Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 29
Found at i:1458970 original size:11 final size:11
Alignment explanation
Indices: 1458946--1458990 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1458936 TTTGTGCTGG
1458946 AAACAAGATAA
1 AAACAAGATAA
* *
1458957 AAATAAGATTA
1 AAACAAGATAA
1458968 AAACAAGATAA
1 AAACAAGATAA
1458979 AGAA-AAGATAA
1 A-AACAAGATAA
1458990 A
1 A
1458991 TGACTCCATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:1458974 original size:22 final size:22
Alignment explanation
Indices: 1458946--1458987 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1458936 TTTGTGCTGG
1458946 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
1458968 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
1458988 AAATGACTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:1460177 original size:24 final size:24
Alignment explanation
Indices: 1460150--1460199 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1460140 TGGTGGTTGA
*
1460150 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1460174 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1460198 TT
1 TT
1460200 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1466159 original size:26 final size:25
Alignment explanation
Indices: 1466128--1466198 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 25
1466118 CCTCTTAAAT
1466128 TTTTAACTTTTTCTTTTCTCTTTC-
1 TTTTAACTTTTTCTTTTCTCTTTCA
*
1466152 -TTT-A-TTAATT-TTTTCTCTTTCA
1 TTTTAACTT-TTTCTTTTCTCTTTCA
*
1466174 TTTTAACTTTTACTTTTTCTCTTTC
1 TTTTAACTTTTTC-TTTTCTCTTTC
1466199 CTTCATTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
21 13 0.35
22 3 0.08
23 6 0.16
24 2 0.05
25 2 0.05
26 11 0.30
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTAACTTTTTCTTTTCTCTTTCA
Found at i:1466218 original size:47 final size:46
Alignment explanation
Indices: 1466128--1466218 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 46
1466118 CCTCTTAAAT
* * * *
1466128 TTTTAACTTTTTCTTTTCTCTTTCTTTATTAATTTTTTCTCTTTCA
1 TTTTAACTTTTACTTTTCTCTTTCTTCATTAATCTTCTCTCTTTCA
*
1466174 TTTTAACTTTTACTTTTTCTCTTTCCTTCATTCATCTTCT-TCTTT
1 TTTTAACTTTTAC-TTTTCTCTTT-CTTCATTAATCTTCTCTCTTT
1466219 TGTTATTCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
46 12 0.32
47 15 0.39
48 11 0.29
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (46 bp):
TTTTAACTTTTACTTTTCTCTTTCTTCATTAATCTTCTCTCTTTCA
Found at i:1469513 original size:24 final size:24
Alignment explanation
Indices: 1469486--1469535 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1469476 TGGTGGTTGA
*
1469486 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1469510 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1469534 TT
1 TT
1469536 GGTTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1471037 original size:32 final size:32
Alignment explanation
Indices: 1470996--1471081 Score: 136
Period size: 33 Copynumber: 2.7 Consensus size: 32
1470986 TCTAATTCAT
1470996 ATATTCGGGTCGGGTCGGGTTTTTTAAGTGTG
1 ATATTCGGGTCGGGTCGGGTTTTTTAAGTGTG
*
1471028 ATATTCGGGTCGAGTCGGGCTTTTTTAAGTGTG
1 ATATTCGGGTCGGGTCGGG-TTTTTTAAGTGTG
* *
1471061 CTATTCGGGTCGGGTAGGGTT
1 ATATTCGGGTCGGGTCGGGTT
1471082 CGAGTTTAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 20 0.41
33 29 0.59
ACGTcount: A:0.13, C:0.12, G:0.37, T:0.38
Consensus pattern (32 bp):
ATATTCGGGTCGGGTCGGGTTTTTTAAGTGTG
Found at i:1471205 original size:264 final size:255
Alignment explanation
Indices: 1470685--1471270 Score: 730
Period size: 264 Copynumber: 2.2 Consensus size: 255
1470675 CTTATTCATA
* *
1470685 TATTGAATAAAAATATTTTTTTATTATTTCGGGTTGGGTCGGGTTTCTAATTCATAT-TTTGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGT
** *
1470749 CGGGTCAGGTGAAACTTTATTTTGGTCGGGCCGGGTCAGTTTTTTTAAGTGTGATATTCAGGTCG
66 CGGGTCAGGTGAAACTTTATTCGGGTCGAGCCGGGTCA--TTTTTTAAGTGTGATATTCAGGTCG
* * * *
1470814 GGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATACATATAATTTTACCTTATATA
129 GGTAGAGTTCGAGTTTAGGGTGAAAAATAACCGACCCGAAAAAACATATAATTTTACCTTATATA
* *
1470879 TTTAGGAATAATTACAATAATACCCCTCTATGTATATATTTTTTCAATTAAATCACTGTTTT
194 TTTAGGAATAATTACAATAATACCCCTCTATATATATATTTTTTCAATTAAATCAATGTTTT
* *
1470941 TATTGAATAAAAATACTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGT
* ** * * * *
1471006 CGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGG-C-TTTTTTAAGTGTGCTATTCGG
66 CGGGTCAGG---TGAAACT-T--TATTCGGGTCGAGCCGGGTCATTTTTTAAGTGTGATATTCAG
* *
1471069 GTCGGGTAGGGTTCGAGTTTAGGGTGAAAAAAATCGAACCGACCCGAAAAAAATATATAATTTTA
125 GTCGGGTAGAGTTCGAGTTTAGGGTG--AAAAAT--AACCGACCCG-AAAAAACATATAATTTTA
* *
1471134 CCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATA-ATTTTTTTTAATTAAGTCA
185 CCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATATA-TTTTTTCAATTAAATCA
1471198 ATGTTTT
249 ATGTTTT
* *
1471205 TATTGAATAAAAATAATTTTTTTATTATTTTGTGTCGTGTCGGGTCGGGTTTCTAATTCTTATAT
1 TATTGAATAAAAAT-ATTTTTTTATTA---T-T-TCGGGTCGGGTCGGGTTTCTAATTCATATAT
1471270 T
60 T
1471271 GAATAAAAAT
Statistics
Matches: 283, Mismatches: 28, Indels: 24
0.84 0.08 0.07
Matches are distributed among these distances:
256 54 0.19
257 14 0.05
259 42 0.15
260 4 0.01
261 7 0.02
262 1 0.00
263 24 0.08
264 95 0.34
265 11 0.04
268 1 0.00
269 1 0.00
270 29 0.10
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (255 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGT
CGGGTCAGGTGAAACTTTATTCGGGTCGAGCCGGGTCATTTTTTAAGTGTGATATTCAGGTCGGG
TAGAGTTCGAGTTTAGGGTGAAAAATAACCGACCCGAAAAAACATATAATTTTACCTTATATATT
TAGGAATAATTACAATAATACCCCTCTATATATATATTTTTTCAATTAAATCAATGTTTT
Found at i:1471826 original size:64 final size:64
Alignment explanation
Indices: 1471666--1471849 Score: 203
Period size: 65 Copynumber: 2.8 Consensus size: 64
1471656 AATTAAATTG
* *
1471666 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACCAAGGATGTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCAC-TACCATGCACCGATGCACCAAGGATATTATGAA
* * * * *
1471731 AACATCGAATGCATTTGATGCATCGATGCACTAGTCATGCATCGATGCACTC-TGGCTATTTTG-
1 AACATCGAATGCATTTGATGCATCGATGCACTA-CCATGCACCGATGCAC-CAAGGATATTATGA
1471794 A
64 A
* * * *
1471795 AACATCGAATGCACTTGATGCATTGATGCACT-CTTAGTGCACCGATGCACTAAGG
1 AACATCGAATGCATTTGATGCATCGATGCACTAC-CA-TGCACCGATGCACCAAGG
1471850 GAGTGCACTG
Statistics
Matches: 100, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
63 1 0.01
64 47 0.47
65 51 0.51
66 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTACCATGCACCGATGCACCAAGGATATTATGAA
Found at i:1471856 original size:21 final size:21
Alignment explanation
Indices: 1471830--1471871 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1471820 ATGCACTCTT
1471830 AGTGCACCGATGCACTAAGGG
1 AGTGCACCGATGCACTAAGGG
*
1471851 AGTGCACTGATGCACTAAGGG
1 AGTGCACCGATGCACTAAGGG
1471872 TCCAACGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.33, T:0.17
Consensus pattern (21 bp):
AGTGCACCGATGCACTAAGGG
Found at i:1472897 original size:17 final size:17
Alignment explanation
Indices: 1472863--1472908 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
1472853 TATGGAATTG
*
1472863 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
1472880 GATT-CAATTCCTTCACA
1 GATTCCAATTCC-TCACA
1472897 GATTCCAATTCC
1 GATTCCAATTCC
1472909 CTCGTAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.27
17 12 0.46
18 7 0.27
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:1473009 original size:19 final size:19
Alignment explanation
Indices: 1472985--1473023 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1472975 TCATCTTATG
* *
1472985 AAACTAAAATTAAGAAATA
1 AAACTAAAAATAAAAAATA
1473004 AAACTAAAAATAAAAAATA
1 AAACTAAAAATAAAAAATA
1473023 A
1 A
1473024 CAAAAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (19 bp):
AAACTAAAAATAAAAAATA
Found at i:1475125 original size:14 final size:14
Alignment explanation
Indices: 1475106--1475144 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
1475096 GAACATTAAT
1475106 ATAAACAAACGAAC
1 ATAAACAAACGAAC
1475120 ATAAACAAACGAAC
1 ATAAACAAACGAAC
1475134 ATAAACAAACG
1 ATAAACAAACG
1475145 CTATACGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.64, C:0.21, G:0.08, T:0.08
Consensus pattern (14 bp):
ATAAACAAACGAAC
Found at i:1479197 original size:23 final size:23
Alignment explanation
Indices: 1479171--1479221 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1479161 TTTATTACTA
1479171 ATTTAATTTTAAAAATAT-TTTTT
1 ATTTAA-TTTAAAAATATATTTTT
* *
1479194 ATTTTCATTTAAATATATATTTTT
1 A-TTTAATTTAAAAATATATTTTT
1479218 ATTT
1 ATTT
1479222 TAAAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTTAATTTAAAAATATATTTTT
Found at i:1479216 original size:24 final size:23
Alignment explanation
Indices: 1479178--1479222 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1479168 CTAATTTAAT
1479178 TTTAAAAATATTTTTTATTTTCA
1 TTTAAAAATATTTTTTATTTTCA
*
1479201 TTTAAATATATATTTTTATTTT
1 TTTAAAAATAT-TTTTTATTTT
1479223 AAAATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTAAAAATATTTTTTATTTTCA
Found at i:1480055 original size:20 final size:19
Alignment explanation
Indices: 1480032--1480078 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1480022 TGATATACCA
*
1480032 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGAAAAAACC
*
1480052 GGTATCAAAATGAAAAAACC
1 GGTA-AAAAATGAAAAAACC
1480072 GGTAAAA
1 GGTAAAA
1480079 CGTTACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGAAAAAACC
Found at i:1480155 original size:181 final size:183
Alignment explanation
Indices: 1479820--1480293 Score: 704
Period size: 182 Copynumber: 2.6 Consensus size: 183
1479810 GATCCAAATT
* * * **
1479820 AAAA-ATATGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGAT
1 AAAATATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
* * * * *
1479884 AAAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
66 AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* *
1479949 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCTTATAAAGTGTCGATACTTTTAA
131 CGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATAC-TTTAA
* * * *
1480003 AAAATGTAT-T-GATCCAAAATGATATACCAGGTAAAAATATGATAAAACCGGTATCAAAATGAA
1 AAAATATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
*
1480066 AAAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTT
66 AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* ** *
1480130 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 CGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
*
1480183 AAAATATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAATATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
*
1480248 AAAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1480294 CGTAAGTACA
Statistics
Matches: 262, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
180 13 0.05
181 61 0.23
182 180 0.69
183 5 0.02
184 3 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (183 bp):
AAAATATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
CGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:1480228 original size:20 final size:19
Alignment explanation
Indices: 1480214--1480260 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1480204 CGATATAACA
1480214 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1480234 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1480254 GGTAAAA
1 GGTAAAA
1480261 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1480262 original size:17 final size:19
Alignment explanation
Indices: 1480223--1480265 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1480213 AGGTAAAAAT
1480223 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1480243 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1480260 ATGATA
1 ATGATA
1480266 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1482518 original size:21 final size:21
Alignment explanation
Indices: 1482492--1482556 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1482482 AAGACAATCA
*
1482492 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
1482513 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1482534 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1482555 AG
1 AG
1482557 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1482632 original size:33 final size:33
Alignment explanation
Indices: 1482590--1482655 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1482580 AAATAGATGG
*
1482590 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1482623 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1482656 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:1484468 original size:19 final size:19
Alignment explanation
Indices: 1484444--1484492 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1484434 AATGTAGGGT
1484444 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1484463 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1484482 TAATTTTGTAT
1 TAATTTTGTAT
1484493 GTGAATACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1485080 original size:200 final size:199
