Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 48 of 128
Found at i:15187926 original size:24 final size:24
Alignment explanation
Indices: 15187894--15188027 Score: 142
Period size: 24 Copynumber: 5.6 Consensus size: 24
15187884 TCGTGTACGG
** *
15187894 AATCAGTCATACAAATCACATACA
1 AATCAGTCATTTAAATCACAGACA
*
15187918 AATCAGTCATTTAAGTCACAGACA
1 AATCAGTCATTTAAATCACAGACA
* *
15187942 AATCAATCATTTAAATCAAAGACA
1 AATCAGTCATTTAAATCACAGACA
* * * *
15187966 AATCAGTCATTTACATCTCGGATA
1 AATCAGTCATTTAAATCACAGACA
* * *
15187990 AATCATTCATTTACATCACAGAAA
1 AATCAGTCATTTAAATCACAGACA
*
15188014 AATCAATCATTTAA
1 AATCAGTCATTTAA
15188028 CCTCGAGGGC
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 91 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.28
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGACA
Found at i:15188075 original size:27 final size:27
Alignment explanation
Indices: 15188045--15188209 Score: 213
Period size: 27 Copynumber: 6.1 Consensus size: 27
15188035 GGCAAAAATA
15188045 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
15188072 GTCATTTTGCCGTACAGAGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
15188099 GTTATTTTACCCCATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
15188126 GTCATTTTACCCTACAGGAGTATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
*
15188153 GTCATTTTACCCTACATGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
15188180 GTCATTTTACCTTACAGGGGTACTACG
1 GTCATTTTACCCTACAGGGGCATTACG
15188207 GTC
1 GTC
15188210 TACAGTCGCC
Statistics
Matches: 115, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 115 1.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:15197626 original size:29 final size:30
Alignment explanation
Indices: 15197593--15197654 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
15197583 CCTTTCCTTT
* *
15197593 ATTCGATAGCCGAGGCTA-CCGTTTTCATA
1 ATTCGATAGCCAAAGCTATCCGTTTTCATA
* *
15197622 ATTCGATGGCCAAAGCTATCCTTTTTCATA
1 ATTCGATAGCCAAAGCTATCCGTTTTCATA
15197652 ATT
1 ATT
15197655 TGATGATCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (30 bp):
ATTCGATAGCCAAAGCTATCCGTTTTCATA
Found at i:15197678 original size:30 final size:30
Alignment explanation
Indices: 15197639--15197835 Score: 122
Period size: 30 Copynumber: 6.7 Consensus size: 30
15197629 GGCCAAAGCT
* *
15197639 ATCCTTTTTCATAATTTGATGATCTTCACC
1 ATCCCTTTTCATAATTCGATGATCTTCACC
** * *
15197669 ATCCCTTTTCATTGTTCGAGGGT-TGTCACC
1 ATCCCTTTTCATAATTCGATGATCT-TCACC
* * * ***
15197699 ATCTCTTTTCATAATTTGAT-AGCGAAAGCC
1 ATCCCTTTTCATAATTCGATGATCTTCA-CC
* **
15197729 ATCCCTTTTCATGA-TCGAT-AGTC-GAAGCC
1 ATCCCTTTTCATAATTCGATGA-TCTTCA-CC
* * *
15197758 ATCCCTTTTCATAGTTCGATGGTCATCACC
1 ATCCCTTTTCATAATTCGATGATCTTCACC
*
15197788 ATCCCTTTTCATAATT-GATGGT-TGTCACC
1 ATCCCTTTTCATAATTCGATGATCT-TCACC
15197817 ATCCCTTTTCATAA-TCGAT
1 ATCCCTTTTCATAATTCGAT
15197836 AGCCGAAGTT
Statistics
Matches: 130, Mismatches: 28, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
28 1 0.01
29 52 0.40
30 76 0.58
31 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGATGATCTTCACC
Found at i:15197758 original size:29 final size:29
Alignment explanation
Indices: 15197697--15197872 Score: 135
Period size: 29 Copynumber: 6.0 Consensus size: 29
15197687 AGGGTTGTCA
* *
15197697 CCATCTCTTTTCATAATTTGATAG-CGAAAG
1 CCATCCCTTTTCATAA-TCGATAGTCG-AAG
*
15197727 CCATCCCTTTTCATGATCGATAGTCGAAG
1 CCATCCCTTTTCATAATCGATAGTCGAAG
* *
15197756 CCATCCCTTTTCATAGTTCGATGGTC-ATCA-
1 CCATCCCTTTTCATA-ATCGATAGTCGA--AG
* * * *
15197786 CCATCCCTTTTCATAATTGATGGTTGTCA-
1 CCATCCCTTTTCATAATCGATAGTCG-AAG
*
15197815 CCATCCCTTTTCATAATCGATAGCCGAAG
1 CCATCCCTTTTCATAATCGATAGTCGAAG
** * * *
15197844 TTATCCCTTTTCATAGTCTATAGCCGAAG
1 CCATCCCTTTTCATAATCGATAGTCGAAG
15197873 TTATCCCATT
Statistics
Matches: 120, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
28 1 0.01
29 79 0.66
30 39 0.32
31 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.35
Consensus pattern (29 bp):
CCATCCCTTTTCATAATCGATAGTCGAAG
Found at i:15197819 original size:59 final size:59
Alignment explanation
Indices: 15197639--15197831 Score: 185
Period size: 59 Copynumber: 3.3 Consensus size: 59
15197629 GGCCAAAGCT
* * * ** *
15197639 ATCCTTTTTCATAATTTGATGATCTTCACCATCCCTTTTCATTGTTCGAGGGTTGTCACC
1 ATCCCTTTTCATAATTTGATGGTCATCACCATCCCTTTTCATAATT-GATGGTTGTCACC
* * * * * * * *
15197699 ATCTCTTTTCATAATTTGATAG-CGA-AAGCCATCCCTTTTCATGATCGATAGTCG-AAGCC
1 ATCCCTTTTCATAATTTGATGGTC-ATCA-CCATCCCTTTTCATAATTGATGGTTGTCA-CC
* *
15197758 ATCCCTTTTCATAGTTCGATGGTCATCACCATCCCTTTTCATAATTGATGGTTGTCACC
1 ATCCCTTTTCATAATTTGATGGTCATCACCATCCCTTTTCATAATTGATGGTTGTCACC
15197817 ATCCCTTTTCATAAT
1 ATCCCTTTTCATAAT
15197832 CGATAGCCGA
Statistics
Matches: 103, Mismatches: 24, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
58 1 0.01
59 66 0.64
60 36 0.35
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.39
Consensus pattern (59 bp):
ATCCCTTTTCATAATTTGATGGTCATCACCATCCCTTTTCATAATTGATGGTTGTCACC
Found at i:15197873 original size:29 final size:29
Alignment explanation
Indices: 15197817--15197885 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
15197807 GGTTGTCACC
15197817 ATCCCTTTTCATAATCGATAGCCGAAGTT
1 ATCCCTTTTCATAATCGATAGCCGAAGTT
* *
15197846 ATCCCTTTTCATAGTCTATAGCCGAAGTT
1 ATCCCTTTTCATAATCGATAGCCGAAGTT
*
15197875 ATCCCATTTCA
1 ATCCCTTTTCA
15197886 CCCGTCAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCGAAGTT
Found at i:15205175 original size:27 final size:27
Alignment explanation
Indices: 15205139--15205230 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 27
15205129 TTTTAATTTC
*
15205139 TTTTAATATTATATGTTTTAAATGTTA
1 TTTTATTATTATATGTTTTAAATGTTA
* ***** *
15205166 TTTTATTATTAAAATAAAGAATAAT-TTC
1 TTTTATTATT-ATATGTTTTA-AATGTTA
15205194 TTTTAATT-TTATATGTTTTAAATGTTA
1 TTTT-ATTATTATATGTTTTAAATGTTA
15205221 TTTTATTATT
1 TTTTATTATT
15205231 CAAATAAATA
Statistics
Matches: 45, Mismatches: 15, Indels: 10
0.64 0.21 0.14
Matches are distributed among these distances:
26 6 0.13
27 21 0.47
28 12 0.27
29 6 0.13
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (27 bp):
TTTTATTATTATATGTTTTAAATGTTA
Found at i:15205216 original size:55 final size:55
Alignment explanation
Indices: 15205132--15205238 Score: 196
Period size: 55 Copynumber: 1.9 Consensus size: 55
15205122 GTTTAAGTTT
15205132 TAATTTCTTTTAATATTATATGTTTTAAATGTTATTTTATTATTAAAATAAAGAA
1 TAATTTCTTTTAATATTATATGTTTTAAATGTTATTTTATTATTAAAATAAAGAA
* *
15205187 TAATTTCTTTTAATTTTATATGTTTTAAATGTTATTTTATTATTCAAATAAA
1 TAATTTCTTTTAATATTATATGTTTTAAATGTTATTTTATTATTAAAATAAA
15205239 TAAAATATAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (55 bp):
TAATTTCTTTTAATATTATATGTTTTAAATGTTATTTTATTATTAAAATAAAGAA
Found at i:15221037 original size:50 final size:50
Alignment explanation
Indices: 15220978--15221122 Score: 146
Period size: 50 Copynumber: 2.9 Consensus size: 50
15220968 CATTGAGATT
* * *
15220978 ATGAGAGGTCTCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGAAAGACCATGTTTGGGACATGGCATTGGCACCGAG
*** * * * *
15221028 ATGAGAGGTCCCCCAAAAGACCATGTCTGGGACATGACATGGGCACCGAT
1 ATGAGAGGTCCCATGAAAGACCATGTTTGGGACATGGCATTGGCACCGAG
** * * * *
15221078 ATGAGAACTCCCATGAAAGACCATATCTAGGATATGGCATTGGCA
1 ATGAGAGGTCCCATGAAAGACCATGTTTGGGACATGGCATTGGCA
15221123 GTATAGAAAA
Statistics
Matches: 75, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGAAAGACCATGTTTGGGACATGGCATTGGCACCGAG
Found at i:15228585 original size:50 final size:50
Alignment explanation
Indices: 15228482--15228674 Score: 165
Period size: 50 Copynumber: 3.7 Consensus size: 50
15228472 GAGAATGAGA
* * *
15228482 TCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGAATATGAGAGG
1 TCCCATGTAAGACCATTTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* * *
15228538 TCCCATGTAACACTATTTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATTTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * **
15228588 TCTCC-CGTAAGACCATGTCTGGGACATGACATGGGCACCGATACGAGAAC
1 TC-CCATGTAAGACCATTTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
15228638 TCCCATGTAAGACCATATT-TGGGATATGGCATTGGCA
1 TCCCATGTAAGACCAT-TTCTGGGACATGGCATTGGCA
15228675 GTATAGAAAA
Statistics
Matches: 112, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
49 2 0.02
50 71 0.63
51 3 0.03
53 3 0.03
55 1 0.01
56 32 0.29
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATTTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:15228674 original size:100 final size:103
Alignment explanation
Indices: 15228488--15228674 Score: 229
Period size: 100 Copynumber: 1.8 Consensus size: 103
15228478 GAGATCCCAT
* * ** *
