Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 15 of 66
Found at i:5017325 original size:27 final size:27
Alignment explanation
Indices: 5017261--5017333 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
5017251 ATTAAACACC
* * *
5017261 TTAAACATGGCATATAATAACTTTTTTT
1 TTAAACATGACATGTAACAA-TTTTTTT
5017289 TTAAACATGACATGTAACAATTTTTTT
1 TTAAACATGACATGTAACAATTTTTTT
* * *
5017316 TTTAATATGACTTGTAAC
1 TTAAACATGACATGTAAC
5017334 TTATTCTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (27 bp):
TTAAACATGACATGTAACAATTTTTTT
Found at i:5017368 original size:126 final size:127
Alignment explanation
Indices: 5017181--5017460 Score: 305
Period size: 126 Copynumber: 2.2 Consensus size: 127
5017171 TATAATAATT
* * * *
5017181 TTTTTTTCTTTCAACATGACATGTAACTTGGTCTTTATCACTGTGTTTCACTAAGACATAAATTC
1 TTTTTTT-TTT-AACATGACATGTAACTTAGTCTTTATCACTATATTTCACTAAGACATAAACTC
* *
5017246 TTGAAA-TTAAACACCTTAAACATGGCATATAATAACTTTTTTTTTAAACAT-GACATGTAACAA
64 TT-AAAGTTAAACACCTTAAACATGACATATAACAACTTTTTTTTTAAACATAG-CATGTAACAA
5017309 -
127 C
* * * ** *
5017309 TTTTTTTTTTAATATGACTTGTAACTTATTCTTTATCTTTATATTTCACTAAGATATAAACTCTT
1 TTTTTTTTTTAACATGACATGTAACTTAGTCTTTATCACTATATTTCACTAAGACATAAACTCTT
* ** * * * * *
5017374 AAAGTTAAGCATTTTAAACATGACGTGTAACAACTTTTTTTTTCAACATAGTATGTAATAAC
66 AAAGTTAAACACCTTAAACATGACATATAACAACTTTTTTTTTAAACATAGCATGTAACAAC
* *
5017436 TTTTTTTTTTAACATGGCGTGTAAC
1 TTTTTTTTTTAACATGACATGTAAC
5017461 AATATTATTT
Statistics
Matches: 126, Mismatches: 23, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
125 3 0.02
126 90 0.71
127 26 0.21
128 7 0.06
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (127 bp):
TTTTTTTTTTAACATGACATGTAACTTAGTCTTTATCACTATATTTCACTAAGACATAAACTCTT
AAAGTTAAACACCTTAAACATGACATATAACAACTTTTTTTTTAAACATAGCATGTAACAAC
Found at i:5017422 original size:28 final size:28
Alignment explanation
Indices: 5017385--5017462 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
5017375 AAGTTAAGCA
5017385 TTTTAAACATGACGTGTAACAACTTTTT
1 TTTTAAACATGACGTGTAACAACTTTTT
* *
5017413 TTTTCAACAT-A-GTATGTAATAACTTTTT
1 TTTTAAACATGACG--TGTAACAACTTTTT
* *
5017441 TTTTTAACATGGCGTGTAACAA
1 TTTTAAACATGACGTGTAACAA
5017463 TATTATTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 38 0.93
30 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (28 bp):
TTTTAAACATGACGTGTAACAACTTTTT
Found at i:5020018 original size:13 final size:13
Alignment explanation
Indices: 5020000--5020025 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5019990 TTTCAGAAAA
5020000 TTTATAAAATCAT
1 TTTATAAAATCAT
5020013 TTTATAAAATCAT
1 TTTATAAAATCAT
5020026 AATTTCTCTT
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:5021417 original size:19 final size:19
Alignment explanation
Indices: 5021393--5021430 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5021383 CTGCCAAACC
*
5021393 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
5021412 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
5021431 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:5033622 original size:2 final size:2
Alignment explanation
Indices: 5033615--5033659 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
5033605 ATACATACAT
*
5033615 AC AC AC AC AC GC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5033657 AC A
1 AC A
5033660 TGATGTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.49, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5037215 original size:2 final size:2
Alignment explanation
Indices: 5037208--5037242 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5037198 ATAAATGTAT
5037208 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5037243 TATAGATGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5048127 original size:18 final size:19
Alignment explanation
Indices: 5048104--5048143 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5048094 CAAGGAAAAA
*
5048104 ATTTTA-GAGTAAAATAAT
1 ATTTTATGAATAAAATAAT
*
5048122 ATTTTATTAATAAAATAAT
1 ATTTTATGAATAAAATAAT
5048141 ATT
1 ATT
5048144 AAAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:5048990 original size:34 final size:34
Alignment explanation
Indices: 5048945--5049049 Score: 129
Period size: 34 Copynumber: 3.0 Consensus size: 34
5048935 AGTAGCTTTA
5048945 GCTGCTGATTTTGGAGGCTGAAAAGTGCAGTTTT
1 GCTGCTGATTTTGGAGGCTGAAAAGTGCAGTTTT
* *
5048979 GTTGCTGATTTTGGAGGCTGAGAAGTGCAGATTTTT
1 GCTGCTGATTTTGGAGGCTGAAAAGTGCAG--TTTT
* * * * *
5049015 GCAGCTGATTTTGAAGGTTGTAAGGTGCAGTTTT
1 GCTGCTGATTTTGGAGGCTGAAAAGTGCAGTTTT
5049049 G
1 G
5049050 GTTGTTAATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
34 33 0.55
36 27 0.45
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.37
Consensus pattern (34 bp):
GCTGCTGATTTTGGAGGCTGAAAAGTGCAGTTTT
Found at i:5060346 original size:25 final size:25
Alignment explanation
Indices: 5060298--5060350 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
5060288 TGTATATACA
5060298 CATATATAATCTAAGTGTACAATGT
1 CATATATAATCTAAGTGTACAATGT
5060323 CATATATAATCTAAGTGTACAATGT
1 CATATATAATCTAAGTGTACAATGT
5060348 CAT
1 CAT
5060351 TCTCTCTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (25 bp):
CATATATAATCTAAGTGTACAATGT
Found at i:5062935 original size:44 final size:44
Alignment explanation
Indices: 5062867--5062954 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
5062857 ACCATTTTCT
* **
5062867 TTACATGCACACTAAATAGGTTTAGGTTTAGTTGGCTATTATAA
1 TTACATGCACACCAAATAGGTTTAGGTTTAGTTAACTATTATAA
* *
5062911 TTACTTGCACACCAAGTAGGTTTAGGTTTAGTTAACTATTATAA
1 TTACATGCACACCAAATAGGTTTAGGTTTAGTTAACTATTATAA
5062955 ATAGCTCCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (44 bp):
TTACATGCACACCAAATAGGTTTAGGTTTAGTTAACTATTATAA
Found at i:5063489 original size:34 final size:34
Alignment explanation
Indices: 5063450--5063516 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
5063440 TGAAACCCTC
5063450 ACAATGCTTTTTCACGAT-AGCAAATGGAACCTTT
1 ACAATGCTTTTTCAC-ATGAGCAAATGGAACCTTT
* *
5063484 ACAATGCTTTTTCACTTGAGCAAGTGGAACCTT
1 ACAATGCTTTTTCACATGAGCAAATGGAACCTT
5063517 ACATTGCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 1 0.03
34 29 0.97
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (34 bp):
ACAATGCTTTTTCACATGAGCAAATGGAACCTTT
Found at i:5063538 original size:33 final size:34
Alignment explanation
Indices: 5063450--5063540 Score: 96
Period size: 34 Copynumber: 2.7 Consensus size: 34
5063440 TGAAACCCTC
* * * *
5063450 ACAATGCTTTTTCACGATAGCAAATGGAACCTTT
1 ACAATGCCTTTTCACTAGAGCAAGTGGAACCTTT
* *
5063484 ACAATGCTTTTTCACTTGAGCAAGTGGAACC-TT
1 ACAATGCCTTTTCACTAGAGCAAGTGGAACCTTT
*
5063517 ACATTGCCTTTT-ATCTAGAGCAAG
1 ACAATGCCTTTTCA-CTAGAGCAAG
5063541 CATAACCCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
32 1 0.02
33 21 0.43
34 27 0.55
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (34 bp):
ACAATGCCTTTTCACTAGAGCAAGTGGAACCTTT
Found at i:5064296 original size:43 final size:43
Alignment explanation
Indices: 5064242--5064343 Score: 150
Period size: 43 Copynumber: 2.4 Consensus size: 43
5064232 ATTATCAAAA
* *
5064242 GAATTCCGTTGGAAATAATTTCATAGGAAATGAATTTCCAACG
1 GAATTTCGTTGGAAATAATTCCATAGGAAATGAATTTCCAACG
* * * *
5064285 GAATTTTGTTGGAAATAATTCCGTAGGTAATGAATTTCTAACG
1 GAATTTCGTTGGAAATAATTCCATAGGAAATGAATTTCCAACG
5064328 GAATTTCGTTGGAAAT
1 GAATTTCGTTGGAAAT
5064344 TTCCAACAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (43 bp):
GAATTTCGTTGGAAATAATTCCATAGGAAATGAATTTCCAACG
Found at i:5064500 original size:56 final size:55
Alignment explanation
Indices: 5064391--5064500 Score: 141
Period size: 56 Copynumber: 2.0 Consensus size: 55
5064381 GGAAAAAACG
* * *
5064391 TTGAAAATTTCCAATGAAATTTTTCGTTGGAAAAAAAATTGCTACGAAAAATTCAT
1 TTGAAAATTTCCAACGAAATTTTTCGTT-GAAAAAAAATTCCCACGAAAAATTCAT
* *
5064447 TTGAAAATTTCCAACGAAATTTTTCGTT-AAAAAAACATTTCCCATGAATAATTC
1 TTGAAAATTTCCAACGAAATTTTTCGTTGAAAAAAA-A-TTCCCACGAAAAATTC
5064501 CGTAGGAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
54 7 0.15
55 1 0.02
56 39 0.83
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.35
Consensus pattern (55 bp):
TTGAAAATTTCCAACGAAATTTTTCGTTGAAAAAAAATTCCCACGAAAAATTCAT
Found at i:5067520 original size:2 final size:2
Alignment explanation
Indices: 5067513--5067538 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5067503 CAATCAATTG
5067513 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
5067539 TATTCATGAA
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:5068401 original size:2 final size:2
Alignment explanation
Indices: 5068384--5068417 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
5068374 TTAATTTCTC
* *
5068384 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5068418 TAACTTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5071395 original size:43 final size:43
Alignment explanation
Indices: 5071217--5071691 Score: 209
Period size: 43 Copynumber: 11.3 Consensus size: 43
5071207 TTTTGGCCGA
* * *
5071217 TAACTTTAAAGAAGGAATAAGCTTCTCATCTAGAATGAAGTTATA
1 TAACTTTAAA-AA-GAATAAGCTCCTCATCTAGAATGAAGCTATG
* * * * * * * * *
5071262 TAGCTTTACAAGGAATAAGCTCGTCATTTGGAAGGAGGCTACG
1 TAACTTTAAAAAGAATAAGCTCCTCATCTAGAATGAAGCTATG
* * * * ** *
5071305 TAGCTTTAAAATGAATAA-TTCCTTATCCGGAATGACA-CTACG
1 TAACTTTAAAAAGAATAAGCTCCTCATCTAGAATGA-AGCTATG
* *
5071347 TAACTTTAAAAAGAATAAGCTCCTCATATAGAATGAAGCCATG
1 TAACTTTAAAAAGAATAAGCTCCTCATCTAGAATGAAGCTATG
* *
5071390 TAACTTT-AAAAGAAATAAGCTCCTCATTTAGAATGAGGCTATG
1 TAACTTTAAAAAG-AATAAGCTCCTCATCTAGAATGAAGCTATG
* * * * * **
5071433 TAATTTTAAAAAG--T---CTCTTCATTTGGCAT-AAGGCTACA
1 TAACTTTAAAAAGAATAAGCTCCTCATCTAGAATGAA-GCTATG
* * * * * * *
5071471 TAACTTTAAAATGAATAAACTCTTTATTTGGAAT-AAGGTTATG
1 TAACTTTAAAAAGAATAAGCTCCTCATCTAGAATGAA-GCTATG
** * * *
5071514 TAAC-TTAAAAAGAATGTAA-CTTTTCATCTGGAATGAGGCTACG
1 TAACTTTAAAAAGAA--TAAGCTCCTCATCTAGAATGAAGCTATG
* * * *
5071557 TAA-TTTAAAAAGAATAAGCTCTTCATTTAAAAT-AGGGCTATG
1 TAACTTTAAAAAGAATAAGCTCCTCATCTAGAATGA-AGCTATG
* * * * *
5071599 TAACTTT-AAAAG---GA-CTCCTCATTTGGAAT-AAGGTTACG
1 TAACTTTAAAAAGAATAAGCTCCTCATCTAGAATGAA-GCTATG
* * *
5071637 TAACTTTAAAAGGAAATAAGCTCCTCATATAAAAT-AAGGCTATG
1 TAACTTTAAAAAG-AATAAGCTCCTCATCTAGAATGAA-GCTATG
5071681 TAACTTTAAAA
1 TAACTTTAAAA
5071692 TGATTTTTAA
Statistics
Matches: 332, Mismatches: 73, Indels: 51
0.73 0.16 0.11
Matches are distributed among these distances:
37 1 0.00
38 51 0.15
39 5 0.02
40 1 0.00
41 5 0.02
42 72 0.22
43 149 0.45
44 40 0.12
45 8 0.02
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (43 bp):
TAACTTTAAAAAGAATAAGCTCCTCATCTAGAATGAAGCTATG
Found at i:5071524 original size:166 final size:166
Alignment explanation
Indices: 5071346--5071691 Score: 394
Period size: 166 Copynumber: 2.1 Consensus size: 166
5071336 ATGACACTAC
*
5071346 GTAACTTTAAAAAGAA-TAAGCTCCTCATATAGAATGAAGCCATGTAACTTT-AAAAGAAATAAG
1 GTAACTTTAAAAAGAAGTAA-CTCCTCATATAGAATGAAGCCACGTAA-TTTAAAAAG-AATAAG
* * * * *
5071409 CTCCTCATTTAGAAT-GAGGCTATGTAATTTTAAAAAGTCTCTTCATTTGGCATAAGGCTACATA
63 CTCCTCATTTAAAATAG-GGCTATGTAACTTTAAAAAGACTCCTCATTTGGAATAAGGCTACATA
5071473 ACTTTAAAATGAATAAACTCTTTATTTGGAATAAGGTTAT
127 ACTTTAAAATGAATAAACTCTTTATTTGGAATAAGGTTAT
** * * * *
5071513 GTAAC-TTAAAAAGAATGTAACTTTTCATCTGGAATGAGGCTACGTAATTTAAAAAGAATAAGCT
1 GTAACTTTAAAAAGAA-GTAACTCCTCATATAGAATGAAGCCACGTAATTTAAAAAGAATAAGCT
* * * *
5071577 CTTCATTTAAAATAGGGCTATGTAACTTTAAAAGGACTCCTCATTTGGAATAAGGTTACGTAACT
