Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 379 of 427
Found at i:110226799 original size:18 final size:18
Alignment explanation
Indices: 110226769--110226827 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
110226759 AGTCTATTTA
110226769 TTTTTCATGTTATTTTTTC
1 TTTTTCATGTTA-TTTTTC
110226788 TTTTTCAT-TTATTTTTC
1 TTTTTCATGTTATTTTTC
*
110226805 TTTTT-ATGTTTATTTTTG
1 TTTTTCATG-TTATTTTTC
110226823 TTTTT
1 TTTTT
110226828 ATTTTCATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
16 2 0.05
17 11 0.30
18 16 0.43
19 8 0.22
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTTCATGTTATTTTTC
Found at i:110242735 original size:30 final size:30
Alignment explanation
Indices: 110242699--110242757 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
110242689 TATTTTATTA
*
110242699 TTAATTT-TGTTATTATTTTAAATGCATTTG
1 TTAATTTAT-TTATTATTTTAAAGGCATTTG
*
110242729 TTAATTTATTTATTATTTTAGAGGCATTT
1 TTAATTTATTTATTATTTTAAAGGCATTT
110242758 ACTTGTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.59
Consensus pattern (30 bp):
TTAATTTATTTATTATTTTAAAGGCATTTG
Found at i:110247522 original size:20 final size:21
Alignment explanation
Indices: 110247480--110247522 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
110247470 TGTTTTGATG
*
110247480 TTGATGATAGATTATGAATGT
1 TTGATGATAGATTATGAAAGT
110247501 TTGATGATAG-TTAT-ACAAGT
1 TTGATGATAGATTATGA-AAGT
110247521 TT
1 TT
110247523 TGTTAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 9 0.45
21 10 0.50
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (21 bp):
TTGATGATAGATTATGAAAGT
Found at i:110248147 original size:48 final size:48
Alignment explanation
Indices: 110248076--110248262 Score: 302
Period size: 48 Copynumber: 3.9 Consensus size: 48
110248066 CATTAGGGAA
*
110248076 TACATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCAAGT
1 TACATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGAGT
* * *
110248124 TACATTGATTTAGCTTCGGGCCATGATATTGGCACTTTGGGTGCGAGT
1 TACATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGAGT
* * *
110248172 TACATTGATTTGGCTTTGGGCCATGATATTGGCATTTCGGGTGCGAGT
1 TACATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGAGT
*
110248220 TACATTGATTTGGCTTCGGGCCATGATATCGGCACTTAGGGTG
1 TACATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTG
110248263 TAAGACTCTC
Statistics
Matches: 127, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 127 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.34
Consensus pattern (48 bp):
TACATTGATTTGGCTTCGGGCCATGATATCGGCACTTCGGGTGCGAGT
Found at i:110248804 original size:20 final size:20
Alignment explanation
Indices: 110248775--110248813 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
110248765 TGATTAGTTG
* *
110248775 TGATTGAATTGTATTTGAAT
1 TGATTAAATTGTATGTGAAT
110248795 TGATTAAATTGTATGTGAA
1 TGATTAAATTGTATGTGAA
110248814 ATGTATGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
TGATTAAATTGTATGTGAAT
Found at i:110250141 original size:18 final size:18
Alignment explanation
Indices: 110250118--110250153 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
110250108 TATAAACTTT
110250118 AATAAATAATAAAAATAA
1 AATAAATAATAAAAATAA
*
110250136 AATAAATAATAATAATAA
1 AATAAATAATAAAAATAA
110250154 TGGACCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AATAAATAATAAAAATAA
Found at i:110260347 original size:131 final size:128
Alignment explanation
Indices: 110259985--110260614 Score: 389
Period size: 131 Copynumber: 4.8 Consensus size: 128
110259975 GAAGACGAGA
* * * * * * * **
110259985 TTCGATATTTGGCAATTCGCGGAAT-AGTGCCCTAACGTGTTGGGTTGCAAT-TTCGCGTTTACT
1 TTCGATGTTTGGCAATTCG-AGAATCA-TGCCCTATCGTGCTGGGTTGCGATCTT-TCATTGGCT
* * * * * * * * *
110260048 CAAAATAATCAAATATCCCTTCAAAATTTCACCCATGCCTTTTTAAAATTCTTTGAAACGAAGGT
63 CAAAACAATCGAAGATCCCTTC-GAATTTCACTCATG--TTTTTAAAAATATTTAAAACGAAGGA
*
110260113 GATG
125 AATG
* * ** * * *
110260117 TGCGATATTTGGCAATTTGCG-GAATTGTGCCCTAACGTGCTGGGTTGCAAT-TTCTCGGTT-GC
1 TTCGATGTTTGGCAA-TT-CGAGAATCATGCCCTATCGTGCTGGGTTGCGATCTT-TC-ATTGGC
* * * * * *
110260179 TTAAAATAATCAAATATCCCTTCAAAATTTCATTCATGTCTTTTAAAAATTATTTAAAACGAAGG
62 TCAAAACAATCGAAGATCCCTTC-GAATTTCACTCATGT-TTTTAAAAA-TATTTAAAACGAAGG
* *
110260244 CAATA
124 AAATG
* * * * *
110260249 TTCGATGTTTGACAATTCGAGAATCATGCCTTATCGTGCTGGGTTGTGATCTTTCGTTTGCTCAA
1 TTCGATGTTTGGCAATTCGAGAATCATGCCCTATCGTGCTGGGTTGCGATCTTTCATTGGCTCAA
* * * *
110260314 AACAATCGAATATTCCTT-TATATTCTCACTCATGTTTATTAAAAATACTTTAAAACGAA-GATG
66 AACAATCGAAGATCCCTTCGA-ATT-TCACTCATGTTT-TTAAAAATA-TTTAAAACGAAGGA-A
110260377 ATG
126 ATG
* * * * * * *
110260380 TTCAATGTTTGGCGATTTGAGAATCGTGCCCTATCGTGCTGGGTTGCGCTTTTTCATTGGTTCAA
1 TTCGATGTTTGGCAATTCGAGAATCATGCCCTATCGTGCTGGGTTGCGATCTTTCATTGGCTCAA
* * *
110260445 AACAATTGAAGATCCCTTCGGAATTTCACTCATGTTTTCTAAAAACTCTTGAAAACGGAA-GAAA
66 AACAATCGAAGATCCCTTC-GAATTTCACTCATGTTTT-TAAAAA-TATTTAAAAC-GAAGGAAA
110260509 TG
127 TG
* * * ** * *
110260511 TTCGATGTTTGGCAATTCGGGGAAT-AGTGCCCTATCGTGCTGAGTTGCAATCTCCCATTCGTTC
1 TTCGATGTTTGGCAATTC-GAGAATCA-TGCCCTATCGTGCTGGGTTGCGATCTTTCATTGGCTC
* * *
110260575 AAAATAATCG-AGTATCTCTTCGAAATTTCACTCATATTTT
64 AAAACAATCGAAG-ATCCCTTCG-AATTTCACTCATGTTTT
110260615 CTAAGGCAAG
Statistics
Matches: 408, Mismatches: 67, Indels: 46
0.78 0.13 0.09
Matches are distributed among these distances:
129 1 0.00
130 15 0.04
131 199 0.49
132 185 0.45
133 6 0.01
134 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (128 bp):
TTCGATGTTTGGCAATTCGAGAATCATGCCCTATCGTGCTGGGTTGCGATCTTTCATTGGCTCAA
AACAATCGAAGATCCCTTCGAATTTCACTCATGTTTTTAAAAATATTTAAAACGAAGGAAATG
Found at i:110260618 original size:132 final size:131
Alignment explanation
Indices: 110259985--110260614 Score: 506
Period size: 132 Copynumber: 4.8 Consensus size: 131
110259975 GAAGACGAGA
* * * * * **
110259985 TTCGATATTTGGCAATTCGCGGAATAGTGCCCTAACGTGTTGGGTTGCAATTTCGCGTTTACTCA
1 TTCGATGTTTGGCAATTCGGGGAATAGTGCCCTATCGTGCTGGGTTGCAATTTCCCGTTTGTTCA
* * *
110260050 AAATAATCAAATATCCCTTCAAAATTTCACCCATGCCTTTTT-AAAATTCTTTG-AAACGAAGGT
66 AAATAATCGAATATCCCTTCAAAATTTCACTCATG--TTTTTAAAAATTC-TTGAAAACGAAGGA
*
110260113 GATG
128 AATG
* * * * * * * *
110260117 TGCGATATTTGGCAATTTGCGGAATTGTGCCCTAACGTGCTGGGTTGCAATTTCTCGGTTGCTT-
1 TTCGATGTTTGGCAATTCGGGGAATAGTGCCCTATCGTGCTGGGTTGCAATTTCCCGTTTG-TTC
* * * * *
110260181 AAAATAATCAAATATCCCTTCAAAATTTCATTCATGTCTTTTAAAAATTATTTAAAACGAAGGCA
65 AAAATAATCGAATATCCCTTCAAAATTTCACTCATGT-TTTTAAAAATTCTTGAAAACGAAGGAA
*
110260246 ATA
129 ATG
* * * ** * *
110260249 TTCGATGTTTGACAATTC-GAGAATCA-TGCCTTATCGTGCTGGGTTGTGATCTT-TCGTTTGCT
1 TTCGATGTTTGGCAATTCGGGGAAT-AGTGCCCTATCGTGCTGGGTTGCAAT-TTCCCGTTTGTT
* * * * * *
110260311 CAAAACAATCGAATATTCCTT-TATATTCTCACTCATGTTTATTAAAAATACTTTAAAACGAA-G
64 CAAAATAATCGAATATCCCTTCAAAATT-TCACTCATGTTT-TTAAAAATTCTTGAAAACGAAGG
*
110260374 ATGATG
127 A-AATG
* * * * * ** ** * *
110260380 TTCAATGTTTGGCGATT-TGAGAATCGTGCCCTATCGTGCTGGGTTGCGCTTTTTCATTGGTTCA
1 TTCGATGTTTGGCAATTCGGGGAATAGTGCCCTATCGTGCTGGGTTGCAATTTCCCGTTTGTTCA
* * * ** *
110260444 AAACAATTGAAGATCCCTTCGGAATTTCACTCATGTTTTCTAAAAACTCTTGAAAACGGAA-GAA
66 AAATAATCGAATATCCCTTCAAAATTTCACTCATGTTTT-TAAAAATTCTTGAAAAC-GAAGGAA
110260508 ATG
129 ATG
* * * *
110260511 TTCGATGTTTGGCAATTCGGGGAATAGTGCCCTATCGTGCTGAGTTGCAATCTCCCATTCGTTCA
1 TTCGATGTTTGGCAATTCGGGGAATAGTGCCCTATCGTGCTGGGTTGCAATTTCCCGTTTGTTCA
* * * *
110260576 AAATAATCGAGTATCTCTTCGAAATTTCACTCATATTTT
66 AAATAATCGAATATCCCTTCAAAATTTCACTCATGTTTT
110260615 CTAAGGCAAG
Statistics
Matches: 403, Mismatches: 78, Indels: 34
0.78 0.15 0.07
Matches are distributed among these distances:
130 12 0.03
131 192 0.48
132 198 0.49
133 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (131 bp):
TTCGATGTTTGGCAATTCGGGGAATAGTGCCCTATCGTGCTGGGTTGCAATTTCCCGTTTGTTCA
AAATAATCGAATATCCCTTCAAAATTTCACTCATGTTTTTAAAAATTCTTGAAAACGAAGGAAAT
G
Found at i:110266745 original size:20 final size:19
Alignment explanation
Indices: 110266687--110266743 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
110266677 CTCCCTCAAC
*
110266687 AAAAATTTAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
110266706 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
110266725 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
110266743 A
1 A
110266744 TATTTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:110269072 original size:19 final size:18
Alignment explanation
Indices: 110269027--110269078 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
110269017 GGCCTGTTTG
*
110269027 TATTAAATATTTATATAAT
1 TATTAAA-ATATATATAAT
*
110269046 T-TTTAAATATATATAAT
1 TATTAAAATATATATAAT
*
110269063 ATATTAAAATAAATAT
1 -TATTAAAATATATAT
110269079 TTCTCAACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 10 0.37
18 5 0.19
19 12 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTAAAATATATATAAT
Found at i:110269284 original size:22 final size:22
Alignment explanation
Indices: 110269257--110269299 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
110269247 AAATGGTAGC
**
110269257 AAAATAGGGTGAAAACAACAAG
1 AAAATAGAATGAAAACAACAAG
*
110269279 AAAATAGAATTAAAACAACAA
1 AAAATAGAATGAAAACAACAA
110269300 TAAATAGCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.09, G:0.14, T:0.12
Consensus pattern (22 bp):
AAAATAGAATGAAAACAACAAG
Found at i:110270506 original size:22 final size:23
Alignment explanation
Indices: 110270480--110270522 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
110270470 ACCTAAATTT