Alignment explanation
Indices: 1484726--1485386 Score: 905
Period size: 200 Copynumber: 3.4 Consensus size: 199
1484716 AATTTACAAT
*
1484726 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * * *
1484791 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGATTTT
66 CGAAACCCATAAGTATAACGTAATA-GTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1484856 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
130 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAA
1484921 AATGA
195 AATGA
** * *
1484926 ATGAAAAACATGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1484991 CGAAACCCATAAGTATAACGTAATAAGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAACGTAAT-AGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1485056 ATGAGAGAATAGGTCTAAATAATGTATCGACAATTTTGTAGTTTGTGTCGATATTTTTGGTCCAA
130 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAA
1485121 AATGA
195 AATGA
* *
1485126 ATGGCAAACAGGGTTGCAACAATAAAGTGTCGATCC---CAT--AAA----C-AT--C-GAAAC-
1 ATGGCAAACAGGG-TGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACA
* * * *
1485177 -CCATA---A---GTATAATGTAATAGGTAATTTTTTAATCTAACCGGTACAAGTATACCGGTTT
65 TCGAAACCCATAAGTATAACGTAATA-GTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
* * *
1485235 TATGAGAGAATAGGTCTAAATAATATGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGACCA
129 TATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
*
1485300 TAATGA
194 AAATGA
* * * *
1485306 ATGGCAAACAGGGTGCAACCATAAAGTGTCAATTCATATATAAAAAATGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1485371 CGAAACCCATATGTAT
66 CGAAACCCATAAGTAT
1485387 CGACACTGTT
Statistics
Matches: 404, Mismatches: 33, Indels: 48
0.83 0.07 0.10
Matches are distributed among these distances:
179 20 0.05
180 127 0.31
182 2 0.00
183 1 0.00
184 3 0.01
186 3 0.01
188 5 0.01
189 2 0.00
191 3 0.01
192 5 0.01
194 3 0.01
196 3 0.01
197 1 0.00
198 2 0.00
200 201 0.50
201 23 0.06
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (199 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAACGTAATAGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA
TGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAAA
ATGA
Found at i:1485275 original size:180 final size:179
Alignment explanation
Indices: 1484969--1485335 Score: 635
Period size: 180 Copynumber: 2.0 Consensus size: 179
1484959 CCATATATAA
*
1484969 AAAGTGTCGATCCGATAAACATCGAAACCCATAAGTATAACGTAATAAGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAACGTAATAAGTAATTTTTCAATCTAA
*
1485034 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACAATTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATATATCGACAATTTTGTAGTT
*
1485099 TGTGTCGATATTTTTGGTCCAAAATGAATGGCAAACAGGGTTGCAACAAT
131 TGTGTCGATATTTTTGGACCAAAATGAATGGCAAACAGGG-TGCAACAAT
* * *
1485149 AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTTAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAACGTAATAAGTAATTTTTCAATCTAA
* *
1485214 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATATGTCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATATATCGACAATTTTGTAGTT
* *
1485279 TGTGTCGATATTTTTGGACCATAATGAATGGCAAACAGGGTGCAACCAT
131 TGTGTCGATATTTTTGGACCAAAATGAATGGCAAACAGGGTGCAACAAT
1485328 AAAGTGTC
1 AAAGTGTC
1485336 AATTCATATA
Statistics
Matches: 177, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
179 16 0.09
180 161 0.91
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (179 bp):
AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAACGTAATAAGTAATTTTTCAATCTAA
CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATATATCGACAATTTTGTAGTT
TGTGTCGATATTTTTGGACCAAAATGAATGGCAAACAGGGTGCAACAAT
Found at i:1486905 original size:6 final size:6
Alignment explanation
Indices: 1486894--1486963 Score: 68
Period size: 6 Copynumber: 11.7 Consensus size: 6
1486884 CAAGCGGTCA
* * * * *
1486894 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGACG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * *
1486942 ATGATG ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGA
1486964 TCCAAACAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.23
Consensus pattern (6 bp):
ATGAAG
Found at i:1486916 original size:12 final size:12
Alignment explanation
Indices: 1486894--1486963 Score: 86
Period size: 12 Copynumber: 5.8 Consensus size: 12
1486884 CAAGCGGTCA
*
1486894 ATGAAGATGAAG
1 ATGACGATGAAG
*
1486906 CTGACGATGAAG
1 ATGACGATGAAG
1486918 ATGACGATGAAG
1 ATGACGATGAAG
*
1486930 ATGACGATGATG
1 ATGACGATGAAG
* *
1486942 ATGATGATGATG
1 ATGACGATGAAG
*
1486954 ATGATGATGA
1 ATGACGATGA
1486964 TCCAAACAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 53 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.23
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:1486932 original size:18 final size:18
Alignment explanation
Indices: 1486894--1486963 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
1486884 CAAGCGGTCA
* * *
1486894 ATGAAGATGAAGCTGACG
1 ATGAAGATGATGATGAAG
*
1486912 ATGAAGATGACGATGAAG
1 ATGAAGATGATGATGAAG
* *
1486930 ATGACGATGATGATGATG
1 ATGAAGATGATGATGAAG
*
1486948 ATGATGATGATGATGA
1 ATGAAGATGATGATGA
1486964 TCCAAACAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.23
Consensus pattern (18 bp):
ATGAAGATGATGATGAAG
Found at i:1486943 original size:3 final size:3
Alignment explanation
Indices: 1486911--1486964 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
1486901 TGAAGCTGAC
* * * *
1486911 GAT GAA GAT GAC GAT GAA GAT GAC GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1486959 GAT GAT
1 GAT GAT
1486965 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:1488608 original size:178 final size:182
Alignment explanation
Indices: 1488168--1488914 Score: 1101
Period size: 178 Copynumber: 4.1 Consensus size: 182
1488158 CAAAGTTTTC
*
1488168 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTA-TTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * * * * *
1488233 CAAAAAGTATCG--ATTGAAAAAATATCAGAACCCATAATTATAATGTAATAGATAATTTTGTAA
65 CAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
* *
1488296 TATAATCGGTATAAATATACCGTTTTTATGAGCGAATAGGTCTACAACCTATATCG
127 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1488352 ACACTTTTTAATA-TGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGA-ACCTTGT
1 ACACTTTTTAATATTGTGTCGGTA-TTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1488415 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
65 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
1488480 AACCGGTAT-AA-ATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
130 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1488531 ACACTTTTTAATATTGTGTCGGT-TTTATGTCCAGAATGGAAGAAAAATGTG-CGATACCTTGTC
1 ACACTTTTTAATATTGTGTCGGTATTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTC
1488594 AAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATA
66 AAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATA
1488659 ACC-GTAT-AATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* * * * * **
1488709 ACACTTTTTAATTTTGTGTCGGTACTTTATGT-CAGAATAATGTAAGATAATTTTGTAATATAAC
1 ACACTTTTTAATATTGTGTCGGTA-TTTATGTCCAG---AATGGAAGAAAAATGTGT-CGAT-AC
* *
1488773 CGTATGTCAAAAAGTGTTGAC-TTTAC-CAT-GGAACCCAGAATTATAATATAATAGATAATTTT
60 C-T-TGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTT
1488835 GTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATAT-G
123 GTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
1488894 ACACTTTTGAATATTGTGTCG
1 ACACTTTTTAATATTGTGTCG
1488915 CTAATTTTAA
Statistics
Matches: 526, Mismatches: 20, Indels: 33
0.91 0.03 0.06
Matches are distributed among these distances:
177 9 0.02
178 166 0.32
179 55 0.10
180 18 0.03
181 51 0.10
182 30 0.06
183 43 0.08
184 61 0.12
185 30 0.06
186 47 0.09
187 16 0.03
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (182 bp):
ACACTTTTTAATATTGTGTCGGTATTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTC
AAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATA
ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:1492349 original size:87 final size:86
Alignment explanation
Indices: 1492248--1492466 Score: 340
Period size: 87 Copynumber: 2.6 Consensus size: 86
1492238 TGAGCACTAC
*
1492248 CTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCCCTTAAATACC
1 CTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTTCCCCTTAAATACC
*
1492313 TATTTTATTATATAAGCGTTA
66 TATTTTATTATATAAGCGCTA
* * * *
1492334 TCTATTACATTATATAAGCGTTACCTAATATGTTATTATATTTGATAATATTTCTCGTTAAATAC
1 -CTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTTCCCCTTAAATAC
1492399 CTATTTTATTATATAAGCGCTA
65 CTATTTTATTATATAAGCGCTA
1492421 -TATTAC---ATATAAGCGTTACCTAATATGTTA-TGTACTTGATAATATT
1 CTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATT
1492467 CCGGTTAAAT
Statistics
Matches: 124, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
81 14 0.11
82 24 0.19
85 6 0.05
87 80 0.65
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (86 bp):
CTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTTCCCCTTAAATACC
TATTTTATTATATAAGCGCTA
Found at i:1492371 original size:26 final size:23
Alignment explanation
Indices: 1492309--1492374 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 23
1492299 TCCCCTTAAA
1492309 TACCTATTTTATTATATAAGCGT
1 TACCTATTTTATTATATAAGCGT
* **
1492332 TATCTATTACATTATATAAGCGT
1 TACCTATTTTATTATATAAGCGT
1492355 TACCTAATATGTTATTATAT
1 TACCT-AT-T-TTATTATAT
1492375 TTGATAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 24 0.71
24 2 0.06
25 1 0.03
26 7 0.21
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (23 bp):
TACCTATTTTATTATATAAGCGT
Found at i:1493074 original size:14 final size:14
Alignment explanation
Indices: 1493034--1493067 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1493024 TATTTGATAA
*
1493034 GTTTTTCTAAATAT
1 GTTTTTCAAAATAT
1493048 GTTTTTCAAAATAT
1 GTTTTTCAAAATAT
1493062 GTTTTT
1 GTTTTT
1493068 AGTAATACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (14 bp):
GTTTTTCAAAATAT
Found at i:1500744 original size:55 final size:55
Alignment explanation
Indices: 1500685--1500801 Score: 144
Period size: 55 Copynumber: 2.1 Consensus size: 55
1500675 ACATCCAAAG
* * * * * *
1500685 AATGAAGAAATTTGAACCTGATTGAAGAACGATTCATGAAGAAGGATATCTGATA
1 AATGAAGAAATCTGAAACTGATTGAAGAACGATTCATAAAGAAAGACATCCGATA
* * * *
1500740 AATGATGAAATCTGAAACTGATTGAAGACCGATTTATAAAGAAAGACATCCGATG
1 AATGAAGAAATCTGAAACTGATTGAAGAACGATTCATAAAGAAAGACATCCGATA
1500795 AATGAAG
1 AATGAAG
1500802 TTTGCAGTTG
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.24
Consensus pattern (55 bp):
AATGAAGAAATCTGAAACTGATTGAAGAACGATTCATAAAGAAAGACATCCGATA
Found at i:1501136 original size:13 final size:13
Alignment explanation
Indices: 1501114--1501150 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1501104 ATTAGCACCT
1501114 TTTA-CATTTGCA
1 TTTAGCATTTGCA
1501126 TTTAGCATTTGCA
1 TTTAGCATTTGCA
1501139 TTT-GCA-TTGCA
1 TTTAGCATTTGCA
1501150 T
1 T
1501151 GTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.25
12 7 0.29
13 11 0.46
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.49
Consensus pattern (13 bp):
TTTAGCATTTGCA
Found at i:1501139 original size:6 final size:6
Alignment explanation
Indices: 1501118--1501150 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1501108 GCACCTTTTA
1501118 CATTTG CATTTAG CATTTG CATTTG CA-TTG CAT
1 CATTTG CATTT-G CATTTG CATTTG CATTTG CAT
1501151 GTATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.45
Consensus pattern (6 bp):
CATTTG
Found at i:1504471 original size:114 final size:114
Alignment explanation
Indices: 1504271--1504491 Score: 309
Period size: 114 Copynumber: 1.9 Consensus size: 114
1504261 AAGTTAGGAT
* * * * * * *
1504271 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGTTTCAGACTAAGGAGGCATGAA
1 ATGTTAGGGCACGACTGAACCCACATCATGTTAAGATAACAAGATTCAAACCAAGAAGGCATGAA
* *
1504336 GAATGAGCCTTACAATTTGAGGTGATGAGGCATTTTGAAGGCCCGTACC
66 GAATGAGCATTACAATCTGAGGTGATGAGGCATTTTGAAGGCCCGTACC
*
1504385 ATGTTAGGGCATGACTGAACCCACATCATGTTAAGATAACAAGATTCAAACCAAGAAGGCATTG-
1 ATGTTAGGGCACGACTGAACCCACATCATGTTAAGATAACAAGATTCAAACCAAGAAGGCA-TGA
* * *
1504449 AGAGTGAGCATTACAATCTGAGGTGTTGGGGCATTTTGAAGGC
65 AGAATGAGCATTACAATCTGAGGTGATGAGGCATTTTGAAGGC
1504492 TCATACCAGT
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
114 91 0.98
115 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (114 bp):
ATGTTAGGGCACGACTGAACCCACATCATGTTAAGATAACAAGATTCAAACCAAGAAGGCATGAA
GAATGAGCATTACAATCTGAGGTGATGAGGCATTTTGAAGGCCCGTACC
Found at i:1505794 original size:36 final size:36
Alignment explanation
Indices: 1505715--1506596 Score: 1187
Period size: 36 Copynumber: 24.3 Consensus size: 36
1505705 GGGCAAGTCA
* * *
1505715 ATCTTATGCCTTCACCAAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA-CC
* * * *
1505752 ACCTTAAGCCTTCACCAAAGAGTAGTGAAGCAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