65 CCTCATTTAAAATAGGGCTATGTAACTTTAAAAAGACTCCTCATTTGGAATAAGGCTACATAACT
* * * * * ** *
5071642 TTAAAAGGAAATAAGCTCCTCATATAAAATAAGGCTAT
130 TTAAAATG-AATAAACTCTTTATTTGGAATAAGGTTAT
5071680 GTAACTTTAAAA
1 GTAACTTTAAAA
5071692 TGATTTTTAA
Statistics
Matches: 149, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
166 82 0.55
167 58 0.39
168 9 0.06
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (166 bp):
GTAACTTTAAAAAGAAGTAACTCCTCATATAGAATGAAGCCACGTAATTTAAAAAGAATAAGCTC
CTCATTTAAAATAGGGCTATGTAACTTTAAAAAGACTCCTCATTTGGAATAAGGCTACATAACTT
TAAAATGAATAAACTCTTTATTTGGAATAAGGTTAT
Found at i:5071525 original size:124 final size:120
Alignment explanation
Indices: 5071387--5071691 Score: 292
Period size: 124 Copynumber: 2.5 Consensus size: 120
5071377 GAATGAAGCC
* *
5071387 ATGTAACTTTAAAAGAAATAAGCTCCTCATTTAGAATGAGGCTATGTAATTTTAAAAAG-T-CTC
1 ATGTAACTTAAAAAGAAATAAGCTCCTCATATAGAATGAGGCTATGTAA-TTTAAAAAGATACTC
*** * *
5071450 TTCATTTGGCATAAGGCTACATAACTTTAAAATGAATAAACTCTTTATTTGGAATAAGGTT
65 TTCATTTAAAATAAGGCTACATAACTTTAAAA-G----AACTCCTCATTTGGAATAAGGTT
* ** * * *
5071511 ATGTAACTTAAAAAGAATGTAA-CTTTTCATCTGGAATGAGGCTACGTAATTTAAAAAGAATAAG
1 ATGTAACTTAAAAAGAA-ATAAGCTCCTCATATAGAATGAGGCTATGTAATTTAAAAAG-AT-A-
* ** *
5071575 CTCTTCATTTAAAATAGGGCTATGTAACTTTAAAAGGACTCCTCATTTGGAATAAGGTT
62 CTCTTCATTTAAAATAAGGCTACATAACTTTAAAAGAACTCCTCATTTGGAATAAGGTT
* * * *
5071634 ACGTAACTTTAAAAGGAAATAAGCTCCTCATATAAAATAAGGCTATGTAACTTTAAAA
1 ATGTAAC-TTAAAAAGAAATAAGCTCCTCATATAGAATGAGGCTATGTAA-TTTAAAA
5071692 TGATTTTTAA
Statistics
Matches: 146, Mismatches: 26, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
123 38 0.26
124 67 0.46
125 11 0.08
127 1 0.01
128 29 0.20
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (120 bp):
ATGTAACTTAAAAAGAAATAAGCTCCTCATATAGAATGAGGCTATGTAATTTAAAAAGATACTCT
TCATTTAAAATAAGGCTACATAACTTTAAAAGAACTCCTCATTTGGAATAAGGTT
Found at i:5078956 original size:48 final size:48
Alignment explanation
Indices: 5078856--5078949 Score: 179
Period size: 48 Copynumber: 2.0 Consensus size: 48
5078846 GATCACCAAT
*
5078856 TAGATTGAATTAGAAACCTAGGTTAAACCTTGACGAAGGATATTTAAG
1 TAGATTGAATTAGAAACCTAGGTTAAACCTTGACGAAGGAGATTTAAG
5078904 TAGATTGAATTAGAAACCTAGGTTAAACCTTGACGAAGGAGATTTA
1 TAGATTGAATTAGAAACCTAGGTTAAACCTTGACGAAGGAGATTTA
5078950 GATAGATCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (48 bp):
TAGATTGAATTAGAAACCTAGGTTAAACCTTGACGAAGGAGATTTAAG
Found at i:5108125 original size:14 final size:14
Alignment explanation
Indices: 5108090--5108127 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
5108080 TAATTAAATT
*
5108090 ATTATGAAA-TATA
1 ATTATGAAAGAATA
5108103 ATT-TGAAAGAATA
1 ATTATGAAAGAATA
5108116 ATTATGAAAGAA
1 ATTATGAAAGAA
5108128 AATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 5 0.23
13 9 0.41
14 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (14 bp):
ATTATGAAAGAATA
Found at i:5114576 original size:18 final size:18
Alignment explanation
Indices: 5114550--5114584 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5114540 TCTTTCTTCC
5114550 TCTTCTTCTCCTTGTTCT
1 TCTTCTTCTCCTTGTTCT
* *
5114568 TCTTGTTCTTCTTGTTC
1 TCTTCTTCTCCTTGTTC
5114585 CCTTCCTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.29, G:0.09, T:0.63
Consensus pattern (18 bp):
TCTTCTTCTCCTTGTTCT
Found at i:5126317 original size:2 final size:2
Alignment explanation
Indices: 5126312--5126337 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5126302 GTATATGTGC
5126312 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
5126338 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5131433 original size:26 final size:27
Alignment explanation
Indices: 5131403--5131570 Score: 89
Period size: 26 Copynumber: 6.1 Consensus size: 27
5131393 TATTAATATT
5131403 TTAAAATATTAATGA-TTAAATTAT-AA
1 TTAAAATATTAAT-ATTTAAATTATCAA
5131429 TTAAAATATTAATATTTAAATTATCAA
1 TTAAAATATTAATATTTAAATTATCAA
* * *
5131456 TTCTTAATATTTTAGATAGGTTATAAATTATTAATA
1 ---TTAAAATATTA-ATA--TT-TAAATTA-TCA-A
* * * **
5131492 GTTAAAA-AATAA-A--AAAATAAAAAA
1 -TTAAAATATTAATATTTAAATTATCAA
* *
5131516 TAAAAATAATAATATTTAAATTAT-AA
1 TTAAAATATTAATATTTAAATTATCAA
*
5131542 ATAAAATATTAATATTTAAATTATCAA
1 TTAAAATATTAATATTTAAATTATCAA
5131569 TT
1 TT
5131571 CTTAATTTTT
Statistics
Matches: 108, Mismatches: 18, Indels: 31
0.69 0.11 0.20
Matches are distributed among these distances:
23 5 0.05
24 6 0.06
25 4 0.04
26 50 0.46
27 10 0.09
30 9 0.08
31 4 0.04
32 1 0.01
33 4 0.04
34 12 0.11
35 2 0.02
36 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (27 bp):
TTAAAATATTAATATTTAAATTATCAA
Found at i:5131508 original size:8 final size:8
Alignment explanation
Indices: 5131495--5131527 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
5131485 ATTAATAGTT
5131495 AAAAAATA
1 AAAAAATA
5131503 AAAAAAT-
1 AAAAAATA
5131510 AAAAAATA
1 AAAAAATA
5131518 AAAATAATA
1 AAAA-AATA
5131527 A
1 A
5131528 TATTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.30
8 11 0.48
9 5 0.22
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAAATA
Found at i:5131512 original size:15 final size:16
Alignment explanation
Indices: 5131494--5131527 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
5131484 TATTAATAGT
5131494 TAAAAAATAAAAA-AA
1 TAAAAAATAAAAATAA
5131509 TAAAAAATAAAAATAA
1 TAAAAAATAAAAATAA
5131525 TAA
1 TAA
5131528 TATTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
TAAAAAATAAAAATAA
Found at i:5131522 original size:113 final size:113
Alignment explanation
Indices: 5131405--5131632 Score: 336
Period size: 113 Copynumber: 2.0 Consensus size: 113
5131395 TTAATATTTT
* *
5131405 AAAATATTAATGA-TTAAATTATAATTAAAATATTAATATTTAAATTATCAATTCTTAATATTTT
1 AAAATAATAAT-ATTTAAATTATAAATAAAATATTAATATTTAAATTATCAATTCTTAATATTTT
* **
5131469 AGATAGGTTATAAATTATTAATAGTTAAAAAAT-AAA-AAAATAAAAAATA
65 AAATAAATTATAAATTATTAATA-TTAAAAAATAAAATAAAAT-AAAAATA
*
5131518 AAAATAATAATATTTAAATTATAAATAAAATATTAATATTTAAATTATCAATTCTTAATTTTTTA
1 AAAATAATAATATTTAAATTATAAATAAAATATTAATATTTAAATTATCAATTCTTAATATTTTA
* *
5131583 AATAAATTATATATTATTAATATTTAAAAATAAAATAAAATAAAAATA
66 AATAAATTATAAATTATTAATATTAAAAAATAAAATAAAATAAAAATA
5131631 AA
1 AA
5131633 TAATCATATA
Statistics
Matches: 104, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
112 9 0.09
113 90 0.87
114 5 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (113 bp):
AAAATAATAATATTTAAATTATAAATAAAATATTAATATTTAAATTATCAATTCTTAATATTTTA
AATAAATTATAAATTATTAATATTAAAAAATAAAATAAAATAAAAATA
Found at i:5136044 original size:20 final size:20
Alignment explanation
Indices: 5135922--5136044 Score: 58
Period size: 20 Copynumber: 6.0 Consensus size: 20
5135912 ACTTTCCATA
*
5135922 TAATATTTGTAAATAAAATAT
1 TAATATTT-TAAATAAATTAT
* *
5135943 TAATAATTTAAAATATTAATGAT
1 TAAT-ATTTTAAATA--AATTAT
* * *
5135966 CAA-ATTATAAATAAAATAT
1 TAATATTTTAAATAAATTAT
* *
5135985 TACTA-TTTAAAT-GATCATAT
1 TAATATTTTAAATAAAT--TAT
*
5136005 TAAT-TTTT-AATAATTNTTAT
1 TAATATTTTAAATAA--ATTAT
5136025 TAATATTTTAAATAAATTAT
1 TAATATTTTAAATAAATTAT
5136045 ATATTATTAA
Statistics
Matches: 73, Mismatches: 17, Indels: 25
0.63 0.15 0.22
Matches are distributed among these distances:
18 1 0.01
19 14 0.19
20 21 0.29
21 21 0.29
22 10 0.14
23 6 0.08
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
TAATATTTTAAATAAATTAT
Found at i:5136104 original size:26 final size:25
Alignment explanation
Indices: 5136075--5136134 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
5136065 TAAAATAAAA
*
5136075 TAAAAATAAATAATCATAATAATATT
1 TAAAAATAAATAA-AATAATAATATT
* *
5136101 TAAATTATAAATAAAATATTAATATT
1 TAAA-AATAAATAAAATAATAATATT
*
5136127 TTAAAATA
1 TAAAAATA
5136135 TTAATGACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.11
26 17 0.61
27 8 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAAAATAAATAAAATAATAATATT
Found at i:5136131 original size:20 final size:20
Alignment explanation
Indices: 5135922--5136131 Score: 68
Period size: 19 Copynumber: 10.6 Consensus size: 20
5135912 ACTTTCCATA
5135922 TAATATTTGTAAATAAAATAT
1 TAATATTT-TAAATAAAATAT
* *
5135943 TAATAATTTAAAATATTAATGAT
1 TAAT-ATTTTAAATA-AAAT-AT
* *
5135966 CAA-ATTATAAATAAAATAT
1 TAATATTTTAAATAAAATAT
* **
5135985 TACTA-TTTAAATGATCATAT
1 TAATATTTTAAAT-AAAATAT
**
5136005 TAAT-TTTT-AATAATTNTTAT
1 TAATATTTTAAATAA--AATAT
*
5136025 TAATATTTTAAATAAATTA-
1 TAATATTTTAAATAAAATAT
*
5136044 T-ATATTATTAATATTAAAA-AC
1 TAATATT-TTAA-A-TAAAATAT
* *
5136065 TAA-A-ATAAAATAAAA-AT
1 TAATATTTTAAATAAAATAT
* * * *
5136082 AAATA-ATCATAATAATAT-T
1 TAATATTTTA-AATAAAATAT
*
5136101 TAA-ATTATAAATAAAATAT
1 TAATATTTTAAATAAAATAT
5136120 TAATATTTTAAA
1 TAATATTTTAAA
5136132 ATATTAATGA
Statistics
Matches: 139, Mismatches: 29, Indels: 43
0.66 0.14 0.20
Matches are distributed among these distances:
17 8 0.06
18 19 0.14
19 34 0.24
20 34 0.24
21 27 0.19
22 13 0.09
23 4 0.03
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (20 bp):
TAATATTTTAAATAAAATAT
Found at i:5136195 original size:156 final size:156
Alignment explanation
Indices: 5136021--5136402 Score: 511
Period size: 156 Copynumber: 2.4 Consensus size: 156
5136011 TTAATAATTN
*
5136021 TTATTAATATTTTAAATAAATTATATATTATTAATA-TTAAAAACTAAAATAAAATAAAAATAAA
1 TTATT-ATATTTTAAATAAATTATAAATTATTAATATTTAAAAA-TAAAATAAAATAAAAATAAA
5136085 TAATCATAATAATATTTAAATTATAAATAAAATATTAATATTTTAAAATATTAATGACTAAATTA
64 TAATCATAATAA-ATTTAAATTATAAATAAAATATTAATATTTTAAAATATTAATGACTAAATTA
* *
5136150 T-A-AAAATATTAATATTTAAATGATTAG
128 TAATAAAATATTAATATTTAAATGATCAA
* *
5136177 TTATTGATATTTTGAATAATTTATAAATTATTAATATTTAAAAATAAAATAAAATAAAAATAAAT
1 TTATT-ATATTTTAAATAAATTATAAATTATTAATATTTAAAAATAAAATAAAATAAAAATAAAT
* * * **
5136242 AATCATAATAAATTTAAATTATAAATGAGATCTTAATATTTTTTAATATTAATGACTAAATTATA
65 AATCATAATAAATTTAAATTATAAATAAAATATTAATATTTTAAAATATTAATGACTAAATTATA
* *
5136307 ATAAAATATTCATATTTAAATTATCAA
130 ATAAAATATTAATATTTAAATGATCAA
* * * * * *
5136334 TTATTAAATTTTTATAGAAATAATAAATTATTAATATTTAAAAAATAAAA-ATAAATAAACATAT
1 TTATTATA-TTTTAAATAAATTATAAATTATTAATATTT-AAAAATAAAATA-AAATAAAAATAA
5136398 ATAAT
63 ATAAT
5136403 AAAGGGTACT
Statistics
Matches: 199, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
155 48 0.24
156 67 0.34
157 59 0.30
158 25 0.13
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (156 bp):
TTATTATATTTTAAATAAATTATAAATTATTAATATTTAAAAATAAAATAAAATAAAAATAAATA
ATCATAATAAATTTAAATTATAAATAAAATATTAATATTTTAAAATATTAATGACTAAATTATAA
TAAAATATTAATATTTAAATGATCAA
Found at i:5138378 original size:3 final size:3
Alignment explanation
Indices: 5138370--5138398 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5138360 CATTACGCTT
5138370 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5138399 GGTTTATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5141174 original size:18 final size:17
Alignment explanation
Indices: 5141133--5141173 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
5141123 AGAATATTTG
5141133 GCTTTTTGCTCAAATTA
1 GCTTTTTGCTCAAATTA
5141150 GCTTTTTGCTCAAATTA
1 GCTTTTTGCTCAAATTA
5141167 GCTTTTT
1 GCTTTTT
5141174 TCTCTTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (17 bp):
GCTTTTTGCTCAAATTA
Found at i:5143140 original size:88 final size:88
Alignment explanation
Indices: 5143030--5143207 Score: 277
Period size: 88 Copynumber: 2.0 Consensus size: 88
5143020 CACCCTTCCC
* * *
5143030 TTTATCATTTTTGTCAAGTTTTGTGGAGGGGCTAATAAGAGTCCTAATTGATTTCATATTCATCA