110270480 TTAAA-TTTAAAAAATAAAAAAA
1 TTAAATTTTAAAAAATAAAAAAA
110270502 TTAAATTTTAAAAAATAAAAA
1 TTAAATTTTAAAAAATAAAAA
110270523 TGTAGAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
TTAAATTTTAAAAAATAAAAAAA
Found at i:110270921 original size:22 final size:23
Alignment explanation
Indices: 110270893--110270943 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
110270883 ACAAAAATCC
110270893 TCTCAAATG-TCTC-TCAATTTTT
1 TCTCAAA-GCTCTCTTCAATTTTT
*
110270915 TCTCAAAGCTCTCTTTAATTTTT
1 TCTCAAAGCTCTCTTCAATTTTT
110270938 T-TCAAA
1 TCTCAAA
110270944 AAAGCTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 1 0.04
22 16 0.62
23 9 0.35
ACGTcount: A:0.25, C:0.22, G:0.04, T:0.49
Consensus pattern (23 bp):
TCTCAAAGCTCTCTTCAATTTTT
Found at i:110273375 original size:130 final size:130
Alignment explanation
Indices: 110273141--110273417 Score: 434
Period size: 130 Copynumber: 2.1 Consensus size: 130
110273131 CAACATTGAT
* * *
110273141 TTTTTAAAATATTTGTATAAAATTTTTTATTTTGTTTCATTTAATAAAATAAAAGTTGTTTTTAA
1 TTTTTAATATATTTGTATAAAACTTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTTAA
* * **
110273206 TATTTTAATTATAATTTACTTTTTATATTTTTAATAAAATAAAAGTTTTTTTTTAATAAGGTAAT
66 TATTTTAATTATAATTTACTTTTTATATTTTTAATAAAATAAAAG-TTCTTTTGAATAAGACAAT
110273271 A
130 A
*
110273272 TTTTTAATATATTTGTA-CAAACTTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTTAA
1 TTTTTAATATATTTGTATAAAACTTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTTAA
* *
110273336 TATTTTAATTGTAATTTACTTTTTATATTTTTAATAAAATAAAAGTTCTTTTGAATAAGACAGTA
66 TATTTTAATTATAATTTACTTTTTATATTTTTAATAAAATAAAAGTTCTTTTGAATAAGACAATA
110273401 TTTTTAATAT-TTT-TATA
1 TTTTTAATATATTTGTATA
110273418 TTTTTAATAA
Statistics
Matches: 134, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
127 2 0.01
128 3 0.02
129 25 0.19
130 88 0.66
131 16 0.12
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (130 bp):
TTTTTAATATATTTGTATAAAACTTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTTAA
TATTTTAATTATAATTTACTTTTTATATTTTTAATAAAATAAAAGTTCTTTTGAATAAGACAATA
Found at i:110274911 original size:22 final size:23
Alignment explanation
Indices: 110274886--110274931 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
110274876 CAACCAAATC
110274886 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
110274908 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
110274931 A
1 A
110274932 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:110274937 original size:23 final size:23
Alignment explanation
Indices: 110274893--110274937 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
110274883 ATCAATTCAA
*
110274893 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
110274916 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
110274938 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:110277057 original size:51 final size:50
Alignment explanation
Indices: 110276898--110277054 Score: 242
Period size: 51 Copynumber: 3.1 Consensus size: 50
110276888 ACTTCTGATC
* *
110276898 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAGTGACA
* *
110276949 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
* *
110276999 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
110277050 AGTGA
1 AGTGA
110277055 TAAATGTGAT
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 46 0.47
51 51 0.53
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.30
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:110281147 original size:20 final size:20
Alignment explanation
Indices: 110281106--110281148 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
110281096 AAAGAGATCG
*
110281106 ATTGAGCTGAAACGAGCTGA
1 ATTGAGCTGAAACAAGCTGA
*
110281126 ATTGAGCT-CAACAAGCTGGA
1 ATTGAGCTGAAACAAGCT-GA
110281146 ATT
1 ATT
110281149 TGAACTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (20 bp):
ATTGAGCTGAAACAAGCTGA
Found at i:110285078 original size:46 final size:48
Alignment explanation
Indices: 110284925--110285237 Score: 260
Period size: 46 Copynumber: 6.7 Consensus size: 48
110284915 TTTGTGCGCT
* * *
110284925 AGTGTAAGA-CATGTCTGGGACAT-GCTTCGGCCAT--ATTATTAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCC-TCGA-GATGAGAGCC
* * * * * *
110284971 AGTGTAAGACCATGTCTAGGACATGGCATCAGCATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGAGAGCC
*
110285019 AGTGTAAGA-CATGTCTGGGACAT-GCATTGGCCTCGAGATGTA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATG-AGAGCC
*
110285065 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CTACGAGATG-G-GTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGATGAGAGCC
* * * *
110285109 AGTGTAAGACCATGTCTGGAACATGGCATCAGCATGGAGATGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA--TGAGAGCC
* * * *
110285159 AGTGTAAGACCATGTCTAGGAGATGGCATC-GACT--TGATGGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAT-GA-GAGCC
* *
110285206 AGTGTAAGACCATGTCTGGGATATGACATCGG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG
110285238 TATTACACCC
Statistics
Matches: 219, Mismatches: 31, Indels: 32
0.78 0.11 0.11
Matches are distributed among these distances:
44 11 0.05
45 16 0.07
46 72 0.33
47 63 0.29
48 24 0.11
49 4 0.02
50 29 0.13
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGAGAGCC
Found at i:110285236 original size:47 final size:47
Alignment explanation
Indices: 110284966--110285236 Score: 215
Period size: 47 Copynumber: 5.8 Consensus size: 47
110284956 CATATTATTA
*
110284966 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATC-AGCATTGAGACGA-
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGA-C-TTGAGA-GAT
* * * *
110285014 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATTGGCCTCGAGATG-T
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCA-TCGACTTGAGA-GAT
* *
110285060 AAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-T-ACGAGAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGA-GAGAT
* * * *
110285104 GGGTCAGTGTAAGACCATGTCTGGAACATGGCATC-AGCATG-GAGATGT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGA-CTTGAGAGA--T
* *
110285152 GAGAGCCAGTGTAAGACCATGTCTAGGAGATGGCATCGACTTGATG-GAT
1 --GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGA-GAGAT
* *
110285201 GAGCCAGTGTAAGACCATGTCTGGGATATGACATCG
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
110285237 GTATTACACC
Statistics
Matches: 181, Mismatches: 25, Indels: 35
0.75 0.10 0.15
Matches are distributed among these distances:
43 2 0.01
44 14 0.08
45 16 0.09
46 48 0.27
47 49 0.27
48 14 0.08
49 1 0.01
50 33 0.18
51 3 0.02
52 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.22
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGAGAT
Found at i:110300240 original size:13 final size:13
Alignment explanation
Indices: 110300222--110300254 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
110300212 ATCAAACACG
110300222 GGCGTGTGCCGCA
1 GGCGTGTGCCGCA
*
110300235 GGCGTGTGCCGCG
1 GGCGTGTGCCGCA
110300248 GGCGTGT
1 GGCGTGT
110300255 CCCTGCCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.03, C:0.27, G:0.52, T:0.18
Consensus pattern (13 bp):
GGCGTGTGCCGCA
Found at i:110302492 original size:46 final size:46
Alignment explanation
Indices: 110302095--110302494 Score: 489
Period size: 46 Copynumber: 8.7 Consensus size: 46
110302085 TGATGGCATA
*
110302095 GTATCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCATGTTGCCATG
* * * *
110302141 GTATCTTTCAACTATGGTCTTATTCTTTTCATGTCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
* ***
110302187 GTATCTTTCAACCATGGTCTTATTCATTTCATGTCACACTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
* **
110302233 GTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
* * * *
110302279 GTATCTCTCAACCATGGTCTTATTCTTTTCATGTCACGTT-CTCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGC-CATG
* * *
110302325 GCATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
* * * * *
110302371 GTATCATTCAACCATGGTCTTACACGTTTCATATCATGTTGTCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
* * * * * *
110302417 GTATCTTTCAACCATGATCTTACACATTTCATATCTTATTGTCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
*
110302463 GTATCTTTCAACCATGGTCTTACACATTTCAT
1 GTATCTTTCAACCATGGTCTTACTCATTTCAT
110302495 TTCAAAGAGC
Statistics
Matches: 317, Mismatches: 34, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
45 5 0.02
46 311 0.98
47 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
Found at i:110303530 original size:41 final size:40
Alignment explanation
Indices: 110303484--110303569 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 40
110303474 CAAATACATT
*
110303484 TAAAACAAATATTAAAACAAGAAACAAATAAAAAATGATAC
1 TAAAACAAATATTAAAACAAGAAACAAATAAAAAAT-ATAA
* * * * *
110303525 TAAAACAATTCTTAAAACAATACACAAATTAAAAATATAA
1 TAAAACAAATATTAAAACAAGAAACAAATAAAAAATATAA
110303565 TAAAA
1 TAAAA
110303570 AGTGATTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 8 0.21
41 31 0.79
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.21
Consensus pattern (40 bp):
TAAAACAAATATTAAAACAAGAAACAAATAAAAAATATAA
Found at i:110303627 original size:23 final size:23
Alignment explanation
Indices: 110303585--110303629 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
110303575 TTATATTAAA
***
110303585 ATTAAAAATAAAATGTAAATATG
1 ATTAAAAATAAAAAAAAAATATG
110303608 ATTAAAAATAAAAAAAAAATAT
1 ATTAAAAATAAAAAAAAAATAT
110303630 ATATTTAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (23 bp):
ATTAAAAATAAAAAAAAAATATG
Found at i:110304794 original size:3 final size:3
