Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 176 of 310
Found at i:57341033 original size:51 final size:49
Alignment explanation
Indices: 57340943--57341039 Score: 167
Period size: 51 Copynumber: 1.9 Consensus size: 49
57340933 TTTTTTAAGC
*
57340943 CCCAATAAAGACTTAGATTATTAATGGATAATTAGATAAAGAAAGAAGT
1 CCCAATAAAGACTTAGATTATTAATGGATAATCAGATAAAGAAAGAAGT
57340992 CCCAATAAAGACTTAGATTACATTAATGGATAATCAGATAAAGAAAGA
1 CCCAATAAAGACTTAGATT--ATTAATGGATAATCAGATAAAGAAAGA
57341040 GGGGGTCTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 19 0.42
51 26 0.58
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.25
Consensus pattern (49 bp):
CCCAATAAAGACTTAGATTATTAATGGATAATCAGATAAAGAAAGAAGT
Found at i:57341966 original size:27 final size:27
Alignment explanation
Indices: 57341929--57342082 Score: 177
Period size: 27 Copynumber: 5.7 Consensus size: 27
57341919 ACACGTTAGA
*
57341929 AAAGGAAAGCCTTAT-TGGCGAATCATG
1 AAAGGAAAGCCTT-TGTGGTGAATCATG
* * **
57341956 AAAGAAAAGCCTTTGTAGCAAATCATG
1 AAAGGAAAGCCTTTGTGGTGAATCATG
* * *
57341983 AAAGGAAAGCCTTTATAGTGAAACATG
1 AAAGGAAAGCCTTTGTGGTGAATCATG
*
57342010 AAAGGAAAGCCTTTGTGGTGAAACATG
1 AAAGGAAAGCCTTTGTGGTGAATCATG
57342037 AAAGGAAAGCCTTTGTGGTGAAAT-ATG
1 AAAGGAAAGCCTTTGTGGTG-AATCATG
*
57342064 AAAGAAAAAGCCTTTGTGG
1 AAAG-GAAAGCCTTTGTGG
57342083 CAATAATTTG
Statistics
Matches: 112, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
26 1 0.01
27 96 0.86
28 15 0.13
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (27 bp):
AAAGGAAAGCCTTTGTGGTGAATCATG
Found at i:57342010 original size:54 final size:53
Alignment explanation
Indices: 57341929--57342085 Score: 199
Period size: 54 Copynumber: 2.9 Consensus size: 53
57341919 ACACGTTAGA
* * *
57341929 AAAGGAAAGCC-TTATTGGCGAATCATGAAAGAAAAGCCTTTGTAGCAAATCATG
1 AAAGGAAAGCCTTTA-TGGTGAAACATGAAAGAAAAGCCTTTGTGGCAAA-CATG
* * *
57341983 AAAGGAAAGCCTTTATAGTGAAACATGAAAGGAAAGCCTTTGTGGTGAAACATG
1 AAAGGAAAGCCTTTATGGTGAAACATGAAAGAAAAGCCTTTGTGG-CAAACATG
* *
57342037 AAAGGAAAGCCTTTGTGGTGAAATATGAAAGAAAAAGCCTTTGTGGCAA
1 AAAGGAAAGCCTTTATGGTGAAACATGAAAG-AAAAGCCTTTGTGGCAA
57342086 TAATTTGAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
54 70 0.79
55 19 0.21
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (53 bp):
AAAGGAAAGCCTTTATGGTGAAACATGAAAGAAAAGCCTTTGTGGCAAACATG
Found at i:57342065 original size:81 final size:82
Alignment explanation
Indices: 57341929--57342078 Score: 207
Period size: 81 Copynumber: 1.8 Consensus size: 82
57341919 ACACGTTAGA
* *
57341929 AAAGGAAAGCCTTATTGGCGAATCATGAAAGAAAAGCCTTTGTAGCAAATCATGAAAG-GAAAGC
1 AAAGGAAAGCCTTATTGGCGAAACATGAAAGAAAAGCCTTTGTAGCAAATCATGAAAGAAAAAGC
57341993 CTTTATAGTGAAACATG
66 CTTTATAGTGAAACATG
* * * *
57342010 AAAGGAAAGCCTT-TGTGGTGAAACATGAAAGGAAAGCCTTTGTGGTGAAAT-ATGAAAGAAAAA
1 AAAGGAAAGCCTTAT-TGGCGAAACATGAAAGAAAAGCCTTTGTAG-CAAATCATGAAAGAAAAA
57342073 GCCTTT
64 GCCTTT
57342079 GTGGCAATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
80 1 0.02
81 46 0.77
82 13 0.22
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (82 bp):
AAAGGAAAGCCTTATTGGCGAAACATGAAAGAAAAGCCTTTGTAGCAAATCATGAAAGAAAAAGC
CTTTATAGTGAAACATG
Found at i:57343923 original size:28 final size:28
Alignment explanation
Indices: 57343887--57343964 Score: 68
Period size: 29 Copynumber: 2.7 Consensus size: 28
57343877 TAAGTGATTT
*
57343887 TTGACAAAAATGTTAAATAGGGATTAAA
1 TTGAAAAAAATGTTAAATAGGGATTAAA
* * *
57343915 TTGAGAAAAGTG-TAAATTGAGGGGTTAAA
1 TTGAAAAAAATGTTAAA-T-AGGGATTAAA
*
57343944 TTGTAAAATAAATGTGAAATA
1 TTG-AAAA-AAATGTTAAATA
57343965 TGGGCTTCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
27 4 0.10
28 11 0.28
29 12 0.31
30 4 0.10
31 5 0.13
32 3 0.08
ACGTcount: A:0.47, C:0.01, G:0.22, T:0.29
Consensus pattern (28 bp):
TTGAAAAAAATGTTAAATAGGGATTAAA
Found at i:57344531 original size:43 final size:44
Alignment explanation
Indices: 57344432--57344542 Score: 147
Period size: 43 Copynumber: 2.6 Consensus size: 44
57344422 TTATCGAGAG
*
57344432 GTGATTACATGTAAGACCATGTCTGGGACATTGGCATCATTAAT
1 GTGATTACATGTAAGACCATGTCTGGGACAGTGGCATCATTAAT
* *
57344476 -TGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGA-T-AT
1 GTGATTACATGTAAGACCATGTCTGGGACAGTGGCATC-ATTAAT
* *
57344518 GTGATAACATGTAAGACCATATCTG
1 GTGATTACATGTAAGACCATGTCTG
57344543 AGATATGGCA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
42 2 0.03
43 55 0.95
44 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (44 bp):
GTGATTACATGTAAGACCATGTCTGGGACAGTGGCATCATTAAT
Found at i:57353231 original size:48 final size:47
Alignment explanation
Indices: 57353069--57353251 Score: 154
Period size: 48 Copynumber: 3.8 Consensus size: 47
57353059 TCCATCAAGT
* * * *
57353069 CGATGCCATGTCCCAGACATGGTCTTACACTGACTA-TCGAAATCGAGA
1 CGATGCCATGTCCCAGACATGGCCTTACACTGAC-ACTCTATA-CGTGA
* * * * * * * *
57353117 CCGACGCCATGTCCCA-AGCATGGTCTTTCACTAGCTCACACATTTTCGTGC
1 -CGATGCCATGTCCCAGA-CATGGCCTTACACT-G-ACACTC-TATACGTGA
57353168 CGATGCCATGTCCCAGACATGGCCTTACACTGACACCTCTATACGTGA
1 CGATGCCATGTCCCAGACATGGCCTTACACTGACA-CTCTATACGTGA
* *
57353216 CGATGCCATGTCCCAGACATAGTCTTACACTGACAC
1 CGATGCCATGTCCCAGACATGGCCTTACACTGACAC
57353252 ATCTCATAGT
Statistics
Matches: 107, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
47 1 0.01
48 42 0.39
49 30 0.28
50 28 0.26
51 6 0.06
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGCCTTACACTGACACTCTATACGTGA
Found at i:57353301 original size:46 final size:46
Alignment explanation
Indices: 57353217--57353430 Score: 172
Period size: 46 Copynumber: 4.6 Consensus size: 46
57353207 TATACGTGAC
*
57353217 GATGCCATGTCCCAGACATAGTCTTACACTGAC--ACATCTC-ATAGTT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGA-AGTT
* * *
57353263 GATGCATGTTCCATACATGTCTTACACTGGCTTACATCTCGAGGTT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAAGTT
* * * *
57353309 GATGCATGTCCCAGACA-GATCTTACACTAGCTTTCGTCTC-AATGCT
1 GATGCATGTCCCAGACATG-TCTTACACTGGCTTACATCTCGAA-GTT
* * * ** *
57353355 GATGCCATATCCCAGACACGGTCTTACACTGGCTCT-CATAAT-GTGGCT
1 GATG-CATGTCCCAGACA-TGTCTTACACTGGCT-TACAT-CTCGAAGTT
57353403 GATGCATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
57353431 AGCACACAAC
Statistics
Matches: 138, Mismatches: 19, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
44 12 0.09
45 14 0.10
46 63 0.46
47 25 0.18
48 21 0.15
49 3 0.02
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAAGTT
Found at i:57358424 original size:43 final size:43
Alignment explanation
Indices: 57358376--57358539 Score: 156
Period size: 43 Copynumber: 3.8 Consensus size: 43
57358366 ATCGAGATGT
*
57358376 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
1 GATTACATGTAAGACCATATCTGGGACATTGGCATTGTATTGA
* * * *
57358419 GATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTTAAT-C
1 GATTACATGTAAGACCATATCTGGGACATTGGCATTG-TATTGA
* * * * * * *
57358462 GATTTCGTATAAGACCCTATCTGGGACAGTGGCATCG-ATATGT
1 GATTACATGTAAGACCATATCTGGGACATTGGCATTGTAT-TGA
*
57358505 G-TTAACATGTAAGACCATATCTGGGATATT-GCATT
1 GATT-ACATGTAAGACCATATCTGGGACATTGGCATT
57358540 TTATGAGCTT
Statistics
Matches: 99, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.01
42 7 0.07
43 88 0.89
44 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
GATTACATGTAAGACCATATCTGGGACATTGGCATTGTATTGA
Found at i:57364253 original size:87 final size:86
Alignment explanation
Indices: 57363836--57364251 Score: 575
Period size: 86 Copynumber: 4.8 Consensus size: 86
57363826 GCTCTTATCG
* * * *
57363836 TATAATTAAATGTTTGCTTATATATAATATCATACAACTTTTATCGTACAAGATGAGTAACATGT
1 TATAACTAAATGCTTGCTTGTATATAATATCATACAACTCTTATCGTACAAGATGAGTAACATGT
57363901 TTTTTT-AAGTT-TTGTTCGAAA
66 TTTTTTGAA-TTATT-TTCGAAA
* *
57363922 TATAACTAAATGCTTACTTATATATAATATCATACAACTCTTATCGTACAAGATGAGTAACATGT
1 TATAACTAAATGCTTGCTTGTATATAATATCATACAACTCTTATCGTACAAGATGAGTAACATGT
**
57363987 TTTTTTGGGTTATTTTCGAAA
66 TTTTTTGAATTATTTTCGAAA
* * * *
57364008 TATAACTAAATGCTTACTTGTATATAATTTTATACAACTCTTATGGTACAAGATGAGTAACATGT
1 TATAACTAAATGCTTGCTTGTATATAATATCATACAACTCTTATCGTACAAGATGAGTAACATGT
** *
57364073 TTTTTTGGGTTATTTTTGAAA
66 TTTTTTGAATTATTTTCGAAA
* * * *
57364094 TATGACTAAATGCTTGCTTGTATATAATATCATACAACTCTTATTGTACAAGATGAGTAAAATTT
1 TATAACTAAATGCTTGCTTGTATATAATATCATACAACTCTTATCGTACAAGATGAGTAACA-TG
*
57364159 TTTTTTTGAATTATTTTTGAAA
65 TTTTTTTGAATTATTTTCGAAA
* * * *
57364181 TATGACTAAATGCTTGCTTGTATATAATATTATACAATTTTTATCGTACAAGATGAGTAACATGT
1 TATAACTAAATGCTTGCTTGTATATAATATCATACAACTCTTATCGTACAAGATGAGTAACATGT
57364246 TTTTTT
66 TTTTTT
57364252 TGGGGGTTAT
Statistics
Matches: 301, Mismatches: 26, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
86 221 0.73
87 80 0.27
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (86 bp):
TATAACTAAATGCTTGCTTGTATATAATATCATACAACTCTTATCGTACAAGATGAGTAACATGT
TTTTTTGAATTATTTTCGAAA
Found at i:57373025 original size:3 final size:3
Alignment explanation
Indices: 57373019--57373066 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
57373009 AGGAGAACAT
57373019 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
57373067 TAAGAAAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:57374693 original size:16 final size:17
Alignment explanation
Indices: 57374662--57374695 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
57374652 AACTTTAAAT
57374662 ACAAATTTAGAATATAA
1 ACAAATTTAGAATATAA
57374679 ACAAATTTA-AATATAA
1 ACAAATTTAGAATATAA
57374695 A
1 A
57374696 AATGAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
ACAAATTTAGAATATAA
Found at i:57375198 original size:12 final size:12
Alignment explanation
Indices: 57375181--57375205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57375171 ACAATTAAGT
57375181 TACTTTTTTTTC
1 TACTTTTTTTTC
57375193 TACTTTTTTTTC
1 TACTTTTTTTTC
57375205 T
1 T
57375206 TACACTCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TACTTTTTTTTC
Found at i:57375420 original size:27 final size:27
Alignment explanation
Indices: 57375388--57375456 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 27
57375378 TAGAAATTAG
* *
57375388 AAAATTTTTAAAAAATTTTAAAAATA-