15228488 GTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGAATATGAGAGGTCCCATGTAACACTA
1 GTAAGACCATGTCTGGGACATGACATGGGCATC--T-AGAATACGAGAACTCCCATGTAACACCA
*
15228553 TTTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCTCCC
63 TTTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCTCCC
* *
15228594 GTAAGACCATGTCTGGGACATGACATGGGCA-C-CG-ATACGAGAACTCCCATGTAAGACCATAT
1 GTAAGACCATGTCTGGGACATGACATGGGCATCTAGAATACGAGAACTCCCATGTAACACCAT-T
*
15228656 T-TGGGATATGGCATTGGCA
65 TCTGGGACATGGCATTGGCA
15228675 GTATAGAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
100 37 0.52
101 3 0.04
105 1 0.01
106 30 0.42
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (103 bp):
GTAAGACCATGTCTGGGACATGACATGGGCATCTAGAATACGAGAACTCCCATGTAACACCATTT
CTGGGACATGGCATTGGCACCGAGATGAGAGGTCTCCC
Found at i:15228710 original size:49 final size:50
Alignment explanation
Indices: 15228594--15228728 Score: 141
Period size: 49 Copynumber: 2.7 Consensus size: 50
15228584 GAGGTCTCCC
* * *
15228594 GTAAGACCATGTCTGGGACATGACATGGGCACCG-ATACGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CGTATACGAAAACTCCCAT
* * *
15228644 GTAAGACCATATTTGGGATATGGCATTGGCA-GTATA-GAAAACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACGTATACGAAAAC-TCCCAT
* * * *
15228693 GTAAGACTATGTCTGGGACATAGCTTTGGCATGTAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACGTAT
15228729 TATCAGATAA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
48 6 0.09
49 34 0.49
50 30 0.43
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACGTATACGAAAACTCCCAT
Found at i:15228971 original size:20 final size:20
Alignment explanation
Indices: 15228933--15228971 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15228923 TAAGTAAGTA
*
15228933 AGTAAGTAAACAAGTGAGTG
1 AGTAAGTAAACAAGCGAGTG
*
15228953 AGTAAGTAAAGAAGCGAGT
1 AGTAAGTAAACAAGCGAGT
15228972 AAAGATTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.31, T:0.18
Consensus pattern (20 bp):
AGTAAGTAAACAAGCGAGTG
Found at i:15239807 original size:29 final size:27
Alignment explanation
Indices: 15239766--15239820 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
15239756 AATAAATATT
15239766 TTTAATATTATTA-ATAATTTGATAAAC
1 TTTAATATTATTATATAATTT-ATAAAC
*
15239793 TTTAATATATAATTATATTATTTATAAA
1 TTTAATAT-T-ATTATATAATTTATAAA
15239821 TTATATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 1 0.04
29 9 0.38
30 6 0.25
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTTAATATTATTATATAATTTATAAAC
Found at i:15245057 original size:17 final size:17
Alignment explanation
Indices: 15245037--15245070 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
15245027 AGGAATTTAC
15245037 TTATGCTATG-CATGAAT
1 TTATG-TATGTCATGAAT
15245054 TTATGTATGTCATGAAT
1 TTATGTATGTCATGAAT
15245071 AAACACGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (17 bp):
TTATGTATGTCATGAAT
Found at i:15245140 original size:20 final size:20
Alignment explanation
Indices: 15245115--15245169 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
15245105 AATCTTATGT
15245115 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGGAATGGAAAG
* *
15245135 TAAGTATATGAAATGGAAAG
1 TAAGTAAATGGAATGGAAAG
15245155 TAAGTAAATGGAATG
1 TAAGTAAATGGAATG
15245170 TTATGTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (20 bp):
TAAGTAAATGGAATGGAAAG
Found at i:15252503 original size:25 final size:25
Alignment explanation
Indices: 15252453--15252516 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
15252443 CCGGTTTCAA
*
15252453 CTCGTATGAG-TTACCGATACTCAG
1 CTCGCATGAGCTTACCGATACTCAG
* * *
15252477 CTCGCATGAGCTTACCGTTATTTAG
1 CTCGCATGAGCTTACCGATACTCAG
* *
15252502 CTCGGAGGAGCTTAC
1 CTCGCATGAGCTTAC
15252517 TATTATTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 9 0.27
25 24 0.73
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (25 bp):
CTCGCATGAGCTTACCGATACTCAG
Found at i:15252522 original size:25 final size:25
Alignment explanation
Indices: 15252473--15252539 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
15252463 TTACCGATAC
* * *
15252473 TCAGCTCGCATGAGCTTACCGTTAT
1 TCAGCTCGGAGGAGCTTACCATTAT
* *
15252498 TTAGCTCGGAGGAGCTTACTATTAT
1 TCAGCTCGGAGGAGCTTACCATTAT
* *
15252523 TCAACTCAGAGGAGCTT
1 TCAGCTCGGAGGAGCTT
15252540 GCTGTTTATA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (25 bp):
TCAGCTCGGAGGAGCTTACCATTAT
Found at i:15262992 original size:27 final size:27
Alignment explanation
Indices: 15262962--15263038 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
15262952 ATTTTAGGAC
15262962 AAGGTCTTGTGGTGAAACCATGGAGTT
1 AAGGTCTTGTGGTGAAACCATGGAGTT
** **
15262989 AA-G----GAAGTGAATACC-TTTAGTT
1 AAGGTCTTGTGGTGAA-ACCATGGAGTT
15263011 AAGGTCTTGTGGTGAAACCATGGAGTT
1 AAGGTCTTGTGGTGAAACCATGGAGTT
15263038 A
1 A
15263039 GGGAGGCCAC
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
22 13 0.37
23 4 0.11
26 4 0.11
27 14 0.40
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (27 bp):
AAGGTCTTGTGGTGAAACCATGGAGTT
Found at i:15266467 original size:19 final size:18
Alignment explanation
Indices: 15266426--15266474 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
15266416 TAAAAATAAA
* *
15266426 ATAAAATAAATTTAAATT
1 ATAAAATAAATTAAAAAT
*
15266444 TTAAAATGAAATTAAAAAT
1 ATAAAAT-AAATTAAAAAT
15266463 ATAAATATAAAT
1 ATAAA-ATAAAT
15266475 AAGCCTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 6 0.24
19 17 0.68
20 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAAATAAATTAAAAAT
Found at i:15266956 original size:24 final size:24
Alignment explanation
Indices: 15266927--15266974 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
15266917 TATCGATTTA
*
15266927 TTTTTATATTAGATAAATATAATT
1 TTTTTACATTAGATAAATATAATT
* *
15266951 TTTTTACATTGGATAGATATAATT
1 TTTTTACATTAGATAAATATAATT
15266975 ATTTCTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
TTTTTACATTAGATAAATATAATT
Found at i:15267731 original size:15 final size:15
Alignment explanation
Indices: 15267711--15267741 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15267701 ATAATTTATT
15267711 ATATAAAATTTTTTG
1 ATATAAAATTTTTTG
15267726 ATATAAAATTTTTTG
1 ATATAAAATTTTTTG
15267741 A
1 A
15267742 AAGAGTGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
ATATAAAATTTTTTG
Found at i:15268574 original size:10 final size:11
Alignment explanation
Indices: 15268530--15268576 Score: 53
Period size: 10 Copynumber: 4.3 Consensus size: 11
15268520 CATGCTTTTT
*
15268530 AAATAATTATAA
1 AAAT-ATTATTA
15268542 AAATATTA-TA
1 AAATATTATTA
15268552 AAATATTATTTA
1 AAATATTA-TTA
15268564 AAAT-TTATTA
1 AAATATTATTA
15268574 AAA
1 AAA
15268577 CTGACAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATATTATTA
Found at i:15276495 original size:19 final size:18
Alignment explanation
Indices: 15276454--15276502 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
15276444 TAAAAATAAA
* *
15276454 ATAAAATAAATTTAAATT
1 ATAAAATAAATTAAAAAT
*
15276472 TTAAAATGAAATTAAAAAT
1 ATAAAAT-AAATTAAAAAT
15276491 ATAAATATAAAT
1 ATAAA-ATAAAT
15276503 AAGCCTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 6 0.24
19 17 0.68
20 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAAATAAATTAAAAAT
Found at i:15276984 original size:24 final size:24
Alignment explanation
Indices: 15276955--15277002 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
15276945 TATCGATTTA
*
15276955 TTTTTATATTAGATAAATATAATT
1 TTTTTACATTAGATAAATATAATT
* *
15276979 TTTTTACATTGGATAGATATAATT
1 TTTTTACATTAGATAAATATAATT
15277003 ATTTCTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
TTTTTACATTAGATAAATATAATT
Found at i:15277759 original size:15 final size:15
Alignment explanation
Indices: 15277739--15277769 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15277729 ATAATTTATT
15277739 ATATAAAATTTTTTG
1 ATATAAAATTTTTTG
15277754 ATATAAAATTTTTTG
1 ATATAAAATTTTTTG
15277769 A
1 A
15277770 AAGAGTGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
ATATAAAATTTTTTG
Found at i:15278602 original size:10 final size:11
Alignment explanation
Indices: 15278558--15278604 Score: 53
Period size: 10 Copynumber: 4.3 Consensus size: 11
15278548 CATGCTTTTT
*
15278558 AAATAATTATAA
1 AAAT-ATTATTA
15278570 AAATATTA-TA
1 AAATATTATTA
15278580 AAATATTATTTA
1 AAATATTA-TTA
15278592 AAAT-TTATTA
1 AAATATTATTA
15278602 AAA
1 AAA
15278605 CTGACAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATATTATTA
Found at i:15281866 original size:70 final size:69
Alignment explanation
Indices: 15281790--15281933 Score: 270
Period size: 70 Copynumber: 2.1 Consensus size: 69
15281780 GACACACACA
15281790 TTAAAAAAATAAGGGATTTTGCAAAATTTAATTATTTCGCAAGGGAAGGGATTCTAACTTGGGAC