Alignment explanation
Indices: 110304788--110304815 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
110304778 AAAGCTTTTT
110304788 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
110304816 CACGTTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:110304892 original size:11 final size:11
Alignment explanation
Indices: 110304876--110304923 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
110304866 CTTTATATAC
110304876 TAATAAAATAA
1 TAATAAAATAA
*
110304887 TAATAAAATATCT
1 TAATAAAATA--A
* *
110304900 TATTAAAATAT
1 TAATAAAATAA
110304911 TAATAAAATAA
1 TAATAAAATAA
110304922 TA
1 TA
110304924 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:110309618 original size:20 final size:19
Alignment explanation
Indices: 110309574--110309619 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
110309564 CATCTAAACG
*
110309574 CTAGAAATGTAAATCATTT
1 CTAGAAAAGTAAATCATTT
*
110309593 CCAGAAAAGTAAATCATTTT
1 CTAGAAAAGTAAATCA-TTT
110309613 CTAGAAA
1 CTAGAAA
110309620 TTATTTTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (19 bp):
CTAGAAAAGTAAATCATTT
Found at i:110309954 original size:124 final size:125
Alignment explanation
Indices: 110309729--110310116 Score: 582
Period size: 125 Copynumber: 3.1 Consensus size: 125
110309719 ATAGGAACTG
* * * * *
110309729 CTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTAGTT
1 CTGTAGAAAAAAAGCGT-CACGTAGGAGCTTTTTTCAGTAATTTTGCTAACAGTCCATCCTACTT
* * * * * * *
110309794 GAAGCGTTTTGGACACTATTTATTTAGAAACATCTTCTCAAAATTATTTTTTCAGAGACTA
65 AAAGCGTTTTCGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAGATACTA
110309855 CTGTAGAAAAAAAGCGTCACGTAGGAGCTTTTTT-AGTAATTTTGCTAACAGTCCATCCTACTTA
1 CTGTAGAAAAAAAGCGTCACGTAGGAGCTTTTTTCAGTAATTTTGCTAACAGTCCATCCTACTTA
*
110309919 AAGCGTTTTCGACACTATTTGTTCAAAAATGTCTTCTCAAAATTA-TTTTTCAGATACTA
66 AAGCGTTTTCGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAGATACTA
*
110309978 CTGTAGAAAAAAAGCGTTCACGTAGGAGCTTTTTTCAGTAATTTTGCTAACAGTCCATCCTGCTT
1 CTGTAGAAAAAAAGCG-TCACGTAGGAGCTTTTTTCAGTAATTTTGCTAACAGTCCATCCTACTT
* * * *
110310043 AAAGCGTTTTCAACACTGTTTGTTCAAAAGCGTCTTTTCAAAATTATTTTTTCAGATACTA
65 AAAGCGTTTTCGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAGATACTA
110310104 CTGTAGAAAAAAA
1 CTGTAGAAAAAAA
110310117 ATAAAAAGTT
Statistics
Matches: 240, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
123 29 0.12
124 83 0.35
125 85 0.35
126 43 0.18
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (125 bp):
CTGTAGAAAAAAAGCGTCACGTAGGAGCTTTTTTCAGTAATTTTGCTAACAGTCCATCCTACTTA
AAGCGTTTTCGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAGATACTA
Found at i:110310147 original size:125 final size:121
Alignment explanation
Indices: 110309755--110310116 Score: 402
Period size: 124 Copynumber: 2.9 Consensus size: 121
110309745 TCCACGTGGG
* * * * * ** * *
110309755 AGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTAGTTGAAGCGTTTTGGACACTATTTATTTA
1 AGCTTTTTTCAATAATTTTGCTAACAGTCCATCCTACTTAAAGCGTTTTCAACACTATTTGTTCA
* * * * **
110309820 GAAACATCTTCTCAAAATTATTTTTTCAGAGACTACTGTAGAAAAAAAGCGTCACGTAGG
66 AAAACGTCTTCTCAAAATTA-TTTTTCAGATACTACTGTAGAAAAAAAG-ATCAC--AAA
* *
110309880 AGCTTTTTT-AGTAATTTTGCTAACAGTCCATCCTACTTAAAGCGTTTTCGACACTATTTGTTCA
1 AGCTTTTTTCAATAATTTTGCTAACAGTCCATCCTACTTAAAGCGTTTTCAACACTATTTGTTCA
* * **
110309944 AAAATGTCTTCTCAAAATTATTTTTCAGATACTACTGTAGAAAAAAAGCGTTCACGTAGG
66 AAAACGTCTTCTCAAAATTATTTTTCAGATACTACTGTAGAAAAAAA--GATCAC--AAA
* * *
110310004 AGCTTTTTTCAGTAATTTTGCTAACAGTCCATCCTGCTTAAAGCGTTTTCAACACTGTTTGTTCA
1 AGCTTTTTTCAATAATTTTGCTAACAGTCCATCCTACTTAAAGCGTTTTCAACACTATTTGTTCA
* *
110310069 AAAGCGTCTTTTCAAAATTATTTTTTCAGATACTACTGTAGAAAAAAA
66 AAAACGTCTTCTCAAAATTA-TTTTTCAGATACTACTGTAGAAAAAAA
110310117 ATAAAAAGTT
Statistics
Matches: 215, Mismatches: 18, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
123 26 0.12
124 83 0.39
125 79 0.37
126 27 0.13
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (121 bp):
AGCTTTTTTCAATAATTTTGCTAACAGTCCATCCTACTTAAAGCGTTTTCAACACTATTTGTTCA
AAAACGTCTTCTCAAAATTATTTTTCAGATACTACTGTAGAAAAAAAGATCACAAA
Found at i:110310264 original size:36 final size:37
Alignment explanation
Indices: 110310205--110310278 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
110310195 ATTTAATTAA
* * *
110310205 TTAACCCTAAAACCTTAAGCCCTAAATTAATTGATTT
1 TTAACCCTAAAACCCTAAACCCTAAATTAATTAATTT
* *
110310242 TTAACTCT-AAACCCTAAACCCTAATTTAATTAATTT
1 TTAACCCTAAAACCCTAAACCCTAAATTAATTAATTT
110310278 T
1 T
110310279 CCTTAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
36 25 0.78
37 7 0.22
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (37 bp):
TTAACCCTAAAACCCTAAACCCTAAATTAATTAATTT
Found at i:110312098 original size:53 final size:53
Alignment explanation
Indices: 110312035--110312145 Score: 204
Period size: 53 Copynumber: 2.1 Consensus size: 53
110312025 ACAAAAGTAA
*
110312035 ATATAATTTTAATTGAATATACTTTCATTTGTTATAGTTTTTCGTATACACAC
1 ATATAATTTTAATTGAATATACTTTCATTTGTTATAGTTTTTCATATACACAC
*
110312088 ATATAATTTTAATTGAATATACTTTCATTTGTTATATTTTTTCATATACACAC
1 ATATAATTTTAATTGAATATACTTTCATTTGTTATAGTTTTTCATATACACAC
110312141 ATATA
1 ATATA
110312146 TATATAGTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (53 bp):
ATATAATTTTAATTGAATATACTTTCATTTGTTATAGTTTTTCATATACACAC
Found at i:110313600 original size:11 final size:11
Alignment explanation
Indices: 110313584--110313615 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
110313574 TCTTTCACTG
110313584 AAAAGAAAAAA
1 AAAAGAAAAAA
110313595 AAAAGAAAAAA
1 AAAAGAAAAAA
110313606 AAAAGAAAAA
1 AAAAGAAAAA
110313616 GAAGCAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:110313616 original size:6 final size:6
Alignment explanation
Indices: 110313584--110313618 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
110313574 TCTTTCACTG
110313584 AAAAGA AAAA-A AAAAGA AAAA-A AAAAGA AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA A
110313619 GCAAAGCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:110315094 original size:11 final size:11
Alignment explanation
Indices: 110315078--110315112 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
110315068 GTTGTGGAAC
110315078 CAAAAAAAAAA
1 CAAAAAAAAAA
110315089 CAAAAAAAAAA
1 CAAAAAAAAAA
110315100 -AAACAAAAAAA
1 CAAA-AAAAAAA
110315111 CA
1 CA
110315113 GATGATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 18 0.82
12 1 0.05
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:110315098 original size:14 final size:14
Alignment explanation
Indices: 110315079--110315110 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
110315069 TTGTGGAACC
110315079 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
110315093 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
110315107 AAAA
1 AAAA
110315111 CAGATGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:110318278 original size:2 final size:2
Alignment explanation
Indices: 110318271--110318300 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
110318261 GTACTACTAC
110318271 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
110318301 TTAATATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110320141 original size:20 final size:20
Alignment explanation
Indices: 110320115--110320167 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
110320105 ATTCTTATTT
110320115 TTTTTTTAAAAAAACCTT-AAA
1 TTTTTTTAAAAAAA--TTAAAA
*
110320136 TTTTTTTAAAAGAATTAAAA
1 TTTTTTTAAAAAAATTAAAA
*
110320156 -TTTGTTAAAAAA
1 TTTTTTTAAAAAA
110320168 TATAAGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (20 bp):
TTTTTTTAAAAAAATTAAAA
Found at i:110320153 original size:19 final size:20
Alignment explanation
Indices: 110320115--110320167 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
110320105 ATTCTTATTT
110320115 TTTTTTTAAAAAAACCTTAAA
1 TTTTTTTAAAAAAA-CTTAAA
*
110320136 TTTTTTTAAAAGAA-TTAAA
1 TTTTTTTAAAAAAACTTAAA
* *
110320155 ATTTGTTAAAAAA
1 TTTTTTTAAAAAA
110320168 TATAAGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 15 0.54
21 13 0.46
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (20 bp):
TTTTTTTAAAAAAACTTAAA
Found at i:110323787 original size:19 final size:18
Alignment explanation
Indices: 110323763--110323802 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
110323753 TTTAATACAC
110323763 ATAAAAAATTAAATTTATA
1 ATAAAAAATTAAA-TTATA
* *
110323782 ATAAAATATTATATTATA
1 ATAAAAAATTAAATTATA
110323800 ATA
1 ATA
110323803 TAAATATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAAAAATTAAATTATA
Found at i:110325353 original size:47 final size:47
Alignment explanation
Indices: 110325244--110325355 Score: 120
Period size: 47 Copynumber: 2.4 Consensus size: 47
110325234 CCGGGATAAG
* * * *
110325244 CACATAGTGTTTCATCGAAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGTCTCATCGAAACAAATCCGAAACTTTAACAGTATAGTA
* * * *
110325291 CACAAAGT-ACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGTC-TCATCGAAACAAATCCGAAACTTTAACAGTA-TAGTA
110325338 CACATAGTGTCTCATCGA
1 CACATAGTGTCTCATCGA
110325356 CTCAATGTCG
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
47 48 0.94
48 3 0.06
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (47 bp):
CACATAGTGTCTCATCGAAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:110327704 original size:47 final size:47
Alignment explanation
Indices: 110327607--110327717 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
110327597 CCGGGATAAG
* * * *