* * *
1505788 ATCTTAAGCCTTCACTGGAGAGTAGTGAAGCAAACT
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
*
1505824 ATCTTAAGCCTTCACC-AGAGAGTTA-TGAAGCGAATCC
1 ATCTTAAGCCTTCACCGA-AGAG-TAGTGAAGC-AAACC
* *
1505861 ATCTTAAGCCTTCACCAAAGAGTAGTGAAACAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
* * *
1505897 ATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
* *
1505933 ATCTTAAGCCTTCACCGAAAAGGAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
* *
1505969 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
* * *
1506005 ATCTTAAGCCTTCACC-AGAGAGTAGTGAAACAGATC
1 ATCTTAAGCCTTCACCGA-AGAGTAGTGAAGCAAACC
* *
1506041 ATCTTAAGCATTCACCGAAGAGTAGTGAAGCAGACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
**
1506077 ATCTTAAGCCTTCA-TTAGAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGA-AGAGTAGTGAAGCAAACC
* *
1506113 ATCTTAAGCATTCACCGGAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
*
1506149 ATCTTAAGCCTTCATCGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
* *
1506185 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAAATC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
*
1506221 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
* *
1506257 ATCTTAAACCTTCACCGAAGAGTAGTGAAACAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
* *
1506293 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
*
1506329 ATCCTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
* *
1506365 ATCTTAAGCCTTCACCGGATAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
*
1506401 ATCCTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
* *
1506437 ATATTAAGCCTTCACCGGAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
* *
1506473 ATCCTAAGCCTTCACCGAAGAGTAGTGAAGCAAATTC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA-CC
*
1506510 ATTTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA-CC
* * * * *
1506547 ATTTTCAGCATTCACCAAAGAGTAGTGAAGCAAATTC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA-CC
1506584 ATCTGTAAGCCTT
1 ATCT-TAAGCCTT
1506597 TAGAGCAAGA
Statistics
Matches: 749, Mismatches: 85, Indels: 21
0.88 0.10 0.02
Matches are distributed among these distances:
35 2 0.00
36 607 0.81
37 133 0.18
38 7 0.01
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
Found at i:1506853 original size:13 final size:13
Alignment explanation
Indices: 1506835--1506859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1506825 TGAAGCAAAC
1506835 CCATCAGTAAGTG
1 CCATCAGTAAGTG
1506848 CCATCAGTAAGT
1 CCATCAGTAAGT
1506860 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:1507035 original size:80 final size:80
Alignment explanation
Indices: 1506890--1507141 Score: 362
Period size: 80 Copynumber: 3.1 Consensus size: 80
1506880 GTCATTCTGG
* * *
1506890 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGATAATTTGTAAGCCTTCACT-GAA
1 CCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCA-TGGAA
*
1506954 GAATAGTGAAGCAAGT
65 GAATAGTGAAGCAAAT
* **
1506970 CCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTAAATTGTAAGTTTTCATGGAAG
1 CCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCATGGAAG
* * *
1507035 ATTAGTCAAGAAAAT
66 AATAGTGAAGCAAAT
* * *
1507050 CCATCAGTAAGTCTTTCAAGCATGATGTTTAAATCCTTCGGGTAATTTGTAAGCCTTCACGAAAG
1 CCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCATGGAAG
*
1507115 AGTAGTGAAGCAAAT
66 AATAGTGAAGCAAAT
1507130 CCATCAGTAAGT
1 CCATCAGTAAGT
1507142 GCCATCAGTA
Statistics
Matches: 152, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
79 1 0.01
80 151 0.99
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCATGGAAG
AATAGTGAAGCAAAT
Found at i:1507148 original size:13 final size:13
Alignment explanation
Indices: 1507130--1507154 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1507120 TGAAGCAAAT
1507130 CCATCAGTAAGTG
1 CCATCAGTAAGTG
1507143 CCATCAGTAAGT
1 CCATCAGTAAGT
1507155 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:1511092 original size:14 final size:15
Alignment explanation
Indices: 1511060--1511092 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1511050 TTTTTTAGTT
1511060 TTAATTTATTTAATC
1 TTAATTTATTTAATC
1511075 -TAATTTATTT-ATC
1 TTAATTTATTTAATC
1511088 TTAAT
1 TTAAT
1511093 GGTGACACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAATTTATTTAATC
Found at i:1516367 original size:104 final size:104
Alignment explanation
Indices: 1516187--1516394 Score: 416
Period size: 104 Copynumber: 2.0 Consensus size: 104
1516177 ACTTAAGGTA
1516187 AACTTTTATAGAATGGCAATAAGACCATCGCTGCTGTATGGATCAAAATGTTGGGCAATCAAGAA
1 AACTTTTATAGAATGGCAATAAGACCATCGCTGCTGTATGGATCAAAATGTTGGGCAATCAAGAA
1516252 GGATCACGTAAGGAAGATGGAGGCCGCAGAAATGAGAAT
66 GGATCACGTAAGGAAGATGGAGGCCGCAGAAATGAGAAT
1516291 AACTTTTATAGAATGGCAATAAGACCATCGCTGCTGTATGGATCAAAATGTTGGGCAATCAAGAA
1 AACTTTTATAGAATGGCAATAAGACCATCGCTGCTGTATGGATCAAAATGTTGGGCAATCAAGAA
1516356 GGATCACGTAAGGAAGATGGAGGCCGCAGAAATGAGAAT
66 GGATCACGTAAGGAAGATGGAGGCCGCAGAAATGAGAAT
1516395 GCTTATGACA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (104 bp):
AACTTTTATAGAATGGCAATAAGACCATCGCTGCTGTATGGATCAAAATGTTGGGCAATCAAGAA
GGATCACGTAAGGAAGATGGAGGCCGCAGAAATGAGAAT
Found at i:1521307 original size:6 final size:7
Alignment explanation
Indices: 1521291--1521316 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1521281 TAAACATTCA
1521291 TTTTTCT
1 TTTTTCT
1521298 TTTTTCT
1 TTTTTCT
1521305 TTTTTCT
1 TTTTTCT
1521312 TTTTT
1 TTTTT
1521317 AAATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:1522581 original size:3 final size:3
Alignment explanation
Indices: 1522573--1522619 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1522563 TTGGATCCTG
1522573 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1522620 GTGGTAATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1522820 original size:41 final size:42
Alignment explanation
Indices: 1522759--1522873 Score: 151
Period size: 41 Copynumber: 2.8 Consensus size: 42
1522749 GATAAGGGTC
* * * *
1522759 TGTTCCGCTGTCACTCAGAGAATATCATATCTGGGGCACACT
1 TGTTCCACTGTCACTCAGAGAATATCAAATCTAGGACACACT
* * *
1522801 TGTTCC-CTGTCACTTAGAGAATATCAGATCTAGGACAGACT
1 TGTTCCACTGTCACTCAGAGAATATCAAATCTAGGACACACT
*
1522842 TGTTCCACTGTCACTCAGGGAATATCAAATCT
1 TGTTCCACTGTCACTCAGAGAATATCAAATCT
1522874 TGGAAGAGAG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 36 0.56
42 28 0.44
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (42 bp):
TGTTCCACTGTCACTCAGAGAATATCAAATCTAGGACACACT
Found at i:1523162 original size:111 final size:111
Alignment explanation
Indices: 1522836--1523694 Score: 1023
Period size: 111 Copynumber: 7.7 Consensus size: 111
1522826 AGATCTAGGA
*
1522836 CAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGTGATTTGTTCCGCTTCT
1 CAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGTGATCTGTTCCGCTTCT
* *
1522901 TCTAGGGGAATATCATATATGGGGGAGTTGATCTATTGAATCAGGG
66 TCTAAGGGAATATCAGATATGGGGGAGTTGATCTATTGAATCAGGG
*** * * * *
1522947 CAGACTTGTTATGCTGTCACTCAGGGAATGTCAAATCTTGGAAGAGAGGGA-CT-ATCTCACTTC
1 CAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGTGATCTGTTC-CGCTTC
* *
1523010 TTCTAAGGGAATATCAGATATGGGGGAGTTGATTTATTGAATCGGGG
65 TTCTAAGGGAATATCAGATATGGGGGAGTTGATCTATTGAATCAGGG
* * * * * * **
1523057 TAGACTTGTTCCACT-TCTTCTAAGGGAATATCAAATCTTGGAGGCGAGGGATCTGTTTTGCTTC
1 CAGACTTGTTCCACTGTC-ACTCAGGGAATATCAAATCTTGGAAGAGAGTGATCTGTTCCGCTTC
* * *
1523121 TTCTAAGGGAAAATCAGATCTGGGGGAATTGATCTATTGAATCAGGG
65 TTCTAAGGGAATATCAGATATGGGGGAGTTGATCTATTGAATCAGGG
* * * * * *
1523168 TAGGCTTGTTCCACT-TCTTCTAAGGGAATATCAAATCTTGGAAGAGAGTGATTTGTTTCGCTTC
1 CAGACTTGTTCCACTGTC-ACTCAGGGAATATCAAATCTTGGAAGAGAGTGATCTGTTCCGCTTC
* * * **
1523232 TTCTAAGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATTTGGG
65 TTCTAAGGGAATATCAGATATGGGGGAGTTGATCTATTGAATCAGGG
* * * * **
1523279 AAGACTTCTTCCACTGTTACTCAGGGAATATCAAATCTTGGAAGAGAGTGATTTGTTCTACTTCT
1 CAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGTGATCTGTTCCGCTTCT
* *
1523344 TCTAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATC-GGTG
66 TCTAAGGGAATATCAGATATGGGGGAGTTGATCTATTGAATCAGG-G
* * * * * * *
1523390 CAGACTTGTTCCGCTCTCACTTAGGGAATATCAAATCTTGGAAAAGAGTGATATGTTCCGTTTTT
1 CAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGTGATCTGTTCCGCTTCT
* *
1523455 TCTAAGAGAATATCAGATATGGGGGAGTTAATAC-ATTGAATC-GGTG
66 TCTAAGGGAATATCAGATATGGGGGAGTTGAT-CTATTGAATCAGG-G
* * * *
1523501 CAGACTTGTTTCGCTGTCACTCATGGAATATCAAATCTTGGAAGAGAGTGATATGTTCCGCTTCT
1 CAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGTGATCTGTTCCGCTTCT
* * *
1523566 TCTAAGGGAATATCAGATATGGGGGAGTTGATTTGTTGAATCAGTG
66 TCTAAGGGAATATCAGATATGGGGGAGTTGATCTATTGAATCAGGG
* * * * * *
1523612 CAGACTTGTT-TAGCTATCACTCAAGGAATGTCAAATCTTAGAAGAGAGTGATCTGTTCCGTTTC
1 CAGACTTGTTCCA-CTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGTGATCTGTTCCGCTTC
1523676 TTCTAAGGGAATATCAGAT
65 TTCTAAGGGAATATCAGAT
1523695 CTGCAAATTA
Statistics
Matches: 650, Mismatches: 88, Indels: 20
0.86 0.12 0.03
Matches are distributed among these distances:
109 4 0.01
110 90 0.14
111 552 0.85
112 4 0.01
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (111 bp):
CAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGTGATCTGTTCCGCTTCT
TCTAAGGGAATATCAGATATGGGGGAGTTGATCTATTGAATCAGGG
Found at i:1525632 original size:6 final size:6
Alignment explanation
Indices: 1525601--1525649 Score: 53
Period size: 6 Copynumber: 7.5 Consensus size: 6
1525591 TTTATTATTT
*
1525601 TTTTTC TTCTTTC TTTCTTA TTTTTC TTTTTC TTTTTC TATTTTTC TTT
1 TTTTTC TT-TTTC TTT-TTC TTTTTC TTTTTC TTTTTC --TTTTTC TTT
1525650 ATTTTTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 20 0.54
7 11 0.30
8 6 0.16
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:1525663 original size:13 final size:13
Alignment explanation
Indices: 1525647--1525671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1525637 TCTATTTTTC
1525647 TTTATTTTTTATA
1 TTTATTTTTTATA
1525660 TTTATTTTTTAT
1 TTTATTTTTTAT
1525672 CTTTTGCTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTTTATA
Found at i:1525670 original size:20 final size:20
Alignment explanation
Indices: 1525601--1525676 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
1525591 TTTATTATTT
* *
1525601 TTTTTCTTCTTTCTTTCT-TA
1 TTTTTCTT-TATCTTTTTATA
* *
1525621 TTTTTCTTTTTCTTTTTCTA
1 TTTTTCTTTATCTTTTTATA
1525641 TTTTTCTTTAT-TTTTTATA
1 TTTTTCTTTATCTTTTTATA
*
1525660 TTTATTTTTTATCTTTT
1 TTT-TTCTTTATCTTTT
1525677 GCTATATCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 18 0.37
20 27 0.55
21 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTATCTTTTTATA
Found at i:1525931 original size:2 final size:2
Alignment explanation
Indices: 1525924--1525964 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1525914 TGGGACAACA
1525924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1525965 AGGATAAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1527048 original size:14 final size:15
Alignment explanation
Indices: 1527028--1527064 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
1527018 GCAAATGCAA
*
1527028 AGATGCAAAAATGGG
1 AGATGCAAAAATGCG
1527043 AG-TGC-AAAATGCG
1 AGATGCAAAAATGCG
1527056 AGATGCAAA
1 AGATGCAAA
1527065 TCCAACAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.47
14 6 0.32
15 4 0.21
ACGTcount: A:0.46, C:0.11, G:0.30, T:0.14
Consensus pattern (15 bp):
AGATGCAAAAATGCG
Found at i:1527065 original size:13 final size:14
Alignment explanation
Indices: 1527002--1527064 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
1526992 GTATATACTA
*
1527002 ATGCAAAGATGC-AC
1 ATGCAAA-ATGCGAG
*
1527016 ATGC-AAATGCAAAG
1 ATGCAAAATGC-GAG
*
1527030 ATGCAAAAATGGGAG
1 ATGC-AAAATGCGAG
1527045 -TGCAAAATGCGAG
1 ATGCAAAATGCGAG
1527058 ATGCAAA
1 ATGCAAA
1527065 TCCAACAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 4 0.10
13 11 0.28
14 18 0.45
15 2 0.05
16 5 0.12
ACGTcount: A:0.46, C:0.14, G:0.25, T:0.14
Consensus pattern (14 bp):
ATGCAAAATGCGAG
Found at i:1529934 original size:12 final size:12
Alignment explanation
Indices: 1529917--1529944 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1529907 TTTAATTTCG
1529917 AAAACTAAAAAT
1 AAAACTAAAAAT
1529929 AAAACTAAAAAT
1 AAAACTAAAAAT
1529941 AAAA
1 AAAA
1529945 ATACCAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAACTAAAAAT
Found at i:1530763 original size:3 final size:3
Alignment explanation
Indices: 1530755--1530823 Score: 86
Period size: 3 Copynumber: 22.7 Consensus size: 3
1530745 TTGGATCCTG
* * *
1530755 TAA TAA TAA TAA CAA -AA AAA GTTAA TAA TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA --TAA TAA TAA TAA TAA TAA TAA TAA
1530801 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
1530824 TTAGCTGTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 55 0.93
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1531554 original size:16 final size:16
Alignment explanation