1 AAAATTTTTAAAAAAATATAAAAATAT
57375414 ATAAA-TTTTAATAAAAATATAAAAATAT
1 A-AAATTTTTAA-AAAAATATAAAAATAT
57375442 AAAATTTATTAAAAA
1 AAAATTT-TTAAAAA
57375457 TTAGAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
26 7 0.19
27 19 0.53
28 6 0.17
29 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
AAAATTTTTAAAAAAATATAAAAATAT
Found at i:57375437 original size:26 final size:26
Alignment explanation
Indices: 57375406--57375457 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
57375396 TAAAAAATTT
*
57375406 TAAAAATAATAAATTTTAATAAAAATA
1 TAAAAAT-ATAAAATTTAATAAAAATA
*
57375433 TAAAAATATAAAATTTATTAAAAAT
1 TAAAAATATAAAATTTAATAAAAAT
57375458 TAGAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAAAATATAAAATTTAATAAAAATA
Found at i:57375513 original size:19 final size:19
Alignment explanation
Indices: 57375466--57375513 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
57375456 ATTAGAATTT
57375466 TTTTATAAAAATTGTAAAA
1 TTTTATAAAAATTGTAAAA
*** *
57375485 AAATAAAAAAATTGTAAAA
1 TTTTATAAAAATTGTAAAA
57375504 TTTTATAAAA
1 TTTTATAAAA
57375514 TCATAAAAAA
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
TTTTATAAAAATTGTAAAA
Found at i:57375769 original size:19 final size:19
Alignment explanation
Indices: 57375700--57375790 Score: 57
Period size: 19 Copynumber: 4.7 Consensus size: 19
57375690 TTTTTTTTAC
*
57375700 ATTTGTATAATTTTCT-TAT
1 ATTT-TATAAATTTCTATAT
*
57375719 GACTTTATAAAATTT-TATA-
1 -ATTTTAT-AAATTTCTATAT
* *
57375738 ATTTTTTATATTTCTATAT
1 ATTTTATAAATTTCTATAT
57375757 ATTTTATAAATTT-TCACTAT
1 ATTTTATAAATTTCT-A-TAT
57375777 -TTTTATAAAATTTC
1 ATTTTAT-AAATTTC
57375791 ACAATTTTGT
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
17 5 0.09
18 10 0.18
19 22 0.39
20 19 0.34
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTATAAATTTCTATAT
Found at i:57375771 original size:20 final size:20
Alignment explanation
Indices: 57375722--57375790 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 20
57375712 TTCTTATGAC
57375722 TTTATAAAATTT-TATA-AT
1 TTTATAAAATTTCTATATAT
* *
57375740 TTT-TTATATTTCTATATAT
1 TTTATAAAATTTCTATATAT
*
57375759 TTTATAAATTTTC-ACTAT-T
1 TTTATAAAATTTCTA-TATAT
57375778 TTTATAAAATTTC
1 TTTATAAAATTTC
57375791 ACAATTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 6 0.15
18 7 0.17
19 19 0.46
20 9 0.22
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATAAAATTTCTATATAT
Found at i:57375777 original size:28 final size:27
Alignment explanation
Indices: 57375730--57375783 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
57375720 ACTTTATAAA
* *
57375730 ATTTTATAATTTTTTATATTTCTATAT
1 ATTTTATAAATTTTCATATTTCTATAT
*
57375757 ATTTTATAAATTTTCACTATTTTTATA
1 ATTTTATAAATTTTCA-TATTTCTATA
57375784 AAATTTCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTTTATAAATTTTCATATTTCTATAT
Found at i:57375803 original size:20 final size:19
Alignment explanation
Indices: 57375758--57375803 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
57375748 TTTCTATATA
* *
57375758 TTTTATAAATTTTCACTAT
1 TTTTATAAAATTTCACAAT
57375777 TTTTATAAAATTTCACAAT
1 TTTTATAAAATTTCACAAT
57375796 TTTGTATA
1 TTT-TATA
57375804 TTTGTTATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (19 bp):
TTTTATAAAATTTCACAAT
Found at i:57377108 original size:19 final size:18
Alignment explanation
Indices: 57377075--57377110 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
57377065 GAAACCGGTC
*
57377075 GGTTAACCGAAAAAATTT
1 GGTTAACCAAAAAAATTT
57377093 GGTTAACCTAAAAAAATT
1 GGTTAACC-AAAAAAATT
57377111 AATAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (18 bp):
GGTTAACCAAAAAAATTT
Found at i:57377287 original size:7 final size:6
Alignment explanation
Indices: 57377246--57377286 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
57377236 ATAATTTAAT
*
57377246 AAATAA AAATAA AAATCTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
57377287 ACATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:57377287 original size:20 final size:20
Alignment explanation
Indices: 57377249--57377288 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
57377239 ATTTAATAAA
**
57377249 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATAAAAAAC
57377269 TAAAAATAAAAATAAAAAAC
1 TAAAAATAAAAATAAAAAAC
57377289 ATATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:57377320 original size:9 final size:9
Alignment explanation
Indices: 57377306--57377355 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
57377296 TTTATATAAA
57377306 TAATTCGGT
1 TAATTCGGT
*
57377315 TAATTCGGG
1 TAATTCGGT
*
57377324 TAATTCAGT
1 TAATTCGGT
**
57377333 TAATTCAAT
1 TAATTCGGT
57377342 TAATTCGGT
1 TAATTCGGT
57377351 TAATT
1 TAATT
57377356 TTATACTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:57384073 original size:60 final size:60
Alignment explanation
Indices: 57383995--57384112 Score: 191
Period size: 60 Copynumber: 2.0 Consensus size: 60
57383985 AGAATTTATA
* *
57383995 GGGGAGTCGCGACCTTAGAATGGATGAATCCTTTTTCAGGCTAGAAAGTGGAACATTTTG
1 GGGGAGTCGCAACCTTAGAAAGGATGAATCCTTTTTCAGGCTAGAAAGTGGAACATTTTG
* * *
57384055 GGGGAGTCGCAACTTTAGAAAGGATGAATCCTTTTTCAGGCTAGTAAGTGGAGCATTT
1 GGGGAGTCGCAACCTTAGAAAGGATGAATCCTTTTTCAGGCTAGAAAGTGGAACATTT
57384113 GAGTTATACT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (60 bp):
GGGGAGTCGCAACCTTAGAAAGGATGAATCCTTTTTCAGGCTAGAAAGTGGAACATTTTG
Found at i:57387782 original size:3 final size:3
Alignment explanation
Indices: 57387774--57387805 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
57387764 TATTTATTAA
57387774 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
57387806 CAAATAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:57388064 original size:12 final size:12
Alignment explanation
Indices: 57388049--57388080 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
57388039 TATTATAATA
57388049 ATAATTATTATT
1 ATAATTATTATT
57388061 ATAATTATTATT
1 ATAATTATTATT
57388073 ATTAATTA
1 A-TAATTA
57388081 GTGTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAATTATTATT
Found at i:57388075 original size:15 final size:15
Alignment explanation
Indices: 57388038--57388076 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
57388028 AAAAAGATAT
*
57388038 TTATTATAATAATAA
1 TTATTATTATAATAA
*
57388053 TTATTATTATAATTA
1 TTATTATTATAATAA
57388068 TTATTATTA
1 TTATTATTA
57388077 ATTAGTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATTATTATAATAA
Found at i:57388965 original size:18 final size:18
Alignment explanation
Indices: 57388942--57388978 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
57388932 TTTGTGATCA
57388942 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
57388960 AAATTGAAATTGAACGTG
1 AAATTGAAAGTGAAAGTG
57388978 A
1 A
57388979 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:57389538 original size:13 final size:13
Alignment explanation
Indices: 57389520--57389554 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
57389510 TTGGTTTAGT
57389520 AAAATAAAAATAA
1 AAAATAAAAATAA
57389533 AAAATAAAAATAA
1 AAAATAAAAATAA
57389546 ATAAATAAA
1 A-AAATAAA
57389555 GTTATATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:57390641 original size:17 final size:18
Alignment explanation
Indices: 57390610--57390658 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
57390600 GATAGGTGTC
57390610 ATATAAAATATAATAAA-AT
1 ATATAAAA-A-AATAAATAT
* *
57390629 ATTTTAAAAAATAAATAT
1 ATATAAAAAAATAAATAT
57390647 ATATAAAAAAAT
1 ATATAAAAAAAT
57390659 GAAACAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 6 0.24
18 13 0.52
19 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATAAAAAAATAAATAT
Found at i:57391412 original size:23 final size:23
Alignment explanation
Indices: 57391364--57391412 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
57391354 TATAATATAT
* *
57391364 AATTTATTTTTAAAAAATTTTTA
1 AATTTATTTTTAAAAAATTCTAA
* *
57391387 AATTTTTTTTTATAAAATTCTAA
1 AATTTATTTTTAAAAAATTCTAA
57391410 AAT
1 AAT
57391413 AAATAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTTATTTTTAAAAAATTCTAA
Found at i:57391452 original size:18 final size:18
Alignment explanation
Indices: 57391429--57391465 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
57391419 TTTTAAATTT
*
57391429 TAAAAAGTCAAAAAAATA
1 TAAAAAGTAAAAAAAATA
*
57391447 TAAAAATTAAAAAAAATA
1 TAAAAAGTAAAAAAAATA
57391465 T
1 T
57391466 TTTTAATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (18 bp):
TAAAAAGTAAAAAAAATA
Found at i:57391668 original size:19 final size:19
Alignment explanation
Indices: 57391646--57391687 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
57391636 TATTAAATTT
* *
57391646 TATTTTTATAATTTATATG
1 TATTTTTATAAATTATATA
*
57391665 TATTTTTCTAAATTATATA
1 TATTTTTATAAATTATATA
57391684 TATT
1 TATT
57391688 CTGAATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTTTATAAATTATATA
Found at i:57393604 original size:86 final size:86
Alignment explanation
Indices: 57393459--57393632 Score: 285
Period size: 86 Copynumber: 2.0 Consensus size: 86
57393449 GTCGTTCCTG
* *
57393459 GCTTTTAACCGAACAGTCTTCTCCGCTAGTCTTGTACCACGAACTGCTTTGAGTGTGGGCTCGAA
1 GCTTTCAACCGAACAGTCTTCTCCGCTAGTCTTGTACCACGAACTGCTTCGAGTGTGGGCTCGAA
57393524 CGATTCGAATCAAACACAAAT
66 CGATTCGAATCAAACACAAAT
* * * *
57393545 GCTTTCAACCGAATAGTCTTCTCCGCTATTCTTGTACCACGAATTGCTTCGAGTGTGGGCTTGAA
1 GCTTTCAACCGAACAGTCTTCTCCGCTAGTCTTGTACCACGAACTGCTTCGAGTGTGGGCTCGAA
*
57393610 CGATTCGAATCAAACACAGAT
66 CGATTCGAATCAAACACAAAT
57393631 GC
1 GC
57393633 AGAAATAGTT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (86 bp):
GCTTTCAACCGAACAGTCTTCTCCGCTAGTCTTGTACCACGAACTGCTTCGAGTGTGGGCTCGAA
CGATTCGAATCAAACACAAAT
Found at i:57394243 original size:13 final size:13
Alignment explanation
Indices: 57394225--57394250 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57394215 CATTTCTATA
57394225 TCATTTTCATTTT
1 TCATTTTCATTTT
57394238 TCATTTTCATTTT
1 TCATTTTCATTTT
57394251 GGAGAAAACT
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:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TCATTTTCATTTT
Found at i:57394295 original size:51 final size:51
