Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 182 of 211
Found at i:56298941 original size:26 final size:27
Alignment explanation
Indices: 56298890--56298943 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
56298880 TTTTTATTAT
* *
56298890 TATTATTATTTCTCTCATTTTAGTTCA
1 TATTATTACTTCTCTCATTGTAGTTCA
56298917 TATTGATTACTTCTCT-ATTGT-GTTCA
1 TATT-ATTACTTCTCTCATTGTAGTTCA
56298943 T
1 T
56298944 TTTGTGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.25
27 8 0.33
28 10 0.42
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (27 bp):
TATTATTACTTCTCTCATTGTAGTTCA
Found at i:56306242 original size:57 final size:58
Alignment explanation
Indices: 56306146--56306265 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 58
56306136 AGAAATGGTA
* ***
56306146 AAAATGGAGAAATGAGAAATATTTGGAAATGGTTATGGTTTTCTCCAAAATGAAAATG
1 AAAATAGAGAAATGAGAAATATTTGGAAATAAATATGGTTTTCTCCAAAATGAAAATG
* *
56306204 AAAATAGAGAAATG-G-AATCATTTGGAAATAAATGTGGTTTTCTTCAAAATGAAAATG
1 AAAATAGAGAAATGAGAAAT-ATTTGGAAATAAATATGGTTTTCTCCAAAATGAAAATG
56306261 AAAAT
1 AAAAT
56306266 GACCTGAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
56 3 0.05
57 39 0.71
58 13 0.24
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (58 bp):
AAAATAGAGAAATGAGAAATATTTGGAAATAAATATGGTTTTCTCCAAAATGAAAATG
Found at i:56311279 original size:16 final size:15
Alignment explanation
Indices: 56311242--56311298 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
56311232 TTTAAACATT
*
56311242 TTAAAAATTAAAATA
1 TTAAAAAATAAAATA
56311257 -TAGAAAAATAATAATA
1 TTA-AAAAATAA-AATA
* *
56311273 TTAAAAATATAAGACA
1 TTAAAAA-ATAAAATA
56311289 TTAAAAAATA
1 TTAAAAAATA
56311299 GAAAAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 2 0.06
15 10 0.29
16 17 0.49
17 6 0.17
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (15 bp):
TTAAAAAATAAAATA
Found at i:56311680 original size:19 final size:21
Alignment explanation
Indices: 56311653--56311691 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
56311643 ATATTTATTT
56311653 AATTATTAAAAATT-ATTTTA
1 AATTATTAAAAATTAATTTTA
*
56311673 AATT-TTAAATATTAATTTT
1 AATTATTAAAAATTAATTTT
56311692 TAAAACTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTATTAAAAATTAATTTTA
Found at i:56313191 original size:13 final size:13
Alignment explanation
Indices: 56313175--56313203 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
56313165 AAAAGAAAAA
56313175 GAAGAAAATAAGG
1 GAAGAAAATAAGG
56313188 GAAGAAAATAAGG
1 GAAGAAAATAAGG
56313201 GAA
1 GAA
56313204 AATGAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.07
Consensus pattern (13 bp):
GAAGAAAATAAGG
Found at i:56320363 original size:54 final size:54
Alignment explanation
Indices: 56320273--56320394 Score: 145
Period size: 54 Copynumber: 2.3 Consensus size: 54
56320263 GTGTTTCAAG
* ** * *
56320273 TCAGTGAGTTACATGGCCTAACACATGGCCTGGCACACGGACGTATGTGGTAAC
1 TCAGTGAGTTACACGGCCTAACACACAGCCTAGCACACGGACGCATGTGGTAAC
* * * ** *
56320327 TCAGAGAGTTACACGGCCTAGCACACAGCTTAGCACACGGGTGCGTGTGGTAAC
1 TCAGTGAGTTACACGGCCTAACACACAGCCTAGCACACGGACGCATGTGGTAAC
56320381 TCAGTGAGTTACAC
1 TCAGTGAGTTACAC
56320395 AGGTGTGTGT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (54 bp):
TCAGTGAGTTACACGGCCTAACACACAGCCTAGCACACGGACGCATGTGGTAAC
Found at i:56320405 original size:30 final size:30
Alignment explanation
Indices: 56320361--56320424 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
56320351 ACAGCTTAGC
* *
56320361 ACACGGGTGCGTGTGGTAACTCAGTGAGTT
1 ACACAGGTGCGTGTGGCAACTCAGTGAGTT
*
56320391 ACACAGGTGTGTGTGGCAACTCAGTGAGTT
1 ACACAGGTGCGTGTGGCAACTCAGTGAGTT
56320421 ACAC
1 ACAC
56320425 TTGTGAGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (30 bp):
ACACAGGTGCGTGTGGCAACTCAGTGAGTT
Found at i:56328178 original size:24 final size:24
Alignment explanation
Indices: 56328151--56328202 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
56328141 TTAGTAAGTC
*
56328151 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
56328175 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
56328199 AAAT
1 AAAT
56328203 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:56332125 original size:7 final size:7
Alignment explanation
Indices: 56332113--56332155 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
56332103 AACATTATTG
56332113 AAAACAA
1 AAAACAA
56332120 AAAACAA
1 AAAACAA
56332127 AAAGA-AA
1 AAA-ACAA
*
56332134 AGAATCAA
1 A-AAACAA
56332142 AAAACAA
1 AAAACAA
56332149 AAAACAA
1 AAAACAA
56332156 TTTTGAAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.81, C:0.12, G:0.05, T:0.02
Consensus pattern (7 bp):
AAAACAA
Found at i:56332709 original size:3 final size:3
Alignment explanation
Indices: 56332703--56332748 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
56332693 TTTTTTTTTA
*
56332703 TAT TAT TAAT T-T TAT TA- TAT TAAT TAT TAT TGT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
56332748 T
1 T
56332749 TCAATAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 27 0.73
4 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:56343877 original size:42 final size:42
Alignment explanation
Indices: 56343825--56343938 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
56343815 TACTTCAATT
* * * *
56343825 TATCCGATGATGCATTTATGTGCCAGTATAACTACTTTGGTA
1 TATCCAATGATACACTTATGTGCCAGTATAACTACTTCGGTA
* * ** *
56343867 TATCCAATGATACACTTATATGTCAGTATATTTGCTTCGGTA
1 TATCCAATGATACACTTATGTGCCAGTATAACTACTTCGGTA
* * *
56343909 TATTCAATGATACACTTACGTGCTAGTATA
1 TATCCAATGATACACTTATGTGCCAGTATA
56343939 TTTGCTTTAG
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (42 bp):
TATCCAATGATACACTTATGTGCCAGTATAACTACTTCGGTA
Found at i:56343952 original size:42 final size:42
Alignment explanation
Indices: 56343859--56343952 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
56343849 AGTATAACTA
*
56343859 CTTTGGTATATCCAATGATACACTTATATGTCAGTATATTTG
1 CTTTGGTATATCCAATGATACACTTACATGTCAGTATATTTG
* * *
56343901 CTTCGGTATATTCAATGATACACTTACGTG-CTAGTATATTTG
1 CTTTGGTATATCCAATGATACACTTACATGTC-AGTATATTTG
*
56343943 CTTTAGTATA
1 CTTTGGTATA
56343953 CCCGATTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.02
42 44 0.98
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (42 bp):
CTTTGGTATATCCAATGATACACTTACATGTCAGTATATTTG
Found at i:56344455 original size:30 final size:30
Alignment explanation
Indices: 56344420--56344486 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
56344410 GATACAAGGG
56344420 ACACACGACCGTATCATCTGGCCGTGTGTC
1 ACACACGACCGTATCATCTGGCCGTGTGTC
*
56344450 ACACACGACCGTGTCATCTGGCCGTGTGTC
1 ACACACGACCGTATCATCTGGCCGTGTGTC
56344480 ACACACG
1 ACACACG
56344487 GCTGAGACAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.21, C:0.34, G:0.24, T:0.21
Consensus pattern (30 bp):
ACACACGACCGTATCATCTGGCCGTGTGTC
Found at i:56345499 original size:25 final size:25
Alignment explanation
Indices: 56345455--56345573 Score: 109
Period size: 25 Copynumber: 4.8 Consensus size: 25
56345445 CGAGCATGTA
* **
56345455 AACGGGAAGCTCTTCCGAGCCATAT
1 AACGGGAAGCTCATGAGAGCCATAT
*
56345480 AACGGGAAGCTCATGAGAGCCGTA-
1 AACGGGAAGCTCATGAGAGCCATAT
* * *
56345504 AATCGGGTAGCTCAAGAGAGCTAT-T
1 AA-CGGGAAGCTCATGAGAGCCATAT
*
56345529 AATCGGGAAGCTCAT-ATGAGCCAAAT
1 AA-CGGGAAGCTCATGA-GAGCCATAT
*
56345555 ATCGGGAAGCTCATGAGAG
1 AACGGGAAGCTCATGAGAG
56345574 TTGTGGTGTG
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
24 3 0.04
25 70 0.92
26 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (25 bp):
AACGGGAAGCTCATGAGAGCCATAT
Found at i:56348841 original size:33 final size:33
Alignment explanation
Indices: 56348799--56348862 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
56348789 ATCAATCATG
56348799 TATTCATCGCTCGTAAAGTATACAAAAGTTTCT
1 TATTCATCGCTCGTAAAGTATACAAAAGTTTCT
56348832 TATTCATCGCTCGTAAAGTATACAAAAGTTT
1 TATTCATCGCTCGTAAAGTATACAAAAGTTT
56348863 TTGACGATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (33 bp):
TATTCATCGCTCGTAAAGTATACAAAAGTTTCT
Found at i:56354214 original size:13 final size:13
Alignment explanation
Indices: 56354196--56354220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56354186 ACAAACGAGA
56354196 AAATTTTCACACG
1 AAATTTTCACACG
56354209 AAATTTTCACAC
1 AAATTTTCACAC
56354221 TTATCAATTC
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:56361218 original size:18 final size:18
Alignment explanation
Indices: 56361195--56361229 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
56361185 TAAATCGAAA
56361195 AGATACAATTTTAATTAG
1 AGATACAATTTTAATTAG
56361213 AGATACAATTTTAATTA
1 AGATACAATTTTAATTA
56361230 AGTGTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (18 bp):
AGATACAATTTTAATTAG
Found at i:56366986 original size:96 final size:96
Alignment explanation
Indices: 56366822--56367008 Score: 338
Period size: 96 Copynumber: 1.9 Consensus size: 96
56366812 TGCTACAGTA
* * **
56366822 GGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGGAAATAGTATAAAATCGCTTCTAGCTGG
1 GGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTAGAAAATCGCTTCTAGCAAG
56366887 ATGCTATTTGAGAAGAATTTGTGAAACTGTT
66 ATGCTATTTGAGAAGAATTTGTGAAACTGTT
56366918 GGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTAGAAAATCGCTTCTAGCAAG
1 GGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTAGAAAATCGCTTCTAGCAAG
56366983 ATGCTATTTGAGAAGAATTTGTGAAA
66 ATGCTATTTGAGAAGAATTTGTGAAA
56367009 TCGCGCCCTC
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (96 bp):
GGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTAGAAAATCGCTTCTAGCAAG
ATGCTATTTGAGAAGAATTTGTGAAACTGTT
Found at i:56369288 original size:28 final size:27
Alignment explanation
Indices: 56369255--56369353 Score: 110
Period size: 28 Copynumber: 3.6 Consensus size: 27
56369245 TAATGAGATT
56369255 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTTTAATTGAA
* * **
56369282 ATGCACTAAGTGTGTGAGTATAAGGGTAA
1 A-GCACTAAGTGTGCGAGTTTAATTG-AA
*
56369311 AGCACTAAGTGTGCGAGTTTGATT-ATTA
1 AGCACTAAGTGTGCGAGTTTAATTGA--A
56369339 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
56369354 TACTTATTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 54 0.92
29 3 0.05
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTTAATTGAA
Found at i:56370399 original size:47 final size:46
Alignment explanation
Indices: 56370287--56370403 Score: 137
Period size: 47 Copynumber: 2.5 Consensus size: 46
56370277 TTGTGTTATA
* * * *
56370287 AATTTAATGTATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCT
1 AATTTGATGTATAATGCTGTCC-ATTTAGAGCATATTTAAGCTGTCC
* *
56370334 AATTCGATGTATAATGCTGTCCATTTAGAGCATA-TTATTGCTGTCC
1 AATTTGATGTATAATGCTGTCCATTTAGAGCATATTTA-AGCTGTCC
*
56370380 AATTTGATGAATAATTGCTGTCCA
1 AATTTGATGTATAA-TGCTGTCCA
56370404 AAACAGGGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 3 0.05
46 28 0.47
47 29 0.48
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (46 bp):
AATTTGATGTATAATGCTGTCCATTTAGAGCATATTTAAGCTGTCC
Found at i:56370400 original size:23 final size:23
Alignment explanation
Indices: 56370287--56370404 Score: 93
Period size: 23 Copynumber: 5.1 Consensus size: 23
56370277 TTGTGTTATA
*
56370287 AATTTAATGTATAA-TGCTGTCC
1 AATTTGATGTATAATTGCTGTCC
* *
56370309 AATTTTGA-GTATATTTAAGCTGTCT
1 AA-TTTGATGTATAATT--GCTGTCC
*
56370334 AATTCGATGTATAA-TGCTGTCC
1 AATTTGATGTATAATTGCTGTCC
*
56370356 -ATTTAGA-GCATATTATTGCTGTCC
1 AATTT-GATG--TATAATTGCTGTCC
*
56370380 AATTTGATGAATAATTGCTGTCC
1 AATTTGATGTATAATTGCTGTCC
56370403 AA
1 AA
56370405 AACAGGGTTG
Statistics
Matches: 75, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
21 4 0.05
22 15 0.20
23 23 0.31
24 15 0.20
25 18 0.24
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (23 bp):
AATTTGATGTATAATTGCTGTCC
Found at i:56372876 original size:25 final size:25
Alignment explanation
Indices: 56372848--56373053 Score: 193
Period size: 25 Copynumber: 8.6 Consensus size: 25
56372838 TAAGCTCATG
56372848 TTATTACATCAAATAAACTTCTATT
1 TTATTACATCAAATAAACTTCTATT
56372873 TTATTACATCAAAT-AA-TATC-A--
1 TTATTACATCAAATAAACT-TCTATT
** * * *
56372894 AAATAAC-TCAAAAAAATTTCTATT
1 TTATTACATCAAATAAACTTCTATT
*
56372918 TTATTACATCAATTAAACTTCTATT
1 TTATTACATCAAATAAACTTCTATT
56372943 TTATTACATCAAATAAACTTCTATT
1 TTATTACATCAAATAAACTTCTATT
* *
56372968 TTATTACAT-AAA-ATA--T-TATC
1 TTATTACATCAAATAAACTTCTATT
** * * *
56372988 AAAATA-ACTCAAAAAAAATTCTATT
1 TTATTACA-TCAAATAAACTTCTATT
56373013 TTATTACATCAAATAAACTTCTATT
1 TTATTACATCAAATAAACTTCTATT
56373038 TTATTACATCAAATAA
1 TTATTACATCAAATAA
56373054 TATCATAATA
Statistics
Matches: 144, Mismatches: 23, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.01
20 12 0.08
21 12 0.08
22 4 0.03
23 4 0.03
24 12 0.08
25 98 0.68
26 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (25 bp):
TTATTACATCAAATAAACTTCTATT
Found at i:56372962 original size:95 final size:95
Alignment explanation
Indices: 56372848--56373053 Score: 376
Period size: 95 Copynumber: 2.2 Consensus size: 95
56372838 TAAGCTCATG
* *
56372848 TTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAATTT
1 TTATTACATCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAACTCAAAAAAAATT
*
56372913 CTATTTTATTACATCAATTAAACTTCTATT
66 CTATTTTATTACATCAAATAAACTTCTATT
*
56372943 TTATTACATCAAATAAACTTCTATTTTATTACATAAAATATTATCAAAATAACTCAAAAAAAATT
1 TTATTACATCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAACTCAAAAAAAATT
56373008 CTATTTTATTACATCAAATAAACTTCTATT
66 CTATTTTATTACATCAAATAAACTTCTATT
56373038 TTATTACATCAAATAA
1 TTATTACATCAAATAA
56373054 TATCATAATA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 107 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (95 bp):
TTATTACATCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAACTCAAAAAAAATT
CTATTTTATTACATCAAATAAACTTCTATT
Found at i:56373010 original size:70 final size:70
Alignment explanation
Indices: 56372936--56373097 Score: 281
Period size: 70 Copynumber: 2.3 Consensus size: 70
56372926 TCAATTAAAC
*
56372936 TTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATAAAATATTATCAAAATAACTCAAA
1 TTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAACTCAAA
56373001 AAAAA
66 AAAAA
* *
56373006 TTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCATAATAACTCAAA
1 TTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAACTCAAA
56373071 AAAAA
66 AAAAA
*
56373076 -TCTATTTTATTACATAAAATAA
1 TTCTATTTTATTACATCAAATAA
56373098 TATTAAAATA
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
69 21 0.24
70 67 0.76
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.40
Consensus pattern (70 bp):
TTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAACTCAAA
AAAAA
Found at i:56373076 original size:95 final size:94
Alignment explanation
Indices: 56372848--56373076 Score: 273
Period size: 95 Copynumber: 2.4 Consensus size: 94
56372838 TAAGCTCATG
* * * * ** *
56372848 TTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAATTT
1 TTATTACATCAAATAAAC-TCTATATAATCAAAAAAAATAATATCAAAATAACTCAAAAAAAATT
*
56372913 CTATTTTATTACATCAATTAAACTTCTATT
65 CTATTTTATTACATCAAATAAACTTCTATT
* * * * * *
56372943 TTATTACATCAAATAAACTTCTATTTTATTACATAAAATATTATCAAAATAACTCAAAAAAAATT
1 TTATTACATCAAATAAAC-TCTATATAATCAAAAAAAATAATATCAAAATAACTCAAAAAAAATT
56373008 CTATTTTATTACATCAAATAAACTTCTATT
65 CTATTTTATTACATCAAATAAACTTCTATT
56373038 TTATTACATCAAATAATA-TC-ATAATAACTCAAAAAAAAT
1 TTATTACATCAAATAA-ACTCTAT-ATAA-TCAAAAAAAAT
56373077 CTATTTTATT
Statistics
Matches: 122, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
93 2 0.02
94 4 0.03
95 115 0.94
96 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (94 bp):
TTATTACATCAAATAAACTCTATATAATCAAAAAAAATAATATCAAAATAACTCAAAAAAAATTC
TATTTTATTACATCAAATAAACTTCTATT
Found at i:56374764 original size:23 final size:24
Alignment explanation
Indices: 56374736--56374782 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
56374726 AACGTATACT
*
56374736 AAAAAACATATGTGCAT-TATATA
1 AAAAAACATATGCGCATGTATATA
*
56374759 AAAAAACCTATGCGCATGTATATA
1 AAAAAACATATGCGCATGTATATA
56374783 CAGTAGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.28
Consensus pattern (24 bp):
AAAAAACATATGCGCATGTATATA
Found at i:56376625 original size:7 final size:7
Alignment explanation
Indices: 56376615--56376639 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56376605 TTATATACAT
56376615 AATACTA
1 AATACTA
56376622 AATACTA
1 AATACTA
56376629 AATACTA
1 AATACTA
56376636 AATA
1 AATA
56376640 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:56376847 original size:20 final size:20
Alignment explanation
Indices: 56376809--56376847 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
56376799 TTTTATTTTT
*
56376809 TAAAATCTACATAATAATTG
1 TAAAATCTACATAAAAATTG
56376829 TAAAATCTA-ATATAAAATT
1 TAAAATCTACATA-AAAATT
56376848 TACCTCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAATCTACATAAAAATTG
Found at i:56377856 original size:11 final size:11
Alignment explanation
Indices: 56377842--56377908 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
56377832 TTAAATATGG
56377842 ATTTGAGAGAA
1 ATTTGAGAGAA
56377853 ATTTTGTAG-G-A
1 A-TTTG-AGAGAA
*
56377864 ATTTGAGAGCA
1 ATTTGAGAGAA
*
56377875 AGTTGAGAGGAA
1 ATTTGAGA-GAA
56377887 A-TTGAGAGGAA
1 ATTTGAGA-GAA
56377898 ATTTGAGAGAA
1 ATTTGAGAGAA
56377909 GATTAGTTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
9 2 0.04
10 5 0.10
11 25 0.52
12 14 0.29
13 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.31, T:0.27
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:56383165 original size:31 final size:31
Alignment explanation
Indices: 56383130--56383190 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
56383120 TCGGGTTGTC
*
56383130 TAGCAACAATAACTTGCCACCCTA-GATTGCT
1 TAGCAACAATAACTTACCACCC-AGGATTGCT
*
56383161 TAGCAACAATGACTTACCACCCAGGATTGC
1 TAGCAACAATAACTTACCACCCAGGATTGC
56383191 CCGACAACGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (31 bp):
TAGCAACAATAACTTACCACCCAGGATTGCT
Found at i:56387159 original size:16 final size:16
Alignment explanation
Indices: 56387138--56387202 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
56387128 TTCGCTGTAT
*
56387138 TGGAATAAAGGCGTAA
1 TGGAATAGAGGCGTAA
*
56387154 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
56387170 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
56387186 TGGAATAGAGTCGTAA
1 TGGAATAGAGGCGTAA
56387202 T
1 T
56387203 AGCAAATCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.40, C:0.06, G:0.32, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:56387657 original size:13 final size:12
Alignment explanation
Indices: 56387633--56387673 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