110327607 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
110327654 CACAAAGTACTTCATCGGAACAAATTCGAAACTTTAACAGTAGTCG-A
1 CACATAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
110327701 CACATAGTA-TCTCATCG
1 CACATAGTACT-TCATCG
110327718 ACTCAATGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 1 0.02
47 51 0.94
48 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (47 bp):
CACATAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:110334392 original size:26 final size:27
Alignment explanation
Indices: 110334363--110334418 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
110334353 TTTCCATATG
* *
110334363 ACCAATTCTTGTA-AA-CATTTCATACA
1 ACCAATT-TTGTATAACCAATTCATAAA
110334389 ACC-ATTTTGTATAACCAATTCATAAA
1 ACCAATTTTGTATAACCAATTCATAAA
110334415 ACCA
1 ACCA
110334419 TTCATCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 5 0.20
25 5 0.20
26 15 0.60
ACGTcount: A:0.41, C:0.23, G:0.04, T:0.32
Consensus pattern (27 bp):
ACCAATTTTGTATAACCAATTCATAAA
Found at i:110334568 original size:46 final size:46
Alignment explanation
Indices: 110334503--110334640 Score: 206
Period size: 46 Copynumber: 3.0 Consensus size: 46
110334493 TTTATTTCGA
* * * * *
110334503 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCACTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGT
*
110334549 CATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
110334595 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
110334641 TACGTTGTAA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 4 0.05
46 80 0.95
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
Found at i:110336829 original size:44 final size:45
Alignment explanation
Indices: 110336739--110336867 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
110336729 GACAGAACGA
*
110336739 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
110336785 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
110336829 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
110336868 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:110344210 original size:44 final size:45
Alignment explanation
Indices: 110344120--110344248 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
110344110 GACAGAACGA
*
110344120 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
110344166 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
110344210 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
110344249 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:110345994 original size:14 final size:15
Alignment explanation
Indices: 110345975--110346054 Score: 101
Period size: 15 Copynumber: 5.4 Consensus size: 15
110345965 CAAAGATAAC
*
110345975 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
110345989 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
110346004 AAGAAACCCAGAATA
1 AAGAAATCCAGAATA
110346019 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
110346034 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
110346049 AAGAAA
1 AAGAAA
110346055 CCCAAGATAC
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
14 9 0.16
15 47 0.82
16 1 0.02
ACGTcount: A:0.60, C:0.14, G:0.16, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:110346006 original size:15 final size:15
Alignment explanation
Indices: 110345986--110346063 Score: 88
Period size: 15 Copynumber: 5.2 Consensus size: 15
110345976 AGAAAACCGA
110345986 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
110346001 ATAAAGAAA-CCCAG
1 ATAAAGAAATCCAAG
110346015 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
110346030 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
110346046 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
110346061 ATA
1 ATA
110346064 CGATACTATG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.07
15 47 0.87
16 3 0.06
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:110346020 original size:30 final size:30
Alignment explanation
Indices: 110345975--110346063 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
110345965 CAAAGATAAC
110345975 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
*
110346004 AAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
110346034 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
110346064 CGATACTATG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 10 0.19
30 40 0.77
31 2 0.04
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:110348054 original size:46 final size:46
Alignment explanation
Indices: 110347987--110348133 Score: 150
Period size: 58 Copynumber: 2.9 Consensus size: 46
110347977 GATATTACAT
* *
110347987 ACGTTGCTATGGTATCTTTCAACCATGGTCTTACACATTTCATGTC
1 ACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATC
110348033 ACGTTGCCATGGTATCTTTCAACCATGGTTTCAACCATGGTCTTACACATTTCATATC
1 ACGTTGCCATGGTA----T----C----TTTCAACCATGGTCTTACACATTTCATATC
* *
110348091 ATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 ACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
110348134 TTCAGAGAGC
Statistics
Matches: 85, Mismatches: 4, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
46 40 0.47
50 2 0.02
54 2 0.02
58 41 0.48
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.37
Consensus pattern (46 bp):
ACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATC
Found at i:110348065 original size:58 final size:58
Alignment explanation
Indices: 110348003--110348119 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
110347993 CTATGGTATC
* *
110348003 TTTCAACCATGGTCTTACACATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGG
1 TTTCAACCATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGG
*
110348061 TTTCAACCATGGTCTTACACATTTCATATCATGCTGCCATGGTATCTTTCAACCATGG
1 TTTCAACCATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGG
110348119 T
1 T
110348120 CTTACACATT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.37
Consensus pattern (58 bp):
TTTCAACCATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGG
Found at i:110348066 original size:12 final size:12
Alignment explanation
Indices: 110348049--110348073 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
110348039 CCATGGTATC
110348049 TTTCAACCATGG
1 TTTCAACCATGG
110348061 TTTCAACCATGG
1 TTTCAACCATGG
110348073 T
1 T
110348074 CTTACACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTCAACCATGG
Found at i:110350273 original size:11 final size:11
Alignment explanation
Indices: 110350257--110350309 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
110350247 TATACTAAAT
110350257 AAATAATAATA
1 AAATAATAATA
110350268 AAATAATAAT-
1 AAATAATAATA
* *
110350278 AAATATCTCATTA
1 AAATA-AT-AATA
*
110350291 AAATATTAATA
1 AAATAATAATA
110350302 AAATAATA
1 AAATAATA
110350310 TTTATCTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 5 0.15
11 21 0.62
12 3 0.09
13 5 0.15
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATAATA
Found at i:110350316 original size:31 final size:33
Alignment explanation
Indices: 110350257--110350322 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
110350247 TATACTAAAT
*
110350257 AAATAATAATAAAATAATAATAAATATCTCATTA
1 AAATAATAATAAAATAATAAT-AATATCTAATTA
* *
110350291 AAATATTAATAAAATAAT-AT-TTATCTAATTA
1 AAATAATAATAAAATAATAATAATATCTAATTA
110350322 A
1 A
110350323 TTAATTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 10 0.34
33 2 0.07
34 17 0.59
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (33 bp):
AAATAATAATAAAATAATAATAATATCTAATTA
Found at i:110351074 original size:12 final size:12
Alignment explanation
Indices: 110351057--110351103 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
110351047 ATGGTTGAAC
*
110351057 ATGATTTTTTTA
1 ATGATTTATTTA
110351069 ATGATTTATTT-
1 ATGATTTATTTA
*
110351080 A-G-TTTTTTTA
1 ATGATTTATTTA
110351090 ATGATTTATTTA
1 ATGATTTATTTA
110351102 AT
1 AT
110351104 CGAATTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 2 0.07
12 19 0.66
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.64
Consensus pattern (12 bp):
ATGATTTATTTA
Found at i:110351087 original size:21 final size:21
Alignment explanation
Indices: 110351061--110351101 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
110351051 TTGAACATGA
110351061 TTTTTTTAATGATTTATTTAG
1 TTTTTTTAATGATTTATTTAG
110351082 TTTTTTTAATGATTTATTTA
1 TTTTTTTAATGATTTATTTA
110351102 ATCGAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
TTTTTTTAATGATTTATTTAG
Found at i:110353330 original size:4 final size:4
Alignment explanation
Indices: 110353323--110353353 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
110353313 TTTATATCTT
110353323 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
110353354 TTCTTTGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:110367619 original size:38 final size:38
Alignment explanation
Indices: 110367575--110367647 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
110367565 TTATAAAAAA
110367575 ACAATTACATATTAAAAGGATAAACCCAAAGAAAACCG
1 ACAATTACATATTAAAAGGATAAACCCAAAGAAAACCG
110367613 ACAATTACATATTAAAAGGATAAACCCAAAGAAAA
1 ACAATTACATATTAAAAGGATAAACCCAAAGAAAA
110367648 AAAAACAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.58, C:0.16, G:0.10, T:0.16
Consensus pattern (38 bp):
ACAATTACATATTAAAAGGATAAACCCAAAGAAAACCG
Found at i:110370342 original size:41 final size:39
Alignment explanation
Indices: 110370227--110370348 Score: 108
Period size: 37 Copynumber: 3.1 Consensus size: 39
110370217 ACCCAATGCT
* *
110370227 TCATCGAATAATTCGAAGTAATAACTTGACACCCAGTGTC
