Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 26
Found at i:1111145 original size:26 final size:26
Alignment explanation
Indices: 1111109--1111172 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
1111099 TAAGGAGTGG
1111109 TCCTTCGAGACATATGTGATATGTGA
1 TCCTTCGAGACATATGTGATATGTGA
*
1111135 TCCTTCGAGACATATGTGATATGTGG
1 TCCTTCGAGACATATGTGATATGTGA
*
1111161 TCCTTCGGGACA
1 TCCTTCGAGACA
1111173 AATTCTAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (26 bp):
TCCTTCGAGACATATGTGATATGTGA
Found at i:1113503 original size:131 final size:123
Alignment explanation
Indices: 1113277--1113642 Score: 451
Period size: 131 Copynumber: 2.9 Consensus size: 123
1113267 CCAAATATAA
* *
1113277 TCTTAAATGCTTAACTATAAAAATATATATTTTATTAATTTTTATTAATTTATCGAATATATTTT
1 TCTTAAAT-C-TAACTAT-AAAATATATATTTTATTATTTTTTCTTAATTTATCGAATATA-TTT
* * *
1113342 TTTGGTTTAAAGTAGGCCAAGTTTGTTATTTGAGGTAAGAATATATATTTAAAATATTTTAAAAT
62 TTTGGTTTAAAGTA-GCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATA-TTT-AAAT
1113407 AT-TTAAATTCATAACTATAAAATATATATTTTATTATTTTTTCTTAATTTATCGATTATATATA
1 -TCTTAAA-TC-TAACTATAAAATATATATTTTATTATTTTTTCTTAATTTATCGA--ATATAT-
*
1113471 TTTTTGGTTTAAAGTATGCTAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATATTTAAAT
60 TTTTTGGTTTAAAGTA-GCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATATTTAAAT
* *
1113536 TCTT-AA-CT-A-TA-AAAATATGTATTTTATTATTTTTTCTTAATTTATCG-A-ATATTTTTTA
1 TCTTAAATCTAACTATAAAATATATATTTTATTATTTTTTCTTAATTTATCGAATATATTTTTTG
* *
1113594 ATTTAAAGTAGTCCAAGTTTATTATTTAAGTTAAGAATATATGTTTAAA
66 GTTTAAAGTAG-CCAAGTTTATTATTTAAGTTAAGAATATATATTTAAA
1113643 TTCTTAACTA
Statistics
Matches: 216, Mismatches: 13, Indels: 26
0.85 0.05 0.10
Matches are distributed among these distances:
116 1 0.00
117 49 0.23
118 4 0.02
119 1 0.00
122 35 0.16
123 2 0.01
124 1 0.00
125 1 0.00
126 1 0.00
128 3 0.01
129 41 0.19
130 17 0.08
131 60 0.28
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.50
Consensus pattern (123 bp):
TCTTAAATCTAACTATAAAATATATATTTTATTATTTTTTCTTAATTTATCGAATATATTTTTTG
GTTTAAAGTAGCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATATTTAAAT
Found at i:1113641 original size:117 final size:116
Alignment explanation
Indices: 1113395--1113703 Score: 390
Period size: 117 Copynumber: 2.7 Consensus size: 116
1113385 TATATTTAAA
*
1113395 ATATTTTAAAATATTTAAATTCATAACTAT-AAAATATATATTTTATTATTTTTTCTTAATTTAT
1 ATATTTTAAAATATTTAAATTCTTAACTATAAAAATAT-TATTTTATTATTTTTTCTTAATTTAT
** *
1113459 CGATTATATATATTTTTGGTTTAAAGTATGCTAAGTTTATTATTTAAGTTAAGAAT
65 CG---A-ATATATTTTTAATTTAAAGTATGCCAAGTTTATTATTTAAGTTAAGAAT
1113515 ATATATTTAAAATATTTAAATTCTTAACTATAAAAATATGTATTTTATTATTTTTTCTTAATTTA
1 ATAT-TTTAAAATATTTAAATTCTTAACTATAAAAATAT-TATTTTATTATTTTTTCTTAATTTA
1113580 TCGAATAT-TTTTTAATTTAAAGTA-GTCCAAGTTTATTATTTAAGTTAAG-A-
64 TCGAATATATTTTTAATTTAAAGTATG-CCAAGTTTATTATTTAAGTTAAGAAT
*
1113630 ATA---T---ATGTTTAAATTCTTAACTATAAAAAATATT-TTTTATTATTTTTTCTTAATTTAT
1 ATATTTTAAAATATTTAAATTCTTAACTAT-AAAAATATTATTTTATTATTTTTTCTTAATTTAT
*
1113688 TGAATATATATTTTAA
65 CGAATATAT-TTTTAA
1113704 AATATTATAA
Statistics
Matches: 176, Mismatches: 7, Indels: 23
0.85 0.03 0.11
Matches are distributed among these distances:
107 30 0.17
108 21 0.12
109 14 0.08
111 1 0.01
115 3 0.02
116 2 0.01
117 36 0.20
118 4 0.02
119 1 0.01
120 4 0.02
121 25 0.14
122 35 0.20
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.52
Consensus pattern (116 bp):
ATATTTTAAAATATTTAAATTCTTAACTATAAAAATATTATTTTATTATTTTTTCTTAATTTATC
GAATATATTTTTAATTTAAAGTATGCCAAGTTTATTATTTAAGTTAAGAAT
Found at i:1122004 original size:20 final size:21
Alignment explanation
Indices: 1121970--1122010 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1121960 AACTACAACT
1121970 AAAATTTAAATTAG-TATATA
1 AAAATTTAAATTAGTTATATA
1121990 AAAATATTAAA-TAGTTATATA
1 AAAAT-TTAAATTAGTTATATA
1122011 TCCATATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (21 bp):
AAAATTTAAATTAGTTATATA
Found at i:1123873 original size:20 final size:19
Alignment explanation
Indices: 1123850--1123894 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1123840 CGATATAACA
1123850 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1123870 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1123890 -GTAAA
1 GGTAAA
1123895 CGATACCGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.05
19 3 0.14
20 15 0.68
21 3 0.14
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.20
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1123874 original size:180 final size:183
Alignment explanation
Indices: 1123456--1123927 Score: 648
Period size: 180 Copynumber: 2.6 Consensus size: 183
1123446 GATCCAAATT
* * * *
1123456 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-TCAAATGATA
* * * * * * * * *
1123521 AAACTGATAAAGCGCTACCAGATACATTTAAAGTGTCGGTACTTTATTATAAGGATTGACACTTC
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATTATAAGGATCGACACTTC
* * **
1123586 GTGAATTTAAAAGGGAATCAGTTTTAAATTCTATAAAGTGTCGATACTTTTAAA
130 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTTAAA
* *
1123640 AAAAATGTATCGATCCAAAATGATATACCAGGTAAAAATATGATAAAACCGGTATCAAATGATAA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAATGATAA
* *
1123705 AACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTTA-TATAAGGATCGACACTTTG
66 AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATTATAAGGATCGACACTTCG
** * *
1123769 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATTC-TTT-AA
131 TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTTAAA
* *
1123820 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATC-AAATGATA
1123885 AAACC-GT-AAACGATACCGGATATATTGAAAGTGTCGATACTTT
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1123928 CGTAAGTACA
Statistics
Matches: 258, Mismatches: 29, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
179 35 0.14
180 56 0.22
181 16 0.06
182 55 0.21
183 47 0.18
184 49 0.19
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (183 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAATGATAA
AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATTATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTTAAA
Found at i:1126148 original size:20 final size:21
Alignment explanation
Indices: 1126111--1126171 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 21
1126101 AAGACAATCA
*
1126111 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
1126132 AGAGTCGAAGA-AAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1126152 AGAGTCGAAGATACACTTGA
1 AGAGTCGAAGAGAAACTTGA
1126172 AGGCATAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 19 0.51
21 18 0.49
ACGTcount: A:0.43, C:0.11, G:0.28, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1126249 original size:33 final size:33
Alignment explanation
Indices: 1126207--1126272 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1126197 AAATAGATGG
*
1126207 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1126240 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1126273 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1128098 original size:19 final size:19
Alignment explanation
Indices: 1128053--1128101 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1128043 AATGTAAGGT
*
1128053 TAATTTTATATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1128072 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1128091 TAATTTTGTAT
1 TAATTTTGTAT
1128102 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1128678 original size:200 final size:200
Alignment explanation
Indices: 1128335--1129477 Score: 1871
Period size: 200 Copynumber: 5.8 Consensus size: 200
1128325 AATTTACAAT
* *
1128335 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAGAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
1128400 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1128465 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1128530 AATGA
196 AATGA
* *
1128535 ATGGCAAACAGAGTGCAACCATAAAGTGTCGATCCATATATAAAGAA-TGTCGATCCCATAAACA
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAA-AAGTGTCGATCCCATAAACA
* * *
1128599 TCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCTGTTT
65 TCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
*
1128664 TATGAGAGAATAGGTCTAAATAATATATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
130 TATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
1128729 GAATGA
195 GAATGA
* *
1128735 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCC---GAT--AAA----C-AT--C-GAAAC--
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
**
1128785 C----CATA-A-GTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1128844 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTAGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1128909 AATGA
196 AATGA
*
1128914 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1128979 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
1129044 ATGAGAGAATAGATCTAAATAATGTTTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1129109 AATGA
196 AATGA
1129114 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1129179 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
1129244 ATGAGAGAATAGGTCTAAATAATATGTCGACACTTTTGTAGTTTGTTTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
*
1129309 ATTGA
196 AATGA
*
1129314 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * * *
1129379 CTAAACCCATAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTACAAGTATATCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1129444 ATGAGAGAATAGGTCTAAATAATGTATCGACACT
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACT
1129478 GTTTAATGTT
Statistics
Matches: 884, Mismatches: 37, Indels: 44
0.92 0.04 0.05
Matches are distributed among these distances:
179 154 0.17
180 1 0.00
181 2 0.00
182 2 0.00
184 3 0.00
185 1 0.00
187 4 0.00
188 2 0.00
189 2 0.00
190 2 0.00
191 1 0.00
192 4 0.00
194 3 0.00
195 1 0.00
197 2 0.00
198 2 0.00
199 1 0.00
200 696 0.79
201 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:1129079 original size:379 final size:379
Alignment explanation
Indices: 1128380--1129477 Score: 1793
Period size: 379 Copynumber: 2.8 Consensus size: 379
1128370 ATATATAAAG
* * *
1128380 AGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATC
1 AGTGTCGATCCGATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACC
1128445 GGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTG
66 GGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTG
*
1128510 TGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGAGTGCAACCATAAAGTGTCGATCCATATA
131 TGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATA
*
1128575 TAAAGAA-TGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAAT
196 TAAA-AAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAAT
* * *
1128639 CTAATCGGTACAAGTATACCTGTTTTATGAGAGAATAGGTCTAAATAATATATCGACACTTTTGT
260 CTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGT
1128704 AGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAA
325 AGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAA
1128759 AGTGTCGATCCGATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACC
1 AGTGTCGATCCGATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACC
1128824 GGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTG
66 GGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTG
* *
1128889 TGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATA
131 TGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATA
*
1128954 TAAAAAGTGTCGATCCGATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATC
196 TAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATC
* * *
1129019 TAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGATCTAAATAATGTTTCGACACTTTTTTA
261 TAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTA
1129084 GTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAA
326 GTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAA
1129138 AGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAAT
1 AGTGTCGAT-C---------------CG-----ATAAACATCGAAACCCATAAGTATAATGTAAT
*
1129203 AGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATA
45 AGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATG
* * *
1129268 TGTCGACACTTTTGTAGTTTGTTTCGATATTTTTGGTCCAGATTGAATGGCAAACAGGGTGCAAC
110 TATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAAC
*
1129333 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCTAAACCCATAAGTATAAT
175 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAAT
* * *
1129398 GTATTAGGTAATTTTTCAATCTAACCGGTACAAGTATATCGGATTTATGAGAGAATAGGTCTAAA
240 GTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAA
1129463 TAATGTATCGACACT
305 TAATGTATCGACACT
1129478 GTTTAATGTT
Statistics
Matches: 670, Mismatches: 27, Indels: 23
0.93 0.04 0.03
Matches are distributed among these distances:
378 2 0.00
379 371 0.55
380 1 0.00
395 2 0.00
400 294 0.44
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (379 bp):
AGTGTCGATCCGATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACC
GGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTG
TGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATA
TAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATC
TAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTA
GTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAA
Found at i:1130994 original size:18 final size:18
Alignment explanation
Indices: 1130971--1131016 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1130961 CAAGCGGTCA
1130971 ATGAAGATGAAGATGACG
1 ATGAAGATGAAGATGACG
* *
1130989 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
*
1131007 ATGATGATGA
1 ATGAAGATGA
1131017 TGATCCAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.22
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:1131008 original size:3 final size:3
Alignment explanation
Indices: 1130971--1131020 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
1130961 CAAGCGGTCA
* * * * *
1130971 ATG AAG ATG AAG ATG ACG ATG AAG ATG ACG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1131019 AT
1 AT
1131021 CCAAACAAGT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.40, C:0.04, G:0.32, T:0.24
Consensus pattern (3 bp):
ATG
Found at i:1131020 original size:12 final size:12
Alignment explanation
Indices: 1130971--1131016 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1130961 CAAGCGGTCA
*
1130971 ATGAAGATGAAG
1 ATGACGATGAAG
1130983 ATGACGATGAAG
1 ATGACGATGAAG
*
1130995 ATGACGATGATG
1 ATGACGATGAAG
*
1131007 ATGATGATGA
1 ATGACGATGA
1131017 TGATCCAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:1132538 original size:183 final size:183
Alignment explanation
Indices: 1132230--1132817 Score: 1059
Period size: 183 Copynumber: 3.2 Consensus size: 183
1132220 CAAATTTTTC
*
1132230 ACACTTTTTAATATTGTGTCGGTACTTTATGTCTAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1132295 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
1132360 AACCGGTATAAATATATCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
1132413 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCATAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* *
1132478 CAAAAAGTTTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
1132543 AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* * *
1132596 ACACTTTTTAATATTGTATCGGTACTTTATGTTCAGAATAGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* *
1132661 CAAAAAGTGTCGACATTTACACATCGGAATCGAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
1132726 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
1132779 ATACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAAT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAAT
1132818 TATAATATAC
Statistics
Matches: 386, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 386 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:1132906 original size:120 final size:120
Alignment explanation
Indices: 1132693--1132910 Score: 382
Period size: 120 Copynumber: 1.8 Consensus size: 120
1132683 ATCGGAATCG
*
1132693 AGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGA
1 AGAATTATAATATAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGA
*
1132758 ATAGGTCTACAACCTATATCGATACTTTTTAATTTTGTGTCGGTACTTTATGTCC
66 ATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCC
* * *
1132813 AGAATTATAATATACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGA
1 AGAATTATAATATAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGA
*
1132878 ATAGGTCTACAACCTATGTCGACACTTTTTAAT
66 ATAGGTCTACAACCTATATCGACACTTTTTAAT
1132911 AGAGAAAATA
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 92 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (120 bp):
AGAATTATAATATAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGA
ATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCC
Found at i:1132959 original size:120 final size:119
Alignment explanation
Indices: 1132699--1132936 Score: 271
Period size: 120 Copynumber: 2.0 Consensus size: 119
1132689 ATCGAGAATT
* * *
1132699 ATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGT
1 ATAATATACTAGACAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGT
* * * **** * * * * *
1132764 CTACAACCTATATCGATACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAATT
66 CTACAACCTATATCGACACTTTTTAA-TTAGAGAAAATACCTCATGACCAAAATC
* * *
1132819 ATAATATACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGT
1 ATAATATACTAGACAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGT
*
1132884 CTACAACCTATGTCGACACTTTTTAA-TAGAGAAAATAACCTCAGTGACCAAAA
66 CTACAACCTATATCGACACTTTTTAATTAGAGAAAAT-ACCTCA-TGACCAAAA
1132937 ATCCTAGATA
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
118 4 0.04
119 4 0.04
120 92 0.92
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (119 bp):
ATAATATACTAGACAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGT
CTACAACCTATATCGACACTTTTTAATTAGAGAAAATACCTCATGACCAAAATC
Found at i:1133108 original size:20 final size:20
Alignment explanation
Indices: 1133085--1133149 Score: 130
Period size: 20 Copynumber: 3.2 Consensus size: 20
1133075 AAATCGCAAC
1133085 GCGATTTTCCATTTCGCGTT
1 GCGATTTTCCATTTCGCGTT
1133105 GCGATTTTCCATTTCGCGTT
1 GCGATTTTCCATTTCGCGTT
1133125 GCGATTTTCCATTTCGCGTT
1 GCGATTTTCCATTTCGCGTT
1133145 GCGAT
1 GCGAT
1133150 AGTCTACAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.43
Consensus pattern (20 bp):
GCGATTTTCCATTTCGCGTT
Found at i:1133169 original size:22 final size:22
Alignment explanation
Indices: 1133141--1133193 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1133131 TTCCATTTCG
1133141 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
1133163 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1133185 CGTTGCGAT
1 CGTTGCGAT
1133194 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1133336 original size:10 final size:11
Alignment explanation
Indices: 1133305--1133338 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
1133295 GACACGTATT
1133305 ACCACGACCACG
1 ACCACGACC-CG
1133317 ACCACGACCCG
1 ACCACGACCCG
1133328 ACC-CGACCCG
1 ACCACGACCCG
1133338 A
1 A
1133339 GACGGACGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:1134011 original size:19 final size:19
Alignment explanation
Indices: 1133989--1134036 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1133979 ACTGTAGACC
1133989 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
1134008 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
1134027 ATCGCAACGA
1 ATCGCAACGA
1134037 CAATTGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:1134055 original size:22 final size:22
Alignment explanation
Indices: 1133944--1134057 Score: 96
Period size: 22 Copynumber: 5.5 Consensus size: 22
1133934 GAATTTAAAA
*
1133944 AATCGCAACGACAACTGTAGAC
1 AATCGCAACGACAATTGTAGAC
* * *
1133966 TATCGCAACAACAACTGTAGAC
1 AATCGCAACGACAATTGTAGAC
* * *
1133988 CATCGCAACG--AATT-TGGAA
1 AATCGCAACGACAATTGTAGAC
* *
1134007 AATCGCAACG--AATT-TGGAA
1 AATCGCAACGACAATTGTAGAC
1134026 AATCGCAACGACAATTGTAGAC
1 AATCGCAACGACAATTGTAGAC
*
1134048 TATCGCAACG
1 AATCGCAACG
1134058 CGAAATGGAA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 31 0.40
20 3 0.04
21 4 0.05
22 40 0.51
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (22 bp):
AATCGCAACGACAATTGTAGAC
Found at i:1134074 original size:20 final size:20
Alignment explanation
Indices: 1134002--1134156 Score: 85
Period size: 20 Copynumber: 8.0 Consensus size: 20
1133992 GCAACGAATT
*
1134002 TGGAAAATCGCAA--CGAATT
1 TGGAAAATCGCAACGCGAA-A
*
1134021 TGGAAAATCGCAACGAC-AAT
1 TGGAAAATCGCAACG-CGAAA
**
1134041 TGTAGACTATCGCAACGCGAAA
1 TG--GAAAATCGCAACGCGAAA
**
1134063 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAA
** * *
1134083 TTCAACTATCGCAACGCGAAC
1 TGGAA-AATCGCAACGCGAAA
1134104 TGGAAAATCGCAACGCG--A
1 TGGAAAATCGCAACGCGAAA
* *
1134122 T----TATCGCTACGCGAAA
1 TGGAAAATCGCAACGCGAAA
*
1134138 TGAAAAATCGCAACGCGAA
1 TGGAAAATCGCAACGCGAA
1134157 TTTGCGATAG
Statistics
Matches: 103, Mismatches: 20, Indels: 25
0.70 0.14 0.17
Matches are distributed among these distances:
14 10 0.10
16 2 0.02
18 1 0.01
19 13 0.13
20 43 0.42
21 18 0.17
22 16 0.16
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:1134091 original size:41 final size:41
Alignment explanation
Indices: 1134021--1134123 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
1134011 GCAACGAATT
*
1134021 TGGAAAATCGCAACGACAATTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGATTGTAGACTATCGCAACGCGAAA
* *
1134063 TGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACGCGAAC
1 TGGAAAATCGCAACGCGATTGT-AGACTATCGCAACGCGAAA
1134104 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGATT
1134124 ATCGCTACGC
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
41 41 0.72
42 16 0.28
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.18
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGATTGTAGACTATCGCAACGCGAAA
Found at i:1134094 original size:82 final size:81
Alignment explanation
Indices: 1133927--1134118 Score: 201
Period size: 82 Copynumber: 2.3 Consensus size: 81
1133917 CAACGAATTT
** * **
1133927 TCGCAACGAATTTAAAAAATCGCAACGACAACTGTAGACTATCGCAACAACAACTGTAGACCATC
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACAACAAATG-AGAAAATC
*
1133992 GCAACGAATTTGGAAAA
65 GCAACGAATTTGCAAAA
* *
1134009 TCGCAACGAATTTGGAAAATCGCAACGACAATTGTAGACTATCGCAAC-GCGAAATG-GAAAATC
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACAAC-AAATGAGAAAATC
* * *
1134072 GCAACGCGATTTTCAACTA
65 GCAACG-AATTTGCAA-AA
*
1134091 TCGCAACGCGAA-CTGGAAAATCGCAACG
1 TCGCAA--CGAATTTGGAAAATCGCAACG
1134119 CGATTATCGC
Statistics
Matches: 93, Mismatches: 12, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
80 11 0.12
81 7 0.08
82 56 0.60
83 15 0.16
84 4 0.04
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (81 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACAACAAATGAGAAAATCG
CAACGAATTTGCAAAA
Found at i:1134134 original size:34 final size:34
Alignment explanation
Indices: 1134089--1134155 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
1134079 GATTTTCAAC
* *
1134089 TATCGCAACGCGAACTGGAAAATCGCAACGCGAT
1 TATCGCAACGCGAAATGAAAAATCGCAACGCGAT
*
1134123 TATCGCTACGCGAAATGAAAAATCGCAACGCGA
1 TATCGCAACGCGAAATGAAAAATCGCAACGCGA
1134156 ATTTGCGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.15
Consensus pattern (34 bp):
TATCGCAACGCGAAATGAAAAATCGCAACGCGAT
Found at i:1134594 original size:120 final size:120
Alignment explanation
Indices: 1134381--1134627 Score: 449
Period size: 120 Copynumber: 2.1 Consensus size: 120
1134371 ACATCGGAAC
1134381 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
*
1134446 GAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
* * *
1134501 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
*
1134566 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
1134621 CCAGAAT
1 CCAGAAT
1134628 GGAAGAAAAA
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 122 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:1134834 original size:120 final size:120
Alignment explanation
Indices: 1134688--1134930 Score: 414
Period size: 120 Copynumber: 2.0 Consensus size: 120
1134678 CGGAACCCAT
* *
1134688 AATTATAATGTAATAGATAATTTTGTAATATAACTGGTATAAATATACCAGTTTTATGAGCGAAT
1 AATTATAATATAATAGATAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGAGCGAAT
*
1134753 AGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAG
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
* * * *
1134808 AATTATAATATAATAGATAATTTTGTAATATAACCGTTATAAGTATACCGGTTTTATTAGCGAAT
1 AATTATAATATAATAGATAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGAGCGAAT
*
1134873 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
1134928 AAT
1 AAT
1134931 GGAAGAAAAA
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 115 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (120 bp):
AATTATAATATAATAGATAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
Found at i:1134836 original size:303 final size:303
Alignment explanation
Indices: 1134289--1135398 Score: 2085
Period size: 303 Copynumber: 3.7 Consensus size: 303
1134279 TTATTTTCTC
1134289 CTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGTCAA
1 CTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGTCAA
1134354 AAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
66 AAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
*
1134419 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATTTT
131 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1134484 GTGTCGGTACTTTATGTCCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGT
196 GTGTCGGTACTTTATGTCCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGT
1134549 ATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCGACA
261 ATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCGACA
* *
1134592 CTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTTGATACCTTGTCAA
1 CTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGTCAA
*
1134657 AAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
66 AAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
* * *
1134722 TGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATTTT
131 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
* * *
1134787 GTGTCGGTACTTTATGTCCAGAATTATAATATAATAGATAATTTTGTAATATAACCGTTATAAGT
196 GTGTCGGTACTTTATGTCCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGT
1134852 ATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCGACA
261 ATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCGACA
*
1134895 CTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAA
1 CTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGTCAA
* *
1134960 AAAGTGTCGACATTTACACATCGGAACCGATAATTATAATGTAATAGATAATTTTGTAATATAAC
66 AAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
1135025 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
131 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1135090 GTGTCGGTACTTTATGTCCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGT
196 GTGTCGGTACTTTATGTCCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGT
1135155 ATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCGACA
261 ATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCGACA
*
1135198 CTTTTTAATATTATGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGTCAA
1 CTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGTCAA
*
1135263 AAAGTGTCGACATTTACACATCGGAACCGAGAATTATAATGTAATAGATAATTTTGTAATATAAC
66 AAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
1135328 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
131 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1135393 GTGTCG
196 GTGTCG
1135399 CTAATTTTAA
Statistics
Matches: 788, Mismatches: 19, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
303 788 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (303 bp):
CTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGTCAA
AAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
GTGTCGGTACTTTATGTCCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGT
ATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCGACA
Found at i:1135143 original size:120 final size:120
Alignment explanation
Indices: 1134991--1135233 Score: 441
Period size: 120 Copynumber: 2.0 Consensus size: 120
1134981 CGGAACCGAT
1134991 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
*
1135056 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
66 AGGTCTACAACCTATATCGACACTTTTTAATATTATGTCGGTACTTTATGTCCAG
* * *
1135111 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
*
1135176 AGGTCTACAACCTATGTCGACACTTTTTAATATTATGTCGGTACTTTATGTCCAG
66 AGGTCTACAACCTATATCGACACTTTTTAATATTATGTCGGTACTTTATGTCCAG
1135231 AAT
1 AAT
1135234 AGAAGAAAAA
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 118 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (120 bp):
AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTATGTCGGTACTTTATGTCCAG
Found at i:1137216 original size:23 final size:23
Alignment explanation
Indices: 1137185--1137257 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1137175 ATAAGTAAAA
* *
1137185 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGTTT
1137208 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
*
1137231 ATATAATGTAATAGGTAGTGTTT
1 ATATAATGTAATAGGTAGCGTTT
1137254 ATAT
1 ATAT
1137258 TGTAAAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGTTT
Found at i:1139130 original size:20 final size:20
Alignment explanation
Indices: 1139105--1139149 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1139095 AAATCGCAAC
1139105 GCGATTTTCCATTTCACGTT
1 GCGATTTTCCATTTCACGTT
*
1139125 GCGATTTTCCATTTCGCGTT
1 GCGATTTTCCATTTCACGTT
1139145 GCGAT
1 GCGAT
1139150 AGTCTACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.42
Consensus pattern (20 bp):
GCGATTTTCCATTTCACGTT
Found at i:1139167 original size:21 final size:19
Alignment explanation
Indices: 1139141--1139196 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 19
1139131 TTCCATTTCG
1139141 CGTTGCGATAGTCTACAATGT
1 CGTTGCGATAGTCTA-AAT-T
** *
1139162 CGTTGCGATTTTTTAAATT
1 CGTTGCGATAGTCTAAATT
1139181 CGTTGCGATAGT-TAAA
1 CGTTGCGATAGTCTAAA
1139197 AAAAAAGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 4 0.13
19 11 0.37
20 3 0.10
21 12 0.40
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCTAAATT
Found at i:1139844 original size:13 final size:13
Alignment explanation
Indices: 1139826--1139851 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1139816 TTTTTAACTA
1139826 TCACAACGAATTT
1 TCACAACGAATTT
1139839 TCACAACGAATTT
1 TCACAACGAATTT
1139852 GGAAAATCGC
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:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
TCACAACGAATTT
Found at i:1139866 original size:19 final size:19
Alignment explanation
Indices: 1139842--1139907 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
1139832 CGAATTTTCA
1139842 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
1139861 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
1139883 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
1139902 CAACGA
1 CAACGA
1139908 CAACTGTAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:1139884 original size:22 final size:22
Alignment explanation
Indices: 1139857--1139928 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
1139847 AATTTGGAAA
1139857 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
1139879 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
1139898 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1139920 ATCGCAACG
1 ATCGCAACG
1139929 CGATTTTCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1139887 original size:41 final size:41
Alignment explanation
Indices: 1139842--1139928 Score: 174
Period size: 41 Copynumber: 2.1 Consensus size: 41
1139832 CGAATTTTCA
1139842 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
1 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
1139883 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
1 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
1139924 CAACG
1 CAACG
1139929 CGATTTTCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (41 bp):
CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
Found at i:1139943 original size:21 final size:21
Alignment explanation
Indices: 1139917--1139993 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
1139907 ACAACTGTAG
1139917 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
* ** **
1139938 ACTATCGCAACTCGAAATGGA
1 ACTATCGCAACGCGATTTTCA
*
1139959 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
*
1139979 ATTATCGCAACGCGA
1 ACTATCGCAACGCGA
1139994 ATTTGCGATA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:1140368 original size:43 final size:42
Alignment explanation
Indices: 1140259--1140511 Score: 206
Period size: 43 Copynumber: 5.9 Consensus size: 42
1140249 CAAATTGATA
* ** * *
1140259 CTTTAGCGGCGTTTGTTGTAAAAAAGCCGCTATATATATCTGAC
1 CTTTTGCGGCGTTTGTTCCAAAAAAGCCGC--TATAGATCTAAC
* * ** * *
1140303 CTTTTGTGGCATTT-TTGGAAAAAATGCCACTATATATCTAAC
1 CTTTTGCGGCGTTTGTTCCAAAAAA-GCCGCTATAGATCTAAC
* *
1140345 CTTTTGCTGCGTTTGTT-CTAAAAAGCCGCTATAGATCTCAAC
1 CTTTTGCGGCGTTTGTTCCAAAAAAGCCGCTATAGATCT-AAC
* * * *
1140387 TTTTTGCGGCGTTTGTTCCAATACACGCCGCTATAGATCTGAC
1 CTTTTGCGGCGTTTGTTCCAA-AAAAGCCGCTATAGATCTAAC
*
1140430 CTTTTGCGGCGTTTGTTCCAAAAACA-CCGCTATAGATCTCGAC
1 CTTTTGCGGCGTTTGTTCCAAAAA-AGCCGCTATAGATCT-AAC
* * * * * *
1140473 CTTCTGTGGCATTTGTTACAAAAACGTCGCTATAGATCT
1 CTTTTGCGGCGTTTGTTCCAAAAAAGCCGCTATAGATCT
1140512 TGACCTATGG
Statistics
Matches: 173, Mismatches: 28, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
41 12 0.07
42 60 0.35
43 70 0.40
44 31 0.18
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (42 bp):
CTTTTGCGGCGTTTGTTCCAAAAAAGCCGCTATAGATCTAAC
Found at i:1140504 original size:85 final size:84
Alignment explanation
Indices: 1140259--1140517 Score: 270
Period size: 85 Copynumber: 3.0 Consensus size: 84
1140249 CAAATTGATA
* * * *
1140259 CTTTAGCGGCGTTTGTTGTAAAAAAGCCGCTATATATATCTGACCTTTTGTGGCATTT-TTGGA-
1 CTTTTGCGGCGTTTGTTCTAAAAAA-CCGCTATAGATCTC-GACCTTTTGTGGCATTTGTT--AC
* * * *
1140322 AAAAATGCCACTATATATCTAAC
62 AAAAACGCCGCTATAGATCTGAC
* * * * * * *