1 TTTATCATCTTTATCAAGTTTTGTGAAGGGGCTAATAAGAGTCCTAATTGATTTCATATTCATCA
* *
5143095 CACT-GAACTTTTTCAACATTTCT
66 CA-TAAAACTTTTTCAACATATCT
* *
5143118 TTTATCATCTTTATCAAGTTTTGTGAAGGGGCTAATAGGAGTTCTAATTGATTTCATATTCATCA
1 TTTATCATCTTTATCAAGTTTTGTGAAGGGGCTAATAAGAGTCCTAATTGATTTCATATTCATCA
5143183 CATAAAACTTTTTCAACATATCT
66 CATAAAACTTTTTCAACATATCT
5143206 TT
1 TT
5143208 GGTATACTTC
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
87 1 0.01
88 81 0.99
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (88 bp):
TTTATCATCTTTATCAAGTTTTGTGAAGGGGCTAATAAGAGTCCTAATTGATTTCATATTCATCA
CATAAAACTTTTTCAACATATCT
Found at i:5143867 original size:17 final size:18
Alignment explanation
Indices: 5143845--5143878 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5143835 ATTTCAAATT
*
5143845 TGAGTTT-AAGCTTAAAA
1 TGAGTTTCAAACTTAAAA
5143862 TGAGTTTCAAACTTAAA
1 TGAGTTTCAAACTTAAA
5143879 TAAATTGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (18 bp):
TGAGTTTCAAACTTAAAA
Found at i:5154335 original size:20 final size:21
Alignment explanation
Indices: 5154307--5154348 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5154297 GAATTGGAGC
*
5154307 ACTCAAAAA-TAGATTTTGAA
1 ACTCAAAAATTAGAATTTGAA
*
5154327 ACTCTAAAATTAGAATTTGAA
1 ACTCAAAAATTAGAATTTGAA
5154348 A
1 A
5154349 GCAAAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (21 bp):
ACTCAAAAATTAGAATTTGAA
Found at i:5160647 original size:17 final size:17
Alignment explanation
Indices: 5160625--5160657 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5160615 GTAAAATAAG
5160625 CACACACTAAGGGGGAA
1 CACACACTAAGGGGGAA
*
5160642 CACACACTTAGGGGGA
1 CACACACTAAGGGGGA
5160658 GAAATCCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.24, G:0.30, T:0.09
Consensus pattern (17 bp):
CACACACTAAGGGGGAA
Found at i:5178842 original size:25 final size:24
Alignment explanation
Indices: 5178788--5178835 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
5178778 GTTGTCAAAA
*
5178788 TATTTTTTAATTACTTATTTTGCAT
1 TATTTTTTAATTAATTATTTTG-AT
*
5178813 TATTTTTTTATTAATTCATTTTG
1 TATTTTTTAATTAATT-ATTTTG
5178836 TTAATTTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.67
Consensus pattern (24 bp):
TATTTTTTAATTAATTATTTTGAT
Found at i:5204758 original size:75 final size:76
Alignment explanation
Indices: 5204669--5204831 Score: 213
Period size: 77 Copynumber: 2.1 Consensus size: 76
5204659 AAAAGTATTG
* *
5204669 TTTCAATAGTCACCTTATGAAAGAACAACTATTCATTT-TATGAGACAACTTTTGAG-TTACAAT
1 TTTC-ATA-TCACCTTATGAAAGAACAACTATTCATTTATAAGAAACAACTTTTGAGCTT-CAAT
5204732 ATGAAAAGATAACT
63 ATGAAAAGATAACT
* * *
5204746 TTTCATATCACCTTATGAAAGGACAACTATTCATTTCATAAGAAATAACTTTTTAGCTTCAATAT
1 TTTCATATCACCTTATGAAAGAACAACTATTCATTT-ATAAGAAACAACTTTTGAGCTTCAATAT
*
5204811 GAAAAGATAATT
65 GAAAAGATAACT
*
5204823 TTTTATATC
1 TTTCATATC
5204832 CGAACTTTTG
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
75 28 0.37
76 3 0.04
77 43 0.57
78 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (76 bp):
TTTCATATCACCTTATGAAAGAACAACTATTCATTTATAAGAAACAACTTTTGAGCTTCAATATG
AAAAGATAACT
Found at i:5206504 original size:25 final size:25
Alignment explanation
Indices: 5206459--5206518 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
5206449 TTGTTGTTAT
5206459 TTATTATTA-TTTTCTTAATTA-TCA
1 TTATTATTATTTTTCTTAATTACT-A
* * *
5206483 TTATTATTATTTTTGTTCATTACTT
1 TTATTATTATTTTTCTTAATTACTA
5206508 TTATTATTATT
1 TTATTATTATT
5206519 CTTTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.29
25 21 0.68
26 1 0.03
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.67
Consensus pattern (25 bp):
TTATTATTATTTTTCTTAATTACTA
Found at i:5209029 original size:42 final size:43
Alignment explanation
Indices: 5208972--5209062 Score: 148
Period size: 43 Copynumber: 2.1 Consensus size: 43
5208962 TTATGTGATA
* *
5208972 ATGATGACCTAGCTATGAGCGTGT-GGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGAGCGAGTGGGGAGTGCACATGAGCTG
*
5209014 ATGATGACCCAGCTATGTGCGAGTGGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGAGCGAGTGGGGAGTGCACATGAGCTG
5209057 ATGATG
1 ATGATG
5209063 GTGGGATGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 21 0.47
43 24 0.53
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.23
Consensus pattern (43 bp):
ATGATGACCCAGCTATGAGCGAGTGGGGAGTGCACATGAGCTG
Found at i:5209496 original size:21 final size:22
Alignment explanation
Indices: 5209451--5209496 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5209441 GCCACTTCAA
*
5209451 TCTCGCTGCAACGAGAATGCTT
1 TCTCGCTGCAACGAGAATACTT
*
5209473 TCTCGCTGCAGCGAGAA-ACTT
1 TCTCGCTGCAACGAGAATACTT
5209494 TCT
1 TCT
5209497 ATCCAGCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (22 bp):
TCTCGCTGCAACGAGAATACTT
Found at i:5210810 original size:62 final size:62
Alignment explanation
Indices: 5210639--5211798 Score: 1190
Period size: 62 Copynumber: 18.8 Consensus size: 62
5210629 GCATACCAGT
* * ** * * *
5210639 TAAATTGGGCTTAAACTC-CTTCGTGCCAACGTAACAGGACTTATACATCTTGGATGCCAGC
1 TAAATTGGGCTTAAACTCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * * * *
5210700 TAAATTGGGCTT-AACTCTTTTTGTGCCAACATAGCTAGACTTAAACATCTTGAATGCTAGG
1 TAAATTGGGCTTAAACTCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * *
5210761 TAAATTGGGCTTAAACTCTTTTTGTGTCAATATAACTGGACTTATACATCTTGGATGCTAGG
1 TAAATTGGGCTTAAACTCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
** ** *
5210823 TAAATTACGCTTAAACTCTTTTTGTGCCAACGTAACTGGACTTACACATCTTGGATGCTAGC
1 TAAATTGGGCTTAAACTCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * * *
5210885 TAAATTGGGCAT-AACTCTTTTTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGC
1 TAAATTGGGCTTAAACTCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * * * ** *
5210946 TAAATTTGGCTTAAACT-TCTTTCGTGCCAATGTAACTGGACTTATACATCTTGGACACCAAG-
1 TAAATTGGGCTTAAACTCT-TTTTGTGCCAATATAACTGGACTTAAACATCTTGGA-TGCTAGC
* * * *
5211008 TAAATTGGGCTTAAACTCATTTTGTGCCAACT-TAGCTAGACTTAAACATCTTGGCTGCTAGC
1 TAAATTGGGCTTAAACTCTTTTTGTGCCAA-TATAACTGGACTTAAACATCTTGGATGCTAGC
* * * *
5211070 TAAATTGGGCTTAAACATC--TTTGTGCCAATATAATTGGGCTTAAACAGCTTGGATGCCAGC
1 TAAATTGGGCTTAAAC-TCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * * *
5211131 TAAATTGGGCTT-AA-TCATCTTTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGC
1 TAAATTGGGCTTAAACTC-TTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * * * * *
5211192 TGAATTGGGCTTAAACTCCTTTTGTGCCAATGTAACTAGACTTATACATCTTGGATGCTAGG
1 TAAATTGGGCTTAAACTCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * * * * * *
5211254 TAAATTGGGTTTAAACTCCTTTTGTGCCAATGTAATTGGACTTATACATCTTGGACGCCAGC
1 TAAATTGGGCTTAAACTCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * * * * ** * *
5211316 TAAATTAGG-TTTAACTTTTTTTGTGCCAACATAGCTAAACTTAAACATATTGGATGCTAGT
1 TAAATTGGGCTTAAACTCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * * * * *
5211377 TAAATTGGGCTTAAACTCCTTTTGTGCCAATGTAATTGGACTTATACATTTTGGATGCCAAG-
1 TAAATTGGGCTTAAACTCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATG-CTAGC
* * * * *
5211439 TAAATTGGGCTTAAACTCCTTTTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGT
1 TAAATTGGGCTTAAACTCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * * *
5211501 TAAATTGGGTTTAAACT-TCTTTTGTGCCAATGTAACTGGACTTATACATCTTGGATGCCA-C
1 TAAATTGGGCTTAAACTCT-TTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * **
5211562 GTAAATTGGGCTTAAACTAC-TTTTGTGCCAACATAGCTATACTTAAACATCTTGGATGCTAGC
1 -TAAATTGGGCTTAAACT-CTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* ** *
5211625 TAAATTGGGCTTAAACATC--TTTGTGCTAATATAACTGGGTTTAAACATCTTGGATGCCAGC
1 TAAATTGGGCTTAAAC-TCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * * * * *
5211686 TAAATTGGGCTT-AA-TCATCTTTGTGCCAACATAGCTAGACTTAAACATCTTAGATGTTAGC
1 TAAATTGGGCTTAAACTC-TTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
* * * *
5211747 TAAATTGGGCTTAGACTCCTTTTGTGCTAATGTAACTAGG-CTTAAACATCTT
1 TAAATTGGGCTTAAACTCTTTTTGTGCCAATATAACT-GGACTTAAACATCTT
5211799 TGATTGCCTA
Statistics
Matches: 911, Mismatches: 158, Indels: 59
0.81 0.14 0.05
Matches are distributed among these distances:
58 4 0.00
60 10 0.01
61 347 0.38
62 534 0.59
63 16 0.02
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (62 bp):
TAAATTGGGCTTAAACTCTTTTTGTGCCAATATAACTGGACTTAAACATCTTGGATGCTAGC
Found at i:5210984 original size:185 final size:185
Alignment explanation
Indices: 5210639--5211798 Score: 1298
Period size: 185 Copynumber: 6.3 Consensus size: 185
5210629 GCATACCAGT
* * * *
5210639 TAAATTGGGCTTAAACTCC-TTCGTGCCAACGTAACAGGACTTATACATCTTGGATGCCAGCTAA
1 TAAATTGGGCTTAAACTCCTTTTGTGCCAACGTAACTGGACTTAAACATCTTGGATGCTAGCTAA
* * * *
5210703 ATTGGGCTT-AACTCTTTTTGTGCCAACATAGCTAGACTTAAACATCTTGAATGCTAGGTAAATT
66 ATTGGGCTTAAACTC-TTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCCAGCTAAATT
* * * *
5210767 GGGCTTAAAC-TCTTTTTGTGTCAATATAACTGGACTTATACATCTTGGATGCTAGG
130 GGGCTTAAACTTC-TTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCTAGG
** * *
5210823 TAAATTACGCTTAAACTCTTTTTGTGCCAACGTAACTGGACTTACACATCTTGGATGCTAGCTAA
1 TAAATTGGGCTTAAACTCCTTTTGTGCCAACGTAACTGGACTTAAACATCTTGGATGCTAGCTAA
* * *
5210888 ATTGGGCAT-AACTCTTTTTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGCTAAATT
66 ATTGGGCTTAAACTC-TTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCCAGCTAAATT
* * ** * * ** * *
5210952 TGGCTTAAACTTCTTTCGTGCCAATGTAACTGGACTTATACATCTTGGACACCAAG
130 GGGCTTAAACTTCTTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCTAGG
* * * * *
5211008 TAAATTGGGCTTAAACTCATTTTGTGCCAACTTAGCTAGACTTAAACATCTTGGCTGCTAGCTAA
1 TAAATTGGGCTTAAACTCCTTTTGTGCCAACGTAACTGGACTTAAACATCTTGGATGCTAGCTAA
* * * * *
5211073 ATTGGGCTTAAACATC-TTTGTGCCAATATAATTGGGCTTAAACAGCTTGGATGCCAGCTAAATT
66 ATTGGGCTTAAAC-TCTTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCCAGCTAAATT
* * * *
5211137 GGGCTTAATCATC-TTTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGC
130 GGGCTTAAACTTCTTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCTAGG
* * * * *
5211192 TGAATTGGGCTTAAACTCCTTTTGTGCCAATGTAACTAGACTTATACATCTTGGATGCTAGGTAA
1 TAAATTGGGCTTAAACTCCTTTTGTGCCAACGTAACTGGACTTAAACATCTTGGATGCTAGCTAA
* ** * * * *
5211257 ATTGGGTTTAAACTCCTTTTGTGCCAATGTAATTGGACTTATACATCTTGGACGCCAGCTAAATT
66 ATTGGGCTTAAACT-CTTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCCAGCTAAATT
* * * * * * *
5211322 AGG-TTTAACTTTTTTTGTGCCAACATAGCTAAACTTAAACATATTGGATGCTAGT
130 GGGCTTAAACTTCTTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCTAGG
* * * * *
5211377 TAAATTGGGCTTAAACTCCTTTTGTGCCAATGTAATTGGACTTATACATTTTGGATGCCAAG-TA
1 TAAATTGGGCTTAAACTCCTTTTGTGCCAACGTAACTGGACTTAAACATCTTGGATG-CTAGCTA
* * *
5211441 AATTGGGCTTAAACTCCTTTTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGTTAAAT
65 AATTGGGCTTAAACT-CTTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCCAGCTAAAT
* ** * * * *
5211506 TGGGTTTAAACTTCTTTTGTGCCAATGTAACTGGACTTATACATCTTGGATGCCACG
129 TGGGCTTAAACTTCTTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCTAGG
* * * **
5211563 TAAATTGGGCTTAAACTACTTTTGTGCCAACATAGCTATACTTAAACATCTTGGATGCTAGCTAA
1 TAAATTGGGCTTAAACTCCTTTTGTGCCAACGTAACTGGACTTAAACATCTTGGATGCTAGCTAA
* * * **
5211628 ATTGGGCTTAAACATC-TTTGTGCTAATATAACTGGGTTTAAACATCTTGGATGCCAGCTAAATT
66 ATTGGGCTTAAAC-TCTTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCCAGCTAAATT
* * * * * *
5211692 GGGCTTAATCATC-TTTGTGCCAACATAGCTAGACTTAAACATCTTAGATGTTAGC
130 GGGCTTAAACTTCTTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCTAGG
* * *
5211747 TAAATTGGGCTTAGACTCCTTTTGTGCTAATGTAACTAGG-CTTAAACATCTT
1 TAAATTGGGCTTAAACTCCTTTTGTGCCAACGTAACT-GGACTTAAACATCTT
5211799 TGATTGCCTA
Statistics
Matches: 827, Mismatches: 137, Indels: 24
0.84 0.14 0.02
Matches are distributed among these distances:
183 1 0.00
184 197 0.24
185 513 0.62
186 113 0.14
187 3 0.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (185 bp):
TAAATTGGGCTTAAACTCCTTTTGTGCCAACGTAACTGGACTTAAACATCTTGGATGCTAGCTAA
ATTGGGCTTAAACTCTTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCCAGCTAAATTG
GGCTTAAACTTCTTTTGTGCCAACATAACTAGACTTAAACATCTTGGATGCTAGG
Found at i:5211083 original size:31 final size:30
Alignment explanation
Indices: 5210924--5211713 Score: 185
Period size: 31 Copynumber: 25.6 Consensus size: 30
5210914 CATAGCTAGA
* *
5210924 CTTAAACATCTTGGATGCTAGCTAAATTTGG
1 CTTAAACATCTTGG-TGCCAGCTAAATTGGG
* * * *
5210955 CTTAAACTTCTTTCGTGCCAATG-T-AACTGGA
1 CTTAAACATC-TTGGTGCC-A-GCTAAATTGGG
* **
5210986 CTTATACATCTTGGACACCAAG-TAAATTGGG
1 CTTAAACATCTTGG-TGCC-AGCTAAATTGGG
* * * ** * *
5211017 CTTAAAC-TCATTTTGTGCCAACTTAGCTAGA
1 CTTAAACATC--TTGGTGCCAGCTAAATTGGG
*
5211048 CTTAAACATCTTGGCTGCTAGCTAAATTGGG
1 CTTAAACATCTTGG-TGCCAGCTAAATTGGG
* *
5211079 CTTAAACATCTTTGTGCCA-ATATAATTGGG
1 CTTAAACATCTTGGTGCCAGCTA-AATTGGG
*
5211109 CTTAAACAGCTTGGATGCCAGCTAAATTGGG
1 CTTAAACATCTTGG-TGCCAGCTAAATTGGG
* * * ** * *
5211140 CTTAATCATCTTTGTGCCAAC-ATAGCTAGA
1 CTTAAACATCTTGGTGCCAGCTA-AATTGGG
* *
5211170 CTTAAACATCTTGGATGCTAGCTGAATTGGG
1 CTTAAACATCTTGG-TGCCAGCTAAATTGGG
* * * *
5211201 CTTAAAC-TCCTTTTGTGCCAATG-T-AACTAGA
1 CTTAAACAT-C-TTGGTGCC-A-GCTAAATTGGG
* * *
5211232 CTTATACATCTTGGATGCTAGGTAAATTGGG
1 CTTAAACATCTTGG-TGCCAGCTAAATTGGG
* * *
5211263 TTTAAAC-TCCTTTTGTGCCAATG-T-AATTGGA
1 CTTAAACAT-C-TTGGTGCC-A-GCTAAATTGGG
* * *
5211294 CTTATACATCTTGGACGCCAGCTAAATTAGG
1 CTTAAACATCTTGG-TGCCAGCTAAATTGGG
* * * * * ** ***
5211325 -TTTAACTTTTTTTGTGCCAAC-ATAGCTAAA
1 CTTAAAC-ATCTTGGTGCCAGCTA-AATTGGG
* * *
5211355 CTTAAACATATTGGATGCTAGTTAAATTGGG
1 CTTAAACATCTTGG-TGCCAGCTAAATTGGG
* *
5211386 CTTAAAC-TCCTTTTGTGCCAATG-T-AATTGGA
1 CTTAAACAT-C-TTGGTGCC-A-GCTAAATTGGG
* *
5211417 CTTATACATTTTGGATGCCAAG-TAAATTGGG
1 CTTAAACATCTTGG-TGCC-AGCTAAATTGGG
* * ** * *
5211448 CTTAAAC-TCCTTTTGTGCCAAC-ATAGCTAGA
1 CTTAAACAT-C-TTGGTGCCAGCTA-AATTGGG
* *
5211479 CTTAAACATCTTGGATGCTAGTTAAATTGGG
1 CTTAAACATCTTGG-TGCCAGCTAAATTGGG
* * * * *
5211510 TTTAAACTTCTTTTGTGCCAATG-T-AACTGGA
1 CTTAAACATC-TTGGTGCC-A-GCTAAATTGGG
*
5211541 CTTATACATCTTGGATGCCA-CGTAAATTGGG
1 CTTAAACATCTTGG-TGCCAGC-TAAATTGGG
* * ** *
5211572 CTTAAAC-TACTTTTGTGCCAACATAGCTAT--A
1 CTTAAACAT-C-TTGGTGCCAGC-TAAAT-TGGG
*
5211603 CTTAAACATCTTGGATGCTAGCTAAATTGGG
1 CTTAAACATCTTGG-TGCCAGCTAAATTGGG
* * * *
5211634 CTTAAACATCTTTGTGCTA-ATATAACTGGG
1 CTTAAACATCTTGGTGCCAGCTA-AATTGGG
*
5211664 TTTAAACATCTTGGATGCCAGCTAAATTGGG
1 CTTAAACATCTTGG-TGCCAGCTAAATTGGG
* *
5211695 CTTAATCATCTTTGTGCCA
1 CTTAAACATCTTGGTGCCA
5211714 ACATAGCTAG
Statistics
Matches: 532, Mismatches: 158, Indels: 139
0.64 0.19 0.17
Matches are distributed among these distances:
29 9 0.02
30 135 0.25
31 331 0.62
32 51 0.10
33 6 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (30 bp):
CTTAAACATCTTGGTGCCAGCTAAATTGGG
Found at i:5211442 original size:431 final size:429
Alignment explanation
Indices: 5210639--5211773 Score: 1551
Period size: 431 Copynumber: 2.6 Consensus size: 429
5210629 GCATACCAGT
* * *
5210639 TAAATTGGGCTTAAACTCCTTCGTGCCAACGTAACAGGACTTATACATCTTGGATGCCAGCTAAA
1 TAAATTGGGCTTAAACT-CTTTGTGCCAATGTAACTGGACTTATACATCTTGGATGCCAGCTAAA
* * *
5210704 TTGGGCTTAACTCTTTTTGTGCCAACATAGCTAGACTTAAACATCTTGAATGCTAGGTAAATTGG
65 TTGGGCTTAA-TCTCTTTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGCTAAATTGG
* * **
5210769 GCTTAAACTCTTTTTGTGTCAATATAACTGGACTTATACATCTTGGATGCTAGGTAAATTACGCT
129 GCTTAAACTCCTTTTGTGCCAATATAACTGGACTTATACATCTTGGATGCTAGGTAAATTGGGCT
* * * *
5210834 TAAACTCTTTTTGTGCCAACGTAACTGGACTTACACATCTTGGATGCTAGCTAAATTGGGCATAA
194 TAAACTCCTTTTGTGCCAACGTAACTGGACTTACACATCTTGGACGCCAGCTAAATTAGGCATAA
* * * *
5210899 CTCTTTTTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGCTAAATTTGGCTTAAACTT
259 CTCTTTTTGTGCCAACATAGCTAAACTTAAACATATTGGATGCTAGCTAAATTGGGCTTAAACTC
5210964 CTTTCGTGCCAATGTAACTGGACTTATACATCTTGGACACCAAGTAAATTGGGCTTAAACTCATT
324 CTTTCGTGCCAATGTAACTGGACTTATACATCTTGGACACCAAGTAAATTGGGCTTAAACTCATT
* *
5211029 TTGTGCCAACTTAGCTAGACTTAAACATCTTGGCTGCTAGC
389 TTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGC
* * * * *
5211070 TAAATTGGGCTTAAACATCTTTGTGCCAATATAATTGGGCTTAAACAGCTTGGATGCCAGCTAAA
1 TAAATTGGGCTTAAAC-TCTTTGTGCCAATGTAACTGGACTTATACATCTTGGATGCCAGCTAAA
*
5211135 TTGGGCTTAATCATCTTTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGCTGAATTGG
65 TTGGGCTTAATC-TCTTTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGCTAAATTGG
* * *
5211200 GCTTAAACTCCTTTTGTGCCAATGTAACTAGACTTATACATCTTGGATGCTAGGTAAATTGGGTT
129 GCTTAAACTCCTTTTGTGCCAATATAACTGGACTTATACATCTTGGATGCTAGGTAAATTGGGCT
* * * **
5211265 TAAACTCCTTTTGTGCCAATGTAATTGGACTTATACATCTTGGACGCCAGCTAAATTAGGTTTAA
194 TAAACTCCTTTTGTGCCAACGTAACTGGACTTACACATCTTGGACGCCAGCTAAATTAGGCATAA
* *
5211330 CTTTTTTTGTGCCAACATAGCTAAACTTAAACATATTGGATGCTAGTTAAATTGGGCTTAAACTC
259 CTCTTTTTGTGCCAACATAGCTAAACTTAAACATATTGGATGCTAGCTAAATTGGGCTTAAACTC
* * * ** *
5211395 CTTTTGTGCCAATGTAATTGGACTTATACATTTTGGATGCCAAGTAAATTGGGCTTAAACTCCTT
324 CTTTCGTGCCAATGTAACTGGACTTATACATCTTGGACACCAAGTAAATTGGGCTTAAACTCATT
*
5211460 TTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGT
389 TTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGC
*
5211501 TAAATTGGGTTTAAACTTCTTTTGTGCCAATGTAACTGGACTTATACATCTTGGATGCCA-CGTA
1 TAAATTGGGCTTAAAC-TC-TTTGTGCCAATGTAACTGGACTTATACATCTTGGATGCCAGC-TA
* *
5211565 AATTGGGCTTAAACTACTTTTGTGCCAACATAGCTATACTTAAACATCTTGGATGCTAGCTAAAT
63 AATTGGGCTTAATCT-C-TTTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGCTAAAT
* ** * * *
5211630 TGGGCTTAAACAT-C-TTTGTGCTAATATAACTGGGTTTAAACATCTTGGATGCCAGCTAAATTG
126 TGGGCTTAAAC-TCCTTTTGTGCCAATATAACTGGACTTATACATCTTGGATGCTAGGTAAATTG
* * * * * * * ** *
5211693 GGCTT-AA-TCATCTTTGTGCCAACATAGCTAGACTTAAACATCTTAGATGTTAGCTAAATTGGG
190 GGCTTAAACTCCT-TTTGTGCCAACGTAACTGGACTTACACATCTTGGACGCCAGCTAAATTAGG
* *
5211756 CTTAGACTCCTTTTGTGC
254 CATA-ACTCTTTTTGTGC
5211774 TAATGTAACT
Statistics
Matches: 618, Mismatches: 77, Indels: 17
0.87 0.11 0.02
Matches are distributed among these distances:
430 5 0.01
431 447 0.72
432 108 0.17
433 57 0.09
434 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (429 bp):
TAAATTGGGCTTAAACTCTTTGTGCCAATGTAACTGGACTTATACATCTTGGATGCCAGCTAAAT
TGGGCTTAATCTCTTTGTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGCTAAATTGGGC
TTAAACTCCTTTTGTGCCAATATAACTGGACTTATACATCTTGGATGCTAGGTAAATTGGGCTTA
AACTCCTTTTGTGCCAACGTAACTGGACTTACACATCTTGGACGCCAGCTAAATTAGGCATAACT
CTTTTTGTGCCAACATAGCTAAACTTAAACATATTGGATGCTAGCTAAATTGGGCTTAAACTCCT
TTCGTGCCAATGTAACTGGACTTATACATCTTGGACACCAAGTAAATTGGGCTTAAACTCATTTT
GTGCCAACATAGCTAGACTTAAACATCTTGGATGCTAGC
Found at i:5223118 original size:25 final size:25
Alignment explanation
Indices: 5223065--5223129 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
5223055 GTTATTGTTA
5223065 TTTATTATTAT-TTTCTTAATTATC
1 TTTATTATTATATTTCTTAATTATC
* * *
5223089 ATTATTATTATATTTGTTCATTA-C
1 TTTATTATTATATTTCTTAATTATC
5223113 TTTTATTATTATTATTT
1 -TTTATTATTA-TATTT
5223130 TTTATTCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 11 0.32
25 18 0.53
26 5 0.15
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTATTATTATATTTCTTAATTATC
Found at i:5223961 original size:24 final size:24
Alignment explanation
Indices: 5223934--5223979 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5223924 TTTTTTGTCT
*
5223934 TTTTGATATTTT-TTTGTTTGTGAG
1 TTTTGAT-TTTTCTTTGATTGTGAG
5223958 TTTTGATTTTTCTTTGATTGTG
1 TTTTGATTTTTCTTTGATTGTG
5223980 GCTAGGGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.11, C:0.02, G:0.20, T:0.67
Consensus pattern (24 bp):
TTTTGATTTTTCTTTGATTGTGAG
Found at i:5224391 original size:13 final size:13
Alignment explanation
Indices: 5224369--5224421 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
5224359 TTTAATTTTT
*
5224369 ATTATATTATTTA
1 ATTATTTTATTTA
5224382 ATTATTTTATTTA
1 ATTATTTTATTTA
* **
5224395 TTTATTTTGGTTA
1 ATTATTTTATTTA
*
5224408 ATATATTTTTTTTA
1 AT-TATTTTATTTA
5224422 TTTGGGGAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 23 0.72
14 9 0.28
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (13 bp):
ATTATTTTATTTA
Found at i:5229221 original size:278 final size:277
Alignment explanation
Indices: 5228724--5229278 Score: 1092
Period size: 278 Copynumber: 2.0 Consensus size: 277
5228714 GATCATAATA
5228724 TTCACCTCTTCTAACACTTCATAAACATTTGATAAGCAATTCACAATGCAATTCAATTTCATTTT
1 TTCACCTCTTCTAACACTTCATAAACATTTGATAAGCAATTCACAATGCAATTCAATTTCATTTT
5228789 TATAGATTATAAATTTCTCCATTACTTCATCTTTAGCATGCAATAAGTAAACATAACAATATCTA
66 TATAGATTATAAATTTCTCCATTACTTCATCTTTAGCATGCAATAAGTAAACATAACAATATCTA
5228854 GAAAAGTCATCTATAAATGTTGCAAAGTATTTCTTTCCACTAATAGATGGAGTACTATGCATATG
131 GAAAAGTCATCTATAAATGTTGCAAAGTATTTCTTTCCACTAATAGATGGAGTACTATGCATATG
5228919 ACAAAAATTGGAATGTATTAATGCAAGCAATTTGAAGTTTCTTTCTATCTTAGGAAATAAGCTTC
196 ACAAAAATTGGAATGTATTAATGCAAGCAATTTGAAGTTTCTTTCTATCTTAGGAAATAAGCTTC
5228984 TTGTGATTTTAGTAAGC
261 TTGTGATTTTAGTAAGC
5229001 NTTCACCTCTTCTAACACTTCATAAACATTTGATAAGCAATTCACAATGCAATTCAATTTCATTT
1 -TTCACCTCTTCTAACACTTCATAAACATTTGATAAGCAATTCACAATGCAATTCAATTTCATTT
5229066 TTATAGATTATAAATTTCTCCATTACTTCATCTTTAGCATGCAATAAGTAAACATAACAATATCT
65 TTATAGATTATAAATTTCTCCATTACTTCATCTTTAGCATGCAATAAGTAAACATAACAATATCT
5229131 AGAAAAGTCATCTATAAATGTTGCAAAGTATTTCTTTCCACTAATAGATGGAGTACTATGCATAT
130 AGAAAAGTCATCTATAAATGTTGCAAAGTATTTCTTTCCACTAATAGATGGAGTACTATGCATAT
*
5229196 GACAAAAATTGGAATGTATTAATGCAAGCAATTTGAAGTTTCTTTCTATCTTAGGAAATGAGCTT
195 GACAAAAATTGGAATGTATTAATGCAAGCAATTTGAAGTTTCTTTCTATCTTAGGAAATAAGCTT
5229261 CTTGTGATTTTAGTAAGC
260 CTTGTGATTTTAGTAAGC
5229279 ATGTATTTCT
Statistics
Matches: 276, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
278 276 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (277 bp):
TTCACCTCTTCTAACACTTCATAAACATTTGATAAGCAATTCACAATGCAATTCAATTTCATTTT
TATAGATTATAAATTTCTCCATTACTTCATCTTTAGCATGCAATAAGTAAACATAACAATATCTA
GAAAAGTCATCTATAAATGTTGCAAAGTATTTCTTTCCACTAATAGATGGAGTACTATGCATATG
ACAAAAATTGGAATGTATTAATGCAAGCAATTTGAAGTTTCTTTCTATCTTAGGAAATAAGCTTC
TTGTGATTTTAGTAAGC
Found at i:5229630 original size:218 final size:218
Alignment explanation
Indices: 5229252--5229668 Score: 771
Period size: 218 Copynumber: 1.9 Consensus size: 218
5229242 TATCTTAGGA
* * *
5229252 AATGAGCTTCTTGTGATTTTAGTAAGCATGTATTTCTTGCACATATCATTATTTCCATCAATATT
1 AATGAGCTTCTTGTGATTTTAGAAACCATGTATTTCTTGCACAAATCATTATTTCCATCAATATT
5229317 AGGTATCAACTCTAATTTAGTCATATCATGCATTTTTCTATAATGAACATGACTTAATCTATTAT
66 AGGTATCAACTCTAATTTAGTCATATCATGCATTTTTCTATAATGAACATGACTTAATCTATTAT
5229382 GCCATAAATTAGACAATGTTGCTTCACTATCATGAACATTAAATGAGGCATCAATATAAGTAAAA
131 GCCATAAATTAGACAATGTTGCTTCACTATCATGAACATTAAATGAGGCATCAATATAAGTAAAA
5229447 CTAGCAGCATTTTTACCTTAGAC
196 CTAGCAGCATTTTTACCTTAGAC
5229470 AATGAGCTTCTTGTGATTTTAGAAACCATGTATTTCTTGCACAAATCATTATTTCCATCAATATT
1 AATGAGCTTCTTGTGATTTTAGAAACCATGTATTTCTTGCACAAATCATTATTTCCATCAATATT
* * *