1 TTAAAAAAATAA-GGATTTTGCAAAATTTAATTATTTCGCAAGGGAAGGGATTCTAACTTGGGAC
15281855 CTCAT
65 CTCAT
15281860 TTAAAAAAAATAAGGATTTTGCAAAATTTAATTATTTCGCAAGGGAAGGGATTCTAACTTGGGAC
1 TT-AAAAAAATAAGGATTTTGCAAAATTTAATTATTTCGCAAGGGAAGGGATTCTAACTTGGGAC
15281925 CTCAT
65 CTCAT
15281930 TTAA
1 TTAA
15281934 TTTTCATGCT
Statistics
Matches: 73, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
69 2 0.03
70 61 0.84
71 10 0.14
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (69 bp):
TTAAAAAAATAAGGATTTTGCAAAATTTAATTATTTCGCAAGGGAAGGGATTCTAACTTGGGACC
TCAT
Found at i:15296513 original size:2 final size:2
Alignment explanation
Indices: 15296508--15296538 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15296498 TTATTGATAC
15296508 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15296539 ATCATACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15297386 original size:25 final size:25
Alignment explanation
Indices: 15297357--15297406 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
15297347 GAAGAAATGG
15297357 TTAAAAACTCAAGAAAGCAACACTT
1 TTAAAAACTCAAGAAAGCAACACTT
15297382 TTAAAAACTCAAGAAAGCAACACTT
1 TTAAAAACTCAAGAAAGCAACACTT
15297407 ACACTAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (25 bp):
TTAAAAACTCAAGAAAGCAACACTT
Found at i:15298000 original size:21 final size:21
Alignment explanation
Indices: 15297976--15298022 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
15297966 GCCTAGTAAA
15297976 AAGTCTTGAGAACTTAGGTTC
1 AAGTCTTGAGAACTTAGGTTC
15297997 AAGTCTTGAGAACTTAGGTTC
1 AAGTCTTGAGAACTTAGGTTC
15298018 AAGTC
1 AAGTC
15298023 ACATTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (21 bp):
AAGTCTTGAGAACTTAGGTTC
Found at i:15323848 original size:27 final size:27
Alignment explanation
Indices: 15323818--15323873 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
15323808 GTAACCAATA
* *
15323818 TATTCCACTAGGACAGTAAACACAGGG
1 TATTCCACCAGGACAGTAAACACAAGG
* *
15323845 TATTCCTCCAGGATAGTAAACACAAGG
1 TATTCCACCAGGACAGTAAACACAAGG
15323872 TA
1 TA
15323874 GACCTTTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (27 bp):
TATTCCACCAGGACAGTAAACACAAGG
Found at i:15323913 original size:27 final size:27
Alignment explanation
Indices: 15323855--15323923 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
15323845 TATTCCTCCA
*
15323855 GGATAGTAAACACAAGGTAGACCTTTG
1 GGATAGTAAACACAAGGTAGACCGTTG
* * * **
15323882 AGATAATAAACACAGGGTAGTTCGTTG
1 GGATAGTAAACACAAGGTAGACCGTTG
*
15323909 GGATAGTAAGCACAA
1 GGATAGTAAACACAA
15323924 AGAACTCTGT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (27 bp):
GGATAGTAAACACAAGGTAGACCGTTG
Found at i:15328572 original size:21 final size:22
Alignment explanation
Indices: 15328546--15328601 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
15328536 GAGCACTCAA
*
15328546 ATGCATCCACAACAAG-GCTAG
1 ATGCATCCACAACAAGACCTAG
* *
15328567 ATGCATGCAC-ACCAGACCTAG
1 ATGCATCCACAACAAGACCTAG
*
15328588 ACGCATCCACAACA
1 ATGCATCCACAACA
15328602 TTCTTCAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 4 0.15
21 21 0.78
22 2 0.07
ACGTcount: A:0.38, C:0.34, G:0.16, T:0.12
Consensus pattern (22 bp):
ATGCATCCACAACAAGACCTAG
Found at i:15332910 original size:6 final size:6
Alignment explanation
Indices: 15332899--15332924 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
15332889 GATTGTTTTA
15332899 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
15332925 GCAGAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:15338666 original size:21 final size:21
Alignment explanation
Indices: 15338642--15338683 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
15338632 AAATGTGGGA
* *
15338642 ATGTTCGCCAGAGTTAAACGT
1 ATGTTCACCAGAGCTAAACGT
15338663 ATGTTCACCAGAGCTAAACGT
1 ATGTTCACCAGAGCTAAACGT
15338684 TTATTGAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (21 bp):
ATGTTCACCAGAGCTAAACGT
Found at i:15339867 original size:17 final size:17
Alignment explanation
Indices: 15339845--15339884 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
15339835 ATGGTAAATA
15339845 ATGATACATAATCTAGC
1 ATGATACATAATCTAGC
15339862 ATGATACATAATCTAGC
1 ATGATACATAATCTAGC
15339879 ATGATA
1 ATGATA
15339885 ATTTCTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (17 bp):
ATGATACATAATCTAGC
Found at i:15340328 original size:27 final size:27
Alignment explanation
Indices: 15340298--15340359 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
15340288 CTATCGGGAC
*
15340298 AGTAAACATGGGGCAGTCTACCAAGAT
1 AGTAAACATGGAGCAGTCTACCAAGAT
* * *
15340325 AGTAAACATGGAGTAGTCTACTAGGAT
1 AGTAAACATGGAGCAGTCTACCAAGAT
*
15340352 AATAAACA
1 AGTAAACA
15340360 CGGGATAGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (27 bp):
AGTAAACATGGAGCAGTCTACCAAGAT
Found at i:15340368 original size:27 final size:27
Alignment explanation
Indices: 15340312--15340369 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
15340302 AACATGGGGC
* *
15340312 AGTCTACCAAGATAGTAAACATGGAGT
1 AGTCTACCAAGATAATAAACAGGGAGT
* *
15340339 AGTCTACTAGGATAATAAACACGGGA-T
1 AGTCTACCAAGATAATAAACA-GGGAGT
15340366 AGTC
1 AGTC
15340370 CACCGGGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (27 bp):
AGTCTACCAAGATAATAAACAGGGAGT
Found at i:15340457 original size:27 final size:27
Alignment explanation
Indices: 15340400--15340477 Score: 66
Period size: 27 Copynumber: 2.9 Consensus size: 27
15340390 TGTAGTCCAT
* *
15340400 CGAGACAATAATCACAGGGTAGTCTGC
1 CGAGACAATAAACACAGGGTAGTCTGA
* * * *
15340427 CGAGACAATAAACACTGGTTTGTTTGA
1 CGAGACAATAAACACAGGGTAGTCTGA
** * *
15340454 CGAGGTAGTAAACACAAGGTAGTC
1 CGAGACAATAAACACAGGGTAGTC
15340478 CACTGGGACA
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.22
Consensus pattern (27 bp):
CGAGACAATAAACACAGGGTAGTCTGA
Found at i:15345397 original size:39 final size:40
Alignment explanation
Indices: 15345329--15345429 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 40
15345319 TAGTATAGAA
* *
15345329 GGCATGTTTCAACATGCAATCAGTTTAGTAG-AAATA-GTT-
1 GGCATGTTT-AACATGCAATCAGTATAGTAGCAAA-ACATTG
*
15345368 GGCATGTTTAACATGCAATTAGTAATAGTAGCAAAACATTG
1 GGCATGTTTAACATGCAATCAGT-ATAGTAGCAAAACATTG
* *
15345409 GGCATGCTTAACATGCGATCA
1 GGCATGTTTAACATGCAATCA
15345430 ATTTCAATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
38 13 0.25
39 16 0.31
40 5 0.10
41 18 0.35
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.30
Consensus pattern (40 bp):
GGCATGTTTAACATGCAATCAGTATAGTAGCAAAACATTG
Found at i:15348226 original size:14 final size:15
Alignment explanation
Indices: 15348207--15348235 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
15348197 AAAAATATTT
15348207 TAACATTT-AAAACC
1 TAACATTTGAAAACC
15348221 TAACATTTGAAAACC
1 TAACATTTGAAAACC
15348236 CTTTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (15 bp):
TAACATTTGAAAACC
Found at i:15349284 original size:19 final size:19
Alignment explanation
Indices: 15349254--15349309 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
15349244 TTTTTTAAAA
15349254 TATAAA-ATTTAGAATTTT
1 TATAAATATTTAGAATTTT
15349272 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
15349291 T-TAAATTATTTTGAATTTT
1 TATAAA-TATTTAGAATTTT
15349310 CTTTTTGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
18 10 0.29
19 25 0.71
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:15358709 original size:21 final size:23
Alignment explanation
Indices: 15358677--15358723 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 23
15358667 TTAATTATTG
*
15358677 ATTTAATGCACATCTT-TAT-CA
1 ATTTAATGCACAACTTGTATACA
15358698 ATTTACAT-CACAACTTGTATACA
1 ATTTA-ATGCACAACTTGTATACA
15358721 ATT
1 ATT
15358724 CATGCTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 12 0.55
22 5 0.23
23 5 0.23
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (23 bp):
ATTTAATGCACAACTTGTATACA
Found at i:15360638 original size:14 final size:14
Alignment explanation
Indices: 15360619--15360649 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
15360609 AAGGTATAAG
*
15360619 TGATTAATTTTCAC
1 TGATTAATTCTCAC
15360633 TGATTAATTCTCAC
1 TGATTAATTCTCAC
15360647 TGA
1 TGA
15360650 GTTTTTTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (14 bp):
TGATTAATTCTCAC
Found at i:15361762 original size:18 final size:18
Alignment explanation
Indices: 15361739--15361816 Score: 93
Period size: 18 Copynumber: 4.3 Consensus size: 18
15361729 AGCTGTACCA
15361739 TAAAATGGCGAACTATAT
1 TAAAATGGCGAACTATAT
* *
15361757 TAAAATGGCGGACTGTAT
1 TAAAATGGCGAACTATAT
* *
15361775 TAAAATGGCAAACAATAT
1 TAAAATGGCGAACTATAT
* * *
15361793 AAAAATGGTGGACTATAT
1 TAAAATGGCGAACTATAT
15361811 TAAAAT
1 TAAAAT