1140345 CTTTTGCTGCGTTTGTTCTAAAAAGCCGCTATAGATCTCAACTTTTTGCGGCGTTTGTTCCAATA
1 CTTTTGCGGCGTTTGTTCTAAAAAACCGCTATAGATCTCGACCTTTTGTGGCATTTGTTACAA-A
*
1140410 CACGCCGCTATAGATCTGAC
65 AACGCCGCTATAGATCTGAC
* *
1140430 CTTTTGCGGCGTTTGTTCCAAAAACACCGCTATAGATCTCGACCTTCTGTGGCATTTGTTACAAA
1 CTTTTGCGGCGTTTGTTCTAAAAA-ACCGCTATAGATCTCGACCTTTTGTGGCATTTGTTACAAA
*
1140495 AACGTCGCTATAGATCTTGAC
65 AACGCCGCTATAGATC-TGAC
1140516 CT
1 CT
1140518 ATGGCAGCGT
Statistics
Matches: 141, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
84 15 0.11
85 67 0.48
86 59 0.42
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (84 bp):
CTTTTGCGGCGTTTGTTCTAAAAAACCGCTATAGATCTCGACCTTTTGTGGCATTTGTTACAAAA
ACGCCGCTATAGATCTGAC
Found at i:1140528 original size:86 final size:85
Alignment explanation
Indices: 1140353--1140529 Score: 212
Period size: 86 Copynumber: 2.1 Consensus size: 85
1140343 ACCTTTTGCT
* * * * * * *
1140353 GCGTTTGTTCTAAAAAGCCGCTATAGATCTCAACTTTTTGCGGCGTTTGTTCCAATACACGCCGC
1 GCGTTTGTTCCAAAAAACCGCTATAGATCTCAACCTTCTGCGGCATTTGTTACAATAAACGCCGC
* * *
1140418 TATAGATCTGACCTTTTGCG
66 TATAGATCTGACCTATGGCA
* * *
1140438 GCGTTTGTTCCAAAAACACCGCTATAGATCTCGACCTTCTGTGGCATTTGTTACAA-AAACGTCG
1 GCGTTTGTTCCAAAAA-ACCGCTATAGATCTCAACCTTCTGCGGCATTTGTTACAATAAACGCCG
1140502 CTATAGATCTTGACCTATGGCA
65 CTATAGATC-TGACCTATGGCA
1140524 GCGTTT
1 GCGTTT
1140530 TTGGTTCTCA
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
85 30 0.39
86 47 0.61
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (85 bp):
GCGTTTGTTCCAAAAAACCGCTATAGATCTCAACCTTCTGCGGCATTTGTTACAATAAACGCCGC
TATAGATCTGACCTATGGCA
Found at i:1142687 original size:43 final size:43
Alignment explanation
Indices: 1142577--1142782 Score: 186
Period size: 43 Copynumber: 4.9 Consensus size: 43
1142567 CGGTGTTTTA
* * * *
1142577 AAAAACACCGAAATAGGTATTGATATTTAGCGGCG--T-T-AC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAG
*
1142616 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAG
* * * * * *
1142659 AAAAATGTCGTAATAGGTGTTGATATTTAGCGGTGTTTTTTAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAG
* ** * * **
1142702 ATAAACGCCGCAATAGGTAATGATATTTAGCGACGTTTTTCTC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAG
* * * *
1142745 TAAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
1142783 TCCCATAAAT
Statistics
Matches: 132, Mismatches: 31, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
39 31 0.23
41 1 0.01
42 1 0.01
43 99 0.75
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAG
Found at i:1142762 original size:86 final size:86
Alignment explanation
Indices: 1142577--1142783 Score: 215
Period size: 86 Copynumber: 2.5 Consensus size: 86
1142567 CGGTGTTTTA
* * * * * **
1142577 AAAAACACCGAAATAGGTATTGATATTTAGCGGCG----TTACACAAACGCCGCAATAGGTGTTG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTAGATAAACGCCGCAATAGGTAATG
* *
1142638 ATATTTAGCGGCGTTTGTCAG
66 ATATTTAGCGACGTTTGTCAC
* * * *
1142659 AAAAATGTCGTAATAGGTGTTGATATTTAGCGGTGTTTTTTAGATAAACGCCGCAATAGGTAATG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTAGATAAACGCCGCAATAGGTAATG
* *
1142724 ATATTTAGCGACGTTTTTCTC
66 ATATTTAGCGACGTTTGTCAC
* * * *
1142745 TAAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTT
1142784 CCCATAAATA
Statistics
Matches: 99, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
82 29 0.29
86 70 0.71
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (86 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTAGATAAACGCCGCAATAGGTAATG
ATATTTAGCGACGTTTGTCAC
Found at i:1142783 original size:43 final size:43
Alignment explanation
Indices: 1142615--1142954 Score: 260
Period size: 43 Copynumber: 8.0 Consensus size: 43
1142605 AGCGGCGTTA
* * * *
1142615 CACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCA
1 CACAAACGCCGCAATAGGTGTTGATGTTTTGCGGCGTTTTTCT
* * * * * * * *
1142658 GAAAAATGTCGTAATAGGTGTTGATATTTAGCGGTGTTTTT-T
1 CACAAACGCCGCAATAGGTGTTGATGTTTTGCGGCGTTTTTCT
* * ** * * *
1142700 AGATAAACGCCGCAATAGGTAATGATATTTAGCGACGTTTTTCT
1 -CACAAACGCCGCAATAGGTGTTGATGTTTTGCGGCGTTTTTCT
* *
1142744 CTA-AAACGCCGCAGTAGGTGTTGATGTTTTGCGGCG-TTTTCC
1 C-ACAAACGCCGCAATAGGTGTTGATGTTTTGCGGCGTTTTTCT
* ** * * * * *
1142786 CATAAATACTGCAGTAGATGTTGATGTTTTGCGGCG-TTGTCC
1 CACAAACGCCGCAATAGGTGTTGATGTTTTGCGGCGTTTTTCT
* * * *
1142828 CACAAACGTCGCAGTAGATTTTGATGTTTTGCGGCGTTTATTC-
1 CACAAACGCCGCAATAGGTGTTGATGTTTTGCGGCGTTT-TTCT
* *
1142871 CACAAACGCCGCAGTAGGTTTTGATGTTTTGCGGCGTTTTTCT
1 CACAAACGCCGCAATAGGTGTTGATGTTTTGCGGCGTTTTTCT
* * *
1142914 CACAAACGCCGCAATATGTATTGAT-TTTGTGCGACGTTTTT
1 CACAAACGCCGCAATAGGTGTTGATGTTT-TGCGGCGTTTTT
1142955 GCTAAAAATA
Statistics
Matches: 247, Mismatches: 42, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.00
42 76 0.31
43 166 0.67
44 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (43 bp):
CACAAACGCCGCAATAGGTGTTGATGTTTTGCGGCGTTTTTCT
Found at i:1142801 original size:42 final size:40
Alignment explanation
Indices: 1142754--1142910 Score: 170
Period size: 42 Copynumber: 3.8 Consensus size: 40
1142744 CTAAAACGCC
*
1142754 GCAGTAGGTGTTGATGTTTTGCGGCGTTTTCCCATAAATACT
1 GCAGTAGATGTTGATGTTTTGCGGCGTTTTCCCA-AAA-ACT
* *
1142796 GCAGTAGATGTTGATGTTTTGCGGCGTTGTCCCACAAACGT
1 GCAGTAGATGTTGATGTTTTGCGGCGTTTTCCCAAAAAC-T
* ** *
1142837 CGCAGTAGATTTTGATGTTTTGCGGCGTTTATTCCACAAACGCC
1 -GCAGTAGATGTTGATGTTTTGCGGCG-TT-TTCC-CAAAAACT
* *
1142881 GCAGTAGGTTTTGATGTTTTGCGGCGTTTT
1 GCAGTAGATGTTGATGTTTTGCGGCGTTTT
1142911 TCTCACAAAC
Statistics
Matches: 100, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
40 2 0.02
41 5 0.05
42 59 0.59
43 27 0.27
44 3 0.03
45 4 0.04
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (40 bp):
GCAGTAGATGTTGATGTTTTGCGGCGTTTTCCCAAAAACT
Found at i:1143418 original size:23 final size:21
Alignment explanation
Indices: 1143369--1143454 Score: 120
Period size: 21 Copynumber: 4.1 Consensus size: 21
1143359 TGATACGTTT
*
1143369 CTTCTCTTTGTGTTGCCGCTG
1 CTTCTCTCTGTGTTGCCGCTG
*
1143390 CTTCTCTCTGTGTTGCCGTTG
1 CTTCTCTCTGTGTTGCCGCTG
1143411 CTTCTCTCTGTGTTGCCGCTG
1 CTTCTCTCTGTGTTGCCGCTG
* *
1143432 CTTCTTTCTCTGCTT-CCGCTG
1 CTTCTCTCTGTG-TTGCCGCTG
1143453 CT
1 CT
1143455 GCTTTAGCTG
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 57 0.97
22 2 0.03
ACGTcount: A:0.00, C:0.33, G:0.21, T:0.47
Consensus pattern (21 bp):
CTTCTCTCTGTGTTGCCGCTG
Found at i:1143459 original size:21 final size:21
Alignment explanation
Indices: 1143426--1143490 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1143416 CTCTGTGTTG
*
1143426 CCGCTGCTTCTTTCTCTGCTT
1 CCGCTGCTGCTTTCTCTGCTT
**
1143447 CCGCTGCTGCTTTAGCTGCTT
1 CCGCTGCTGCTTTCTCTGCTT
** *
1143468 CTACTGCTGCTCTCTCTGCTT
1 CCGCTGCTGCTTTCTCTGCTT
1143489 CC
1 CC
1143491 CTTGCTTCAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.03, C:0.38, G:0.17, T:0.42
Consensus pattern (21 bp):
CCGCTGCTGCTTTCTCTGCTT
Found at i:1144538 original size:9 final size:10
Alignment explanation
Indices: 1144515--1144541 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1144505 TAATTGCTCC
1144515 AAAAAGCAAG
1 AAAAAGCAAG
1144525 AAAAAGCAAG
1 AAAAAGCAAG
1144535 AAAAAGC
1 AAAAAGC
1144542 TGTGAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.11, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAGCAAG
Found at i:1146772 original size:134 final size:134
Alignment explanation
Indices: 1146474--1146799 Score: 359
Period size: 134 Copynumber: 2.4 Consensus size: 134
1146464 GCCACTAAAT
* * * * * *
1146474 TACAACTCTATTGCGCCGTTTATGTCAAAAACACCACTAAAGTATAACTTTTTAGCAGCGTTTGG
1 TACAACTCTATTACGGCGCTTATATCAAAAATACCACTAAAGTATAACTTTTTAGCGGCGTTTGG
* * ** * *
1146539 TAACAAACGCCACTAAATTTAGAGTATTTTATGGCGTTTTCTTAAAAAATGCCGTTATAAATAAC
66 TAACAAACGCCACTAAATTAAGAGTATTTTACGGCGTTTGATTAAAAAACGCCGCTATAAATAAC
1146604 AATA
131 AATA
* * ** *
1146608 TACAACTCTATTACGGCGTTTATATCAAAAATGCCTTTAAAGTATAACTTTTTAGCGGCGTTTGT
1 TACAACTCTATTACGGCGCTTATATCAAAAATACCACTAAAGTATAACTTTTTAGCGGCGTTTGG
* * * * * *
1146673 TACCAAACGCTACTAAATTAATAGTATTTTGCGGCGTTTGATTGAAAAACGCCGCTATAAATGAC
66 TAACAAACGCCACTAAATTAAGAGTATTTTACGGCGTTTGATTAAAAAACGCCGCTATAAATAAC
1146738 AATA
131 AATA
* * * * * * *
1146742 TGCAAC-CATTTTACGGCGCTTGTTTGAAAAATACCACT-AAGTATTACTATTTAGCGGC
1 TACAACTC-TATTACGGCGCTTATATCAAAAATACCACTAAAGTATAACTTTTTAGCGGC
1146800 ATTTTTGGAT
Statistics
Matches: 159, Mismatches: 32, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
133 19 0.12
134 140 0.88
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (134 bp):
TACAACTCTATTACGGCGCTTATATCAAAAATACCACTAAAGTATAACTTTTTAGCGGCGTTTGG
TAACAAACGCCACTAAATTAAGAGTATTTTACGGCGTTTGATTAAAAAACGCCGCTATAAATAAC
AATA
Found at i:1148270 original size:41 final size:41
Alignment explanation
Indices: 1148115--1148273 Score: 214
Period size: 41 Copynumber: 3.9 Consensus size: 41
1148105 CGTTTATAAA
* *
1148115 AAAAACGCCACTATTGATT-ACACTATTGTGGCATTTGT-T
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
* * *
1148154 AAAAAACGCCACTATTGATTAAAACTATTGCGGCTTTTTTCT
1 -AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
*
1148196 AAAAACACCACTATTGATTAACACTATTGCGGCGTTTGTCT
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
* * *
1148237 AAAAATGCCACTATTTATTATCACTATTGCGGCGTTT
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTT
1148274 TAAGAATAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
40 19 0.18
41 85 0.81
42 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.35
Consensus pattern (41 bp):
AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
Found at i:1148304 original size:82 final size:80
Alignment explanation
Indices: 1148099--1148316 Score: 226
Period size: 82 Copynumber: 2.6 Consensus size: 80
1148089 ATTTAACATT
* *
1148099 TTGCGGCGTTTATAAAAAAAACGCCACTATTGATTACACTATTGTGGCATTTGTTAAAAAACGCC
1 TTGCGGCGTTT-T-AAAAAAACGCCACTATTGATTACACTATTGCGGCGTTTGTTAAAAAACGCC
1148164 ACTATTGATTAAAACTA
64 ACTATTGATTAAAACTA
* ** * *
1148181 TTGCGGCTTTTTTCTAAAAACACCACTATTGATTAACACTATTGCGGCGTTTGTCT-AAAAATGC
1 TTGCGGC-GTTTTAAAAAAACGCCACTATTGATT-ACACTATTGCGGCGTTTGT-TAAAAAACGC
* **
1148245 CACTATTTATTATCACTA
63 CACTATTGATTAAAACTA
* *
1148263 TTGCGGCGTTTTAAGAATAAATGCCACTATATG-TGTA-ACTATTACGGCGTTTGT
1 TTGCGGCGTTTTAA-AA-AAACGCCACTAT-TGAT-TACACTATTGCGGCGTTTGT
1148317 GGTATACACG
Statistics
Matches: 113, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
81 22 0.19
82 72 0.64
83 16 0.14
84 3 0.03
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (80 bp):
TTGCGGCGTTTTAAAAAAACGCCACTATTGATTACACTATTGCGGCGTTTGTTAAAAAACGCCAC
TATTGATTAAAACTA
Found at i:1148408 original size:41 final size:42
Alignment explanation
Indices: 1148157--1148410 Score: 140
Period size: 41 Copynumber: 6.2 Consensus size: 42
1148147 ATTTGTTAAA
* * ** *
1148157 AAACGCCACTAT-TGATTAAAACTATTGCGGC-TTTTTTCTAA
1 AAACGCCACTATATG-TTAATACTATTGCGGCGTTTGTGGTAT
* * * *
1148198 AAACACCACTAT-TGATTAACACTATTGCGGCGTTTGT-CTAA
1 AAACGCCACTATATG-TTAATACTATTGCGGCGTTTGTGGTAT
* * * * *
1148239 AAATGCCACTATTTATT-ATCACTATTGCGGCGTTT-TAAGAAT
1 AAACGCCACTATATGTTAAT-ACTATTGCGGCGTTTGT-GGTAT
* *
1148281 AAATGCCACTATATGTGT-A-ACTATTACGGCGTTTGTGGTAT
1 AAACGCCACTATATGT-TAATACTATTGCGGCGTTTGTGGTAT
* * * * *
1148322 ACACGTCGCTA-AT-TT-ATCGATCTATTACGCCGTTT-TGGCTA-
1 AAACGCCACTATATGTTAAT--A-CTATTGCGGCGTTTGTGG-TAT
1148363 AAACGCCACTATATGTTAATA-TATTGCGGCGTTTGTGGTAT
1 AAACGCCACTATATGTTAATACTATTGCGGCGTTTGTGGTAT
1148404 AAACGCC
1 AAACGCC
1148411 GCTAATTTAC
Statistics
Matches: 171, Mismatches: 25, Indels: 34
0.74 0.11 0.15