1 TCATCGAATAATTCGAAGTAATAAATTGACA-CTAGTGTC
** ** *
110370267 TCATCGGCTAAACCGAAG---TAAATT-AGCATCTAGTGCC
1 TCATCGAATAATTCGAAGTAATAAATTGA-CA-CTAGTGTC
110370304 TCATCGAATATATTCGAAGTAATAAATTGACACGTAGTGTC
1 TCATCGAATA-ATTCGAAGTAATAAATTGACAC-TAGTGTC
110370345 TCAT
1 TCAT
110370349 TGACTCGAAG
Statistics
Matches: 62, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
36 1 0.02
37 21 0.34
38 6 0.10
40 15 0.24
41 18 0.29
42 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (39 bp):
TCATCGAATAATTCGAAGTAATAAATTGACACTAGTGTC
Found at i:110370936 original size:18 final size:19
Alignment explanation
Indices: 110370910--110370945 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
110370900 TAAACTAAAT
*
110370910 TTAACTCCCT-AATTTCAC
1 TTAAATCCCTAAATTTCAC
110370928 TTAAATCCCTAAATTTCA
1 TTAAATCCCTAAATTTCA
110370946 AATTTTCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATCCCTAAATTTCAC
Found at i:110372043 original size:21 final size:21
Alignment explanation
Indices: 110372019--110372073 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
110372009 ATAGCGGTGA
* * *
110372019 CGGTAAGATTAGTTACTGTAG
1 CGGTGAGATTAGATAATGTAG
110372040 CGGTGAGATTAGATAATGTAG
1 CGGTGAGATTAGATAATGTAG
*
110372061 CAGTGAGATTAGA
1 CGGTGAGATTAGA
110372074 AACAATGGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.07, G:0.31, T:0.29
Consensus pattern (21 bp):
CGGTGAGATTAGATAATGTAG
Found at i:110375524 original size:22 final size:20
Alignment explanation
Indices: 110375499--110375544 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
110375489 AAATTTTAAT
*
110375499 TTAAAATCTATTTAATTTATTA
1 TTAAAATAT-TTTAA-TTATTA
110375521 TT-AAATATTTTAATTATTA
1 TTAAAATATTTTAATTATTA
110375540 TTAAA
1 TTAAA
110375545 TTTAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 8 0.36
20 7 0.32
21 5 0.23
22 2 0.09
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAAAATATTTTAATTATTA
Found at i:110375548 original size:16 final size:18
Alignment explanation
Indices: 110375507--110375553 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
110375497 ATTTAAAATC
110375507 TATTTAATTTATTATTAAA
1 TATTTAA-TTATTATTAAA
110375526 TATTTTAATTATTATT-AA
1 TA-TTTAATTATTATTAAA
110375544 -ATTTAATTAT
1 TATTTAATTAT
110375554 AAATTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 9 0.33
17 1 0.04
18 2 0.07
19 10 0.37
20 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTAATTATTATTAAA
Found at i:110376223 original size:14 final size:13
Alignment explanation
Indices: 110376192--110376230 Score: 55
Period size: 11 Copynumber: 3.1 Consensus size: 13
110376182 ATTATATTTT
110376192 TTAAAAAATAATA
1 TTAAAAAATAATA
110376205 -T-AAAAATAATA
1 TTAAAAAATAATA
110376216 TTAAAAAATTAATA
1 TTAAAAAA-TAATA
110376230 T
1 T
110376231 GTGCGGACGC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 10 0.43
12 2 0.09
13 5 0.22
14 6 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TTAAAAAATAATA
Found at i:110376884 original size:23 final size:23
Alignment explanation
Indices: 110376835--110376884 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
110376825 TATAATTTTT
* **
110376835 TAAATTAAAAATATAAAATTAGT
1 TAAATTAAAAATATAAAATAAAA
110376858 TAAATTGAAAAATA-AAAATAAAA
1 TAAATT-AAAAATATAAAATAAAA
110376881 TAAA
1 TAAA
110376885 AAATAAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (23 bp):
TAAATTAAAAATATAAAATAAAA
Found at i:110380624 original size:20 final size:20
Alignment explanation
Indices: 110380588--110380626 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
110380578 TCTTTCTTAG
*
110380588 TCTCTTTTTCTTCTCTTCCA
1 TCTCTTTTTCCTCTCTTCCA
110380608 TCTCTTTTCTCCT-TCTTCC
1 TCTCTTTT-TCCTCTCTTCC
110380627 TTAGAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (20 bp):
TCTCTTTTTCCTCTCTTCCA
Found at i:110384428 original size:107 final size:108
Alignment explanation
Indices: 110384228--110384443 Score: 407
Period size: 107 Copynumber: 2.0 Consensus size: 108
110384218 AAAAAACACG
110384228 TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTGTTAGAAATTTTATTATTT
1 TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTGTTAGAAATTTTATTATTT
110384293 AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA
66 AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA
*
110384336 TCAAAAATTTTAT-AGAGTAATTAACAAAAATTTTAATACAATTTTGTTTGAAATTTTATTATTT
1 TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTGTTAGAAATTTTATTATTT
*
110384400 AAAACTTATTCTAACTTAACATATCATTGTTTTGTTAAACTAA
66 AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA
110384443 T
1 T
110384444 TTTTTGTTTA
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
107 93 0.88
108 13 0.12
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (108 bp):
TCAAAAATTTTATCAGAGTAATTAACAAAAATTTTAATACAATTTTGTTAGAAATTTTATTATTT
AAAACTTATTCCAACTTAACATATCATTGTTTTGTTAAACTAA
Found at i:110385279 original size:158 final size:158
Alignment explanation
Indices: 110384991--110385306 Score: 632
Period size: 158 Copynumber: 2.0 Consensus size: 158
110384981 TTAGGGGACC
110384991 GTGTTTGTGTTTAGCAGAACCATTGAAATAGTTAAAGGTCAAGAGAGATGGGCCTATGGAAGGCA
1 GTGTTTGTGTTTAGCAGAACCATTGAAATAGTTAAAGGTCAAGAGAGATGGGCCTATGGAAGGCA
110385056 GACTTCTAGTTCTTGGTTAGGCACTCACCCAACTTCTGTGATAATCTAAAGGAAGTGCTCTGGAT
66 GACTTCTAGTTCTTGGTTAGGCACTCACCCAACTTCTGTGATAATCTAAAGGAAGTGCTCTGGAT
110385121 TTAAGGTACTTGCAAATGTGTCTTACAT
131 TTAAGGTACTTGCAAATGTGTCTTACAT
110385149 GTGTTTGTGTTTAGCAGAACCATTGAAATAGTTAAAGGTCAAGAGAGATGGGCCTATGGAAGGCA
1 GTGTTTGTGTTTAGCAGAACCATTGAAATAGTTAAAGGTCAAGAGAGATGGGCCTATGGAAGGCA
110385214 GACTTCTAGTTCTTGGTTAGGCACTCACCCAACTTCTGTGATAATCTAAAGGAAGTGCTCTGGAT
66 GACTTCTAGTTCTTGGTTAGGCACTCACCCAACTTCTGTGATAATCTAAAGGAAGTGCTCTGGAT
110385279 TTAAGGTACTTGCAAATGTGTCTTACAT
131 TTAAGGTACTTGCAAATGTGTCTTACAT
110385307 ATAACAATAA
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 158 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (158 bp):
GTGTTTGTGTTTAGCAGAACCATTGAAATAGTTAAAGGTCAAGAGAGATGGGCCTATGGAAGGCA
GACTTCTAGTTCTTGGTTAGGCACTCACCCAACTTCTGTGATAATCTAAAGGAAGTGCTCTGGAT
TTAAGGTACTTGCAAATGTGTCTTACAT
Found at i:110387613 original size:12 final size:12
Alignment explanation
Indices: 110387593--110387640 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
110387583 TGTCATTAAC
*
110387593 ATATGAAACCAA
1 ATATAAAACCAA
*
110387605 ATATAAAACTTTAA
1 ATATAAAAC--CAA
110387619 CATATAAAACCAA
1 -ATATAAAACCAA
110387632 ATATAAAAC
1 ATATAAAAC
110387641 TTTACTCCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 17 0.57
13 2 0.07
14 2 0.07
15 9 0.30
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (12 bp):
ATATAAAACCAA
Found at i:110387625 original size:15 final size:14
Alignment explanation
Indices: 110387603--110387644 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
110387593 ATATGAAACC
110387603 AAATATAAAACTTT
1 AAATATAAAACTTT
*
110387617 AACATATAAAAC--C
1 AA-ATATAAAACTTT
110387630 AAATATAAAACTTT
1 AAATATAAAACTTT
110387644 A
1 A
110387645 CTCCCACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
12 9 0.39
13 2 0.09
14 3 0.13
15 9 0.39
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATATAAAACTTT
Found at i:110387628 original size:27 final size:27
Alignment explanation
Indices: 110387588--110387644 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
110387578 CAGTATGTCA
*
110387588 TTAACATATGAAACCAAATATAAAACT
1 TTAACATATAAAACCAAATATAAAACT
110387615 TTAACATATAAAACCAAATATAAAACT
1 TTAACATATAAAACCAAATATAAAACT
110387642 TTA
1 TTA
110387645 CTCCCACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (27 bp):
TTAACATATAAAACCAAATATAAAACT
Found at i:110396105 original size:18 final size:18
Alignment explanation
Indices: 110396078--110396116 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
110396068 AAACCTATAC
* *
110396078 TAATATTACATATAATAA
1 TAATACTACAAATAATAA
*
110396096 TAATACTACAAATAGTAA
1 TAATACTACAAATAATAA
110396114 TAA
1 TAA
110396117 CTAATAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (18 bp):
TAATACTACAAATAATAA
Found at i:110396213 original size:21 final size:21
Alignment explanation
Indices: 110396168--110396239 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 21
110396158 TCAGGATGCC
*
110396168 AATAATAACAATAATATTAGGAAA
1 AATAATAACAAT-ATA-TA-AAAA
110396192 AATAATAACAATATATAAAAA
1 AATAATAACAATATATAAAAA
* * *
110396213 ACGAAAATAA-AATAAATAAATA
1 A--ATAATAACAATATATAAAAA
110396235 AATAA
1 AATAA
110396240 AATGAAAAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.07
21 4 0.10
22 13 0.32
23 9 0.22
24 12 0.29
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (21 bp):
AATAATAACAATATATAAAAA
Found at i:110398373 original size:75 final size:75
Alignment explanation
Indices: 110398250--110398417 Score: 246
Period size: 75 Copynumber: 2.2 Consensus size: 75
110398240 AGTAAAAATT
* * * *
110398250 AAAAACAGAATTTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAATT
1 AAAAATAGAATTTGAAAATACCTCAGCGTGCCCCGAGGCCCAACTCACCTCTCGCAATATGAATT
110398315 GATTTTTTTG
66 GATTTTTTTG
* * * *
110398325 AAAAATAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCCCAACTCACCTGTCGCAATATGAGTT
1 AAAAATAGAATTTGAAAATACCTCAGCGTGCCCCGAGGCCCAACTCACCTCTCGCAATATGAATT
110398390 GATTTTTTTG
66 GATTTTTTTG
* *
110398400 CAAAGTAGAATTTGAAAA
1 AAAAATAGAATTTGAAAA
110398418 ACAGAAATTG
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 81 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (75 bp):
