Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 131 of 186
Found at i:43066216 original size:48 final size:48
Alignment explanation
Indices: 43065865--43066197 Score: 296
Period size: 48 Copynumber: 6.9 Consensus size: 48
43065855 AAGAGGGTGA
* * * * * *
43065865 AATGCTGATACCATGTTCCAAACATGGTCTTACACGAGCTCACATGTC
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATC
* * * * * *
43065913 GA-GACTGATGCCATGTCCCATATATGGTCTTACATTAGCTCTCATCTC
1 AATG-CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATC
* * * * * * * *
43065961 AATGCCGATGCCATGTCCCAGAGATGGTTTTATATTATCTCTCGTCTC
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATC
* * * *
43066009 AATGCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTCCCATATC
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATC
* * *
43066057 -ATGGTCGATGCTATGTCCCAAACATGGTCTTACACTAG-TGCACATATC
1 AAT-GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCT-CTCATATC
* *
43066105 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTTAT-TAC
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATAT-C
* * * * *
43066153 ATTGTCGATGTCATGTTCCAAACATGGTCTTACACTAGTTCTCAT
1 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCAT
43066198 GTTGTGGCCG
Statistics
Matches: 235, Mismatches: 43, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
47 5 0.02
48 226 0.96
49 4 0.02
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (48 bp):
AATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATC
Found at i:43072904 original size:18 final size:18
Alignment explanation
Indices: 43072881--43072918 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
43072871 ATTGAGGAAC
43072881 AAATCTAAACAATGGTTG
1 AAATCTAAACAATGGTTG
43072899 AAATCTAAACAATGGTTG
1 AAATCTAAACAATGGTTG
43072917 AA
1 AA
43072919 TTCTTTACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (18 bp):
AAATCTAAACAATGGTTG
Found at i:43076364 original size:26 final size:24
Alignment explanation
Indices: 43076311--43076366 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
43076301 CCATTTCTTT
* *
43076311 TTATTTCTTTTCTTGTTCTATTTC
1 TTATTTCTTTTCTTATTCTAATTC
43076335 TTATTT-TTCTTCTTATTCTAGATTC
1 TTATTTCTT-TTCTTATTCTA-ATTC
43076360 ATTATTT
1 -TTATTT
43076367 AGCTATGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.07
24 16 0.59
25 3 0.11
26 6 0.22
ACGTcount: A:0.14, C:0.14, G:0.04, T:0.68
Consensus pattern (24 bp):
TTATTTCTTTTCTTATTCTAATTC
Found at i:43078008 original size:22 final size:21
Alignment explanation
Indices: 43077974--43078018 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
43077964 ACCATTAAGT
*
43077974 TTATTTTTTTTGTTTTTATTG
1 TTATTTTTGTTGTTTTTATTG
43077995 TTATTTTTAGTTGTTTTTATTG
1 TTATTTTT-GTTGTTTTTATTG
43078017 TT
1 TT
43078019 TTTCTTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (21 bp):
TTATTTTTGTTGTTTTTATTG
Found at i:43078033 original size:22 final size:22
Alignment explanation
Indices: 43077986--43078033 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
43077976 ATTTTTTTTG
* *
43077986 TTTTTATTGTTATTTTTAGTTG
1 TTTTTATTGTTATTTTTACTTA
43078008 TTTTTATTGTT-TTTCTTACTTA
1 TTTTTATTGTTATTT-TTACTTA
43078030 TTTT
1 TTTT
43078034 GTTTCTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.75
Consensus pattern (22 bp):
TTTTTATTGTTATTTTTACTTA
Found at i:43110682 original size:50 final size:50
Alignment explanation
Indices: 43110618--43110712 Score: 190
Period size: 50 Copynumber: 1.9 Consensus size: 50
43110608 TTAATTTATT
43110618 ATGAATTTCCAAAGTCGGAGCAGGGAATCCAGAAACCGTTCTGGCTTGTA
1 ATGAATTTCCAAAGTCGGAGCAGGGAATCCAGAAACCGTTCTGGCTTGTA
43110668 ATGAATTTCCAAAGTCGGAGCAGGGAATCCAGAAACCGTTCTGGC