Indices: 1531533--1531583 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
1531523 AATAGAAAGC
*
1531533 AACCCGAATCAAAATT
1 AACCCGAACCAAAATT
*
1531549 AACCCGAACCAAAAGT
1 AACCCGAACCAAAATT
*
1531565 AACCTGAACCAAAATT
1 AACCCGAACCAAAATT
1531581 AAC
1 AAC
1531584 TCAAACTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.51, C:0.27, G:0.08, T:0.14
Consensus pattern (16 bp):
AACCCGAACCAAAATT
Found at i:1531605 original size:32 final size:32
Alignment explanation
Indices: 1531528--1531605 Score: 75
Period size: 32 Copynumber: 2.4 Consensus size: 32
1531518 AGCGAAATAG
* * * *
1531528 AAAGCAACCCGAATCAAAATTAACCCGAACCA
1 AAAGAAACCTGAACCAAAATTAACCCAAACCA
* * **
1531560 AAAGTAACCTGAACCAAAATTAACTCAAACTG
1 AAAGAAACCTGAACCAAAATTAACCCAAACCA
*
1531592 AAAGAAACTTGAAC
1 AAAGAAACCTGAAC
1531606 TGAATTTTAA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.51, C:0.24, G:0.10, T:0.14
Consensus pattern (32 bp):
AAAGAAACCTGAACCAAAATTAACCCAAACCA
Found at i:1531649 original size:32 final size:34
Alignment explanation
Indices: 1531592--1531660 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 34
1531582 ACTCAAACTG
* *
1531592 AAAGAAACTTGAACTGAATTTTAACCTGATCC-GA
1 AAAGAAACTCGAACCGAATTTTAACCTG-TCCTGA
1531626 AAAG-AACTCGAACCGAA-TTTAACCTGTCCTGA
1 AAAGAAACTCGAACCGAATTTTAACCTGTCCTGA
1531658 AAA
1 AAA
1531661 CAATCCGAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 3 0.09
32 14 0.44
33 11 0.34
34 4 0.12
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.23
Consensus pattern (34 bp):
AAAGAAACTCGAACCGAATTTTAACCTGTCCTGA
Found at i:1531913 original size:19 final size:19
Alignment explanation
Indices: 1531889--1531944 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1531879 TTATTATTTT
1531889 TTAAATTTTAATAAAAATA
1 TTAAATTTTAATAAAAATA
*
1531908 TTAAATTTATAATTATAAATA
1 TTAAATTT-TAA-TAAAAATA
1531929 --AAATTTTTAATAAAAA
1 TTAAA-TTTTAATAAAAA
1531945 AATATTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 5 0.16
19 14 0.44
20 6 0.19
21 7 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAATTTTAATAAAAATA
Found at i:1532767 original size:2 final size:2
Alignment explanation
Indices: 1532760--1532800 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1532750 ATCTTTATGT
1532760 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1532801 GTTAACAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1533949 original size:19 final size:18
Alignment explanation
Indices: 1533892--1533957 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 18
1533882 TCGTAGATGT
1533892 TAATATATATATATATCTAA
1 TAATATATATA-ATAT-TAA
* *
1533912 TAAT-TA-CTAATATTCA
1 TAATATATATAATATTAA
1533928 TAATATATATAATCATTAA
1 TAATATATATAAT-ATTAA
1533947 TAATATATATA
1 TAATATATATA
1533958 TGATAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 6 0.15
17 6 0.15
18 6 0.15
19 17 0.44
20 4 0.10
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATATATATAATATTAA
Found at i:1533977 original size:5 final size:5
Alignment explanation
Indices: 1533967--1534023 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
1533957 ATGATAAAAT
* * * * *
1533967 ATAAA ATAAA ACT-AC ATAAA ATAGA AGAAA ATAAA ATAAA ATACA AGAAA
1 ATAAA ATAAA A-TAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1534017 ATAAA AT
1 ATAAA AT
1534024 CACATTAATT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
4 1 0.03
5 38 0.95
6 1 0.03
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (5 bp):
ATAAA
Found at i:1534005 original size:20 final size:20
Alignment explanation
Indices: 1533982--1534023 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1533972 ATAAAACTAC
*
1533982 ATAAAATAGAAGAAAATAAA
1 ATAAAATACAAGAAAATAAA
1534002 ATAAAATACAAGAAAATAAA
1 ATAAAATACAAGAAAATAAA
1534022 AT
1 AT
1534024 CACATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (20 bp):
ATAAAATACAAGAAAATAAA
Found at i:1537142 original size:16 final size:15
Alignment explanation
Indices: 1537121--1537150 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1537111 ATGATACAAT
1537121 ATATGTGATTATATGC
1 ATATGTGA-TATATGC
1537137 ATATGTGATATATG
1 ATATGTGATATATG
1537151 TTATGAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.43
Consensus pattern (15 bp):
ATATGTGATATATGC
Found at i:1539231 original size:6 final size:6
Alignment explanation
Indices: 1539220--1539252 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1539210 GATATCTCAG
*
1539220 AGAGGA AGAGGA AGAGGA AGAGGT AGAGGA AGA
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGA
1539253 AATCAACCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.03
Consensus pattern (6 bp):
AGAGGA
Found at i:1546299 original size:16 final size:16
Alignment explanation
Indices: 1546278--1546318 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1546268 GAGATGTGAG
1546278 TGAGAGTTTAAAACTT
1 TGAGAGTTTAAAACTT
* *
1546294 TGAGAGTTTAAGAGTT
1 TGAGAGTTTAAAACTT
*
1546310 TTAGAGTTT
1 TGAGAGTTT
1546319 GATATTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.41
Consensus pattern (16 bp):
TGAGAGTTTAAAACTT
Found at i:1546889 original size:170 final size:168
Alignment explanation
Indices: 1546514--1547181 Score: 516
Period size: 170 Copynumber: 3.9 Consensus size: 168
1546504 TGTTCCCAAT
* * * * * * * *
1546514 TTCACGTCAACCCCTCATTTGTTTGATGGGATAAGAGACTATGAAATGATAGAGATTCTTTGGAA
1 TTCACGTCAA-CCCT-ATCTATTTGATGGGATGAGACATTATGACATGATAGAGATTCTCT-AAA
* ** * * * *
1546579 ACGGTGAAAGTGA-TTCTTGTGGGATGAGTCTTTCCCTTTCTTTCTAGATGTTCTCTATCA-TTT
63 AAGGTGAAA-ACACTTCTTGAGGGACGAGCCTTTCCCTTTTTTTCTAGA--TTCTCTATCATTTT
* * * *
1546642 GCAATCAATT-TCATGAAGTAGATGATGTCCCCATTTGAGGAACAA
125 TCAATCAATTAT-ATGAA-TATATGATGTTCCCATTTGAGGAACTA
* * *
1546687 TTCACATCAACCCTCATCTATTTGATGGGATGAGACATTATGACATAACAGAGATTCTCTATAAA
1 TTCACGTCAACCCT-ATCTATTTGATGGGATGAGACATTATGACATGATAGAGATTCTCTA-AAA
* * *
1546752 AGGTGAAATCGCTTCTTGAGGGACGAGCCTTTCCTTTTTTTTC-AGATTATCTCTAT-ATTTTTC
64 AGGTGAAAACACTTCTTGAGGGACGAGCCTTTCCCTTTTTTTCTAGA-T-TCTCTATCATTTTTC
* **
1546815 AATCAATTATATGCATATATGATGTTCCTGTTTGAGGAACTA
127 AATCAATTATATGAATATATGATGTTCCCATTTGAGGAACTA
* * * * * *
1546857 TTCATGTCATCTCCTATCTAGTTAATGGGATGAGACACTATGACATGGTAGAGATTCTCTGAAAA
1 TTCACGTCAAC-CCTATCTATTTGATGGGATGAGACATTATGACATGATAGAGATTCTCT-AAAA
* * * * *
1546922 CGGTGAAAACACTTATTGTA-GGACAAGCC-TTCCCTTTTTATC-ATATAT-TCTATGCATTTTT
64 AGGTGAAAACACTTCTTG-AGGGACGAGCCTTTCCCTTTTTTTCTAGAT-TCTCTAT-CATTTTT
* * * * * * *
1546983 TAGTCAATTATATGAAAATATAATGTTCCCAATCGAGAAACTA
126 CAATCAATTATATGAATATATGATGTTCCCATTTGAGGAACTA
* * * *
1547026 TTCACGTCAACCCCATATCTATTTGATGGGATGAGACATAATGACATGATA-ATTATTCTATGGA
1 TTCACGTCAA-CCC-TATCTATTTGATGGGATGAGACATTATGACATGATAGA-GATTCTCT-AA
** * *
1547090 AAAGGAAAAAACTCTTCTTGTGGGACGAGCC-TTCCCTTTTTTTGTCATAGATTCT-T-TGCATT
62 AAAGGTGAAAACACTTCTTGAGGGACGAGCCTTTCCC-TTTTTT-TC-TAGATTCTCTAT-CATT
* *
1547152 TTTCAGTCAATTATATGCATATATGATGTT
123 TTTCAATCAATTATATGAATATATGATGTT
1547182 TCTGTTTCAG
Statistics
Matches: 399, Mismatches: 77, Indels: 39
0.77 0.15 0.08
Matches are distributed among these distances:
167 5 0.01
168 3 0.01
169 63 0.16
170 164 0.41
171 37 0.09
172 112 0.28
173 11 0.03
174 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (168 bp):
TTCACGTCAACCCTATCTATTTGATGGGATGAGACATTATGACATGATAGAGATTCTCTAAAAAG
GTGAAAACACTTCTTGAGGGACGAGCCTTTCCCTTTTTTTCTAGATTCTCTATCATTTTTCAATC
AATTATATGAATATATGATGTTCCCATTTGAGGAACTA
Found at i:1549999 original size:17 final size:19
Alignment explanation
Indices: 1549963--1549999 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
1549953 AACTAAAATA
*
1549963 AAAATATATATTTCTTATC
1 AAAATATATATTTCTAATC
1549982 AAAATA-ATA-TTCTAATC
1 AAAATATATATTTCTAATC
1549999 A
1 A
1550000 TATAAAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATATATATTTCTAATC
Found at i:1550955 original size:18 final size:19
Alignment explanation
Indices: 1550934--1550969 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1550924 TTAAACTTTG
*
1550934 AAATAATAT-TAAAAAATT
1 AAATAAAATATAAAAAATT
1550952 AAATAAAATATAAAAAAT
1 AAATAAAATATAAAAAAT
1550970 AAAAATAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAAAATATAAAAAATT
Found at i:1550977 original size:20 final size:18
Alignment explanation
Indices: 1550934--1550973 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1550924 TTAAACTTTG
* *
1550934 AAATAATATTAAAAAATT
1 AAATAAAATTAAAAAATA
1550952 AAATAAAATATAAAAAATA
1 AAATAAAAT-TAAAAAATA
1550971 AAA
1 AAA
1550974 ATAACATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AAATAAAATTAAAAAATA
Found at i:1558749 original size:2 final size:2
Alignment explanation
Indices: 1558742--1558788 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1558732 TTAAATGTAT
1558742 TA TA TA TA TA TA TA TA TA T- 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
1558783 TA TA TA
1 TA TA TA
1558789 GCTTAAGCTG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1559363 original size:21 final size:21
Alignment explanation
Indices: 1559339--1559382 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1559329 GTGCCAGAGG
* *
1559339 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAACT
* *
1559360 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
1559381 AG
1 AG
1559383 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:1560969 original size:23 final size:21
Alignment explanation
Indices: 1560939--1560993 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
1560929 TGTATATATT
*
1560939 CACATTCAAGGTGTGCATCGGTG
1 CACATTCAAGGTGT--ATCGATG
* *
1560962 CACCTTCATGGTGTATCGATG
1 CACATTCAAGGTGTATCGATG
1560983 CACATTCAAGG
1 CACATTCAAGG
1560994 ATGCTTCGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 15 0.56
23 12 0.44
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (21 bp):
CACATTCAAGGTGTATCGATG
Found at i:1566367 original size:21 final size:23
Alignment explanation
Indices: 1566327--1566368 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1566317 AATTAAATTG
1566327 AATATACTTAGAAAATCATTTGT
1 AATATACTTAGAAAATCATTTGT
*
1566350 AATAT-CTTA-AAATTCATTT
1 AATATACTTAGAAAATCATTT
1566369 AACTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (23 bp):
AATATACTTAGAAAATCATTTGT
Found at i:1574320 original size:31 final size:29
Alignment explanation
Indices: 1574246--1574329 Score: 80
Period size: 31 Copynumber: 2.9 Consensus size: 29
1574236 AAAAATTTTG
* *
1574246 GTTT-GTGACCAAAATATAAATTTTGAAA
1 GTTTAGTGACCAAAGTATAAATTTAGAAA
* *
1574274 GTTTAATGGCCAAAGTATAAACTTTAGAAAA
1 GTTTAGTGACCAAAGTATAAA-TTTAG-AAA
* * *
1574305 GTTTAGTGACTAAAGTGTAATTTTA
1 GTTTAGTGACCAAAGTATAAATTTA
1574330 AAACAAATTA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
28 4 0.09
29 13 0.30
30 8 0.18
31 19 0.43
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (29 bp):
GTTTAGTGACCAAAGTATAAATTTAGAAA
Found at i:1577030 original size:36 final size:36
Alignment explanation
Indices: 1576983--1577053 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
1576973 TTGTGAATAT
1576983 GTTGTAAAACCCAGGAAGAACACGATGTCTATTTTC
1 GTTGTAAAACCCAGGAAGAACACGATGTCTATTTTC
1577019 GTTGTAAAACCCAGGAAGAACACGATGTCTATTTT
1 GTTGTAAAACCCAGGAAGAACACGATGTCTATTTT
1577054 TCTACAGCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (36 bp):
GTTGTAAAACCCAGGAAGAACACGATGTCTATTTTC
Found at i:1584995 original size:22 final size:21
Alignment explanation
Indices: 1584958--1585039 Score: 103
Period size: 22 Copynumber: 3.9 Consensus size: 21
1584948 TGGTGCCATA
*
1584958 ATAGAGTGTCGATACCATAGT
1 ATAGAGTATCGATACCATAGT
* *
1584979 ATAGTAGTATCAATACCATGGT
1 ATAG-AGTATCGATACCATAGT
*
1585001 A-AGGGTATCGATACCATAGT
1 ATAGAGTATCGATACCATAGT
1585021 ATAGAAGTATCGATACCAT
1 ATAG-AGTATCGATACCAT
1585040 GGAAGGGGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
20 15 0.29
21 8 0.16
22 28 0.55
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (21 bp):
ATAGAGTATCGATACCATAGT
Found at i:1585030 original size:42 final size:42
Alignment explanation
Indices: 1584966--1585056 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
1584956 TAATAGAGTG
*
1584966 TCGATACCATAGTATAGTAGTATCAATACCATGGTAA-GGGTA
1 TCGATACCATAGTATAGAAGTATCAATACCATGG-AAGGGGTA
*
1585008 TCGATACCATAGTATAGAAGTATCGATACCATGGAAGGGGTA
1 TCGATACCATAGTATAGAAGTATCAATACCATGGAAGGGGTA
*
1585050 TCAATAC
1 TCGATAC
1585057 TATTGAGACA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 2 0.04
42 43 0.96
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.26
Consensus pattern (42 bp):
TCGATACCATAGTATAGAAGTATCAATACCATGGAAGGGGTA
Found at i:1585056 original size:20 final size:20
Alignment explanation
Indices: 1584985--1585056 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
1584975 TAGTATAGTA
1584985 GTATCAATACCATGGTAA-GG
1 GTATCAATACCATGG-AAGGG
* * **
1585005 GTATCGATACCATAGTATAGAA
1 GTATCAATACCAT-GGA-AGGG
*
1585027 GTATCGATACCATGGAAGGG
1 GTATCAATACCATGGAAGGG
1585047 GTATCAATAC
1 GTATCAATAC
1585057 TATTGAGACA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
