Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_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: 5609167
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 23
Found at i:5049803 original size:81 final size:81
Alignment explanation
Indices: 5049699--5049888 Score: 292
Period size: 81 Copynumber: 2.3 Consensus size: 81
5049689 TGAAAGGTTA
* *
5049699 AATGTAAGTTAGATGAAAGGTTAAATGCCTTTGGATGAAAGACTACATGCCTAACTGTGC-TTTT
1 AATGCAAGTTAGATGAAAGGTTAAATGCCTTTGGATGAAAGACTAAATGCCTAACTGTGCATTTT
*
5049763 GGAAGAAAGGTGCCAAT
66 -GAAGAAAGGTGACAAT
* * *
5049780 AATGCAAGTTAGACGAAATGTTAAATGCCTTTGGATGAAAGACTAAATGCCTAACTGTTCATTTT
1 AATGCAAGTTAGATGAAAGGTTAAATGCCTTTGGATGAAAGACTAAATGCCTAACTGTGCATTTT
*
5049845 GCAGAAAGGTGACAAT
66 GAAGAAAGGTGACAAT
*
5049861 AATACAAGTTAGATGAAAGGTTAAATGC
1 AATGCAAGTTAGATGAAAGGTTAAATGC
5049889 AAGTTAGATG
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 94 0.96
82 4 0.04
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (81 bp):
AATGCAAGTTAGATGAAAGGTTAAATGCCTTTGGATGAAAGACTAAATGCCTAACTGTGCATTTT
GAAGAAAGGTGACAAT
Found at i:5049888 original size:104 final size:104
Alignment explanation
Indices: 5049780--5049992 Score: 336
Period size: 104 Copynumber: 2.0 Consensus size: 104
5049770 AGGTGCCAAT
* * *
5049780 AATGCAAGTTAGACGAAATGTTAAATGCCTTTGGATGAAAGACTAAATGCCTAACTGTTCATTTT
1 AATGCAAGTTAGACGAAAGGTTAAATGCCTTTGGATGAAAGACTAAATGCCTAACTGTGCATTTG
5049845 GCAGAAAGGTGACAATAATACAAGTTAGATGAAAGGTTA
66 GCAGAAAGGTGACAATAATACAAGTTAGATGAAAGGTTA
*
5049884 AATGCAAGTTAGATGAAAGGTTAAATGCCTTTGGATGAAAGACTAAATGCCTAACTGTGCATTTG
1 AATGCAAGTTAGACGAAAGGTTAAATGCCTTTGGATGAAAGACTAAATGCCTAACTGTGCATTTG
* *** * *
5049949 GCAGAAAGGTGCCAATAATGTGAGTTATATGAAATGTTA
66 GCAGAAAGGTGACAATAATACAAGTTAGATGAAAGGTTA
5049988 AATGC
1 AATGC
5049993 CTTTGGATGA
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (104 bp):
AATGCAAGTTAGACGAAAGGTTAAATGCCTTTGGATGAAAGACTAAATGCCTAACTGTGCATTTG
GCAGAAAGGTGACAATAATACAAGTTAGATGAAAGGTTA
Found at i:5049895 original size:23 final size:23
Alignment explanation
Indices: 5049865--5049911 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5049855 GACAATAATA
5049865 CAAGTTAGATGAAAGGTTAAATG
1 CAAGTTAGATGAAAGGTTAAATG
5049888 CAAGTTAGATGAAAGGTTAAATG
1 CAAGTTAGATGAAAGGTTAAATG
5049911 C
1 C
5049912 CTTTGGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.26
Consensus pattern (23 bp):
CAAGTTAGATGAAAGGTTAAATG
Found at i:5049923 original size:22 final size:22
Alignment explanation
Indices: 5049869--5049935 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
5049859 ATAATACAAG
**
5049869 TTAGATGAAAGGTTAAATGCAAG
1 TTAGATGAAAGGTTAAATGC-CT
5049892 TTAGATGAAAGGTTAAATGCCT
1 TTAGATGAAAGGTTAAATGCCT
* **
5049914 TTGGATGAAAGACTAAATGCCT
1 TTAGATGAAAGGTTAAATGCCT
5049936 AACTGTGCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 19 0.49
23 20 0.51
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (22 bp):
TTAGATGAAAGGTTAAATGCCT
Found at i:5050170 original size:46 final size:46
Alignment explanation
Indices: 5050114--5050207 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
5050104 TTAGATGAAG
* * *
5050114 AACAATGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGTAT
1 AACAATGCATAATTAGCATGAAAGGATGCCACAAATGAAAATATAT
*
5050160 AACAGTGCATAATTAGCATGAAAGGATGCCACAAATGAAAATATAT
1 AACAATGCATAATTAGCATGAAAGGATGCCACAAATGAAAATATAT
5050206 AA
1 AA
5050208 AGGTGTATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (46 bp):
AACAATGCATAATTAGCATGAAAGGATGCCACAAATGAAAATATAT
Found at i:5054706 original size:20 final size:20
Alignment explanation
Indices: 5054678--5054726 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
5054668 ACTGATGTGA
*
5054678 GTATCGATACTAAGAGAAAT
1 GTATCGATACTAAGAGAAAG
*
5054698 GTATAGATACTAAGAGAAAG
1 GTATCGATACTAAGAGAAAG
5054718 GTATCGATA
1 GTATCGATA
5054727 TCATGGATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.24
Consensus pattern (20 bp):
GTATCGATACTAAGAGAAAG
Found at i:5055341 original size:81 final size:81
Alignment explanation
Indices: 5055202--5055507 Score: 495
Period size: 81 Copynumber: 3.8 Consensus size: 81
5055192 CTATTATAAA
* * *
5055202 ATAAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCACGTTAGTTGAAA
1 ATAAAAGACTAAATGCCTAACTATGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
5055267 GGTTAAATGCCTTTGG
66 GGTTAAATGCCTTTGG
*
5055283 ATAAAAGACTAAATGCCTAACTATGCATTTGGAAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
1 ATAAAAGACTAAATGCCTAACTATGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
5055348 GGTTAAATGCCTTTGG
66 GGTTAAATGCCTTTGG
* * *
5055364 ATGAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCGAGTTAGATGAAA
1 ATAAAAGACTAAATGCCTAACTATGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
5055429 GGTTAAATGCCTTTGG
66 GGTTAAATGCCTTTGG
* * * * *
5055445 ATGAAAGACTAAATGCTTAACTATGCTTTTTGGCAGAAAGGTGCCATTAATGCAAGTTGGATG
1 ATAAAAGACTAAATGCCTAACTATGC-ATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATG
5055508 CCTAACGATA
Statistics
Matches: 210, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
81 178 0.85
82 32 0.15
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (81 bp):
ATAAAAGACTAAATGCCTAACTATGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
GGTTAAATGCCTTTGG
Found at i:5055615 original size:46 final size:46
Alignment explanation
Indices: 5055563--5055694 Score: 194
Period size: 46 Copynumber: 2.9 Consensus size: 46
5055553 GATGAAGAAT
*
5055563 AATGCATAATTGGCATGAAAGGATGCCATCAATGAAAATGTATAAC
1 AATGCATAATTGGCATGAAAGGATGCCATCAATGAAAATATATAAC
* *
5055609 AATGCATAATTGGCATGAAAGGATGTCATAAATGAAAATATATAAC
1 AATGCATAATTGGCATGAAAGGATGCCATCAATGAAAATATATAAC
* * *
5055655 AGTGCATAATTAGCATGAAATGATGCCA-CAAATGAAAATA
1 AATGCATAATTGGCATGAAAGGATGCCATC-AATGAAAATA
5055695 CCTAAAGATT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.24
Consensus pattern (46 bp):
AATGCATAATTGGCATGAAAGGATGCCATCAATGAAAATATATAAC
Found at i:5057947 original size:13 final size:13
Alignment explanation
Indices: 5057929--5057972 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
5057919 TTTAATTTAG
5057929 CTTTATTTATTTT
1 CTTTATTTATTTT
5057942 CTTTATTTAATTTT
1 CTTTATTT-ATTTT
* *
5057956 C-TTCTTTAATTT
1 CTTTATTTATTTT
5057968 CTTTA
1 CTTTA
5057973 CAATATTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 5 0.19
13 15 0.58
14 6 0.23
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.70
Consensus pattern (13 bp):
CTTTATTTATTTT
Found at i:5064667 original size:21 final size:21
Alignment explanation
Indices: 5064643--5064684 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5064633 TGGGTATCGG
5064643 TACTACTTCAACAAGTATTGA
1 TACTACTTCAACAAGTATTGA
5064664 TACTACTTCAACAAGTATTGA
1 TACTACTTCAACAAGTATTGA
5064685 CACCATAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (21 bp):
TACTACTTCAACAAGTATTGA
Found at i:5064764 original size:20 final size:20
Alignment explanation
Indices: 5064736--5064774 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5064726 AATACCTAGG
*
5064736 AAGGTAGGTATCGATACCAT
1 AAGGAAGGTATCGATACCAT
5064756 AAGGAAGGTATCGATACCA
1 AAGGAAGGTATCGATACCA
5064775 GAAAATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (20 bp):
AAGGAAGGTATCGATACCAT
Found at i:5064765 original size:24 final size:22
Alignment explanation
Indices: 5064721--5064765 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5064711 TATTCAAAGA
5064721 GTATCAATACCTAGGAAGGTAG
1 GTATCAATACCTAGGAAGGTAG
*
5064743 GTATCGATACCATAAGGAAGGTA
1 GTATCAATACC-T-AGGAAGGTA
5064766 TCGATACCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 1 0.05
24 9 0.45
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (22 bp):
GTATCAATACCTAGGAAGGTAG
Found at i:5065345 original size:22 final size:22
Alignment explanation
Indices: 5065297--5065346 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5065287 CACATATATG
5065297 TGATATGTGATAGAAGAGAAGA
1 TGATATGTGATAGAAGAGAAGA
* *
5065319 -AATATGTGATCATAAGAGAA-A
1 TGATATGTGAT-AGAAGAGAAGA
5065340 TGATATG
1 TGATATG
5065347 AATACATGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.46, C:0.02, G:0.26, T:0.26
Consensus pattern (22 bp):
TGATATGTGATAGAAGAGAAGA
Found at i:5067235 original size:127 final size:127
Alignment explanation
Indices: 5067009--5067273 Score: 521
Period size: 127 Copynumber: 2.1 Consensus size: 127
5066999 GTTCTGCACC
5067009 ACCCAAGAGAGGTAGAGATTATGGCTTTCGATCTTAAGTGAGGTTTGAATCGGTGGCATCCTCTA
1 ACCCAAGAGAGGTAGAGATTATGGCTTTCGATCTTAAGTGAGGTTTGAATCGGTGGCATCCTCTA
5067074 TTAGAGAATCAAATCAGACGAGAGCTAGATAGACTCAATCAGTATGGTCTGGTGATGGAAGA
66 TTAGAGAATCAAATCAGACGAGAGCTAGATAGACTCAATCAGTATGGTCTGGTGATGGAAGA
5067136 ACCCAAGAGAGGTAGAGATTATGGCTTTCGATCTTAAGTGAGGTTTGAATCGGTGGCATCCTCTA
1 ACCCAAGAGAGGTAGAGATTATGGCTTTCGATCTTAAGTGAGGTTTGAATCGGTGGCATCCTCTA
5067201 TTAGAGAATCAAATCAGACGAGAGCTAGATAGACTCAATCAGTATGGTCTGGTGATGGAAGA
66 TTAGAGAATCAAATCAGACGAGAGCTAGATAGACTCAATCAGTATGGTCTGGTGATGGAAGA
*
5067263 ACCCAATAGAG
1 ACCCAAGAGAG
5067274 ACACGGTCAG
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 137 1.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.25
Consensus pattern (127 bp):
ACCCAAGAGAGGTAGAGATTATGGCTTTCGATCTTAAGTGAGGTTTGAATCGGTGGCATCCTCTA
TTAGAGAATCAAATCAGACGAGAGCTAGATAGACTCAATCAGTATGGTCTGGTGATGGAAGA
Found at i:5072338 original size:22 final size:22
Alignment explanation
Indices: 5072290--5072339 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5072280 CACATATATG
5072290 TGATATGTGATAGAAGAGAAGA
1 TGATATGTGATAGAAGAGAAGA
* *
5072312 -AATATGTGATCATAAGAGAA-A
1 TGATATGTGAT-AGAAGAGAAGA
5072333 TGATATG
1 TGATATG
5072340 AATACATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.46, C:0.02, G:0.26, T:0.26
Consensus pattern (22 bp):
TGATATGTGATAGAAGAGAAGA
Found at i:5074909 original size:24 final size:23
Alignment explanation
Indices: 5074881--5074933 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
5074871 ATTTTCAGAT
5074881 TTTATTTTCTTTAATTTACTTTTC
1 TTTATTTTCTTTAA-TTACTTTTC
*
5074905 TTTATTTTCTTTAATTATTTTTC
1 TTTATTTTCTTTAATTACTTTTC
5074928 -TTATTT
1 TTTATTT
5074934 AATTTCTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 6 0.21
23 8 0.29
24 14 0.50
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTATTTTCTTTAATTACTTTTC
Found at i:5078177 original size:19 final size:19
Alignment explanation
Indices: 5078144--5078192 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
5078134 TTAAAACATA
5078144 ATTTAATATTATAATATTC
1 ATTTAATATTATAATATTC
5078163 ATTT-ATATTACTAATATT-
1 ATTTAATATTA-TAATATTC
*
5078181 ACTTAATATTAT
1 ATTTAATATTAT
5078193 TTATTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTAATATTATAATATTC
Found at i:5085147 original size:23 final size:23
Alignment explanation
Indices: 5085121--5085184 Score: 56
Period size: 25 Copynumber: 2.7 Consensus size: 23
5085111 TATTCGTATT
5085121 ATATTAATAAATATATGAATATA
1 ATATTAATAAATATATGAATATA
* * *** *
5085144 ATATTTTATATTATATATTTTTATT
1 ATA-TTAATA-AATATATGAATATA
5085169 ATATTAATAAATATAT
1 ATATTAATAAATATAT
5085185 ATAATATTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
23 9 0.29
24 10 0.32
25 12 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATTAATAAATATATGAATATA
Found at i:5085170 original size:13 final size:14
Alignment explanation
Indices: 5085144--5085172 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5085134 TATGAATATA
5085144 ATATTTTATATTAT
1 ATATTTTATATTAT
5085158 ATATTTT-TATTAT
1 ATATTTTATATTAT
5085171 AT
1 AT
5085173 TAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTATATTAT
Found at i:5085183 original size:25 final size:25
Alignment explanation
Indices: 5085117--5085193 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 25
5085107 TTACTATTCG
5085117 TATTATATTAATAAATATATGA-ATA
1 TATTATATTAATAAATATAT-ATATA
* * * * *
5085142 TAATAT-TTTAT-ATTATATATTTT
1 TATTATATTAATAAATATATATATA
5085165 TATTATATTAATAAATATATATA-A
1 TATTATATTAATAAATATATATATA
5085189 TATTA
1 TATTA
5085194 AATATTAACA
Statistics
Matches: 39, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
22 1 0.03
23 12 0.31
24 13 0.33
25 13 0.33
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (25 bp):
TATTATATTAATAAATATATATATA
Found at i:5085662 original size:25 final size:25
Alignment explanation
Indices: 5085628--5085678 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5085618 TATTTAGATA
5085628 GTTGGATGGTTTGTTTGATCAAATT
1 GTTGGATGGTTTGTTTGATCAAATT
5085653 GTTGGATGGTTTGTTTGATCAAATT
1 GTTGGATGGTTTGTTTGATCAAATT
5085678 G
1 G
5085679 AAACATCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.04, G:0.29, T:0.47
Consensus pattern (25 bp):
GTTGGATGGTTTGTTTGATCAAATT
Found at i:5090930 original size:54 final size:54
Alignment explanation
Indices: 5090848--5091154 Score: 341
Period size: 54 Copynumber: 5.7 Consensus size: 54
5090838 CTATAGACAA
* * * *
5090848 TATGTGTGTAACCCAC-AGAATTCATCATATGTTGATGAGCAACCATTCAGGAAC
1 TATGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACAACCGTTCAGGCAC
* * * * *
5090902 TATGTGTGCAACCCACAAAATTCATCATATATTGATGAATAATCGTTCA-TCAC
1 TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTTCAGGCAC
* * * * *
5090955 TATGTGTACAACCCACGAAATTAATCATATATTGATGAATAGCCGTTCAGGCAC
1 TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTTCAGGCAC
* * *
5091009 TATGTGTACAACCCACGAAATTCATCATATGTTGATGAACAACCATTTAGGCAC
1 TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTTCAGGCAC
* * * **
5091063 TCTGTTTGCAACCCACGAAATTCATCATATGGTGATGAACAACCGTTTGGGCAC
1 TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTTCAGGCAC
* * * * *
5091117 TAGGTGTGCAA-CCACGGAATTCATAATATTTTTATGAA
1 TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAA
5091155 TGAACATATT
Statistics
Matches: 217, Mismatches: 34, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
53 68 0.31
54 148 0.68
55 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (54 bp):
TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTTCAGGCAC
Found at i:5091034 original size:107 final size:108
Alignment explanation
Indices: 5090848--5091155 Score: 343
Period size: 107 Copynumber: 2.9 Consensus size: 108
5090838 CTATAGACAA
* * * *
5090848 TATGTGTGTAACCCAC-AGAATTCATCATATGTTGATGAGCAACCATTCAGGAACTATGTGTGCA
1 TATGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACAACCGTTCAGGCACTATGTGTGCA
* * * *
5090912 ACCCACAAAATTCATCATATATTGATGAATAATCGTTCA-TCAC
65 ACCCACGAAATTCATCATATATTGATGAATAACCATTCAGGCAC
* * * * * *
5090955 TATGTGTACAACCCACGAAATTAATCATATATTGATGAATAGCCGTTCAGGCACTATGTGTACAA
1 TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTTCAGGCACTATGTGTGCAA
* * *
5091020 CCCACGAAATTCATCATATGTTGATGAACAACCATTTAGGCAC
66 CCCACGAAATTCATCATATATTGATGAATAACCATTCAGGCAC
* * * ** *
5091063 TCTGTTTGCAACCCACGAAATTCATCATATGGTGATGAACAACCGTTTGGGCACTAGGTGTGCAA
1 TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTTCAGGCACTATGTGTGCAA
* * * *
5091128 -CCACGGAATTCATAATATTTTTATGAAT
66 CCCACGAAATTCATCATATATTGATGAAT
5091156 GAACATATTG
Statistics
Matches: 165, Mismatches: 34, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
107 108 0.65
108 57 0.35
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (108 bp):
TATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTTCAGGCACTATGTGTGCAA
CCCACGAAATTCATCATATATTGATGAATAACCATTCAGGCAC
Found at i:5091171 original size:161 final size:161
Alignment explanation
Indices: 5090848--5091155 Score: 368
Period size: 161 Copynumber: 1.9 Consensus size: 161
5090838 CTATAGACAA
** *
5090848 TATGTGTGTAACCCACAGAATTCATCATATGTTGATGAGCAACCATTCAGGAACTATGTGTGCAA
1 TATGTGTACAACCCACAGAATTCATCATATGTTGATGAACAACCATTCAGGAACTATGTGTGCAA
* * * * *
5090913 CCCACAAAATTCATCATATATTGATGAATAATCGTTCATCACTATGTGTACAACCCACGAAATTA
66 CCCACAAAATTCATCATATAGTGATGAACAACCGTTCAGCACTAGGTGTACAACCCACGAAATTA
* * *
5090978 ATCATATATTGATGAATAGCCGTTCAGGCAC
131 ATAATATATTGATGAATAGACATTCAGGCAC
* * * *
5091009 TATGTGTACAACCCAC-GAAATTCATCATATGTTGATGAACAACCATTTAGGCACTCTGTTTGCA
1 TATGTGTACAACCCACAG-AATTCATCATATGTTGATGAACAACCATTCAGGAACTATGTGTGCA
* * ** * *
5091073 ACCCACGAAATTCATCATATGGTGATGAACAACCGTTTGGGCACTAGGTGTGCAA-CCACGGAAT
65 ACCCACAAAATTCATCATATAGTGATGAACAACCG-TTCAGCACTAGGTGTACAACCCACGAAAT
* * *
5091137 TCATAATATTTTTATGAAT
129 TAATAATATATTGATGAAT
5091156 GAACATATTG
Statistics
Matches: 123, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
160 1 0.01
161 108 0.88
162 14 0.11
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (161 bp):
TATGTGTACAACCCACAGAATTCATCATATGTTGATGAACAACCATTCAGGAACTATGTGTGCAA
CCCACAAAATTCATCATATAGTGATGAACAACCGTTCAGCACTAGGTGTACAACCCACGAAATTA
ATAATATATTGATGAATAGACATTCAGGCAC
Found at i:5091407 original size:46 final size:46
Alignment explanation
Indices: 5091340--5091435 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 46
5091330 ATGAAGGACT
* * * *
5091340 AAATGTATAATAATGCATAATTGGCATGAAAGTATGTCATAAATGA
1 AAATGTATAACAATGCATAATTGGCATGAAAGGATGTCACAAATAA
* *
5091386 AAATGTATAACAGTGCATAATTGGCATTAAAGGATGTCACAAATAA
1 AAATGTATAACAATGCATAATTGGCATGAAAGGATGTCACAAATAA
5091432 AAAT
1 AAAT
5091436 ACATAACGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (46 bp):
AAATGTATAACAATGCATAATTGGCATGAAAGGATGTCACAAATAA
Found at i:5095900 original size:27 final size:27
Alignment explanation
Indices: 5095870--5096009 Score: 71
Period size: 27 Copynumber: 5.2 Consensus size: 27
5095860 ATTCAGGCTC
5095870 TATGTGTGCAACCCACAGAATTCATCA
1 TATGTGTGCAACCCACAGAATTCATCA
* * * *
5095897 TATGTTGATG-AA-CAACCG--TTTAGGCA
1 TATG-TG-TGCAACCCACAGAATTCA-TCA
*
5095923 CTATGTGTACAACCCACAGAATTCATCA
1 -TATGTGTGCAACCCACAGAATTCATCA
* * * *
5095951 TATGTTGATG-AA-CAACCG--TTTAGGCA
1 TATG-TG-TGCAACCCACAGAATTCA-TCA
5095977 CTATGTGTGCAACCCACAGAATTCATCA
1 -TATGTGTGCAACCCACAGAATTCATCA
5096005 TATGT
1 TATGT
5096010 TGATGAACAA
Statistics
Matches: 79, Mismatches: 18, Indels: 32
0.61 0.14 0.25
Matches are distributed among these distances:
25 9 0.11
26 12 0.15
27 37 0.47
28 12 0.15
29 9 0.11
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (27 bp):
TATGTGTGCAACCCACAGAATTCATCA
Found at i:5096077 original size:54 final size:54
Alignment explanation
Indices: 5095701--5096095 Score: 524
Period size: 54 Copynumber: 7.3 Consensus size: 54
5095691 ATGTGTACTA
*
5095701 TAGGCACTATGTGTGCAACCCAC-GAAATTCATCATATGTTGATGAAAAACCGTT
1 TAGGCACTATGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACAACCGTT
* * * * * **
5095755 CAGGCACTATGTGTGCAACCCACGGAACTCATCATATGTTAATGAATAGTCGTT
1 TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
* * * * ** *
5095809 CAGGCACTATGTGTGCAACCTACATAATTCATCATATGTTGATGAATAGTCATT
1 TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
* *
5095863 CAGGCTCTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
1 TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
*
5095917 TAGGCACTATGTGTACAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
1 TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
5095971 TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
1 TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
* * * * * **
5096025 TAGGCACTATATGTGCAACCCACAAAATTCATAATAAGTTTATGAATGACCGTAT
1 TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGT-T
*
5096080 T-GGCACTACGTGTGCA
1 TAGGCACTATGTGTGCA
5096096 TCTCAATGAA
Statistics
Matches: 307, Mismatches: 32, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
54 304 0.99
55 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (54 bp):
TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
Found at i:5096309 original size:46 final size:46
Alignment explanation
Indices: 5096256--5096351 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
5096246 ATGAAGGACT
*
5096256 AAATGTATAACAATGCATAATTGGCATGAAAGGATGCCATAAATGA
1 AAATGTATAACAATGCATAATTGGCATGAAAGGATGCCACAAATGA
* * * *
5096302 AAATGTATAACAGTGCCTAATTGGCATTAAAGGATGTCACAAATGA
1 AAATGTATAACAATGCATAATTGGCATGAAAGGATGCCACAAATGA
5096348 AAAT
1 AAAT
5096352 ACATAACGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (46 bp):
AAATGTATAACAATGCATAATTGGCATGAAAGGATGCCACAAATGA
Found at i:5097109 original size:22 final size:23
Alignment explanation
Indices: 5097083--5097126 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
5097073 GGGAGCGTGT
* *
5097083 GGGTATCGATACT-CCTTTATAG
1 GGGTATAGATACTACCTCTATAG
5097105 GGGTATAGATACTACCTCTATA
1 GGGTATAGATACTACCTCTATA
5097127 AAATTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (23 bp):
GGGTATAGATACTACCTCTATAG
Found at i:5098014 original size:17 final size:17
Alignment explanation
Indices: 5097989--5098044 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