56387623 TATAATACTA
56387633 TAAAATATAATT
1 TAAAATATAATT
56387645 TAAAATAATAATT
1 TAAAAT-ATAATT
*
56387658 ATTAAATATAATT
1 -TAAAATATAATT
56387671 TAA
1 TAA
56387674 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:56387659 original size:121 final size:123
Alignment explanation
Indices: 56387437--56387692 Score: 430
Period size: 121 Copynumber: 2.1 Consensus size: 123
56387427 TTTTTATTAA
56387437 ATATAATTTAATAAAATTCTTAATATTAGATATTCTTAATATTAAATTACTAAAATCATAATATA
1 ATATAATTTAATAAAATTCTTAATATTAGATATTCTTAATATTAAATTACTAAAATCATAATATA
* *
56387502 TATAATACTATAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAAAT
66 TATAATACTATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
* *
56387560 ATATAATTTAATAAAATTCTTAATATTAAATATATTCTT-ATA-TGAATTACTAAAATCAT-A-A
1 ATATAATTTAATAAAATTCTTAATATT--AGATATTCTTAATATTAAATTACTAAAATCATAATA
56387621 TATATAATACTATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
64 TATATAATACTATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
56387681 ATATAATTTAAT
1 ATATAATTTAAT
56387693 CTAAAGTTTG
Statistics
Matches: 127, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
121 71 0.56
122 1 0.01
123 43 0.34
124 3 0.02
125 9 0.07
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (123 bp):
ATATAATTTAATAAAATTCTTAATATTAGATATTCTTAATATTAAATTACTAAAATCATAATATA
TATAATACTATAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
Found at i:56389503 original size:9 final size:9
Alignment explanation
Indices: 56389491--56389515 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
56389481 GATGATGTAT
56389491 TTATTATTG
1 TTATTATTG
56389500 TTATTATTG
1 TTATTATTG
56389509 TTATTAT
1 TTATTAT
56389516 AGCATTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTATTG
Found at i:56389925 original size:98 final size:98
Alignment explanation
Indices: 56389792--56389988 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
56389782 TTAAAAATAA
* * * *
56389792 TAAAGGAAATATTTCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
56389857 TTAAATCTTGGGTAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
56389890 TAAAGGAAATATTCCGAGTTTGAGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
56389955 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
56389988 T
1 T
56389989 TTTATTGTAC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:56401498 original size:45 final size:45
Alignment explanation
Indices: 56401392--56401953 Score: 280
Period size: 45 Copynumber: 12.8 Consensus size: 45
56401382 TCGCATCTAG
* *
56401392 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAT-GGCAAA
* *
56401436 TATTATC-CTCCTGAAGTTACAGT-GAGGCAGACTAAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAAGATGGCAAA
* **
56401481 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CCG-ATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATGGCA-AA
* * * * * * *** *
56401525 TCCTATCTCTCTGAAGTTGCATTAGAGCGGATTAAA-ACCTCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATGGCAAA
* * * * *
56401569 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCAT--CTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG-ATGGCAAA
* ** *
56401609 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGACT-AAGCAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG-ATGGCAAA
*
56401654 TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGGCTGAAA-ATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAAGATGGCAAA
* * ** *
56401699 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGAC-AA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATGGCAAA
* * * * *** *
56401743 TCCTATCTCCCTGAAGTTGCATTGGAGCGGATTAAA-ACCTCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATGGCAAA
* * * ** * *
56401787 TTTTATCTCTCTGAAGTTGCAG-AGAGC--A-TATCGCAT--CTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG-ATGGCAAA
* * ** *
56401827 TCTTATCTCCTTGAAGTTGTAGTGGAGCAGACT-AAGCAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG-ATGGCAAA
* * *
56401872 TCTTATC-CTCCTGAAGTTACAAT-GAGGCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAAGATGGCAAA
* * * *
56401917 TTTTATCTCCCTGAAGTTGCGGTGGAACAGATTAAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG
56401954 CTGACAATGG
Statistics
Matches: 400, Mismatches: 81, Indels: 73
0.72 0.15 0.13
Matches are distributed among these distances:
40 44 0.11
41 12 0.03
42 4 0.01
43 24 0.06
44 146 0.37
45 155 0.39
46 13 0.03
47 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATGGCAAA
Found at i:56401759 original size:218 final size:217
Alignment explanation
Indices: 56401379--56401961 Score: 963
Period size: 218 Copynumber: 2.7 Consensus size: 217
56401369 TGAAGACAAT
* *
56401379 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-TAAGCAAGTATTATC
1 AGATCGCATCTAGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCTTATC
56401443 CTCCTGAAGTTACAGTGAGGCAGACT-AAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGA
65 CTCCTGAAGTTACAGTGAGGCAGACTGAAA-ATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGA
* *
56401507 GCAGATTAAAGCCGATAATCCTATCTCTCTGAAGTTGCATTAGAGCGGATTAAAACCTCAGATCT
129 GCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCATTAGAGCGGATTAAAACCTCAGATCT
56401572 TATCTCTCTGAAGTTGCAGAGAGC
194 TATCTCTCTGAAGTTGCAGAGAGC
56401596 AGATCGCATCTAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCTTATC
1 AGATCGCATCTAGTCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCTTATC
* * *
56401661 CTCCTGAAGTTGCAGTGAGGCAGGCTGAAAATGGCAAATCTTATCTCCCTAAAGTTGCAGTGGAG
65 CTCCTGAAGTTACAGTGAGGCAGACTGAAAATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAG
* *
56401726 CAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCATTGGAGCGGATTAAAACCTCAGATTTT
130 CAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCATTAGAGCGGATTAAAACCTCAGATCTT
56401791 ATCTCTCTGAAGTTGCAGAGAGC
195 ATCTCTCTGAAGTTGCAGAGAGC
* *
56401814 ATATCGCATCTAGTCTTATCTCCTTGAAGTTGTAGTGGAGCAGACTAAGCAAAGCAAGTCTTATC
1 AGATCGCATCTAGTCTTATCTCC-TGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCTTATC
* * * * *
56401879 CTCCTGAAGTTACAATGAGGCAGACTGAAGATGGCAAATTTTATCTCCCTGAAGTTGCGGTGGAA
65 CTCCTGAAGTTACAGTGAGGCAGACTGAAAATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAG
*
56401944 CAGATTAAAGCTGACAAT
130 CAGATTAAAGCCGACAAT
56401962 GGAGCGGGTT
Statistics
Matches: 342, Mismatches: 20, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
216 1 0.00
217 48 0.14
218 290 0.85
219 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (217 bp):
AGATCGCATCTAGTCTTATCTCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCTTATCC
TCCTGAAGTTACAGTGAGGCAGACTGAAAATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
AGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCATTAGAGCGGATTAAAACCTCAGATCTTA
TCTCTCTGAAGTTGCAGAGAGC
Found at i:56403519 original size:24 final size:25
Alignment explanation
Indices: 56403478--56403525 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
56403468 CATATATATA
56403478 TATTTTTTAAAAACGAATATTTTCT
1 TATTTTTTAAAAACGAATATTTTCT
* *
56403503 TATTTTTT-TAAATGAATATTTTC
1 TATTTTTTAAAAACGAATATTTTC
56403526 ATATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.56
Consensus pattern (25 bp):
TATTTTTTAAAAACGAATATTTTCT
Found at i:56403905 original size:9 final size:9
Alignment explanation
Indices: 56403893--56403917 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
56403883 GATGATGTAT
56403893 TTATTATTG
1 TTATTATTG
56403902 TTATTATTG
1 TTATTATTG
56403911 TTATTAT
1 TTATTAT
56403918 AGCATTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTATTG
Found at i:56404312 original size:98 final size:98
Alignment explanation
Indices: 56404193--56404389 Score: 322
Period size: 98 Copynumber: 2.0 Consensus size: 98
56404183 TTAAAAATAA
* * *
56404193 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTTACATATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
*
56404258 TTAAATCTTGGGTAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* * * *
56404291 TAAATGAAATATTCTGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
56404356 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
56404389 T
1 T
56404390 TTTATTGTAC
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:56406631 original size:33 final size:31
Alignment explanation
Indices: 56406594--56406665 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
56406584 AATAAATACC
56406594 AAAAATTTATTTTAAAAATTAAAATTAAAATTA
1 AAAAATTTATTTTAAAAA-T-AAATTAAAATTA
** **
56406627 AAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATTTATTTTAAAAATAAATTAAAATTA
56406658 AAAAATTT
1 AAAAATTT
56406666 TAAAAAAGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 16 0.48
32 1 0.03
33 16 0.48
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (31 bp):
AAAAATTTATTTTAAAAATAAATTAAAATTA
Found at i:56406648 original size:11 final size:11
Alignment explanation
Indices: 56406628--56406727 Score: 72
Period size: 11 Copynumber: 9.4 Consensus size: 11
56406618 TTAAAATTAA
56406628 AAAAAGTATTTT
1 AAAAA-TATTTT
56406640 AAAAATATTTT
1 AAAAATATTTT
56406651 --AAA-A--TT
1 AAAAATATTTT
56406657 AAAAA-ATTTT
1 AAAAATATTTT
56406667 AAAAAAGTATTTT
1 -AAAAA-TATTTT
*
56406680 AAAAA-A-ATT
1 AAAAATATTTT
*
56406689 AAAAAAATTTT
1 AAAAATATTTT
56406700 AAAAAAGTATTTT
1 -AAAAA-TATTTT
*
56406713 AAAAGTATTTT
1 AAAAATATTTT