15361817 TGTGAATTGT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (18 bp):
TAAAATGGCGAACTATAT
Found at i:15361780 original size:36 final size:36
Alignment explanation
Indices: 15361739--15361816 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
15361729 AGCTGTACCA
* * * *
15361739 TAAAATGGCGAACTATATTAAAATGGCGGACTGTAT
1 TAAAATGGCAAACAATATAAAAATGGCGGACTATAT
*
15361775 TAAAATGGCAAACAATATAAAAATGGTGGACTATAT
1 TAAAATGGCAAACAATATAAAAATGGCGGACTATAT
15361811 TAAAAT
1 TAAAAT
15361817 TGTGAATTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (36 bp):
TAAAATGGCAAACAATATAAAAATGGCGGACTATAT
Found at i:15361849 original size:18 final size:18
Alignment explanation
Indices: 15361828--15361866 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
15361818 GTGAATTGTA
*
15361828 TTAATTTGGAAAACTTTG
1 TTAATTTGGAAAACTATG
*
15361846 TTAATTTGGCAAACTATG
1 TTAATTTGGAAAACTATG
15361864 TTA
1 TTA
15361867 TTTATGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (18 bp):
TTAATTTGGAAAACTATG
Found at i:15368220 original size:21 final size:19
Alignment explanation
Indices: 15368188--15368231 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
15368178 GATGTAGTTC
15368188 AAAAAATTTTAAAAATTATT
1 AAAAAATTTTAAAAATTA-T
* *
15368208 AAAAAGTTGTTAAATATTAT
1 AAAAAATT-TTAAAAATTAT
15368228 AAAA
1 AAAA
15368232 TAACTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
AAAAAATTTTAAAAATTAT
Found at i:15368337 original size:19 final size:19
Alignment explanation
Indices: 15368314--15368363 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
15368304 TAAAAATGCT
15368314 ATAAAATGTTA-AAATATA
1 ATAAAATGTTATAAATATA
* *
15368332 AGTAAATTATTATAAATATA
1 A-TAAAATGTTATAAATATA
*
15368352 ATAAAAAGTTAT
1 ATAAAATGTTAT
15368364 TCAAATTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 1 0.04
19 16 0.64
20 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (19 bp):
ATAAAATGTTATAAATATA
Found at i:15368659 original size:21 final size:22
Alignment explanation
Indices: 15368635--15368701 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 22
15368625 CTTTAAGTTT
* *
15368635 AATTTAAT-TTTCATATCATTA
1 AATTTAATATATCACATCATTA
15368656 AA-TTAATATATCACATCATTA
1 AATTTAATATATCACATCATTA
*
15368677 TATTT--TATAT-A-ATCATTA
1 AATTTAATATATCACATCATTA
*
15368695 ATTTTAA
1 AATTTAA
15368702 ATGTTATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
18 10 0.27
19 1 0.03
20 10 0.27
21 14 0.38
22 2 0.05
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTAATATATCACATCATTA
Found at i:15373145 original size:13 final size:12
Alignment explanation
Indices: 15373115--15373142 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
15373105 AACTTAAATA
15373115 TTTTAATTTAGT
1 TTTTAATTTAGT
15373127 TTTTAATTTAGT
1 TTTTAATTTAGT
15373139 TTTT
1 TTTT
15373143 TAACATAGCT
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:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (12 bp):
TTTTAATTTAGT
Found at i:15375686 original size:13 final size:15
Alignment explanation
Indices: 15375665--15375696 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
15375655 TGACAAAATC
*
15375665 AAAATATATTTTAAA
1 AAAATATATGTTAAA
15375680 AAAATATATGTTAAA
1 AAAATATATGTTAAA
15375695 AA
1 AA
15375697 TGTTAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAATATATGTTAAA
Found at i:15376039 original size:22 final size:21
Alignment explanation
Indices: 15376004--15376057 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
15375994 TTGGGAAAAC
*
15376004 ATATAATAATACAGTAATAATA
1 ATATAATAA-ACAGTAATAACA
*
15376026 ATATAAATAAACAGTATTAACA
1 ATAT-AATAAACAGTAATAACA
15376048 ATATAATAAA
1 ATATAATAAA
15376058 AAACTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 18 0.62
23 5 0.17
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.30
Consensus pattern (21 bp):
ATATAATAAACAGTAATAACA
Found at i:15377519 original size:127 final size:126
Alignment explanation
Indices: 15377293--15377521 Score: 298
Period size: 127 Copynumber: 1.8 Consensus size: 126
15377283 AGTCTAATGT
* * * * * * *
15377293 GATCTGTTCTCTGCAATCTCAAAGAGATGAGATCTGATTTTAATCCGCTCCACTGCAACTTCAGG
1 GATCTGCTCTCTGCAACCTCAAAGAGATAAGATCTAATGTTAATCCGCTCCACTACAACTTCAGA
* * *
15377358 GAGATAGGATTATTGGCTTCAGTCTGCTCCACTGCAACTTCAGGGAGTTAAGACTTGATGC
66 GAGATAGGATTATTGACTTCAATCTGCTCAACTGCAACTTCAGGGAGTTAAGACTTGATGC
*
15377419 GATCTGCTCTCTGCAACCTCAGAA-AGATAAGATCTTAATGTTAATCCGCTTCACTACAACTTCA
1 GATCTGCTCTCTGCAACCTCA-AAGAGATAAGATC-TAATGTTAATCCGCTCCACTACAACTTCA
* * * *
15377483 GAGAGATAGGATTATTTACTTCAATTTGTTTAACTGCAA
64 GAGAGATAGGATTATTGACTTCAATCTGCTCAACTGCAA
15377522 TGTCGGGGAA
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
126 28 0.33
127 58 0.67
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (126 bp):
GATCTGCTCTCTGCAACCTCAAAGAGATAAGATCTAATGTTAATCCGCTCCACTACAACTTCAGA
GAGATAGGATTATTGACTTCAATCTGCTCAACTGCAACTTCAGGGAGTTAAGACTTGATGC
Found at i:15377595 original size:50 final size:50
Alignment explanation
Indices: 15377527--15377709 Score: 152
Period size: 50 Copynumber: 3.7 Consensus size: 50
15377517 TGCAATGTCG
** * * *
15377527 GGGAAACAAGATTTGCCGTCGCAACTTCAATCTATTCCACTACACCGCCA
1 GGGAAACAAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCA
* * * ** * ** * *
15377577 GGGAAATAAGATCCGCCGTTGTGGCTTCAATCCT-TTTAATTGCAATGTCG
1 GGGAAACAAGATCCGCCGTCGTAGCTTCAAT-CTATTCCACTGCACCGCCA
* * *
15377627 GGGAAACCAGATTCGCCGTCGTAGCTTTAATCTATTCCACTGCACCGCCA
1 GGGAAACAAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCA
* * * *
15377677 GGGAAATAAGATCCGCCATTGTGGCTTCAATCT
1 GGGAAACAAGATCCGCCGTCGTAGCTTCAATCT
15377710 TTTTAATTGC
Statistics
Matches: 96, Mismatches: 35, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
49 2 0.02
50 92 0.96
51 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (50 bp):
GGGAAACAAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCA
Found at i:15377674 original size:100 final size:100
Alignment explanation
Indices: 15377511--15377722 Score: 343
Period size: 100 Copynumber: 2.1 Consensus size: 100
15377501 CTTCAATTTG
* *
15377511 TTTAACTGCAATGTCGGGGAAACAAGATTTGCCGTCGCAACTTCAATCTATTCCACTACACCGCC
1 TTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGCAACTTCAATCTATTCCACTACACCGCC
*
15377576 AGGGAAATAAGATCCGCCGTTGTGGCTTCAATCCT
66 AGGGAAATAAGATCCGCCATTGTGGCTTCAATCCT
* * * * *
15377611 TTTAATTGCAATGTCGGGGAAACCAGATTCGCCGTCGTAGCTTTAATCTATTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGCAACTTCAATCTATTCCACTACACCGCC
*
15377676 AGGGAAATAAGATCCGCCATTGTGGCTTCAATCTT
66 AGGGAAATAAGATCCGCCATTGTGGCTTCAATCCT
15377711 TTTAATTGCAAT
1 TTTAATTGCAAT
15377723 TCCAAATAAA
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 103 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (100 bp):
TTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGCAACTTCAATCTATTCCACTACACCGCC
AGGGAAATAAGATCCGCCATTGTGGCTTCAATCCT
Found at i:15381841 original size:17 final size:17
Alignment explanation
Indices: 15381819--15381853 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
15381809 TAGTCCAAAG
15381819 GGCATCACTTTATAACA
1 GGCATCACTTTATAACA
15381836 GGCATCACTTTATAACA
1 GGCATCACTTTATAACA
15381853 G
1 G
15381854 AACATTCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (17 bp):
GGCATCACTTTATAACA
Found at i:15382057 original size:8 final size:8
Alignment explanation
Indices: 15382044--15382068 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
15382034 CTGTAATCCA
15382044 CACACATT
1 CACACATT
15382052 CACACATT
1 CACACATT
15382060 CACACATT
1 CACACATT
15382068 C
1 C
15382069 CCATCTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (8 bp):
CACACATT
Found at i:15382669 original size:23 final size:24
Alignment explanation
Indices: 15382635--15382688 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
15382625 TGAACAAAAT
*
15382635 ATGATTATG-AAATCAATAAAAGA
1 ATGATTATGAAAAACAATAAAAGA
*
15382658 ATGATGTA-GAAAAAGAATAAAAGA
1 ATGAT-TATGAAAAACAATAAAAGA
*
15382682 ATAATTA
1 ATGATTA
15382689 CTCAAAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (24 bp):
ATGATTATGAAAAACAATAAAAGA
Found at i:15382718 original size:26 final size:25
Alignment explanation
Indices: 15382667--15382722 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
15382657 AATGATGTAG
*
15382667 AAAAAGAATAAAAGAATAATTACTC
1 AAAAAGAATAAAAGAATAATGACTC
* * *
15382692 AAAAGAGAATGAAAGAATACTGGCTC
1 AAAA-AGAATAAAAGAATAATGACTC
15382718 AAAAA
1 AAAAA
15382723 TGCATACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.61, C:0.09, G:0.14, T:0.16
Consensus pattern (25 bp):
AAAAAGAATAAAAGAATAATGACTC
Found at i:15390214 original size:14 final size:14