5229535 AGGTATCAACTCTAATTTAGTCATATCATGCATTTTTCTATAATGAATATGACTTAGTTTATTAT
66 AGGTATCAACTCTAATTTAGTCATATCATGCATTTTTCTATAATGAACATGACTTAATCTATTAT
*
5229600 GCCATAAATTAGACAATGTTGTTTCACTATCATGAACATTAAATGAGGCATCAATATAAGTAAAA
131 GCCATAAATTAGACAATGTTGCTTCACTATCATGAACATTAAATGAGGCATCAATATAAGTAAAA
5229665 CTAG
196 CTAG
5229669 TAGTGTTTTT
Statistics
Matches: 192, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
218 192 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (218 bp):
AATGAGCTTCTTGTGATTTTAGAAACCATGTATTTCTTGCACAAATCATTATTTCCATCAATATT
AGGTATCAACTCTAATTTAGTCATATCATGCATTTTTCTATAATGAACATGACTTAATCTATTAT
GCCATAAATTAGACAATGTTGCTTCACTATCATGAACATTAAATGAGGCATCAATATAAGTAAAA
CTAGCAGCATTTTTACCTTAGAC
Found at i:5231238 original size:77 final size:77
Alignment explanation
Indices: 5231121--5231276 Score: 213
Period size: 77 Copynumber: 2.0 Consensus size: 77
5231111 TACGAGAGAG
* * * * * *
5231121 TCACCTTATGAAAGGACAATCATTCATTCCATAAGACATAATTTTTTAGCTACAATATGAAAAGA
1 TCACCTTATGAAAGGACAACCACTCATTCCATAAGACATAACTTTTGAACTACAATATGAAAAAA
5231186 TAACTTTTCATA
66 TAACTTTTCATA
* * * *
5231198 TCACTTTATGAAAGGACGACCACTCATTCCATAATACATAACTTTTGAACTTCAATATGAAAAAA
1 TCACCTTATGAAAGGACAACCACTCATTCCATAAGACATAACTTTTGAACTACAATATGAAAAAA
*
5231263 TAATTTTTCATA
66 TAACTTTTCATA
5231275 TC
1 TC
5231277 TAAGCTTTTG
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (77 bp):
TCACCTTATGAAAGGACAACCACTCATTCCATAAGACATAACTTTTGAACTACAATATGAAAAAA
TAACTTTTCATA
Found at i:5232855 original size:144 final size:144
Alignment explanation
Indices: 5232606--5232866 Score: 341
Period size: 144 Copynumber: 1.8 Consensus size: 144
5232596 AAAAATACTC
* * *
5232606 CAATGATGAAATCTCAAGGATGCTAAAAGAGGTGGATTTTTGGGAATTTCTATATAAGGAAATCT
1 CAATGATGAAATCTCAAGGATGCCAAAAGAGGTGGATTCTTGGAAATTTCTATATAA-GAAATCT
* *
5232671 TCCAAAATTATGCCATAAGAGTTCAGAGATTTTAGAAAATTTTCAATGCCAAGGATTTACATAAA
65 TCCAAAATTATGCCATAAGAGTTCAGAGATTTTAGAAAATTATCAATACCAAGGATTTACATAAA
5232736 TAAATAAGATCTCTT
130 TAAATAAGATCTCTT
* *
5232751 CAATGATGAAATCTTAAGGATGCCAAAA-ACGGTGGCTTCTTGAGAAATTT-TAGT-TGAA-AAA
1 CAATGATGAAATCTCAAGGATGCCAAAAGA-GGTGGATTCTTG-GAAATTTCTA-TAT-AAGAAA
* * ** *
5232812 TCTTCCAAAATTATGTCATGAGAGTTTGGAGATTTTGGAAAATTATCAATACCAA
62 TCTTCCAAAATTATGCCATAAGAGTTCAGAGATTTTAGAAAATTATCAATACCAA
5232867 TATTTTTATT
Statistics
Matches: 100, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
144 52 0.52
145 39 0.39
146 9 0.09
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (144 bp):
CAATGATGAAATCTCAAGGATGCCAAAAGAGGTGGATTCTTGGAAATTTCTATATAAGAAATCTT
CCAAAATTATGCCATAAGAGTTCAGAGATTTTAGAAAATTATCAATACCAAGGATTTACATAAAT
AAATAAGATCTCTT
Found at i:5234115 original size:18 final size:18
Alignment explanation
Indices: 5234084--5234119 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5234074 GAAAATAAAG
*
5234084 ACTTTGCTATCCTCCATA
1 ACTTTGCTAACCTCCATA
*
5234102 ACTTTTCTAACCTCCATA
1 ACTTTGCTAACCTCCATA
5234120 TTTTGTTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.33, G:0.03, T:0.39
Consensus pattern (18 bp):
ACTTTGCTAACCTCCATA
Found at i:5244721 original size:28 final size:29
Alignment explanation
Indices: 5244654--5244721 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 29
5244644 AACCATATGG
5244654 ACTTATTTAACTTAAAATAAAAATACAAAA
1 ACTTATTTAAC-TAAAATAAAAATACAAAA
* *
5244684 ACTTCA-TTAA-TACAATAAAAGA-ATAAAA
1 ACTT-ATTTAACTAAAATAAAA-ATACAAAA
5244712 ACTTATTTAA
1 ACTTATTTAA
5244722 ATTTTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
27 1 0.03
28 22 0.67
29 1 0.03
30 8 0.24
31 1 0.03
ACGTcount: A:0.57, C:0.10, G:0.01, T:0.31
Consensus pattern (29 bp):
ACTTATTTAACTAAAATAAAAATACAAAA
Found at i:5246854 original size:15 final size:16
Alignment explanation
Indices: 5246809--5246854 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
5246799 TCTTTTAAAT
5246809 ATTAATAACTTATAATTA
1 ATTAATAA-TT-TAATTA
5246827 ATTAA-AATATTAA-TA
1 ATTAATAAT-TTAATTA
5246842 ATTAATAATTTAA
1 ATTAATAATTTAA
5246855 ATATCACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 11 0.42
16 7 0.27
17 3 0.12
18 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTAATAATTTAATTA
Found at i:5246894 original size:40 final size:41
Alignment explanation
Indices: 5246836--5246925 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 41
5246826 AATTAAAATA
*
5246836 TTAATAATTAATAATTTAAAT-ATCACTATTTTA-GTATAAT
1 TTAATTATTAATAATTTAAATAATCA-TATTTTATGTATAAT
* * *
5246876 TTAATTATTAA-AATTTTAATTAATGATATTTTATTTATAAT
1 TTAATTATTAATAA-TTTAAATAATCATATTTTATGTATAAT
5246917 TTAA-TATTA
1 TTAATTATTA
5246926 TTGTGATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
39 2 0.05
40 28 0.65
41 13 0.30
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (41 bp):
TTAATTATTAATAATTTAAATAATCATATTTTATGTATAAT
Found at i:5247261 original size:19 final size:19
Alignment explanation
Indices: 5247239--5247301 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 19
5247229 ATGATTGATA
5247239 ATTTAAATATTAATATTTT
1 ATTTAAATATTAATATTTT
*
5247258 ATTTATAAT-TTAATATTAAT
1 ATTTA-AATATTAATATT-TT
5247278 ATTTTAAAATATTAATATTTT
1 A-TTT-AAATATTAATATTTT
5247299 ATT
1 ATT
5247302 ACAAATTGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 13 0.35
20 7 0.19
21 8 0.22
22 9 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTAAATATTAATATTTT
Found at i:5247274 original size:14 final size:14
Alignment explanation
Indices: 5247226--5247299 Score: 55
Period size: 16 Copynumber: 5.2 Consensus size: 14
5247216 ATTTATTTTA
*
5247226 TTAATGATTGATAAT
1 TTAAT-ATTAATAAT
5247241 TTAAATATTAAT-AT
1 TT-AATATTAATAAT
*
5247255 TT--TATTTATAAT
1 TTAATATTAATAAT
*
5247267 TTAATATTAATATT
1 TTAATATTAATAAT
*
5247281 TTAAAATATTAATATT
1 TT--AATATTAATAAT
5247297 TTA
1 TTA
5247300 TTACAAATTG
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
11 6 0.12
12 4 0.08
14 15 0.31
15 7 0.14
16 17 0.35
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (14 bp):
TTAATATTAATAAT
Found at i:5247290 original size:16 final size:16
Alignment explanation
Indices: 5247269--5247299 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5247259 TTTATAATTT
5247269 AATATTAATATTTTAA
1 AATATTAATATTTTAA
5247285 AATATTAATATTTTA
1 AATATTAATATTTTA
5247300 TTACAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTAATATTTTAA
Found at i:5247295 original size:22 final size:20
Alignment explanation
Indices: 5247224--5247301 Score: 70
Period size: 22 Copynumber: 3.8 Consensus size: 20
5247214 TAATTTATTT
5247224 TATTAATGATTGATAATTT-AAA
1 TATTAAT-ATT-AT-ATTTAAAA
* *
5247246 TATTAATATTTTATTTATAA
1 TATTAATATTATATTTAAAA
5247266 T-TTAATATTAATATTTTAAAA
1 TATTAATATT-ATA-TTTAAAA
*
5247287 TATTAATATTTTATT
1 TATTAATATTATATT
5247302 ACAAATTGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
19 12 0.26
20 8 0.17
21 12 0.26
22 15 0.32
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TATTAATATTATATTTAAAA
Found at i:5257805 original size:11 final size:11
Alignment explanation
Indices: 5257789--5257814 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5257779 TTTGTGTCAT
5257789 TAATATATATA
1 TAATATATATA
5257800 TAATATATATA
1 TAATATATATA
5257811 TAAT
1 TAAT
5257815 TAAAGCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATATATATA
Found at i:5261022 original size:15 final size:15
Alignment explanation
Indices: 5260998--5261038 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
5260988 TCTTTATCTT
*
5260998 TTTCTT-CTTTTTCC
1 TTTCTTCCTTTCTCC
5261012 TTTCTTCCTTTCTCC
1 TTTCTTCCTTTCTCC
5261027 TTTCTT-CTTTCT
1 TTTCTTCCTTTCT
5261039 TCTGTCTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTCTTCCTTTCTCC
Found at i:5261039 original size:7 final size:7
Alignment explanation
Indices: 5260994--5261046 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
5260984 ACCTTCTTTA
5260994 TCTT-TT
1 TCTTCTT
5261000 TCTTCTT
1 TCTTCTT
5261007 T-TTCCTT
1 TCTT-CTT
5261014 TCTTCCTT
1 TCTT-CTT
*
5261022 TCTCCTT
1 TCTTCTT
5261029 TCTTCTT
1 TCTTCTT
*
5261036 TCTTCTG
1 TCTTCTT
5261043 TCTT
1 TCTT
5261047 TCTCAACTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
6 6 0.15
7 26 0.63
8 9 0.22
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (7 bp):
TCTTCTT
Found at i:5369909 original size:13 final size:13
Alignment explanation
Indices: 5369891--5369917 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5369881 AAGAAAATAA
5369891 AATATTTTTATTT
1 AATATTTTTATTT
5369904 AATATTTTTATTT
1 AATATTTTTATTT
5369917 A
1 A
5369918 GTTTGATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
AATATTTTTATTT
Found at i:5381916 original size:15 final size:16
Alignment explanation
Indices: 5381893--5381926 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5381883 ATTTCTAGTG
*
5381893 AAAATGAAAAAA-AAA
1 AAAAAGAAAAAAGAAA
5381908 AAAAAGAAAAAAGAAA
1 AAAAAGAAAAAAGAAA
5381924 AAA
1 AAA
5381927 GAGAGACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAA
Found at i:5384208 original size:30 final size:29
Alignment explanation
Indices: 5384107--5384208 Score: 84
Period size: 29 Copynumber: 3.5 Consensus size: 29
5384097 AAAAAATTCG
* *
5384107 AATAAGTCCTTAGACTTTTA-TTACATTCA
1 AATAAGTCCTTATACTTTTATTTA-AGTCA
* * *
5384136 ATTAAGT-CTCTATATTTTTATTTAAGTTA
1 AATAAGTCCT-TATACTTTTATTTAAGTCA
*
5384165 AATAA-ACCTTTATACTTTTATCTTAAGTCA
1 AATAAGTCC-TTATACTTTTAT-TTAAGTCA
*
5384195 AATAAGTTCTTATA
1 AATAAGTCCTTATA
5384209 ATTAATGATT
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
28 2 0.04
29 32 0.57
30 21 0.38
31 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (29 bp):
AATAAGTCCTTATACTTTTATTTAAGTCA
Found at i:5387419 original size:16 final size:15
Alignment explanation
Indices: 5387398--5387427 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5387388 TATTATAAGA
5387398 TATTATTTTAATATAT
1 TATTATTTT-ATATAT
5387414 TATTATTTTATATA
1 TATTATTTTATATA
5387428 AGTAGTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATTTTATATAT
Found at i:5387913 original size:23 final size:23
Alignment explanation
Indices: 5387876--5387940 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
5387866 ATACCATTAC
5387876 TTAATATCTTATATAATTATAGTAT
1 TTAATAT-TT-TATAATTATAGTAT
* * *
5387901 TTAGTATTTTATAGTTATATTAT
1 TTAATATTTTATAATTATAGTAT
5387924 TTAATATTTTATTAATT
1 TTAATATTTTA-TAATT
5387941 TTAATACTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 22 0.65
24 6 0.18
25 6 0.18
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (23 bp):
TTAATATTTTATAATTATAGTAT
Found at i:5396438 original size:24 final size:24
Alignment explanation
Indices: 5396406--5396462 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
5396396 ACTGCTTAAC
5396406 AAGGAAGAAGCTCATTAGTTGAAT
1 AAGGAAGAAGCTCATTAGTTGAAT
5396430 AAGGAAGAAGCTCATTAGTTGAAT
1 AAGGAAGAAGCTCATTAGTTGAAT
5396454 AAGGAAGAA
1 AAGGAAGAA
5396463 TGTTGGTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.46, C:0.07, G:0.26, T:0.21
Consensus pattern (24 bp):
AAGGAAGAAGCTCATTAGTTGAAT
Found at i:5398237 original size:150 final size:150
Alignment explanation
Indices: 5398071--5398389 Score: 534
Period size: 150 Copynumber: 2.1 Consensus size: 150
5398061 TTATGAGCTG
* * *
5398071 AAGCTTAAAGAAGAAGAAGAAGAAGATAGAAGGGAAGTAAAGGAAAAAAAAAAGAGTATTGCACT
1 AAGCTTAAAGAGGAAGAAGAAGAAGATAGAAGGGAAGCAAAGGAAAAAAAAAAGAGCATTGCACT
* * *
5398136 GAAAGCCAGCATCCTTGAAGAAGAGCTGGAAGAGCTATCATGTGATGATGATGAAGAGTTAGCTC
66 AAAAGCCAGCATCCTTAAAGAAAAGCTGGAAGAGCTATCATGTGATGATGATGAAGAGTTAGCTC
*