5097979 CATTCAAAAT
*
5097989 CAAACATCCAAAACACA
1 CAAATATCCAAAACACA
5098006 CAAATATCCAAAACA-A
1 CAAATATCCAAAACACA
5098022 CCAAATATCCAAAACACA
1 -CAAATATCCAAAACACA
*
5098040 TAAAT
1 CAAAT
5098045 CCATCAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 1 0.03
17 33 0.94
18 1 0.03
ACGTcount: A:0.59, C:0.29, G:0.00, T:0.12
Consensus pattern (17 bp):
CAAATATCCAAAACACA
Found at i:5104306 original size:13 final size:13
Alignment explanation
Indices: 5104288--5104312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5104278 AACATAATTA
5104288 AATTAAAAACAAC
1 AATTAAAAACAAC
5104301 AATTAAAAACAA
1 AATTAAAAACAA
5104313 AACATTTTTT
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:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (13 bp):
AATTAAAAACAAC
Found at i:5104804 original size:21 final size:21
Alignment explanation
Indices: 5104739--5104816 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
5104729 CATTCAAAGA
*
5104739 GGGTATCGATACAC-GTTGAAG
1 GGGTATCGATAC-CTGTTCAAG
*
5104760 GAGTATCGATACCTAG--CAAGG
1 GGGTATCGATACCT-GTTCAA-G
*
5104781 GGGTATCGATACCTGTTTAAG
1 GGGTATCGATACCTGTTCAAG
*
5104802 GGGTATTGATACCTG
1 GGGTATCGATACCTG
5104817 GTGCACAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
20 4 0.09
21 40 0.85
22 3 0.06
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (21 bp):
GGGTATCGATACCTGTTCAAG
Found at i:5109072 original size:18 final size:18
Alignment explanation
Indices: 5109031--5109074 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5109021 AACTCCAACA
*
5109031 TTCTTCTTTTTCTCTGTC
1 TTCTTCTTTGTCTCTGTC
*
5109049 TCCTTCTTTGTCTC-GTCC
1 TTCTTCTTTGTCTCTGT-C
5109067 TTCTTCTT
1 TTCTTCTT
5109075 GAGGTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.00, C:0.32, G:0.07, T:0.61
Consensus pattern (18 bp):
TTCTTCTTTGTCTCTGTC
Found at i:5109589 original size:21 final size:21
Alignment explanation
Indices: 5109563--5109602 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5109553 GGTTCAGTGT
5109563 ATCCGTTCACCACGATTTTCC
1 ATCCGTTCACCACGATTTTCC
5109584 ATCCGTTCACCACGATTTT
1 ATCCGTTCACCACGATTTT
5109603 TCATGCTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.35, G:0.10, T:0.35
Consensus pattern (21 bp):
ATCCGTTCACCACGATTTTCC
Found at i:5116224 original size:18 final size:18
Alignment explanation
Indices: 5116201--5116238 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5116191 ATTCGAATAA
*
5116201 TTGAATCGAATATAAAAT
1 TTGAATAGAATATAAAAT
5116219 TTGAATAGAATATAAAAT
1 TTGAATAGAATATAAAAT
5116237 TT
1 TT
5116239 TAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.37
Consensus pattern (18 bp):
TTGAATAGAATATAAAAT
Found at i:5117755 original size:2 final size:2
Alignment explanation
Indices: 5117739--5117882 Score: 181
Period size: 2 Copynumber: 73.0 Consensus size: 2
5117729 TTATATCTAA
* *
5117739 AT AT AT AA AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5117781 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
5117821 A- AA AGT AT GT A- AGT A- AT AT GAA AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT A-T AT AT AT -AT AT AT AT AT AT AT AT AT AT
5117861 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
5117883 TTTTAAAATA
Statistics
Matches: 125, Mismatches: 9, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
1 5 0.04
2 117 0.94
3 3 0.02
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5118466 original size:20 final size:19
Alignment explanation
Indices: 5118413--5118467 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
5118403 ATCGTTATTA
*
5118413 TAAGAACAATATCAATACT
1 TAAGAACAATATCGATACT
* *
5118432 TAATGAACAGTATCGGTACT
1 TAA-GAACAATATCGATACT
5118452 GTAAGAACAATATCGA
1 -TAAGAACAATATCGA
5118468 CACTAGATGC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.10
20 23 0.79
21 3 0.10
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (19 bp):
TAAGAACAATATCGATACT
Found at i:5120052 original size:21 final size:21
Alignment explanation
Indices: 5120026--5120072 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
5120016 ACTCTAGAAG
5120026 CTTGTTTTAAACCATATAAAT
1 CTTGTTTTAAACCATATAAAT
5120047 CTTGTTTTAAACCATATAAAT
1 CTTGTTTTAAACCATATAAAT
5120068 CTTGT
1 CTTGT
5120073 CAATTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.45
Consensus pattern (21 bp):
CTTGTTTTAAACCATATAAAT
Found at i:5124213 original size:24 final size:23
Alignment explanation
Indices: 5124185--5124233 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
5124175 ATTTGAATGG
*
5124185 TTGAATCAAATATAAGCTTGAAAA
1 TTGAATCAAAAATAAGCTT-AAAA
* *
5124209 TTGAATTAAAAATAATCTTAAAA
1 TTGAATCAAAAATAAGCTTAAAA
5124232 TT
1 TT
5124234 TCTTTAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (23 bp):
TTGAATCAAAAATAAGCTTAAAA
Found at i:5130747 original size:2 final size:2
Alignment explanation
Indices: 5130729--5130795 Score: 100
Period size: 2 Copynumber: 33.5 Consensus size: 2
5130719 GCATCAAACC
* *
5130729 TA TA CA TA TA CA TA TA TA TA TA T- 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
5130770 TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA T-A TA T
5130796 TGCAATGGTC
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 56 0.95
3 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5133106 original size:37 final size:36
Alignment explanation
Indices: 5133028--5133295 Score: 205
Period size: 37 Copynumber: 7.6 Consensus size: 36
5133018 AAGTTTTGTT
* *
5133028 TCAAGTGATATGAAA-TTTTTT-AAGGGAAAATATC
1 TCAAGTGAGATGAAATTTTTTTCGAGGGAAAATATC
* * *
5133062 TCAAGTGAGATGAAATTTTATTTTGAGTGAAACTATC
1 TCAAGTGAGATGAAATTTT-TTTCGAGGGAAAATATC
* * * *
5133099 TCGAGTGAGACGAAGA--GTTTTCAAGGGAAAATATC
1 TCAAGTGAGATGAA-ATTTTTTTCGAGGGAAAATATC
* *
5133134 TCAAGTGAAATGAAATTTTGTTTCGAGAGG-AAATGTC
1 TCAAGTGAGATGAAATTTT-TTTCGAG-GGAAAATATC
* * *
5133171 TCGAGTGAGATGAAA--ATTTTCAAGGGAAAATATC
1 TCAAGTGAGATGAAATTTTTTTCGAGGGAAAATATC
* * * ***
5133205 TCAAGTGAAATGAAATTTCCTTTCGAGAGAAACCGTC
1 TCAAGTGAGATGAAATTT-TTTTCGAGGGAAAATATC
* * *
5133242 TCAAGTGAGACGAAA--ATTTTCAAGGGAAAATATC
1 TCAAGTGAGATGAAATTTTTTTCGAGGGAAAATATC
*
5133276 TCAAGTGAGATG-CATTTTTT
1 TCAAGTGAGATGAAATTTTTT
5133296 GTTTCAAAGA
Statistics
Matches: 177, Mismatches: 43, Indels: 27
0.72 0.17 0.11
Matches are distributed among these distances:
33 3 0.02
34 63 0.36
35 31 0.18
36 5 0.03
37 72 0.41
38 3 0.02
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (36 bp):
TCAAGTGAGATGAAATTTTTTTCGAGGGAAAATATC
Found at i:5133213 original size:71 final size:71
Alignment explanation
Indices: 5133039--5133283 Score: 348
Period size: 71 Copynumber: 3.4 Consensus size: 71
5133029 CAAGTGATAT
* * * * * *
5133039 GAAATTTTTTAAGGGAAAATATCTCAAGTGAGATGAAATTTTATTTTGAGTGAAACTATCTCGAG
1 GAAAATTTTCAAGGGAAAATATCTCAAGTGAAATGAAATTTTATTTCGAGAGAAACTGTCTCGAG
5133104 TGAGAC
66 TGAGAC
* *
5133110 GAAGAGTTTTCAAGGGAAAATATCTCAAGTGAAATGAAATTTTGTTTCGAGAGGAAA-TGTCTCG
1 GAA-AATTTTCAAGGGAAAATATCTCAAGTGAAATGAAATTTTATTTCGAGA-GAAACTGTCTCG
*
5133174 AGTGAGAT
64 AGTGAGAC
** * *
5133182 GAAAATTTTCAAGGGAAAATATCTCAAGTGAAATGAAATTTCCTTTCGAGAGAAACCGTCTCAAG
1 GAAAATTTTCAAGGGAAAATATCTCAAGTGAAATGAAATTTTATTTCGAGAGAAACTGTCTCGAG
5133247 TGAGAC
66 TGAGAC
5133253 GAAAATTTTCAAGGGAAAATATCTCAAGTGA
1 GAAAATTTTCAAGGGAAAATATCTCAAGTGA
5133284 GATGCATTTT
Statistics
Matches: 157, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
70 4 0.03
71 91 0.58
72 58 0.37
73 4 0.03
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (71 bp):
GAAAATTTTCAAGGGAAAATATCTCAAGTGAAATGAAATTTTATTTCGAGAGAAACTGTCTCGAG
TGAGAC
Found at i:5133314 original size:71 final size:70
Alignment explanation
Indices: 5133028--5133322 Score: 331
Period size: 71 Copynumber: 4.1 Consensus size: 70
5133018 AAGTTTTGTT
* * * * * * * *
5133028 TCAAGTGATATGAAATTTTTTAAGGGAAAATATCTCAAGTGAGATGAAATTTTATTTTGAGTGAA
1 TCAAGTGAGACGAAAATTTTCAAGGGAAAATATCTCAAGTGAAATGAAATTTT-GTTTCAGAGAA
*
5133093 ACTATC
65 ACTGTC
* *
5133099 TCGAGTGAGACGAAGAGTTTTCAAGGGAAAATATCTCAAGTGAAATGAAATTTTGTTTCGAGAGG
1 TCAAGTGAGACGAA-AATTTTCAAGGGAAAATATCTCAAGTGAAATGAAATTTTGTTTC-AGA-G
5133164 AAA-TGTC
63 AAACTGTC
* * **
5133171 TCGAGTGAGATGAAAATTTTCAAGGGAAAATATCTCAAGTGAAATGAAATTTCCTTTCGAGAGAA
1 TCAAGTGAGACGAAAATTTTCAAGGGAAAATATCTCAAGTGAAATGAAATTTTGTTTC-AGAGAA
*
5133236 ACCGTC
65 ACTGTC
* ** * *
5133242 TCAAGTGAGACGAAAATTTTCAAGGGAAAATATCTCAAGTGAGATGCATTTTTTGTTTCAAAGAG
1 TCAAGTGAGACGAAAATTTTCAAGGGAAAATATCTCAAGTGAAATG-AAATTTTGTTTCAGAGAA
*
5133307 ATTGTC
65 ACTGTC
5133313 TCAAGTGAGA
1 TCAAGTGAGA
5133323 ATAAATTCGC
Statistics
Matches: 193, Mismatches: 26, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
70 4 0.02
71 123 0.64
72 62 0.32
73 4 0.02
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.31
Consensus pattern (70 bp):
TCAAGTGAGACGAAAATTTTCAAGGGAAAATATCTCAAGTGAAATGAAATTTTGTTTCAGAGAAA
CTGTC
Found at i:5137717 original size:17 final size:17
Alignment explanation
Indices: 5137676--5137717 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
5137666 ATAGGCTCTC
*
5137676 AAAAACCCTAAAAGCAA
1 AAAAACCTTAAAAGCAA
*
5137693 AAAAACCTTAAAAGTAA
1 AAAAACCTTAAAAGCAA
5137710 AAAAACCT
1 AAAAACCT
5137718 AGAATCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.64, C:0.19, G:0.05, T:0.12
Consensus pattern (17 bp):
AAAAACCTTAAAAGCAA
Found at i:5138362 original size:7 final size:7
Alignment explanation
Indices: 5138330--5138408 Score: 74
Period size: 7 Copynumber: 11.4 Consensus size: 7
5138320 GATCATCTTT
5138330 AAATATA
1 AAATATA
*
5138337 AAATTACA
1 AAA-TATA
*
5138345 AAATTAAA
1 AAA-TATA
5138353 AAATATA
1 AAATATA
5138360 AAATATA
1 AAATATA
5138367 AAATATA
1 AAATATA
5138374 AAATATA
1 AAATATA
*
5138381 AAGT-TA
1 AAATATA
*
5138387 AATTAT-
1 AAATATA
*
5138393 CAATA-A
1 AAATATA
5138399 AAATATA
1 AAATATA
5138406 AAA
1 AAA
5138409 AATTAACAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
6 12 0.20
7 35 0.58
8 13 0.22
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (7 bp):
AAATATA
Found at i:5140538 original size:20 final size:23
Alignment explanation
Indices: 5140493--5140541 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
5140483 GGATAAAATA
5140493 TTAAAAAATAAATTATTTTAAGT
1 TTAAAAAATAAATTATTTTAAGT
*
5140516 TTAAATAATAAA-TA-TTTAA-T
1 TTAAAAAATAAATTATTTTAAGT