Alignment explanation
Indices: 15390175--15390282 Score: 65
Period size: 13 Copynumber: 8.2 Consensus size: 14
15390165 GCATATACGC
15390175 ATATATAA-ATA-A
1 ATATATAATATATA
*
15390187 GTATAATAAT-TATA
1 ATAT-ATAATATATA
15390201 ATATATAATATATA
1 ATATATAATATATA
15390215 ATATAATAATA-ATA
1 ATAT-ATAATATATA
*
15390229 A-A-CTAATA-ATA
1 ATATATAATATATA
*
15390240 ATACAATAATA-ATA
1 ATA-TATAATATATA
*
15390254 ATATA-AATAAATA
1 ATATATAATATATA
* *
15390267 GTAT-TAAAATATA
1 ATATATAATATATA
15390280 ATA
1 ATA
15390283 AAAAACTAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
11 9 0.12
12 8 0.10
13 27 0.35
14 27 0.35
15 6 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (14 bp):
ATATATAATATATA
Found at i:15390225 original size:3 final size:3
Alignment explanation
Indices: 15390189--15390256 Score: 70
Period size: 3 Copynumber: 23.0 Consensus size: 3
15390179 ATAAATAAGT
* *
15390189 ATA ATA ATT ATA ATA TATA ATA TATA AT- ATA ATA ATA ATA A-A CTA
1 ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
*
15390234 ATA ATA AT- ACA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
15390257 TAAATAAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
2 4 0.07
3 44 0.81
4 6 0.11
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:15390228 original size:11 final size:11
Alignment explanation
Indices: 15390189--15390283 Score: 65
Period size: 11 Copynumber: 8.4 Consensus size: 11
15390179 ATAAATAAGT
15390189 ATAATAAT-T-
1 ATAATAATATA
15390198 ATAAT-ATATA
1 ATAATAATATA
15390208 ATATATAATATA
1 ATA-ATAATATA
15390220 ATAATAATAAACTA
1 ATAATAAT--A-TA
*
15390234 ATAATAATACA
1 ATAATAATATA
15390245 ATAATAATA-A
1 ATAATAATATA
15390255 TATAAATAAATAGTA
1 -AT-AAT-AATA-TA
*
15390270 TTAA-AATATA
1 ATAATAATATA
15390280 ATAA
1 ATAA
15390284 AAAACTAAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 23
0.73 0.03 0.24
Matches are distributed among these distances:
8 2 0.03
9 6 0.08
10 9 0.13
11 23 0.32
12 12 0.17
13 7 0.10
14 11 0.15
15 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (11 bp):
ATAATAATATA
Found at i:15398032 original size:26 final size:26
Alignment explanation
Indices: 15398003--15398108 Score: 88
Period size: 26 Copynumber: 4.1 Consensus size: 26
15397993 ATCCACTCAT
* *
15398003 GGTCCTCCAACTAACTCAAACTCCAG
1 GGTCCTCCAACCAACTCAAACTCAAG
*** * *
15398029 GGTCCTTGGACCCATTCAAACTCAAG
1 GGTCCTCCAACCAACTCAAACTCAAG
* * *
15398055 GGACCTCCAACCAACCCAAACTCAAA
1 GGTCCTCCAACCAACTCAAACTCAAG
* *
15398081 GGTCCT-CAGACTAACTCAAACTTAAG
1 GGTCCTCCA-ACCAACTCAAACTCAAG
15398107 GG
1 GG
15398109 ATCATCTTGA
Statistics
Matches: 59, Mismatches: 20, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
25 2 0.03
26 57 0.97
ACGTcount: A:0.33, C:0.34, G:0.15, T:0.18
Consensus pattern (26 bp):
GGTCCTCCAACCAACTCAAACTCAAG
Found at i:15401084 original size:29 final size:29
Alignment explanation
Indices: 15401052--15401111 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
15401042 TTATTTATAT
15401052 TTTCAATTGTAACT-ATTTAATTTTTAAAG
1 TTTCAATTGTAA-TGATTTAATTTTTAAAG
15401081 TTTCAATTGTAATGATTTAATTTTTAAAG
1 TTTCAATTGTAATGATTTAATTTTTAAAG
15401110 TT
1 TT
15401112 AAATTTATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.53
Consensus pattern (29 bp):
TTTCAATTGTAATGATTTAATTTTTAAAG
Found at i:15405217 original size:25 final size:25
Alignment explanation
Indices: 15405189--15405257 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
15405179 AAGAGAATGG
* *
15405189 AAAATAAAGAAAA-AAAAGAAAGTT
1 AAAAAAAAGAAAAGAAAAAAAAGTT
* *
15405213 AAAAAACATAAAAGAAAAAAAAGTT
1 AAAAAAAAGAAAAGAAAAAAAAGTT
* *
15405238 AAAAAACATAAAAGAAAAAA
1 AAAAAAAAGAAAAGAAAAAA
15405258 TTAAATTGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 10 0.25
25 30 0.75
ACGTcount: A:0.78, C:0.03, G:0.09, T:0.10
Consensus pattern (25 bp):
AAAAAAAAGAAAAGAAAAAAAAGTT
Found at i:15407955 original size:24 final size:24
Alignment explanation
Indices: 15407928--15407986 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
15407918 TTATATGATA
15407928 TGAATATAATATGACAAAATTTAT
1 TGAATATAATATGACAAAATTTAT
** *
15407952 TGAA-ATATATATGTTAAATTTTAT
1 TGAATATA-ATATGACAAAATTTAT
*
15407976 T-TATATAATAT
1 TGAATATAATAT
15407987 ATAATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 8 0.28
24 21 0.72
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (24 bp):
TGAATATAATATGACAAAATTTAT
Found at i:15408617 original size:122 final size:123
Alignment explanation
Indices: 15408389--15408633 Score: 474
Period size: 122 Copynumber: 2.0 Consensus size: 123
15408379 TTGCACAATT
15408389 ATAATTGTAATACCCAATTTTTGACCCGGGCCCAACTAAGCCTAAAGCCCAAACCCATTACAAGC
1 ATAATTGTAATACCCAATTTTTGACCCGGGCCCAACTAAGCCTAAAGCCCAAACCCATTACAAGC
*
15408454 ACAAGTCGTTAACCCGAATACCTGACCCACTAGCCTAAAATAAAAAAAATGAACAGCA
66 ACAAGTCGTTAACCCGAATACCTGACCCAATAGCCTAAAATAAAAAAAATGAACAGCA
15408512 ATAATTGTAA-ACCCAATTTTTGACCCGGGCCCAACTAAGCCTAAAGCCCAAACCCATTACAAGC
1 ATAATTGTAATACCCAATTTTTGACCCGGGCCCAACTAAGCCTAAAGCCCAAACCCATTACAAGC
15408576 ACAAGTCGTTAACCCGAATACCTGACCCAATAGCCTAAAATAAAAAAAATGAACAGCA
66 ACAAGTCGTTAACCCGAATACCTGACCCAATAGCCTAAAATAAAAAAAATGAACAGCA
15408634 GAAACATTTG
Statistics
Matches: 121, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
122 111 0.92
123 10 0.08
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.18
Consensus pattern (123 bp):
ATAATTGTAATACCCAATTTTTGACCCGGGCCCAACTAAGCCTAAAGCCCAAACCCATTACAAGC
ACAAGTCGTTAACCCGAATACCTGACCCAATAGCCTAAAATAAAAAAAATGAACAGCA
Found at i:15413624 original size:2 final size:2
Alignment explanation
Indices: 15413607--15413661 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
15413597 TTCTGAGATG
* *
15413607 AC AC AC AA AC AG 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
15413649 AC AC AC AC AC AC A
1 AC AC AC AC AC AC A
15413662 TATGGATGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.53, C:0.45, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:15416099 original size:18 final size:18
Alignment explanation
Indices: 15416062--15416099 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
15416052 AAAAAATGAC
*
15416062 ATTTTTTACATTTAATAT
1 ATTTTTTACATTTAAAAT
15416080 ATTTTTTA-ATTTCAAAAT
1 ATTTTTTACATTT-AAAAT
15416098 AT
1 AT
15416100 ATAGTGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTTACATTTAAAAT
Found at i:15416232 original size:19 final size:19
Alignment explanation
Indices: 15416208--15416256 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
15416198 AGTTAATAAT
15416208 AAATTTGATTATGGTGGGC
1 AAATTTGATTATGGTGGGC
15416227 AAATTTGATTATGGTGGGC
1 AAATTTGATTATGGTGGGC
15416246 AAATTTGATTA
1 AAATTTGATTA
15416257 CAATGACTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.39
Consensus pattern (19 bp):
AAATTTGATTATGGTGGGC
Found at i:15416940 original size:15 final size:15
Alignment explanation
Indices: 15416920--15416949 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15416910 ACTTAGCCTT
15416920 AATTACATGTAACAA
1 AATTACATGTAACAA
*
15416935 AATTACATGTGACAA
1 AATTACATGTAACAA
15416950 TTATTCGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (15 bp):
AATTACATGTAACAA
Found at i:15421848 original size:23 final size:23
Alignment explanation
Indices: 15421821--15421865 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
15421811 TTCAATATCA
*
15421821 TTCATAT-AATTTAATCATCATAT
1 TTCATATGAATGTAATC-TCATAT
*
15421844 TTCATTTGAATGTAATCTCATA
1 TTCATATGAATGTAATCTCATA
15421866 ACAATTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (23 bp):
TTCATATGAATGTAATCTCATAT
Found at i:15422007 original size:20 final size:20
Alignment explanation
Indices: 15421977--15422402 Score: 415
Period size: 20 Copynumber: 21.3 Consensus size: 20
15421967 CATAGTGCTG
* *
15421977 AACAAAGGCACCAAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* * *
15421997 TATAGAGGCACTGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* ** * *
15422017 AATAGAGGTGCTGGAGTGCA
1 AACAGAGGCACCGAAGTGCA
* * *
15422037 AACAGAGACATCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
*
15422057 AATAGAGGCACC-AGAGTGCA
1 AACAGAGGCACCGA-AGTGCA
*
15422077 AACAAAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
15422097 AACAAAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
* *
15422117 TACAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
*
15422137 AACAGAGGCACTGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* **
15422157 TACAGAGGCATTGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
*
15422177 AACAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
15422197 AACAGAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