5398201 TGGTTGCAAGAAAATTTAGA
131 TGGTTGCAAGAAAATTCAGA
* *
5398221 AAGCTTAAAGAGGAAGAAGAAGAAGATAGGAGGGAAGCAAAGGAAAAGAAAAAGAGCATTGCACT
1 AAGCTTAAAGAGGAAGAAGAAGAAGATAGAAGGGAAGCAAAGGAAAAAAAAAAGAGCATTGCACT
5398286 AAAAGCCAGCATCCTTAAAGAAAAGCTGGAAGAGCTATCATGTGATGATGATGAAGAGTTAGCTC
66 AAAAGCCAGCATCCTTAAAGAAAAGCTGGAAGAGCTATCATGTGATGATGATGAAGAGTTAGCTC
5398351 TGGTTGCAAGAAAATTCAGA
131 TGGTTGCAAGAAAATTCAGA
*
5398371 AAGCTT-ATG-GGAAGAAGAA
1 AAGCTTAAAGAGGAAGAAGAA
5398390 ATCAAAGACT
Statistics
Matches: 159, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
148 10 0.06
149 2 0.01
150 147 0.92
ACGTcount: A:0.45, C:0.10, G:0.28, T:0.18
Consensus pattern (150 bp):
AAGCTTAAAGAGGAAGAAGAAGAAGATAGAAGGGAAGCAAAGGAAAAAAAAAAGAGCATTGCACT
AAAAGCCAGCATCCTTAAAGAAAAGCTGGAAGAGCTATCATGTGATGATGATGAAGAGTTAGCTC
TGGTTGCAAGAAAATTCAGA
Found at i:5408348 original size:20 final size:20
Alignment explanation
Indices: 5408331--5408368 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5408321 CCTCAAATCT
5408331 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
5408351 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
5408369 GGGGCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:5415388 original size:20 final size:19
Alignment explanation
Indices: 5415365--5415403 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5415355 ATTTCAGTTC
*
5415365 TTTTAGTTTAATTTTACTTT
1 TTTTACTTTAA-TTTACTTT
*
5415385 TTTTTCTTTAATTTACTTT
1 TTTTACTTTAATTTACTTT
5415404 AAGAATAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTACTTTAATTTACTTT
Found at i:5417719 original size:21 final size:22
Alignment explanation
Indices: 5417693--5417735 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
5417683 CTACAAATAT
*
5417693 ATAATAAAAA-TAAAAATAGTA
1 ATAATAAAAAGGAAAAATAGTA
5417714 ATAATAAAAAGGAAAAATAGTA
1 ATAATAAAAAGGAAAAATAGTA
5417736 GTAGTATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (22 bp):
ATAATAAAAAGGAAAAATAGTA
Found at i:5417957 original size:14 final size:14
Alignment explanation
Indices: 5417935--5417986 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
5417925 AAATTACTCA
5417935 ATAAA-AATAATAG
1 ATAAATAATAATAG
5417948 ATAAATAATAATAG
1 ATAAATAATAATAG
* *
5417962 ATAAAAAATGATA-
1 ATAAATAATAATAG
*
5417975 AAAAATAATAAT
1 ATAAATAATAAT
5417987 TCAAATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
13 14 0.42
14 19 0.58
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (14 bp):
ATAAATAATAATAG
Found at i:5418261 original size:15 final size:16
Alignment explanation
Indices: 5418241--5418273 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5418231 TACGAAAAAT
*
5418241 AATATAATAAT-ATAA
1 AATATAAAAATGATAA
5418256 AATATAAAAATGATAA
1 AATATAAAAATGATAA
5418272 AA
1 AA
5418274 AAAATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AATATAAAAATGATAA
Found at i:5425710 original size:11 final size:11
Alignment explanation
Indices: 5425617--5425719 Score: 91
Period size: 9 Copynumber: 10.2 Consensus size: 11
5425607 ATCAATCAAA
5425617 AAAAAAAAAG-
1 AAAAAAAAAGC
5425627 AAAAAAAAA--
1 AAAAAAAAAGC
5425636 AAAAAAAAA--
1 AAAAAAAAAGC
5425645 AAAAAAAAA--
1 AAAAAAAAAGC
5425654 AAAAAAAAA--
1 AAAAAAAAAGC
*
5425663 AAAAAAAAA-A
1 AAAAAAAAAGC
**
5425673 AAAAAAAAAAA
1 AAAAAAAAAGC
5425684 AAAAAAAAAGC
1 AAAAAAAAAGC
*
5425695 AAAAAAAAAGGG
1 AAAAAAAAA-GC
5425707 AAAAAAAAAGC
1 AAAAAAAAAGC
5425718 AA
1 AA
5425720 GTGTGAAAGA
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
9 36 0.42
10 18 0.21
11 22 0.26
12 10 0.12
ACGTcount: A:0.92, C:0.02, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGC
Found at i:5425710 original size:12 final size:12
Alignment explanation
Indices: 5425683--5425716 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5425673 AAAAAAAAAA
*
5425683 AAAAAAAAAAGC
1 AAAAAAAAAGGC
*
5425695 AAAAAAAAAGGG
1 AAAAAAAAAGGC
5425707 AAAAAAAAAG
1 AAAAAAAAAG
5425717 CAAGTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGGC
Found at i:5425715 original size:1 final size:1
Alignment explanation
Indices: 5425614--5425703 Score: 153
Period size: 1 Copynumber: 90.0 Consensus size: 1
5425604 ACAATCAATC
*
5425614 AAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
**
5425679 AAAAAAAAAAAAAAGCAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
5425704 GGGAAAAAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 84 1.00
ACGTcount: A:0.97, C:0.01, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:5427376 original size:142 final size:142
Alignment explanation
Indices: 5427016--5427627 Score: 926
Period size: 142 Copynumber: 4.3 Consensus size: 142
5427006 AGATAATCAA
**
5427016 TGTCAAGA-TTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCTTAAATCCTCTAG
1 TGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCTTAAATCCTCCGG
* * * * *
5427080 GTACATTTTCAAGACCTCCGGGCACATTATTCTCTTAAAT-CTTTCCGGTGCATCTTCTAAAACC
66 GTACATTCTGAAGACCTTCGGGCACATTATTCTCTTAAATCCTCT-GGGTGCATCTTCTAAAACC
*
5427144 TCCGAGTAATTAC
130 TCCGAGTAATTAG
*
5427157 TGTCAAGATTTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCTTAAATCCTTCG
1 TGTCAAGA-TTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCTTAAATCCTCCG
* *
5427222 GGTACATTCTGAAGACCTTCGAGTACATTATTCTCTTAAATCCTCTGGGTGCATCTTCTAAAACC
65 GGTACATTCTGAAGACCTTCGGGCACATTATTCTCTTAAATCCTCTGGGTGCATCTTCTAAAACC
* *
5427287 TTCGGGTAATTAG
130 TCCGAGTAATTAG
** *
5427300 TGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTTAAGGAGCCACATTTTTTAAATCCTCCGG
1 TGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCTTAAATCCTCCGG
* * *
5427365 GTACATTCTGAAGACC-TCTGGGCACATTTTTCTCTTAAATCCTCCGAGTGCATCTTCTAAAACC
66 GTACATTCTGAAGACCTTC-GGGCACATTATTCTCTTAAATCCTCTGGGTGCATCTTCTAAAACC
5427429 TCC-AGGTAATTAG
130 TCCGA-GTAATTAG
* *
5427442 TGTCAAGATTTTTTAAAGTTACGTTGCCTTAGTTTTCGAGGAGCCACATTTCCTAAATCCTCCGG
1 TGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCTTAAATCCTCCGG
* * *
5427507 GTACATTCTGAAGACCTTTGGGTACATTATTCTCTTAAATTCTCTGGGTGCATCTTCTAAAACCT
66 GTACATTCTGAAGACCTTCGGGCACATTATTCTCTTAAATCCTCTGGGTGCATCTTCTAAAACCT
5427572 CCGAGTAATTAG
131 CCGAGTAATTAG
* *
5427584 TGTTAAGATTTTTTAAAGTTACGTTACCTCAGTTTTCGAGGAGC
1 TGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGC
5427628 TATATTTTTC
Statistics
Matches: 426, Mismatches: 38, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
141 10 0.02
142 287 0.67
143 126 0.30
144 3 0.01
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (142 bp):
TGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCACATTTCTTAAATCCTCCGG
GTACATTCTGAAGACCTTCGGGCACATTATTCTCTTAAATCCTCTGGGTGCATCTTCTAAAACCT
CCGAGTAATTAG
Found at i:5427668 original size:21 final size:21
Alignment explanation
Indices: 5427642--5427761 Score: 143
Period size: 21 Copynumber: 5.7 Consensus size: 21
5427632 TTTTTCTCTT
*
5427642 AAAACCTTCGGGTATATTTTC
1 AAAACCTTCGGGTACATTTTC
*
5427663 AAAACCTCCGGGTACATTTTC
1 AAAACCTTCGGGTACATTTTC
* *
5427684 AAAATCTCCGGGTACATTCTAT-
1 AAAACCTTCGGGTACATT-T-TC
* *
5427706 AAAACCTTCGGGTACATTCTG
1 AAAACCTTCGGGTACATTTTC
*
5427727 AAGACCTTCGGGTACATTTTC
1 AAAACCTTCGGGTACATTTTC
*
5427748 AAAGCCTTCGGGTA
1 AAAACCTTCGGGTA
5427762 ATTAATTTGA
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
20 1 0.01
21 66 0.78
22 17 0.20
23 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (21 bp):
AAAACCTTCGGGTACATTTTC
Found at i:5427739 original size:43 final size:42
Alignment explanation
Indices: 5427642--5427761 Score: 143
Period size: 43 Copynumber: 2.8 Consensus size: 42
5427632 TTTTTCTCTT
* * *
5427642 AAAACCTTCGGGTATATTTTCAAAACCTCCGGGTACATTTTC
1 AAAACCTTCGGGTACATTTTCAAAACCTTCGGGTACATTCTC
* * *
5427684 AAAATCTCCGGGTACATTCTAT-AAAACCTTCGGGTACATTCTG
1 AAAACCTTCGGGTACATT-T-TCAAAACCTTCGGGTACATTCTC
* *
5427727 AAGACCTTCGGGTACATTTTCAAAGCCTTCGGGTA
1 AAAACCTTCGGGTACATTTTCAAAACCTTCGGGTA
5427762 ATTAATTTGA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 29 0.45
43 34 0.52
44 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (42 bp):
AAAACCTTCGGGTACATTTTCAAAACCTTCGGGTACATTCTC
Found at i:5427760 original size:64 final size:64
Alignment explanation
Indices: 5427641--5427761 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 64
5427631 ATTTTTCTCT
* * *
5427641 TAAAACCTTCGGGTATATTTTCAAAACCTCCGGGTACATTTTCAAAATCTCCGGGTACATTCTA
1 TAAAACCTTCGGGTACATTCTCAAAACCTCCGGGTACATTTTCAAAACCTCCGGGTACATTCTA
* * * * *
5427705 TAAAACCTTCGGGTACATTCTGAAGACCTTCGGGTACATTTTCAAAGCCTTCGGGTA
1 TAAAACCTTCGGGTACATTCTCAAAACCTCCGGGTACATTTTCAAAACCTCCGGGTA
5427762 ATTAATTTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 49 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (64 bp):
TAAAACCTTCGGGTACATTCTCAAAACCTCCGGGTACATTTTCAAAACCTCCGGGTACATTCTA
Found at i:5428137 original size:142 final size:141
Alignment explanation
Indices: 5427828--5428201 Score: 588
Period size: 142 Copynumber: 2.6 Consensus size: 141
5427818 TCCTAAATCT
* *
5427828 TCCGGGCACATTATTTTCTTAAATCCTCTGGGTGCATCTTCTAAAACCTCCGAGTAATTAGTGTC
1 TCCGGGCACATTATTCTCTTAAATCCTCCGGGTGCATCTTCTAAAACCTCCGAGTAATTAGTGTC
* * * * *
5427893 AAGATTTTTAAAGTTACGTTACCTCAGTTTTCGAGGAGCCACATTTCCTAAATCCTCCAGGTACA
66 AAGATTTTTAAAGTTACGTTGCCTCAATTTTCAAGGAACCACATTTCCTAAATCCTCCAAGTACA
5427958 TTCTGAAGACC
131 TTCTGAAGACC
* *
5427969 TTCGGGCACATTATTCTCTTAAATCCTCCGGGTGCATCTTTTAAAACCTCCGAGTAATTAGTGTC
1 TCCGGGCACATTATTCTCTTAAATCCTCCGGGTGCATCTTCTAAAACCTCCGAGTAATTAGTGTC
*
5428034 AAGATTTTTTAAAAGTTACGTTGTCTCAATTTTCAAGGAACCACATTTCCTAAATCCTCCAAGTA
66 AAGA-TTTTT-AAAGTTACGTTGCCTCAATTTTCAAGGAACCACATTTCCTAAATCCTCCAAGTA
5428099 CA-TCTGAAGACC
129 CATTCTGAAGACC
* * * *
5428111 TCCGGGCACATTATTCTCTTAAATCCTCCAGGTGCATCTTCTAAAACCTCTGGGTAATTAGTTTC
1 TCCGGGCACATTATTCTCTTAAATCCTCCGGGTGCATCTTCTAAAACCTCCGAGTAATTAGTGTC
*
5428176 AAGATTTTTAAAGTTATGTTGCCTCA
66 AAGATTTTTAAAGTTACGTTGCCTCA
5428202 GCTTTGGGGA
Statistics
Matches: 213, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
140 15 0.07
141 70 0.33
142 78 0.37
143 50 0.23
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (141 bp):
TCCGGGCACATTATTCTCTTAAATCCTCCGGGTGCATCTTCTAAAACCTCCGAGTAATTAGTGTC
AAGATTTTTAAAGTTACGTTGCCTCAATTTTCAAGGAACCACATTTCCTAAATCCTCCAAGTACA
TTCTGAAGACC
Found at i:5428321 original size:37 final size:38
Alignment explanation
Indices: 5428179--5428324 Score: 188
Period size: 38 Copynumber: 3.9 Consensus size: 38
5428169 TAGTTTCAAG
*
5428179 ATTTTTAAAGTTAT-GTTGCCTCAGCTTTGGGGAGTTTC
1 ATTTTTAAAGTT-TCGTTGCCTCAGCTTTGAGGAGTTTC
* *
5428217 ATTTTTAAAGTTTCGTTGCCTCAGTTTTAAGGAGTTTC
1 ATTTTTAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTTC
* ** **
5428255 ATTTTTAAAGTTTCATAACCTCAATTTTGAGGAG-TTC
1 ATTTTTAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTTC
*
5428292 ATTTTTAAAGTTTCGTTGCCTTAGCTTTGAGGA
1 ATTTTTAAAGTTTCGTTGCCTCAGCTTTGAGGA
5428325 CTCATTTAGT
Statistics
Matches: 93, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
37 31 0.33
38 62 0.67
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (38 bp):
ATTTTTAAAGTTTCGTTGCCTCAGCTTTGAGGAGTTTC
Found at i:5428355 original size:10 final size:9
Alignment explanation
Indices: 5428335--5428382 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 9
5428325 CTCATTTAGT
5428335 AAAAAA-AA
1 AAAAAACAA
5428343 AAAAAAC--
1 AAAAAACAA
*
5428350 ACAAAAC-A
1 AAAAAACAA
5428358 AAAAAACAA
1 AAAAAACAA
5428367 AACAAAACAA
1 AA-AAAACAA
5428377 AAAAAA
1 AAAAAA
5428383 AAAGGAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