20 24 0.59
21 4 0.10
22 13 0.32
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (20 bp):
GTATCAATACCATGGAAGGG
Found at i:1585450 original size:55 final size:55
Alignment explanation
Indices: 1585377--1585648 Score: 420
Period size: 55 Copynumber: 5.0 Consensus size: 55
1585367 ATTACCTAAT
* * *
1585377 GGCACTATGTGTGCAAAACTAAGAAACTCATAATAAGTTTATGAATTTTCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* *
1585432 GGAACTTTGTGTGCAAAACTAAGAAATTCATAACAAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
*
1585487 GGCACTTTGAGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
1585542 AGC-CTTTGTATGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * *
1585596 GGCACTTTGTGTACAAAACTAGGAAATTCATAATAAGTTTATAAATTTTCGTA
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTA
1585649 AACTAAGAAA
Statistics
Matches: 197, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
54 50 0.25
55 147 0.75
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (55 bp):
GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
Found at i:1585661 original size:37 final size:37
Alignment explanation
Indices: 1585611--1585685 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
1585601 TTTGTGTACA
* *
1585611 AAACTAGGAAATTCATAATAAGTTTATAAATTTTCGT
1 AAACTAAGAAATTCATAATAAGTTTATAAATTTCCGT
*
1585648 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGT
1 AAACTAAGAAATTCATAATAAGTTTATAAATTTCCGT
1585685 A
1 A
1585686 TGGGCACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (37 bp):
AAACTAAGAAATTCATAATAAGTTTATAAATTTCCGT
Found at i:1585714 original size:92 final size:92
Alignment explanation
Indices: 1585556--1585827 Score: 481
Period size: 92 Copynumber: 3.0 Consensus size: 92
1585546 TTTGTATGCA
* * *
1585556 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGCACTTTGTGTACAAAACTAGGAA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAA
*
1585621 ATTCATAATAAGTTTATAAATTTTCGT
66 ATTCATAATAAGTTTATGAATTTTCGT
1585648 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAA
*
1585713 ATTCATATTAAGTTTATGAATTTTCGT
66 ATTCATAATAAGTTTATGAATTTTCGT
1585740 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAA
* *
1585805 ACTCGTAATAAGTTTATGAATTT
66 ATTCATAATAAGTTTATGAATTT
1585828 CCATATGGGC
Statistics
Matches: 172, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 172 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (92 bp):
AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAACTAAGAA
ATTCATAATAAGTTTATGAATTTTCGT
Found at i:1585753 original size:37 final size:37
Alignment explanation
Indices: 1585703--1585777 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
1585693 TTTGTGTGCA
* *
1585703 AAACTAAGAAATTCATATTAAGTTTATGAATTTTCGT
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGT
1585740 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGT
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGT
1585777 A
1 A
1585778 TGGGCACTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (37 bp):
AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGT
Found at i:1586125 original size:55 final size:55
Alignment explanation
Indices: 1585740--1586108 Score: 632
Period size: 55 Copynumber: 6.7 Consensus size: 55
1585730 GAATTTTCGT
1585740 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* * *
1585795 AAACTAAGAAACTCGTAATAAGTTTATGAATTTCCATATGGGCACTTTGTGTGCA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* *
1585850 AAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGACACTTTGTGTGCA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* *
1585905 AAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTACT-TGTGCA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACT-TTGTGTGCA
1585960 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
* *
1586015 AAACTAAGAAAATCATAATAAGTTTATGAATTTCCGTATGGGCACTATGTGTGCA
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
*
1586070 AAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
1 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1586109 TGGTAGTGGG
Statistics
Matches: 294, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
54 1 0.00
55 292 0.99
56 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (55 bp):
AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCA
Found at i:1601969 original size:21 final size:20
Alignment explanation
Indices: 1601943--1601981 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1601933 ATATGCTAAA
1601943 CTATCA-AAGTGTGAGTTTTGG
1 CTATCAGAAGT-TGA-TTTTGG
1601964 CTATCAGAAGTTGATTTT
1 CTATCAGAAGTTGATTTT
1601982 CTTAGTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (20 bp):
CTATCAGAAGTTGATTTTGG
Found at i:1602076 original size:12 final size:13
Alignment explanation
Indices: 1602033--1602090 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
1602023 ATATTATATT
1602033 AAAAACAAGA-AAC
1 AAAAA-AAGAGAAC
* *
1602046 AGAAAAAGA-AAG
1 AAAAAAAGAGAAC
1602058 AAGAAAAAGAGAA-
1 AA-AAAAAGAGAAC
*
1602071 AAAAAAACAGAAC
1 AAAAAAAGAGAAC
1602084 AAAAAAA
1 AAAAAAA
1602091 ATAATAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
12 16 0.42
13 20 0.53
14 2 0.05
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAAC
Found at i:1603601 original size:28 final size:28
Alignment explanation
Indices: 1603565--1603627 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
1603555 TAAAGAGGTT
1603565 CAAAATCTAATGATTTGCATGATCTTCA
1 CAAAATCTAATGATTTGCATGATCTTCA
1603593 CAAAATCTAATGATTTGCATGATCTTCA
1 CAAAATCTAATGATTTGCATGATCTTCA
1603621 CAAAATC
1 CAAAATC
1603628 CTCAAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (28 bp):
CAAAATCTAATGATTTGCATGATCTTCA
Found at i:1606452 original size:45 final size:45
Alignment explanation
Indices: 1606318--1606499 Score: 240
Period size: 45 Copynumber: 4.0 Consensus size: 45
1606308 GGTAACCAGG
* * * * *
1606318 AAAATAAGTTTATGAGCTTATGCAAT-AGTGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * *
1606362 AAAATAAGCTTACGAGCTTATGGAAATAAATTGTTAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGG-AATAAATGGTAAGTATATTGGT
*
1606408 AAAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * *
1606453 AAAATAAGCTTACGAGCTTATGGGATAAATGATATGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1606498 AA
1 AA
1606500 GAAAGTTGTA
Statistics
Matches: 120, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
44 20 0.17
45 64 0.53
46 36 0.30
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.34
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:1609881 original size:544 final size:544
Alignment explanation
Indices: 1608864--1609942 Score: 1795
Period size: 544 Copynumber: 2.0 Consensus size: 544
1608854 ACGTACAAAT
*
1608864 ACGAAAGTTCTTTAGTGTGGTTATTATTGGTCTTCATCATTCAAAGATATTAATGATATTTTAAG
1 ACGAAAGTTCTTCAGTGTGGTTATTATTGGTCTTCATCATTCAAAGATATTAATGATATTTTAAG
* **
1608929 CAATATGATTGATGCCAATGAACAGGCGACATTTCTCAACGTAACAAAATGCCGATGCAGCTGAT
66 CAATATGATTGATGCCAACGAACAGGCGACATTTCTCAAAATAACAAAATGCCGATGCAGCTGAT
* * *
1608994 TTGGAACTTGAATTGTTTAATGTATGGGGATTAGATTTCATGGGATCATACCCTTCATCATGTGG
131 TTGGAAATTAAACTGTTTAATGTATGGGGATTAGATTTCATGGGATCATACCCTTCATCATGTGG
* * *
1609059 GAAATGTTTTCTCTTGGTTGTTGTTGACTATCTCATATGGGTGGAAGTTGTAGCATTTCCCACCA
196 GAAATGTTTTCTCTTAGTTGTTGTTGACTATCTCAAATGGGTGAAAGTTGTAGCATTTCCCACCA
* *
1609124 GTAATGCTAAAGTGGTTTTACGATTCCTCCAACAAAACATATTCACTCATTTTGGAACAGCCTGT
261 ATAATGCTAAAGCGGTTTTACGATTCCTCCAACAAAACATATTCACTCATTTTGGAACAGCCTGT
1609189 GCATTCATCAATGATGAAGGTTCTCAGTTCATTTGGACACACGTTTCTAGAGCATTGAATTGTTA
326 GCATTCATCAATGATGAAGGTTCTCAGTTCATTTGGACACACGTTTCTAGAGCATTGAATTGTTA
* * *
1609254 TCGAGTTAAGCATCGGATTGCTAAAGTATATCATCCGTTGACCAACGACTAAGCAGAAGTGTCGA
391 TAGAGTTAAGCATCAGATTGCTAAAGTATATCATCCATTGACCAACGACTAAGCAGAAGTGTCGA
* *
1609319 ACTGTAAGATCAAACAAATTCTAGAAAAGGTTGTTAATCTTTCTCGAAAAGACTAATCTCAAAAC
456 ACCGTAAGATCAAACAAATTCTAGAAAAGGTTGTTAATCCTTCTCGAAAAGACTAATCTCAAAAC
1609384 CTTGAGGAAACATTACGTACAGCA
521 CTTGAGGAAACATTACGTACAGCA
* *
1609408 ACGAAAGTTCTTCAGTGTGGTTATTATTGGTCTTCATCATTCAAAGATGTTAATGATTTTTTAAG
1 ACGAAAGTTCTTCAGTGTGGTTATTATTGGTCTTCATCATTCAAAGATATTAATGATATTTTAAG
* * * **
1609473 CAATATGATTGCTGCTAACGAACATGCGACATTTCTCAAAATAACAAAATGTTGATGCAGGC-GA
66 CAATATGATTGATGCCAACGAACAGGCGACATTTCTCAAAATAACAAAATGCCGATGCA-GCTGA
*
1609537 TTTGGAAATTAAACTGTTTGATGTATGGGGATTAGATTTCATGGGATCATACCCTTCATCATGTG
130 TTTGGAAATTAAACTGTTTAATGTATGGGGATTAGATTTCATGGGATCATACCCTTCATCATGTG
*
1609602 GGAAACT-TTTTCTCTTAGTTGTTGTTGACTATCTCAAATGGGTGAAAGTTGTAGTATTTCCCAC
195 GGAAA-TGTTTTCTCTTAGTTGTTGTTGACTATCTCAAATGGGTGAAAGTTGTAGCATTTCCCAC
*
1609666 CAATAATGCTAAAGCGGTTTTACGATTCCTCCAACAAAACATATTCACTCGTTTTGGAACAGCAC
259 CAATAATGCTAAAGCGGTTTTACGATTCCTCCAACAAAACATATTCACTCATTTTGGAACAGC-C
* * * *
1609731 -GTGCATTCATCAGTGATGAATGTTCTCAGTTCATTTGGGCACACGTTTCTAGAGCTTTGAATTG
323 TGTGCATTCATCAATGATGAAGGTTCTCAGTTCATTTGGACACACGTTTCTAGAGCATTGAATTG
1609795 TTATAGAGTTAAGCATCAGATTGCTAAAGTATATCATCCATTGACCAACGACTAAGCAGAAGTGT
388 TTATAGAGTTAAGCATCAGATTGCTAAAGTATATCATCCATTGACCAACGACTAAGCAGAAGTGT
* * *
1609860 CGAACCGTAAGATCAAACAAATTCTGGAAAAGGTTGTTAATCCTTCTCGAAAAGACTAGTTTCAA
453 CGAACCGTAAGATCAAACAAATTCTAGAAAAGGTTGTTAATCCTTCTCGAAAAGACTAATCTCAA
*
1609925 AGCCTTGAGGAAACATTA
518 AACCTTGAGGAAACATTA
1609943 TAGGATTATA
Statistics
Matches: 497, Mismatches: 35, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
544 493 0.99
545 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (544 bp):
ACGAAAGTTCTTCAGTGTGGTTATTATTGGTCTTCATCATTCAAAGATATTAATGATATTTTAAG
CAATATGATTGATGCCAACGAACAGGCGACATTTCTCAAAATAACAAAATGCCGATGCAGCTGAT
TTGGAAATTAAACTGTTTAATGTATGGGGATTAGATTTCATGGGATCATACCCTTCATCATGTGG
GAAATGTTTTCTCTTAGTTGTTGTTGACTATCTCAAATGGGTGAAAGTTGTAGCATTTCCCACCA
ATAATGCTAAAGCGGTTTTACGATTCCTCCAACAAAACATATTCACTCATTTTGGAACAGCCTGT
GCATTCATCAATGATGAAGGTTCTCAGTTCATTTGGACACACGTTTCTAGAGCATTGAATTGTTA
TAGAGTTAAGCATCAGATTGCTAAAGTATATCATCCATTGACCAACGACTAAGCAGAAGTGTCGA
ACCGTAAGATCAAACAAATTCTAGAAAAGGTTGTTAATCCTTCTCGAAAAGACTAATCTCAAAAC
CTTGAGGAAACATTACGTACAGCA
Found at i:1611119 original size:20 final size:21
Alignment explanation
Indices: 1611089--1611127 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1611079 ATTACAGGTA
*
1611089 CAAATATGACAAAATCGGTCT
1 CAAATATGACAAAACCGGTCT
1611110 CAAA-ATGACAAAACCGGT
1 CAAATATGACAAAACCGGT
1611128 AAAACGCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (21 bp):
CAAATATGACAAAACCGGTCT
Found at i:1611347 original size:182 final size:182
Alignment explanation
Indices: 1611069--1612262 Score: 1743
Period size: 182 Copynumber: 6.5 Consensus size: 182
1611059 ATGGATTGAC
* * * *
1611069 CCATAGCAATATTACAGGTACAAATATGACAAAATC-GGTCTC-AAAATGACAAAACCGGTAAAA
1 CCATAACAATATAACAGGTAAAAATATGATAAAA-CAGGTCTCAAAAATGACAAAACCGG-AAAA
* * ** *
1611132 CGCTACCGGATATGTGT-CGAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAA
64 AGTTACCGGATATGT-TAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAA
*
1611196 AGAGAAGAAGTTATAGCACCTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
128 AGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
* * *
1611251 CCTTACCAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAAAAAACCGGAAAAAG
1 CCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAAAG
1611316 TTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGA
66 TTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGA
* * *
1611381 GAAAAAGTTATTGCGCTTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
131 GAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
* * * *
1611433 CCATAATAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAATTGACAAAACCAGTAAAAC
1 CCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACC-GGAAAAA
* *
1611498 GTTACCGGATATATTAAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAAAG
65 GTTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAG
* * * * *
1611563 AGAAGAAGTTATAGCGCCTATAAAGTGTCGATAATTTA-AAAATATATATCGAT
130 AGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAA-ATGTATCGAT
* * * *
1611616 CCACAACAATATAACAGGTAAAAATATGATAAAACATGTCTCAAAAATGAGAAAATCGGAAAAAG
1 CCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAAAG
*
1611681 TTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTTGAATTTAAAAGA
66 TTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGA
1611746 GAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
131 GAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
* * * * * *
1611798 CCATAACAATATAATATGTAAAAATATAATAAAACAGGTCTCAAAATTGACAAAACCAGTAAAAC
1 CCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACC-GGAAAAA
* * * * *
1611863 GCTACCGAATATATTGAAAGTGTCGATAATTTAATATTAGTATCGACACTTTCTGAATTTAAAAG
65 GTTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAG
1611928 AGAAGAAGTTATAGCGCCTAAAAAGTGTCGAC-CTTATATGAAAATGTATCGAT
130 AGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTT-TATGAAAATGTATCGAT
* * * * *
1611981 CCTTACCAATATAACAGGTAAAAATATAATAAAACAGGTCTCAAAAATGACAAAACCAGAAAATG