AAAAATAGAATTTGAAAATACCTCAGCGTGCCCCGAGGCCCAACTCACCTCTCGCAATATGAATT
GATTTTTTTG
Found at i:110398472 original size:89 final size:87
Alignment explanation
Indices: 110398321--110399012 Score: 809
Period size: 89 Copynumber: 7.9 Consensus size: 87
110398311 AATTGATTTT
* * * * * *
110398321 TTTGAAAAATAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCCCAACTCACCTGTCGCAATATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
* *
110398386 AGTTGATTTTTTTGCAAAGTAGAA
66 AGTTGA--TTTTTGAAAAATAGAA
* *
110398410 TTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATA
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
*
110398475 AGTTGATTTTTGAAAAGTAGAA
66 AGTTGATTTTTGAAAAATAGAA
* * * *
110398497 ATTGAAAAACATAAATTGAAATTACCTCAGCGTGTGAGCC-AAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGT---CCTGAGGCTCAACTCACCTCTCGCAAT
*
110398561 ATGAGTTGATTTTTGAAAAATATAGA
63 ATGAGTTGATTTTTGAAAAATAGA-A
* * *
110398587 -TTGAAAAAAATAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCACAATA
1 TTTG--AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
* *
110398651 TGAGTTGA---TTCAAAAACAGACA
64 TGAGTTGATTTTTGAAAAATAGA-A
*
110398673 -TT-AAGAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
*
110398736 AGTTGATTTTTGAAAAATATAGA
66 AGTTGATTTTTGAAAAATAGA-A
* * *
110398759 TTGGAAAAACAGAAATTGAAAATACCTTATCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
*
110398824 AGTTCG---TTT-AAAAACAGAAA
66 AGTT-GATTTTTGAAAAATAG-AA
** *
110398844 TTTGAAAAACAGATTTTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTTACCTCTCGCAATATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
110398909 AGTTGATTTTTGAAAACAT-GAA
66 AGTTGATTTTTGAAAA-ATAGAA
** * * *
110398931 TTAAAAAAATAGAAATTGAAAATACCTCGGCATGCGAG-CC-AAGGCTCAACTCACCTCTCGCAA
1 TTTGAAAAACAGAAATTGAAAATACCT---CA-GCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
*
110398994 TATGAGTTGATTTCTGAAA
62 TATGAGTTGATTTTTGAAA
110399013 GCAGAAATAA
Statistics
Matches: 527, Mismatches: 53, Indels: 46
0.84 0.08 0.07
Matches are distributed among these distances:
83 63 0.12
84 1 0.00
85 70 0.13
86 26 0.05
87 76 0.14
88 68 0.13
89 184 0.35
90 7 0.01
91 32 0.06
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (87 bp):
TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTGAAAAATAGAA
Found at i:110398597 original size:16 final size:16
Alignment explanation
Indices: 110398573--110398609 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
110398563 GAGTTGATTT
*
110398573 TTGAAAAATATAG--A
1 TTGAAAAAAATAGAAA
110398587 TTGAAAAAAATAGAAA
1 TTGAAAAAAATAGAAA
110398603 TTGAAAA
1 TTGAAAA
110398610 TACCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 12 0.60
16 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (16 bp):
TTGAAAAAAATAGAAA
Found at i:110398861 original size:14 final size:15
Alignment explanation
Indices: 110398833--110398865 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
110398823 GAGTTCGTTT
110398833 AAAAACAGAAATTTG
1 AAAAACAGAAATTTG
*
110398848 AAAAACAG-ATTTTG
1 AAAAACAGAAATTTG
110398862 AAAA
1 AAAA
110398866 TACCTCAGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.21
Consensus pattern (15 bp):
AAAAACAGAAATTTG
Found at i:110398951 original size:434 final size:422
Alignment explanation
Indices: 110398022--110399012 Score: 1144
Period size: 434 Copynumber: 2.3 Consensus size: 422
110398012 GTGATCTTGA
** * * * * *
110398022 GCTCAACTCATTTCTCGCAATATGAATTGACTCTTTAAATAACATAAACT-AAAAAATAGAAATT
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAA-AACATGAATTAAAAAAATAGAAATT
* * *
110398086 GAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGGTCTTTTTG-
64 GAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTT-G-ATTTTTGA
* * *** * *
110398150 AAACTTAATTTGAAAAGTAGGTTTTGAAAGTACCTCGTCATGTGACCCGAGGCTCAACTCATCTC
127 AAAATTAATTTGAAAAATAGAAATTGAAAATACCTCGTCA-GTGACCCGAGGCTCAACTCACCTC
* * * *
110398215 TCGCAATATGAGTTGATTTTTAAAAAGTAAAAATTAAAAACAGAATTTGAAAATACCTCAGCGTG
191 TCACAATATGAGTTGA-TTTCAAAAAGCAAAAATTAAAAACAGAAATTGAAAATACCTCAGCGTG
* *
110398280 TCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGAAAAATAGAAATTGAAATTA
255 TCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGAAAAACAGAAATTGAAAATA
* ***
110398345 CCTCAGCGTGCCCCGAGGCCCAACTCACCTGTCGCAATATGAGTTGATTTTTTTGCAAAGTAGAA
320 CCTCAGCGTGCCCCGAGGCCCAACTCACCTCTCGCAATATGAGTTG---TTTTAAAAAAGTAGAA
*
110398410 TTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAG
382 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAG
* * *
110398451 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAA-GTAGAAATTGAAAAACAT--AAAT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAT-G-AATT-AAAAAAATAGAAAT
*
110398513 TGAAATTACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
63 TGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
* **
110398578 AAATATAGA-TTGAAAAAAATAGAAATTGAAAATACCTCAG-C-GTGTCTTGAGGCTCAACTCAC
128 AAAT-TA-ATTTG--AAAAATAGAAATTGAAAATACCTC-GTCAGTGACCCGAGGCTCAACTCAC
* * *
110398640 CTCTCACAATATGAGTTGA-TTCAAAAA-CAGACATTAAGAACAGAAATTGAAAATACCTCAGCG
188 CTCTCACAATATGAGTTGATTTCAAAAAGCAAAAATTAAAAACAGAAATTGAAAATACCTCAGCG
*
110398703 TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAGATTGGAAAAA
253 TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGA--TTT------T-T---TT-GAAAAA
* * * * *
110398768 CAGAAATTGAAAATACCTTATCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTCG-TT
305 CAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCCCAACTCACCTCTCGCAATATGAGTT-GTTT
**
110398832 TAAAAACAG-A-AATTTGAAAAACAGATTTTGAAAATACCTCAGCGTGTCCTGAG
369 TAAAAA-AGTAGAATTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAG
*
110398885 GCTCAACTTACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTAAAAAAATAGAAATTGA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTAAAAAAATAGAAATTGA
* * * *
110398950 AAATACCTCGGCATGCGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTCTGAAA
66 AAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
110399013 GCAGAAATAA
Statistics
Matches: 479, Mismatches: 55, Indels: 51
0.82 0.09 0.09
Matches are distributed among these distances:
425 69 0.14
426 14 0.03
427 10 0.02
428 105 0.22
429 27 0.06
430 26 0.05
431 1 0.00
432 7 0.01
433 5 0.01
434 145 0.30
435 7 0.01
436 2 0.00
437 2 0.00
438 58 0.12
439 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (422 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTAAAAAAATAGAAATTGA
AAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
TTAATTTGAAAAATAGAAATTGAAAATACCTCGTCAGTGACCCGAGGCTCAACTCACCTCTCACA
ATATGAGTTGATTTCAAAAAGCAAAAATTAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGA
GGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAG
CGTGCCCCGAGGCCCAACTCACCTCTCGCAATATGAGTTGTTTTAAAAAAGTAGAATTTGAAAAA
CAGAAATTGAAAATACCTCAGCGTGTCCTGAG
Found at i:110411930 original size:12 final size:12
Alignment explanation
Indices: 110411913--110411978 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
110411903 TCAGGATGTC
110411913 AATAATAACAAT
1 AATAATAACAAT
110411925 AATAATAGA-AAT
1 AATAATA-ACAAT
**
110411937 AATAATATTAAT
1 AATAATAACAAT
* ** *
110411949 AATATTAGGAAA
1 AATAATAACAAT
110411961 AATAATAACAAT
1 AATAATAACAAT
110411973 ATATAA
1 A-ATAA
110411979 AAACGAAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
12 37 0.88
13 5 0.12
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.29
Consensus pattern (12 bp):
AATAATAACAAT
Found at i:110412596 original size:15 final size:15
Alignment explanation
Indices: 110412576--110412604 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
110412566 TCCTTTTTTT
110412576 TATTTTTTTATATTA
1 TATTTTTTTATATTA
110412591 TATTTTTTTATATT
1 TATTTTTTTATATT
110412605 TGCAATATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTTTTTATATTA
Found at i:110414913 original size:31 final size:31
Alignment explanation
Indices: 110414857--110414915 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
110414847 CTAACTATGC
*
110414857 AATTGTTCCCATATTGAGACATAAACTTGAT
1 AATTGTTCCCATATGGAGACATAAACTTGAT
*
110414888 AATTGTTCCCATAGTGGAGA-TTAAACTT
1 AATTGTTCCCATA-TGGAGACATAAACTT
110414916 TAAGGTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (31 bp):
AATTGTTCCCATATGGAGACATAAACTTGAT
Found at i:110427171 original size:5 final size:5
Alignment explanation
Indices: 110427161--110427194 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
110427151 AAATGTTGAA
110427161 GGGTC GGGTC GGGTC GGGTC GGGTC GGGTC GGGT
1 GGGTC GGGTC GGGTC GGGTC GGGTC GGGTC GGGT
110427195 TTATATCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.18, G:0.62, T:0.21
Consensus pattern (5 bp):
GGGTC
Found at i:110427360 original size:50 final size:50
Alignment explanation
Indices: 110427283--110427380 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
110427273 TAAACTCAAT
* * * *
110427283 TTAATTTAAGAATAGTAAATTTGGGTTCGACCTGATTCATCTGTATTTGA
1 TTAATTTAAGAAAAGTAAATTTAGGTTCGACCCGATTCATCTATATTTGA
*
110427333 TTAATTTAA-AAAAGGTAAATTTAGGTTCGACCCGGTTCATCTATATTT
1 TTAATTTAAGAAAA-GTAAATTTAGGTTCGACCCGATTCATCTATATTT
110427381 AATTTTTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 3 0.07
50 39 0.93
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (50 bp):
TTAATTTAAGAAAAGTAAATTTAGGTTCGACCCGATTCATCTATATTTGA
Found at i:110427649 original size:2 final size:2
Alignment explanation
Indices: 110427630--110427664 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
110427620 TAGTGATTTA
* *