7 6 0.18
8 12 0.35
9 7 0.21
10 9 0.26
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:5428360 original size:13 final size:13
Alignment explanation
Indices: 5428339--5428384 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
5428329 TTTAGTAAAA
*
5428339 AAAAAAAAAACAC
1 AAAACAAAAACAC
*
5428352 AAAACAAAAAAAC
1 AAAACAAAAACAC
5428365 AAAAC-AAAACA-
1 AAAACAAAAACAC
5428376 AAAA-AAAAA
1 AAAACAAAAA
5428385 AGGAGAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 8 0.28
12 5 0.17
13 16 0.55
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAACAC
Found at i:5428362 original size:18 final size:17
Alignment explanation
Indices: 5428335--5428385 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 17
5428325 CTCATTTAGT
5428335 AAAA-AAAAAAAAAACAC
1 AAAACAAAAAAAAAA-AC
5428352 AAAACAAAAAAACAAAAC
1 AAAACAAAAAAA-AAAAC
5428370 AAAACAAAAAAAAAAA
1 AAAACAAAAAAAAAAA
5428386 GGAGAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.25
18 21 0.66
19 3 0.09
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAACAAAAAAAAAAAC
Found at i:5429275 original size:106 final size:106
Alignment explanation
Indices: 5428993--5429287 Score: 369
Period size: 106 Copynumber: 2.8 Consensus size: 106
5428983 TACTACCAAT
* * * *
5428993 GAAGGGAGAAAGACCGAGTGATCGTCGGTTGTTGGTGTTGCCGACCATCGGGCCACCAGATTCGA
1 GAAGGGAGGAAGACCGAGTGATCGTCGGTTGTTGGTGTTACCGACCATCGCGCCACTAGATTCGA
* * *
5429058 CGAAAGGTAGCCCACAACAAGGAAAGAGAGAGAATGCCGAT
66 CGAAAGGTAGCCCACAGCAAGGAAAGAGAGAGAACGCCGAC
* * *
5429099 GAAAGGAGGAAGACCGAGTGATCGTTGGTTGTTGGTGTTACCGACCATCGCGCCA-TCAAATTCG
1 GAAGGGAGGAAGACCGAGTGATCGTCGGTTGTTGGTGTTACCGACCATCGCGCCACT-AGATTCG
* * *
5429163 ACGAAAGGCAGCCCACAGCAAGGAAGGAGAGAGAACGTCGAC
65 ACGAAAGGTAGCCCACAGCAAGGAAAGAGAGAGAACGCCGAC
* * * * * *
5429205 GAAGGGAGGAAGCCCGAGT-AGTCGCCGGTTGTTGGTGCTACCGACCATTGTGCCACTAGATCCG
1 GAAGGGAGGAAGACCGAGTGA-TCGTCGGTTGTTGGTGTTACCGACCATCGCGCCACTAGATTCG
**
5429269 GTGAAAGGTAGCCCACAGC
65 ACGAAAGGTAGCCCACAGC
5429288 TCTTGAGGTT
Statistics
Matches: 161, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
105 1 0.01
106 159 0.99
107 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.33, T:0.16
Consensus pattern (106 bp):
GAAGGGAGGAAGACCGAGTGATCGTCGGTTGTTGGTGTTACCGACCATCGCGCCACTAGATTCGA
CGAAAGGTAGCCCACAGCAAGGAAAGAGAGAGAACGCCGAC
Found at i:5430087 original size:17 final size:17
Alignment explanation
Indices: 5430067--5430099 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5430057 ACTCAATGAA
5430067 AATA-ATAAATAAATAAC
1 AATAGATAAA-AAATAAC
5430084 AATAGATAAAAAATAA
1 AATAGATAAAAAATAA
5430100 TAAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
AATAGATAAAAAATAAC
Found at i:5430394 original size:25 final size:25
Alignment explanation
Indices: 5430365--5430413 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5430355 GCTTACGAAA
* *
5430365 AATATAATAATAATAAATAATAAAT
1 AATATAAAAATAATAAAAAATAAAT
*
5430390 AATATAAAAATGATAAAAAATAAA
1 AATATAAAAATAATAAAAAATAAA
5430414 ATTTTTGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (25 bp):
AATATAAAAATAATAAAAAATAAAT
Found at i:5432145 original size:8 final size:8
Alignment explanation
Indices: 5432123--5432161 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
5432113 AAAAATTATG
5432123 AAAATAAAT
1 AAAA-AAAT
5432132 -AAAAAAT
1 AAAAAAAT
5432139 AAAAAAAT
1 AAAAAAAT
5432147 AAAAAAAT
1 AAAAAAAT
5432155 AAAAAAA
1 AAAAAAA
5432162 GAATAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:5438439 original size:31 final size:31
Alignment explanation
Indices: 5438379--5438439 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
5438369 TTATTCCAAC
* *
5438379 ATTGTGTTGGATAATAGGGAAAGAGGAAGAT
1 ATTGTGTTGGATAAAAGGGAAACAGGAAGAT
* *
5438410 ATTGTGTTTGATAAAAGGGAAACATGAAGA
1 ATTGTGTTGGATAAAAGGGAAACAGGAAGA
5438440 CAACAAAGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.02, G:0.31, T:0.26
Consensus pattern (31 bp):
ATTGTGTTGGATAAAAGGGAAACAGGAAGAT
Found at i:5440279 original size:31 final size:31
Alignment explanation
Indices: 5440244--5440441 Score: 306
Period size: 31 Copynumber: 6.4 Consensus size: 31
5440234 AGTGATTGGT
5440244 GTGTTACAACATTTTACGTTATATGCATGGC
1 GTGTTACAACATTTTACGTTATATGCATGGC
*
5440275 GTGTTACAATATTTTACGTTATATGCATGGC
1 GTGTTACAACATTTTACGTTATATGCATGGC
*
5440306 GTGTTACAATATTTTACGTTATATGCATGGC
1 GTGTTACAACATTTTACGTTATATGCATGGC
* *
5440337 GTGTTACAACATTTTACGTTATATGCGTGAC
1 GTGTTACAACATTTTACGTTATATGCATGGC
* * *
5440368 TTGTTACAACATTTTACGTTATATGCGTGAC
1 GTGTTACAACATTTTACGTTATATGCATGGC
* *
5440399 TTGTTACAACATTTTATGTTATATGCATGGC
1 GTGTTACAACATTTTACGTTATATGCATGGC
*
5440430 GTGTTATAACAT
1 GTGTTACAACAT
5440442 GACTGACAAA
Statistics
Matches: 157, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 157 1.00
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.41
Consensus pattern (31 bp):
GTGTTACAACATTTTACGTTATATGCATGGC
Found at i:5444636 original size:118 final size:118
Alignment explanation
Indices: 5444246--5444818 Score: 590
Period size: 118 Copynumber: 4.9 Consensus size: 118
5444236 TGCATGCAGA
* * * * *
5444246 TTCTGTGGTGACATGCTGACTTCTTGCATTATCGTGGGGTGACACGGCACGCCTCATCTTATGGT
1 TTCTGTGGTGACACGCTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGT
* * * *
5444311 GACATGTTGAGTGGAAGCAAATAGTTGGCGTAACACGCTGACTTCTTACTGAT
66 GACATGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGACTTCTTGCTGAT
* * * * *
5444364 TTCTGTGATGACATGCTGACTTCTTGTAGTATTGTGGGGTGACACAAG-ACGCCCCATCTTGTGG
1 TTCTGTGGTGACACGCTGACTTCTTGCAATATTGTGGGGTGACAC-GGCACGCCCCATCTTGTGG
* * *
5444428 TGACATGTTGAGT-GAAGTAGATAGTTGGCGTGACACGCTGA----GTGC--AT
65 TGACATGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGACTTCTTGCTGAT
* ** * * * *
5444475 TTTTGTGGTGACACATTGACTTCTTGCATTATTGTGGAGTGACACGGTACGCCCCATCTTGTAGT
1 TTCTGTGGTGACACGCTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGT
* * *
5444540 GACACGCTGAGTGGAAGTAAATAGTTGGCGTGACACGCTGACTTCTTGCTGAT
66 GACATGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGACTTCTTGCTGAT
* * * * **
5444593 TTCTGTGATGACACACTGACTTTTTACAATATTGTGGGGTGACACGGCGTGCCCCATCTTGTGGT
1 TTCTGTGGTGACACGCTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGT
** * * *
5444658 GACATGCTGAGTGGAAGCAGATAGTTGGCGTGACATTCTGAGTGCATG-TAGAT
66 GACATGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGACTTCTTGCT-GAT
* * *** * * *
5444711 TTTTGTGGTGACACGTTGACTTCTTATTATATTGTGGGGTGACACGGCATGCCTCA-ATTGTGGT
1 TTCTGTGGTGACACGCTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGT
* * * * * *
5444775 GATACGCTGAGTGGAACCAGATACTTGGCATGACACACTGACTT
66 GACATGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGACTT
5444819 GTTCCAGTTT
Statistics
Matches: 381, Mismatches: 64, Indels: 21
0.82 0.14 0.05
Matches are distributed among these distances:
110 1 0.00
111 65 0.17
112 27 0.07
113 2 0.01
116 3 0.01
117 68 0.18
118 214 0.56
119 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (118 bp):
TTCTGTGGTGACACGCTGACTTCTTGCAATATTGTGGGGTGACACGGCACGCCCCATCTTGTGGT
GACATGCTGAGTGGAAGCAGATAGTTGGCGTGACACGCTGACTTCTTGCTGAT
Found at i:5444650 original size:229 final size:230
Alignment explanation
Indices: 5444262--5444818 Score: 703
Period size: 229 Copynumber: 2.4 Consensus size: 230
5444252 GGTGACATGC
* * * *
5444262 TGACTTCTTGCATTATCGTGGGGTGACACGGCACGCCTCATCTTATGGTGACATGTTGAGTGGAA
1 TGACTTCTTGCATTATTGTGGGGTGACACGGCACGCCTCATCTTGTGGTGACACGCTGAGTGGAA
* ** **
5444327 GCAAATAGTTGGCGTAACACGCTGACTTCTTACTGATTTCTGTGATGACATGCTGACTTCTTGTA
66 GCAAATAGTTGGCGTGACACGCTGACTTCTTACTGATTTCTGTGATGACACACTGACTTCTTACA
* * *
5444392 GTATTGTGGGGTGACACAAGACGCCCCATCTTGTGGTGACATGTTGAGT-GAAGTAGATAGTTGG
131 ATATTGTGGGGTGACAC-AGACGCCCCATCTTGTGGTGACATGCTGAGTGGAAGCAGATAGTTGG
5444456 CGTGACACGCTGAGTGC-ATTTTTGTGGTGACACAT
195 CGTGACACGCTGAGTGCAATTTTTGTGGTGACACAT
* * * *
5444491 TGACTTCTTGCATTATTGTGGAGTGACACGGTACGCCCCATCTTGTAGTGACACGCTGAGTGGAA
1 TGACTTCTTGCATTATTGTGGGGTGACACGGCACGCCTCATCTTGTGGTGACACGCTGAGTGGAA
* * *
5444556 GTAAATAGTTGGCGTGACACGCTGACTTCTTGCTGATTTCTGTGATGACACACTGACTTTTTACA
66 GCAAATAGTTGGCGTGACACGCTGACTTCTTACTGATTTCTGTGATGACACACTGACTTCTTACA
*
5444621 ATATTGTGGGGTGACAC-GGCGTGCCCCATCTTGTGGTGACATGCTGAGTGGAAGCAGATAGTTG
131 ATATTGTGGGGTGACACAGAC--GCCCCATCTTGTGGTGACATGCTGAGTGGAAGCAGATAGTTG
** *
5444685 GCGTGACATTCTGAGTGCATGTAGATTTTTGTGGTGACACGT
194 GCGTGACACGCTGAGTGC----A-ATTTTTGTGGTGACACAT
* * *
5444727 TGACTTCTT--ATTATATTGTGGGGTGACACGGCATGCCTCA-ATTGTGGTGATACGCTGAGTGG
1 TGACTTCTTGCA-T-TATTGTGGGGTGACACGGCACGCCTCATCTTGTGGTGACACGCTGAGTGG
* * * * *
5444789 AACCAGATACTTGGCATGACACACTGACTT
64 AAGCAAATAGTTGGCGTGACACGCTGACTT
5444819 GTTCCAGTTT
Statistics
Matches: 281, Mismatches: 36, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
227 2 0.01
229 156 0.56
230 29 0.10
234 1 0.00
235 44 0.16
236 49 0.17
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (230 bp):
TGACTTCTTGCATTATTGTGGGGTGACACGGCACGCCTCATCTTGTGGTGACACGCTGAGTGGAA
GCAAATAGTTGGCGTGACACGCTGACTTCTTACTGATTTCTGTGATGACACACTGACTTCTTACA
ATATTGTGGGGTGACACAGACGCCCCATCTTGTGGTGACATGCTGAGTGGAAGCAGATAGTTGGC
GTGACACGCTGAGTGCAATTTTTGTGGTGACACAT
Found at i:5444722 original size:31 final size:31
Alignment explanation
Indices: 5444651--5444723 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
5444641 GTGCCCCATC
*
5444651 TTGTGGTGACATGCTGAGTGGAAGCAGATAG
1 TTGTGGTGACATGCTGAGTGCAAGCAGATAG
* * * **
5444682 TTG-GCGTGACATTCTGAGTGCATGTAGATTT
1 TTGTG-GTGACATGCTGAGTGCAAGCAGATAG
5444713 TTGTGGTGACA
1 TTGTGGTGACA
5444724 CGTTGACTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 1 0.03
31 32 0.94
32 1 0.03
ACGTcount: A:0.22, C:0.11, G:0.34, T:0.33
Consensus pattern (31 bp):
TTGTGGTGACATGCTGAGTGCAAGCAGATAG
Found at i:5446943 original size:145 final size:145
Alignment explanation
Indices: 5446775--5447035 Score: 373
Period size: 145 Copynumber: 1.8 Consensus size: 145
5446765 GATGGGGTTG
* * * *
5446775 TTAGCACTGTGCGTCTGAAGAGGACCTCTCAGT-GGTTGAGGAGCTGTCGTCGCATGGTCCAACT
1 TTAGCACTGTGAGTCTGAAGAGGACCTATC-GTGGGTTGAGGAACTATCGTCGCATGGTCCAACT
* ** *
5446839 GC-AAGCATTGATATGTTATTCGATAATCACATATGGAATTGTTGAACACAAATTGTTATAACCG
65 ACGAA-CACAGATATGTTATTCGATAATCACATATGGAATTGTTAAACACAAATTGTTATAACCG
5446903 TCCTTATCGGCTCCTTA
129 TCCTTATCGGCTCCTTA
* * * * *
5446920 TTAGCACTGTGAGTTTGAGGAGGACCTATCGTGGGTTGTGGAATTATCGTCGTATGGTCCAACTA
1 TTAGCACTGTGAGTCTGAAGAGGACCTATCGTGGGTTGAGGAACTATCGTCGCATGGTCCAACTA
5446985 CGAACACAGATATGTTATTCGATAATCACATATGGAATTGTTAAACACAAA
66 CGAACACAGATATGTTATTCGATAATCACATATGGAATTGTTAAACACAAA
5447036 CCTTTAGAAC
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
144 2 0.02
145 97 0.96
146 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (145 bp):
TTAGCACTGTGAGTCTGAAGAGGACCTATCGTGGGTTGAGGAACTATCGTCGCATGGTCCAACTA
CGAACACAGATATGTTATTCGATAATCACATATGGAATTGTTAAACACAAATTGTTATAACCGTC
CTTATCGGCTCCTTA
Found at i:5448487 original size:31 final size:31
Alignment explanation
Indices: 5448445--5448709 Score: 370
Period size: 31 Copynumber: 8.5 Consensus size: 31
5448435 GTTAACCCAT
*
5448445 AATGTGGTAACACGCCATGCATATAATGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* *
5448476 AATATGGTAACACGCCATGCATATAATGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
5448507 AATGTGGTAACACGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* *
5448538 AATGTTGTAACACACCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* *