1 CCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAAAG
*
1612046 TTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGA
66 TTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGA
* *
1612111 GAAGAAGTTATAGCGCTTAAAAAGTGTCGACATTTTATGAAAATGTATCGAT
131 GAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
* * * *
1612163 CCAGAACAATATAACATGTAAAAATATGATAAAACCGGTCTC-AAAATGACAAAACCGGTAAATA
1 CCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGG-AAAAA
* * * *
1612227 GATACCGGATATGTTGAAAGTATCGATACTTTAATA
65 GTTACCGGATATGTTAAAAGTGTCGATAATTTAATA
1612263 AGTACGCCTA
Statistics
Matches: 912, Mismatches: 90, Indels: 20
0.89 0.09 0.02
Matches are distributed among these distances:
181 17 0.02
182 550 0.60
183 345 0.38
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
CCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAAAG
TTACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGA
GAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
Found at i:1611722 original size:365 final size:363
Alignment explanation
Indices: 1611069--1612262 Score: 1858
Period size: 365 Copynumber: 3.3 Consensus size: 363
1611059 ATGGATTGAC
* * * * *
1611069 CCATAGCAATATTACAGGTACAAATATGACAAAATC-GGTCTCAAAATGACAAAACCGGTAAAAC
1 CCATAACAATATAACAGGTAAAAATATGATAAAA-CAGGTCTCAAAATGACAAAACCAGTAAAAC
*
1611133 GCTACCGGATATGTGTCG--AGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAA
65 GCTACCGGATATAT-T-GAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAA
*
1611196 AGAGAAGAAGTTATAGCACCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCTTACCAAT
128 AGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGA-ACTTTATGAAAATGTATCGATCCTTACCAAT
1611261 ATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAAAAAACCGGAAAAAGTTACCGGATA
192 ATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAAAAAACCGGAAAAAGTTACCGGATA
*
1611326 TGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAAAAGTTA
257 TGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTA
*
1611391 TTGCGCTTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
322 TAGCGCTTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
*
1611433 CCATAATAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAATTGACAAAACCAGTAAAAC
1 CCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAA-TGACAAAACCAGTAAAAC
* *
1611498 GTTACCGGATATATTAAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAAAG
65 GCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAAAG
* * * * ** *
1611563 AGAAGAAGTTATAGCGCCTATAAAGTGTCGATAATTTA-AAAATATATATCGATCCACAACAATA
130 AGAAGAAGTTATAGCGCCTAAAAAGTGTCGA-ACTTTATGAAA-ATGTATCGATCCTTACCAATA
* * *
1611627 TAACAGGTAAAAATATGATAAAACATGTCTCAAAAATGAGAAAATCGGAAAAAGTTACCGGATAT
193 TAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAAAAAACCGGAAAAAGTTACCGGATAT
*
1611692 GTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTTGAATTTAAAAGAGAAGAAGTTAT
258 GTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTAT
*
1611757 AGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
323 AGCGCTTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
* * *
1611798 CCATAACAATATAATATGTAAAAATATAATAAAACAGGTCTCAAAATTGACAAAACCAGTAAAAC
1 CCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAA-TGACAAAACCAGTAAAAC
* * *
1611863 GCTACCGAATATATTGAAAGTGTCGATAATTTAATATTAGTATCGACACTTTCTGAATTTAAAAG
65 GCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAAAG
*
1611928 AGAAGAAGTTATAGCGCCTAAAAAGTGTCGACCTTATATGAAAATGTATCGATCCTTACCAATAT
130 AGAAGAAGTTATAGCGCCTAAAAAGTGTCGAACTT-TATGAAAATGTATCGATCCTTACCAATAT
* * * *
1611993 AACAGGTAAAAATATAATAAAACAGGTCTCAAAAATGACAAAACCAGAAAATGTTACCGGATATG
194 AACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAAAAAACCGGAAAAAGTTACCGGATATG
*
1612058 TTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATA
259 TTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATA
*
1612123 GCGCTTAAAAAGTGTCGACATTTTATGAAAATGTATCGAT
324 GCGCTTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
* * * *
1612163 CCAGAACAATATAACATGTAAAAATATGATAAAACCGGTCTCAAAATGACAAAACCGGTAAATA-
1 CCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAATGACAAAACCAGTAAA-AC
* * * *
1612227 GATACCGGATATGTTGAAAGTATCGATACTTTAATA
65 GCTACCGGATATATTGAAAGTGTCGATAATTTAATA
1612263 AGTACGCCTA
Statistics
Matches: 760, Mismatches: 62, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
363 1 0.00
364 91 0.12
365 665 0.88
366 3 0.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (363 bp):
CCATAACAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAATGACAAAACCAGTAAAACG
CTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAAAGA
GAAGAAGTTATAGCGCCTAAAAAGTGTCGAACTTTATGAAAATGTATCGATCCTTACCAATATAA
CAGGTAAAAATATGATAAAACAGGTCTCAAAAATGAAAAAACCGGAAAAAGTTACCGGATATGTT
AAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGC
GCTTAAAAAGTGTCGACACTTTATGAAAATGTATCGAT
Found at i:1612074 original size:547 final size:545
Alignment explanation
Indices: 1611075--1612262 Score: 1799
Period size: 547 Copynumber: 2.2 Consensus size: 545
1611065 TGACCCATAG
* * * * *
1611075 CAATATTACAGGTACAAATATGACAAAATCGGTCTCAAAATGACAAAACCGGTAAAACGCTACCG
1 CAATATAACAGGTAAAAATATGATAAAA-CGGTCTCAAAATGACAAAACCGGTAAAAAGATACCG
**
1611140 GATATGTGTCGAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAAAGAGAAGAA
65 GATATGT-TAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAAAGAGAAGAA
* *
1611205 GTTATAGCACCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCTTACCAATATAACAGGT
129 GTTATAGCACCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGT
* * * *
1611270 AAAAATATGATAAAACAGGTCTCAAAAATGAAAAAACCGGAAAAAGTTACCGGATATGTTAAAAG
194 AAAAATATAATAAAACAGGTCTCAAAAATGAAAAAACCGGAAAAAGCTACCGAATATATTAAAAG
* *
1611335 TGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAAAAGTTATTGCGCTTA
259 TGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAAAAGTTATAGCGCCTA
* *
1611400 AAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGATAA
324 AAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAATAA
*
1611465 AACAGGTCTCAAAATTGACAAAACCAGTAAAACGTTACCGGATATATTAAAAGTGTCGATAATTT
389 AACAGGTCTCAAAAATGACAAAACCAGTAAAACGTTACCGGATATATTAAAAGTGTCGATAATTT
* *
1611530 AATATAAGTATCGAAACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGAT
454 AATATAAGTATCGAAACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGAC
1611595 AATTTA-AAAATATATATCGATCCACAA
519 AATTTATAAAA-ATATATCGATCCACAA
* * * *
1611622 CAATATAACAGGTAAAAATATGATAAAACATGTCTCAAAAATGAGAAAATCGG-AAAAAGTTACC
1 CAATATAACAGGTAAAAATATGATAAAAC-GGTCTC-AAAATGACAAAACCGGTAAAAAGATACC
* *
1611686 GGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTTTTTGAATTTAAAAGAGAAGA
64 GGATATGTT-AAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAAAGAGAAGA
* * *
1611751 AGTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAATATG
128 AGTTATAGCACCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGG
* * * * *
1611816 TAAAAATATAATAAAACAGGTCTCAAAATTGACAAAACCAGTAAAACGCTACCGAATATATTGAA
193 TAAAAATATAATAAAACAGGTCTCAAAAATGAAAAAACC-GGAAAAAGCTACCGAATATATTAAA
* *
1611881 AGTGTCGATAATTTAATATTAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCC
257 AGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAAAAGTTATAGCGCC
* *
1611946 TAAAAAGTGTCGAC-CTTATATGAAAATGTATCGATCCTTACCAATATAACAGGTAAAAATATAA
322 TAAAAAGTGTCGACACTT-TATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAA
* * *
1612010 TAAAACAGGTCTCAAAAATGACAAAACCAG-AAAATGTTACCGGATATGTTGAAAGTGTCGATAA
386 TAAAACAGGTCTCAAAAATGACAAAACCAGTAAAACGTTACCGGATATATTAAAAGTGTCGATAA
* *
1612074 TTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCTTAAAAAGTGTC
451 TTTAATATAAGTATCGAAACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTC
* * * *
1612139 GACATTTTATGAAAATGTATCGATCCAGAA
516 GACAATTTATAAAAATATATCGATCCACAA
* *
1612169 CAATATAACATGTAAAAATATGATAAAACCGGTCTCAAAATGACAAAACCGGTAAATAGATACCG
1 CAATATAACAGGTAAAAATATGATAAAA-CGGTCTCAAAATGACAAAACCGGTAAAAAGATACCG
* *
1612234 GATATGTTGAAAGTATCGATACTTTAATA
65 GATATGTT-AAAGTGTCGATAATTTAATA
1612263 AGTACGCCTA
Statistics
Matches: 578, Mismatches: 55, Indels: 16
0.89 0.08 0.02
Matches are distributed among these distances:
546 16 0.03
547 379 0.66
548 183 0.32
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (545 bp):
CAATATAACAGGTAAAAATATGATAAAACGGTCTCAAAATGACAAAACCGGTAAAAAGATACCGG
ATATGTTAAAGTGTCGATAATTTAATATAAGTATCGAAACTTTCTGAATTTAAAAGAGAAGAAGT
TATAGCACCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAA
AAATATAATAAAACAGGTCTCAAAAATGAAAAAACCGGAAAAAGCTACCGAATATATTAAAAGTG
TCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAAAAGTTATAGCGCCTAAA
AAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATAATAAAA
CAGGTCTCAAAAATGACAAAACCAGTAAAACGTTACCGGATATATTAAAAGTGTCGATAATTTAA
TATAAGTATCGAAACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACAA
TTTATAAAAATATATCGATCCACAA
Found at i:1612673 original size:18 final size:19
Alignment explanation
Indices: 1612650--1612694 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1612640 TAGTTAATAT
1612650 TTATAGGTA-AAAATGATA
1 TTATAGGTAGAAAATGATA
1612668 TTATAGGTAGAAAATGATA
1 TTATAGGTAGAAAATGATA
*
1612687 TTTTAGGT
1 TTATAGGT
1612695 TGTATAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (19 bp):
TTATAGGTAGAAAATGATA
Found at i:1612975 original size:18 final size:18
Alignment explanation
Indices: 1612940--1612978 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1612930 TTGAAATGGT
1612940 AATTGCATTAAAACTTTA
1 AATTGCATTAAAACTTTA
*
1612958 AATTG-ATTACAAATTTTA
1 AATTGCATTA-AAACTTTA
1612976 AAT
1 AAT
1612979 GTTGACAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (18 bp):
AATTGCATTAAAACTTTA
Found at i:1613992 original size:22 final size:22
Alignment explanation
Indices: 1613941--1613996 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
1613931 ATGTTTTTGT
*
1613941 TTTTTTTATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAG-A
*
1613964 TGGTTATTATATAAAATGATA-A
1 T-TTTATTATATAAAATGATAGA
1613986 CTTTTATTATA
1 -TTTTATTATA
1613997 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 2 0.07
24 17 0.61
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (22 bp):
TTTTATTATATAAAATGATAGA
Found at i:1614724 original size:22 final size:18
Alignment explanation
Indices: 1614675--1614713 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1614665 GAAAAAATTT
*
1614675 GAAGAAGAGAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1614693 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1614711 GAA
1 GAA
1614714 ATGAGGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:1616207 original size:19 final size:19
Alignment explanation
Indices: 1616181--1616229 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1616171 AAATGCATGG
1616181 TTAA-TTTGTATAAGATTT
1 TTAATTTTGTATAAGATTT
*
1616199 TTAATTTTGTATACGATTT
1 TTAATTTTGTATAAGATTT
*
1616218 ATAATTTTGTAT
1 TTAATTTTGTAT
1616230 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:1617205 original size:199 final size:199
Alignment explanation
Indices: 1616850--1618059 Score: 1910
Period size: 199 Copynumber: 6.1 Consensus size: 199
1616840 GTAGATTAGC
* *
1616850 AATATAACTGGTTTTTGAGAAAACAAGTGTAAAAAAAGTATCGACACAAATCGAACAAGTGTCGA
1 AATAT-ACCGGTTTTTGAGAAAACAAGTGTAAAAAAAGTATCGACACAAATCAAACAAGTGTCGA
1616915 TACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTGTAACAA
65 TACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTGTAACAA
*
1616980 GTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGTAATATAACCG
130 GTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAATATAACCG
1617045 GTCTA
195 GTCTA
* *
1617050 AATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTATCGACACAATTCAAACAAGTGTCGAT
1 AATATACCGGTTTTTGAGAAAACAAGTGTAAAAAAAGTATCGACACAAATCAAACAAGTGTCGAT
* *
1617115 ACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAAAAAGTGTCGATACATTTGTAACAAG
66 ACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTGTAACAAG
* * *
1617180 TGTCGATCCAAAAAATATTGAAAACTATAATTATAATGTAATAGGTAGATTAGCAATATAACCGG
131 TGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAATATAACCGG
1617245 TCTA
196 TCTA
**
1617249 AATATACCAATTTTTGAGAAAACAAGTG-AAAAACAAGTATCGACACAAATCAAACAAGTGTCGA
1 AATATACCGGTTTTTGAGAAAACAAGTGTAAAAA-AAGTATCGACACAAATCAAACAAGTGTCGA
1617313 TACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTGTAACAA
65 TACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTGTAACAA
* **
1617378 GTGTCGATCCAAAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAATATAATT
130 GTGTCGATCC-CAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAATATAACC
*
1617443 GGTATA
194 GGTCTA
*
1617449 AATATACCGGTTTTTGAGAAAACATGTGT-AAAAAAGTATCGACACAAATCAAACAAGTGTCGAT
1 AATATACCGGTTTTTGAGAAAACAAGTGTAAAAAAAGTATCGACACAAATCAAACAAGTGTCGAT
* *
1617513 ACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAAAAAGTGTCGATACATTTGTAACAAG
66 ACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTGTAACAAG
* * * * *
1617578 TGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGATAAATTAGAAATATAACCAG
131 TGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAATATAACCGG
1617643 TCTA
196 TCTA
* * * * * * **
1617647 AATATACCGGTTTAAATT--GAAAACAGGT-TACCATAATGTATCGACACATTAT-TAACTTGTG
1 AATATACCGGTTT---TTGAGAAAACAAGTGTA-AAAAAAGTATCGACACA-AATCAAACAAGTG
1617708 TCGATACCTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTGT
61 TCGATA-CTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTGT
* * *
1617773 AACAAGTGTCGATCCGAAAAACATTGAAAACTATAATTATAATGTAATAGATAGATTAGCAATAT
125 AACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAATAT
1617838 AACCGGTCTA
190 AACCGGTCTA
*
1617848 AATATACCGGTTTTTGAGAAAACATGTGTAAAAAAAGTATCGACACAAATCAAACAAGTGTCGAT
1 AATATACCGGTTTTTGAGAAAACAAGTGTAAAAAAAGTATCGACACAAATCAAACAAGTGTCGAT
* * *
1617913 ACTTTTTGTCCAGAATGCATTTCAAAACCAAGTGCCCTAAAAAGTGTCGATACATTTGTAACAAG
66 ACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTGTAACAAG
* * * *
1617978 TGTCGATCCCAAAAACATCAAAAACCATAATTATAATGTAATAGGTAAATTAGCAATATAACCAG
131 TGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAATATAACCGG
1618043 TCTA
196 TCTA
1618047 AATATACCGGTTT
1 AATATACCGGTTT
1618060 AAATTGAAAA
Statistics
Matches: 927, Mismatches: 69, Indels: 29
0.90 0.07 0.03
Matches are distributed among these distances:
198 72 0.08
199 561 0.61
200 150 0.16
201 144 0.16
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (199 bp):
AATATACCGGTTTTTGAGAAAACAAGTGTAAAAAAAGTATCGACACAAATCAAACAAGTGTCGAT
ACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTTGTAACAAG
TGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAATATAACCGG
TCTA
Found at i:1617488 original size:398 final size:395
Alignment explanation
Indices: 1616576--1618054 Score: 2374
Period size: 398 Copynumber: 3.8 Consensus size: 395
1616566 TAAACTTATA
* *
1616576 TGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAG
1 TGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAG
*
1616641 GTAAATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTAT
66 GTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTAT
* *
1616706 CGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAA
131 CGACACAAATCAAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAA
*
1616771 AAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATTGAAAACCATAATTATAATGTA
196 AAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTA
* **
1616836 ATAGGTAGATTAGCAATAT-A--A--C------T-GGTTTTTGAGAAAACAAGTGTAAAAAAAGT
261 ATAGGTAAATTAGCAATATAACCAGTCTAAATATACCTTTTTGAGAAAACAAGTG-AAAAAAAGT
*
1616889 ATCGACACAAATCGAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACT
325 ATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACT
1616954 AAAAAG
390 AAAAAG
1616960 TGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAG
1 TGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAG
*
1617025 GTAGATTAGTAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTAT
66 GTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTAT
*
1617090 CGACACAATTCAAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAA
131 CGACACAAATCAAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAA
* * * *
1617155 AAAGTGTCGATACATTTGTAACAAGTGTCGATCCAAAAAATATTGAAAACTATAATTATAATGTA
196 AAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTA
* *
1617220 ATAGGTAGATTAGCAATATAACCGGTCTAAATATACCAATTTTTGAGAAAACAAGTGAAAAACAA
261 ATAGGTAAATTAGCAATATAACCAGTCTAAATATACC--TTTTTGAGAAAACAAGTGAAAAA-AA
1617285 GTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCA
323 GTATCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCA
1617350 CTAAAAAG
388 CTAAAAAG
*
1617358 TGTCGATACATTTGTAACAAGTGTCGATCCAAAAAAACATCGAAAACTATAATTATAATGTAATA
1 TGTCGATACATTTGTAACAAGTGTCGATCC-CAAAAACATCGAAAACTATAATTATAATGTAATA
** * *
1617423 GGTAGATTAGCAATATAATTGGTATAAATATACCGGTTTTTGAGAAAACATGTGT-AAAAAAGTA
65 GGTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTA
1617487 TCGACACAAATCAAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTA
130 TCGACACAAATCAAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTA
1617552 AAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGT
195 AAAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGT
* * * ** * * * *
1617617 AATAGATAAATTAGAAATATAACCAGTCTAAATATACCGGTTTAAATTGAAAACAGGTTACCATA
260 AATAGGTAAATTAGCAATATAACCAGTCTAAATATACC-TTTTTGA--GAAAACAAGTGA-AAAA
* * * **
1617682 ATGTATCGACACATTAT-TAACTTGTGTCGATACCTTTTGGTCCAGAATGTATTTCAAAACCAAG
321 AAGTATCGACACA-AATCAAACAAGTGTCGATA-CTTTTGGTCCAGAATGTATTTCAAAACCAAG
1617746 TGCACTAAAAAG
384 TGCACTAAAAAG
* *
1617758 TGTCGATACATTTGTAACAAGTGTCGATCCGAAAAACATTGAAAACTATAATTATAATGTAATAG
1 TGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAG
* *
1617823 ATAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTAAAAAAAGTAT
66 GTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTAT
*
1617888 CGACACAAATCAAACAAGTGTCGATACTTTTTGTCCAGAATGCATTTCAAAACCAAGTGCCCTAA
131 CGACACAAATCAAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAA
*
1617953 AAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCAAAAACCATAATTATAATGTA
196 AAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTA
1618018 ATAGGTAAATTAGCAATATAACCAGTCTAAATATACC
261 ATAGGTAAATTAGCAATATAACCAGTCTAAATATACC
1618055 GGTTTAAATT
Statistics
Matches: 1021, Mismatches: 52, Indels: 28
0.93 0.05 0.03
Matches are distributed among these distances:
384 269 0.26
385 1 0.00
389 1 0.00
395 1 0.00
397 9 0.01
398 290 0.28
399 200 0.20
400 250 0.24
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (395 bp):
TGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAG
GTAGATTAGCAATATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTAT
CGACACAAATCAAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAA
AAAGTGTCGATACATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTA
ATAGGTAAATTAGCAATATAACCAGTCTAAATATACCTTTTTGAGAAAACAAGTGAAAAAAAGTA
TCGACACAAATCAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTA
AAAAG
Found at i:1617937 original size:400 final size:399
Alignment explanation
Indices: 1616908--1618119 Score: 2040
Period size: 400 Copynumber: 3.0 Consensus size: 399
1616898 AATCGAACAA
1616908 GTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTT
1 GTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTT
* *
1616973 GTAACAAGTGTCGATCCCAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGTAAT
66 GTAACAAGTGTCGATCCAAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAAT
* *
1617038 ATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTAAAAAAAGTATCGACACAATTCAA
131 ATAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTAAAAAAAGTATCGACACAAATCAA
1617103 ACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAAAAAGTGTCGATAC
196 ACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAAAAAGTGTCGATAC
* * * * *
1617168 ATTTGTAACAAGTGTCGATCCAAAAAATATTGAAAACTATAATTATAATGTAATAGGTAGATTAG
261 ATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAG
* ** * * * *
1617233 CAATATAACCGGTCTAAATATACCAATTT---TTGAGAAAACAAGTGA-AAAACAAGTATCGACA
326 CAATATAACCAGTCTAAATATACCGGTTTAAATT--GAAAACAAGTTACCATA-ATGTATCGACA
* * **
1617294 CA-AATCAAACAA
388 CATTAT-TAACTT
1617306 GTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTT
1 GTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTT
1617371 GTAACAAGTGTCGATCCAAAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAA
66 GTAACAAGTGTCGATCC-AAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAA
** *
1617436 TATAATTGGTATAAATATACCGGTTTTTGAGAAAACATGTGT-AAAAAAGTATCGACACAAATCA
130 TATAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTAAAAAAAGTATCGACACAAATCA
1617500 AACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAAAAAGTGTCGATA
195 AACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAAAAAGTGTCGATA
*
1617565 CATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGATAAATTA
260 CATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTA
* *
1617630 GAAATATAACCAGTCTAAATATACCGGTTTAAATTGAAAACAGGTTACCATAATGTATCGACACA
325 GCAATATAACCAGTCTAAATATACCGGTTTAAATTGAAAACAAGTTACCATAATGTATCGACACA
1617695 TTATTAACTT
390 TTATTAACTT
1617705 GTGTCGATACCTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATT
1 GTGTCGATA-CTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATT
* * *
1617770 TGTAACAAGTGTCGATCCGAAAAACATTGAAAACTATAATTATAATGTAATAGATAGATTAGCAA
65 TGTAACAAGTGTCGATCCAAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAA
1617835 TATAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTAAAAAAAGTATCGACACAAATCA
130 TATAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTAAAAAAAGTATCGACACAAATCA
*
1617900 AACAAGTGTCGATACTTTTTGTCCAGAATGCATTTCAAAACCAAGTGCCCTAAAAAGTGTCGATA
195 AACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAAAAAGTGTCGATA
*
1617965 CATTTGTAACAAGTGTCGATCCCAAAAACATCAAAAACCATAATTATAATGTAATAGGTAAATTA
260 CATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTA
1618030 GCAATATAACCAGTCTAAATATACCGGTTTAAATTGAAAACAAGTTACCATAATGTATCGACACA
325 GCAATATAACCAGTCTAAATATACCGGTTTAAATTGAAAACAAGTTACCATAATGTATCGACACA
1618095 TTATTAACTT
390 TTATTAACTT
1618105 GTGTCGATACCTTTT
1 GTGTCGATA-CTTTT
1618120 TAAATTACTC
Statistics
Matches: 769, Mismatches: 37, Indels: 14
0.94 0.05 0.02
Matches are distributed among these distances:
398 253 0.33
399 200 0.26
400 314 0.41
401 2 0.00
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.29
Consensus pattern (399 bp):
GTGTCGATACTTTTGGTCCAGAATGTATTTCAAAACCAAGTGCACTAAAAAGTGTCGATACATTT
GTAACAAGTGTCGATCCAAAAAACATCGAAAACTATAATTATAATGTAATAGGTAGATTAGCAAT
ATAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTAAAAAAAGTATCGACACAAATCAA
ACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAAAACCAAGTGCCCTAAAAAGTGTCGATAC
ATTTGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTATAATGTAATAGGTAAATTAG
CAATATAACCAGTCTAAATATACCGGTTTAAATTGAAAACAAGTTACCATAATGTATCGACACAT
TATTAACTT
Found at i:1618419 original size:15 final size:15
Alignment explanation
Indices: 1618399--1618435 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1618389 TTTCTCAAAT
1618399 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAC
* *
1618414 CTCTTCCCAACCCAG
1 CTCTTCTCAACCCAC
1618429 CTCTTCT
1 CTCTTCT
1618436 GAGGAAATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.16, C:0.51, G:0.03, T:0.30
Consensus pattern (15 bp):
CTCTTCTCAACCCAC
Found at i:1620200 original size:199 final size:198
Alignment explanation
Indices: 1619595--1620832 Score: 1831
Period size: 199 Copynumber: 6.2 Consensus size: 198
1619585 GTAACATAAA
1619595 TAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCA
1 TAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCA
*
1619660 TATAAACGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTAAAAAAGGTATCGACACAAATCA
66 TATAAACGGTCTAAATATACCGGTTTTTGAGAAAACAAGTGTAAAAAA-GTATCGACACAAATCA
*
1619725 AACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACATAAAAGTGTCGATA
130 AACAAGTGTCAATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACATAAAAGTGTCGATA
1619790 CATT
195 CATT
*
1619794 TAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAAAGTAATAGGTAAATTATTCA
1 TAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCA
* * *
1619859 TGTAAACGGTCTAAATATACCAGTTTTTGAGAAAACATGTGTAAAAAAGTATCGACACAAATCAA
66 TATAAACGGTCTAAATATACCGGTTTTTGAGAAAACAAGTGTAAAAAAGTATCGACACAAATCAA
*
1619924 ACAAGTGTCAATACTTTTGGTCCAAAATGTATTTCAAAACTAAGTGCAC-TAAAAAGTGTCGATA
131 ACAAGTGTCAATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACAT-AAAAGTGTCGATA
1619988 CATT
195 CATT
* * ** ***
1619992 TATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTAGAAA
1 TAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCA
* *
1620057 TATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAAGTGTACAAACAGTATCGACACAAAT-A
66 TATAAACGGTCTAAATATACCGGTTTTTGAGAAAACAAGTGTA-AAAAAGTATCGACACAAATCA
* *
1620121 GAACAAGTGTCAATACTTTTGGTCCAGAATGTATTTCAGAACCAAGTGCACATAAAAGTGTCGAT
130 -AACAAGTGTCAATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACATAAAAGTGTCGAT
1620186 ACATT
194 ACATT
1620191 TAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCA
1 TAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCA
* * *
1620256 TGTAAACGGTCTAAATATATCGGTTTTTGAGAAAACAGGTGTAAAACAAGTATCGACACAAATCA
66 TATAAACGGTCTAAATATACCGGTTTTTGAGAAAACAAGTGTAAAA-AAGTATCGACACAAATCA
* * *
1620321 AATAAGTGTCAATACTTTTGGTCCAAAATGTATTTCAAAACTAAGTGCACATAAAAGTGTTGATA
130 AACAAGTGTCAATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACATAAAAGTGTCGATA
1620386 CATT
195 CATT
*
1620390 TAAAACAAGTGTCGATCCCGAAAACATCAAAAAACATAATTATAATGTAATAGGTAAATTATTCA
1 TAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCA
* * *
1620455 TGTAACCGGTCTAAATATACCAGTTTTTGAGAAAACATA-TGTAAAAAAAGTATCGACACAAATC
66 TATAAACGGTCTAAATATACCGGTTTTTGAGAAAACA-AGTGT-AAAAAAGTATCGACACAAATC
* * * * *