Alignment explanation
Indices: 57394232--57394349 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
57394222 ATATCATTTT
* * *
57394232 CATTTTTCATTTTCATTTTGGAGAAAACTACATTCATTTTTAAATGTTT-C
1 CATTTCTCATTTTCATTTTGGAGAAAACCACATTCATTTTCAAATGTTTCC
*
57394282 CATTTCTCTATTTTTATTTTGGAGAAAACCACATTCATTTTCAAATGTTTCC
1 CATTTCTC-ATTTTCATTTTGGAGAAAACCACATTCATTTTCAAATGTTTCC
57394334 CATTTCTCCATTTTCA
1 CATTTCT-CATTTTCA
57394350 CCATTTCTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 7 0.12
51 38 0.63
52 14 0.23
53 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (51 bp):
CATTTCTCATTTTCATTTTGGAGAAAACCACATTCATTTTCAAATGTTTCC
Found at i:57395712 original size:24 final size:24
Alignment explanation
Indices: 57395685--57395733 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
57395675 ATTAACTTCG
*
57395685 GTAGCATTTGGCCCTTGAATCATT
1 GTAGCATTTGGCCATTGAATCATT
57395709 GTAGCATTTGGCCATTGAATCATT
1 GTAGCATTTGGCCATTGAATCATT
57395733 G
1 G
57395734 ATCACTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (24 bp):
GTAGCATTTGGCCATTGAATCATT
Found at i:57397831 original size:11 final size:12
Alignment explanation
Indices: 57397806--57397835 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
57397796 TTTACAATTT
57397806 TTAATTTTTTAA
1 TTAATTTTTTAA
57397818 TTAATTTTTT-A
1 TTAATTTTTTAA
57397829 TTAATTT
1 TTAATTT
57397836 AGTAATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTAATTTTTTAA
Found at i:57398259 original size:27 final size:28
Alignment explanation
Indices: 57398223--57398275 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
57398213 AAATGAAAAA
**
57398223 TAAATATAAAATACTTTAAATTTTAATT
1 TAAATATAAAATACAATAAATTTTAATT
57398251 TAAAT-TAAAATACAATAAATTTTAA
1 TAAATATAAAATACAATAAATTTTAA
57398276 AAAAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAATATAAAATACAATAAATTTTAATT
Found at i:57402402 original size:26 final size:26
Alignment explanation
Indices: 57402366--57402553 Score: 349
Period size: 26 Copynumber: 7.2 Consensus size: 26
57402356 TGATACAAAT
*
57402366 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
57402392 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
57402418 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
57402444 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
57402470 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
57402496 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
57402522 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
57402548 TGATAA
1 TGATAA
57402554 GAATTTCATG
Statistics
Matches: 160, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 160 1.00
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:57404868 original size:14 final size:14
Alignment explanation
Indices: 57404849--57404877 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
57404839 TTTCAACTGT
57404849 ATACCAGCATCTAC
1 ATACCAGCATCTAC
57404863 ATACCAGCATCTAC
1 ATACCAGCATCTAC
57404877 A
1 A
57404878 CCTATGGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.34, G:0.07, T:0.21
Consensus pattern (14 bp):
ATACCAGCATCTAC
Found at i:57413698 original size:51 final size:50
Alignment explanation
Indices: 57413637--57413867 Score: 285
Period size: 51 Copynumber: 4.7 Consensus size: 50
57413627 TACAAATCAA
* * * * * *
57413637 ATCTCGAAGAATATAAAATCATATTTTCTAAGATTACATATCGTATCTAAG
1 ATCTCTAAGATTATAATATCATATCTTATAAGATT-CATATCATATCTAAG
* * *
57413688 ATCTCTAAGAATATAAAATAATATCTTATAAGATTTCATATCATATCTAAG
1 ATCTCTAAGATTATAATATCATATCTTATAAGA-TTCATATCATATCTAAG
*
57413739 ATCTCTAAGATTATAATATCATATC--AT---A-TCATATCATATCCAAG
1 ATCTCTAAGATTATAATATCATATCTTATAAGATTCATATCATATCTAAG
*
57413783 ATCTCTAAGATTATAATATAATATCTTATAAGATTCCATATCATATCTAAG
1 ATCTCTAAGATTATAATATCATATCTTATAAGATT-CATATCATATCTAAG
*
57413834 ATCTCTAAGATTATAATATCATATCTTTTAAGAT
1 ATCTCTAAGATTATAATATCATATCTTATAAGAT
57413868 CATGTTTCCA
Statistics
Matches: 159, Mismatches: 13, Indels: 16
0.85 0.07 0.09
Matches are distributed among these distances:
44 39 0.25
46 3 0.02
49 3 0.02
50 1 0.01
51 111 0.70
52 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (50 bp):
ATCTCTAAGATTATAATATCATATCTTATAAGATTCATATCATATCTAAG
Found at i:57413764 original size:5 final size:5
Alignment explanation
Indices: 57413754--57413778 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
57413744 TAAGATTATA
57413754 ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC
57413779 CAAGATCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATC
Found at i:57413807 original size:95 final size:95
Alignment explanation
Indices: 57413673--57413858 Score: 327
Period size: 95 Copynumber: 2.0 Consensus size: 95
57413663 TCTAAGATTA
* * *
57413673 CATATCGTATCTAAGATCTCTAAGAATATAAAATAATATCTTATAAGATTTCATATCATATCTAA
1 CATATCATATCCAAGATCTCTAAGAATATAAAATAATATCTTATAAGATTCCATATCATATCTAA
57413738 GATCTCTAAGATTATAATATCATATCATAT
66 GATCTCTAAGATTATAATATCATATCATAT
* *
57413768 CATATCATATCCAAGATCTCTAAGATTATAATATAATATCTTATAAGATTCCATATCATATCTAA
1 CATATCATATCCAAGATCTCTAAGAATATAAAATAATATCTTATAAGATTCCATATCATATCTAA
57413833 GATCTCTAAGATTATAATATCATATC
66 GATCTCTAAGATTATAATATCATATC
57413859 TTTTAAGATC
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 86 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (95 bp):
CATATCATATCCAAGATCTCTAAGAATATAAAATAATATCTTATAAGATTCCATATCATATCTAA
GATCTCTAAGATTATAATATCATATCATAT
Found at i:57415098 original size:71 final size:72
Alignment explanation
Indices: 57415018--57415165 Score: 178
Period size: 73 Copynumber: 2.1 Consensus size: 72
57415008 AAAATACCTT
* ** *
57415018 TTTTATTTTCTTTAAAAAAT-AA-AGGAAA-ATGAAAAGAAAAATCATTTAT-ATGAACTGAAGT
1 TTTTGTTTTCTTTAAAAAATAAACAAAAAATATGAAAA-AAAAATCATTTATGA-GAACTCAAG-
57415079 AAAAAATCCA
63 AAAAAATCCA
* * *
57415089 TTTTGTTTTCTTTAAAAAGTAAACAAAAAATATGAAAAAGAAATCATTTATGAGAACTCAAGGAA
1 TTTTGTTTTCTTTAAAAAATAAACAAAAAATATGAAAAAAAAATCATTTATGAGAACTCAAGAAA
57415154 AAATCCA
66 AAATCCA
57415161 TTTTG
1 TTTTG
57415166 ATACGAGTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
71 18 0.27
72 16 0.24
73 24 0.36
74 8 0.12
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (72 bp):
TTTTGTTTTCTTTAAAAAATAAACAAAAAATATGAAAAAAAAATCATTTATGAGAACTCAAGAAA
AAATCCA
Found at i:57418792 original size:17 final size:15
Alignment explanation
Indices: 57418752--57418796 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
57418742 TCTACATTTG
*
57418752 ATATTTTTTTCTTAT
1 ATATTTTTTTCATAT
*
57418767 ATATATTTTTCATAT
1 ATATTTTTTTCATAT
57418782 ATCAATTTTTTTCAT
1 AT--ATTTTTTTCAT
57418797 TGGCATTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 15 0.60
17 10 0.40
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (15 bp):
ATATTTTTTTCATAT
Found at i:57420211 original size:30 final size:30
Alignment explanation
Indices: 57420172--57420244 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
57420162 TTTAATAACT
*
57420172 AATTAAGCCCTCAATATAGTTTAAGTACTC
1 AATTAAGCCCTCAATAGAGTTTAAGTACTC
* * *
57420202 AATTGAGCCCTCAGTCGAGTTTAAGTACTC
1 AATTAAGCCCTCAATAGAGTTTAAGTACTC
57420232 AATTAAGCCCTCA
1 AATTAAGCCCTCA
57420245 TCCCTTGACA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (30 bp):
AATTAAGCCCTCAATAGAGTTTAAGTACTC
Found at i:57424932 original size:47 final size:46
Alignment explanation
Indices: 57424881--57424994 Score: 129
Period size: 47 Copynumber: 2.5 Consensus size: 46
57424871 CGTATAAAAT
* *
57424881 CATATCTGGGATATGGCATCGGTGTGATATATGCTACTATATAAGAC
1 CATATCTGGGATATGGCATCGGTGAGATATATGATAC-ATATAAGAC
* * * * * *
57424928 CATATTTGGGATATGGCATCAGTGAGATATGTGATTCGTGTAAGAC
1 CATATCTGGGATATGGCATCGGTGAGATATATGATACATATAAGAC
* *
57424974 CATAGCTGGGCTATGGCATCG
1 CATATCTGGGATATGGCATCG
57424995 ATATGTGATA
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
46 24 0.44
47 31 0.56
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (46 bp):
CATATCTGGGATATGGCATCGGTGAGATATATGATACATATAAGAC
Found at i:57425024 original size:49 final size:48
Alignment explanation
Indices: 57424922--57425093 Score: 189
Period size: 42 Copynumber: 3.7 Consensus size: 48
57424912 TGCTACTATA
** * * * *
57424922 TAAGACCATATTTGGGATATGGCATCA-GTGAGATATGTGATT-CGTG
1 TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTATGTG
57424968 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTATGTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATTATGTG
* *
57425017 TAAGACCATAGTTGGGCTATGGCATC------GATATGTGAATATGTG
1 TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTATGTG
*
57425059 TAAGACCATAGCTAGGCTATGGCATCATTATGTGA
1 TAAGACCATAGCTGGGCTATGGCATCA-TATGTGA
57425094 AGATGTGTGA
Statistics
Matches: 106, Mismatches: 10, Indels: 17
0.80 0.08 0.13
Matches are distributed among these distances:
42 39 0.37
46 23 0.22
47 1 0.01
48 13 0.12
49 30 0.28
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.31
Consensus pattern (48 bp):
TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTATGTG
Found at i:57425060 original size:42 final size:42
Alignment explanation
Indices: 57425001--57425128 Score: 168
Period size: 42 Copynumber: 3.0 Consensus size: 42
57424991 ATCGATATGT
*
57425001 GATATGTGATTATGTGTAAGACCATAGTTGGGCTATGGCATC
1 GATATGTGAATATGTGTAAGACCATAGTTGGGCTATGGCATC
* *
57425043 GATATGTGAATATGTGTAAGACCATAGCTAGGCTATGGCATC
1 GATATGTGAATATGTGTAAGACCATAGTTGGGCTATGGCATC
* * ** *
57425085 -ATTATGTGAAGATGTGTGAGACCATAGTTGAACTATGGCGTC
1 GA-TATGTGAATATGTGTAAGACCATAGTTGGGCTATGGCATC
57425127 GA
1 GA
57425129 GAAAACGAAG
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
41 1 0.01
42 72 0.97
43 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.30
Consensus pattern (42 bp):
GATATGTGAATATGTGTAAGACCATAGTTGGGCTATGGCATC
Found at i:57432525 original size:65 final size:66
Alignment explanation
Indices: 57432380--57432554 Score: 237
Period size: 65 Copynumber: 2.7 Consensus size: 66
57432370 CAAGTTCATC
*
57432380 TAAATAATTAAAGTTGATACAATAATGAAAATTCAATAAAAAACAGAAACGTAATGCAAATATAT
1 TAAATAATTAAAGTTGATACAATAATGAAAATTCAATAAAAAACAGAAACATAATGCAAATATAT
*
57432445 G
66 A
* * ** *