1 ATGAATTTCCAAAGTCGGAGCAGGGAATCCAGAAACCGTTCTGGC
43110713 CCTGTCCCAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (50 bp):
ATGAATTTCCAAAGTCGGAGCAGGGAATCCAGAAACCGTTCTGGCTTGTA
Found at i:43111632 original size:27 final size:27
Alignment explanation
Indices: 43111602--43111779 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
43111592 ATATTGAGTC
* *
43111602 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
43111629 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
43111656 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** **
43111684 CGCACACTTAGTGCCGCATGGTCAGTT
1 CGCACACTTAGTGCTACATAATCAACT
* **
43111711 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
43111738 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
43111765 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43111780 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:43111741 original size:82 final size:81
Alignment explanation
Indices: 43111628--43111778 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
43111618 TATAATCAAC
* *
43111628 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
43111693 AGTGCCGCATGGTCAGT
65 AGTGCCGCATGGTCAGT
* **
43111710 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
43111774 AGTGC
65 AGTGC
43111779 TGTACAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.25
82 47 0.75
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCAGT
Found at i:43116324 original size:18 final size:17
Alignment explanation
Indices: 43116297--43116332 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
43116287 ACAAAAAATT
43116297 TAAAAATATAATAAATAA
1 TAAAAATAT-ATAAATAA
*
43116315 TAAAATTATATAAATAA
1 TAAAAATATATAAATAA
43116332 T
1 T
43116333 TTAATATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAATATATAAATAA
Found at i:43122289 original size:37 final size:37
Alignment explanation
Indices: 43122145--43122281 Score: 211
Period size: 37 Copynumber: 3.7 Consensus size: 37
43122135 GCTCAGACGA
* * * * *
43122145 AATCTCCACACGAAGTTATTGGGTTTTACCCGGACAA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
43122182 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
* *
43122219 ACTCTCCACACGTAGTCATCGGGGCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
43122256 AATCTCCACACGTAGTCATCGGGTCT
1 AATCTCCACACGTAGTCATCGGGTCT
43122282 CAACCGGAAT
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 91 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:43122573 original size:47 final size:47
Alignment explanation
Indices: 43122495--43122875 Score: 564
Period size: 47 Copynumber: 8.1 Consensus size: 47
43122485 ATATATATTC
* * * * *
43122495 CACATTGACCATTCGGCTTTACCACATATATGCATGTTCATATTCAC
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
* *
43122542 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
*
43122589 CACATTGGCCACTCGGCCTTATCACATATATGCATGTTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
* * * *
43122636 CACATAGGCCATTCGGCCTTATCACACATATGTATGCTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
* *
43122683 CACATTGGCCACTCGGCCTTATCACATATATGCAAGTTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
* * *
43122730 CACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCAC
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
* *
43122777 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
* **
43122824 CACATTGGCCATTCGGCCTTATCACATATATACACATTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
43122871 CACAT
1 CACAT
43122876 AAAATCCTAA
Statistics
Matches: 298, Mismatches: 36, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 298 1.00
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (47 bp):
CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
Found at i:43145004 original size:68 final size:65
Alignment explanation
Indices: 43144894--43145145 Score: 201
Period size: 68 Copynumber: 3.8 Consensus size: 65
43144884 ATACAGATGG
** * * * * *
43144894 TATGTAGCTAGGTCACATGTAT-AGTGCTAAGTGCACATCATGTGTACAAGAGAGCTACAAGACA
1 TATGTAGCTAGGTCACATGGGTGA-TACTATGTGTACACCATGTGTACAAGAGAGCTAC-AGAGA
43144958 TTA
64 -TA
*
43144961 TGATGTAGCTAGGTCACATGGGTGATACTATGTGTACACCATGTATACAAGAGAGCTACAG-GAT
1 T-ATGTAGCTAGGTCACATGGGTGATACTATGTGTACACCATGTGTACAAGAGAGCTACAGAGAT
43145025 A
65 A
* * * * * * *
43145026 TATGTAGCTAGGTCGCATGCGTGGCTCCAAGTGAAGGACACCATGTAG-ACAAGAGAGCTAC-GA
1 TATGTAGCTAGGTCACATGGGT-GATACTA-TG-TGTACACCATGT-GTACAAGAGAGCTACAGA
43145089 GATA
62 GATA
* * * * *
43145093 AAT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCGTGTGTACAAGAGAG
1 TATGTAGCTAGGTCACATGGGTGATACT-ATGTGTACACCATGTGTACAAGAGAG
43145146 TTGAACTCTA
Statistics
Matches: 149, Mismatches: 27, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
62 1 0.01
63 17 0.11
64 20 0.13
65 10 0.07
66 20 0.13
67 32 0.21
68 48 0.32
69 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (65 bp):
TATGTAGCTAGGTCACATGGGTGATACTATGTGTACACCATGTGTACAAGAGAGCTACAGAGATA
Found at i:43147678 original size:27 final size:27
Alignment explanation
Indices: 43147648--43147887 Score: 286
Period size: 27 Copynumber: 8.9 Consensus size: 27
43147638 CCTTAATCAA
* * * *
43147648 TAAAATGATTATTTTTCCCTTATGGGG
1 TAAAATGACTGTTTTGCCCTTATGAGG
*
43147675 TAAAATGACTGTTTTGCCCTTATGTGG
1 TAAAATGACTGTTTTGCCCTTATGAGG
* *
43147702 TAAAATCACTGTTTTGCCTTTATGAGG
1 TAAAATGACTGTTTTGCCCTTATGAGG
43147729 TAAAATGACTGTTTTGCCCTTATGAGG
1 TAAAATGACTGTTTTGCCCTTATGAGG
* * * *
43147756 TAAATTGACTATTTTGGCCTTATGGGG
1 TAAAATGACTGTTTTGCCCTTATGAGG
* * *
43147783 TAAAATGATTATTTTACCCTTATGAGG
1 TAAAATGACTGTTTTGCCCTTATGAGG
*
43147810 TAAAATGACTGTTTTGCCCTGAT-ATGG
1 TAAAATGACTGTTTTGCCCTTATGA-GG
*
43147837 TAAAATGACTGTTTTGCCCTT-TTATGG
1 TAAAATGACTGTTTTGCCCTTATGA-GG
* *
43147864 TAAGATGACTGTTTTACCCTTATG
1 TAAAATGACTGTTTTGCCCTTATG
43147888 TGATGTATGT
Statistics
Matches: 184, Mismatches: 26, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
26 2 0.01
27 181 0.98
28 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCCCTTATGAGG
Found at i:43148209 original size:18 final size:18
Alignment explanation
Indices: 43148186--43148257 Score: 92
Period size: 18 Copynumber: 4.1 Consensus size: 18
43148176 GAACTTGCAT
*
43148186 ACTGTTTACTATTACTAC
1 ACTGTTTACTATTACTGC
*
43148204 ACTGTTTACTGTTACTGC
1 ACTGTTTACTATTACTGC
*
43148222 ACTG-CTACTATTACTGC
1 ACTGTTTACTATTACTGC
* *
43148239 ACTATTTACTGTTACTGC
1 ACTGTTTACTATTACTGC
43148257 A
1 A
43148258 TTGGGCCAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
17 14 0.30
18 32 0.70
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.42
Consensus pattern (18 bp):
ACTGTTTACTATTACTGC
Found at i:43151648 original size:27 final size:27
Alignment explanation
Indices: 43151511--43151639 Score: 186
Period size: 27 Copynumber: 4.8 Consensus size: 27
43151501 CCTTAATCGA
*
43151511 TAAAATGACTATTTTTCCCTTATGGGG
1 TAAAATGACTATTTTGCCCTTATGGGG
* *
43151538 TAAAATGATTGTTTTGCCCTTATGGGG
1 TAAAATGACTATTTTGCCCTTATGGGG
* * *
43151565 TAAAATGATTATTTTTCCCTTATGAGG
1 TAAAATGACTATTTTGCCCTTATGGGG
*
43151592 TAAAATGACTATTTTGCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGGGG
*
43151619 TAAAATGACTGTTTTGCCCTT
1 TAAAATGACTATTTTGCCCTT
43151640 TTATGGTAAG
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.42
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATGGGG
Found at i:43151648 original size:54 final size:53