5140536 TTAAAA
1 TTAAAA
5140542 CATTGAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 5 0.21
22 2 0.08
23 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TTAAAAAATAAATTATTTTAAGT
Found at i:5142235 original size:24 final size:24
Alignment explanation
Indices: 5142208--5142285 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
5142198 TCCATTGCCT
* *
5142208 TCACCGTTGCGATCACCAGCAGCA
1 TCACCATTGCGACCACCAGCAGCA
* *
5142232 TCACCTTTGCGACCAGCAGCAGCA
1 TCACCATTGCGACCACCAGCAGCA
* * *
5142256 TCACCACTGCGACCACCATCAGCT
1 TCACCATTGCGACCACCAGCAGCA
5142280 TCACCA
1 TCACCA
5142286 CCACCAACAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.26, C:0.41, G:0.17, T:0.17
Consensus pattern (24 bp):
TCACCATTGCGACCACCAGCAGCA
Found at i:5142538 original size:45 final size:45
Alignment explanation
Indices: 5142470--5142605 Score: 157
Period size: 45 Copynumber: 3.0 Consensus size: 45
5142460 TAAGATCCTT
*
5142470 AGCACCACCATAT-TTGCAGCCAAATGCAGTATCAGGAGGACCACC
1 AGCACCACCAT-TGTTGCAGCCAAATGCAGTATCAGGAAGACCACC
* * ** * * * *
5142515 AGCACCATCGTTGTTGCCTCCAAATGCAATCTCAGGAAGAGCGCC
1 AGCACCACCATTGTTGCAGCCAAATGCAGTATCAGGAAGACCACC
* *
5142560 GGCACCACCATTGTTGCAGCCAAATGTAGTATCAGGAAGACCACC
1 AGCACCACCATTGTTGCAGCCAAATGCAGTATCAGGAAGACCACC
5142605 A
1 A
5142606 TTGCCCCCAC
Statistics
Matches: 70, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
44 1 0.01
45 69 0.99
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.18
Consensus pattern (45 bp):
AGCACCACCATTGTTGCAGCCAAATGCAGTATCAGGAAGACCACC
Found at i:5142917 original size:36 final size:36
Alignment explanation
Indices: 5142869--5143168 Score: 229
Period size: 36 Copynumber: 8.3 Consensus size: 36
5142859 AGTTCCACCA
*
5142869 CCACCACCTCCTCCTCCTGGAACAGCATCAACAATG
1 CCACCACCTCCTCCTCCTGGAACAGCATCCACAATG
* *
5142905 TCACCA---CCTCCTCCTGGAACAGCA-CCGA-ATATTT
1 CCACCACCTCCTCCTCCTGGAACAGCATCC-ACA-A-TG
* * * ***
5142939 CCGCCACTTCCTCCTCCTGGAACAGTATCGTTAATG
1 CCACCACCTCCTCCTCCTGGAACAGCATCCACAATG
* ***
5142975 CCACCACCTCCTCCTTCTGGAACAGCATCGTTAATG
1 CCACCACCTCCTCCTCCTGGAACAGCATCCACAATG
* * ****
5143011 CCACCACCACCTCCTCCTGGAACAACATTGTTAATG
1 CCACCACCTCCTCCTCCTGGAACAGCATCCACAATG
* *
5143047 CCACCA---CCACCTCCTGGAACAGTATCCACAATG
1 CCACCACCTCCTCCTCCTGGAACAGCATCCACAATG
* * *
5143080 CAACCTCCTTCTCCTCCTCCAGGAACAGCATCCACAATG
1 CCACC-AC--CTCCTCCTCCTGGAACAGCATCCACAATG
* *
5143119 CCACCACCAATTACTCCTCATGGAACAGCATCCACAATG
1 CCACCACC---TCCTCCTCCTGGAACAGCATCCACAATG
5143158 CCACCACCTCC
1 CCACCACCTCC
5143169 CCCTGGTGCC
Statistics
Matches: 212, Mismatches: 35, Indels: 34
0.75 0.12 0.12
Matches are distributed among these distances:
32 2 0.01
33 44 0.21
34 5 0.02
36 79 0.37
37 18 0.08
38 3 0.01
39 61 0.29
ACGTcount: A:0.26, C:0.41, G:0.12, T:0.21
Consensus pattern (36 bp):
CCACCACCTCCTCCTCCTGGAACAGCATCCACAATG
Found at i:5142920 original size:33 final size:33
Alignment explanation
Indices: 5142872--5143174 Score: 169
Period size: 33 Copynumber: 8.5 Consensus size: 33
5142862 TCCACCACCA
* *
5142872 CCACCTCCTCCTCCTGGAACAGCATCAACAATG
1 CCACCACCTCCTCCTGGAACAGCATCCACAATG
*
5142905 TCACCACCTCCTCCTGGAACAGCA-CCGA-ATATTTCCG
1 CCACCACCTCCTCCTGGAACAGCATCC-ACA-A--T--G
** * ***
5142942 CCACTTCCTCCTCCTGGAACAGTATCGTTAATG
1 CCACCACCTCCTCCTGGAACAGCATCCACAATG
***
5142975 CCACCACCTCCTCCTTCTGGAACAGCATCGTTAATG
1 CCACCACCTCCT-C--CTGGAACAGCATCCACAATG
* ****
5143011 CCACCACCACCTCCTCCTGGAACAACATTGTTAATG
1 ---CCACCACCTCCTCCTGGAACAGCATCCACAATG
* *
5143047 CCACCACCACCTCCTGGAACAGTATCCACAATG
1 CCACCACCTCCTCCTGGAACAGCATCCACAATG
* *
5143080 CAACCTCCTTCTCCTCCTCCAGGAACAGCATCCACAATG
1 CCACC-AC--CTCCTCCT---GGAACAGCATCCACAATG
*
5143119 CCACCACCAATTACTCCTCATGGAACAGCATCCACAATG
1 CCACCA-C-----CTCCTCCTGGAACAGCATCCACAATG
*
5143158 CCACCACCTCCCCCTGG
1 CCACCACCTCCTCCTGG
5143175 TGCCACAAAA
Statistics
Matches: 215, Mismatches: 31, Indels: 48
0.73 0.11 0.16
Matches are distributed among these distances:
32 2 0.01
33 73 0.34
34 2 0.01
35 2 0.01
36 44 0.20
37 22 0.10
38 4 0.02
39 58 0.27
42 8 0.04
ACGTcount: A:0.26, C:0.41, G:0.12, T:0.21
Consensus pattern (33 bp):
CCACCACCTCCTCCTGGAACAGCATCCACAATG
Found at i:5143113 original size:39 final size:39
Alignment explanation
Indices: 5143056--5143165 Score: 125
Period size: 39 Copynumber: 2.8 Consensus size: 39
5143046 GCCACCACCA
* * * * *
5143056 CCTCCTGGAACAGTATCCACAATGCAACCTCC-TTCTCCT
1 CCTCCAGGAACAGCATCCACAATGCAACCACCAAT-TACT
*
5143095 CCTCCAGGAACAGCATCCACAATGCCACCACCAATTACT
1 CCTCCAGGAACAGCATCCACAATGCAACCACCAATTACT
*
5143134 CCT-CATGGAACAGCATCCACAATGCCACCACC
1 CCTCCA-GGAACAGCATCCACAATGCAACCACC
5143166 TCCCCCTGGT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.03
39 60 0.95
40 1 0.02
ACGTcount: A:0.29, C:0.42, G:0.11, T:0.18
Consensus pattern (39 bp):
CCTCCAGGAACAGCATCCACAATGCAACCACCAATTACT
Found at i:5145006 original size:20 final size:20
Alignment explanation
Indices: 5144912--5145280 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
5144902 GATTTTCCAT
* ** *
5144912 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
5144932 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
5144952 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5144972 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
5144992 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
5145012 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
5145032 TATCGCAACGCGTATTCGTA
1 AATCGCAACGCGTATCCGTA
5145052 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5145072 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
5145092 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5145112 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
5145132 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5145152 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
5145172 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5145192 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
5145212 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
5145232 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
5145252 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
5145272 AATCACAAC
1 AATCGCAAC
5145281 ACTTAAATTT
Statistics
Matches: 303, Mismatches: 36, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.01
20 295 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:5146002 original size:24 final size:24
Alignment explanation
Indices: 5145963--5146009 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5145953 AAATTTGGTC
5145963 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
5145987 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
5146010 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:5148511 original size:19 final size:19
Alignment explanation
Indices: 5148489--5148781 Score: 383
Period size: 19 Copynumber: 16.4 Consensus size: 19
5148479 CGGAAAATAC
*
5148489 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5148508 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
5148522 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
5148542 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5148556 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5148575 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5148594 AATCGCAA--CGACAT---
1 AATCGCAATGCGAAATGAA
* *
5148608 AATCGCAATGCAAAATTAA
1 AATCGCAATGCGAAATGAA
5148627 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5148646 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5148665 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5148684 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5148703 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5148722 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
5148736 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5148755 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5148774 AATCGCAA
1 AATCGCAA
5148782 CGAGATAATC
Statistics
Matches: 244, Mismatches: 9, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 38 0.16
15 1 0.00
16 13 0.05
17 13 0.05
18 2 0.01
19 164 0.67
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5148604 original size:52 final size:55
Alignment explanation
Indices: 5148517--5148803 Score: 347
Period size: 52 Copynumber: 5.4 Consensus size: 55
5148507 AAATCCCAAC
*
5148517 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
*
5148570 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACAT---AATCGCAATGCAAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGA-ATGAAAATCGCAATGCGAA
*
5148622 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
5148679 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
5148734 A-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
5148784 A-GATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAAT
5148804 TATAAACGCA
Statistics
Matches: 219, Mismatches: 4, Indels: 23
0.89 0.02 0.09
Matches are distributed among these distances:
50 2 0.01
52 126 0.58
53 16 0.07
54 6 0.03
55 6 0.03
57 63 0.29
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (55 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:5148919 original size:19 final size:19
Alignment explanation
Indices: 5148810--5148911 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
5148800 AAATTATAAA
5148810 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
5148829 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
5148849 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
5148865 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
5148882 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
5148901 CGCATTGCGAT
1 CGCATTGCGAT
5148912 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:5149037 original size:14 final size:14
Alignment explanation
Indices: 5149018--5149054 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5149008 CATCAATTAC
5149018 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5149032 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5149046 ACAAATCAA
1 ACAAATCAA
5149055 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5151032 original size:14 final size:14
Alignment explanation
Indices: 5151013--5151069 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
5151003 GCGAAATGAA
5151013 AATCGCAACGATAG