56406724 AAAA
1 AAAA
56406728 TTAAAAAATA
Statistics
Matches: 73, Mismatches: 4, Indels: 23
0.73 0.04 0.23
Matches are distributed among these distances:
6 2 0.03
8 5 0.07
9 10 0.14
10 4 0.05
11 23 0.32
12 19 0.26
13 10 0.14
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:56406668 original size:10 final size:10
Alignment explanation
Indices: 56406635--56406705 Score: 60
Period size: 10 Copynumber: 7.1 Consensus size: 10
56406625 TAAAAAAAGT
56406635 ATTTTAAAAA
1 ATTTTAAAAA
56406645 TATTTT--AAA
1 -ATTTTAAAAA
56406654 A--TTAAAAA
1 ATTTTAAAAA
56406662 ATTTTAAAAAA
1 ATTTT-AAAAA
56406673 GTATTTTAAAAA
1 --ATTTTAAAAA
* *
56406685 AATTAAAAAA
1 ATTTTAAAAA
56406695 ATTTTAAAAA
1 ATTTTAAAAA
56406705 A
1 A
56406706 GTATTTTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
6 2 0.04
8 5 0.10
9 3 0.06
10 19 0.39
11 10 0.20
12 5 0.10
13 5 0.10
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:56406671 original size:17 final size:17
Alignment explanation
Indices: 56406638--56406670 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
56406628 AAAAAGTATT
56406638 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
56406655 TTAAAAA-ATTTTAAAA
1 TTAAAAATATTTTAAAA
56406671 AAGTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:56406687 original size:32 final size:33
Alignment explanation
Indices: 56406651--56406716 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
56406641 AAAATATTTT
56406651 AAAATT-AAAAAATTTTAAAAAAGTATTTTAAA
1 AAAATTAAAAAAATTTTAAAAAAGTATTTTAAA
56406683 AAAATTAAAAAAATTTTAAAAAAGTATTTTAAA
1 AAAATTAAAAAAATTTTAAAAAAGTATTTTAAA
56406716 A
1 A
56406717 GTATTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.18
33 27 0.82
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (33 bp):
AAAATTAAAAAAATTTTAAAAAAGTATTTTAAA
Found at i:56408341 original size:15 final size:15
Alignment explanation
Indices: 56408323--56408351 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56408313 ATATCTAATT
56408323 TTATTCAAATATTTA
1 TTATTCAAATATTTA
56408338 TTATTCAAATATTT
1 TTATTCAAATATTT
56408352 CGTCTTACAT
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:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATTCAAATATTTA
Found at i:56425042 original size:13 final size:13
Alignment explanation
Indices: 56425024--56425048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56425014 TTAATAAGCT
56425024 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
56425037 TTTTTCTTTTTT
1 TTTTTCTTTTTT
56425049 ATAAAAGGAT
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:56433029 original size:20 final size:20
Alignment explanation
Indices: 56432992--56433029 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56432982 TAGAACTTTT
*
56432992 TAATTTATTTATGTTATTAA
1 TAATTTATTTATGATATTAA
56433012 TAATTATATTTAT-ATATT
1 TAATT-TATTTATGATATT
56433030 TTTCAACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TAATTTATTTATGATATTAA
Found at i:56433838 original size:88 final size:88
Alignment explanation
Indices: 56433694--56433871 Score: 207
Period size: 88 Copynumber: 2.0 Consensus size: 88
56433684 ATAAAAAATT
* * * * ** *
56433694 CTCAAATTTTTTCAAAAAAAGTAATTAAGTCTCTACTTTTTTTTGCACTCGTTTAGGTACTTAAA
1 CTCAAACTTTTTCAAAAAAAGCAATTAAGCCTCTACTATTTTTTGCACTCAATTAGGCACTTAAA
* * * *
56433759 CTTTCAAAATGTATCAAAAAGTCC
66 CTGTC-AAATGCATAAAAAAGACC
* *
56433783 CTCAAACTTTTTC-AAAAAAGCAATTAAGCCTCTGA-TATTTTTTGTACTCAATTAGGCACTTTA
1 CTCAAACTTTTTCAAAAAAAGCAATTAAGCCTCT-ACTATTTTTTGCACTCAATTAGGCACTTAA
56433846 ACTGTCAAATGCATAAAAAAGACC
65 ACTGTCAAATGCATAAAAAAGACC
56433870 CT
1 CT
56433872 TTGACCGTTA
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
87 17 0.23
88 45 0.60
89 13 0.17
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (88 bp):
CTCAAACTTTTTCAAAAAAAGCAATTAAGCCTCTACTATTTTTTGCACTCAATTAGGCACTTAAA
CTGTCAAATGCATAAAAAAGACC
Found at i:56434043 original size:21 final size:21
Alignment explanation
Indices: 56433982--56434090 Score: 64
Period size: 21 Copynumber: 5.3 Consensus size: 21
56433972 AATAAAAGTC
* *
56433982 ATAAAAAT-ATTAAATTTTA-
1 ATAAAAATCATAAAAATTTAT
* * **
56434001 ATAAAAATTAGAAAAAAATAT
1 ATAAAAATCATAAAAATTTAT
56434022 ATAAAAATCATAAAAATTTAT
1 ATAAAAATCATAAAAATTTAT
* ** * *
56434043 AAAAAAAATC-TGTAATTTTTT
1 -ATAAAAATCATAAAAATTTAT
*
56434064 ATAAAAGTCATAAAAAATTT-T
1 ATAAAAATCAT-AAAAATTTAT
56434085 ATAAAA
1 ATAAAA
56434091 TGCATTAAAA
Statistics
Matches: 66, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
19 8 0.12
20 13 0.20
21 32 0.48
22 13 0.20
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (21 bp):
ATAAAAATCATAAAAATTTAT
Found at i:56434300 original size:21 final size:18
Alignment explanation
Indices: 56434273--56434318 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 18
56434263 TTAGTACTAT
*
56434273 CATTTTTATACTTATTTTTA
1 CATTTTTATA-TT-TCTTTA
56434293 CGATTTTTATATTTCTTTA
1 C-ATTTTTATATTTCTTTA
56434312 CATTTTT
1 CATTTTT
56434319 TTATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
19 6 0.25
20 3 0.12
21 9 0.38
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.65
Consensus pattern (18 bp):
CATTTTTATATTTCTTTA
Found at i:56434328 original size:29 final size:27
Alignment explanation
Indices: 56434296--56434397 Score: 82
Period size: 29 Copynumber: 3.6 Consensus size: 27
56434286 ATTTTTACGA
56434296 TTTTTATATTTCTTTACATTTTTTTATATT
1 TTTTTATATTT-TTTA-ATTTTTTTATA-T
* *
56434326 TTTTTATGATTTTATAATTTTTTTCTAAT
1 TTTTTAT-ATTTTTTAATTTTTTTAT-AT
*
56434355 TTTTAATAGTTTTTTATAGTTTTTTTA-A-
1 TTTTTATA-TTTTTTA-A-TTTTTTTATAT
*
56434383 TTTTAATATTTTTTA
1 TTTTTATATTTTTTA
56434398 TAACTTATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
27 7 0.11
28 9 0.15
29 23 0.37
30 12 0.19
31 11 0.18
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (27 bp):
TTTTTATATTTTTTAATTTTTTTATAT
Found at i:56434338 original size:20 final size:20
Alignment explanation
Indices: 56434275--56434386 Score: 79
Period size: 20 Copynumber: 5.6 Consensus size: 20
56434265 AGTACTATCA
*
56434275 TTTTTATACTTATTTTTACGA-
1 TTTTTATA-TT-TTTTTATGAT
* *
56434296 TTTTTATATTTCTTTA-CATT
1 TTTTTATATTTTTTTATGA-T
56434316 TTTTTATATTTTTTTATGAT
1 TTTTTATATTTTTTTATGAT
* * *
56434336 TTTATA-ATTTTTTTCTAAT
1 TTTTTATATTTTTTTATGAT
* * *
56434355 TTTTAATAGTTTTTTATAGTT
1 TTTTTATATTTTTTTAT-GAT
56434376 TTTTTA-ATTTT
1 TTTTTATATTTT
56434387 AATATTTTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
18 1 0.01
19 20 0.28
20 35 0.49
21 15 0.21
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTTATATTTTTTTATGAT
Found at i:56434349 original size:11 final size:10
Alignment explanation
Indices: 56434296--56434386 Score: 80
Period size: 10 Copynumber: 9.2 Consensus size: 10
56434286 ATTTTTACGA
56434296 TTTTTATATT
1 TTTTTATATT
* *
56434306 TCTTTACATT
1 TTTTTATATT
56434316 TTTTTATATT
1 TTTTTATATT
56434326 TTTTTATGA-T
1 TTTTTAT-ATT
*
56434336 TTTATA-ATT
1 TTTTTATATT
* *
56434345 TTTTTCTAAT
1 TTTTTATATT
* *
56434355 TTTTAATAGT
1 TTTTTATATT
56434365 TTTTTATAGTT
1 TTTTTATA-TT
56434376 TTTTTA-ATT
1 TTTTTATATT
56434385 TT
1 TT
56434387 AATATTTTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 9
0.74 0.15 0.10
Matches are distributed among these distances:
8 1 0.02
9 9 0.14
10 46 0.72
11 8 0.12
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.71
Consensus pattern (10 bp):
TTTTTATATT
Found at i:56434358 original size:39 final size:37
Alignment explanation
Indices: 56434275--56434386 Score: 98
Period size: 39 Copynumber: 2.8 Consensus size: 37
56434265 AGTACTATCA
* *
56434275 TTTTTATACTTATTTTTACGATTTTTATATTTCTTTACATT
1 TTTTTATA-TT-TTTTTATGATTTTTA-ATTT-TTTACAAT
*
56434316 TTTTTATATTTTTTTATGATTTTATAATTTTTTTCTAAT
1 TTTTTATATTTTTTTATGATTTT-TAATTTTTTAC-AAT
* * *
56434355 TTTTAATAGTTTTTTATAGTTTTTTTAATTTT
1 TTTTTATATTTTTTTAT-G-ATTTTTAATTTT
56434387 AATATTTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
38 4 0.07
39 33 0.54
40 12 0.20
41 12 0.20
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (37 bp):
TTTTTATATTTTTTTATGATTTTTAATTTTTTACAAT
Found at i:56434361 original size:18 final size:18
Alignment explanation
Indices: 56434316--56434378 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
56434306 TCTTTACATT
*
56434316 TTTTTATATTTTTTTATGA
1 TTTTTA-ATTTTTTTATAA
*
56434335 TTTTATAATTTTTTTCTAA
1 TTTT-TAATTTTTTTATAA
*
56434354 TTTTTAATAGTTTTTTATAG
1 TTTTTAAT--TTTTTTATAA
56434374 TTTTT
1 TTTTT
56434379 TTAATTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.11
19 18 0.49
20 15 0.41
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTTTAATTTTTTTATAA
Found at i:56434396 original size:10 final size:9
Alignment explanation
Indices: 56434296--56434399 Score: 68
Period size: 10 Copynumber: 10.9 Consensus size: 9
56434286 ATTTTTACGA
56434296 TTTTTATAT
1 TTTTTATAT
*
56434305 TTCTTTACATT
1 TT-TTTATA-T
56434316 TTTTTATAT
1 TTTTTATAT
56434325 TTTTT-TAT
1 TTTTTATAT
*
56434333 GATTTTATAATT
1 -TTTTTAT-A-T
*
56434345 TTTTTCTAAT
1 TTTTTAT-AT
*
56434355 TTTTAATAGT
1 TTTTTATA-T
56434365 TTTTTATAGT
1 TTTTTATA-T
*
56434375 TTTTT-TAA
1 TTTTTATAT
*
56434383 TTTTAATAT
1 TTTTTATAT
56434392 TTTTTATA
1 TTTTTATA
56434400 ACTTATATTG
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
8 7 0.09
9 24 0.32
10 32 0.43
11 11 0.15
12 1 0.01
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (9 bp):