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 17 0.10
41 106 0.62
42 39 0.23
43 4 0.02
44 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (42 bp):
AAACGCCACTATATGTTAATACTATTGCGGCGTTTGTGGTAT
Found at i:1149008 original size:2 final size:2
Alignment explanation
Indices: 1148997--1149045 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1148987 GTATTAATTA
1148997 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1149038 AT AT AT AT
1 AT AT AT AT
1149046 TTGAAAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1149381 original size:19 final size:20
Alignment explanation
Indices: 1149357--1149394 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1149347 TCCATGTTTA
1149357 TAAAATTTATAA-AAAAAAT
1 TAAAATTTATAATAAAAAAT
1149376 TAAAATTTATAATAAAAAA
1 TAAAATTTATAATAAAAAA
1149395 AAACCTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAATTTATAATAAAAAAT
Found at i:1165604 original size:32 final size:29
Alignment explanation
Indices: 1165567--1165665 Score: 87
Period size: 28 Copynumber: 3.3 Consensus size: 29
1165557 AATAATTTGA
* **
1165567 AATATTTGTTATTATGGTTTTAATTTTTTTCT
1 AATATTTATTATTATGGGCTT-A-TTTTTT-T
*
1165599 AATATTTATTATTTTGGGCTTATTTTTTT
1 AATATTTATTATTATGGGCTTATTTTTTT
*
1165628 AATATTTATTATTA-GGTAC-TATTTTTTT
1 AATATTTATTATTATGG-GCTTATTTTTTT
1165656 -ATAATTTATT
1 AAT-ATTTATT
1165666 TTTTCTAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.03
28 18 0.31
29 15 0.25
30 6 0.10
31 1 0.02
32 17 0.29
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (29 bp):
AATATTTATTATTATGGGCTTATTTTTTT
Found at i:1165653 original size:29 final size:30
Alignment explanation
Indices: 1165589--1165660 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
1165579 TATGGTTTTA
* * *
1165589 ATTTTTTTCTAATATTTATTATTTTGGGCT
1 ATTTTTTTATAATATTTATTATTTAGGACT
1165619 -TATTTTTT-TAATATTTATTA-TTAGGTACT
1 AT-TTTTTTATAATATTTATTATTTAGG-ACT
1165648 ATTTTTTTATAAT
1 ATTTTTTTATAAT
1165661 TTATTTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
28 4 0.11
29 21 0.58
30 11 0.31
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (30 bp):
ATTTTTTTATAATATTTATTATTTAGGACT
Found at i:1166487 original size:24 final size:24
Alignment explanation
Indices: 1166460--1166518 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
1166450 CAAGTTGTGA
* *
1166460 TATTTTAATTATATTATTTCATTG
1 TATTTAAATCATATTATTTCATTG
1166484 TATTTAAATCATATTATTTCATTG
1 TATTTAAATCATATTATTTCATTG
1166508 TATTTAAATCA
1 TATTTAAATCA
1166519 ATAGATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (24 bp):
TATTTAAATCATATTATTTCATTG
Found at i:1173750 original size:60 final size:62
Alignment explanation
Indices: 1173682--1173803 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 62
1173672 AGGTCTTTAT
* * *
1173682 TATCTATTTACCTTTGAATA-TTAAAGATAA-TTATA-TATTAAATATTTCAAATTAAAATAA
1 TATCTATTTAACTTTGAATAGTAAAAGA-AATTTATACTATTAAATATTTAAAATTAAAATAA
* * *
1173742 TATCTATTTAAGTTTGAATAGTAAAAGAAATTTATATCTTTTGAATATTTAAAATTAAAATA
1 TATCTATTTAACTTTGAATAGTAAAAGAAATTTATA-CTATTAAATATTTAAAATTAAAATA
1173804 TATTACTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
60 20 0.38
61 11 0.21
63 21 0.40
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (62 bp):
TATCTATTTAACTTTGAATAGTAAAAGAAATTTATACTATTAAATATTTAAAATTAAAATAA
Found at i:1175476 original size:63 final size:63
Alignment explanation
Indices: 1175396--1175517 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 63
1175386 GGTATTTATC
* * ** *
1175396 ATCTCTTTAACTTTGAATATTAAATGTAA-TTATATAATTTCT-AATATTTTAAATTAAAATAAT
1 ATCTATTTAACTTTGAATAGTAAAAATAATTTATAT-ATTT-TGAATATTTCAAATTAAAATAAT
* *
1175459 ATCTATTTAAGTTTGAATAGTAAAAATAGTTTATATATTTTGAATATTTCAAATTAAAA
1 ATCTATTTAACTTTGAATAGTAAAAATAATTTATATATTTTGAATATTTCAAATTAAAA
1175518 GATATTATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.02
63 43 0.86
64 6 0.12
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (63 bp):
ATCTATTTAACTTTGAATAGTAAAAATAATTTATATATTTTGAATATTTCAAATTAAAATAAT
Found at i:1178073 original size:11 final size:11
Alignment explanation
Indices: 1178057--1178088 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1178047 ATTAAAATCA
1178057 TTTAAATATAT
1 TTTAAATATAT
*
1178068 TTTAAATTTAT
1 TTTAAATATAT
1178079 TTTAAATATA
1 TTTAAATATA
1178089 GATTGATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTAAATATAT
Found at i:1178085 original size:22 final size:21
Alignment explanation
Indices: 1178057--1178386 Score: 137
Period size: 22 Copynumber: 15.3 Consensus size: 21
1178047 ATTAAAATCA
*
1178057 TTTAAATATATTTTAAATTTAT
1 TTTAAATATATATT-AATTTAT
* *
1178079 TTTAAATATAGATTGATTTAT
1 TTTAAATATATATTAATTTAT
*
1178100 TTTAAA-ATATGGATTGATTTAT
1 TTTAAATATAT--ATTAATTTAT
** *
1178122 TTTAAA-ATATGAAAAAATTAT
1 TTTAAATATAT-ATTAATTTAT
*
1178143 TTTAAA-ATATTGATTGATTTAT
1 TTTAAATATA-T-ATTAATTTAT
**
1178165 TTTAAA-ATATGGAAAAATTTAT
1 TTTAAATATAT--ATTAATTTAT
*
1178187 TTTAAA-ATATGGATTGATTTAT
1 TTTAAATATAT--ATTAATTTAT
** *
1178209 TTTAAA-ATATGAAAAAATTAT
1 TTTAAATATAT-ATTAATTTAT
*** *
1178230 TTTAAATACGGATTGATTTAT
1 TTTAAATATATATTAATTTAT
*
1178251 TTTAAA-ATATGGATTGATTTAT
1 TTTAAATATAT--ATTAATTTAT
*
1178273 TTTAAA-ATATGGA-AAATTTTAT
1 TTTAAATATAT--ATTAA-TTTAT
*
1178295 TTTAAA-ATATGGATTGATTTAT
1 TTTAAATATAT--ATTAATTTAT
*
1178317 TTTAAA-ATATGGATTGATTTAT
1 TTTAAATATAT--ATTAATTTAT
*
1178339 TTTAAA-ATATGGA-AAATTTAT
1 TTTAAATATAT--ATTAATTTAT
** *
1178360 TTTAAATATGGATTGATTTAT
1 TTTAAATATATATTAATTTAT
1178381 TTTAAA
1 TTTAAA
1178387 AAATTTATTA
Statistics
Matches: 255, Mismatches: 42, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
20 5 0.02
21 79 0.31
22 170 0.67
23 1 0.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (21 bp):
TTTAAATATATATTAATTTAT
Found at i:1178251 original size:108 final size:108
Alignment explanation
Indices: 1178071--1178387 Score: 471
Period size: 108 Copynumber: 2.9 Consensus size: 108
1178061 AATATATTTT
* *
1178071 AAATTTATTTT-AAATATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAA
1 AAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATA-GGA
* *
1178135 AAAATTATTTTAAAATATTGATTGATTTATTTTAAAATATGGAA
65 AAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAA
*** *
1178179 AAATTTATTTTAAAATATGGATTGATTTATTTTAAAATAT-GAAAAAATTATTTT-AAATACGGA
1 AAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATA-GGA
**
1178242 TTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAA
65 -AAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAA
*
1178287 AATTTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGA
1 AAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATA-GGA
1178352 AAATTTATTTT-AAATATGGATTGATTTATTTTAAAA
65 AAATTTATTTTAAAATATGGATTGATTTATTTTAAAA
1178388 AATTTATTAT
Statistics
Matches: 186, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
107 7 0.04
108 125 0.67
109 46 0.25
110 8 0.04
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (108 bp):
AAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATAGGAA
AATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAA
Found at i:1178390 original size:44 final size:43
Alignment explanation
Indices: 1178094--1178387 Score: 423
Period size: 44 Copynumber: 6.8 Consensus size: 43
1178084 ATATAGATTG
*
1178094 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAAA
* *
1178137 AATTATTTTAAAATATTGATTGATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGG-AAA
*
1178181 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAAA
* * **
1178224 AATTATTTT-AAATACGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGA-AA
** **
1178267 ATTTATTTTAAAATATGGA-AAATTTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGA-TTTATTTTAAAATATGGA-AA
1178311 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAAA
1178354 ATTTATTTT-AAATATGGATTGATTTATTTTAAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAA
1178388 AATTTATTAT
Statistics
Matches: 227, Mismatches: 19, Indels: 11
0.88 0.07 0.04
Matches are distributed among these distances:
42 54 0.24
43 66 0.29
44 106 0.47
45 1 0.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (43 bp):
ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAAA
Found at i:1178421 original size:64 final size:65
Alignment explanation
Indices: 1178094--1178390 Score: 330
Period size: 64 Copynumber: 4.6 Consensus size: 65
1178084 ATATAGATTG
* *** * * * * *
1178094 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATAT-GAAAAAATTATTTTAAAATATTGATT
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAAAATGGATTGATTTAGTGTAAAATATGGA-A
*
1178158 G
65 A
*** * * * *
1178159 ATTTATTTTAAAATATGGAAAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAAAATGGATTGATTTAGTGTAAAATATGGAAA
* * * * *
1178224 AATTATTTT-AAATACGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAAAATGGATTGATTTAGTGTAAAATATGGAAA
* * *
1178288 ATTTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAA
1 A-TTTATTTTAAAATATGGATTGATTTATTTTAAAAAATGGATTGATTTAGTGTAAAATATGGAA
1178353 A
65 A
1178354 ATTTATTTT-AAATATGGATTGATTTATTTTAAAAAAT
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAAAAT
1178391 TTATTATTGT
Statistics
Matches: 209, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
64 78 0.37
65 58 0.28
66 73 0.35
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (65 bp):
ATTTATTTTAAAATATGGATTGATTTATTTTAAAAAATGGATTGATTTAGTGTAAAATATGGAAA
Found at i:1182148 original size:22 final size:22
Alignment explanation
Indices: 1182123--1182164 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1182113 GGCTGCCTAA
*
1182123 CTTTGAAATTTAAAGCAGCCCC
1 CTTTGAAAATTAAAGCAGCCCC
*
1182145 CTTTGAAAATTCAAGCAGCC
1 CTTTGAAAATTAAAGCAGCC
1182165 ACCGGCTGCT
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:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (22 bp):
CTTTGAAAATTAAAGCAGCCCC
Found at i:1200827 original size:16 final size:15
Alignment explanation
Indices: 1200802--1200846 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1200792 ATTTTGAATA
*
1200802 TTTGGATTGTTTGAT
1 TTTGGATTGTTTGAC
*
1200817 TTTGTGATTGTTAGAC
1 TTTG-GATTGTTTGAC
1200833 TTTGGATTTGTTTG
1 TTTGGA-TTGTTTG
1200847 GATGTTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.13, C:0.02, G:0.27, T:0.58
Consensus pattern (15 bp):
TTTGGATTGTTTGAC
Found at i:1202459 original size:20 final size:23
Alignment explanation
Indices: 1202424--1202483 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
1202414 TTACTAACTA
*
1202424 TTGTTGAAATTTAAA-T-CTGAAT
1 TTGTTG-AATTCAAATTGCTGAAT
1202446 TTGTT-AATTCAAATTAGGCTGAAT
1 TTGTTGAATTCAAATT--GCTGAAT
1202470 TTGTTGAATTCAAA
1 TTGTTGAATTCAAA
1202484 GTGGGCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.22
21 1 0.03
22 5 0.16
24 11 0.34
25 8 0.25
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (23 bp):
TTGTTGAATTCAAATTGCTGAAT
Found at i:1208779 original size:16 final size:16
Alignment explanation
Indices: 1208758--1208789 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1208748 TCCAACAGTG
1208758 TTATTTTTAATTTTTT
1 TTATTTTTAATTTTTT
*
1208774 TTATTTTTTATTTTTT
1 TTATTTTTAATTTTTT
1208790 GGGTATAACT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTATTTTTAATTTTTT
Found at i:1209679 original size:2 final size:2
Alignment explanation
Indices: 1209672--1209702 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1209662 GAGAAAATAA
1209672 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1209703 AATTCATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1211006 original size:18 final size:18