Alignment explanation
Indices: 43151511--43151671 Score: 187
Period size: 54 Copynumber: 3.0 Consensus size: 53
43151501 CCTTAATCGA
** * *
43151511 TAAAATGACTATTTTTCCCTTATGGGGTAAAATGATTGTTTTGCCCTTATGGGG
1 TAAAATGACTATTTTTCCCTT-TTAGGTAAAATGACTGTTTTGCCCTTATGTGG
* * *
43151565 TAAAATGATTATTTTTCCCTTATGAGGTAAAATGACTATTTTGCCCTTATGTGG
1 TAAAATGACTATTTTTCCCTT-TTAGGTAAAATGACTGTTTTGCCCTTATGTGG
* * * * *
43151619 TAAAATGACTGTTTTGCCCTTTTATGGTAAGATGACTGTTTTACCCCTATGTG
1 TAAAATGACTATTTTTCCCTTTTA-GGTAAAATGACTGTTTTGCCCTTATGTG
43151672 ATGTATTTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 2 0.02
54 91 0.98
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (53 bp):
TAAAATGACTATTTTTCCCTTTTAGGTAAAATGACTGTTTTGCCCTTATGTGG
Found at i:43151653 original size:27 final size:27
Alignment explanation
Indices: 43151511--43151660 Score: 158
Period size: 27 Copynumber: 5.6 Consensus size: 27
43151501 CCTTAATCGA
* * **
43151511 TAAAATGACTATTTTTCCCTTATGGGG
1 TAAAATGACTGTTTTGCCCTTATATGG
* **
43151538 TAAAATGATTGTTTTGCCCTTATGGGG
1 TAAAATGACTGTTTTGCCCTTATATGG
* * *
43151565 TAAAATGATTATTTTTCCCTTATGA-GG
1 TAAAATGACTGTTTTGCCCTTAT-ATGG
* *
43151592 TAAAATGACTATTTTGCCCTTATGTGG
1 TAAAATGACTGTTTTGCCCTTATATGG
*
43151619 TAAAATGACTGTTTTGCCCTTTTATGG
1 TAAAATGACTGTTTTGCCCTTATATGG
*
43151646 TAAGATGACTGTTTT
1 TAAAATGACTGTTTT
43151661 ACCCCTATGT
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
27 108 1.00
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCCCTTATATGG
Found at i:43152015 original size:17 final size:18
Alignment explanation
Indices: 43151988--43152025 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
43151978 GGACTTGCAT
43151988 ACTGTTTACTGTTACTAC
1 ACTGTTTACTGTTACTAC
43152006 ACTG-TTACTGTTACTAC
1 ACTGTTTACTGTTACTAC
43152023 ACT
1 ACT
43152026 ACAATGGGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.42
Consensus pattern (18 bp):
ACTGTTTACTGTTACTAC
Found at i:43159841 original size:42 final size:42
Alignment explanation
Indices: 43159779--43159861 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
43159769 CTAAAACATA
* *
43159779 TGTAACACCCCTCACCCGTATTCAACGCTAGAATAGGGTTAT
1 TGTAACACCCCTCACACGTATTCAACGCCAGAATAGGGTTAT
*
43159821 TGTAACACCCCTCACACGTATTCAACTCCAGAATAGGGTTA
1 TGTAACACCCCTCACACGTATTCAACGCCAGAATAGGGTTA
43159862 CGGTGCATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (42 bp):
TGTAACACCCCTCACACGTATTCAACGCCAGAATAGGGTTAT
Found at i:43168662 original size:27 final size:28
Alignment explanation
Indices: 43168632--43168689 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
43168622 AATTTTTGAT
43168632 AAAATGAGCTATTTG-GG-CTAATTTGTG
1 AAAATGAGCT-TTTGAGGACTAATTTGTG
*
43168659 AAAATGAGGTTTTGAAGGACTAATTTGTG
1 AAAATGAGCTTTTG-AGGACTAATTTGTG
43168688 AA
1 AA
43168690 TTTAACATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
27 9 0.33
28 2 0.07
29 12 0.44
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (28 bp):
AAAATGAGCTTTTGAGGACTAATTTGTG
Found at i:43178153 original size:15 final size:15
Alignment explanation
Indices: 43178135--43178165 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43178125 TCCAGGACAA
43178135 AGAAATCCAAGATAC
1 AGAAATCCAAGATAC
*
43178150 AGAAATCTAAGATAC
1 AGAAATCCAAGATAC
43178165 A
1 A
43178166 ATATCATAAT
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:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (15 bp):
AGAAATCCAAGATAC
Found at i:43181963 original size:37 final size:37
Alignment explanation
Indices: 43181901--43182009 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
43181891 AGCTCAGATG
* * *
43181901 AAATCTCCACACGAAGTTATTGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