57432446 TAAATAATTTAAGTTAATACAATAATGAAAATTGTAT-AAAAATAGAAACATAATGCAAATATAT
1 TAAATAATTAAAGTTGATACAATAATGAAAATTCAATAAAAAACAGAAACATAATGCAAATATAT
57432510 A
66 A
* *
57432511 TAAATAATTGAAGTTGATA-AGATAATGAAATTTCAATACAAAAA
1 TAAATAATTAAAGTTGATACA-ATAATGAAAATTCAATA-AAAAA
57432555 TCACATTCTA
Statistics
Matches: 94, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
64 1 0.01
65 55 0.59
66 33 0.35
67 5 0.05
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.29
Consensus pattern (66 bp):
TAAATAATTAAAGTTGATACAATAATGAAAATTCAATAAAAAACAGAAACATAATGCAAATATAT
A
Found at i:57434649 original size:31 final size:32
Alignment explanation
Indices: 57434614--57434678 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
57434604 AATATTAAAA
57434614 ATAATATAACTTAA-TTTTTTTCCTTTTTTCT
1 ATAATATAACTTAATTTTTTTTCCTTTTTTCT
*
57434645 ATAATATAACTTAATTTTTTTTTCTTTTTTCT
1 ATAATATAACTTAATTTTTTTTCCTTTTTTCT
57434677 AT
1 AT
57434679 CTTTCCCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 14 0.44
32 18 0.56
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (32 bp):
ATAATATAACTTAATTTTTTTTCCTTTTTTCT
Found at i:57434727 original size:27 final size:29
Alignment explanation
Indices: 57434669--57434727 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
57434659 TTTTTTTTTC
*
57434669 TTTTTTCTATCTTTCCCTTTTTCCTTTAT
1 TTTTTTCTATCTTTCCCTTTTTCCGTTAT
57434698 TTTTTTCTAT-TTT-CCTTTTTCCCGTT-T
1 TTTTTTCTATCTTTCCCTTTTT-CCGTTAT
57434725 TTT
1 TTT
57434728 AATAATAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 11 0.39
28 7 0.25
29 10 0.36
ACGTcount: A:0.05, C:0.22, G:0.02, T:0.71
Consensus pattern (29 bp):
TTTTTTCTATCTTTCCCTTTTTCCGTTAT
Found at i:57435389 original size:16 final size:17
Alignment explanation
Indices: 57435368--57435406 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
57435358 TCTTTTATAA
57435368 TTTTTAAAATTC-AATT
1 TTTTTAAAATTCGAATT
*
57435384 TTTTTAAATTTCTGAATT
1 TTTTTAAAATTC-GAATT
57435402 TTTTT
1 TTTTT
57435407 TTTAAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
18 9 0.45
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTTAAAATTCGAATT
Found at i:57438046 original size:11 final size:10
Alignment explanation
Indices: 57438029--57438099 Score: 56
Period size: 10 Copynumber: 7.1 Consensus size: 10
57438019 GATTTCTAAT
57438029 ATTTTTTAAA
1 ATTTTTTAAA
*
57438039 ATTTTTTTACA
1 A-TTTTTTAAA
*
57438050 ATATTTTAAA
1 ATTTTTTAAA
* *
57438060 A-TTTCTAAT
1 ATTTTTTAAA
*
57438069 A-GTTTTATAA
1 ATTTTTTA-AA
*
57438079 TTTTTTTAAA
1 ATTTTTTAAA
57438089 ATTTTTTAAA
1 ATTTTTTAAA
57438099 A
1 A
57438100 AATTACACAT
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
9 10 0.22
10 22 0.48
11 14 0.30
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:57438075 original size:39 final size:40
Alignment explanation
Indices: 57438001--57438099 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 40
57437991 AAATTAATAA
* * ** *
57438001 TTTTTCACAATCTTTTATGATTTCTAATATTTTTTAAAAT
1 TTTTTTACAATATTTTAAAATTTCTAATATGTTTTAAAAT
*
57438041 TTTTTTACAATATTTTAAAATTTCTAATA-GTTTTATAAT
1 TTTTTTACAATATTTTAAAATTTCTAATATGTTTTAAAAT
* *
57438080 TTTTTTAAAATTTTTTAAAA
1 TTTTTTACAATATTTTAAAA
57438100 AATTACACAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 26 0.51
40 25 0.49
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (40 bp):
TTTTTTACAATATTTTAAAATTTCTAATATGTTTTAAAAT
Found at i:57438152 original size:11 final size:11
Alignment explanation
Indices: 57438071--57438171 Score: 71
Period size: 11 Copynumber: 9.1 Consensus size: 11
57438061 TTTCTAATAG
57438071 TTTTATAATTT
1 TTTTATAATTT
*
57438082 TTTTAAAATTT
1 TTTTATAATTT
* * *
57438093 TTTAAAAAATT
1 TTTTATAATTT
****
57438104 ACACATAATTT
1 TTTTATAATTT
*
57438115 TATTTATATATAT
1 T-TTTATA-ATTT
57438128 TTTTATAA--T
1 TTTTATAATTT
57438137 TTTTATAATTT
1 TTTTATAATTT
57438148 TTTTATAACTTT
1 TTTTATAA-TTT
*
57438160 TTTTATACTTT
1 TTTTATAATTT
57438171 T
1 T
57438172 AAAGATATTT
Statistics
Matches: 70, Mismatches: 15, Indels: 10
0.74 0.16 0.11
Matches are distributed among these distances:
9 9 0.13
11 38 0.54
12 19 0.27
13 4 0.06
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:57438152 original size:20 final size:22
Alignment explanation
Indices: 57438117--57438166 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
57438107 CATAATTTTA
57438117 TTTATATATATTTTTATAA-TT
1 TTTATATATATTTTTATAACTT
*
57438138 TTTATA-ATTTTTTTATAACTT
1 TTTATATATATTTTTATAACTT
*
57438159 TTTTTATA
1 TTTATATA
57438167 CTTTTAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.44
21 13 0.52
22 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTATATATATTTTTATAACTT
Found at i:57438163 original size:32 final size:33
Alignment explanation
Indices: 57438108--57438171 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
57438098 AAAATTACAC
57438108 ATAATTTTATTTATATATATTTTTATAATTTTT
1 ATAATTTTATTTATATATATTTTTATAATTTTT
* *
57438141 ATAATTTT-TTTATA-ACTTTTTTTATACTTTT
1 ATAATTTTATTTATATA-TATTTTTATAATTTT
57438172 AAAGATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 1 0.04
32 19 0.68
33 8 0.29
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (33 bp):
ATAATTTTATTTATATATATTTTTATAATTTTT
Found at i:57438171 original size:9 final size:9
Alignment explanation
Indices: 57438116--57438149 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
57438106 ACATAATTTT
*
57438116 ATTTATATA
1 ATTTTTATA
57438125 TATTTTTATA
1 -ATTTTTATA
57438135 ATTTTTATA
1 ATTTTTATA
57438144 ATTTTT
1 ATTTTT
57438150 TTATAACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTTTATA
Found at i:57440294 original size:27 final size:27
Alignment explanation
Indices: 57440264--57440319 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
57440254 TCAAATTATT
* * *
57440264 TTATGCAAATATTTTCTTTTAAATTTA
1 TTATACAAATATTTCCTTTAAAATTTA
* *
57440291 TTATATATATATTTCCTTTAAAATTTA
1 TTATACAAATATTTCCTTTAAAATTTA
57440318 TT
1 TT
57440320 TAAGTACAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (27 bp):
TTATACAAATATTTCCTTTAAAATTTA
Found at i:57452440 original size:64 final size:64
Alignment explanation
Indices: 57452361--57452482 Score: 190
Period size: 64 Copynumber: 1.9 Consensus size: 64
57452351 ATAACAAATA
* *
57452361 TAGTTGGGAGTATTTGATTCATTTCGATCATAGCATCCTAATTACTTAACATAAGCATCACATC
1 TAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTACTTAACATAAGCATCACATC
* * **
57452425 TAGTTAGGAGCATTTGATTTATTTCGATCATAGCATCCTAATTATTTGGCATAAGCAT
1 TAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTACTTAACATAAGCAT
57452483 AGATATATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (64 bp):
TAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTACTTAACATAAGCATCACATC
Found at i:57452600 original size:44 final size:45
Alignment explanation
Indices: 57452550--57452868 Score: 222
Period size: 44 Copynumber: 7.2 Consensus size: 45
57452540 AGAAGTGAAC
* *
57452550 CTTATCTTCCTGAAGTTGAAGTGGAGCAGGTTGAA-ATGACAAGT
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGATGACAAGT
* * * **
57452594 CTTATC-TCATTGAAGTTGTAGTGGAGCAGACTGAAGATAGTGAA-T
1 CTTATCTTC-CTGAAGTTGCAGTGGAGCAGATTGAAGAT-GACAAGT
* *
57452639 CTTAT-TTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAT-AAACAGAT
1 CTTATCTT-CCTGAAGTTGCAGTGGAGCAGATTGAAG--ATGACA-AG-T
* * * * *
57452687 CTTATC-TCTCTGAAGTTGCAGTAGAGTAGATT-ATGGT-A-AA-C
1 CTTATCTTC-CTGAAGTTGCAGTGGAGCAGATTGAAGATGACAAGT
*
57452728 CTTATCTCCCTGAAGTTGCAGTGGAGCATG-TTGAAG-TGACAAGT
1 CTTATCTTCCTGAAGTTGCAGTGGAGCA-GATTGAAGATGACAAGT
* ** * *
57452772 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTCAATATG-CAAGT
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGATGACAAGT
* * *
57452816 CTTATCTTCCTGAAGTTGCAG-GAAGCAGACT-AAG-TTAC-AGAT
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGATGACAAG-T
57452858 CTTATCTTCCT
1 CTTATCTTCCT
57452869 AAGCAGTAGT
Statistics
Matches: 222, Mismatches: 31, Indels: 46
0.74 0.10 0.15
Matches are distributed among these distances:
41 29 0.13
42 20 0.09
43 14 0.06
44 85 0.38
45 37 0.17
46 5 0.02
47 5 0.02
48 27 0.12
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (45 bp):
CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGATGACAAGT
Found at i:57452652 original size:89 final size:87
Alignment explanation
Indices: 57452537--57452800 Score: 261
Period size: 89 Copynumber: 3.0 Consensus size: 87
57452527 GTAGTAACAT
*
57452537 TGAAGA-AGTGAACCTTATCTT-CCTGAAGTTGAAGTGGAGCAGGTTGAAATGACAAGTCTTATC
1 TGAAGATAGTGAACCTTAT-TTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATGACAAGTCTTATC
*
57452600 TCATTGAAGTTGTAGTGGAGCAGA
65 TC-TTGAAGTTGCAGTGGAGCAGA
* * * *
57452624 CTGAAGATAGTGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAT-AAACAGATC
1 -TGAAGATAGTGAACCTTATTTCCCTGAAGTTGCAGTGGAGCAGGTTGAA---ATGACA-AG-TC
* *
57452688 TTATCTCTCTGAAGTTGCAGTAGAGTAGA
60 TTATCTCT-TGAAGTTGCAGTGGAGCAGA
* * * * * *
57452717 T---TATGGTAAACCTTATCTCCCTGAAGTTGCAGTGGAGCATGTTGAAGTGACAAGTCTTATCT
1 TGAAGATAGTGAACCTTATTTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATGACAAGTCTTATCT
*
57452779 CCCTGAAGTTGCAGTGGAGCAG
66 -CTTGAAGTTGCAGTGGAGCAG
57452801 GCTCAATATG
Statistics
Matches: 145, Mismatches: 21, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
85 25 0.17
86 4 0.03
87 2 0.01
88 8 0.06
89 72 0.50
91 2 0.01
92 6 0.04
93 26 0.18
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (87 bp):
TGAAGATAGTGAACCTTATTTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATGACAAGTCTTATCT
CTTGAAGTTGCAGTGGAGCAGA
Found at i:57453085 original size:45 final size:45
Alignment explanation
Indices: 57452983--57453092 Score: 125
Period size: 45 Copynumber: 2.4 Consensus size: 45
57452973 AGGTTGAAGG
* * *
57452983 TACAAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAAAT
1 TACAAGTCTTATCTTCCTGAAGTAGCAAGAAAGCAGACTCAAAAT
* *
57453028 TAC-AGATCTTATCTTCCTGAAGTTGC-AGTAAAGCAGGCTCAAAAT
1 TACAAG-TCTTATCTTCCTGAAGTAGCAAG-AAAGCAGACTCAAAAT
* *
57453073 TACAAGTTTTATCTCCCTGA
1 TACAAGTCTTATCTTCCTGA
57453093 GGTCGCAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
44 4 0.07
45 49 0.89