1 AATCGCAACGATAG
*
5151027 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--AT-AG
*
5151046 AATCGCAACGAAAG
1 AATCGCAACGATAG
5151060 AATCGCAACG
1 AATCGCAACG
5151070 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 2 0.06
19 9 0.26
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (14 bp):
AATCGCAACGATAG
Found at i:5151040 original size:33 final size:33
Alignment explanation
Indices: 5150994--5151086 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
5150984 GCGAAACCAA
*
5150994 AATCGCAACGCGAAATGAAAATCGCAACGATAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5151027 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5151060 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5151087 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5151051 original size:19 final size:19
Alignment explanation
Indices: 5150957--5151091 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
5150947 TAGTTTACTT
* *
5150957 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
5150977 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
5150996 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5151015 TCGCAA--CG--AT-AGAA
1 TCGCAACGCGAAATGAAAA
*
5151029 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5151048 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5151062 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5151081 TCGCAATGCGA
1 TCGCAACGCGA
5151092 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 17 0.18
15 2 0.02
16 8 0.08
17 8 0.08
18 2 0.02
19 48 0.49
20 12 0.12
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:5151109 original size:19 final size:19
Alignment explanation
Indices: 5151087--5151215 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
5151077 AAAATCGCAA
5151087 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5151106 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
5151120 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5151139 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
5151153 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5151172 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
5151191 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
5151211 TGCGA
1 TGCGA
5151216 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:5151129 original size:33 final size:33
Alignment explanation
Indices: 5151087--5151178 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
5151077 AAAATCGCAA
5151087 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
5151120 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
5151153 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
5151179 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:5151430 original size:92 final size:93
Alignment explanation
Indices: 5151259--5151729 Score: 894
Period size: 92 Copynumber: 5.1 Consensus size: 93
5151249 TTGAATGGAT
*
5151259 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAATGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5151324 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5151352 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5151416 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5151444 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5151509 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
5151537 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5151601 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5151629 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
5151693 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5151721 AAATTTACT
1 AAATTTACT
5151730 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 4, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
91 10 0.03
92 231 0.62
93 131 0.35
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5151571 original size:185 final size:185
Alignment explanation
Indices: 5151259--5151729 Score: 908
Period size: 185 Copynumber: 2.6 Consensus size: 185
5151249 TTGAATGGAT
*
5151259 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAATGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5151324 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
5151389 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
5151444 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5151509 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
5151574 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
5151629 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
5151693 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
5151730 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
184 72 0.25
185 211 0.75
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5153455 original size:14 final size:14
Alignment explanation
Indices: 5153436--5153525 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
5153426 TTGAAATGAA
5153436 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5153450 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
5153467 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
5153483 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5153502 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5153516 AATCGCAACG
1 AATCGCAACG
5153526 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5153473 original size:33 final size:33
Alignment explanation
Indices: 5153428--5153542 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
5153418 TCTTTTGGTT
5153428 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
5153461 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5153494 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5153527 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
5153543 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5153474 original size:19 final size:18
Alignment explanation
Indices: 5153435--5153547 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
5153425 GTTGAAATGA
5153435 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
5153450 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
5153467 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
5153483 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
5153500 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
5153516 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
5153533 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
5153548 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:5153578 original size:14 final size:14
Alignment explanation
Indices: 5153559--5153613 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5153549 TTTGGTTTCG
5153559 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5153573 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5153592 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5153606 CGTTGCGA
1 CGTTGCGA
5153614 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5153591 original size:33 final size:33
Alignment explanation
Indices: 5153543--5153613 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
5153533 AAAATCGCAA
**
5153543 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5153576 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5153609 TGCGA
1 TGCGA
5153614 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:5153621 original size:33 final size:33
Alignment explanation
Indices: 5153554--5153635 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
5153544 GCGATTTTGG
***
5153554 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
5153587 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
5153620 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
5153636 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:5153640 original size:20 final size:20
Alignment explanation
Indices: 5153566--5153654 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
5153556 TCGCGTTGCG
5153566 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
5153586 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
5153599 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
5153619 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
5153639 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
5153655 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:5153776 original size:33 final size:33
Alignment explanation
Indices: 5153734--5153804 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5153724 AATACTAACT
*
5153734 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
5153767 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
5153800 TGAAA
1 TGAAA
5153805 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:5154038 original size:22 final size:22
Alignment explanation
Indices: 5153986--5154040 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5153976 TGGTTGTGAG
**
5153986 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
5154008 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
5154030 GGATTTCTTCG
1 GGATTTCTTCG
5154041 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:5154211 original size:20 final size:20
Alignment explanation
Indices: 5154186--5154378 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
5154176 CTTTAAATAT
5154186 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5154206 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
5154228 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5154247 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
5154267 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
5154287 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5154307 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5154327 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
5154347 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
5154367 CGCGTTGCGATT
1 CGCGTTGCGATT
5154379 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5154373 original size:60 final size:60
Alignment explanation
Indices: 5154186--5154378 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
5154176 CTTTAAATAT
**
5154186 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
5154247 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
5154307 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
5154367 CGCGTTGCGATT
1 CGCGTTGCGATT