TTTTTATAT
Found at i:56434413 original size:28 final size:28
Alignment explanation
Indices: 56434355--56434414 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
56434345 TTTTTCTAAT
* * *
56434355 TTTTAATAGTTTTTTATAGTTTTTTTAA
1 TTTTAATAGTTTTTTATACTTATATTAA
*
56434383 TTTTAATA-TTTTTTATAACTTATATTGA
1 TTTTAATAGTTTTTTAT-ACTTATATTAA
56434411 TTTT
1 TTTT
56434415 TTTATCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (28 bp):
TTTTAATAGTTTTTTATACTTATATTAA
Found at i:56435730 original size:45 final size:45
Alignment explanation
Indices: 56435679--56435766 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
56435669 GGTCCTTGAA
* *
56435679 AAAATTAGTATAAAT-AATTAATAGTAACTACTATGTAATTTAAAT
1 AAAATTAGTATAAATAAATT-ATAATAAATACTATGTAATTTAAAT
**
56435724 AAAATTAGTATAAATAAATTATAATAAATTTTATGTAATTTAA
1 AAAATTAGTATAAATAAATTATAATAAATACTATGTAATTTAA
56435767 TTAATTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 34 0.89
46 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (45 bp):
AAAATTAGTATAAATAAATTATAATAAATACTATGTAATTTAAAT
Found at i:56441054 original size:24 final size:23
Alignment explanation
Indices: 56441027--56441073 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
56441017 GTTATAATTT
56441027 TTTTTTATTTACCAAAAATATATA
1 TTTTTTATTTACC-AAAATATATA
56441051 TTTTTTATTTACCAAAATATATA
1 TTTTTTATTTACCAAAATATATA
56441074 AAAAAAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTTTATTTACCAAAATATATA
Found at i:56441160 original size:27 final size:27
Alignment explanation
Indices: 56441122--56441173 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
56441112 CATTGGTCAC
*
56441122 GCCAATGGCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
56441149 GCCAATGCCATTGGCGGCACCAATG
1 GCCAATGCCATTGGCGGCACCAATG
56441174 TATAATAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.29, G:0.31, T:0.17
Consensus pattern (27 bp):
GCCAATGCCATTGGCGGCACCAATGGT
Found at i:56441222 original size:4 final size:4
Alignment explanation
Indices: 56441213--56441318 Score: 69
Period size: 4 Copynumber: 25.0 Consensus size: 4
56441203 GAAGGAGAGG
*
56441213 GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAAA GGAAA GGAGAA GAGAA
1 GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA G-AAA -GAAA -GA-AA GA-AA
56441264 -AAA -AAA GAAA GAAA G-AA G-AA GAAAA GGAAA GGAGAA GAAA -AAA
1 GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA -GA-AA GAAA GAAA
56441307 GAAA GAAA GAAA
1 GAAA GAAA GAAA
56441319 AGGAAAGGAG
Statistics
Matches: 89, Mismatches: 2, Indels: 22
0.79 0.02 0.19
Matches are distributed among these distances:
3 14 0.16
4 40 0.45
5 28 0.31
6 7 0.08
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:56441271 original size:41 final size:41
Alignment explanation
Indices: 56441215--56441325 Score: 154
Period size: 41 Copynumber: 2.7 Consensus size: 41
56441205 AGGAGAGGGA
*
56441215 AAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAAGGAAAGGAG
1 AAGAAA-AAAGAAAGAAAGGAAAGGAAAGAAAAGGAAAGGAG
*
56441257 AAGAGAAAAA-AAAGAAA-GAAAGAAGAAGAAAAGGAAAGGAG
1 AAGA-AAAAAGAAAGAAAGGAAAGGA-AAGAAAAGGAAAGGAG
*
56441298 AAGAAAAAAGAAAGAAAGAAAAGGAAAG
1 AAGAAAAAAGAAAGAAAGGAAAGGAAAG
56441326 GAGAAGAGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
40 10 0.16
41 37 0.61
42 12 0.20
43 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (41 bp):
AAGAAAAAAGAAAGAAAGGAAAGGAAAGAAAAGGAAAGGAG
Found at i:56441277 original size:31 final size:31
Alignment explanation
Indices: 56441239--56441348 Score: 112
Period size: 31 Copynumber: 3.2 Consensus size: 31
56441229 GAAAGGAGAG
56441239 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAA
1 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAA
*
56441270 GAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAA
1 GAAAG-AA-AAG--G-AAAGG--AGAAG-AG-AAAAA-AAA
56441311 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAA
1 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAA
*
56441342 AAAAGAA
1 GAAAGAA
56441349 GGAAGGAAGG
Statistics
Matches: 66, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
31 14 0.21
32 7 0.11
33 5 0.08
34 4 0.06
35 1 0.02
36 10 0.15
37 1 0.02
38 4 0.06
39 5 0.08
40 7 0.11
41 8 0.12
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (31 bp):
GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAA
Found at i:56446727 original size:18 final size:18
Alignment explanation
Indices: 56446704--56446748 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
56446694 ATCCCAATGA
*
56446704 TCGCCACCACCTTCTTCT
1 TCGCCACCACATTCTTCT
*
56446722 TCGCCAGCACATTCTTCT
1 TCGCCACCACATTCTTCT
*
56446740 TCACCACCA
1 TCGCCACCA
56446749 ACCATATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.47, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACATTCTTCT
Found at i:56447751 original size:11 final size:11
Alignment explanation
Indices: 56447725--56447755 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
56447715 AAAAAAATAC
56447725 CTTCTTTTTCT
1 CTTCTTTTTCT
56447736 C-TCTTTTTCT
1 CTTCTTTTTCT
56447746 CTTCTTTTTC
1 CTTCTTTTTC
56447756 CGCAGCACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:56447883 original size:27 final size:27
Alignment explanation
Indices: 56447839--56447938 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
56447829 ACACGAGTAA
*
56447839 TGCCGCCAATGCCTTTGGCA-CTATTGG
1 TGCCGCCAATGGCTTTGGCACCT-TTGG
*
56447866 TGCCGCCAATGGCATTGGCACCTTTGG
1 TGCCGCCAATGGCTTTGGCACCTTTGG
*
56447893 TGCCGCCAATGGTTTTGGCACCTTTGG
1 TGCCGCCAATGGCTTTGGCACCTTTGG
* *
56447920 TGCCGCCAATCGTTTTGGC
1 TGCCGCCAATGGCTTTGGC
56447939 GTGACCAAGG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
27 65 0.97
28 2 0.03
ACGTcount: A:0.13, C:0.29, G:0.28, T:0.30
Consensus pattern (27 bp):
TGCCGCCAATGGCTTTGGCACCTTTGG
Found at i:56448028 original size:22 final size:22
Alignment explanation
Indices: 56447998--56448042 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
56447988 TTGTTTTTTT
56447998 ATATATTTTGGTAAATAAAAAA
1 ATATATTTTGGTAAATAAAAAA
*
56448020 ATATTTTTTGGTAAATAAAAAA
1 ATATATTTTGGTAAATAAAAAA
56448042 A
1 A
56448043 GTTATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (22 bp):
ATATATTTTGGTAAATAAAAAA
Found at i:56448534 original size:32 final size:32
Alignment explanation
Indices: 56448496--56448557 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
56448486 CCCGTTTTTT
* * **
56448496 AAATAAATACCAAAAATTTATTTTAAAAATTA
1 AAATAAAAACAAAAAAAGTATTTTAAAAATTA
*
56448528 AAATAAAAATAAAAAAAGTATTTTAAAAAT
1 AAATAAAAACAAAAAAAGTATTTTAAAAAT
56448558 ATTTTAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (32 bp):
AAATAAAAACAAAAAAAGTATTTTAAAAATTA
Found at i:56448584 original size:29 final size:30
Alignment explanation
Indices: 56448552--56448613 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
56448542 AAAGTATTTT
56448552 AAAAATATTTTAAA-ATTAAAAAATAAAAA
1 AAAAATATTTTAAATATTAAAAAATAAAAA
* *
56448581 AAAAGTATTTTAAATTTTAAAAAATAAAAA
1 AAAAATATTTTAAATATTAAAAAATAAAAA
56448611 AAA
1 AAA
56448614 TAAAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (30 bp):
AAAAATATTTTAAATATTAAAAAATAAAAA
Found at i:56448592 original size:40 final size:43
Alignment explanation
Indices: 56448514--56448594 Score: 132
Period size: 40 Copynumber: 2.0 Consensus size: 43
56448504 ACCAAAAATT
56448514 TATTTTAAAAATTAAAATAAAAATAAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATTAAAATAAAAATAAAAAAAGTATTTTAAAAA
*
56448557 TATTTT-AAAATTAAAA-AATAA-AAAAAAAGTATTTTAAA
1 TATTTTAAAAATTAAAATAAAAATAAAAAAAGTATTTTAAA
56448595 TTTTAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
40 17 0.46
41 4 0.11
42 10 0.27
43 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (43 bp):
TATTTTAAAAATTAAAATAAAAATAAAAAAAGTATTTTAAAAA
Found at i:56448605 original size:38 final size:38
Alignment explanation
Indices: 56448515--56448619 Score: 124
Period size: 37 Copynumber: 2.7 Consensus size: 38
56448505 CCAAAAATTT
*
56448515 ATTTTAAAAATTAAAATAAAAATAAAAAAAGTATTTTAAAA
1 ATTTTAAAAATTAAAA-AATAA-AAAAAAAGTATTTT-AAA
*
56448556 ATATTTTAAAATTAAAAAATAAAAAAAAAGTATTTT-AA
1 AT-TTTAAAAATTAAAAAATAAAAAAAAAGTATTTTAAA
* *
56448594 ATTTTAAAAAATAAAAAA-AATAAAAA
1 ATTTTAAAAATTAAAAAATAAAAAAAA
56448620 TATTTATTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
36 7 0.12
37 14 0.24
38 4 0.07
40 14 0.24
41 6 0.10
42 13 0.22
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (38 bp):
ATTTTAAAAATTAAAAAATAAAAAAAAAGTATTTTAAA
Found at i:56451047 original size:30 final size:32
Alignment explanation
Indices: 56450995--56451065 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
56450985 AAAAGTTACA
* *
56450995 ATTT-AGTCATTGAATTATTTTAAA-TATTTC
1 ATTTAAGTCATTAAACTATTTTAAATTATTTC
* *
56451025 ATTTAAGTCATTAAACTA-TTTAAATTTTTTT
1 ATTTAAGTCATTAAACTATTTTAAATTATTTC
56451056 ATTTAAGTCA
1 ATTTAAGTCA
56451066 CTCGTTAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.52
Consensus pattern (32 bp):
ATTTAAGTCATTAAACTATTTTAAATTATTTC
Found at i:56454064 original size:25 final size:25
Alignment explanation
Indices: 56453926--56454064 Score: 67
Period size: 25 Copynumber: 5.6 Consensus size: 25
56453916 GTCCCGATAT
*
56453926 ATGGCTCTTCGGAGTTTCCTGATTA
1 ATGGCTCTTCGGAGCTTCCTGATTA
* *
56453951 AAGGCTCTTTGTGAGCTTCAC-G-TTA
1 ATGGCTCTTCG-GAGCTTC-CTGATTA