Alignment explanation
Indices: 1210983--1211017 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1210973 AAATATTACA
*
1210983 TACAATTTGGACAAAACG
1 TACAATTTGAACAAAACG
1211001 TACAATTTGAACAAAAC
1 TACAATTTGAACAAAAC
1211018 TAACTGCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (18 bp):
TACAATTTGAACAAAACG
Found at i:1211888 original size:70 final size:70
Alignment explanation
Indices: 1211804--1211944 Score: 239
Period size: 70 Copynumber: 2.0 Consensus size: 70
1211794 ATATCAAGGG
*
1211804 AAATTGATGGCCCAATAGTAAATTTTT-AAGTTGTAGTTCAGTTTAGGAACCTGTGGAAGTTAAG
1 AAATTGATGACCCAATAGT-AATTTTTAAAGTTGTAGTTCAGTTTAGGAACCTGTGGAAGTTAAG
1211868 GGACTT
65 GGACTT
* *
1211874 AAATTGATGACCCAATTGTAATTTTTAAAGTTGTAGTTCGGTTTAGGAACCTGTGGAAGTTAAGG
1 AAATTGATGACCCAATAGTAATTTTTAAAGTTGTAGTTCAGTTTAGGAACCTGTGGAAGTTAAGG
1211939 GACTT
66 GACTT
1211944 A
1 A
1211945 TCCTTGAATT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 7 0.10
70 60 0.90
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (70 bp):
AAATTGATGACCCAATAGTAATTTTTAAAGTTGTAGTTCAGTTTAGGAACCTGTGGAAGTTAAGG
GACTT
Found at i:1213657 original size:34 final size:34
Alignment explanation
Indices: 1213614--1213717 Score: 208
Period size: 34 Copynumber: 3.1 Consensus size: 34
1213604 GCTCTGAAAT
1213614 TAATAAATCAACCTCGTATACCAATATGACTATA
1 TAATAAATCAACCTCGTATACCAATATGACTATA
1213648 TAATAAATCAACCTCGTATACCAATATGACTATA
1 TAATAAATCAACCTCGTATACCAATATGACTATA
1213682 TAATAAATCAACCTCGTATACCAATATGACTATA
1 TAATAAATCAACCTCGTATACCAATATGACTATA
1213716 TA
1 TA
1213718 TATGACTAAG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 70 1.00
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (34 bp):
TAATAAATCAACCTCGTATACCAATATGACTATA
Found at i:1214744 original size:36 final size:36
Alignment explanation
Indices: 1214704--1214784 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
1214694 CATCGACTGA
*
1214704 TAATTCCTTATATGTGGCAGGTTCAGTCGCTGCTAG
1 TAATTCCTTAAATGTGGCAGGTTCAGTCGCTGCTAG
*
1214740 TAATTCCTTAAATGTGGCAGGTTCAGTCGCTGCTGG
1 TAATTCCTTAAATGTGGCAGGTTCAGTCGCTGCTAG
1214776 TAATTCCTT
1 TAATTCCTT
1214785 GAATAGGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (36 bp):
TAATTCCTTAAATGTGGCAGGTTCAGTCGCTGCTAG
Found at i:1214796 original size:31 final size:33
Alignment explanation
Indices: 1214704--1214816 Score: 97
Period size: 36 Copynumber: 3.3 Consensus size: 33
1214694 CATCGACTGA
* *
1214704 TAATTCCTTATATGTGGCAGGTTCAGTCGCTGCTAG
1 TAATTCCTTA-AAGT-G-AGGTTCAGTCGCTGCTGG
1214740 TAATTCCTTAAATGTGGCAGGTTCAGTCGCTGCTGG
1 TAATTCCTTAAA-GT-G-AGGTTCAGTCGCTGCTGG
* * *
1214776 TAATTCCTTGAA-T-AGGTTCAG-CACCGACTGG
1 TAATTCCTTAAAGTGAGGTTCAGTCGCTG-CTGG
1214807 TAATTCCTTA
1 TAATTCCTTA
1214817 TGGACCTAAG
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
30 3 0.04
31 21 0.30
34 1 0.01
35 1 0.01
36 43 0.62
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (33 bp):
TAATTCCTTAAAGTGAGGTTCAGTCGCTGCTGG
Found at i:1219751 original size:22 final size:21
Alignment explanation
Indices: 1219723--1219775 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 21
1219713 TGGGTTTTGT
1219723 AATATTATAA-TATTAATAATA
1 AATATTATAATTA-TAATAATA
1219744 ATATATTATAATTATAATAATA
1 A-ATATTATAATTATAATAATA
1219766 AATTATTATA
1 AA-TATTATA
1219776 TAATAACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.07
22 25 0.86
23 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATATTATAATTATAATAATA
Found at i:1219762 original size:19 final size:19
Alignment explanation
Indices: 1219724--1219781 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
1219714 GGGTTTTGTA
1219724 ATATTATAATATTAATAATAAT
1 ATATTAT-A-ATT-ATAATAAT
1219746 ATATTATAATTATAATAAT
1 ATATTATAATTATAATAAT
* *
1219765 AAATTATTA-TATAATAA
1 ATATTATAATTATAATAA
1219782 CATTAAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.24
19 15 0.44
20 3 0.09
21 1 0.03
22 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATTATAATTATAATAAT
Found at i:1219773 original size:16 final size:16
Alignment explanation
Indices: 1219754--1219786 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1219744 ATATATTATA
1219754 ATTATAATAATAA-ATT
1 ATTAT-ATAATAACATT
1219770 ATTATATAATAACATT
1 ATTATATAATAACATT
1219786 A
1 A
1219787 AAATGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTATATAATAACATT
Found at i:1220219 original size:38 final size:38
Alignment explanation
Indices: 1220130--1220238 Score: 154
Period size: 38 Copynumber: 2.9 Consensus size: 38
1220120 CATTATGAAT
1220130 TTCTTCTTTCAGATGAGTTCTCTCATTATGAA---ATTC
1 TTCTTC-TTCAGATGAGTTCTCTCATTATGAACTTATTC
*
1220166 TTCTTCTTCAGATGAGTTCT-TCATTATGAACTTCTTC
1 TTCTTCTTCAGATGAGTTCTCTCATTATGAACTTATTC
1220203 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 TT-CTTCTTCAGATGAGTTC-TCTCATTATGAACTT
1220239 TCTCTGGAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
34 10 0.15
35 14 0.21
36 6 0.09
37 5 0.08
38 17 0.26
39 1 0.02
40 13 0.20
ACGTcount: A:0.20, C:0.21, G:0.11, T:0.48
Consensus pattern (38 bp):
TTCTTCTTCAGATGAGTTCTCTCATTATGAACTTATTC
Found at i:1220414 original size:109 final size:112
Alignment explanation
Indices: 1220186--1221159 Score: 1439
Period size: 109 Copynumber: 8.8 Consensus size: 112
1220176 GATGAGTTCT
*
1220186 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTT-TCTGGAAAAG
*
1220251 CTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
65 CTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
*
1220299 TCATTATGAACTTCTTC-TCC-TATTCAGATGAGTTCTTCTTATTATGAACTTTTCTGGAAAAGC
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTTCTGGAAAAGC
*
1220362 TGATCTATCAAGTGATGGA-TTGAGCAAAAGGTTGAACAAGCTCTTC
66 TGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
*
1220408 TCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTTA-TATGAACTTCTCTGGAAAAGC
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTTCTGGAAAAGC
*
1220471 TGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAAC-AGCTCTTC
66 TGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
1220517 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATG-ACTTCTTCTGGAAAAG
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTT-TTCTGGAAAAG
1220581 CTGATCC--CAAGTGATGGATTTGAGC-AAAGGTTGAACAAGCTCTTC
65 CTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
1220626 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAG
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTT-TTCTGGAAAAG
*
1220691 CTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAGCTCTTC
65 CTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
*
1220739 TCATTATGAACTTCTTGTTCC-T-TTCAGATGAGTTCTTCTTATTATGAACTTCTTC-GGAAAAG
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTT-TTCTGGAAAAG
1220801 CTGATCCATC-AGTGATGGATTTGAGC-AAAGG-TGAACAAGCTCTTC
65 CTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
1220846 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAG
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTT-TTCTGGAAAAG
* **
1220911 CTGATCCATCAAGTGATGGATTTGAGCATAAGGTTGAACAAATTCTTC
65 CTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
* * * * **
1220959 TCATTATGAATTTATTCTTCCTCCTTCAAGTAATGAGTTCTTCTCATTATGAACTCTACCTGGAA
1 TCATTATGAACTTCTTCTTCCTTCTTC-AG--ATGAGTTCTTCTTATTATGAACT-TTTCTGGAA
*** * * ** * * **
1221024 ATTTTAATCCATCACA-TGATGAATTCAAACAAAAGGTTAAACAAATTCTTC
62 AAGCTGATCCATCA-AGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
*
1221075 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTT-TCTGGAAAAG
*
1221140 TTGAT-C--CAAGTGATGGATTT
65 CTGATCCATCAAGTGATGGATTT
1221160 AAATCTTTGC
Statistics
Matches: 794, Mismatches: 43, Indels: 51
0.89 0.05 0.06
Matches are distributed among these distances:
107 34 0.04
108 17 0.02
109 232 0.29
110 160 0.20
111 100 0.13
112 27 0.03
113 127 0.16
114 2 0.00
115 2 0.00
116 91 0.11
117 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (112 bp):
TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTTCTGGAAAAGC
TGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
Found at i:1220767 original size:220 final size:224
Alignment explanation
Indices: 1220186--1221161 Score: 1431
Period size: 220 Copynumber: 4.4 Consensus size: 224
1220176 GATGAGTTCT
*
1220186 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT-TCTCTGGAAAA
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCT-TCTGGAAAA
* *
1220250 GCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT
65 GCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT
* *
1220315 C-TCCTATTCAGATGAGTTCTTCTTATTATGAACTT-TTCTGGAAAAGCTGAT-CTATCAAGTGA
130 CTTCCTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAGCTGATCCCA-C-AGTGA
1220377 TGGA-TTGAGCAAAAGGTTGAACAAGCTCTTC
193 TGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
1220408 TCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTTA-TATGAACTTC-TCTGGAAAAG
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAG
1220470 CTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAAC-AGCTCTTCTCATTATGAACTTCTTC
66 CTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
1220534 TTCCTTCTTCAGATGAGTTCTTCTTATTATG-ACTTCTTCTGGAAAAGCTGATCCCA-AGTGATG
131 TTCC-TCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAGCTGATCCCACAGTGATG
1220597 GATTTGAGC-AAAGGTTGAACAAGCTCTTC
195 GATTTGAGCAAAAGGTTGAACAAGCTCTTC
1220626 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAG
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAG
*
1220691 CTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTG
66 CTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
1220756 TTCCT-TTCAGATGAGTTCTTCTTATTATGAACTTCTTC-GGAAAAGCTGAT-CCATCAGTGATG
131 TTCCTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAGCTGATCCCA-CAGTGATG
1220818 GATTTGAGC-AAAGG-TGAACAAGCTCTTC
195 GATTTGAGCAAAAGGTTGAACAAGCTCTTC
1220846 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAG
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAG
* * ** * *
1220911 CTGATCCATCAAGTGATGGATTTGAGCATAAGGTTGAACAAATTCTTCTCATTATGAATTTATTC
66 CTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* * *** *
1220976 TTCCTCCTTCAAGTAATGAGTTCTTCTCATTATGAAC-TCTACCTGGAAATTTTAATCCATCACA
131 TTCCT-CTTC-AG--ATGAGTTCTTCTTATTATGAACTTCT-TCTGGAAAAGCTGATCC--CACA
* ** * * **
1221040 -TGATGAATTCAAACAAAAGGTTAAACAAATTCTTC
189 GTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTC
*
1221075 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT-TCTCTGGAAAA
1 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCT-TCTGGAAAA
*
1221139 GTTGAT-C--CAAGTGATGGATTTAA
65 GCTGATCCATCAAGTGATGGATTTAA
1221162 ATCTTTGCTA
Statistics
Matches: 699, Mismatches: 29, Indels: 48
0.90 0.04 0.06
Matches are distributed among these distances:
218 73 0.10
219 86 0.12
220 238 0.34
221 103 0.15
222 50 0.07
223 2 0.00
224 3 0.00
225 22 0.03
226 23 0.03
227 11 0.02
228 9 0.01
229 79 0.11
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (224 bp):
TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAG
CTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
TTCCTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAGCTGATCCCACAGTGATGG
ATTTGAGCAAAAGGTTGAACAAGCTCTTC
Found at i:1221530 original size:52 final size:52
Alignment explanation
Indices: 1221452--1221556 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
1221442 CAACATGTTA
1221452 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