46 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (45 bp):
TACAAGTCTTATCTTCCTGAAGTAGCAAGAAAGCAGACTCAAAAT
Found at i:57454689 original size:24 final size:24
Alignment explanation
Indices: 57454658--57454703 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
57454648 TTTTATGCAA
*
57454658 ATATTTT-CTTTTAAATTTATTAT
1 ATATTTTCCTTTAAAATTTATTAT
57454681 ATATGTTTCCTTTAAAATTTATT
1 ATAT-TTTCCTTTAAAATTTATT
57454704 TAAGTACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 3 0.15
25 13 0.65
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (24 bp):
ATATTTTCCTTTAAAATTTATTAT
Found at i:57462539 original size:127 final size:128
Alignment explanation
Indices: 57462401--57462719 Score: 507
Period size: 129 Copynumber: 2.5 Consensus size: 128
57462391 AGTCCAACGA
* *
57462401 AAAATCGAAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCTAAACATTGAACATTGCCTTGC
1 AAAATCGAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTG-
* *
57462466 TTT-AGAATTT-ATAAAACACGAGTGAAATTCTAAAGGAATATTCAATTATTTTGAACAAACCG
65 TTTCAGAATTTAAAAAAACACGAGTGAAATTCTAAAGGAACATTCAATTATTTTGAACAAACCG
*
57462528 AAAATCAAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGT
1 AAAATCGAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGT
* * *
57462593 TTCAGAATTTGAAAAAAATACGAGTGAAATTCTAAAGGAACATTCGATTATTTTGAACAAACGG
66 TTCAGAATTT-AAAAAAACACGAGTGAAATTCTAAAGGAACATTCAATTATTTTGAACAAACCG
* * *
57462657 GAAATCGAAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATTAAACATTGCCTT
1 AAAATCGAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTT
57462720 TTTTTTAAGG
Statistics
Matches: 177, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
126 3 0.02
127 68 0.38
129 106 0.60
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (128 bp):
AAAATCGAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGCCTTGT
TTCAGAATTTAAAAAAACACGAGTGAAATTCTAAAGGAACATTCAATTATTTTGAACAAACCG
Found at i:57462935 original size:24 final size:23
Alignment explanation
Indices: 57462896--57462940 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
57462886 ATACAATGCC
57462896 AATTAACAAACTAATAATTAACA
1 AATTAACAAACTAATAATTAACA
57462919 AATTAACAAAACTAATAATTAA
1 AATTAAC-AAACTAATAATTAA
57462941 GTATAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (23 bp):
AATTAACAAACTAATAATTAACA
Found at i:57467375 original size:44 final size:44
Alignment explanation
Indices: 57467274--57467432 Score: 133
Period size: 44 Copynumber: 3.6 Consensus size: 44
57467264 CTTTGATCCA
** ** * *
57467274 CTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGCTTTAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCAATCTG
* * ** *
57467318 TTCTACTATAACTTCAGGGAGATAAGACTTGTATCTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCAATCTG
* * * *
57467362 CTCCACTGCAACTTCAGAGAGATAAG-GTT-AATGGCTTCCATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAT--CTTCAATCTG
* *
57467406 CTCCACTGCAACTTTAAGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
57467433 TTTGCCATGA
Statistics
Matches: 89, Mismatches: 23, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 85 0.96
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTATCTTCAATCTG
Found at i:57467575 original size:43 final size:43
Alignment explanation
Indices: 57467519--57467661 Score: 144
Period size: 43 Copynumber: 3.3 Consensus size: 43
57467509 CCTTTGTAAT
*
57467519 TTCAAGGGGATAAGACTTGTAACTTTAACCTATTCCTTGCAAC
1 TTCAAGGAGATAAGACTTGTAACTTTAACCTATTCCTTGCAAC
* * * * ** * * * *
57467562 TTCAAGGAAATAAGATTTGCTATCTTCAGTCTGTCCCGTTGTAAT
1 TTCAAGGAGATAAGACTTG-TAACTTTAACCTATTCC-TTGCAAC
*
57467607 TTC-AGGGGATAAGACTTGTAACTTTAACCTATTCCTTGCAAC
1 TTCAAGGAGATAAGACTTGTAACTTTAACCTATTCCTTGCAAC
*
57467649 TTCAGGGAGATAA
1 TTCAAGGAGATAA
57467662 AGTTAGTGGC
Statistics
Matches: 73, Mismatches: 24, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
42 8 0.11
43 34 0.47
44 23 0.32
45 8 0.11
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (43 bp):
TTCAAGGAGATAAGACTTGTAACTTTAACCTATTCCTTGCAAC
Found at i:57467705 original size:87 final size:87
Alignment explanation
Indices: 57467519--57467707 Score: 226
Period size: 87 Copynumber: 2.2 Consensus size: 87
57467509 CCTTTGTAAT
*
57467519 TTCAAGGGGATAAGACTTGTAACTTTAACCTATTCCTTGCAACTTCAAGGAAATAAGATTTGCTA
1 TTCAAGGGGATAAGACTTGTAACTTTAACCTATTCCTTGCAACTTCAAGGAAATAAGATTAGCTA
* * *
57467584 TCTTCAGTCTGTCCCGTTGTAAT
66 GCTTCAGTCTGTCCCG-TGCAAC
* *
57467607 TTC-AGGGGATAAGACTTGTAACTTTAACCTATTCCTTGCAACTTCAGGGAGATAA-AGTTAG-T
1 TTCAAGGGGATAAGACTTGTAACTTTAACCTATTCCTTGCAACTTCAAGGAAATAAGA-TTAGCT
*
57467669 GGCTTC-GATCTGCTCCAC-TGCAAC
65 AGCTTCAG-TCTG-TCC-CGTGCAAC
*
57467693 TTCAAGGAGATAAGA
1 TTCAAGGGGATAAGA
57467708 TTCGCCATGG
Statistics
Matches: 88, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
85 1 0.01
86 17 0.19
87 66 0.75
88 4 0.05
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (87 bp):
TTCAAGGGGATAAGACTTGTAACTTTAACCTATTCCTTGCAACTTCAAGGAAATAAGATTAGCTA
GCTTCAGTCTGTCCCGTGCAAC
Found at i:57467890 original size:44 final size:45
Alignment explanation
Indices: 57467781--57467890 Score: 114
Period size: 44 Copynumber: 2.5 Consensus size: 45
57467771 TCCGCTCTAC
* * * * *
57467781 TGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCCCCAC
1 TGCAACTTCAGGGAGATAAGACTTGCTAACTTCAGCCTGCCCCAA
* * * * * *
57467826 TACAATTTTAGGGGGATAAGACTTG-TAACTTTAGCCTGCTCCAA
1 TGCAACTTCAGGGAGATAAGACTTGCTAACTTCAGCCTGCCCCAA
57467870 TGCAACTTCAGGGAGATAAGA
1 TGCAACTTCAGGGAGATAAGA
57467891 TTCGCCATAA
Statistics
Matches: 50, Mismatches: 15, Indels: 1
0.76 0.23 0.02
Matches are distributed among these distances:
44 31 0.62
45 19 0.38
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (45 bp):
TGCAACTTCAGGGAGATAAGACTTGCTAACTTCAGCCTGCCCCAA
Found at i:57469713 original size:16 final size:17
Alignment explanation
Indices: 57469682--57469714 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
57469672 TTCATAAGTA
57469682 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
57469699 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
57469715 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:57470060 original size:46 final size:46
Alignment explanation
Indices: 57469995--57470310 Score: 341
Period size: 46 Copynumber: 6.9 Consensus size: 46
57469985 TTATCTTTGA
* * * * * * * *
57469995 CATGATGCCATAGTGTCTTTCGACTATAGTCTTACTCATTTTCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTAT
* * *** *
57470041 CAGGTTGCCATGGTATCTTTCAACCACGGTCTTGTTCA-TTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TAT
* ** * ** * ***
57470087 TACATTGCCATAGTATCTTTCAACCATGGTCTTATTCA-TTCCCGC
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTAT
*
57470132 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTAT
* *
57470178 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTAT
*
57470224 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TAT
57470270 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT
57470311 NNNNNNNNNN
Statistics
Matches: 233, Mismatches: 33, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
45 40 0.17
46 191 0.82
47 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTAT
Found at i:57473996 original size:38 final size:38
Alignment explanation
Indices: 57473953--57474031 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
57473943 TAATTTTCTC
*
57473953 TCTTCTTCAGCTTTCATTCCTTGAATCCAACTTGATAT
1 TCTTCTTCAGCTTGCATTCCTTGAATCCAACTTGATAT
*
57473991 TCTTCTTCAGCTTGCATTTCTTGAATCCAACTTGATAT
1 TCTTCTTCAGCTTGCATTCCTTGAATCCAACTTGATAT
57474029 TCT
1 TCT
57474032 AACTTCCCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.46
Consensus pattern (38 bp):
TCTTCTTCAGCTTGCATTCCTTGAATCCAACTTGATAT
Found at i:57474031 original size:20 final size:20
Alignment explanation
Indices: 57473972--57474031 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
57473962 GCTTTCATTC
57473972 CTTGAATCCAACTTGATATT
1 CTTGAATCCAACTTGATATT
* * *
57473992 CTT--CTTCAGCTTGCAT-TT
1 CTTGAATCCAACTTG-ATATT
57474010 CTTGAATCCAACTTGATATT
1 CTTGAATCCAACTTGATATT
57474030 CT
1 CT
57474032 AACTTCCCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
18 12 0.40
19 4 0.13
20 14 0.47
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.43
Consensus pattern (20 bp):
CTTGAATCCAACTTGATATT
Found at i:57475388 original size:26 final size:25
Alignment explanation
Indices: 57475365--57475413 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
57475355 TCTGTTTCTT
* *
57475365 ATTCTTT-TTGTTTCTTTTTATTTC
1 ATTCTTTATTCTTTCTATTTATTTC
57475389 ATTCTTTCATTCTTTCTATTTATTT
1 ATTCTTT-ATTCTTTCTATTTATTT
57475414 TAAATATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
26 14 0.67
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.71
Consensus pattern (25 bp):
ATTCTTTATTCTTTCTATTTATTTC
Found at i:57481696 original size:292 final size:290
Alignment explanation
Indices: 57481172--57481753 Score: 1146
Period size: 292 Copynumber: 2.0 Consensus size: 290
57481162 TAACATAATT
57481172 TTTTTAACTTAATGTATACATATAATTTATATGCAACTACCTAGTACATGTCACTTAACCAAAGG
1 TTTTTAACTTAATGTATACATATAATTTATATGCAACTACCTAGTACATGTCACTTAACCAAAGG
57481237 AAGAAATACATCACCAAAATCTTTTTGTTGGAGTCGGGTTTGTTTTGGATGCTAGACCGAATCTG
66 AAGAAATACATCACCAAAATCTTTTTGTTGGAGTCGGGTTTGTTTTGGATGCTAGACCGAATCTG
57481302 AAACTCTAATAACCTGCGCATGAAAATAACCGTACGCTGAGTATTTCATACTCAATTGTATTACT
131 AAACTCTAATAACCTGCGCATGAAAATAACCGTACGCTGAGTATTTCATACTCAATTGTATTACT
57481367 ATAAATCAAGACTATTTAACATTAATAAATTACAAACATCAACCATAAATTTTATAATTATTTAA
196 ATAAATCAAGACTATTTAACATTAATAAATTACAAACATCAACCATAAATTTTATAATTATTTAA
57481432 ACTAATTTTATATATAATTATTTTACTTCATA
261 ACTAA-TTTATATATAA-TATTTTACTTCATA
57481464 TTTTTAACTTAATGTATACATATAATTTATATGCAACTACCTAGTACATGTCACTTAACCAAAGG
1 TTTTTAACTTAATGTATACATATAATTTATATGCAACTACCTAGTACATGTCACTTAACCAAAGG
57481529 AAGAAATACATCACCAAAATCTTTTTGTTGGAGTCGGGTTTGTTTTGGATGCTAGACCGAATCTG
66 AAGAAATACATCACCAAAATCTTTTTGTTGGAGTCGGGTTTGTTTTGGATGCTAGACCGAATCTG
57481594 AAACTCTAATAACCTGCGCATGAAAATAACCGTACGCTGAGTATTTCATACTCAATTGTATTACT
131 AAACTCTAATAACCTGCGCATGAAAATAACCGTACGCTGAGTATTTCATACTCAATTGTATTACT