110427630 AT AT AA AT AT AA AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
110427665 ATTATTACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:110429459 original size:39 final size:39
Alignment explanation
Indices: 110429405--110429482 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
110429395 AGTTTACTCG
110429405 AGCACAAATAAAGATAAAATTTAAACATTTTTTTAAAGT
1 AGCACAAATAAAGATAAAATTTAAACATTTTTTTAAAGT
110429444 AGCACAAATAAAGATAAAATTTAAACATTTTTTTAAAGT
1 AGCACAAATAAAGATAAAATTTAAACATTTTTTTAAAGT
110429483 TAAAGACAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (39 bp):
AGCACAAATAAAGATAAAATTTAAACATTTTTTTAAAGT
Found at i:110434348 original size:22 final size:21
Alignment explanation
Indices: 110434307--110434348 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
110434297 TTTATCAGTC
*
110434307 AATTTCTCAATTCCATATCAT
1 AATTTCTCAATTCAATATCAT
110434328 AATTTCATCAA-TCAATCATCA
1 AATTTC-TCAATTCAAT-ATCA
110434349 ATTCACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTTCTCAATTCAATATCAT
Found at i:110435943 original size:21 final size:21
Alignment explanation
Indices: 110435900--110435943 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
110435890 TTACTATAGA
* *
110435900 AAGTGACTTGACTTGTTTCGC
1 AAGTAACTTGACTTGTCTCGC
110435921 AAGTAACTTGACTTGATCT-GC
1 AAGTAACTTGACTTG-TCTCGC
110435942 AA
1 AA
110435944 TAAATCAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (21 bp):
AAGTAACTTGACTTGTCTCGC
Found at i:110443036 original size:18 final size:18
Alignment explanation
Indices: 110443013--110443073 Score: 113
Period size: 18 Copynumber: 3.4 Consensus size: 18
110443003 GTTCATTGTT
110443013 ATTCAGTAACAATCAGTC
1 ATTCAGTAACAATCAGTC
*
110443031 ATTCAGTAACAATCAATC
1 ATTCAGTAACAATCAGTC
110443049 ATTCAGTAACAATCAGTC
1 ATTCAGTAACAATCAGTC
110443067 ATTCAGT
1 ATTCAGT
110443074 GTATTTATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (18 bp):
ATTCAGTAACAATCAGTC
Found at i:110444186 original size:16 final size:16
Alignment explanation
Indices: 110444146--110444205 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
110444136 TTATTCTTTT
*
110444146 ATTTAAT-TTTTATTA
1 ATTTAATATTATATTA
*
110444161 ATTGT-TTATTATATT-
1 ATT-TAATATTATATTA
110444176 ATTCTAATATTATATTA
1 ATT-TAATATTATATTA
110444193 ATTTAATAATTAT
1 ATTTAAT-ATTAT
110444206 GACCGGTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
15 8 0.22
16 20 0.56
17 8 0.22
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTAATATTATATTA
Found at i:110446239 original size:28 final size:28
Alignment explanation
Indices: 110446207--110446263 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
110446197 GAAAGTTTCG
110446207 ATAATGTAACGACTTTTGAAAGCCCCGT
1 ATAATGTAACGACTTTTGAAAGCCCCGT
110446235 ATAATGTAACGACTTTTGAAAGCCCCGT
1 ATAATGTAACGACTTTTGAAAGCCCCGT
110446263 A
1 A
110446264 CGAACCATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (28 bp):
ATAATGTAACGACTTTTGAAAGCCCCGT
Found at i:110446447 original size:43 final size:42
Alignment explanation
Indices: 110446369--110446475 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 42
110446359 GAGATTTATG
*
110446369 TGTAAGACCATGTCTAGGACATCAGCAGCGTATTTGATTTCA
1 TGTAAGACCATGTCTAGGACATCAGCAGCGTATTTGATTACA
* * *
110446411 TGTAAGACCCTGTCTAGGACAGTGA-CATCGATATTTGATTACA
1 TGTAAGACCATGTCTAGGACA-TCAGCAGCG-TATTTGATTACA
* *
110446454 TGTAAGACCACGTCTGGGACAT
1 TGTAAGACCATGTCTAGGACAT
110446476 TGGCATTGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 25 0.45
43 31 0.55
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATGTCTAGGACATCAGCAGCGTATTTGATTACA
Found at i:110447176 original size:23 final size:22
Alignment explanation
Indices: 110447145--110447187 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
110447135 TTTCGAAACA
*
110447145 TATGTTTTGGTATGACTTTGGCT
1 TATGATTTGGTATGA-TTTGGCT
110447168 TATGATTTGGTATGATTTGG
1 TATGATTTGGTATGATTTGG
110447188 TATGGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.16, C:0.05, G:0.28, T:0.51
Consensus pattern (22 bp):
TATGATTTGGTATGATTTGGCT
Found at i:110447183 original size:10 final size:10
Alignment explanation
Indices: 110447145--110447196 Score: 59
Period size: 10 Copynumber: 4.8 Consensus size: 10
110447135 TTTCGAAACA
*
110447145 TATGTTTTGG
1 TATGATTTGG
110447155 TATGACTTTGG
1 TATGA-TTTGG
110447166 CTTATGATTTGG
1 --TATGATTTGG
110447178 TATGATTTGG
1 TATGATTTGG
110447188 TATGGATTT
1 TAT-GATTT
110447197 TAAGCATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 17 0.46
11 10 0.27
12 5 0.14
13 5 0.14
ACGTcount: A:0.17, C:0.04, G:0.27, T:0.52
Consensus pattern (10 bp):
TATGATTTGG
Found at i:110448376 original size:5 final size:5
Alignment explanation
Indices: 110448355--110448407 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
110448345 TGTTAAAATA
* *
110448355 TATAT TAAAT TATTAT TATAT TATAG TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
110448403 TATAT
1 TATAT
110448408 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.76
6 6 0.15
7 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:110448386 original size:10 final size:9
Alignment explanation
Indices: 110448352--110448408 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
110448342 ATGTGTTAAA
110448352 ATATATATT
1 ATATATATT
*
110448361 AAAT-TATT
1 ATATATATT
110448369 AT-TATATT
1 ATATATATT
110448377 ATAGTATATT
1 ATA-TATATT
110448387 ATAT-TA-T
1 ATATATATT
110448394 ATATTATATT
1 ATA-TATATT
110448404 ATATA
1 ATATA
110448409 AATAAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.35
9 8 0.20
10 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:110448398 original size:12 final size:12
Alignment explanation
Indices: 110448353--110448408 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
110448343 TGTGTTAAAA
*
110448353 TATATATTAAAT
1 TATATATTATAT
110448365 TAT-TATTATATT
1 TATATATTATA-T
110448377 ATAGTATATTATAT
1 -TA-TATATTATAT
110448391 TATATATTATAT
1 TATATATTATAT
110448403 TATATA
1 TATATA
110448409 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:110449749 original size:18 final size:19
Alignment explanation
Indices: 110449726--110449764 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
110449716 TTATATAGAT
110449726 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
110449744 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
110449763 AT
1 AT
110449765 TGAATCGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:110450114 original size:39 final size:39
Alignment explanation
Indices: 110450004--110450138 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
110449994 GACCTCGAGT
* * * *
110450004 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
110450045 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
110450083 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
110450122 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
110450139 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:110450282 original size:18 final size:19
Alignment explanation
Indices: 110450261--110450301 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
110450251 AATGAAATGA
110450261 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
110450279 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
110450298 GAAA
1 GAAA
110450302 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:110454143 original size:20 final size:20
Alignment explanation
Indices: 110454120--110454159 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
110454110 AAATTTTAGG
110454120 ATTTATTT-TCATTTATCTTT
1 ATTTATTTGT-ATTTATCTTT
110454140 ATTTATTTGTATTTATCTTT
1 ATTTATTTGTATTTATCTTT
110454160 TAGAATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (20 bp):
ATTTATTTGTATTTATCTTT
Found at i:110462550 original size:4 final size:4
Alignment explanation
Indices: 110462541--110462569 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
110462531 CCCTTTTCTA
110462541 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
110462570 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:110470923 original size:42 final size:42
Alignment explanation
Indices: 110470866--110470959 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
110470856 TGAGATTTAT
* *
110470866 GTGTAAGACCATGTCTGGGACA-TCGGCATC-ATATTTGATTTC
1 GTGTAAGA-CATGTCTGAGACAGT-GGCATCGATATTTGATTAC
110470908 GTGTAAGACATTGTCTGAGACAGTGGCATCGATATTTGATTAC
1 GTGTAAGACA-TGTCTGAGACAGTGGCATCGATATTTGATTAC
*
110470951 ATGTAAGAC
1 GTGTAAGAC
110470960 CACATCTGGG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
41 2 0.04
42 24 0.52
43 20 0.43
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (42 bp):
GTGTAAGACATGTCTGAGACAGTGGCATCGATATTTGATTAC
Found at i:110470978 original size:43 final size:43
Alignment explanation
Indices: 110470808--110470979 Score: 145
Period size: 43 Copynumber: 4.0 Consensus size: 43
110470798 CGTAGGATTC
* * *
110470808 CGATATGTGATTTCATGTAAGACCACATCTAGGACGTTGGCAT
1 CGATATTTGATTACATGTAAGACCACATCTGGGACGTTGGCAT
* ** ** * *
110470851 CGAT-TTGAGATTTATGTGTAAGACCATGTCTGGGACATCGGCAT
1 CGATATT-TGA-TTACATGTAAGACCACATCTGGGACGTTGGCAT
* * ** *
110470895 C-ATATTTGATTTCGTGTAAGA-CATTGTCTGAGACAG-TGGCAT
1 CGATATTTGATTACATGTAAGACCA-CATCTGGGAC-GTTGGCAT
110470937 CGATATTTGATTACATGTAAGACCACATCTGGGACGTTGGCAT
1 CGATATTTGATTACATGTAAGACCACATCTGGGACGTTGGCAT
110470980 TGTACAAGTT
Statistics
Matches: 100, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
41 2 0.02
42 27 0.27
43 41 0.41
44 30 0.30
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (43 bp):