1 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
1221504 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
1 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
1221556 A
1 A
1221557 GATATCGATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.36
Consensus pattern (52 bp):
ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
Found at i:1223213 original size:16 final size:18
Alignment explanation
Indices: 1223168--1223214 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1223158 ATTCATAGAA
*
1223168 GAAATAAATTGAATTTTC
1 GAAATAAATTGAATTCTC
1223186 GAAA-ATAATTGAA-TCTC
1 GAAATA-AATTGAATTCTC
1223203 -AAATAAATTGAA
1 GAAATAAATTGAA
1223215 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 10 0.38
17 5 0.19
18 11 0.42
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (18 bp):
GAAATAAATTGAATTCTC
Found at i:1223562 original size:19 final size:21
Alignment explanation
Indices: 1223540--1223590 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1223530 TTGACCCCCC
1223540 TTTTTTCT-TTTTTTT-TTTT
1 TTTTTTCTCTTTTTTTCTTTT
1223559 TTTTTTCTCTTTTTTTCTTTT
1 TTTTTTCTCTTTTTTTCTTTT
*
1223580 CTTTTTCTCTT
1 TTTTTTCTCTT
1223591 CAAGCATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 8 0.28
20 7 0.24
21 14 0.48
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTTTTCTCTTTTTTTCTTTT
Found at i:1223569 original size:21 final size:21
Alignment explanation
Indices: 1223541--1223590 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1223531 TGACCCCCCT
* *
1223541 TTTTTCT-TTTTTTTTTTTTT
1 TTTTTCTCTTTTTTTCTTTTC
1223561 -TTTTCTCTTTTTTTCTTTTC
1 TTTTTCTCTTTTTTTCTTTTC
1223581 TTTTTCTCTT
1 TTTTTCTCTT
1223591 CAAGCATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 6 0.23
20 11 0.42
21 9 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTTTCTCTTTTTTTCTTTTC
Found at i:1223590 original size:8 final size:7
Alignment explanation
Indices: 1223539--1223590 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
1223529 CTTGACCCCC
1223539 CTTTTTT
1 CTTTTTT
1223546 CTTTTTT
1 CTTTTTT
1223553 -TTTTTT
1 CTTTTTT
1223559 -TTTTTT
1 CTTTTTT
1223565 CTCTTTTT
1 CT-TTTTT
1223573 -TTCTTTT
1 CTT-TTTT
1223580 CTTTTTCT
1 CTTTTT-T
1223588 CTT
1 CTT
1223591 CAAGCATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
6 13 0.32
7 16 0.40
8 11 0.28
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
CTTTTTT
Found at i:1230741 original size:15 final size:15
Alignment explanation
Indices: 1230718--1230749 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1230708 TGAAATGAAT
1230718 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1230733 AATGCATGTATGCAA
1 AATGAATGTATGCAA
1230748 AA
1 AA
1230750 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1235217 original size:9 final size:9
Alignment explanation
Indices: 1235203--1235241 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
1235193 ATTATTAATA
1235203 ATAATTATT
1 ATAATTATT
*
1235212 ATAATTATA
1 ATAATTATT
1235221 ATAATTATT
1 ATAATTATT
*
1235230 ATTATTA-T
1 ATAATTATT
1235238 ATAA
1 ATAA
1235242 ATAACATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
8 4 0.15
9 22 0.85
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATAATTATT
Found at i:1235223 original size:18 final size:18
Alignment explanation
Indices: 1235178--1235238 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
1235168 GGTTTTGTAA
1235178 TATTA-AATAA-TATATAT
1 TATTATAATAATTAT-TAT
1235195 TATTAATAATAATTATTAT
1 TATT-ATAATAATTATTAT
*
1235214 AATTATAATAATTATTAT
1 TATTATAATAATTATTAT
1235232 TATTATA
1 TATTATA
1235239 TAAATAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.10
18 21 0.54
19 11 0.28
20 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTATAATAATTATTAT
Found at i:1240735 original size:22 final size:23
Alignment explanation
Indices: 1240669--1240737 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
1240659 CGTGCGAGCC
*
1240669 GCCATCGAGCCACTGTCGAACAT
1 GCCATCGAGCCACTGCCGAACAT
* ** * *
1240692 GTCATATAGCCA-TTCACAAACAT
1 GCCATCGAGCCACTGC-CGAACAT
1240715 -CCATCGAGCCACTGCCGAACAT
1 GCCATCGAGCCACTGCCGAACAT
1240737 G
1 G
1240738 TCATATAGCC
Statistics
Matches: 32, Mismatches: 11, Indels: 6
0.65 0.22 0.12
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.19
Consensus pattern (23 bp):
GCCATCGAGCCACTGCCGAACAT
Found at i:1243865 original size:2 final size:2
Alignment explanation
Indices: 1243858--1243899 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1243848 AATTGGATCC
1243858 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1243900 ATATATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1243904 original size:2 final size:2
Alignment explanation
Indices: 1243899--1243941 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1243889 TCTCTCTCTC
1243899 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1243941 T
1 T
1243942 TATGACCCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1245498 original size:18 final size:19
Alignment explanation
Indices: 1245456--1245492 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1245446 AACTAAGGGT
1245456 CAAGTTTTTCTTCTTTCCC
1 CAAGTTTTTCTTCTTTCCC
1245475 CAAGTTTTTCTTCTTTCC
1 CAAGTTTTTCTTCTTTCC
1245493 TAAGTTCAAA
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:0.11, C:0.30, G:0.05, T:0.54
Consensus pattern (19 bp):
CAAGTTTTTCTTCTTTCCC
Found at i:1246957 original size:133 final size:134
Alignment explanation
Indices: 1246719--1247252 Score: 770
Period size: 133 Copynumber: 4.0 Consensus size: 134
1246709 AAATTTCAAA
* * * * *
1246719 CCATCCAGTAAG-GAAACATATAGGAAAGTATGACAAATAGTTTTCAGCGTGACTATAACA--CA
1 CCATCCGGTAAGAG-AACATATAGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATAA-ATGCA
* * *
1246781 AACATTCACAGGATATATAACATAATTTCAGAAACACATAGAAATGAAGATTCACTTCCAAAGAA
64 AACATTCACAGGAAATATAACATAATTTCAGAAACAAATAGAAATGAAGATTCAATTCCAAAGAA
* *
1246846 ATAAAT
129 AGAAAG
*
1246852 CCATCCGGTAAGAGAACATACAGGAAAGCATGATAAGTAG-TTTCAGTGTGACTATAAATGCAAA
1 CCATCCGGTAAGAGAACATATAGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATAAATGCAAA
* * *
1246916 CATTTACAGGAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCATTTCCAAAGAAAG
66 CATTCACAGGAAATATAACATAATTTCAGAAACAAATAGAAATGAAGATTCAATTCCAAAGAAAG
1246981 AAAG
131 AAAG
* * * *
1246985 CCATCCTGTAAGAAAACATATGGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATTAATGCAAA
1 CCATCCGGTAAGAGAACATATAGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATAAATGCAAA
* * *
1247050 CATTCACATGGAAATACAACATAATTTCAAAAACAAATAGAAATGAAGATTCAATTTCAAAGAAA
66 CATTCACA-GGAAATATAACATAATTTCAGAAACAAATAGAAATGAAGATTCAATTCCAAAGAAA
1247115 GAAAG
130 GAAAG
* * * *
1247120 CCATACGGTGATAGAACATATAGGAAAGCATGATAAGTAGTTTTCAGTGAGACTATAAATGCAAA
1 CCATCCGGTAAGAGAACATATAGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATAAATGCAAA
* *
1247185 CATTCACAGGAAATATAACATAATTTCAGAAACAGATAGAAATGAAGATTCAGTTCCAAAGAAAG
66 CATTCACAGGAAATATAACATAATTTCAGAAACAAATAGAAATGAAGATTCAATTCCAAAGAAAG
1247250 AAA
131 AAA
1247253 TTTCAATAAT
Statistics
Matches: 360, Mismatches: 36, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
131 1 0.00
132 16 0.04
133 135 0.38
134 86 0.24
135 122 0.34
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (134 bp):
CCATCCGGTAAGAGAACATATAGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATAAATGCAAA
CATTCACAGGAAATATAACATAATTTCAGAAACAAATAGAAATGAAGATTCAATTCCAAAGAAAG
AAAG
Found at i:1247231 original size:269 final size:266
Alignment explanation
Indices: 1246719--1247252 Score: 807
Period size: 268 Copynumber: 2.0 Consensus size: 266
1246709 AAATTTCAAA
* *
1246719 CCATCCAGTAAGGAAACATATAGGAAAGTATGACAAATAGTTTTCAGCGTGACTATAACACAAAC
1 CCATCCAGTAAGAAAACATATAGGAAAGCATGACAAATAGTTTTCAGCGTGACTATAACACAAAC
* * * * * *
1246784 ATTCACAGGATATATAACATAATTTCAGAAACACATAGAAATGAAGATTCACTTCCAAAGAAATA
66 ATTCACAGGAAATACAACATAATTTCAAAAACAAATAGAAATGAAGATTCAATTCCAAAGAAAGA
* * *
1246849 AATCCATCCGGTAAGAGAACATACAGGAAAGCATGATAAGTAGTTTCAGTGTGACTATAAATGCA
131 AAGCCATACGGTAAGAGAACATACAGGAAAGCATGATAAGTAGTTTCAGTGAGACTATAAATGCA
* *
1246914 AACATTTACAGGAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCATTTCCAAAGAA
196 AACATTCACAGGAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCAGTTCCAAAGAA
1246979 AGAAAG
261 AGAAAG
* * * * * **
1246985 CCATCCTGTAAGAAAACATATGGGAAAGCATGATAAGTAGTTTTCAGTGTGACTATTAATGCAAA
1 CCATCCAGTAAGAAAACATATAGGAAAGCATGACAAATAGTTTTCAGCGTGACTA-TAACACAAA
*
1247050 CATTCACATGGAAATACAACATAATTTCAAAAACAAATAGAAATGAAGATTCAATTTCAAAGAAA
65 CATTCACA-GGAAATACAACATAATTTCAAAAACAAATAGAAATGAAGATTCAATTCCAAAGAAA
* * *
1247115 GAAAGCCATACGGTGATAGAACATATAGGAAAGCATGATAAGTAGTTTTCAGTGAGACTATAAAT
129 GAAAGCCATACGGTAAGAGAACATACAGGAAAGCATGATAAGTAG-TTTCAGTGAGACTATAAAT
* *
1247180 GCAAACATTCACAGGAAATATAACATAATTTCAGAAACAGATAGAAATGAAGATTCAGTTCCAAA
193 GCAAACATTCACAGGAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCAGTTCCAAA
1247245 GAAAGAAA
258 GAAAGAAA
1247253 TTTCAATAAT
Statistics
Matches: 239, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
266 48 0.20
267 15 0.06
268 89 0.37
269 87 0.36
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (266 bp):
CCATCCAGTAAGAAAACATATAGGAAAGCATGACAAATAGTTTTCAGCGTGACTATAACACAAAC
ATTCACAGGAAATACAACATAATTTCAAAAACAAATAGAAATGAAGATTCAATTCCAAAGAAAGA
AAGCCATACGGTAAGAGAACATACAGGAAAGCATGATAAGTAGTTTCAGTGAGACTATAAATGCA
AACATTCACAGGAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCAGTTCCAAAGAA
AGAAAG
Found at i:1253805 original size:15 final size:15
Alignment explanation
Indices: 1253787--1253819 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1253777 ATCAACAGAT
1253787 ATAATTTTTATATAA
1 ATAATTTTTATATAA
*
1253802 ATAATTTTTATTTAA
1 ATAATTTTTATATAA
1253817 ATA
1 ATA
1253820 TTTAGAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTATATAA
Found at i:1255529 original size:23 final size:22
Alignment explanation
Indices: 1255502--1255576 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
1255492 TGATATATGA
1255502 ATATGCAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
* ** *
1255525 ATATG-ATATGAAATAACATATG
1 ATATGAATACGTGAT-ACATGTG
1255547 AATATGTAATACGTGATACATGTG
1 -ATATG-AATACGTGATACATGTG
1255571 ATATGA
1 ATATGA
1255577 TATGAAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 6 0.15
22 7 0.17
23 15 0.38
24 6 0.15
25 6 0.15
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (22 bp):
ATATGAATACGTGATACATGTG
Found at i:1255546 original size:46 final size:46
Alignment explanation
Indices: 1255476--1255585 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
1255466 GAGATAAGCT
* *
1255476 ATGTGAT-T-ATATGAAATGATATATGAATATGCAATACGTGATAC
1 ATGTGATATGATATGAAATAACATATGAATATGCAATACGTGATAC
*
1255520 ATGTGATATGATATGAAATAACATATGAATATGTAATACGTGATAC
1 ATGTGATATGATATGAAATAACATATGAATATGCAATACGTGATAC
1255566 ATGTGATATGATATGAAATA
1 ATGTGATATGATATGAAATA
1255586 CATGGTTACA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 7 0.11
45 1 0.02
46 53 0.87
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (46 bp):
ATGTGATATGATATGAAATAACATATGAATATGCAATACGTGATAC
Found at i:1255805 original size:38 final size:38
Alignment explanation
Indices: 1255737--1255832 Score: 122
Period size: 38 Copynumber: 2.5 Consensus size: 38
1255727 TATAAGACAT
* *
1255737 ATGATAGGTCC-TACGGGACACAGATTACATCCTTCAGG
1 ATGATAGGTCCTTA-GGGATACAGATGACATCCTTCAGG
* * *
1255775 ATGACAGGTCCTTAGGGATACATATGACATCCTTCGGG
1 ATGATAGGTCCTTAGGGATACAGATGACATCCTTCAGG
*