15422217 TACAGAGGCATCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* ** * *
15422237 TACAGAGATATCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
* *
15422257 AATAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
*
15422277 AACAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
15422297 AACAGAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
15422317 TACAGAGGCATCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
15422337 TACAGAGGCACCGAACTGCA
1 AACAGAGGCACCGAAGTGCA
* * * ** *
15422357 AATAAAGGCATCGTGGTACA
1 AACAGAGGCACCGAAGTGCA
*
15422377 AATAGAGGCACCGAAGTAG-A
1 AACAGAGGCACCGAAGT-GCA
15422397 AACAGA
1 AACAGA
15422403 TACATTTCAA
Statistics
Matches: 337, Mismatches: 66, Indels: 6
0.82 0.16 0.01
Matches are distributed among these distances:
19 1 0.00
20 335 0.99
21 1 0.00
ACGTcount: A:0.42, C:0.21, G:0.27, T:0.11
Consensus pattern (20 bp):
AACAGAGGCACCGAAGTGCA
Found at i:15422402 original size:80 final size:80
Alignment explanation
Indices: 15421977--15422393 Score: 487
Period size: 80 Copynumber: 5.2 Consensus size: 80
15421967 CATAGTGCTG
* * * * ** * * *
15421977 AACAAAGGCACCAAAGTGCATATAGAGGCA-CTGAAGTGCAAATAGAGGTGCTGGAGTGCAAACA
1 AACAGAGGCACCGAAGTGCATACAGAGGCATC-GAAGTGCAAACAGAGGCACCGAAGTACAAACA
* *
15422041 GAGACATCGAAGTACA
65 GAGGCACCGAAGTACA
* * * * * *
15422057 AATAGAGGCACC-AGAGTGCAAACAAAGGCACCGAAGTGCAAACAAAGGCACCGAAGTACATACA
1 AACAGAGGCACCGA-AGTGCATACAGAGGCATCGAAGTGCAAACAGAGGCACCGAAGTACAAACA
15422121 GAGGCACCGAAGTACA
65 GAGGCACCGAAGTACA
* *
15422137 AACAGAGGCACTGAAGTGCATACAGAGGCATTGAAGTGCAAACAGAGGCACCGAAGTACAAACAG
1 AACAGAGGCACCGAAGTGCATACAGAGGCATCGAAGTGCAAACAGAGGCACCGAAGTACAAACAG
*
15422202 AGGCACCGAAGTGCA
66 AGGCACCGAAGTACA
* * ** * *
15422217 TACAGAGGCATCGAAGTGCATACAGAGATATCGAAGTACAAATAGAGGCACCGAAGTACAAACAG
1 AACAGAGGCACCGAAGTGCATACAGAGGCATCGAAGTGCAAACAGAGGCACCGAAGTACAAACAG
15422282 AGGCACCGAAGTACA
66 AGGCACCGAAGTACA
* * * * *
15422297 AACAGAGGCACCGAAGTGCATACAGAGGCATCGAAGTGCATACAGAGGCACCGAACTGCAAATAA
1 AACAGAGGCACCGAAGTGCATACAGAGGCATCGAAGTGCAAACAGAGGCACCGAAGTACAAACAG
* **
15422362 AGGCATCGTGGTACA
66 AGGCACCGAAGTACA
*
15422377 AATAGAGGCACCGAAGT
1 AACAGAGGCACCGAAGT
15422394 AGAAACAGAT
Statistics
Matches: 286, Mismatches: 48, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
79 1 0.00
80 283 0.99
81 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.27, T:0.11
Consensus pattern (80 bp):
AACAGAGGCACCGAAGTGCATACAGAGGCATCGAAGTGCAAACAGAGGCACCGAAGTACAAACAG
AGGCACCGAAGTACA
Found at i:15424948 original size:12 final size:12
Alignment explanation
Indices: 15424910--15424948 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
15424900 ACTAAAATGG
15424910 TTTAATAAAATT
1 TTTAATAAAATT
*
15424922 CTTAATAACATATT
1 TTTAATAA-A-ATT
15424936 TTTAATAAAATT
1 TTTAATAAAATT
15424948 T
1 T
15424949 CTAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.48
13 2 0.09
14 10 0.43
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (12 bp):
TTTAATAAAATT
Found at i:15425194 original size:16 final size:17
Alignment explanation
Indices: 15425175--15425212 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
15425165 TGAAGTTTTT
15425175 TTTTAAATTT-TGAAAA
1 TTTTAAATTTCTGAAAA
* *
15425191 TTTTAATTTTCTGAAAT
1 TTTTAAATTTCTGAAAA
15425208 TTTTA
1 TTTTA
15425213 TTAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTTAAATTTCTGAAAA
Found at i:15425194 original size:20 final size:19
Alignment explanation
Indices: 15425155--15425194 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
15425145 AAGTTGATAG
**
15425155 TTTTTAATTTTGAAGTTTT
1 TTTTTAATTTTGAAAATTT
15425174 TTTTTAAATTTTGAAAATTT
1 TTTTT-AATTTTGAAAATTT
15425194 T
1 T
15425195 AATTTTCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (19 bp):
TTTTTAATTTTGAAAATTT
Found at i:15425220 original size:37 final size:35
Alignment explanation
Indices: 15425156--15425227 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 35
15425146 AGTTGATAGT
* * *
15425156 TTTTAATTTTGAAGTTTTTTTTTAAATTTTGAAAA
1 TTTTAATTTTGAAATTTTTATTAAAATTTTGAAAA
15425191 TTTTAATTTTCTGAAATTTTTATTAAAATTTTGAAAA
1 TTTTAA-TTT-TGAAATTTTTATTAAAATTTTGAAAA
15425228 AGTTTAGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 6 0.19
36 3 0.09
37 23 0.72
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.57
Consensus pattern (35 bp):
TTTTAATTTTGAAATTTTTATTAAAATTTTGAAAA
Found at i:15425225 original size:20 final size:19
Alignment explanation
Indices: 15425160--15425226 Score: 50
Period size: 20 Copynumber: 3.5 Consensus size: 19
15425150 GATAGTTTTT
* *
15425160 AATTTTGAAGTTTTTTTTTA
1 AATTTTGAA-ATTTTTATTA
*
15425180 AATTTTGAAAATTTTAATT-
1 AATTTTG-AAATTTTTATTA
*
15425199 --TTCTGAAATTTTTATTAA
1 AATTTTGAAATTTTTATT-A
15425217 AATTTTGAAA
1 AATTTTGAAA
15425227 AAGTTTAGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
16 10 0.28
17 4 0.11
20 20 0.56
21 2 0.06
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (19 bp):
AATTTTGAAATTTTTATTA
Found at i:15431394 original size:126 final size:126
Alignment explanation
Indices: 15431167--15431633 Score: 645
Period size: 126 Copynumber: 3.6 Consensus size: 126
15431157 TAATTTCGAG
**
15431167 TTGACGTTTCTGATAAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* *
15431232 AAATCGCGCCCTCG-TGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCGCGCCCTCGTTAG-CGCACTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
* *
15431293 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGCAGGATGCTATTTGTGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * *
15431358 AAATCGCGGCCTCGTTAGCGCACTTTTGCTATAGTAGGTCATGTAAGAAAT-A--ATTTTT
66 AAATCGCGCCCTCGTTAGCGCACTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
*
15431416 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* **
15431481 AAATCGCGCCCTCATGGACGCGCTTTTGCGCGCAAGTTTGCTACAGTAGGTCACGGAAGAAATAA
66 AAATCGCG-CC-C-T-----CG---TT-AGCGCACTTTTGCTACAGTAGGTCACGGAAGAAATAA
15431546 TTATTTTT
119 TTATTTTT
* *
15431554 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
15431619 AAATCGCGCCCTCGT
66 AAATCGCGCCCTCGT
15431634 GGACGCGATN
Statistics
Matches: 302, Mismatches: 23, Indels: 31
0.85 0.06 0.09
Matches are distributed among these distances:
123 76 0.25
124 1 0.00
125 2 0.01
126 104 0.34
127 3 0.01
130 2 0.01
131 2 0.01
134 2 0.01
135 30 0.10
136 2 0.01
137 2 0.01
138 76 0.25
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (126 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTTAGCGCACTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
Found at i:15431620 original size:138 final size:135
Alignment explanation
Indices: 15431382--15431640 Score: 428
Period size: 138 Copynumber: 1.9 Consensus size: 135
15431372 TTAGCGCACT
* * *
15431382 TTTGCTATAGTAGGTCATGTAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAATATAAAATCG
1 TTTGCTACAGTAGGTCACGGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAATATAAAATCG
* *
15431447 CTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCATGGACGCGCTTTTGCGC
66 CTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCATGGACGCGCTTTTGCGC
15431512 GCAAG
131 GCAAG
*
15431517 TTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAGTATAAAA
1 TTTGCTACAGTAGGTCACGGAAGAAAT-A--ATTTTTTTGACGTTTCTGAGCAAATAATATAAAA
*
15431582 TCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCG
63 TCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCATGGACGCG
15431641 ATNNNNNNNN
Statistics
Matches: 114, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
135 24 0.21
136 1 0.01
138 89 0.78
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (135 bp):
TTTGCTACAGTAGGTCACGGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAATATAAAATCG
CTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCATGGACGCGCTTTTGCGC
GCAAG
Found at i:15434502 original size:29 final size:29
Alignment explanation
Indices: 15434460--15434519 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
15434450 NNNNNNNNNN
*
15434460 TTAGGGTTTTTAATTAAATTAGGTTAAGG
1 TTAGAGTTTTTAATTAAATTAGGTTAAGG
* *
15434489 TTAGAGTTTTTAATTAATTTAGGTTAGGG
1 TTAGAGTTTTTAATTAAATTAGGTTAAGG
15434518 TT
1 TT
15434520 TAGGGTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.48
Consensus pattern (29 bp):
TTAGAGTTTTTAATTAAATTAGGTTAAGG
Found at i:15434570 original size:25 final size:25
Alignment explanation
Indices: 15434542--15434654 Score: 94
Period size: 25 Copynumber: 4.7 Consensus size: 25
15434532 AGGTGAGGGT
15434542 TTTTATTACATCAAATAAATTTCTA
1 TTTTATTACATCAAATAAATTTCTA
*
15434567 TTTTATTACATCAAAT-AATATC-A
1 TTTTATTACATCAAATAAATTTCTA
** * * ** *
15434590 --AAATAAC-TCGAAT-TTTTTATTA
1 TTTTATTACATCAAATAAATTT-CTA
*