5154379 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:5154459 original size:20 final size:20
Alignment explanation
Indices: 5154434--5154485 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
5154424 AAGAATCGCG
*
5154434 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
5154454 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
5154474 TTGCGATTCTGG
1 TTGCGATTCTGG
5154486 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:5154939 original size:21 final size:21
Alignment explanation
Indices: 5154898--5154939 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5154888 TAAAACGTCT
*
5154898 AATAATAATATTTTCGGTAAA
1 AATAATAATATTTTCGATAAA
*
5154919 AATAATAATATTTTTGATAAA
1 AATAATAATATTTTCGATAAA
5154940 TTTTTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (21 bp):
AATAATAATATTTTCGATAAA
Found at i:5159517 original size:21 final size:21
Alignment explanation
Indices: 5159484--5159526 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5159474 TTCTGAATCC
*
5159484 TTGCTGTCATCATCATCGTCG
1 TTGCCGTCATCATCATCGTCG
* *
5159505 TTGCCGTCGTCATCGTCGTCG
1 TTGCCGTCATCATCATCGTCG
5159526 T
1 T
5159527 CGTCATCCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.30, G:0.23, T:0.37
Consensus pattern (21 bp):
TTGCCGTCATCATCATCGTCG
Found at i:5161557 original size:111 final size:111
Alignment explanation
Indices: 5161418--5161639 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
5161408 ATTACAAAAA
*
5161418 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAATTACTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATACTACTAATAATTTAAATTA
*
5161483 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
* *
5161529 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATACTACTAATAATTTAAATTA
*
5161594 AATTAAAACGTTAAAATGTTGCCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
5161640 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATACTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:5161794 original size:20 final size:19
Alignment explanation
Indices: 5161765--5161806 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
5161755 CTTAAAAAGA
*
5161765 TAGAGTATTTGAGAGAAATT
1 TAGAGAATTTGAGAG-AATT
5161785 TAGAGAATTTGAGAGAATT
1 TAGAGAATTTGAGAGAATT
5161804 TAG
1 TAG
5161807 TGTGATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.33
Consensus pattern (19 bp):
TAGAGAATTTGAGAGAATT
Found at i:5168635 original size:29 final size:29
Alignment explanation
Indices: 5168579--5168633 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
5168569 AACTACAAAA
5168579 TATTTAAATTTATAAAAAATATAAAAATG
1 TATTTAAATTTATAAAAAATATAAAAATG
*
5168608 TATTTACA-TTATAAAAAATATAAAAA
1 TATTTAAATTTATAAAAAATATAAAAA
5168634 ATATACAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (29 bp):
TATTTAAATTTATAAAAAATATAAAAATG
Found at i:5168649 original size:25 final size:26
Alignment explanation
Indices: 5168589--5168665 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 26
5168579 TATTTAAATT
* *
5168589 TATAAAAAATATAAAAATGTATTTACAT
1 TATAAAAAATATAAAAA--TATATACAA
5168617 TATAAAAAATATAAAAA-ATATACAA
1 TATAAAAAATATAAAAATATATACAA
* *
5168642 TATGAAAAATTGTAAAAATATATA
1 TAT-AAAAAATATAAAAATATATA
5168666 AAAATTAGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
25 9 0.21
26 12 0.28
27 5 0.12
28 17 0.40
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (26 bp):
TATAAAAAATATAAAAATATATACAA
Found at i:5169122 original size:59 final size:60
Alignment explanation
Indices: 5169021--5169165 Score: 204
Period size: 59 Copynumber: 2.5 Consensus size: 60
5169011 CAATGAAGTG
* * *
5169021 ATCATTTTGTAACTTTTAATAGTCG-GGGACTCAAAAAAGAAACGTCCTATAATTTGAGA
1 ATCATTTTGTAACTATTAATAGTCGTGGGACTCAAAAAAGAAACATCCTATAATTAGAGA
* * *
5169080 ATCATTTTGTAACTATTAATAGTCGTGGGACTC-AAAATGAAACATCCTATGATTAGATA
1 ATCATTTTGTAACTATTAATAGTCGTGGGACTCAAAAAAGAAACATCCTATAATTAGAGA
* *
5169139 ACCATTTTGTAACTGTTAATAGTCGTG
1 ATCATTTTGTAACTATTAATAGTCGTG
5169166 AATAAAGCAA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 70 0.91
60 7 0.09
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (60 bp):
ATCATTTTGTAACTATTAATAGTCGTGGGACTCAAAAAAGAAACATCCTATAATTAGAGA
Found at i:5172335 original size:22 final size:23
Alignment explanation
Indices: 5172305--5172349 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5172295 AACCTTAAAC
* *
5172305 TAAACCCTAAA-CTAAGCCCAAA
1 TAAAACCTAAACCCAAGCCCAAA
5172327 TAAAACCTAAACCCAAGCCCAAA
1 TAAAACCTAAACCCAAGCCCAAA
5172350 CATATCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.51, C:0.33, G:0.04, T:0.11
Consensus pattern (23 bp):
TAAAACCTAAACCCAAGCCCAAA
Found at i:5185281 original size:5 final size:5
Alignment explanation
Indices: 5185273--5185318 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
5185263 CTAAAAAGAA
*
5185273 AAAAG AAAAG AAAAG -AAAG AAAGAA AAAAG AAAAG AAAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG -AAAAG AAAAG
5185319 GGAGAGGTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 4 0.11
5 23 0.64
6 9 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5185297 original size:25 final size:26
Alignment explanation
Indices: 5185267--5185316 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
5185257 CAACGCCTAA
5185267 AAAGAAAAAAGAAAAG-AAAAGAAAG
1 AAAGAAAAAAGAAAAGAAAAAGAAAG
5185292 AAAGAAAAAAGAAAAGAAAAAGAAA
1 AAAGAAAAAAGAAAAGAAAAAGAAA
5185317 AGGGAGAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (26 bp):
AAAGAAAAAAGAAAAGAAAAAGAAAG
Found at i:5200120 original size:81 final size:80
Alignment explanation
Indices: 5199970--5200510 Score: 410
Period size: 81 Copynumber: 6.7 Consensus size: 80
5199960 GTCTCGTTTC
* * * * * * * *
5199970 CAAAATTGATCTGAATACCCAAAAAAGCGGAACAAATCGAGTCTTATTTCCCTT-AAAGAAAAAT
1 CAAAATAGATCTGACTACCCAAAAAAGAGGAACAAATCAAGTC-TATCTCCCTTGAATGAATAGT
* * *
5200034 AGAGAAAACTCGTTTT
65 GGAGAAAACCCGTCTT
* * *
5200050 CAAAAATTGATTTGACTACTCAAAAAAGAGGAACAAATCAAGTCGTATCT-CCTTGAATGAATAG
1 C-AAAATAGATCTGACTACCCAAAAAAGAGGAACAAATCAAGTC-TATCTCCCTTGAATGAATAG
* * *
5200114 TGGAGAAGACCCATCTG
64 TGGAGAAAACCCGTCTT
* * * * *
5200131 C-AAATAGATCTGACTACACGAAAAAGAGGAATATATCAAGTCTGATCTCCCCTGAATGAATAGT
1 CAAAATAGATCTGACTACCCAAAAAAGAGGAACAAATCAAGTCT-ATCTCCCTTGAATGAATAGT
* *
5200195 GGAGCATACCCGTCTT
65 GGAGAAAACCCGTCTT
* * * * * *
5200211 CAAAATAAATATGACTACCCAAAAAAAAGGAACATATCAAGTCTAATATCCCCTG-ATAGAATAG
1 CAAAATAGATCTGACTACCCAAAAAAGAGGAACAAATCAAGTCT-ATCTCCCTTGAAT-GAATAG
* *
5200275 TGGAGCAGACCCGTCTT
64 TGGAGAAAACCCGTCTT
* * * *
5200292 CAAAATAGACCTGACTACCC-AAAAAGAGGAA-AAGATCAAGTCTGATCTCCCATAAAAGAATAG
1 CAAAATAGATCTGACTACCCAAAAAAGAGGAACAA-ATCAAGTCT-ATCTCCCTTGAATGAATAG
* * ** *
5200355 TGAAGCATGCCCATCTT
64 TGGAGAAAACCCGTCTT
* * * * * *
5200372 CAAAATATATCTAACTACCCGAAAAAGAGGAACAAATCAAGTTTGATCTCCCTTGAAAGAAGAGT
1 CAAAATAGATCTGACTACCCAAAAAAGAGGAACAAATCAAGTCT-ATCTCCCTTGAATGAATAGT
* * * *
5200437 GGAGCAGACACATCTT
65 GGAGAAAACCCGTCTT
* ** ** * * *
5200453 CCAAAATTGATCCAACTACCTGAAAAAGAGGAACATATCAAGTCCGATCTCCCCTGAA
1 -CAAAATAGATCTGACTACCCAAAAAAGAGGAACAAATCAAGT-CTATCTCCCTTGAA
5200511 AAAAGAGTGG
Statistics
Matches: 380, Mismatches: 69, Indels: 22
0.81 0.15 0.05
Matches are distributed among these distances:
78 1 0.00
79 40 0.11
80 96 0.25
81 193 0.51
82 50 0.13
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (80 bp):
CAAAATAGATCTGACTACCCAAAAAAGAGGAACAAATCAAGTCTATCTCCCTTGAATGAATAGTG
GAGAAAACCCGTCTT
Found at i:5200322 original size:161 final size:159
Alignment explanation
Indices: 5200062--5200511 Score: 519
Period size: 161 Copynumber: 2.8 Consensus size: 159
5200052 AAAATTGATT
* * *
5200062 TGACTACTCAAAAAAGAGGAACAAATCAAGTC-GTATCTCCTTGAATGAATAGTGGAGAAGACCC
1 TGACTACCCAAAAAAGAGGAACAAATCAAGTCTATATC-CCTTGAA-GAATAGTGGAGCAGACCC
* * * *
5200126 ATCTGC-AAATAGATCTGACTACACGAAAAAGAGGAATATATCAAGTCTGATCTCCCCTGAATGA
64 ATCTTCAAAATAGACCTGACTAC-CGAAAAAGAGGAAAATATCAAGTCTGATCTCCCCTGAAAGA
* *
5200190 ATAGTGGAGCATACCCGTCTTCAAAATAAATA
128 ATAGTGAAGCATACCCATCTTCAAAATAAATA
* * *
5200222 TGACTACCCAAAAAAAAGGAACATATCAAGTCTAATATCCCCTGATAGAATAGTGGAGCAGACCC
1 TGACTACCCAAAAAAGAGGAACAAATCAAGTCT-ATATCCCTTGA-AGAATAGTGGAGCAGACCC
* * * * *
5200287 GTCTTCAAAATAGACCTGACTACCCAAAAAGAGGAAAAGATCAAGTCTGATCTCCCATAAAAGAA
64 ATCTTCAAAATAGACCTGACTACCGAAAAAGAGGAAAATATCAAGTCTGATCTCCCCTGAAAGAA
* * *
5200352 TAGTGAAGCATGCCCATCTTCAAAATATATC
129 TAGTGAAGCATACCCATCTTCAAAATAAATA
* * * * * *
5200383 TAACTACCCGAAAAAGAGGAACAAATCAAGTTTGATCTCCCTTGAAAGAAGAGTGGAGCAGACAC
1 TGACTACCCAAAAAAGAGGAACAAATCAAGTCT-ATATCCCTTG-AAGAATAGTGGAGCAGACCC
* * * *
5200448 ATCTTCCAAAATTGATCC-AACTACCTGAAAAAGAGGAACATATCAAGTCCGATCTCCCCTGAAA
64 ATCTT-CAAAATAGA-CCTGACTACC-GAAAAAGAGGAAAATATCAAGTCTGATCTCCCCTGAAA
5200512 AAAGAGTGGA
Statistics
Matches: 243, Mismatches: 39, Indels: 13
0.82 0.13 0.04
Matches are distributed among these distances:
160 29 0.12
161 145 0.60
162 35 0.14
163 34 0.14
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.21
Consensus pattern (159 bp):
TGACTACCCAAAAAAGAGGAACAAATCAAGTCTATATCCCTTGAAGAATAGTGGAGCAGACCCAT
CTTCAAAATAGACCTGACTACCGAAAAAGAGGAAAATATCAAGTCTGATCTCCCCTGAAAGAATA
GTGAAGCATACCCATCTTCAAAATAAATA
Found at i:5200372 original size:80 final size:80
Alignment explanation
Indices: 5200052--5200522 Score: 459
Period size: 81 Copynumber: 5.8 Consensus size: 80
5200042 CTCGTTTTCA
* * * * *
5200052 AAAATTGATTTGACTACTCAAAAAAGAGGAACAA-ATCAAGTC-GTATCT-CCTTGAATGAATAG
1 AAAATAGATCTGACTAC-CCAAAAAGAGGAA-AATATCAAGTCTG-ATCTCCCCTGAAAGAATAG
* *
5200114 TGGAGAAGACCCATCTGC
63 TGGAGCAGACCCATCTTC
* * *
5200132 -AAATAGATCTGACTACACGAAAAAGAGGAATATATCAAGTCTGATCTCCCCTGAATGAATAGTG
1 AAAATAGATCTGACTAC-CCAAAAAGAGGAAAATATCAAGTCTGATCTCCCCTGAAAGAATAGTG
* *
5200196 GAGCATACCCGTCTTC
65 GAGCAGACCCATCTTC
* * * * * * *
5200212 AAAATAAATATGACTACCCAAAAAAAAGGAACATATCAAGTCTAATATCCCCTGATAGAATAGTG
1 AAAATAGATCTGACTACCC-AAAAAGAGGAAAATATCAAGTCTGATCTCCCCTGAAAGAATAGTG
*
5200277 GAGCAGACCCGTCTTC
65 GAGCAGACCCATCTTC
* * * * *
5200293 AAAATAGACCTGACTACCCAAAAAGAGGAAAAGATCAAGTCTGATCTCCCATAAAAGAATAGTGA
1 AAAATAGATCTGACTACCCAAAAAGAGGAAAATATCAAGTCTGATCTCCCCTGAAAGAATAGTGG
5200358 AGCATG-CCCATCTTC
66 AGCA-GACCCATCTTC
* * * * *
5200373 AAAATATATCTAACTACCCGAAAAAGAGGAACAA-ATCAAGTTTGATCTCCCTTGAAAGAAGAGT