57481659 ATAAATCAAGACTATTTAACATTAATAAATTACAAACATCAACCATAAATTTTATAATTATTTAA
196 ATAAATCAAGACTATTTAACATTAATAAATTACAAACATCAACCATAAATTTTATAATTATTTAA
57481724 ACTAATTTATATATAATATTTTACTTCATA
261 ACTAATTTATATATAATATTTTACTTCATA
57481754 AATCTTAAAT
Statistics
Matches: 290, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
290 14 0.05
291 11 0.04
292 265 0.91
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (290 bp):
TTTTTAACTTAATGTATACATATAATTTATATGCAACTACCTAGTACATGTCACTTAACCAAAGG
AAGAAATACATCACCAAAATCTTTTTGTTGGAGTCGGGTTTGTTTTGGATGCTAGACCGAATCTG
AAACTCTAATAACCTGCGCATGAAAATAACCGTACGCTGAGTATTTCATACTCAATTGTATTACT
ATAAATCAAGACTATTTAACATTAATAAATTACAAACATCAACCATAAATTTTATAATTATTTAA
ACTAATTTATATATAATATTTTACTTCATA
Found at i:57483958 original size:19 final size:19
Alignment explanation
Indices: 57483934--57483970 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
57483924 ATATAATCCT
57483934 TTTTTTCT-TTTTCTTTTTC
1 TTTTTTCTCTTTT-TTTTTC
57483953 TTTTTTCTCTTTTTTTTT
1 TTTTTTCTCTTTTTTTTT
57483971 GAATGCCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTTTCTCTTTTTTTTTC
Found at i:57487256 original size:45 final size:44
Alignment explanation
Indices: 57487201--57487342 Score: 157
Period size: 44 Copynumber: 3.2 Consensus size: 44
57487191 CAACTTTAGG
* *
57487201 GGAA-ATAAGACTTGTGATTTTCAGTCTGCT-TCCTTGCTACCTCA
1 GGAAGATAAGACTTGT-ATCTTCAGCCTGCTCT-CTTGCTACCTCA
* *
57487245 GGAAGATAAGACTTGTATCTTC-GACCTGCTCTCTTACTACTTCA
1 GGAAGATAAGACTTGTATCTTCAG-CCTGCTCTCTTGCTACCTCA
* * *
57487289 AGAAGATAAGATTTGTATCTTCAACCTGCTCTCTTGCTACCTCA
1 GGAAGATAAGACTTGTATCTTCAGCCTGCTCTCTTGCTACCTCA
57487333 -GAGAGATAAG
1 GGA-AGATAAG
57487343 GTTGGTGGCT
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
43 3 0.04
44 69 0.82
45 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (44 bp):
GGAAGATAAGACTTGTATCTTCAGCCTGCTCTCTTGCTACCTCA
Found at i:57487443 original size:45 final size:44
Alignment explanation
Indices: 57487356--57487452 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 44
57487346 GGTGGCTAAA
* * *
57487356 ATCTGCTCCATAGCAGATACATGGATATAAGACTTGCCATTTTT
1 ATCTGCTCCATAACAGATACATGGAGATAAGACTTGCAATTTTT
* *
57487400 GATCTGCTCCATAACCGATACATGGAGATAAGA-TCTGTAATTTTT
1 -ATCTGCTCCATAACAGATACATGGAGATAAGACT-TGCAATTTTT
57487445 AGTCTGCT
1 A-TCTGCT
57487453 TCCTTGTTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
44 2 0.04
45 43 0.96
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (44 bp):
ATCTGCTCCATAACAGATACATGGAGATAAGACTTGCAATTTTT
Found at i:57487510 original size:178 final size:178
Alignment explanation
Indices: 57487294--57487624 Score: 520
Period size: 178 Copynumber: 1.9 Consensus size: 178
57487284 CTTCAAGAAG
* * **
57487294 ATAAGATTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGTTGGTGGCTAAAATC
1 ATAAGACTTGTATCTTCAACCTACTCTCTTGCTACCTCAGAGAGATAAGACTGGTGGCTAAAATC
* * ** ***
57487359 TGCTCCATAG-CAGATACATGGATATAAGACTTGCCATTTTTGATCTGCTCCATAACCGATACAT
66 TACTCCATAGTC-GATACATGGAGATAAGACTCACCATTTCCAATCTGCTCCATAACCGATACAT
57487423 GGAGATAAGATCTGTAATTTTTAGTCTGCTTCCTTGTTACCTCAGGAAT
130 GGAGATAAGATCTGTAATTTTTAGTCTGCTTCCTTGTTACCTCAGGAAT
*
57487472 ATAAGACTTGTATCTTCAACCTACTCTCTTGCTACCTCAGAGAGATACGACTGGTGGCTAAAATC
1 ATAAGACTTGTATCTTCAACCTACTCTCTTGCTACCTCAGAGAGATAAGACTGGTGGCTAAAATC
* *
57487537 TACTCCATAGTCGATACATGGAGATAAGACTCACCATTTCCAATCTGCTCCATAGCCGATACTTG
66 TACTCCATAGTCGATACATGGAGATAAGACTCACCATTTCCAATCTGCTCCATAACCGATACATG
57487602 GAGATAAGATCTGTAATTTTTAG
131 GAGATAAGATCTGTAATTTTTAG
57487625 CCTATTACCC
Statistics
Matches: 138, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
178 137 0.99
179 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (178 bp):
ATAAGACTTGTATCTTCAACCTACTCTCTTGCTACCTCAGAGAGATAAGACTGGTGGCTAAAATC
TACTCCATAGTCGATACATGGAGATAAGACTCACCATTTCCAATCTGCTCCATAACCGATACATG
GAGATAAGATCTGTAATTTTTAGTCTGCTTCCTTGTTACCTCAGGAAT
Found at i:57489105 original size:20 final size:20
Alignment explanation
Indices: 57489082--57489121 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
57489072 AGGCCTTCTG
*
57489082 TATTATATAAGGTCCTTCCT
1 TATTACATAAGGTCCTTCCT
57489102 TATTACATAAGGTCCTTCCT
1 TATTACATAAGGTCCTTCCT
57489122 AGTTTGGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (20 bp):
TATTACATAAGGTCCTTCCT
Found at i:57497825 original size:19 final size:19
Alignment explanation
Indices: 57497783--57497825 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
57497773 TTGTGAATTT
* *
57497783 TAATGCATATGATGCAATG
1 TAATGCAGATGATGAAATG
57497802 TAATGCAGATGTATGAAATG
1 TAATGCAGATG-ATGAAATG
57497822 -AATG
1 TAATG
57497826 AAAAAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (19 bp):
TAATGCAGATGATGAAATG
Found at i:57499580 original size:21 final size:24
Alignment explanation
Indices: 57499511--57499567 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
57499501 GACTTGCATT
*
57499511 ATTTGTTTGGATTAAAATAAAACG
1 ATTTATTTGGATTAAAATAAAACG
57499535 ATTTATTTGGATTAAAATAAAACG
1 ATTTATTTGGATTAAAATAAAACG
57499559 ATTTATTTG
1 ATTTATTTG
57499568 ATAAATGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (24 bp):
ATTTATTTGGATTAAAATAAAACG
Found at i:57507590 original size:33 final size:33
Alignment explanation
Indices: 57507553--57507622 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 33
57507543 TATTTATACA
57507553 ATTATAATATT-TTATT-TAAATT-AGTAGATATTT
1 ATTAT-ATATTATTATTAT-AATTAAG-AGATATTT
*
57507586 ATTATTTATTATTATTATAATTAAGAGATATTT
1 ATTATATATTATTATTATAATTAAGAGATATTT
57507619 ATTA
1 ATTA
57507623 ATTAAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
32 4 0.12
33 26 0.79
34 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (33 bp):
ATTATATATTATTATTATAATTAAGAGATATTT
Found at i:57507644 original size:33 final size:33
Alignment explanation
Indices: 57507542--57507644 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
57507532 TGTAATGATA
* * *
57507542 ATATTTATACAATTATAATATTTTATTTAAATTAGTAG
1 ATATTTAT-TAATTATAATA-ATTA--TAAATAAG-AG
* * * *
57507580 ATATTTATTATTTATTATTATTATAATTAAGAG
1 ATATTTATTAATTATAATAATTATAAATAAGAG
57507613 ATATTTATTAATTA-AATAATTATAAAATAAGA
1 ATATTTATTAATTATAATAATTAT-AAATAAGA
57507645 TTTTTATGTT
Statistics
Matches: 53, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
32 7 0.13
33 22 0.42
34 6 0.11
36 3 0.06
37 7 0.13
38 8 0.15
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.49
Consensus pattern (33 bp):
ATATTTATTAATTATAATAATTATAAATAAGAG
Found at i:57507874 original size:12 final size:12
Alignment explanation
Indices: 57507858--57507901 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
57507848 AAAACAGGGG
57507858 AGAAAAAGAGAA
1 AGAAAAAGAGAA
* *
57507870 GGAAAAAGGGAA
1 AGAAAAAGAGAA
*
57507882 AGAAAAAGAAAAA
1 AGAAAAAG-AGAA
57507895 AGAAAAA
1 AGAAAAA
57507902 CTAGAGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:57510409 original size:30 final size:31
Alignment explanation
Indices: 57510352--57510418 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
57510342 TAGCTCTCAT
*
57510352 TTATTATTTAATATTTATATTAGATATATAA
1 TTATTATTTAATATTTATATTAAATATATAA
*
57510383 TTATTTTTTAA-ATTTAT-TTCAAATATATAA
1 TTATTATTTAATATTTATATT-AAATATATAA
57510413 -TATTAT
1 TTATTAT
57510419 ATATATGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 7 0.22
30 15 0.47
31 10 0.31
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (31 bp):
TTATTATTTAATATTTATATTAAATATATAA
Found at i:57510666 original size:12 final size:12
Alignment explanation
Indices: 57510649--57510676 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
57510639 ATAAGAGGTA
57510649 TTTTAAAATACC
1 TTTTAAAATACC
57510661 TTTTAAAATACC
1 TTTTAAAATACC
57510673 TTTT
1 TTTT
57510677 TTGAAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTTAAAATACC
Found at i:57511518 original size:14 final size:15
Alignment explanation
Indices: 57511499--57511527 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
57511489 TACTAGTATA
57511499 TGTTTTT-ATTTTGT
1 TGTTTTTCATTTTGT
57511513 TGTTTTTCATTTTGT
1 TGTTTTTCATTTTGT
57511528 AATTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.07, C:0.03, G:0.14, T:0.76
Consensus pattern (15 bp):
TGTTTTTCATTTTGT
Found at i:57515203 original size:33 final size:35
Alignment explanation
Indices: 57515149--57515213 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 35
57515139 CACAAATGTG
*
57515149 TTAAAATCATTAATTAAAAATA-ATAAAATATTTT
1 TTAAAATCACTAATTAAAAATATATAAAATATTTT
* *
57515183 TTAAAAT-ACTAATTACAAATATTTAAAATAT
1 TTAAAATCACTAATTAAAAATATATAAAATAT
57515214 AGTTTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 12 0.44
34 15 0.56
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (35 bp):
TTAAAATCACTAATTAAAAATATATAAAATATTTT
Found at i:57518182 original size:18 final size:18
Alignment explanation
Indices: 57518159--57518193 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
57518149 AATTTGGGCC
*
57518159 GTGTGGGCTTACACGGGT
1 GTGTGGGCTCACACGGGT
57518177 GTGTGGGCTCACACGGG
1 GTGTGGGCTCACACGGG
57518194 CAGATCACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.20, G:0.46, T:0.23
Consensus pattern (18 bp):
GTGTGGGCTCACACGGGT
Found at i:57519039 original size:238 final size:238
Alignment explanation
Indices: 57518621--57519099 Score: 958
Period size: 238 Copynumber: 2.0 Consensus size: 238
57518611 GGACTCGTTT
57518621 ACTGCATAATCTATTACTGTATTGATTACTGATACTGTAATGGGCCAAAGCCCAAATGCATGACT
1 ACTGCATAATCTATTACTGTATTGATTACTGATACTGTAATGGGCCAAAGCCCAAATGCATGACT
57518686 GCTTTTGTACTAAGATAGGTTAAAGCCCTAACTGATACTGTCACTGATACTGAAAAGGGCTTAGG
66 GCTTTTGTACTAAGATAGGTTAAAGCCCTAACTGATACTGTCACTGATACTGAAAAGGGCTTAGG
57518751 CCCAGACTAAGTTTATTTTGTATACTGTCTGTTTGTTTGCGCGGGGAATTACATACTGAGTTTAC
131 CCCAGACTAAGTTTATTTTGTATACTGTCTGTTTGTTTGCGCGGGGAATTACATACTGAGTTTAC
57518816 ATAAACTCACCCCTTCTACTTAATCTATGTAGGTAATCCCCAG
196 ATAAACTCACCCCTTCTACTTAATCTATGTAGGTAATCCCCAG
57518859 ACTGCATAATCTATTACTGTATTGATTACTGATACTGTAATGGGCCAAAGCCCAAATGCATGACT
1 ACTGCATAATCTATTACTGTATTGATTACTGATACTGTAATGGGCCAAAGCCCAAATGCATGACT
57518924 GCTTTTGTACTAAGATAGGTTAAAGCCCTAACTGATACTGTCACTGATACTGAAAAGGGCTTAGG