1620519 GAACAAGTGTCGATACTTTTCGTCCAGAATGTATTTCAAAACCAAGTGCAC-TAAAAAGTGTCAA
129 AAACAAGTGTCAATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACAT-AAAAGTGTCGA
1620583 TACATT
193 TACATT
** * * * ***
1620589 TGTAACAAGTGTCGATCCCAAAAACATCGAAAACCATAATTACAATGTAATAGGTAAATTAGAAA
1 TAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCA
* * *
1620654 TATAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTATAAACAGTATCGACACAAAT-A
66 TATAAACGGTCTAAATATACCGGTTTTTGAGAAAACAAGTGTA-AAAAAGTATCGACACAAATCA
* * * * * * *
1620718 GAATAAGTGTCGATACTTTTTGTCCAGAATGTATTTCAGAACCAAGTGCACA-ACAAAGTTTCAA
130 -AACAAGTGTCAATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACATA-AAAGTGTCGA
1620782 TACATT
193 TACATT
* * * * *
1620788 TATAACAATTATCGATCCCAAAAATATCGAAAAACATAATTATAA
1 TAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAA
1620833 CCAAATGTCT
Statistics
Matches: 950, Mismatches: 75, Indels: 28
0.90 0.07 0.03
Matches are distributed among these distances:
197 1 0.00
198 184 0.19
199 759 0.80
200 6 0.01
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.27
Consensus pattern (198 bp):
TAAAACAAGTGTCGATCCCGAAAACATCGAAAAACATAATTATAATGTAATAGGTAAATTATTCA
TATAAACGGTCTAAATATACCGGTTTTTGAGAAAACAAGTGTAAAAAAGTATCGACACAAATCAA
ACAAGTGTCAATACTTTTGGTCCAAAATGTATTTCAAAACCAAGTGCACATAAAAGTGTCGATAC
ATT
Found at i:1623932 original size:182 final size:182
Alignment explanation
Indices: 1623621--1624074 Score: 719
Period size: 182 Copynumber: 2.5 Consensus size: 182
1623611 ATATGTTGAT
* * * * *
1623621 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAATAGGTAAAAAAATGACGAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
** * * * * *
1623686 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGATAGTGTCGATATTTTATTA
66 CGGTCTCGAAATGACAAAACCGGTAAAGAGATACCGGATATATTGATAGTGTCAATACTTTATTA
* *
1623751 TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGAGCTAATAA
131 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGAGCCAATAA
*
1623803 AGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
* *
1623868 CGGTCTCGAAATGACAAAACCGGTAAAGAGATATCGGATATGTTGATAGTGTCAATACTTTATTA
66 CGGTCTCGAAATGACAAAACCGGTAAAGAGATACCGGATATATTGATAGTGTCAATACTTTATTA
*
1623933 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
131 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGAGCCAATAA
*
1623985 AGTGTCGATACTTTATAAAAATGTATCGATCCATGACAATATAACAGGTAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
**
1624050 CTATCTCGAAATGACAAAACCGGTA
66 CGGTCTCGAAATGACAAAACCGGTA
1624075 GTAAAAAAGT
Statistics
Matches: 250, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
182 250 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
CGGTCTCGAAATGACAAAACCGGTAAAGAGATACCGGATATATTGATAGTGTCAATACTTTATTA
TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGAGCCAATAA
Found at i:1624700 original size:23 final size:23
Alignment explanation
Indices: 1624674--1624721 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1624664 AAATAAGTCA
* *
1624674 ATATAAGCGTTAACTATTATATT
1 ATATAAGCGCTAACTAATATATT
*
1624697 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTAACTAATATATT
1624720 AT
1 AT
1624722 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (23 bp):
ATATAAGCGCTAACTAATATATT
Found at i:1629284 original size:2 final size:2
Alignment explanation
Indices: 1629277--1629311 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1629267 AATTTGAGAT
1629277 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1629312 TAGACAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1633005 original size:20 final size:20
Alignment explanation
Indices: 1632961--1633238 Score: 171
Period size: 20 Copynumber: 13.6 Consensus size: 20
1632951 AATGACCAAT
* *
1632961 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1632980 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1633000 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
* **
1633020 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1633041 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1633064 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
1633084 AGAATTGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1633104 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1633124 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1633147 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
1633167 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1633187 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1633207 AGAATCGCAACGCGATTTAA
1 AAAATCGCAACGCGATTTAG
1633227 AAAATCGCAACG
1 AAAATCGCAACG
1633239 TTAAAAAGAT
Statistics
Matches: 201, Mismatches: 50, Indels: 15
0.76 0.19 0.06
Matches are distributed among these distances:
19 17 0.08
20 142 0.71
21 13 0.06
23 29 0.14
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1633117 original size:40 final size:40
Alignment explanation
Indices: 1633045--1633236 Score: 231
Period size: 40 Copynumber: 4.7 Consensus size: 40
1633035 GCTTCCAAGT
* *
1633045 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTT---ATAAAATCGCAATGCGATTGAGAGAA
* * * *
1633088 TTGCAATGCGATTTATATAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTATAAAATCGCAATGCGATTGAGAGAA
* *
1633128 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTT---ATAAAATCGCAATGCGATTGAGAGAA
* *
1633171 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAA
1 TCGCAACGCGATTTATAAAATCGCAATGCGATTGAGAGAA
*
1633211 TCGCAACGCGATTTAAAAAATCGCAA
1 TCGCAACGCGATTTATAAAATCGCAA
1633237 CGTTAAAAAG
Statistics
Matches: 127, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
40 80 0.63
43 47 0.37
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (40 bp):
TCGCAACGCGATTTATAAAATCGCAATGCGATTGAGAGAA
Found at i:1633151 original size:83 final size:83
Alignment explanation
Indices: 1633045--1633236 Score: 318
Period size: 83 Copynumber: 2.3 Consensus size: 83
1633035 GCTTCCAAGT
* * * *
1633045 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATTGCAATGCGATTTATATAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATC
*
1633110 GCAATGCGATTGAGAGAG
66 GCAATGCGATTGAGAGAA
1633128 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATC
1633193 GCAATGCGATTGAGAGAA
66 GCAATGCGATTGAGAGAA
1633211 TCGCAACGCGATTT--AA-AAAATCGCAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAA
1633237 CGTTAAAAAG
Statistics
Matches: 104, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
80 10 0.10
81 2 0.02
83 92 0.88
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATC
GCAATGCGATTGAGAGAA
Found at i:1633336 original size:6 final size:6
Alignment explanation
Indices: 1633325--1633386 Score: 117
Period size: 6 Copynumber: 10.5 Consensus size: 6
1633315 GACACGTATT
1633325 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1633373 ACCACG ACC-CG ACC
1 ACCACG ACCACG ACC
1633387 CGAGATGAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.09
6 51 0.91
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1634221 original size:20 final size:20
Alignment explanation
Indices: 1634198--1634249 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1634188 ATATAAATCG
1634198 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAC
* *
1634218 CGTTGCGATTTTCTTTTTAG
1 CGTTGCGATTTTCTTTTGAC
1634238 CGTTGCGATTTT
1 CGTTGCGATTTT
1634250 ATTGGTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.10, C:0.17, G:0.21, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAC
Found at i:1642312 original size:15 final size:15
Alignment explanation
Indices: 1642277--1642315 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1642267 ATCCGCCTGG
* *
1642277 CATCCACCCGCCCCG
1 CATCCGCCCGCCCCA
1642292 CATCCGCCCGCCCCA
1 CATCCGCCCGCCCCA
1642307 CATCCGCCC
1 CATCCGCCC
1642316 ACCCAGCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.13, C:0.67, G:0.13, T:0.08
Consensus pattern (15 bp):
CATCCGCCCGCCCCA
Found at i:1642315 original size:26 final size:26
Alignment explanation
Indices: 1642256--1642307 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1642246 TTGAGACATT
* *
1642256 ACCCGCCCCGCATCCGCCTGGCATCC
1 ACCCGCCCCGCATCCGCCTCGCACCC
1642282 ACCCGCCCCGCATCCGCC-CGC-CCC
1 ACCCGCCCCGCATCCGCCTCGCACCC
1642306 AC
1 AC
1642308 ATCCGCCCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 2 0.08
26 18 0.75
ACGTcount: A:0.12, C:0.63, G:0.17, T:0.08
Consensus pattern (26 bp):
ACCCGCCCCGCATCCGCCTCGCACCC
Found at i:1645192 original size:15 final size:15
Alignment explanation
Indices: 1645172--1645200 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1645162 AGGAAACAAA
1645172 ACATGGGCGGCTATG
1 ACATGGGCGGCTATG
1645187 ACATGGGCGGCTAT
1 ACATGGGCGGCTAT
1645201 CAAAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (15 bp):
ACATGGGCGGCTATG
Found at i:1649799 original size:15 final size:15
Alignment explanation
Indices: 1649779--1649807 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1649769 AGGAAACAAA
1649779 ACATGGGCGGCTATG
1 ACATGGGCGGCTATG
1649794 ACATGGGCGGCTAT
1 ACATGGGCGGCTAT
1649808 CAAAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (15 bp):
ACATGGGCGGCTATG
Found at i:1651957 original size:7 final size:7
Alignment explanation
Indices: 1651924--1651958 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1651914 TTTGATTCTC
*
1651924 TCTTGAT
1 TCTTGTT
*
1651931 TCTTGAT
1 TCTTGTT
1651938 TCTTGTT
1 TCTTGTT
1651945 TCTTGTT
1 TCTTGTT
1651952 TCTTGTT
1 TCTTGTT
1651959 GTTTCTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.06, C:0.14, G:0.14, T:0.66
Consensus pattern (7 bp):
TCTTGTT
Found at i:1652244 original size:64 final size:64
Alignment explanation
Indices: 1652163--1652318 Score: 235
Period size: 64 Copynumber: 2.4 Consensus size: 64
1652153 CATCGATATT
* *
1652163 AGTGCACCGATGCATAAAATGCATTCGATG-TTTCA-AACAAGCCTGAGTGCATCGATACATGGT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAACCTGAGTGCATCGATACATGG-
1652226 C
64 C
* * *
1652227 TGTGCATCGATGTATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCATGGC
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATACATGGC
1652291 AGTGCATCGATGCATAAAATGCATTCGA
1 AGTGCATCGATGCATAAAATGCATTCGA
1652319 AATGGTGTGT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
64 54 0.65
65 27 0.33
66 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (64 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATACATGGC
Found at i:1655037 original size:21 final size:23
Alignment explanation
Indices: 1654982--1655061 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 23
1654972 ATTGTTCATT
1654982 GATGCACATTCAAGGAGTGCATC
1 GATGCACATTCAAGGAGTGCATC
* * *
1655005 GGTGCATC-TTC-ATGA-TGTATC
1 GATGCA-CATTCAAGGAGTGCATC
1655026 GATGCACATTCAAAGG-GATGCATC
1 GATGCACATTC-AAGGAG-TGCATC
1655050 GATGCACATTCA
1 GATGCACATTCA
1655062 TAGTGTATCG
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
20 1 0.02
21 13 0.29
22 3 0.07
23 11 0.24
24 17 0.38
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (23 bp):
GATGCACATTCAAGGAGTGCATC
Found at i:1655069 original size:45 final size:44
Alignment explanation
Indices: 1654982--1655076 Score: 124
Period size: 45 Copynumber: 2.1 Consensus size: 44
1654972 ATTGTTCATT
*
1654982 GATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGTATC
1 GATGCACATTCAAGGAGTGCATCGATGCATCTTCATGATGTATC
1655026 GATGCACATTCAAAGG-GATGCATCGATGCA-CATTCAT-AGTGTATC
1 GATGCACATTC-AAGGAG-TGCATCGATGCATC-TTCATGA-TGTATC
1655071 GATGCA
1 GATGCA
1655077 TTATGCACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
44 14 0.30
45 32 0.70
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
GATGCACATTCAAGGAGTGCATCGATGCATCTTCATGATGTATC
Found at i:1655073 original size:21 final size:23
Alignment explanation
Indices: 1655018--1655076 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
1655008 GCATCTTCAT
1655018 GATGTATCGATGCACATTCAAAGG
1 GATGTATCGATGCACATTCAAA-G
* *
1655042 GATGCATCGATGCACATTCATA-
1 GATGTATCGATGCACATTCAAAG
1655064 G-TGTATCGATGCA
1 GATGTATCGATGCA
1655077 TTATGCACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.34
22 1 0.03
24 20 0.62
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (23 bp):
GATGTATCGATGCACATTCAAAG
Found at i:1660929 original size:64 final size:63
Alignment explanation
Indices: 1660880--1661031 Score: 218
Period size: 64 Copynumber: 2.4 Consensus size: 63
1660870 TGCACTAAGG
* * *
1660880 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAGCCTGAGTGCATCGATGCATGGTC
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAACATAAGTGCATCGATGCATGG-C
*
1660943 TGTGCATCAATGCATAAAATGCATTCGATGTTTTCATAAAAACATAAGTGCATCGATGCATGGC
1 -GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACATAAGTGCATCGATGCATGGC
1661007 AGTGCATCGATGCATAAAATGCATT
1 -GTGCATCGATGCATAAAATGCATT
1661032 TGAAATGGTA
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
64 52 0.65
65 26 0.32
66 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACATAAGTGCATCGATGCATGGC
Done.