1 AAAATAGATCTGACTACCC-AAAAAGAGGAA-AATATCAAGTCTGATCTCCCCTGAAAGAATAGT
*
5200437 GGAGCAGACACATCTTCC
64 GGAGCAGACCCATCTT-C
* ** * * * * *
5200455 AAAATTGATCCAACTACCTGAAAAAGAGGAACATATCAAGTCCGATCTCCCCTGAAAAAAGAGTG
1 AAAATAGATCTGACTACC-CAAAAAGAGGAAAATATCAAGTCTGATCTCCCCTGAAAGAATAGTG
5200520 GAG
65 GAG
5200523 GGGATTTCCC
Statistics
Matches: 328, Mismatches: 51, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
78 1 0.00
79 38 0.12
80 95 0.29
81 135 0.41
82 59 0.18
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (80 bp):
AAAATAGATCTGACTACCCAAAAAGAGGAAAATATCAAGTCTGATCTCCCCTGAAAGAATAGTGG
AGCAGACCCATCTTC
Found at i:5200654 original size:3 final size:3
Alignment explanation
Indices: 5200646--5200671 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5200636 GTCCTACATA
5200646 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
5200672 AAAAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5202481 original size:18 final size:19
Alignment explanation
Indices: 5202458--5202513 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 19
5202448 CGGTACCTAA
5202458 GGTATTGATACCCAT-AGG
1 GGTATTGATACCCATAAGG
*
5202476 GGTATTGGTACCCATTCCTAAGG
1 GGTATTGATACCCA----TAAGG
5202499 GGTATTGATACCCAT
1 GGTATTGATACCCAT
5202514 TCATAGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 13 0.42
19 1 0.03
22 1 0.03
23 16 0.52
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (19 bp):
GGTATTGATACCCATAAGG
Found at i:5202770 original size:20 final size:20
Alignment explanation
Indices: 5202745--5202788 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5202735 ATGTTTAATG
5202745 AAAAA-GATACAAAATGTTTA
1 AAAAAGGATACAAAATG-TTA
* *
5202765 AAAAAGGATACCAATTGTTA
1 AAAAAGGATACAAAATGTTA
5202785 AAAA
1 AAAA
5202789 GATCCAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.23
Consensus pattern (20 bp):
AAAAAGGATACAAAATGTTA
Found at i:5202774 original size:21 final size:21
Alignment explanation
Indices: 5202732--5202788 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
5202722 CCCCCTTAAT
5202732 AAAATGTTTAATGAAAAAGATAC
1 AAAATGTTTAA--AAAAAGATAC
*
5202755 AAAATGTTTAAAAAAGGATAC
1 AAAATGTTTAAAAAAAGATAC
* *
5202776 CAATTG-TTAAAAA
1 AAAATGTTTAAAAA
5202789 GATCCAATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 13 0.42
23 11 0.35
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.26
Consensus pattern (21 bp):
AAAATGTTTAAAAAAAGATAC
Found at i:5202806 original size:19 final size:19
Alignment explanation
Indices: 5202765--5202800 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
5202755 AAAATGTTTA
5202765 AAAAAGGATACCAATTGTT
1 AAAAAGGATACCAATTGTT
5202784 AAAAA-GAT-CCAATTGTT
1 AAAAAGGATACCAATTGTT
5202801 GGAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (19 bp):
AAAAAGGATACCAATTGTT
Found at i:5205563 original size:33 final size:33
Alignment explanation
Indices: 5205513--5205582 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
5205503 CCTTTATAAC
* * *
5205513 TCCCTAGTTTTTTACGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
* *
5205546 TCCCTAGCTTTTCACGGGATCAGCTAGAACCTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
5205579 TCCC
1 TCCC
5205583 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (33 bp):
TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
Found at i:5205991 original size:40 final size:40
Alignment explanation
Indices: 5205938--5206013 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
5205928 TTGGAGCCAG
* *
5205938 GGGGCATTGATACCTATGCAGGGGTATTGATACCCATGCA
1 GGGGCATTGATACCCATGCAGGGGTATCGATACCCATGCA
* * *
5205978 GGGGTATTGATACCCATGCGGGGGTATCGGTACCCA
1 GGGGCATTGATACCCATGCAGGGGTATCGATACCCA
5206014 GTGTAATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (40 bp):
GGGGCATTGATACCCATGCAGGGGTATCGATACCCATGCA
Found at i:5206013 original size:20 final size:20
Alignment explanation
Indices: 5205938--5206004 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
5205928 TTGGAGCCAG
* *
5205938 GGGGCATTGATACCTATGCA
1 GGGGTATTGATACCCATGCA
5205958 GGGGTATTGATACCCATGCA
1 GGGGTATTGATACCCATGCA
*
5205978 GGGGTATTGATACCCATGCG
1 GGGGTATTGATACCCATGCA
5205998 GGGGTAT
1 GGGGTAT
5206005 CGGTACCCAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.25
Consensus pattern (20 bp):
GGGGTATTGATACCCATGCA
Found at i:5206094 original size:22 final size:22
Alignment explanation
Indices: 5206069--5206112 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5206059 GTTTGAGCCT
* *
5206069 TCATAGGGGTATTGATACCCAG
1 TCATAAGGGTATCGATACCCAG
5206091 TCATAAGGGTATCGATACCCAG
1 TCATAAGGGTATCGATACCCAG
5206113 GGTATGGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (22 bp):
TCATAAGGGTATCGATACCCAG
Found at i:5206116 original size:15 final size:15
Alignment explanation
Indices: 5206096--5206144 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
5206086 CCCAGTCATA
5206096 AGGGTATCGATACCC
1 AGGGTATCGATACCC
* *
5206111 AGGGTATGGATACCTAT
1 AGGGTATCGATACC--C
5206128 AGGGGTATCGATACCC
1 A-GGGTATCGATACCC
5206144 A
1 A
5206145 TTCGTAAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 13 0.48
16 1 0.04
17 1 0.04
18 12 0.44
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (15 bp):
AGGGTATCGATACCC
Found at i:5206190 original size:22 final size:23
Alignment explanation
Indices: 5206128--5206213 Score: 113
Period size: 23 Copynumber: 3.8 Consensus size: 23
5206118 GGATACCTAT
* *
5206128 AGGGGTATCGATACCCATTCGTA
1 AGGGGTATTGATACCCATTCATA
*
5206151 AAGGGTATTGATACCCATTCATA
1 AGGGGTATTGATACCCATTCATA
5206174 AGGGGTATTGATA-CCATTCAT-
1 AGGGGTATTGATACCCATTCATA
* *
5206195 AGGGGTATCGGTACCCATT
1 AGGGGTATTGATACCCATT
5206214 TGCATTTTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.20
22 13 0.23
23 32 0.57
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (23 bp):
AGGGGTATTGATACCCATTCATA
Found at i:5207847 original size:77 final size:77
Alignment explanation
Indices: 5207696--5208125 Score: 419
Period size: 77 Copynumber: 5.6 Consensus size: 77
5207686 GCCATGATTA
* * * * * * *
5207696 ACTAAGAAACACGTTGAGATGTGGAATGTTAAT-TTTTT-TTAATAAAAT-AGGTTGTGCCCAAT
1 ACTAAGAAATAAGTTGAGATCTGAAATGTTAATATTTTTATTAATAAAATGA-GTTTTACCCAAG
*
5207758 AATGACATGGTTC
65 AATGTCATGGTTC
* * * **
5207771 ACTAAGAAATATGTTGTGATCTGAAATGTTAATATGTTTATTAATAAAATGAGTTTTGTCCAAGA
1 ACTAAGAAATAAGTTGAGATCTGAAATGTTAATATTTTTATTAATAAAATGAGTTTTACCCAAGA
5207836 ATGTCATGGTTC
66 ATGTCATGGTTC
* * * * * *
5207848 ACTAATAAATAGGTTGGGATCTGGAATGTTAATATTTTTA-TAATAAAATGGGTTATACCCAAGA
1 ACTAAGAAATAAGTTGAGATCTGAAATGTTAATATTTTTATTAATAAAATGAGTTTTACCCAAGA
*
5207912 ATGCCATGGTTC
66 ATGTCATGGTTC
* * * *
5207924 ACTAAGAAATAAGTT-ACGATATGAAATATTAATATTTTTATTAATAAAATGAGTTTCATCCAAG
1 ACTAAGAAATAAGTTGA-GATCTGAAATGTTAATATTTTTATTAATAAAATGAGTTTTACCCAAG
5207988 AATGTCATGGTTC
65 AATGTCATGGTTC
* * * * * ** ** *
5208001 ACTAAGTAATATGTTGAGATTTGGAATGCTAATATTTTTATTAATAAAATTTGTTACACACAAGA
1 ACTAAGAAATAAGTTGAGATCTGAAATGTTAATATTTTTATTAATAAAATGAGTTTTACCCAAGA
*
5208066 ATGTTAT-GTTC
66 ATGTCATGGTTC
* *
5208077 ACTAAGAAAGCAAGTTGTGATCT-AGAATGTTAAT-TTTTCTATT-ATAAAA
1 ACTAAGAAA-TAAGTTGAGATCTGA-AATGTTAATATTTT-TATTAATAAAA
5208126 AATTTGAAAG
Statistics
Matches: 296, Mismatches: 50, Indels: 17
0.82 0.14 0.05
Matches are distributed among these distances:
75 28 0.09
76 90 0.30
77 176 0.59
78 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (77 bp):
ACTAAGAAATAAGTTGAGATCTGAAATGTTAATATTTTTATTAATAAAATGAGTTTTACCCAAGA
ATGTCATGGTTC
Found at i:5207929 original size:153 final size:153
Alignment explanation
Indices: 5207708--5208110 Score: 508
Period size: 153 Copynumber: 2.6 Consensus size: 153
5207698 TAAGAAACAC
* * * * *
5207708 GTTGAGATGTGGAATGTTAAT-TTTTTTTAATAAAATAGGTTGTGCCCAATAATGACATGGTTCA
1 GTTGAGATCTGGAATGTTAATATTTTTATAATAAAATAGGTTATACCCAAGAATGACATGGTTCA
* **
5207772 CTAAGAAATATGTTGTGATCTGAAATGTTAATATGTTTATTAATAAAATGAGTTTTGTCCAAGAA
66 CTAAGAAATAAGTTGTGATCTGAAATGTTAATATGTTTATTAATAAAATGAGTTTCATCCAAGAA
5207837 TGTCATGGTTCACTAA-TAAATAG
131 TGTCATGGTTCACTAAGT-AATAG
* * *
5207860 GTTGGGATCTGGAATGTTAATATTTTTATAATAAAATGGGTTATACCCAAGAATGCCATGGTTCA
1 GTTGAGATCTGGAATGTTAATATTTTTATAATAAAATAGGTTATACCCAAGAATGACATGGTTCA
** * * *
5207925 CTAAGAAATAAGTTACGATATGAAATATTAATATTTTTATTAATAAAATGAGTTTCATCCAAGAA
66 CTAAGAAATAAGTTGTGATCTGAAATGTTAATATGTTTATTAATAAAATGAGTTTCATCCAAGAA
*
5207990 TGTCATGGTTCACTAAGTAATAT
131 TGTCATGGTTCACTAAGTAATAG
* * ** * * **
5208013 GTTGAGATTTGGAATGCTAATATTTTTATTAATAAAATTTGTTACACACAAGAATGTTAT-GTTC
1 GTTGAGATCTGGAATGTTAATATTTTTA-TAATAAAATAGGTTATACCCAAGAATGACATGGTTC
*
5208077 ACTAAGAAAGCAAGTTGTGATCT-AGAATGTTAAT
65 ACTAAGAAA-TAAGTTGTGATCTGA-AATGTTAAT
5208111 TTTTCTATTA
Statistics
Matches: 215, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
152 19 0.09
153 153 0.71
154 43 0.20
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (153 bp):
GTTGAGATCTGGAATGTTAATATTTTTATAATAAAATAGGTTATACCCAAGAATGACATGGTTCA
CTAAGAAATAAGTTGTGATCTGAAATGTTAATATGTTTATTAATAAAATGAGTTTCATCCAAGAA
TGTCATGGTTCACTAAGTAATAG
Found at i:5208420 original size:60 final size:59
Alignment explanation
Indices: 5208346--5208480 Score: 184
Period size: 60 Copynumber: 2.3 Consensus size: 59
5208336 TGAAGGCTAC
*
5208346 AAAGTATCGATACTTTTAAATTCAAAAGTTAAAATATCA-TTTTCTATTTTTTTAAATTCA
1 AAAGTATCGATACTTTTAAATTCAAAAGTTAAAATACCATTTTTC-ATTTTTTT-AATTCA
* * * *
5208406 AAAGTATTGATACTTATAAATTCAAAAGTTAACATACCATTTTTCATTTTTTTAATTCG
1 AAAGTATCGATACTTTTAAATTCAAAAGTTAAAATACCATTTTTCATTTTTTTAATTCA
*
5208465 AAA-TATGGATACTTTT
1 AAAGTATCGATACTTTT
5208481 CCAAAAGTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
58 11 0.16
59 8 0.12
60 43 0.64
61 5 0.07
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (59 bp):
AAAGTATCGATACTTTTAAATTCAAAAGTTAAAATACCATTTTTCATTTTTTTAATTCA
Found at i:5208859 original size:60 final size:58
Alignment explanation
Indices: 5208765--5208880 Score: 137
Period size: 59 Copynumber: 2.0 Consensus size: 58
5208755 AAATGAGGAA
* * * * *
5208765 TTCGATCTTTTTTATCAATTTTTTAATTTCTAAAAGTATCGATCATCAATATTTTAAAT
1 TTCGATCTTATCTATCAATTTTTTAATTTCTAAAAATATCGATAAT-AATATATTAAAT
5208824 TTCGATCTTATCT-TCAACTTTGTTTAATATT-TAAAAATATCGATAATAATATATTAA
1 TTCGATCTTATCTATCAA-TTT-TTTAAT-TTCTAAAAATATCGATAATAATATATTAA
5208881 GTATCGATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
58 4 0.08
59 23 0.47