CGATATTTGATTACATGTAAGACCACATCTGGGACGTTGGCAT
Found at i:110471219 original size:2 final size:2
Alignment explanation
Indices: 110471212--110471237 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
110471202 ATTCAGGGAA
110471212 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
110471238 TTTTACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110472171 original size:23 final size:22
Alignment explanation
Indices: 110472133--110472193 Score: 90
Period size: 21 Copynumber: 2.8 Consensus size: 22
110472123 GACACATAAA
*
110472133 GTGCCT-AAAACGACACACGAG
1 GTGCCTGAATACGACACACGAG
110472154 GTGCCTG-ATACGACACACGAG
1 GTGCCTGAATACGACACACGAG
110472175 GTGCCTGAAATACGACACA
1 GTGCCTG-AATACGACACA
110472194 TAAAGTGCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 26 0.72
23 10 0.28
ACGTcount: A:0.34, C:0.28, G:0.25, T:0.13
Consensus pattern (22 bp):
GTGCCTGAATACGACACACGAG
Found at i:110472201 original size:23 final size:23
Alignment explanation
Indices: 110472123--110472205 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 23
110472113 ATCAGTATAT
*
110472123 GACACATAAAGTGCCT-AAA-AC
1 GACACACAAAGTGCCTGAAATAC
* *
110472144 GACACACGAGGTGCCTG--ATAC
1 GACACACAAAGTGCCTGAAATAC
* *
110472165 GACACACGAGGTGCCTGAAATAC
1 GACACACAAAGTGCCTGAAATAC
*
110472188 GACACATAAAGTGCCTGA
1 GACACACAAAGTGCCTGA
110472206 TCAATAAAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.02
21 32 0.62
23 19 0.37
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.14
Consensus pattern (23 bp):
GACACACAAAGTGCCTGAAATAC
Found at i:110473683 original size:16 final size:17
Alignment explanation
Indices: 110473648--110473683 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
110473638 CCTAATTCTC
110473648 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
110473664 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
110473679 CCTTC
1 CCTTC
110473684 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:110474796 original size:23 final size:22
Alignment explanation
Indices: 110474765--110474807 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
110474755 TTATGAAACA
*
110474765 TATGTTTTGGTATGACTTTGGCT
1 TATGATTTGGTATGA-TTTGGCT
110474788 TATGATTTGGTATGATTTGG
1 TATGATTTGGTATGATTTGG
110474808 TATGGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.16, C:0.05, G:0.28, T:0.51
Consensus pattern (22 bp):
TATGATTTGGTATGATTTGGCT
Found at i:110474803 original size:10 final size:10
Alignment explanation
Indices: 110474765--110474816 Score: 59
Period size: 10 Copynumber: 4.8 Consensus size: 10
110474755 TTATGAAACA
*
110474765 TATGTTTTGG
1 TATGATTTGG
110474775 TATGACTTTGG
1 TATGA-TTTGG
110474786 CTTATGATTTGG
1 --TATGATTTGG
110474798 TATGATTTGG
1 TATGATTTGG
110474808 TATGGATTT
1 TAT-GATTT
110474817 TAAGCATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 17 0.46
11 10 0.27
12 5 0.14
13 5 0.14
ACGTcount: A:0.17, C:0.04, G:0.27, T:0.52
Consensus pattern (10 bp):
TATGATTTGG
Found at i:110483738 original size:16 final size:15
Alignment explanation
Indices: 110483713--110483749 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
110483703 AACATCTCCG
110483713 AAAAATAAAGAATAC
1 AAAAATAAAGAATAC
110483728 AAAACATAAAGAATAC
1 AAAA-ATAAAGAATAC
110483744 ACAAAA
1 A-AAAA
110483750 CTCTTGAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 13 0.65
17 3 0.15
ACGTcount: A:0.73, C:0.11, G:0.05, T:0.11
Consensus pattern (15 bp):
AAAAATAAAGAATAC
Found at i:110487756 original size:18 final size:18
Alignment explanation
Indices: 110487730--110487805 Score: 116
Period size: 18 Copynumber: 4.2 Consensus size: 18
110487720 ATTGTTATTT
*
110487730 AGTAACAATTAGTCATTC
1 AGTAACAATCAGTCATTC
* *
110487748 AGAAACAATCAATCATTC
1 AGTAACAATCAGTCATTC
*
110487766 AGTAACAATCAGTCATTT
1 AGTAACAATCAGTCATTC
110487784 AGTAACAATCAGTCATTC
1 AGTAACAATCAGTCATTC
110487802 AGTA
1 AGTA
110487806 TATTTATCTA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (18 bp):
AGTAACAATCAGTCATTC
Found at i:110488935 original size:16 final size:16
Alignment explanation
Indices: 110488914--110488944 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
110488904 TTTAATTAAT
*
110488914 ATAATACAATAATATA
1 ATAATAAAATAATATA
110488930 ATAATAAAATAATAT
1 ATAATAAAATAATAT
110488945 TTACTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATAAAATAATATA
Found at i:110498593 original size:5 final size:5
Alignment explanation
Indices: 110498583--110498624 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
110498573 TATCCTCCTC
* *
110498583 TTCTT TTC-T TTATT TTCTT TTACTT TTCTT TTCTT TTATT TT
1 TTCTT TTCTT TTCTT TTCTT TT-CTT TTCTT TTCTT TTCTT TT
110498625 ATTCTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 3 0.09
5 24 0.75
6 5 0.16
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (5 bp):
TTCTT
Found at i:110498625 original size:5 final size:5
Alignment explanation
Indices: 110498591--110498661 Score: 61
Period size: 5 Copynumber: 13.2 Consensus size: 5
110498581 TCTTCTTTTC
* * *
110498591 TTTAT TTTCT TTTACT TTTCT TTTCT TTTAT TTTATT CTTTAT TTTAT
1 TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTA-T -TTTAT TTTAT
*
110498639 TTTAAT TTTAT CTTTCT TTTAT T
1 TTT-AT TTTAT -TTTAT TTTAT T
110498662 CATCCTTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
5 36 0.65
6 15 0.27
7 4 0.07
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:110498641 original size:22 final size:22
Alignment explanation
Indices: 110498587--110498661 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
110498577 CTCCTCTTCT
* *
110498587 TTTC-TTTATTTTCTTTTACT-
1 TTTCTTTTATTTTATTTTATTC
*
110498607 TTTCTTTTCTTTTATTTTATTC
1 TTTCTTTTATTTTATTTTATTC
*
110498629 TTTATTTTATTTTAATTTTA-TC
1 TTTCTTTTATTTT-ATTTTATTC
110498651 TTTCTTTTATT
1 TTTCTTTTATT
110498662 CATCCTTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
22 23 0.50
23 6 0.13
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTCTTTTATTTTATTTTATTC
Found at i:110498642 original size:38 final size:39
Alignment explanation
Indices: 110498588--110498661 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
110498578 TCCTCTTCTT
* * *
110498588 TTCTTTATTTTCTTTTACTTTTCT-TTTCTTTTATTTTA
1 TTCTTTATTTTATTTTAATTTTATCTTTCTTTTATTTTA
110498626 TTCTTTATTTTATTTTAATTTTATCTTTCTTTTATT
1 TTCTTTATTTTATTTTAATTTTATCTTTCTTTTATT
110498662 CATCCTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 21 0.66
39 11 0.34
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.76
Consensus pattern (39 bp):
TTCTTTATTTTATTTTAATTTTATCTTTCTTTTATTTTA
Found at i:110498658 original size:11 final size:10
Alignment explanation
Indices: 110498586--110498661 Score: 64
Period size: 11 Copynumber: 7.2 Consensus size: 10
110498576 CCTCCTCTTC
110498586 TTTTC-TTTA
1 TTTTCTTTTA
110498595 TTTTCTTTTA
1 TTTTCTTTTA
*
110498605 CTTTTCTTTTC
1 -TTTTCTTTTA
*
110498616 TTTTATTTTA
1 TTTTCTTTTA
*
110498626 TTCTTTATTTTA
1 -T-TTTCTTTTA
*
110498638 TTTTAATTTTA
1 TTTT-CTTTTA
110498649 TCTTTCTTTTA
1 T-TTTCTTTTA
110498660 TT
1 TT
110498662 CATCCTTTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
9 5 0.09
10 16 0.28
11 24 0.42
12 12 0.21
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:110498670 original size:38 final size:38
Alignment explanation
Indices: 110498590--110498673 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
110498580 CTCTTCTTTT
* * * * *
110498590 CTTTATTTTCTTTTACTTTTCTTTTCTTTTATTTTATT
1 CTTTATTTTATTTTAATTTTATTTTCTTTTATTTCATC
110498628 CTTTATTTTATTTTAATTTTATCTTTCTTTTA-TTCATC
1 CTTTATTTTATTTTAATTTTAT-TTTCTTTTATTTCATC
110498666 CTTTATTT
1 CTTTATTT
110498674 ATCTACATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 31 0.77
39 9 0.22
ACGTcount: A:0.14, C:0.13, G:0.00, T:0.73
Consensus pattern (38 bp):
CTTTATTTTATTTTAATTTTATTTTCTTTTATTTCATC
Found at i:110511944 original size:31 final size:30
Alignment explanation
Indices: 110511871--110511951 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
110511861 AAATATTTTA
* * *
110511871 TAAAT-TTTAATACAATAATAAATGATATT
1 TAAATATTTAATATAATGATAAATCATATT
110511900 TAAATATTTAATATAATGATAAATCATATT
1 TAAATATTTAATATAATGATAAATCATATT
110511930 TAAATAGTTTAATATAATGATA
1 TAAATA-TTTAATATAATGATA
110511952 CATAAAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 5 0.11
30 27 0.57
31 15 0.32
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
TAAATATTTAATATAATGATAAATCATATT
Found at i:110511965 original size:31 final size:30
Alignment explanation
Indices: 110511869--110511965 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
110511859 TGAAATATTT
* * * *
110511869 TATAAAT-TTTAATACAATAATAAATGATA
1 TATAAATATTTAATATAATGATAAATAAAA
* * *
110511898 TTTAAATATTTAATATAATGATAAATCATA
1 TATAAATATTTAATATAATGATAAATAAAA
* *
110511928 TTTAAATAGTTTAATATAATGATACATAAAA
1 TATAAATA-TTTAATATAATGATAAATAAAA
110511959 TATAAAT
1 TATAAAT
110511966 TAATCTAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 6 0.10
30 27 0.47
31 25 0.43
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (30 bp):
TATAAATATTTAATATAATGATAAATAAAA
Found at i:110512931 original size:21 final size:19
Alignment explanation
Indices: 110512907--110512945 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
110512897 TATAGTTGCT
110512907 TATTAATTATATAATTTTTAC
1 TATT-ATTA-ATAATTTTTAC
*
110512928 TATTATTAATATTTTTTA
1 TATTATTAATAATTTTTA
110512946 TTAAATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATTAATAATTTTTAC
Done.