15434612 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAATTTCTA
15434637 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
15434655 TATCAAAATA
Statistics
Matches: 65, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
20 7 0.11
21 4 0.06
22 1 0.02
23 1 0.02
24 9 0.14
25 41 0.63
26 2 0.03
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.45
Consensus pattern (25 bp):
TTTTATTACATCAAATAAATTTCTA
Found at i:15434668 original size:35 final size:35
Alignment explanation
Indices: 15434562--15434668 Score: 103
Period size: 35 Copynumber: 3.1 Consensus size: 35
15434552 TCAAATAAAT
15434562 TTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TTCTATTTTATTACATCAAATAATATCAAAATAAC
* * *** * *
15434597 -TCGAATTTT-TTATTATTTTATTACATC-AAATAAAC
1 TTC-TATTTTATTA-CATCAAATAATATCAAAAT-AAC
15434632 TTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TTCTATTTTATTACATCAAATAATATCAAAATAAC
15434667 TT
1 TT
15434669 AAAAAATTTC
Statistics
Matches: 52, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
34 9 0.17
35 34 0.65
36 9 0.17
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.44
Consensus pattern (35 bp):
TTCTATTTTATTACATCAAATAATATCAAAATAAC
Found at i:15435811 original size:7 final size:7
Alignment explanation
Indices: 15435801--15435825 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
15435791 TTATATACAT
15435801 AATACTA
1 AATACTA
15435808 AATACTA
1 AATACTA
15435815 AATACTA
1 AATACTA
15435822 AATA
1 AATA
15435826 TCAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:15436751 original size:22 final size:22
Alignment explanation
Indices: 15436726--15436781 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
15436716 AAATATGGAT
15436726 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
15436748 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
15436770 TTGAGAGGAATT
1 TTGAGA-GAATT
15436782 GAGAGGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:15436798 original size:12 final size:11
Alignment explanation
Indices: 15436742--15436798 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
15436732 GAATTTTGGA
15436742 AGGAAATTGAG
1 AGGAAATTGAG
*
15436753 A-GAATTTTG-G
1 AGGAA-ATTGAG
15436763 AAGGAAATTGAG
1 -AGGAAATTGAG
15436775 AGG-AATTGAG
1 AGGAAATTGAG
15436785 AGGAAATATGAG
1 AGGAAAT-TGAG
15436797 AG
1 AG
15436799 AGGATTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 14 0.37
11 14 0.37
12 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:15444084 original size:19 final size:19
Alignment explanation
Indices: 15444060--15444132 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
15444050 AATCTTCAAG
15444060 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
15444079 GATATGTAATCTTAGACAT
1 GATATGCAATCTTAGATAT
*
15444098 GATATGCAATCTTAAATAT
1 GATATGCAATCTTAGATAT
15444117 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
15444133 AGATATGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:15444384 original size:23 final size:23
Alignment explanation
Indices: 15444340--15444384 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
15444330 TTTTATTTTG
* *
15444340 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
15444363 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
15444385 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:15446052 original size:23 final size:23
Alignment explanation
Indices: 15446017--15446060 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
15446007 AAGTATGTAT
15446017 ATATATTAATTACAAATGTATAC
1 ATATATTAATTACAAATGTATAC
** *
15446040 ATATATTTGTTACACATGTAT
1 ATATATTAATTACAAATGTAT
15446061 TTATAATTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (23 bp):
ATATATTAATTACAAATGTATAC
Found at i:15448199 original size:12 final size:12
Alignment explanation
Indices: 15448184--15448210 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15448174 TAATTAATTA
15448184 ATTAATATTATC
1 ATTAATATTATC
15448196 ATTAATATTATC
1 ATTAATATTATC
15448208 ATT
1 ATT
15448211 TTTCCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTAATATTATC
Found at i:15448308 original size:28 final size:28
Alignment explanation
Indices: 15448241--15448308 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
15448231 TATTATTGTT
* *
15448241 ATATTATTATATTAATTAGTTTTGTATTA
1 ATATTATTAT-TTAATTAGTTTTCTAATA
* * *
15448270 TTATT-TGTATTTATTTATTTTTCTAATA
1 ATATTAT-TATTTAATTAGTTTTCTAATA
15448298 ATATTATTATT
1 ATATTATTATT
15448309 ATTATTATCA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
28 23 0.74
29 8 0.26
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (28 bp):
ATATTATTATTTAATTAGTTTTCTAATA
Found at i:15451682 original size:19 final size:19
Alignment explanation
Indices: 15451658--15451705 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
15451648 TAATACCTCT
15451658 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTTCAT-CA
15451677 TTTGCATTACATTTCATCA
1 TTTGCATTACATTTCATCA
*
15451696 TATGCATTAC
1 TTTGCATTAC
15451706 GTTTTACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (19 bp):
TTTGCATTACATTTCATCA
Found at i:15459919 original size:45 final size:45
Alignment explanation
Indices: 15459853--15459938 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
15459843 GTCATCATGG
*
15459853 CGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAA
1 CGAATCTTATCTCCCTAAAGTTGCAGTGGAACAGACTGAAGATAA
* * *
15459898 CGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAG
1 CGAATCTTATCTCCCTAAAGTTGCAGTGGAACAGACTGAAG
15459939 CTATAGATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (45 bp):
CGAATCTTATCTCCCTAAAGTTGCAGTGGAACAGACTGAAGATAA
Found at i:15464978 original size:58 final size:58
Alignment explanation
Indices: 15464887--15465000 Score: 201
Period size: 58 Copynumber: 2.0 Consensus size: 58
15464877 ATGGATTAAT
* *
15464887 TTGAAATTCACCGGACAGTTCGAGTATTCCTATCCCTTGTTCACCATTTTTGTGCTAG
1 TTGAAATTCACCGGACAGTTCGAGTATTCCTATCCCCTGTTCACCATTTTCGTGCTAG
*
15464945 TTGAAATTCACCGGACAGTTCGAGTATTGCTATCCCCTGTTCACCATTTTCGTGCT
1 TTGAAATTCACCGGACAGTTCGAGTATTCCTATCCCCTGTTCACCATTTTCGTGCT
15465001 GCTGGCTAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (58 bp):
TTGAAATTCACCGGACAGTTCGAGTATTCCTATCCCCTGTTCACCATTTTCGTGCTAG
Found at i:15466156 original size:58 final size:58
Alignment explanation
Indices: 15466065--15466178 Score: 201
Period size: 58 Copynumber: 2.0 Consensus size: 58
15466055 ATGGATTAAT
* *
15466065 TTGAAATTCACCGGACAGTTCGAGTATTCCTATCCCTTGTTCACCATTTTTGTGCTAG
1 TTGAAATTCACCGGACAGTTCGAGTATTCCTATCCCCTGTTCACCATTTTCGTGCTAG
*
15466123 TTGAAATTCACCGGACAGTTCGAGTATTGCTATCCCCTGTTCACCATTTTCGTGCT
1 TTGAAATTCACCGGACAGTTCGAGTATTCCTATCCCCTGTTCACCATTTTCGTGCT
15466179 GCTGGCTAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (58 bp):
TTGAAATTCACCGGACAGTTCGAGTATTCCTATCCCCTGTTCACCATTTTCGTGCTAG
Found at i:15467000 original size:40 final size:40
Alignment explanation
Indices: 15466945--15467025 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
15466935 ATTCGTATAT
*
15466945 TGATCCAATTATTATTCTTTCTTCTTTTGAAAGGAATTAC
1 TGATCCAATTATTATTCTTTCCTCTTTTGAAAGGAATTAC
15466985 TGATCCAATTATTATTCTTTCCTCTTTTGAAAGGAATTAC
1 TGATCCAATTATTATTCTTTCCTCTTTTGAAAGGAATTAC
15467025 T
1 T
15467026 ATGATTCTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (40 bp):
TGATCCAATTATTATTCTTTCCTCTTTTGAAAGGAATTAC
Found at i:15467879 original size:15 final size:15
Alignment explanation
Indices: 15467859--15467888 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15467849 GTTATGTAAG
15467859 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
15467874 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
15467889 ATGTTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:15472114 original size:15 final size:15
Alignment explanation
Indices: 15472091--15472121 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15472081 GCTATGTAAG
*
15472091 TGAATGGTCAAGAGT
1 TGAAAGGTCAAGAGT
15472106 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
15472121 T
1 T
15472122 ATGTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:15473143 original size:13 final size:13
Alignment explanation
Indices: 15473127--15473153 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15473117 CTTAAAACTC
15473127 ATGCCATATTCAT
1 ATGCCATATTCAT
15473140 ATGCCATATTCAT
1 ATGCCATATTCAT
15473153 A
1 A
15473154 CTTAGTCAAC
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:0.22, G:0.07, T:0.37
Consensus pattern (13 bp):
ATGCCATATTCAT
Found at i:15473418 original size:25 final size:25
Alignment explanation
Indices: 15473389--15473443 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