1255813 ATGATAGGTCCTTCGGGATA
1 ATGATAGGTCCTTAGGGATA
1255833 TTTATACGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 48 0.96
39 2 0.04
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (38 bp):
ATGATAGGTCCTTAGGGATACAGATGACATCCTTCAGG
Found at i:1267682 original size:2 final size:2
Alignment explanation
Indices: 1267675--1267703 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1267665 CACTGCACTT
1267675 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1267704 AAATATAGGC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1268377 original size:3 final size:3
Alignment explanation
Indices: 1268369--1268399 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1268359 TTTATCTTAA
1268369 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1268400 AACAATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1279538 original size:23 final size:23
Alignment explanation
Indices: 1279471--1279540 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
1279461 CACCACAGTT
* *
1279471 CGTATAAATGCACCGAAGTGTCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1279494 CGTAGAATTTGCACCGTAGTGCCG
1 CGTAGAA-ATGCACCGAAGTGCCA
1279518 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1279541 TATAAAGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1279950 original size:22 final size:19
Alignment explanation
Indices: 1279923--1279972 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
1279913 ATTTTTGTGT
*
1279923 TATCATATAACTTCTCTTTTA
1 TATCATATAA-TT-TCTTATA
1279944 TATTCATATAATTTCTTATA
1 TA-TCATATAATTTCTTATA
1279964 TATCATATA
1 TATCATATA
1279973 GTTTATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 7 0.26
20 8 0.30
21 4 0.15
22 8 0.30
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (19 bp):
TATCATATAATTTCTTATA
Found at i:1284335 original size:20 final size:21
Alignment explanation
Indices: 1284288--1284338 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
1284278 TTTTGTGTCT
*
1284288 TATCATATAACTTCTCTTTTA
1 TATCATATAACTTCTCTTTCA
1284309 TATTCATATAA-TT-TCTTATCA
1 TA-TCATATAACTTCTCTT-TCA
1284330 TATCATATA
1 TATCATATA
1284339 GTTTATCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.41
21 8 0.30
22 8 0.30
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (21 bp):
TATCATATAACTTCTCTTTCA
Found at i:1284349 original size:20 final size:20
Alignment explanation
Indices: 1284312--1284356 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1284302 TCTTTTATAT
* *
1284312 TCATATAATTTCTTATCATA
1 TCATATAATTTATCATCATA
*
1284332 TCATATAGTTTATCATCATA
1 TCATATAATTTATCATCATA
*
1284352 ACATA
1 TCATA
1284357 GTATATTACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (20 bp):
TCATATAATTTATCATCATA
Found at i:1290180 original size:24 final size:26
Alignment explanation
Indices: 1290153--1290202 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1290143 TTATTCTTAT
1290153 AATATT-TTAA-AATTAAGATAAAAA
1 AATATTGTTAATAATTAAGATAAAAA
*
1290177 AATATTGTTAATATTTAAGATAAAAA
1 AATATTGTTAATAATTAAGATAAAAA
1290203 TAAAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.26
25 4 0.17
26 13 0.57
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (26 bp):
AATATTGTTAATAATTAAGATAAAAA
Found at i:1290204 original size:24 final size:23
Alignment explanation
Indices: 1290153--1290202 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 23
1290143 TTATTCTTAT
1290153 AATATTTTAAAATTAAGATAAAAA
1 AATATTTTAAAATTAAGAT-AAAA
*
1290177 AATATTGTTAATATTTAAGATAAAA
1 AATATT-TTAA-AATTAAGATAAAA
1290202 A
1 A
1290203 TAAAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 9 0.39
26 8 0.35
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (23 bp):
AATATTTTAAAATTAAGATAAAA
Found at i:1290237 original size:30 final size:30
Alignment explanation
Indices: 1290191--1290445 Score: 215
Period size: 30 Copynumber: 8.7 Consensus size: 30
1290181 TTGTTAATAT
* *
1290191 TTAAGATAAAAATAAAATATATTTATTAAA
1 TTAAGATAAGAATAAAATATATTTATTAAG
* *
1290221 TTAAAATAAGAATAAAATATACATTT-TTAAA
1 TTAAGATAAGAATAAAATAT--ATTTATTAAG
* **
1290252 TTAAAATAA-AAT---ATATATTT-TTGGG
1 TTAAGATAAGAATAAAATATATTTATTAAG
* * *
1290277 TTGAGATAAGAAT-AAATAATATTTAATAAT
1 TTAAGATAAGAATAAAAT-ATATTTATTAAG
* * *
1290307 TTAAGATAAGAATATAATATATTTAATAAT
1 TTAAGATAAGAATAAAATATATTTATTAAG
* * * *
1290337 TTAAGTTAAGAATATAATATATGTATCAAG
1 TTAAGATAAGAATAAAATATATTTATTAAG
*
1290367 TTAAGATAAAAATAAAATATATTT-TTAAG
1 TTAAGATAAGAATAAAATATATTTATTAAG
*
1290396 TTAAGGTAAGAATAAAATATATTT-TATAAG
1 TTAAGATAAGAATAAAATATATTTAT-TAAG
*
1290426 -TAAGATAAAGATTAAAATAT
1 TTAAGAT-AAGAATAAAATAT
1290446 TTAATATTAA
Statistics
Matches: 188, Mismatches: 27, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
25 13 0.07
26 3 0.02
27 4 0.02
28 2 0.01
29 38 0.20
30 107 0.57
31 17 0.09
32 4 0.02
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (30 bp):
TTAAGATAAGAATAAAATATATTTATTAAG
Found at i:1290252 original size:25 final size:25
Alignment explanation
Indices: 1290221--1290273 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1290211 ATTTATTAAA
*
1290221 TTAAAATAAGAATAAAATATACATTT
1 TTAAATTAA-AATAAAATATACATTT
*
1290247 TTAAATTAAAATAAAATATATATTT
1 TTAAATTAAAATAAAATATACATTT
1290272 TT
1 TT
1290274 GGGTTGAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
TTAAATTAAAATAAAATATACATTT
Found at i:1290351 original size:86 final size:85
Alignment explanation
Indices: 1290194--1290424 Score: 207
Period size: 86 Copynumber: 2.7 Consensus size: 85
1290184 TTAATATTTA
* *
1290194 AGATAAAAATAAAATATATTTATTAAATTAAAATAAGAATAAAATATACATTTTTAAATTAAAAT
1 AGATAAAAATAAAATATATTTAATAAATTAAAATAAGAATAAAATATA-ATTTATAAATTAAAAT
1290259 AAAATATATATTTTTGGGTTG
65 AAAATATATATTTTTGGGTTG
* * * * * **
1290280 AGATAAGAAT-AAATAATATTTAATAATTTAAGATAAGAATATAATAT-ATTTAATAATTTAAGT
1 AGATAAAAATAAAAT-ATATTTAATAAATTAAAATAAGAATAAAATATAATTT-ATAAATTAAAA
*** *
1290343 TAAGAATATAATATATGTATCAAGTTA
64 TAA-AATAT-ATAT-T-T-TTGGGTTG
* * ** *
1290370 AGATAAAAATAAAATATATTT-TTAAGTTAAGGTAAGAATAAAATATATTTTATAA
1 AGATAAAAATAAAATATATTTAATAAATTAAAATAAGAATAAAATATAATTTATAA
1290425 GTAAGATAAA
Statistics
Matches: 117, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
84 4 0.03
85 14 0.12
86 42 0.36
87 4 0.03
88 1 0.01
89 26 0.22
90 22 0.19
91 4 0.03
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (85 bp):
AGATAAAAATAAAATATATTTAATAAATTAAAATAAGAATAAAATATAATTTATAAATTAAAATA
AAATATATATTTTTGGGTTG
Found at i:1290621 original size:15 final size:14
Alignment explanation
Indices: 1290592--1290625 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1290582 TGATCGGTGA
*
1290592 AAATTAAATATATT
1 AAATTAAATAAATT
1290606 AAATTAAAATAAATT
1 AAATT-AAATAAATT
1290621 AAATT
1 AAATT
1290626 CTCTAATCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATTAAATAAATT
Found at i:1293154 original size:31 final size:31
Alignment explanation
Indices: 1293116--1293184 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1293106 CTTTTAAAAC
1293116 TTGCAATACAATCCCCCAACATTTAGTCCGT
1 TTGCAATACAATCCCCCAACATTTAGTCCGT
*** * *
1293147 TTGCAATATGGTCCCTCAACATTTAGTCCTT
1 TTGCAATACAATCCCCCAACATTTAGTCCGT
1293178 TTGCAAT
1 TTGCAAT
1293185 TGACCCCCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.35
Consensus pattern (31 bp):
TTGCAATACAATCCCCCAACATTTAGTCCGT
Found at i:1300609 original size:31 final size:31
Alignment explanation
Indices: 1300537--1300601 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1300527 GTTACGTCGA
* *
1300537 GGACCATATTGCAAACATACTAAATGTTGAG
1 GGACCATATTGCAAACAGACTAAATATTGAG
*
1300568 GGACCATATTGCAAACGGACTAAATATTGAG
1 GGACCATATTGCAAACAGACTAAATATTGAG
1300599 GGA
1 GGA
1300602 TTATATTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (31 bp):
GGACCATATTGCAAACAGACTAAATATTGAG
Found at i:1315421 original size:13 final size:12
Alignment explanation
Indices: 1315394--1315431 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
1315384 ATGTAAAACT
1315394 ATATT-TTTAAA
1 ATATTGTTTAAA
1315405 ATATTGTTTACAA
1 ATATTGTTTA-AA
*
1315418 ATATAGTTTAAA
1 ATATTGTTTAAA
1315430 AT
1 AT
1315432 TCTATCGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 5 0.21
12 8 0.33
13 11 0.46
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (12 bp):
ATATTGTTTAAA
Found at i:1315643 original size:16 final size:15
Alignment explanation
Indices: 1315610--1315652 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
1315600 TTTAAGATAA
* *
1315610 TTTATTAATAAATTT
1 TTTATTAAAAAATAT
1315625 TTTATATAAAAAATAT
1 TTTAT-TAAAAAATAT
1315641 TTTATTAAAAAA
1 TTTATTAAAAAA
1315653 GTATAATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTATTAAAAAATAT
Found at i:1316025 original size:14 final size:15
Alignment explanation
Indices: 1315994--1316023 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1315984 TTAAATTTGT
1315994 ATTGCGATTTTTTAA
1 ATTGCGATTTTTTAA
*
1316009 ATTGTGATTTTTTAA
1 ATTGCGATTTTTTAA
1316024 TTTCGTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (15 bp):
ATTGCGATTTTTTAA
Found at i:1316289 original size:22 final size:22
Alignment explanation
Indices: 1316264--1316307 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1316254 CTCTTTCCGG
1316264 CGACATCTGTTCT-TATATCTAA
1 CGACATCT-TTCTCTATATCTAA
*
1316286 CGACATCTTTCTCTATCTCTAA
1 CGACATCTTTCTCTATATCTAA
1316308 TTTTTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.41
Consensus pattern (22 bp):
CGACATCTTTCTCTATATCTAA
Found at i:1316324 original size:14 final size:16
Alignment explanation
Indices: 1316305--1316341 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1316295 TCTCTATCTC
1316305 TAATTTT-TTT-TACA
1 TAATTTTATTTCTACA
*
1316319 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
1316335 TAATTTT
1 TAATTTT
1316342 CAATGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:1319423 original size:20 final size:20
Alignment explanation
Indices: 1319400--1319442 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1319390 ATCACAAAGT
1319400 GAATTTGACTTTCACGTTGC
1 GAATTTGACTTTCACGTTGC
*
1319420 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCACGTTGC
1319440 GAA
1 GAA
1319443 AGTGTACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (20 bp):
GAATTTGACTTTCACGTTGC
Found at i:1320980 original size:21 final size:21
Alignment explanation
Indices: 1320956--1321054 Score: 110
Period size: 21 Copynumber: 4.7 Consensus size: 21
1320946 GTGGAAGAGA
* *
1320956 CCTCTTTAACGATGATAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
1320977 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
1320998 CCTCTTGAAGGATGATAGGGC
1 CCTCTTGAACGATGAGAGGGG
*
1321019 CCTCTTGAACGAT-AGGAGAGG
1 CCTCTTGAACGATGA-GAGGGG
1321040 CCTCTTGAACGATGA
1 CCTCTTGAACGATGA
1321055 CAGATGAATC
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 1 0.02
21 61 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:1321002 original size:42 final size:42
Alignment explanation
Indices: 1320936--1321054 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
1320926 GTGTATCGGG
* * * *
1320936 CTCTTGAACGGTGGAAGAGACCTCTTTAACGATGATAGGGGC
1 CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGATAGGGCC
* *
1320978 CTCTTGAACGGTGGGAGGGGCCTCTTGAAGGATGATAGGGCC
1 CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGATAGGGCC
* *
1321020 CTCTTGAACGATAGGAGAGGCCTCTTGAACGATGA
1 CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGA
1321055 CAGATGAATC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGATAGGGCC
Done.