5448569 AATGTTGTAACACACCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
5448600 AATGTGGTAACACGCCATGCATATATCGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
*
5448631 AATGTCGTAACACGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACGTAA
* * * * *
5448662 CATCTTGTAACACGCCATGCGTATCAA-GTCA
1 AATGTGGTAACACGCCATGCATAT-AACGTAA
* *
5448693 AATGTTGTAACATGCCA
1 AATGTGGTAACACGCCA
5448710 ACGCTGACAC
Statistics
Matches: 215, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
31 213 0.99
32 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (31 bp):
AATGTGGTAACACGCCATGCATATAACGTAA
Found at i:5449495 original size:47 final size:48
Alignment explanation
Indices: 5449382--5449516 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 48
5449372 CGTCACTGAT
* *
5449382 CTCCATGGAATGTCACCAACTCTGAACGCTAGCGTGTCACAAAATTTC
1 CTCCATGGAATGTCACCAACTCTGAACGCTGGCGTGTCACAAAATTCC
* * * * *
5449430 CTCCATGGCATGTTACCAACTTTGAATGCTGGGGTGTCAC-AAATTCC
1 CTCCATGGAATGTCACCAACTCTGAACGCTGGCGTGTCACAAAATTCC
** *
5449477 CTCCATGGTGTGTCACCAACTCTGAACGCTGGCATGTCAC
1 CTCCATGGAATGTCACCAACTCTGAACGCTGGCGTGTCAC
5449517 CAACTCTAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
47 39 0.53
48 34 0.47
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (48 bp):
CTCCATGGAATGTCACCAACTCTGAACGCTGGCGTGTCACAAAATTCC
Found at i:5449538 original size:24 final size:24
Alignment explanation
Indices: 5449486--5449587 Score: 84
Period size: 24 Copynumber: 4.3 Consensus size: 24
5449476 CCTCCATGGT
* *
5449486 GTGTCACCAACTCTGAACGC-TGGC
1 GTGTCACCAACTCTAAAC-CTTGTC
* *
5449510 ATGTCACCAACTCTAAACCTTGCC
1 GTGTCACCAACTCTAAACCTTGTC
* * *
5449534 GTGTCA-CACATTC-CAACCATGTC
1 GTGTCACCA-ACTCTAAACCTTGTC
* *
5449557 GAGTCACAAACTCTAAACCTTGTC
1 GTGTCACCAACTCTAAACCTTGTC
5449581 GTGTCAC
1 GTGTCAC
5449588 AGTCGTGTTA
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
23 18 0.30
24 42 0.70
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (24 bp):
GTGTCACCAACTCTAAACCTTGTC
Found at i:5449588 original size:24 final size:24
Alignment explanation
Indices: 5449511--5449588 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 24
5449501 AACGCTGGCA
* *
5449511 TGTCACCAACTCTAAACCTTGCCG
1 TGTCACAAACTCTAAACCTTGTCG
* * * *
5449535 TGTCACACATTC-CAACCATGTCG
1 TGTCACAAACTCTAAACCTTGTCG
*
5449558 AGTCACAAACTCTAAACCTTGTCG
1 TGTCACAAACTCTAAACCTTGTCG
5449582 TGTCACA
1 TGTCACA
5449589 GTCGTGTTAC
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
23 17 0.41
24 24 0.59
ACGTcount: A:0.28, C:0.33, G:0.13, T:0.26
Consensus pattern (24 bp):
TGTCACAAACTCTAAACCTTGTCG
Found at i:5457393 original size:7 final size:7
Alignment explanation
Indices: 5457381--5457411 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
5457371 GTTGATTTAC
5457381 TTTTGAG
1 TTTTGAG
5457388 TTTTGAG
1 TTTTGAG
5457395 TTTTGAG
1 TTTTGAG
5457402 TTTTGAG
1 TTTTGAG
5457409 TTT
1 TTT
5457412 AATCATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (7 bp):
TTTTGAG
Found at i:5459332 original size:19 final size:19
Alignment explanation
Indices: 5459305--5459351 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5459295 TACCAAAGAG
*
5459305 ACAAGATAAAATTTT-TAGA
1 ACAAAATAAAATTTTATA-A
*
5459324 ACAAAATAATATTTTATAA
1 ACAAAATAAAATTTTATAA
*
5459343 ATAAAATAA
1 ACAAAATAA
5459352 TATTAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (19 bp):
ACAAAATAAAATTTTATAA
Found at i:5464085 original size:19 final size:19
Alignment explanation
Indices: 5464058--5464094 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5464048 GTTTCGAACT
5464058 AGATCAAATAGAGAATTTA
1 AGATCAAATAGAGAATTTA
* *
5464077 AGATGAAATTGAGAATTT
1 AGATCAAATAGAGAATTT
5464095 TAAAGTCCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.30
Consensus pattern (19 bp):
AGATCAAATAGAGAATTTA
Found at i:5473829 original size:2 final size:2
Alignment explanation
Indices: 5473822--5473869 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
5473812 TGCTCTAAGT
*
5473822 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AA AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5473862 AG AG AG AG
1 AG AG AG AG
5473870 TGTGTGTGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5475757 original size:35 final size:35
Alignment explanation
Indices: 5475718--5475824 Score: 107
Period size: 35 Copynumber: 3.1 Consensus size: 35
5475708 TTACAATGGC
5475718 TTTTCACAGGCTCAGCCACAACCTTTAACAATGAT
1 TTTTCACAGGCTCAGCCACAACCTTTAACAATGAT
* * * * *
5475753 TTTTCA-TGGAATCAACCAAAACC--CAA-AATGGA-
1 TTTTCACAGG-CTCAGCCACAACCTTTAACAAT-GAT
*
5475785 TTTTCACAGGCTCAGCCACAACCTTTAACTATGAT
1 TTTTCACAGGCTCAGCCACAACCTTTAACAATGAT
5475820 TTTTC
1 TTTTC
5475825 CCGGGAGCAA
Statistics
Matches: 54, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
32 19 0.35
33 6 0.11
34 6 0.11
35 23 0.43
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (35 bp):
TTTTCACAGGCTCAGCCACAACCTTTAACAATGAT
Found at i:5475792 original size:67 final size:67
Alignment explanation
Indices: 5475712--5475847 Score: 218
Period size: 67 Copynumber: 2.0 Consensus size: 67
5475702 AAGCTTTTAC
* * *
5475712 AATGGCTTTTCACAGGCTCAGCCACAACCTTTAACAATGATTTTTCATGGAATCAACCAAAACCC
1 AATGGATTTTCACAGGCTCAGCCACAACCTTTAACAATGATTTTTCACGGAAGCAACCAAAACCC
5475777 AA
66 AA
* * *
5475779 AATGGATTTTCACAGGCTCAGCCACAACCTTTAACTATGATTTTTCCCGGGAGCAACCAAAACCC
1 AATGGATTTTCACAGGCTCAGCCACAACCTTTAACAATGATTTTTCACGGAAGCAACCAAAACCC
5475844 AA
66 AA
5475846 AA
1 AA
5475848 CTAACTTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.24
Consensus pattern (67 bp):
AATGGATTTTCACAGGCTCAGCCACAACCTTTAACAATGATTTTTCACGGAAGCAACCAAAACCC
AA
Found at i:5476407 original size:73 final size:73
Alignment explanation
Indices: 5476213--5476416 Score: 212
Period size: 74 Copynumber: 2.8 Consensus size: 73
5476203 GTGCTTAAAT
* * * * * * * *
5476213 TCAATTTTTTGATAGTGTGCTCTTAGTTGACTAACCATACTTCTTAGTTGATTAATTCTTCTCTG
1 TCAAATTTTTGATCGTGAGCTCTTAGTTGGCTAACCATACTTCTTAGTTGATTAAGTCGTCTATC
5476278 TCTAATAA
66 TCTAATAA
* * * * * * *
5476286 TCAAATTCTCTG-GCAGTGAGCTCTTAGCTGGCGAACAATACTTTTTAGTTGACTAAGTCGTCTA
1 TCAAATT-TTTGATC-GTGAGCTCTTAGTTGGCTAACCATACTTCTTAGTTGATTAAGTCGTCTA
**
5476350 TCTCTTGTAA
64 TCTCTAATAA
* *
5476360 TCAAATTTTTGATCGTGAGCTTTTAGTTGGCTAACCATACTTCTTAGTCGATTAAGT
1 TCAAATTTTTGATCGTGAGCTCTTAGTTGGCTAACCATACTTCTTAGTTGATTAAGT
5476417 ATTCTCTGAC
Statistics
Matches: 102, Mismatches: 26, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
73 45 0.44
74 57 0.56
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.42
Consensus pattern (73 bp):
TCAAATTTTTGATCGTGAGCTCTTAGTTGGCTAACCATACTTCTTAGTTGATTAAGTCGTCTATC
TCTAATAA
Found at i:5490594 original size:17 final size:17
Alignment explanation
Indices: 5490572--5490607 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5490562 AAGTAAAATA
5490572 AGCACACACAAAGGGGG
1 AGCACACACAAAGGGGG
*
5490589 AGCACACACTAAGGGGG
1 AGCACACACAAAGGGGG
5490606 AG
1 AG
5490608 AGATCCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.36, T:0.03
Consensus pattern (17 bp):
AGCACACACAAAGGGGG
Found at i:5491073 original size:73 final size:73
Alignment explanation
Indices: 5490980--5491134 Score: 193
Period size: 73 Copynumber: 2.1 Consensus size: 73
5490970 CAAGAAATGG
* * * * * * *
5490980 GTTAGTCGACTAAGAGTCTACTGCCAGAAATCTAGATTTCAAGACAGAACCAACTTAATCGACAA
1 GTTAGTCGACTAAAAATCTACTACCAAAAATCGAGACTTCAAGACAGAAACAACTTAATCGACAA
*
5491045 AGAAGTAA
66 AGAAGGAA
* * * *
5491053 GTTAGTCGACTAAAAATCTACTACCAAAAATCGGGACTTCAAGATAGAAATAACTTAATCGACTA
1 GTTAGTCGACTAAAAATCTACTACCAAAAATCGAGACTTCAAGACAGAAACAACTTAATCGACAA
5491118 AGAAGGAA
66 AGAAGGAA
*
5491126 ATTAGTCGA
1 GTTAGTCGA
5491135 TTAAGTGCTC
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (73 bp):
GTTAGTCGACTAAAAATCTACTACCAAAAATCGAGACTTCAAGACAGAAACAACTTAATCGACAA
AGAAGGAA
Found at i:5491687 original size:35 final size:34
Alignment explanation
Indices: 5491624--5491689 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
5491614 GTTAGTTGTT
* *
5491624 GGGTTTTGGTTGATCCGGTAAAAACCATTGTGAA
1 GGGTTTTGGCTGAGCCGGTAAAAACCATTGTGAA
*
5491658 GGGTTTTGGCTGAGCCTGGTAAAAGCCATTGT
1 GGGTTTTGGCTGAGCC-GGTAAAAACCATTGT
5491690 AAAGCTTGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.23, C:0.14, G:0.32, T:0.32
Consensus pattern (34 bp):
GGGTTTTGGCTGAGCCGGTAAAAACCATTGTGAA
Found at i:5504566 original size:22 final size:23
Alignment explanation
Indices: 5504541--5504586 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5504531 CATTTATGGG
*
5504541 AAATGGTTT-GAATGATGTTATC
1 AAATGGTTTAAAATGATGTTATC
*
5504563 AAATGTTTTAAAATGATGTTATC
1 AAATGGTTTAAAATGATGTTATC
5504586 A
1 A
5504587 TGGATTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (23 bp):
AAATGGTTTAAAATGATGTTATC
Found at i:5524804 original size:21 final size:19
Alignment explanation
Indices: 5524773--5524812 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
5524763 ATGAAATAAT
5524773 AACAATAACATTCATAGCA
1 AACAATAACATTCATAGCA
5524792 AACACATAGACATTCATAGCA
1 AACA-ATA-ACATTCATAGCA
5524813 GGATAGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 12 0.63
ACGTcount: A:0.50, C:0.23, G:0.07, T:0.20
Consensus pattern (19 bp):
AACAATAACATTCATAGCA
Found at i:5527443 original size:25 final size:26
Alignment explanation
Indices: 5527409--5527458 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
5527399 TCCAACTTTT
5527409 AATAAAATATTAATA-TTAAATTATA
1 AATAAAATATTAATATTTAAATTATA
5527434 AATAAAATATTAATATTTAAATTAT
1 AATAAAATATTAATATTTAAATTAT
5527459 CNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATAAAATATTAATATTTAAATTATA
Found at i:5532068 original size:49 final size:48
Alignment explanation
Indices: 5531996--5532089 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 48
5531986 AAGGGGTTAT
* * *
5531996 TTATAATAGCCAACTAAACCTAAACTTACTTGGTGTGCAAGTAAAATAA
1 TTATAATAGCCAACTAAACCTAAACCTACTTGATCTGCAAG-AAAATAA
5532045 TTATAATAGCCAACTAAACCTAAACCTACTTGATCTGCAAGAAAA
1 TTATAATAGCCAACTAAACCTAAACCTACTTGATCTGCAAGAAAA
5532090 GAAAATAGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 4 0.10
49 38 0.90
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.27
Consensus pattern (48 bp):
TTATAATAGCCAACTAAACCTAAACCTACTTGATCTGCAAGAAAATAA
Found at i:5561952 original size:12 final size:12
Alignment explanation
Indices: 5561921--5561952 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5561911 AGTTTTTTTG
*
5561921 TCTTTCTCCCTT
1 TCTTTCTTCCTT
5561933 TCTTTCTTCCTT
1 TCTTTCTTCCTT
5561945 TCTTTCTT
1 TCTTTCTT
5561953 TGCTTCATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (12 bp):
TCTTTCTTCCTT
Found at i:5563087 original size:24 final size:19
Alignment explanation
Indices: 5563033--5563084 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
5563023 ATAATATTTT
5563033 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
*
5563052 AATATTGTTTTATTCATAA
1 AATATTATTTTATTCATAA
5563071 AATATTATTTTATT
1 AATATTATTTTATT
5563085 TTAGAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:5574174 original size:22 final size:22
Alignment explanation
Indices: 5574149--5574190 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5574139 CAAAGAACCA
*
5574149 ATATCTGGAAAAAAAAGAATTG
1 ATATATGGAAAAAAAAGAATTG
* *
5574171 ATATATGGAAAGACAAGAAT
1 ATATATGGAAAAAAAAGAAT
5574191 CAATTCTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.19, T:0.21
Consensus pattern (22 bp):
ATATATGGAAAAAAAAGAATTG
Done.