15473379 TTGTTTGATT
15473389 AATATTAATATTATGATTAATTAAA
1 AATATTAATATTATGATTAATTAAA
* * *
15473414 AATATTGATATTTTGATTAATTAGA
1 AATATTAATATTATGATTAATTAAA
15473439 AATAT
1 AATAT
15473444 ATGAAAACGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (25 bp):
AATATTAATATTATGATTAATTAAA
Found at i:15477045 original size:50 final size:50
Alignment explanation
Indices: 15476920--15477091 Score: 150
Period size: 50 Copynumber: 3.5 Consensus size: 50
15476910 GAATATAACA
* * * * * *
15476920 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTT-TCTTGTA-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATAGG
* * * *
15476969 TACCAATTCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGG
* ** ** * *
15477019 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGG
* *
15477069 TGCCAACGCCATGTCCTAGACAT
1 TGCCAATGCCATGTCCCAGACAT
15477092 TGTTCTCATC
Statistics
Matches: 97, Mismatches: 24, Indels: 3
0.78 0.19 0.02
Matches are distributed among these distances:
48 3 0.03
49 35 0.36
50 59 0.61
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAGG
Found at i:15477112 original size:37 final size:37
Alignment explanation
Indices: 15477058--15477128 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
15477048 ACGGGGGACC
*
15477058 TCTCATCTCGGTGCCAACGCCATGTCCTAGACATTGT
1 TCTCATCTCGGTGCCAACGCCATGTCCCAGACATTGT
* *
15477095 TCTCATCTCGGTTCCAACTCCATGTCCCAGACAT
1 TCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
15477129 GGTCTTACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.20, C:0.35, G:0.15, T:0.30
Consensus pattern (37 bp):
TCTCATCTCGGTGCCAACGCCATGTCCCAGACATTGT
Found at i:15479783 original size:15 final size:16
Alignment explanation
Indices: 15479748--15479790 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
15479738 ATATTGCGAC
*
15479748 AAATCATAAAAAGATT
1 AAATAATAAAAAGATT
*
15479764 TAATAATAAAAA-ATT
1 AAATAATAAAAAGATT
15479779 AAATAACTAAAA
1 AAATAA-TAAAA
15479791 TAAATGAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (16 bp):
AAATAATAAAAAGATT
Found at i:15490232 original size:26 final size:25
Alignment explanation
Indices: 15490194--15490252 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
15490184 ATAGATACTA
*
15490194 TATTTTTAGTTTTTTTATTTAATTTT
1 TATTTTTAGTTTTTTAATTT-ATTTT
* *
15490220 TATTTTTATTTTTTTAATTTCTTTT
1 TATTTTTAGTTTTTTAATTTATTTT
15490245 TAATTTTT
1 T-ATTTTT
15490253 TAGGTTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (25 bp):
TATTTTTAGTTTTTTAATTTATTTT
Found at i:15492327 original size:26 final size:26
Alignment explanation
Indices: 15492291--15492343 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
15492281 TTAGTTGTTC
15492291 TATGCTTTGAGAATTTTTAAAGTAAA
1 TATGCTTTGAGAATTTTTAAAGTAAA
15492317 TATGCTTTGAGAATTTTTAAAGTAAA
1 TATGCTTTGAGAATTTTTAAAGTAAA
15492343 T
1 T
15492344 CAGTATTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (26 bp):
TATGCTTTGAGAATTTTTAAAGTAAA
Found at i:15499110 original size:97 final size:97
Alignment explanation
Indices: 15498944--15499190 Score: 460
Period size: 97 Copynumber: 2.5 Consensus size: 97
15498934 ATTGTAACGG
15498944 TTAATATAAAAATAATATTTTAATATTTTATAATATAGAAAATCTAAAATTGAGCTATTAAATTA
1 TTAATATAAAAATAATATTTTAATATTTTATAATATAGAAAATCTAAAATTGAGCTATTAAATTA
15499009 TGCCAGGCATCAACATGAAAAGTATTTTGGAA
66 TGCCAGGCATCAACATGAAAAGTATTTTGGAA
15499041 TTAATATAAAAATAATATTTTAATATTTTATAATATAGAAAATCTAAAATTGAGCTATTAAATTA
1 TTAATATAAAAATAATATTTTAATATTTTATAATATAGAAAATCTAAAATTGAGCTATTAAATTA
15499106 TGCCAGGCATCAACATGAAAAGTATTTTGGAA
66 TGCCAGGCATCAACATGAAAAGTATTTTGGAA
* *
15499138 TTAATATAAAAATAATATTTAAATATTTTATAATATATG-AAATATAAAATTGA
1 TTAATATAAAAATAATATTTTAATATTTTATAATATA-GAAAATCTAAAATTGA
15499191 CCTAATCTGA
Statistics
Matches: 147, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
97 146 0.99
98 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (97 bp):
TTAATATAAAAATAATATTTTAATATTTTATAATATAGAAAATCTAAAATTGAGCTATTAAATTA
TGCCAGGCATCAACATGAAAAGTATTTTGGAA
Found at i:15499235 original size:21 final size:20
Alignment explanation
Indices: 15499202--15499241 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
15499192 CTAATCTGAT
*
15499202 CAATAGAAAATTTTAATTTA
1 CAATAGAAAATTTGAATTTA
*
15499222 CAATATGATAATTTGAATTT
1 CAATA-GAAAATTTGAATTT
15499242 TGTTATAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (20 bp):
CAATAGAAAATTTGAATTTA
Found at i:15499839 original size:22 final size:21
Alignment explanation
Indices: 15499814--15499854 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15499804 ACTTTTTATA
*
15499814 TATCATAATAATTAAAAATATT
1 TATCA-AATAAATAAAAATATT
*
15499836 TATCAATTAAATAAAAATA
1 TATCAAATAAATAAAAATA
15499855 AATTTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
TATCAAATAAATAAAAATATT
Found at i:15500122 original size:37 final size:37
Alignment explanation
Indices: 15500079--15500164 Score: 138
Period size: 37 Copynumber: 2.3 Consensus size: 37
15500069 TTTGACCCTC
*
15500079 TAAAAATTATAATAAAATAATTTAATTCTCTAAAAAT
1 TAAAAATTATAATAAAATAATTTAATTCTCTAAAAAA
15500116 TAAAAA-TATAAATAAAATAATTTAATTCTCTAAAAAA
1 TAAAAATTAT-AATAAAATAATTTAATTCTCTAAAAAA
15500153 TAAAAATATATA
1 TAAAAAT-TATA
15500165 GGCTATTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
36 3 0.07
37 38 0.84
38 1 0.02
39 3 0.07
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (37 bp):
TAAAAATTATAATAAAATAATTTAATTCTCTAAAAAA
Found at i:15500137 original size:32 final size:30
Alignment explanation
Indices: 15500076--15500137 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
15500066 CACTTTGACC
* **
15500076 CTCTAAAAATTATAATAAAATAATTTAATT
1 CTCTAAAAATTAAAATAAAATAAAATAATT
15500106 CTCTAAAAATTAAAAATATAAATAAAATAATT
1 CTCTAAAAATT-AAAATA-AAATAAAATAATT
15500138 TAATTCTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 11 0.41
31 5 0.19
32 11 0.41
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (30 bp):
CTCTAAAAATTAAAATAAAATAAAATAATT
Found at i:15501537 original size:17 final size:17
Alignment explanation
Indices: 15501515--15501550 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
15501505 GATGGCAGAC
15501515 TATGCATGTGTAACTCG
1 TATGCATGTGTAACTCG
15501532 TATGCATGTGTAACTCG
1 TATGCATGTGTAACTCG
15501549 TA
1 TA
15501551 GCTCTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (17 bp):
TATGCATGTGTAACTCG
Found at i:15505930 original size:27 final size:27
Alignment explanation
Indices: 15505892--15505945 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
15505882 TTGCCACATA
15505892 ACCGTGTGACCCCTATTTTCAAAATTT
1 ACCGTGTGACCCCTATTTTCAAAATTT
15505919 ACCGTGTGACCCCTATTTTCAAAATTT
1 ACCGTGTGACCCCTATTTTCAAAATTT
15505946 TCAACTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (27 bp):
ACCGTGTGACCCCTATTTTCAAAATTT
Found at i:15506505 original size:7 final size:8
Alignment explanation
Indices: 15506475--15506505 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
15506465 TTTTTAAGGG
15506475 GTAAAATA
1 GTAAAATA
15506483 GTAAAATA
1 GTAAAATA
15506491 GTAAAATA
1 GTAAAATA
15506499 G-AAAATA
1 GTAAAATA
15506506 AATGAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.23
Consensus pattern (8 bp):
GTAAAATA
Found at i:15507675 original size:11 final size:11
Alignment explanation
Indices: 15507661--15507698 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15507651 AGCCCGGCCC
15507661 ATATTAAATAT
1 ATATTAAATAT
*
15507672 ATATTTAATAT
1 ATATTAAATAT
15507683 ATA-TAATATAT
1 ATATTAA-ATAT
15507694 ATATT
1 ATATT
15507699 TGATTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 2 0.09
11 20 0.87
12 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:15510857 original size:28 final size:28
Alignment explanation
Indices: 15510821--15510908 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 28
15510811 GGGTGTCTTG
* **
15510821 TTTAA-AGGTTCGCCACTCAGGCATTCC
1 TTTAAGAGGTTTGCCACAAAGGCATTCC
*
15510848 TTTAAGAGGTTTGCCACAAAGGCGTTCC
1 TTTAAGAGGTTTGCCACAAAGGCATTCC
*
15510876 TTTCAGAGGTTTGCCACAAAGGC-TATCC
1 TTTAAGAGGTTTGCCACAAAGGCAT-TCC
15510904 TTTAA
1 TTTAA
15510909 TTGAGTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
27 6 0.11
28 47 0.89
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (28 bp):
TTTAAGAGGTTTGCCACAAAGGCATTCC
Found at i:15519025 original size:25 final size:25
Alignment explanation
Indices: 15518990--15519037 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
15518980 ACATGTATGT
*
15518990 TCATACGAGCTGAATAACAGTAAGC
1 TCATACAAGCTGAATAACAGTAAGC
* *
15519015 TCATACAAGCTGAGTATCAGTAA
1 TCATACAAGCTGAATAACAGTAA
15519038 ATTTATAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (25 bp):
TCATACAAGCTGAATAACAGTAAGC
Done.