* * *
56453976 ATGGCTTTTCGAAGCTTCTTGA-T-
1 ATGGCTCTTCGGAGCTTCCTGATTA
* * *
56453999 ACGGCTCGCTT--GAACTTCCCGA-TA
1 ATGGCT--CTTCGGAGCTTCCTGATTA
* * **
56454023 TATGGCTATCCAAAGCTTCCTGATTA
1 -ATGGCTCTTCGGAGCTTCCTGATTA
56454049 ATGGCTCTTCGGAGCT
1 ATGGCTCTTCGGAGCT
56454065 ACCCGTTATT
Statistics
Matches: 79, Mismatches: 24, Indels: 22
0.63 0.19 0.18
Matches are distributed among these distances:
23 14 0.18
24 8 0.10
25 47 0.59
26 9 0.11
27 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (25 bp):
ATGGCTCTTCGGAGCTTCCTGATTA
Found at i:56454087 original size:24 final size:24
Alignment explanation
Indices: 56454060--56454121 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
56454050 TGGCTCTTCG
*
56454060 GAGCTACCCGTTATTGGCTCACAT
1 GAGCTTCCCGTTATTGGCTCACAT
* **
56454084 GAGCTTTCCGATTA-TGGCTCTTAT
1 GAGCTTCCCG-TTATTGGCTCACAT
56454108 GAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
56454122 ACAGCCCGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 3 0.10
24 25 0.81
25 3 0.10
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCACAT
Found at i:56462782 original size:33 final size:35
Alignment explanation
Indices: 56462745--56462841 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
56462735 ATGGTTATAT
56462745 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
56462778 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
56462813 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAATATA-ATTT-ATATATT
56462842 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 8 0.16
35 11 0.22
36 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:56463182 original size:16 final size:16
Alignment explanation
Indices: 56463161--56463191 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56463151 CATATTCCAA
56463161 AAATAATAAACTAATC
1 AAATAATAAACTAATC
*
56463177 AAATAATAAATTAAT
1 AAATAATAAACTAAT
56463192 TTTTAATACT
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:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAAACTAATC
Found at i:56470881 original size:19 final size:20
Alignment explanation
Indices: 56470857--56470904 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
56470847 TTACATGTCT
*
56470857 AATTTATTAAAAAGG-ACTA
1 AATTTATTAAAAAGGTACAA
* *
56470876 AATTTA-AAAAAAGGTGCAA
1 AATTTATTAAAAAGGTACAA
56470895 AATTTATTAA
1 AATTTATTAA
56470905 TTATAATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 7 0.30
19 14 0.61
20 2 0.09
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.31
Consensus pattern (20 bp):
AATTTATTAAAAAGGTACAA
Found at i:56490544 original size:42 final size:42
Alignment explanation
Indices: 56490495--56490627 Score: 130
Period size: 42 Copynumber: 3.2 Consensus size: 42
56490485 AAGGCTGAAT
* *
56490495 AGAAGCTCATGAGAGCTAAACAGAAACCCT-TAAGCGTTGAAC
1 AGAAGCTCAT-AGAGCTAAACGGAAACCCTATAAGCGTTAAAC
* * *
56490537 -GAAAGCTCGTAAGAGCTGAACGGAAA-CCTATAAGGGTTAAAC
1 AG-AAGCTCAT-AGAGCTAAACGGAAACCCTATAAGCGTTAAAC
* * *
56490579 AGAAGCTCAATAGAGCTAAACGGAAACTC-ATAAGGGTTAAAT
1 AGAAGCTC-ATAGAGCTAAACGGAAACCCTATAAGCGTTAAAC
56490621 AGAAGCT
1 AGAAGCT
56490628 TAGTTGAACT
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
41 4 0.05
42 69 0.91
43 3 0.04
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (42 bp):
AGAAGCTCATAGAGCTAAACGGAAACCCTATAAGCGTTAAAC
Found at i:56490608 original size:21 final size:22
Alignment explanation
Indices: 56490546--56490612 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 22
56490536 CGAAAGCTCG
* *
56490546 TAAGAGCTGAACGGAAAC-CTA
1 TAAGAGCTAAACGGAAACTCAA
* * * *
56490567 TAAGGGTTAAACAGAAGCTCAA
1 TAAGAGCTAAACGGAAACTCAA
56490589 T-AGAGCTAAACGGAAACTC-A
1 TAAGAGCTAAACGGAAACTCAA
56490609 TAAG
1 TAAG
56490613 GGTTAAATAG
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
20 2 0.06
21 29 0.85
22 3 0.09
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.16
Consensus pattern (22 bp):
TAAGAGCTAAACGGAAACTCAA
Found at i:56490619 original size:21 final size:21
Alignment explanation
Indices: 56490555--56490619 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
56490545 GTAAGAGCTG
56490555 AACGGAAAC-CTATAAGGGTTA
1 AACGGAAACTC-ATAAGGGTTA
* * * *
56490576 AACAGAAGCTCA-ATAGAGCTA
1 AACGGAAACTCATA-AGGGTTA
56490597 AACGGAAACTCATAAGGGTTA
1 AACGGAAACTCATAAGGGTTA
56490618 AA
1 AA
56490620 TAGAAGCTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
20 1 0.03
21 30 0.91
22 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (21 bp):
AACGGAAACTCATAAGGGTTA
Found at i:56494818 original size:40 final size:40
Alignment explanation
Indices: 56494759--56495019 Score: 459
Period size: 40 Copynumber: 6.5 Consensus size: 40
56494749 TGATTCCGTA
*
56494759 CACCGGCATGAAGCCTGCTAGACGTATAGTCTGAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
* *
56494799 CACCGGCATTAAGCTTGCTAGACGTATAATCTGAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
56494839 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
*
56494879 CACCGGCATTAAGCCTACTAGACGTATAGTCTGAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
* *
56494919 CACCGGCATTAAGCCTACTAGACGTATAATCTGAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
*
56494959 CACCAGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
56494999 CACCGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
56495020 GCACAAGCCT
Statistics
Matches: 210, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 210 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
Found at i:56496594 original size:13 final size:13
Alignment explanation
Indices: 56496576--56496600 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56496566 TCAAACAATC
56496576 AAATTTTTATACG
1 AAATTTTTATACG
56496589 AAATTTTTATAC
1 AAATTTTTATAC
56496601 ATATCAATTC
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:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
AAATTTTTATACG
Found at i:56499747 original size:17 final size:18
Alignment explanation
Indices: 56499727--56499762 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
56499717 AACACATAAT
56499727 ATTAATTAT-TAAGTTTA
1 ATTAATTATCTAAGTTTA
*
56499744 ATTAATTATCTAATTTTA
1 ATTAATTATCTAAGTTTA
56499762 A
1 A
56499763 ATTGAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTAATTATCTAAGTTTA
Found at i:56499980 original size:27 final size:27
Alignment explanation
Indices: 56499950--56500006 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
56499940 TATCAAATTA
*
56499950 GTATTACTATCAAATTTTATAATAAGT
1 GTATCACTATCAAATTTTATAATAAGT
* * *
56499977 GTATCATTATCAAATTTTGTAGTAAGT
1 GTATCACTATCAAATTTTATAATAAGT
56500004 GTA
1 GTA
56500007 CCATCATGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (27 bp):
GTATCACTATCAAATTTTATAATAAGT
Found at i:56504444 original size:62 final size:59
Alignment explanation
Indices: 56504332--56504448 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 59
56504322 ATCACTTTAA
* * * *
56504332 TATTAAATTAATATAATACTTATCAAGATAAATATTAGACTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTATCAAGATAAACATTAAACTAAATATAATATTAAATCT
* *
56504391 TATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAATTAAATATAATATTAA
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAACATTAAACTAAATATAATATTAA
56504449 GATAACTAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 20 0.41
61 1 0.02
62 28 0.57
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.39
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTATCAAGATAAACATTAAACTAAATATAATATTAAATCT
Found at i:56517435 original size:23 final size:23
Alignment explanation
Indices: 56517386--56517435 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
56517376 TAAAAATGTA
* * *
56517386 AAAAAAATTAAATATATATTTGC
1 AAAAAAATTAAAAATATAATTCC
56517409 AAAAAAA-TAAAAATATAATTCC
1 AAAAAAATTAAAAATATAATTCC
*
56517431 TAAAA
1 AAAAA
56517436 GTGTTCTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAAAAATTAAAAATATAATTCC
Found at i:56526050 original size:100 final size:99
Alignment explanation
Indices: 56525939--56526132 Score: 262
Period size: 100 Copynumber: 1.9 Consensus size: 99
56525929 TTTTTTTAAT
* * * **
56525939 GTTGGTACCTCAATTAGTTAAACCGCTAGTCAAATTATTAAGTCAATTTAAAAAAAAGTTTGACC
1 GTTGATACCTCAATTAGTCAAACCGCTACTCAAATTATTAAGTCAATTTAAAAAAAAGTTCAACC
* *
56526004 CATAAATTAGTACAAAAATTATGCTTTTTTCTCAA
66 CACAAATTAGTAC-AAAACTATGCTTTTTTCTCAA
* * * * *
56526039 GTTGATACCTCAATTAGTCAAACTGCTACTCAAATTGTTAAGTCTATTTAAAAAAAGGTTCAACT
1 GTTGATACCTCAATTAGTCAAACCGCTACTCAAATTATTAAGTCAATTTAAAAAAAAGTTCAACC
*
56526104 CACAAATTGGTACAAAACTATGCTTTTTT
66 CACAAATTAGTACAAAACTATGCTTTTTT
56526133 TTTCCATTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
99 15 0.19
100 66 0.81
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (99 bp):
GTTGATACCTCAATTAGTCAAACCGCTACTCAAATTATTAAGTCAATTTAAAAAAAAGTTCAACC
CACAAATTAGTACAAAACTATGCTTTTTTCTCAA
Found at i:56527601 original size:15 final size:15
Alignment explanation
Indices: 56527592--56527625 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
56527582 CAAATGCTAT
56527592 AATAATAAATACAAC
1 AATAATAAATACAAC
*
56527607 AATAATAAATACATC
1 AATAATAAATACAAC
56527622 AATA
1 AATA
56527626 GCATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:56528249 original size:3 final size:3
Alignment explanation
Indices: 56528243--56528292 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