66 GCTTTTGTACTAAGATAGGTTAAAGCCCTAACTGATACTGTCACTGATACTGAAAAGGGCTTAGG
57518989 CCCAGACTAAGTTTATTTTGTATACTGTCTGTTTGTTTGCGCGGGGAATTACATACTGAGTTTAC
131 CCCAGACTAAGTTTATTTTGTATACTGTCTGTTTGTTTGCGCGGGGAATTACATACTGAGTTTAC
57519054 ATAAACTCACCCCTTCTACTTAATCTATGTAGGTAATCCCCAG
196 ATAAACTCACCCCTTCTACTTAATCTATGTAGGTAATCCCCAG
57519097 ACT
1 ACT
57519100 TGACGAATCG
Statistics
Matches: 241, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
238 241 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (238 bp):
ACTGCATAATCTATTACTGTATTGATTACTGATACTGTAATGGGCCAAAGCCCAAATGCATGACT
GCTTTTGTACTAAGATAGGTTAAAGCCCTAACTGATACTGTCACTGATACTGAAAAGGGCTTAGG
CCCAGACTAAGTTTATTTTGTATACTGTCTGTTTGTTTGCGCGGGGAATTACATACTGAGTTTAC
ATAAACTCACCCCTTCTACTTAATCTATGTAGGTAATCCCCAG
Found at i:57520674 original size:18 final size:18
Alignment explanation
Indices: 57520651--57520686 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
57520641 GAGGTAGGAA
57520651 TAAGAGGGAATCAAAGCT
1 TAAGAGGGAATCAAAGCT
*
57520669 TAAGAGGGAATCGAAGCT
1 TAAGAGGGAATCAAAGCT
57520687 CTCGAATTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (18 bp):
TAAGAGGGAATCAAAGCT
Found at i:57522451 original size:40 final size:41
Alignment explanation
Indices: 57522399--57522493 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 41
57522389 TTAAATAACC
*
57522399 AAATACAT-TTAAAACAAATATTAAAACAAGAAACAAA-TA
1 AAATATATATTAAAACAAATATTAAAACAAGAAACAAATTA
* * * *
57522438 AAATATATATTAAAACAATTCTTAAAACAATACACAAATTA
1 AAATATATATTAAAACAAATATTAAAACAAGAAACAAATTA
* *
57522479 AAAAATATAATAAAA
1 AAATATATATTAAAA
57522494 ATTGATTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 7 0.15
40 25 0.53
41 15 0.32
ACGTcount: A:0.65, C:0.09, G:0.01, T:0.24
Consensus pattern (41 bp):
AAATATATATTAAAACAAATATTAAAACAAGAAACAAATTA
Found at i:57523167 original size:31 final size:31
Alignment explanation
Indices: 57523125--57523241 Score: 171
Period size: 31 Copynumber: 3.8 Consensus size: 31
57523115 ACAAATGAAT
*
57523125 TAGCCGAAGCTACCACTATTCACTGATCAAG
1 TAGCCGAAGCTACCACTTTTCACTGATCAAG
* *
57523156 TAGCCGGAGCTACCATTTTTCACTGATCAAG
1 TAGCCGAAGCTACCACTTTTCACTGATCAAG
* * *
57523187 TAGCCGGAGCTACCACTTTTCAATGATCAGG
1 TAGCCGAAGCTACCACTTTTCACTGATCAAG
*
57523218 GAGCCGAAGCTACCACTTTTCACT
1 TAGCCGAAGCTACCACTTTTCACT
57523242 TGTCATTTGT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (31 bp):
TAGCCGAAGCTACCACTTTTCACTGATCAAG
Found at i:57524694 original size:26 final size:26
Alignment explanation
Indices: 57524661--57524711 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
57524651 AACACAAAAA
57524661 TTTTAAGAAATAATCAAGAATTGAAT
1 TTTTAAGAAATAATCAAGAATTGAAT
*
57524687 TTTTAAGAAATAATCAAGAGTTGAA
1 TTTTAAGAAATAATCAAGAATTGAA
57524712 CTTACTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (26 bp):
TTTTAAGAAATAATCAAGAATTGAAT
Found at i:57528674 original size:24 final size:24
Alignment explanation
Indices: 57528647--57528717 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
57528637 ATCATAGAAA
57528647 GTGTACAT-TGGCACTATGTGTGCG
1 GTGTA-ATATGGCACTATGTGTGCG
*
57528671 GTGTAGTATGGCACTATGTGTGCG
1 GTGTAATATGGCACTATGTGTGCG
*
57528695 GAGTTGAATA--GCACTATGTGTGC
1 GTG-T-AATATGGCACTATGTGTGC
57528718 TGATTTGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.02
24 36 0.88
25 1 0.02
26 3 0.07
ACGTcount: A:0.20, C:0.14, G:0.34, T:0.32
Consensus pattern (24 bp):
GTGTAATATGGCACTATGTGTGCG
Found at i:57528738 original size:26 final size:24
Alignment explanation
Indices: 57528657--57528727 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
57528647 GTGTACATTG
* * * *
57528657 GCACTATGTGTGCGGTGTAGTATG
1 GCACTATGTGTGCGGAGTTGAATA
57528681 GCACTATGTGTGCGGAGTTGAATA
1 GCACTATGTGTGCGGAGTTGAATA
* *
57528705 GCACTATGTGTGCTGATTTGAAT
1 GCACTATGTGTGCGGAGTTGAAT
57528728 GTCAACATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGGAGTTGAATA
Found at i:57535009 original size:565 final size:566
Alignment explanation
Indices: 57533750--57536002 Score: 4332
Period size: 565 Copynumber: 4.0 Consensus size: 566
57533740 TTCACTAACA
57533750 GAAGATCTTTCATTTTTTTCTGCCAAAGTTGATAATTTGTCATTCAATATAATCATCTTACTAAT
1 GAAGATCTTTCATTTTTTTCTGCCAAAGTTGATAATTTGTCATTCAATATAATCATCTTACTAAT
* *
57533815 GATAATTTACATGATTACTAAACACGAAAATCAAGCTCTGATACCATTTTGTTAGAATGAAATTG
66 GATAATTTTCATGATTACTAAACACGAAAATCAAGCTCTGATACTATTTTGTTAGAATGAAATTG
* * * * *
57533880 AACTCGAGGAAACAATGTAGAAGCACAATCAATGTTCTTTCACTCCCTATAAATCAATTTGGTAA
131 AACTCGACGAAACAATATAGAAGTACAATCAGTGTTCTTTCACTCTCTATAAATCAATTTGGTAA
* * * *
57533945 TTATGGCAAATCGAATAATACAATATATCAACAATTAACGCAAATCAACCACAATATCGTAAAAT
196 TTATGGCAAACCGAATAATACAATATATCAATAATCAACGAAAATCAACCACAATATCGTAAAAT
*
57534010 AATAATAATAAATCGAAACACACAATTTTTACATGGAGAACCCCTTTAAAGCAAAGGGT-AAAAC
261 AATAATAATAAATCGAAACACACAATTTTTACATGGAGAACCCCTTTAAAGCGAAGGGTAAAAAC
*
57534074 TACAGAACTTAAAAGTACGCCAAAATTTTCACTATAATCAGAGTCTTGCTATAAGATCACAACCA
326 TACAGAACTTGAAAGTACGCCAAAATTTTCACTATAATCAGAGTCTTGCTATAAGATCACAACCA
*
57534139 AGCCACCATAAAGAGTATACAACTCAAACAAGACTAAAGCAAACTTTAGAGAAAAGTTGAGAATA
391 AGCCACCATAAAGAGTATACAACTCAAACAAGACTAAAGCAAACTTAAGAGAAAAGTTGAGAATA
57534204 TCACAAAAAGAGGTTGACTTTAAAAGTCAAAAATCGCGAAGCTATAGTATATCAAACGAAAATCA
456 TCACAAAAAGAGGTTGACTTTAAAAGTCAAAAATCGCGAAGCTATAGTATATCAAACGAAAATCA
*
57534269 GACCGTACACATTAAATATCTTCAAGTCTACTAGATACTTGAAATT
521 GACCGTACACATTAAATATCTTCAAGTCTACTAGATACCTGAAATT
57534315 GAAGATCTTTCATTTTTTTCTGCCAAAGTTGATAATTTGTCATTCAATATAATCATCTTACTAAT
1 GAAGATCTTTCATTTTTTTCTGCCAAAGTTGATAATTTGTCATTCAATATAATCATCTTACTAAT
57534380 GATAATTTTCATGATTACTAAACACGAAAATCAAGCTCTGATACTATTTTGTTAGAATGAAATTG
66 GATAATTTTCATGATTACTAAACACGAAAATCAAGCTCTGATACTATTTTGTTAGAATGAAATTG
57534445 AACTCGACGAAACAATATAGAAGTACAATCAGTGTTCTTTCACTCTCTATAAATCAATTTGGTAA
131 AACTCGACGAAACAATATAGAAGTACAATCAGTGTTCTTTCACTCTCTATAAATCAATTTGGTAA
57534510 TTATGGCAAACCGAATAATACAATATATCAATAATCAACGAAAATCAACCACAATATCGTAAAAT
196 TTATGGCAAACCGAATAATACAATATATCAATAATCAACGAAAATCAACCACAATATCGTAAAAT
57534575 AATAATAATAAATCGAAACACACAATTTTTACATGGAGAACCCCTTTAAAGCGAAGGGTAAAAAC
261 AATAATAATAAATCGAAACACACAATTTTTACATGGAGAACCCCTTTAAAGCGAAGGGTAAAAAC
57534640 TACAGAACTTGAAAGTACGCCAAAATTTTCACTATAATCAGAGTCTTGCTATAAGATCACAACCA
326 TACAGAACTTGAAAGTACGCCAAAATTTTCACTATAATCAGAGTCTTGCTATAAGATCACAACCA
57534705 AGCCACCATAAAGAGTATACAACTCAAACAAGACTAAAGCAAACTTAAGAGAAAAGTTGAGAATA
391 AGCCACCATAAAGAGTATACAACTCAAACAAGACTAAAGCAAACTTAAGAGAAAAGTTGAGAATA
57534770 TCACAAAAAGAGGTTGACTTTAAAAGTCAAAAATCGCGAAGCTATAGTATATCAAACGAAAATCA
456 TCACAAAAAGAGGTTGACTTTAAAAGTCAAAAATCGCGAAGCTATAGTATATCAAACGAAAATCA
57534835 GACCGTACACATTAAATATCTTCAAGTCTACTAGATACCTGAAATT
521 GACCGTACACATTAAATATCTTCAAGTCTACTAGATACCTGAAATT
57534881 GAAGATCTTTCATTTTTTTCTGCCAAAGTTGATAATTTGTCATTCAATATAATCATCTTACTAAT
1 GAAGATCTTTCATTTTTTTCTGCCAAAGTTGATAATTTGTCATTCAATATAATCATCTTACTAAT
57534946 GATAATTTTCATGATTACTAAACACGAAAATCAAGCTCTGATACTATTTT-TTAGAATGAAATTG
66 GATAATTTTCATGATTACTAAACACGAAAATCAAGCTCTGATACTATTTTGTTAGAATGAAATTG
57535010 AACTCGACGAAACAATATAGAAGTACAATCAGTGTTCTTTCACTCTCTATAAATCAATTTGGTAA
131 AACTCGACGAAACAATATAGAAGTACAATCAGTGTTCTTTCACTCTCTATAAATCAATTTGGTAA
57535075 TTATGGCAAACCGAATAATACAATATATCAATAATCAACGAAAATCAACCACAATATCGTAAAAT
196 TTATGGCAAACCGAATAATACAATATATCAATAATCAACGAAAATCAACCACAATATCGTAAAAT
57535140 AATAATAATAAATCGAAACACACAATTTTTACATGGAGAACCCCTTTAAAGCGAAGGGTAAAAAC
261 AATAATAATAAATCGAAACACACAATTTTTACATGGAGAACCCCTTTAAAGCGAAGGGTAAAAAC
57535205 TACAGAACTTGAAAGTACGCCAAAATTTTCACTATAATCAGAGTCTTGCTATAAGATCACAACCA
326 TACAGAACTTGAAAGTACGCCAAAATTTTCACTATAATCAGAGTCTTGCTATAAGATCACAACCA
57535270 AGCCACCATAAAGAGTATACAACTCAAACAAGACTAAAGCAAACTTAAGAGAAAAGTTGAGAATA
391 AGCCACCATAAAGAGTATACAACTCAAACAAGACTAAAGCAAACTTAAGAGAAAAGTTGAGAATA
57535335 TCACAAAAAGAGGTTGACTTTAAAAGTCAAAAATCGCGAAGCTATAGTATATCAAACGAAAATCA
456 TCACAAAAAGAGGTTGACTTTAAAAGTCAAAAATCGCGAAGCTATAGTATATCAAACGAAAATCA
57535400 GACCGTACACATTAAATATCTTCAAGTCTACTAGATACCTGAAATT
521 GACCGTACACATTAAATATCTTCAAGTCTACTAGATACCTGAAATT
57535446 GAAGATCTTTCATTTTTTTCTGCCAAAGTTGATAATTTGTCATTCAATATAATCATCTTACTAAT
1 GAAGATCTTTCATTTTTTTCTGCCAAAGTTGATAATTTGTCATTCAATATAATCATCTTACTAAT
57535511 GATAATTTTCATGATTACTAAACACGAAAATCAAGCTCTGATACTATTTT-TTAGAATGAAATTG
66 GATAATTTTCATGATTACTAAACACGAAAATCAAGCTCTGATACTATTTTGTTAGAATGAAATTG
57535575 AACTCGACGAAACAATATAGAAGTACAATCAGTGTTCTTTCACTCTCTATAAATCAATTTGGTAA
131 AACTCGACGAAACAATATAGAAGTACAATCAGTGTTCTTTCACTCTCTATAAATCAATTTGGTAA
57535640 TTATGGCAAACCGAATAATACAATATATCAATAATCAACGAAAATCAACCACAATATCGTAAAAT
196 TTATGGCAAACCGAATAATACAATATATCAATAATCAACGAAAATCAACCACAATATCGTAAAAT
57535705 AATAATAATAAATCGAAACACACAATTTTTACATGGAGAACCCCTTTAAAGCGAAGGGTAAAAAC
261 AATAATAATAAATCGAAACACACAATTTTTACATGGAGAACCCCTTTAAAGCGAAGGGTAAAAAC
57535770 TACAGAACTTGAAAGTACGCCAAAATTTTCACTATAATCAGAGTCTTGCTATAAGATCACAACCA
326 TACAGAACTTGAAAGTACGCCAAAATTTTCACTATAATCAGAGTCTTGCTATAAGATCACAACCA
57535835 AGCCACCATAAAGAGTATACAACTCAAACAAGACTAAAGCAAACTTAAGAGAAAAGTTGAGAATA
391 AGCCACCATAAAGAGTATACAACTCAAACAAGACTAAAGCAAACTTAAGAGAAAAGTTGAGAATA
57535900 TCACAAAAAGAGGTTGACTTTAAAAGTCAAAAATCGCGAAGCTATAGTATATCAAACGAAAATCA
456 TCACAAAAAGAGGTTGACTTTAAAAGTCAAAAATCGCGAAGCTATAGTATATCAAACGAAAATCA
* *
57535965 GACCATACACATTAAATATCTTTAAGTCTACTAGATAC
521 GACCGTACACATTAAATATCTTCAAGTCTACTAGATAC
57536003 AATAAAAAAT
Statistics
Matches: 1670, Mismatches: 17, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
565 1312 0.79
566 358 0.21
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (566 bp):
GAAGATCTTTCATTTTTTTCTGCCAAAGTTGATAATTTGTCATTCAATATAATCATCTTACTAAT
GATAATTTTCATGATTACTAAACACGAAAATCAAGCTCTGATACTATTTTGTTAGAATGAAATTG
AACTCGACGAAACAATATAGAAGTACAATCAGTGTTCTTTCACTCTCTATAAATCAATTTGGTAA
TTATGGCAAACCGAATAATACAATATATCAATAATCAACGAAAATCAACCACAATATCGTAAAAT
AATAATAATAAATCGAAACACACAATTTTTACATGGAGAACCCCTTTAAAGCGAAGGGTAAAAAC
TACAGAACTTGAAAGTACGCCAAAATTTTCACTATAATCAGAGTCTTGCTATAAGATCACAACCA
AGCCACCATAAAGAGTATACAACTCAAACAAGACTAAAGCAAACTTAAGAGAAAAGTTGAGAATA
TCACAAAAAGAGGTTGACTTTAAAAGTCAAAAATCGCGAAGCTATAGTATATCAAACGAAAATCA