43181938 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
43181975 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
43182010 ATATATTTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:43182261 original size:98 final size:98
Alignment explanation
Indices: 43182159--43182340 Score: 310
Period size: 98 Copynumber: 1.9 Consensus size: 98
43182149 CATCTCCTAC
*
43182159 ATATTTCACACTAACCATTCAGCTTTACCACATATACATATCTCATACATATTTCACACTAGTCA
1 ATATTTCACACTAACCATTCAGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
43182224 TTCGGCTTTACCACATATACATATCTCAGATAT
66 TTCGGCTTTACCACATATACATATCTCAGATAT
** * * *
43182257 ATATTTCACGTTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
1 ATATTTCACACTAACCATTCAGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
43182322 TTCGGCTTTACCACATATA
66 TTCGGCTTTACCACATATA
43182341 TACACTTCCA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 78 1.00
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (98 bp):
ATATTTCACACTAACCATTCAGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
TTCGGCTTTACCACATATACATATCTCAGATAT
Found at i:43182344 original size:50 final size:48
Alignment explanation
Indices: 43182150--43182340 Score: 292
Period size: 48 Copynumber: 3.9 Consensus size: 48
43182140 ATATACACAC
* * *
43182150 ATCTCCTACATATTTCACACTAACCATTCAGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
43182198 ATCTCATACATATTTCACACTAGTCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* **
43182246 ATCTCAGATATATATTTCACGTTAGCCATTCGGCTTTACCACATATACAT
1 ATCTC--ATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
43182296 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATA
43182341 TACACTTCCA
Statistics
Matches: 131, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
48 87 0.66
50 44 0.34
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:43182384 original size:47 final size:47
Alignment explanation
Indices: 43182310--43182825 Score: 681
Period size: 47 Copynumber: 11.1 Consensus size: 47
43182300 CATACATATT
* * * * * * **
43182310 TCACATTAGCCATTCGGCTTTACCACATATATACACT-TCCACGTTTG
1 TCACATTGGCCATTCGGCCTTATCACATATATGCA-TGTTCACATTCA
** *
43182357 TCACATTGGCCATTTTGCCTTATCACATATATGCATGTTCTCATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
43182404 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTC-
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * * * **
43182450 T---A---GCCATTCGGCTTTACCACATATATACACT-TCCACGTTTG
1 TCACATTGGCCATTCGGCCTTATCACATATATGCA-TGTTCACATTCA
** *
43182491 TCACATTGGCCATTTTGCCTTATCACATATATGCATGTTCTCATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
43182538 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
43182585 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
43182632 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
43182679 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
43182726 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
43182773 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
43182820 TCACAT
1 TCACAT
43182826 AAAATCCTAA
Statistics
Matches: 418, Mismatches: 41, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
40 29 0.07
41 2 0.00
43 1 0.00
44 1 0.00
46 3 0.01
47 382 0.91
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:43182463 original size:134 final size:134
Alignment explanation
Indices: 43182309--43182724 Score: 622
Period size: 134 Copynumber: 3.1 Consensus size: 134
43182299 TCATACATAT
43182309 TTCACA-T-TAGCCATTCGGCTTTACCACATATATACACTTCCACGTTTGTCACATTGGCCATTT
1 TTCACATTCTAGCCATTCGGCTTTACCACATATATACACTTCCACGTTTGTCACATTGGCCATTT