56528233 TTACAATACC
56528243 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56528291 AA
1 AA
56528293 GGAGAAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:56530844 original size:25 final size:26
Alignment explanation
Indices: 56530814--56530866 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
56530804 GGAGGGTTTT
*
56530814 ATTATTATTATTTAATATTAAT-TTA
1 ATTATTATTATTTAATAATAATATTA
*
56530839 ATTATTTTTATTTAATAATAATATTA
1 ATTATTATTATTTAATAATAATATTA
56530865 AT
1 AT
56530867 ATAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTATTATTATTTAATAATAATATTA
Found at i:56548436 original size:21 final size:21
Alignment explanation
Indices: 56548394--56548437 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
56548384 ATATGCATGC
*
56548394 TTTTATACATATATTTTTTAT
1 TTTTATACATATATTTTCTAT
*
56548415 TTTTAATACATGTA-TTTCTAT
1 TTTT-ATACATATATTTTCTAT
56548436 TT
1 TT
56548438 GTTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTATACATATATTTTCTAT
Found at i:56559579 original size:16 final size:16
Alignment explanation
Indices: 56559529--56559580 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 16
56559519 GGGTAAGAAG
56559529 TAAAAGTTTAGAGGGAAAA
1 TAAAAGTTT-GAGGG--AA
56559548 TAAAAAGTTTTG-GGGAA
1 T-AAAAG-TTTGAGGGAA
56559565 TAAAAGTTTGAGGGAA
1 TAAAAGTTTGAGGGAA
56559581 AATAAATAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
15 4 0.13
16 10 0.33
17 3 0.10
19 4 0.13
20 6 0.20
21 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.25
Consensus pattern (16 bp):
TAAAAGTTTGAGGGAA
Found at i:56559600 original size:31 final size:33
Alignment explanation
Indices: 56559527--56559616 Score: 103
Period size: 35 Copynumber: 2.7 Consensus size: 33
56559517 AAGGGTAAGA
56559527 AGTAAAAGTTTAGAGGGAAAATAAAAAGTTTTGGGG
1 AGTAAAAGTTTAGAGGGAAAATAAAAAG---TGGGG
* *
56559563 AATAAAAGTTT-GAGGGAAAATAAATAG-GGGG
1 AGTAAAAGTTTAGAGGGAAAATAAAAAGTGGGG
* *
56559594 AGTAAAATTTTGGAGGGAAAATA
1 AGTAAAAGTTTAGAGGGAAAATA
56559617 TTAAAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 13 0.27
32 11 0.22
35 15 0.31
36 10 0.20
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (33 bp):
AGTAAAAGTTTAGAGGGAAAATAAAAAGTGGGG
Found at i:56565681 original size:11 final size:10
Alignment explanation
Indices: 56565661--56565711 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
56565651 ATTTATGACG
*
56565661 TTTTTATAAT
1 TTTTTTTAAT
56565671 TTTCTTTTAAT
1 TTT-TTTTAAT
56565682 TTTTTTT-AT
1 TTTTTTTAAT
*
56565691 TTTTTTAAAT
1 TTTTTTTAAT
* *
56565701 ATTTTTAAAT
1 TTTTTTTAAT
56565711 T
1 T
56565712 ATTTATTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
9 8 0.23
10 18 0.51
11 9 0.26
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:56574291 original size:14 final size:14
Alignment explanation
Indices: 56574272--56574300 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56574262 TCATCGTGCG
56574272 AAATCACATGGCCT
1 AAATCACATGGCCT
56574286 AAATCACATGGCCT
1 AAATCACATGGCCT
56574300 A
1 A
56574301 CCGCACAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.21
Consensus pattern (14 bp):
AAATCACATGGCCT
Found at i:56576621 original size:41 final size:44
Alignment explanation
Indices: 56576496--56576683 Score: 145
Period size: 45 Copynumber: 4.2 Consensus size: 44
56576486 ATACTCGGAT
* * *
56576496 AATCACATATATCGAACAATGCCAACGTCCCAGACGTGGTCTTACATG
1 AATCACATATATCG----ATGCCAATGTCCCAGACATGGTCTTACACG
* * * * * *
56576544 CTATCTC--ATATCAATGCCACTGTCCCGGACAGGGTCTTACACG
1 -AATCACATATATCGATGCCAATGTCCCAGACATGGTCTTACACG
*
56576587 AATCA-A-ATA-CGATGCCAATGTCCTAGACATGGTCTTACACG
1 AATCACATATATCGATGCCAATGTCCCAGACATGGTCTTACACG
* *
56576628 TAATCACATATATCGATGCC-ATCGTCCCAGACGTGGTCCTACACG
1 -AATCACATATATCGATGCCAAT-GTCCCAGACATGGTCTTACACG
*
56576673 AGAACACATAT
1 A-ATCACATAT
56576684 CGAAAATCCT
Statistics
Matches: 112, Mismatches: 20, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
41 27 0.24
42 11 0.10
43 25 0.22
44 6 0.05
45 34 0.30
47 5 0.04
49 4 0.04
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (44 bp):
AATCACATATATCGATGCCAATGTCCCAGACATGGTCTTACACG
Found at i:56578853 original size:3 final size:3
Alignment explanation
Indices: 56578845--56578885 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
56578835 GTGAATTAAA
*
56578845 TAT TAT TA- TAT TAT TAT TAT ATAT TGT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
56578886 ACTAATACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:56580010 original size:23 final size:24
Alignment explanation
Indices: 56579951--56580013 Score: 94
Period size: 23 Copynumber: 2.7 Consensus size: 24
56579941 GCCGATCATG
* *
56579951 CACTTTATGTGTCATA-CATCAGG
1 CACTTTATGTGTCGTATCATCAGA
56579974 CACTTTATGTGTCGTATC-TCAGA
1 CACTTTATGTGTCGTATCATCAGA
56579997 CACTTTATGTGTCGTAT
1 CACTTTATGTGTCGTAT
56580014 GAAGCACCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 36 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (24 bp):
CACTTTATGTGTCGTATCATCAGA
Found at i:56587080 original size:41 final size:41
Alignment explanation
Indices: 56587035--56587175 Score: 219
Period size: 41 Copynumber: 3.4 Consensus size: 41
56587025 TTTATAATAT
* * *
56587035 TCACCGGCACTTAGCTTGTTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGTTAGGTTTATAACCTGATTCAGA
56587076 TCACCGGCACTTAGCCTGTTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGTTAGGTTTATAACCTGATTCAGA
* * *
56587117 TCACCGGCATTTAGCCTGCTAGGTTTATAACTTGATTCAGA
1 TCACCGGCACTTAGCCTGTTAGGTTTATAACCTGATTCAGA
*
56587158 TCACTGGCACTTAGCCTG
1 TCACCGGCACTTAGCCTG
56587176 CTAGACTTAA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGTTAGGTTTATAACCTGATTCAGA
Found at i:56593118 original size:14 final size:14
Alignment explanation
Indices: 56593099--56593125 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56593089 TGATTCGACA
56593099 TAACCTTTTATGAT
1 TAACCTTTTATGAT
56593113 TAACCTTTTATGA
1 TAACCTTTTATGA
56593126 AATAATCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (14 bp):
TAACCTTTTATGAT
Found at i:56596193 original size:41 final size:41
Alignment explanation
Indices: 56596148--56596256 Score: 182
Period size: 41 Copynumber: 2.7 Consensus size: 41
56596138 TTTAACATAT
* *
56596148 TCACCGGCACTTAGCCTGTTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
56596189 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
56596230 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
56596257 AAGTCCGAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:56596930 original size:25 final size:25
Alignment explanation
Indices: 56596896--56596959 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
56596886 ACAAGAATTT
56596896 ATACATATATATATTTTCGAACATG
1 ATACATATATATATTTTCGAACATG
56596921 ATACATATATATATTTTCGAACATG
1 ATACATATATATATTTTCGAACATG
56596946 ATACATATATATAT
1 ATACATATATATAT
56596960 ATCATTCATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (25 bp):
ATACATATATATATTTTCGAACATG
Found at i:56597983 original size:13 final size:13
Alignment explanation
Indices: 56597965--56597990 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56597955 CACAAACGAT
56597965 GAAATTTTCACAC
1 GAAATTTTCACAC
56597978 GAAATTTTCACAC
1 GAAATTTTCACAC
56597991 AAGTAAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
GAAATTTTCACAC
Found at i:56599677 original size:60 final size:58
Alignment explanation
Indices: 56599600--56599727 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 58
56599590 CCTTTCGTTA
* * * **
56599600 AAGTTTCAGTCTCAACAAAGATGGGCTACTCAAGTTTCTTTGCTTTTTTTCAAACTTTTC
1 AAGTTTCAGTCTCAACAAAGATGGACGACTCAAGTTTCATT--TTAATTTCAAACTTTTC
* * *
56599660 AAGTTTTAGTCTTAACAAAGATGGACGACTCAAGTTTCATTTTAATTTCAAACTTTTT
1 AAGTTTCAGTCTCAACAAAGATGGACGACTCAAGTTTCATTTTAATTTCAAACTTTTC
56599718 AAGTTTCAGT
1 AAGTTTCAGT
56599728 TTTGCTATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 23 0.39
60 36 0.61
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (58 bp):
AAGTTTCAGTCTCAACAAAGATGGACGACTCAAGTTTCATTTTAATTTCAAACTTTTC
Found at i:56606308 original size:42 final size:41
Alignment explanation
Indices: 56606253--56606350 Score: 100
Period size: 36 Copynumber: 2.5 Consensus size: 41
56606243 TTCTCTACGA
* *
56606253 GATGTTAAATTAGTGCAATCTCAGTCCAATACT-TCTTCGGCT
1 GATGTTGACTTAGTGCAATC-CAGTCCAATACTCT-TTCGGCT
*
56606295 GATGTTGACTTAGTG-----CAGTCCAATGCTCTTTCGGCT
1 GATGTTGACTTAGTGCAATCCAGTCCAATACTCTTTCGGCT
*
56606331 GATGTTGACTTGGTGCAATC
1 GATGTTGACTTAGTGCAATC
56606351 ACCAGATGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
36 32 0.70
37 1 0.02
42 13 0.28
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (41 bp):
GATGTTGACTTAGTGCAATCCAGTCCAATACTCTTTCGGCT
Found at i:56606328 original size:36 final size:36
Alignment explanation
Indices: 56606274--56606347 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
56606264 AGTGCAATCT
56606274 CAGTCCAATACTTCTTCGGCTGATGTTGACTTAGTG
1 CAGTCCAATACTTCTTCGGCTGATGTTGACTTAGTG
* *
56606310 CAGTCCAATGC-TCTTTCGGCTGATGTTGACTTGGTG
1 CAGTCCAATACTTC-TTCGGCTGATGTTGACTTAGTG
56606346 CA
1 CA
56606348 ATCACCAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 2 0.06
36 33 0.94
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (36 bp):
CAGTCCAATACTTCTTCGGCTGATGTTGACTTAGTG
Found at i:56606441 original size:69 final size:69