GACCGTACACATTAAATATCTTCAAGTCTACTAGATACCTGAAATT
Found at i:57538121 original size:16 final size:17
Alignment explanation
Indices: 57538102--57538143 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
57538092 TAAGAAATTG
57538102 TTATTATATTATATT-T
1 TTATTATATTATATTAT
57538118 TTATTATATTATATTAT
1 TTATTATATTATATTAT
*
57538135 ATATTATAT
1 TTATTATAT
57538144 AAATAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTATATTATATTAT
Found at i:57538143 original size:5 final size:5
Alignment explanation
Indices: 57538103--57538136 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
57538093 AAGAAATTGT
*
57538103 TATTA TATTA TATTTT TATTA TATTA TATTA TAT
1 TATTA TATTA TA-TTA TATTA TATTA TATTA TAT
57538137 ATTATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TATTA
Found at i:57539947 original size:45 final size:45
Alignment explanation
Indices: 57539848--57539950 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 45
57539838 CGACCACTGT
* * * * *
57539848 TACTGTTGCCGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACTGTTACCGTTACCAATTCAGCACTTTGTGTGTCGAA
* *
57539893 TACTGTTACTGTTACCGTTATCAATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACCGTTACCAATTCAGCACTTTGTGTGTCGAA
57539938 TACTGTTACTGTT
1 TACTGTTACTGTT
57539951 CTGGATTTGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACCGTTACCAATTCAGCACTTTGTGTGTCGAA
Found at i:57540152 original size:18 final size:18
Alignment explanation
Indices: 57540130--57540298 Score: 110
Period size: 18 Copynumber: 9.4 Consensus size: 18
57540120 TGATAATTAT
57540130 TGAATAATTGACTGTTAC
1 TGAATAATTGACTGTTAC
*
57540148 CGAATAATTGACTGTTAC
1 TGAATAATTGACTGTTAC
* * *
57540166 TGAATAACTGAATATTAC
1 TGAATAATTGACTGTTAC
*
57540184 TGAATAATTGA-TCATTAC
1 TGAATAATTGACT-GTTAC
* * *
57540202 TGAATAACTGATTGTCAC
1 TGAATAATTGACTGTTAC
* * *
57540220 TGACTAAATGACCGTTAC
1 TGAATAATTGACTGTTAC
* * * * *
57540238 TCAATAACTTAATTGCTAT
1 TGAATAA-TTGACTGTTAC
* *
57540257 TGAAT-ATCTGAAT-TTAT
1 TGAATAAT-TGACTGTTAC
*
57540274 TAAATAATTGACTGTTAC
1 TGAATAATTGACTGTTAC
*
57540292 TGGATAA
1 TGAATAA
57540299 CCGATCAATT
Statistics
Matches: 114, Mismatches: 31, Indels: 12
0.73 0.20 0.08
Matches are distributed among these distances:
17 13 0.11
18 91 0.80
19 10 0.09
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (18 bp):
TGAATAATTGACTGTTAC
Found at i:57540207 original size:54 final size:54
Alignment explanation
Indices: 57540114--57540222 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 54
57540104 AAAGGTATAA
* * * *
57540114 AATAACTGATAATTATTGAATAATTGACTGTTACCGAATAATTGACTGTTACTG
1 AATAACTGATAATTACTGAATAATTGACTATTACCGAATAACTGACTGTCACTG
* *
57540168 AATAACTGA-ATATTACTGAATAATTGA-TCATTACTGAATAACTGATTGTCACTG
1 AATAACTGATA-ATTACTGAATAATTGACT-ATTACCGAATAACTGACTGTCACTG
57540222 A
1 A
57540223 CTAAATGACC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 2 0.04
54 45 0.96
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (54 bp):
AATAACTGATAATTACTGAATAATTGACTATTACCGAATAACTGACTGTCACTG
Found at i:57552540 original size:29 final size:29
Alignment explanation
Indices: 57552508--57552584 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
57552498 TTATTAATAT
*
57552508 AAAATTTAAATTTATTATTATATTTTTAA
1 AAAATTTATATTTATTATTATATTTTTAA
* * * * *
57552537 AAAATATGTATGTATTTTTATATTTTTTA
1 AAAATTTATATTTATTATTATATTTTTAA
*
57552566 AAATTTTATATATTATTAT
1 AAAATTTATAT-TTATTAT
57552585 ATCTTGTTAG
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
29 31 0.86
30 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (29 bp):
AAAATTTATATTTATTATTATATTTTTAA
Found at i:57552667 original size:18 final size:18
Alignment explanation
Indices: 57552603--57552680 Score: 54
Period size: 18 Copynumber: 4.3 Consensus size: 18
57552593 AGCAATCATT
57552603 TTTTTATATATATT-TTTA
1 TTTTTATATAT-TTATTTA
**
57552621 AATTTAT-TATTTTATTT-
1 TTTTTATATA-TTTATTTA
* *
57552638 TTTTGAAAATATTTATTTA
1 TTTT-TATATATTTATTTA
*
57552657 TTTTTATATATTTCTTTAA
1 TTTTTATATATTTATTT-A
57552676 TTTTT
1 TTTTT
57552681 CTAAAATTAG
Statistics
Matches: 45, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
17 6 0.13
18 27 0.60
19 12 0.27
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (18 bp):
TTTTTATATATTTATTTA
Found at i:57556757 original size:19 final size:21
Alignment explanation
Indices: 57556710--57556753 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 21
57556700 GACATCATTC
57556710 TTAAATGTACTGCATTGCAATGAA
1 TTAAATGTACTGCATTGC-A--AA
57556734 TTAAATGTACTGCATTGCAA
1 TTAAATGTACTGCATTGCAA
57556754 TAAAGGATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.05
23 1 0.05
24 18 0.90
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (21 bp):
TTAAATGTACTGCATTGCAAA
Found at i:57567218 original size:25 final size:25
Alignment explanation
Indices: 57567189--57567237 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
57567179 TGAGCTTAAA
*
57567189 AAATATCCATTATATAGTTGTTGAT
1 AAATAGCCATTATATAGTTGTTGAT
57567214 AAATAGCCATTATATAGTTGTTGA
1 AAATAGCCATTATATAGTTGTTGA
57567238 CATGCCATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (25 bp):
AAATAGCCATTATATAGTTGTTGAT
Found at i:57572614 original size:45 final size:43
Alignment explanation
Indices: 57572564--57572661 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 43
57572554 TTGATTATAC
*
57572564 TTTGTAATACTTTATTTTTATTATAATTGATTTGGTTATACATTA
1 TTTGTAATA--TTATTTTTATTATAATTGATTTGGATATACATTA
*
57572609 TTTGTAGAGTATTATTTTTGTTATAATTGATTTGGATATACATTA
1 TTTGTA-A-TATTATTTTTATTATAATTGATTTGGATATACATTA
*
57572654 TTTATAAT
1 TTTGTAAT
57572662 TATACATGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
43 1 0.02
44 1 0.02
45 43 0.90
46 1 0.02
47 2 0.04
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (43 bp):
TTTGTAATATTATTTTTATTATAATTGATTTGGATATACATTA
Found at i:57573509 original size:7 final size:7
Alignment explanation
Indices: 57573499--57573538 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
57573489 TATTATGTTT
57573499 TATTATA
1 TATTATA
57573506 TATTATA
1 TATTATA
57573513 TATTATA
1 TATTATA
57573520 TTATTATTA
1 -TATTA-TA
57573529 TATTATA
1 TATTATA
57573536 TAT
1 TAT
57573539 AGTAAAGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 19 0.61
8 10 0.32
9 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TATTATA
Found at i:57574396 original size:21 final size:22
Alignment explanation
Indices: 57574368--57574433 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 22
57574358 CGGCTTTGCC
57574368 ATTCAGGCACTATATGTGTCGT
1 ATTCAGGCACTATATGTGTCGT
* ** *
57574390 ATT-AGGCACCACGTGTTTCGT
1 ATTCAGGCACTATATGTGTCGT
* *
57574411 -TTCAGGCACTTTATGTGTAGT
1 ATTCAGGCACTATATGTGTCGT
57574432 AT
1 AT
57574434 ACTGCTTCTG
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
20 2 0.06
21 26 0.81
22 4 0.12
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (22 bp):
ATTCAGGCACTATATGTGTCGT
Found at i:57577830 original size:21 final size:21
Alignment explanation
Indices: 57577806--57577855 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
57577796 TTTTTTAATT
*
57577806 AATTAACTACCGAAACGTTAA
1 AATTAACTAACGAAACGTTAA
** *
57577827 AATTTCCTAACGAAACTTTAA
1 AATTAACTAACGAAACGTTAA
*
57577848 AACTAACT
1 AATTAACT
57577856 CAATAACACT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.28
Consensus pattern (21 bp):
AATTAACTAACGAAACGTTAA
Found at i:57586182 original size:26 final size:26
Alignment explanation
Indices: 57586151--57586206 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
57586141 TGAAATGCCC
57586151 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
57586177 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
57586203 ATCA
1 ATCA
57586207 ATTTGTACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:57587418 original size:19 final size:19
Alignment explanation
Indices: 57587394--57587430 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
57587384 TGGAGACACA
*
57587394 CTTGGCCTAATGAAGCCCG
1 CTTGGCCTAATAAAGCCCG
57587413 CTTGGCCTAATAAAGCCC
1 CTTGGCCTAATAAAGCCC
57587431 CTATCCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (19 bp):
CTTGGCCTAATAAAGCCCG
Found at i:57593728 original size:115 final size:113
Alignment explanation
Indices: 57593519--57593741 Score: 383
Period size: 115 Copynumber: 2.0 Consensus size: 113
57593509 AATTTCTCTT
*
57593519 TTCTTGCAATTTACTAGTCCCGAATTCATGTTCCTGTAATTTCTCCGATTCTTTTTTTGTCCTTT
1 TTCTTGCAATTTACTAGTCCCGAATTCATGTTCCTGTAATTTCTCCCATTCTTTTTTTGTCCTTT
*
57593584 CATACATTGATGTTGATTTTGAAGTACTAAGTAGATCAGTTTCTTTCA
66 CATACATTGATGTTGATTTTGAAGTACTAAGTAGACCAGTTTCTTTCA
* * *
57593632 TTCTTGCAATTTTACTAGTTCTGAATTCATGTTCGTGTAATTTCTCCCATTCTTTTTTTTGTCCT
1 TTCTTGCAA-TTTACTAGTCCCGAATTCATGTTCCTGTAATTTCTCCCATTC-TTTTTTTGTCCT
57593697 TTCATACATTGATGTTGATTTTGAAGTACTAAGTAGACCAGTTTC
64 TTCATACATTGATGTTGATTTTGAAGTACTAAGTAGACCAGTTTC
57593742 CTGACTTGGT
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
113 9 0.09
114 38 0.37
115 56 0.54
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (113 bp):
TTCTTGCAATTTACTAGTCCCGAATTCATGTTCCTGTAATTTCTCCCATTCTTTTTTTGTCCTTT
CATACATTGATGTTGATTTTGAAGTACTAAGTAGACCAGTTTCTTTCA
Found at i:57593913 original size:36 final size:36
Alignment explanation
Indices: 57593866--57593938 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
57593856 TCAGGGAAGT
57593866 CTGATGTTCATTGTAATAGTGTAAAACAGAAACCTA
1 CTGATGTTCATTGTAATAGTGTAAAACAGAAACCTA
*
57593902 CTGATGTTCATTGTAATAGTGTAAAACAGAAGCCTA
1 CTGATGTTCATTGTAATAGTGTAAAACAGAAACCTA
57593938 C
1 C
57593939 ACTTTAGATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (36 bp):
CTGATGTTCATTGTAATAGTGTAAAACAGAAACCTA
Found at i:57596358 original size:13 final size:13
Alignment explanation
Indices: 57596340--57596374 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
57596330 ACTGTTCGAA
57596340 ACTGTTTGGTTAC
1 ACTGTTTGGTTAC
57596353 ACTGTTTGGTTAC
1 ACTGTTTGGTTAC
57596366 ACTGTTTGG
1 ACTGTTTGG
57596375 GTATTGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.26, T:0.46
Consensus pattern (13 bp):
ACTGTTTGGTTAC
Done.