60 20 0.41
61 2 0.04
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.48
Consensus pattern (58 bp):
TTCGATCTTATCTATCAATTTTTTAATTTCTAAAAATATCGATAATAATATATTAAAT
Found at i:5212353 original size:21 final size:21
Alignment explanation
Indices: 5212327--5212379 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
5212317 GTTTTTTGGA
5212327 AGCTTTTGAGCTCCGGTTGAG
1 AGCTTTTGAGCTCCGGTTGAG
*
5212348 AGCTTTTGAGCTCTGGTTGAG
1 AGCTTTTGAGCTCCGGTTGAG
*
5212369 AGCTCTTGAGC
1 AGCTTTTGAGC
5212380 CATCTCTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.15, C:0.19, G:0.32, T:0.34
Consensus pattern (21 bp):
AGCTTTTGAGCTCCGGTTGAG
Found at i:5213574 original size:10 final size:9
Alignment explanation
Indices: 5213554--5213660 Score: 56
Period size: 10 Copynumber: 10.9 Consensus size: 9
5213544 AATAATAAAC
*
5213554 AAAACAAAT
1 AAAAAAAAT
5213563 AAAGAAAAAT
1 AAA-AAAAAT
*
5213573 -AATAAAAT
1 AAAAAAAAT
5213581 AAATAAAAAT
1 AAA-AAAAAT
5213591 AAAACAAAAT
1 AAAA-AAAAT
5213601 AAATAAAATAGT
1 AAA-AAAA-A-T
* *
5213613 AACATAAAT
1 AAAAAAAAT
5213622 AAAAATAAA-
1 AAAAA-AAAT
*
5213631 ACAAAAAAGGT
1 A-AAAAAA-AT
5213642 AAAAGAAAAT
1 AAAA-AAAAT
5213652 AAAGAAAAA
1 AAA-AAAAA
5213661 GAATACAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 25
0.69 0.08 0.23
Matches are distributed among these distances:
8 5 0.07
9 15 0.20
10 43 0.57
11 10 0.13
12 3 0.04
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.14
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:5213609 original size:37 final size:38
Alignment explanation
Indices: 5213543--5213636 Score: 129
Period size: 37 Copynumber: 2.5 Consensus size: 38
5213533 GCGAATATGA
*
5213543 AAATAATAAACAAAAC-AAATAAAGAAAAATAATAAAAT
1 AAATAA-AAATAAAACAAAATAAAGAAAAATAATAAAAT
* * *
5213581 AAATAAAAATAAAACAAAATAAA-TAAAATAGTAACAT
1 AAATAAAAATAAAACAAAATAAAGAAAAATAATAAAAT
5213618 AAATAAAAATAAAACAAAA
1 AAATAAAAATAAAACAAAA
5213637 AAGGTAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
37 38 0.75
38 13 0.25
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (38 bp):
AAATAAAAATAAAACAAAATAAAGAAAAATAATAAAAT
Found at i:5213680 original size:2 final size:2
Alignment explanation
Indices: 5213673--5213740 Score: 86
Period size: 2 Copynumber: 34.5 Consensus size: 2
5213663 ATACAAAATA
* *
5213673 AT AT AT AT AT AT AT AT AT A- AT AA AA AGT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
*
5213714 AG AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5213741 CTAAGTAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.03
2 57 0.95
3 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:5213826 original size:2 final size:2
Alignment explanation
Indices: 5213821--5213864 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5213811 AAAAATAAGG
5213821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5213863 TA
1 TA
5213865 ATCGTATAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5213835 original size:48 final size:48
Alignment explanation
Indices: 5213669--5213836 Score: 155
Period size: 48 Copynumber: 3.4 Consensus size: 48
5213659 AAGAATACAA
* * * * *
5213669 AATAATATATATATATATATA-TAA-TAAAAAGTATATATATATATAAGAT
1 AATAATATATATATATATATACTAAGTAAAAA-CA-A-AAACAAATAAAAT
*
5213718 ATATATATATATATATATATATACTAAGTAAAAATAAAAACAAATAAAAT
1 A-ATA-ATATATATATATATATACTAAGTAAAAACAAAAACAAATAAAAT
* * * *
5213768 ACTAAAATATATATATATATACTAGGTAAAAACAAATA-AAATAAAA-
1 AATAATATATATATATATATACTAAGTAAAAACAAAAACAAATAAAAT
5213814 AATAAGGTATATATATATATATA
1 AATAA--TATATATATATATATA
5213837 TATATATATA
Statistics
Matches: 102, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
46 4 0.04
47 8 0.08
48 45 0.44
49 3 0.03
50 13 0.13
51 18 0.18
52 5 0.05
53 6 0.06
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (48 bp):
AATAATATATATATATATATACTAAGTAAAAACAAAAACAAATAAAAT
Found at i:5215067 original size:65 final size:65
Alignment explanation
Indices: 5214979--5215162 Score: 314
Period size: 65 Copynumber: 2.8 Consensus size: 65
5214969 GTGAAGTTGA
* *
5214979 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTTTTACCGAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAATTTCACCGAATTG
* *
5215044 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATAAATTTCATCGAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAATTTCACCGAATTG
* *
5215109 GCTTTGAGTTGGATATCCTTCGTTATGAAGTTGAAATCCAATCTCGAGTAAATT
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAATT
5215163 GAGTCTCTTC
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 112 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (65 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAATTTCACCGAATTG
Found at i:5216029 original size:61 final size:65
Alignment explanation
Indices: 5215950--5216108 Score: 209
Period size: 61 Copynumber: 2.5 Consensus size: 65
5215940 TCTTCTCCTT
* *
5215950 TTTTCAGTTTAGGGCGCCCTTTCGGGTTTTCACCCTAAA-CATTTTTC-TCT-TTTCTC-TTTTC
1 TTTTCAATTTAGGACGCCCTTTCGGGTTTTCACCCTAAATCATTTTTCTTCTCTTTCTCTTTTTC
** *
5216011 TTTTCAATTTAGGACGCCCTTTCGGGTTTTCACCCTAAATGTTTTTTCTTTTCTTTCTCTTTTTC
1 TTTTCAATTTAGGACGCCCTTTCGGGTTTTCACCCTAAATCATTTTTCTTCTCTTTCTCTTTTTC
* * *
5216076 TTCTTCAACTTAAGACGCCCTCTCGGGTTTTCA
1 TT-TTCAATTTAGGACGCCCTTTCGGGTTTTCA
5216109 TCATAAGTGA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
61 37 0.44
62 6 0.07
63 2 0.02
64 6 0.07
65 7 0.08
66 27 0.32
ACGTcount: A:0.13, C:0.26, G:0.13, T:0.48
Consensus pattern (65 bp):
TTTTCAATTTAGGACGCCCTTTCGGGTTTTCACCCTAAATCATTTTTCTTCTCTTTCTCTTTTTC
Found at i:5229589 original size:20 final size:17
Alignment explanation
Indices: 5229550--5229594 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
5229540 AAGCTCTTCT
*
5229550 CTCTTTTTCTTCCTTGC
1 CTCTTCTTCTTCCTTGC
5229567 CTCTTCTTCTTCCTTGC
1 CTCTTCTTCTTCCTTGC
*
5229584 CTCCTCTTCTT
1 CTCTTCTTCTT
5229595 TTTGCGACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.00, C:0.40, G:0.04, T:0.56
Consensus pattern (17 bp):
CTCTTCTTCTTCCTTGC
Found at i:5238113 original size:22 final size:20
Alignment explanation
Indices: 5238088--5238208 Score: 63
Period size: 22 Copynumber: 5.8 Consensus size: 20
5238078 AAAACAAAGA
5238088 AAGAAAAATAATAAAAATAAAT
1 AAGAAAAATAAT-AAAA-AAAT
* *
5238110 AAGAATAAGAATAAAACAAAAT
1 AAGAAAAATAAT-AAA-AAAAT
* *
5238132 AA-ATAAAATAGTAACACAAAT
1 AAGA-AAAATAATAA-AAAAAT
*
5238153 AA-AAATAA-AACAAACCAAAAT
1 AAGAAA-AATAATAAA--AAAAT
*
5238174 AAGAAAAAAAATAAAACAAA-
1 AAGAAAAATAATAAAA-AAAT
5238194 AAG-AAAATAATAAAA
1 AAGAAAAATAATAAAA
5238209 TAAAATAACT
Statistics
Matches: 79, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
19 12 0.15
20 9 0.11
21 23 0.29
22 34 0.43
23 1 0.01
ACGTcount: A:0.76, C:0.06, G:0.05, T:0.13
Consensus pattern (20 bp):
AAGAAAAATAATAAAAAAAT
Found at i:5238113 original size:26 final size:25
Alignment explanation
Indices: 5238066--5238137 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 25
5238056 TGTAAATATG
5238066 AAAATAATAAACAA-AACA-AAGAAAGA
1 AAAATAATAAA-AATAA-ATAAG-AAGA
*
5238092 AAAATAATAAAAATAAATAAGAATA
1 AAAATAATAAAAATAAATAAGAAGA
* *
5238117 AGAATAAAACAAAATAAATAA
1 AAAATAATA-AAAATAAATAA
5238138 AATAGTAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 13 0.32
26 27 0.68
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (25 bp):
AAAATAATAAAAATAAATAAGAAGA
Found at i:5238140 original size:5 final size:5
Alignment explanation
Indices: 5238092--5238216 Score: 53
Period size: 5 Copynumber: 24.4 Consensus size: 5
5238082 CAAAGAAAGA
* *
5238092 AAAAT AATA- AAAAT -AAAT AAGAAT AAGAAT AAAAC AAAAT -AAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT AAAAT AAAAT AAAAT AAAAT
* * * ** * *
5238141 AGTAAC ACAAAT AAAAAT AAAAC AAACC AAAAT AAGAAAA AAAAT AAAAC
1 A-AAAT A-AAAT -AAAAT AAAAT AAAAT AAAAT -A-AAAT AAAAT AAAAT
*
5238191 AAAA- AGAAA- ATAAT AAAAT AAAAT AA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AA
5238217 CTAAAAAGGA
Statistics
Matches: 92, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
4 14 0.15
5 52 0.57
6 22 0.24
7 4 0.04
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:5238223 original size:29 final size:28
Alignment explanation
Indices: 5238153--5238216 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
5238143 TAACACAAAT
**
5238153 AAAAATAAAAC-AAACCAAAATAAGAAA
1 AAAAATAAAACAAAAAGAAAATAAGAAA
*
5238180 AAAAATAAAACAAAAAGAAAATAATAAA
1 AAAAATAAAACAAAAAGAAAATAAGAAA
5238208 ATAAAATAA
1 A-AAAATAA
5238217 CTAAAAAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 11 0.34
28 14 0.44
29 7 0.22
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (28 bp):
AAAAATAAAACAAAAAGAAAATAAGAAA
Found at i:5238228 original size:29 final size:27
Alignment explanation
Indices: 5238169--5238235 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
5238159 AAAACAAACC
5238169 AAAATAAGAAAAAAAATAAAACAAAAAG
1 AAAATAAGAAAAAAAAT-AAACAAAAAG
*
5238197 AAAATAATAAAATAAAAT-AACTAAAAAG
1 AAAATAAGAAAA-AAAATAAAC-AAAAAG
*
5238225 GAAA-AAGAAAA
1 AAAATAAGAAAA
5238236 TTAAGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.26
28 20 0.59
29 5 0.15
ACGTcount: A:0.79, C:0.03, G:0.07, T:0.10
Consensus pattern (27 bp):
AAAATAAGAAAAAAAATAAACAAAAAG
Found at i:5238326 original size:46 final size:47
Alignment explanation
Indices: 5238241--5238335 Score: 115
Period size: 46 Copynumber: 2.0 Consensus size: 47
5238231 GAAAATTAAG
* *
5238241 AAAAAGAATACAAATAATATATATATAGTGTCTAAT-AAAACAAATA
1 AAAAAGAATACAAATAATATATATAAAATGTCTAATAAAAACAAATA
* *
5238287 AAAAAGAATAATAAAT-ATATATATAAAATGT-TAGGTAAAAACAAATA
1 AAAAAGAAT-ACAAATAATATATATAAAATGTCTA-ATAAAAACAAATA
5238334 AA
1 AA
5238336 GTAAAACATA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 2 0.05
46 23 0.55
47 17 0.40
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.25
Consensus pattern (47 bp):
AAAAAGAATACAAATAATATATATAAAATGTCTAATAAAAACAAATA
Found at i:5238391 original size:12 final size:12
Alignment explanation
Indices: 5238374--5238408 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
5238364 AAATATTAGA
5238374 AAAATAAGA-AAT
1 AAAATAA-ACAAT
5238386 AAAATAAACAAT
1 AAAATAAACAAT
5238398 AAAATAAACAA
1 AAAATAAACAA
5238409 ATAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 1 0.05
12 21 0.95
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (12 bp):
AAAATAAACAAT
Done.