Alignment explanation
Indices: 56606330--56606464 Score: 243
Period size: 69 Copynumber: 2.0 Consensus size: 69
56606320 CTCTTTCGGC
*
56606330 TGATGTTGACTTGGTGCAATCACCAGATGTTTCAAGTGGTAATGCTCGGTCTATCACAAGAACAT
1 TGATGTTGACTTGGAGCAATCACCAGATGTTTCAAGTGGTAATGCTCGGTCTATCACAAGAACAT
56606395 CAAT
66 CAAT
* *
56606399 TGATGTTGACTTGGAGCAATCACCAGATGTTTCAAGTGGTAATGCTTGGTCTATTACAAGAACAT
1 TGATGTTGACTTGGAGCAATCACCAGATGTTTCAAGTGGTAATGCTCGGTCTATCACAAGAACAT
56606464 C
66 C
56606465 TGAAGGTGTC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (69 bp):
TGATGTTGACTTGGAGCAATCACCAGATGTTTCAAGTGGTAATGCTCGGTCTATCACAAGAACAT
CAAT
Found at i:56606447 original size:35 final size:34
Alignment explanation
Indices: 56606339--56606447 Score: 85
Period size: 35 Copynumber: 3.1 Consensus size: 34
56606329 CTGATGTTGA
56606339 CTTGGTGCAATCACCAGATGTTTCAAGTGGTAATG
1 CTTGG-GCAATCACCAGATGTTTCAAGTGGTAATG
* * * * *** * * **
56606374 CTCGGTCTATCACAAGA-ACATCAATTGATGTTG
1 CTTGGGCAATCACCAGATGTTTCAAGTGGTAATG
56606407 ACTTGGAGCAATCACCAGATGTTTCAAGTGGTAATG
1 -CTTGG-GCAATCACCAGATGTTTCAAGTGGTAATG
56606443 CTTGG
1 CTTGG
56606448 TCTATTACAA
Statistics
Matches: 49, Mismatches: 22, Indels: 6
0.64 0.29 0.08
Matches are distributed among these distances:
33 9 0.18
34 13 0.27
35 18 0.37
36 9 0.18
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (34 bp):
CTTGGGCAATCACCAGATGTTTCAAGTGGTAATG
Found at i:56608624 original size:20 final size:19
Alignment explanation
Indices: 56608599--56608636 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
56608589 AAATAATTTG
56608599 AATTTTAAAAATTAATTTTC
1 AATTTTAAAAATT-ATTTTC
*
56608619 AATTTTGAAAATTATTTT
1 AATTTTAAAAATTATTTT
56608637 AAGTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTC
Found at i:56612573 original size:3 final size:3
Alignment explanation
Indices: 56612565--56612629 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
56612555 GGGTTTTAAA
* * * * *
56612565 AAT AAT AAT ACT AAT AAT AAT GAG AAT AAT -AT GAAT GAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
56612610 AAT AAT AAAT AAT GAAT AAT
1 AAT AAT -AAT AAT -AAT AAT
56612630 CTAAGGTTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
2 2 0.04
3 38 0.79
4 8 0.17
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:56613449 original size:2 final size:2
Alignment explanation
Indices: 56613434--56613474 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
56613424 CCCTTTTTAT
*
56613434 TA TA TA TT TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56613475 CAATTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 35 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56614236 original size:44 final size:44
Alignment explanation
Indices: 56614188--56614303 Score: 135
Period size: 44 Copynumber: 2.6 Consensus size: 44
56614178 TGTCAATTTG
*
56614188 ATCCACTCCACTGCAACTTCAGGGAGATAAAACTTGTAGCTTCT-
1 ATCCACTCCACTGCAACTTCAGGGAGATAAAACTTATAGCTT-TA
* * * *
56614232 ATCCATTCCACTGTAACTTTAGGGAGATAAGACTTATAGCTTTA
1 ATCCACTCCACTGCAACTTCAGGGAGATAAAACTTATAGCTTTA
*** *
56614276 ATTTGCTCCGCTGCAACTTCAGGGAGAT
1 ATCCACTCCACTGCAACTTCAGGGAGAT
56614304 GAGATTTGTG
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 1 0.02
44 58 0.98
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCCACTCCACTGCAACTTCAGGGAGATAAAACTTATAGCTTTA
Found at i:56614595 original size:44 final size:44
Alignment explanation
Indices: 56614531--56614824 Score: 205
Period size: 44 Copynumber: 6.5 Consensus size: 44
56614521 GCCCCACTTT
* * * * *
56614531 AACTTCA-AGGAGATACGATTTATAGCTTTAATATGCTCTAGTGC
1 AACTTCAGA-GAGATAAGATTTATAACTTCAATCTGCTCTACTGC
* * * *
56614575 AACTTCAGAGAGAAAAGATTTTCTATCTTCAATCTACTCTACTGC
1 AACTTCAGAGAGATAAGA-TTTATAACTTCAATCTGCTCTACTGC
* * **
56614620 AACTTCAGAGAGATAAGATCTATAACTTCAATCTGCTCCACTAT
1 AACTTCAGAGAGATAAGATTTATAACTTCAATCTGCTCTACTGC
* * * * *
56614664 AACTTCAGGGAGATAAGATTTGTAATTTGTGGCTTTAATCTGTTCCACTGC
1 AACTTCAGAGAGATAAGATTTATAA-------CTTCAATCTGCTCTACTGC
* * * * ** * * *
56614715 AATTTTAGGGAAATAAGATTCGCTATCTTTAGTCTGCTCTACTGC
1 AACTTCAGAGAGATAAGATT-TATAACTTCAATCTGCTCTACTGC
* * *
56614760 AACTTCAGAGAGATAAGATCTATAACTTCAATCTGCTCCATTGC
1 AACTTCAGAGAGATAAGATTTATAACTTCAATCTGCTCTACTGC
56614804 AACTTCATG-GAGATAAGATTT
1 AACTTCA-GAGAGATAAGATTT
56614825 GTAATTTGTA
Statistics
Matches: 194, Mismatches: 45, Indels: 22
0.74 0.17 0.08
Matches are distributed among these distances:
44 90 0.46
45 70 0.36
51 32 0.16
52 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Consensus pattern (44 bp):
AACTTCAGAGAGATAAGATTTATAACTTCAATCTGCTCTACTGC
Found at i:56614725 original size:51 final size:45
Alignment explanation
Indices: 56614696--56614963 Score: 211
Period size: 44 Copynumber: 5.9 Consensus size: 45
56614686 TAATTTGTGG
* * * * *
56614696 CTTTAATCTGTTCCACTGCAATTTTAGGGAAATAAGATTCGCT-AT
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAAT
* * * * *
56614741 CTTTAGTCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATAA-
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAT
* * *
56614785 CTTCAATCTGCTCCATTGCAACTTCATGGAGATAAGATTTGTAATTTGT
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAA----T
* * * * *
56614834 AGCTTTAATATGTTCCACTGCAACTTTAGGGAAATAAGATTCGCT-AT
1 --CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAAT
* * * *
56614881 TTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAACTTGTAA-
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAT
* * *
56614925 CTTCAACCTGCTCCATTGCAACTTCAGGGAGATAAGATT
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
56614964 CACTATAATG
Statistics
Matches: 171, Mismatches: 42, Indels: 21
0.73 0.18 0.09
Matches are distributed among these distances:
44 70 0.41
45 65 0.38
47 1 0.01
51 34 0.20
52 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (45 bp):
CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAT
Found at i:56614761 original size:140 final size:140
Alignment explanation
Indices: 56614548--56614963 Score: 584
Period size: 140 Copynumber: 3.0 Consensus size: 140
56614538 AGGAGATACG
* * * * * * ** * * *
56614548 ATTTATAGCTTTAATATGCTCTAGTGCAACTTCAGAGAGAA-AAGATTTTCTATCTTCAATCTAC
1 ATTTGTAGCTTTAATATGTTCCACTGCAACTTTAGGGA-AATAAGATTCGCTATCTTTAGTCTGC
* **
56614612 TCTACTGCAACTTCAGAGAGATAAGATCTATAACTTCAATCTGCTCCACTATAACTTCAGGGAGA
65 TCTACTGCAACTTCAGAGAGATAAGATCTATAACTTCAATCTGCTCCATTGCAACTTCAGGGAGA
56614677 TAAGATTTGTA
130 TAAGATTTGTA
* * *
56614688 ATTTGTGGCTTTAATCTGTTCCACTGCAATTTTAGGGAAATAAGATTCGCTATCTTTAGTCTGCT
1 ATTTGTAGCTTTAATATGTTCCACTGCAACTTTAGGGAAATAAGATTCGCTATCTTTAGTCTGCT
*
56614753 CTACTGCAACTTCAGAGAGATAAGATCTATAACTTCAATCTGCTCCATTGCAACTTCATGGAGAT
66 CTACTGCAACTTCAGAGAGATAAGATCTATAACTTCAATCTGCTCCATTGCAACTTCAGGGAGAT
56614818 AAGATTTGTA
131 AAGATTTGTA
*
56614828 ATTTGTAGCTTTAATATGTTCCACTGCAACTTTAGGGAAATAAGATTCGCTATTTTTAGTCTGCT
1 ATTTGTAGCTTTAATATGTTCCACTGCAACTTTAGGGAAATAAGATTCGCTATCTTTAGTCTGCT
* * * * *
56614893 CCACTGCAACTTCAGGGAGATAA-AACTTGTAACTTCAACCTGCTCCATTGCAACTTCAGGGAGA
66 CTACTGCAACTTCAGAGAGATAAGATC-TATAACTTCAATCTGCTCCATTGCAACTTCAGGGAGA
56614957 TAAGATT
130 TAAGATT
56614964 CACTATAATG
Statistics
Matches: 246, Mismatches: 28, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
139 4 0.02
140 242 0.98
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (140 bp):
ATTTGTAGCTTTAATATGTTCCACTGCAACTTTAGGGAAATAAGATTCGCTATCTTTAGTCTGCT
CTACTGCAACTTCAGAGAGATAAGATCTATAACTTCAATCTGCTCCATTGCAACTTCAGGGAGAT
AAGATTTGTA
Found at i:56626432 original size:24 final size:24
Alignment explanation
Indices: 56626405--56626478 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
56626395 AATATGAATG
56626405 ATAATAAAAATAATAAATAAAAGA
1 ATAATAAAAATAATAAATAAAAGA
*
56626429 ATAA-ATAAAAGAATAAATAAATA-A
1 ATAATA-AAAATAATAAATAAA-AGA
*
56626453 ATATGATAAAAATCAT--ATAAAAGA
1 ATA--ATAAAAATAATAAATAAAAGA
56626477 AT
1 AT
56626479 GTGAATAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
23 2 0.05
24 30 0.73
25 1 0.02
26 7 0.17
27 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.23
Consensus pattern (24 bp):
ATAATAAAAATAATAAATAAAAGA
Found at i:56626455 original size:12 final size:12
Alignment explanation
Indices: 56626411--56626449 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
56626401 AATGATAATA
*
56626411 AAAATAATAAAT
1 AAAAGAATAAAT
56626423 AAAAGAATAAAT
1 AAAAGAATAAAT
56626435 AAAAGAATAAAT
1 AAAAGAATAAAT
56626447 AAA
1 AAA
56626450 TAAATATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (12 bp):
AAAAGAATAAAT
Found at i:56631380 original size:15 final size:15
Alignment explanation
Indices: 56631358--56631393 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
56631348 CAATTTAAAG
56631358 AAAAATGAATATTGT
1 AAAAATGAATATTGT
* *
56631373 ACAAATGAATGTTGT
1 AAAAATGAATATTGT
56631388 AAAAAT
1 AAAAAT
56631394 ATTGGTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.14, T:0.31
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:56632896 original size:20 final size:20
Alignment explanation
Indices: 56632868--56632905 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56632858 ATCAAAGTAA
56632868 TTTTCAAAATTTGAAAATAAC
1 TTTTCAAAATTT-AAAATAAC
56632889 TTTT-AAAATTTAAAATA
1 TTTTCAAAATTTAAAATA
56632906 TTTATAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
TTTTCAAAATTTAAAATAAC
Done.