43182372 TGCCTTATCACATATATGCATGTTCTCATTCATCACATTGGCCATTCGGCCTTATCACACATATG
66 TGCCTTATCACATATATGCATGTTCTCATTCATCACATTGGCCATTCGGCCTTATCACACATATG
43182437 CATG
131 CATG
43182441 TTCACATTCTAGCCATTCGGCTTTACCACATATATACACTTCCACGTTTGTCACATTGGCCATTT
1 TTCACATTCTAGCCATTCGGCTTTACCACATATATACACTTCCACGTTTGTCACATTGGCCATTT
*
43182506 TGCCTTATCACATATATGCATGTTCTCATTCATCACATTGGCCATTCGGCCTTATCACATATATG
66 TGCCTTATCACATATATGCATGTTCTCATTCATCACATTGGCCATTCGGCCTTATCACACATATG
43182571 CATG
131 CATG
* * * * * * **
43182575 TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCA-TGTTCACATTCATCACATT
1 TTCACATTC-T---A---GCCATTCGGCTTTACCACATATATACACT-TCCACGTTTGTCACATT
** * *
43182639 GGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCA
58 GGCCATTTTGCCTTATCACATATATGCATGTTCTCATTCATCACATTGGCCATTCGGCCTTATCA
43182704 CACATATGCATG
123 CACATATGCATG
43182716 TTCACATTC
1 TTCACATTC
43182725 ATCACATTGG
Statistics
Matches: 260, Mismatches: 14, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
132 6 0.02
133 1 0.00
134 133 0.51
135 1 0.00
138 1 0.00
140 1 0.00
141 117 0.45
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.35
Consensus pattern (134 bp):
TTCACATTCTAGCCATTCGGCTTTACCACATATATACACTTCCACGTTTGTCACATTGGCCATTT
TGCCTTATCACATATATGCATGTTCTCATTCATCACATTGGCCATTCGGCCTTATCACACATATG
CATG
Found at i:43191237 original size:13 final size:13
Alignment explanation
Indices: 43191219--43191247 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
43191209 TTTCAATCTT
43191219 TTTGTTTTGGTCA
1 TTTGTTTTGGTCA
43191232 TTTGTTTTGGTCA
1 TTTGTTTTGGTCA
43191245 TTT
1 TTT
43191248 TTGGTATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.66
Consensus pattern (13 bp):
TTTGTTTTGGTCA
Found at i:43193850 original size:48 final size:49
Alignment explanation
Indices: 43193765--43193951 Score: 186
Period size: 48 Copynumber: 3.8 Consensus size: 49
43193755 GTCATTAGGG
*
43193765 GATA-CATTGATTTGGCTTCGGGCCATGATATTGGCACTTCAGGTGCGA
1 GATATCATTGATTTGGCTTCGGGCCATGATATTAGCACTTCAGGTGCGA
* * * *
43193813 GCT-TCATTTATTTGGTTTTGGGCCATGATATTAGCACTTC-GTGTGCGA
1 GATATCATTGATTTGGCTTCGGGCCATGATATTAGCACTTCAG-GTGCGA
* ** *
43193861 GATAT-ATTGATTTGGGTTCGGGTAATGATATTAGTACTTCAGGTGCGA
1 GATATCATTGATTTGGCTTCGGGCCATGATATTAGCACTTCAGGTGCGA
* * *
43193909 GATATATATATTGAGTTT-GCTTCGGGCCAAGATATTGGCACTT
1 G--ATAT-CATTGA-TTTGGCTTCGGGCCATGATATTAGCACTT
43193952 AGTGTGCAAG
Statistics
Matches: 112, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
47 1 0.01
48 78 0.70
49 2 0.02
50 4 0.04
52 24 0.21
53 3 0.03
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (49 bp):
GATATCATTGATTTGGCTTCGGGCCATGATATTAGCACTTCAGGTGCGA
Found at i:43196150 original size:42 final size:42
Alignment explanation
Indices: 43196091--43196175 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
43196081 ATACATTTGA
43196091 ATGATTACGGAGCATTATCGGGCTTATTTCTAAAATAATCAT
1 ATGATTACGGAGCATTATCGGGCTTATTTCTAAAATAATCAT
43196133 ATGATTACGGAGCATTATCGGGCTTATTTCTAAAATAATCAT
1 ATGATTACGGAGCATTATCGGGCTTATTTCTAAAATAATCAT
43196175 A
1 A
43196176 CATTTCATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (42 bp):
ATGATTACGGAGCATTATCGGGCTTATTTCTAAAATAATCAT
Found at i:43203757 original size:10 final size:10
Alignment explanation
Indices: 43203744--43203783 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
43203734 AAAAATGATC
43203744 AAAATTAATA
1 AAAATTAATA
43203754 AAAATTAGATA
1 AAAATTA-ATA
43203765 TAAAATTAATA
1 -AAAATTAATA
43203776 AAAATTAA
1 AAAATTAA
43203784 ATATGTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 15 0.54
11 6 0.21
12 7 0.25
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (10 bp):
AAAATTAATA
Found at i:43203796 original size:22 final size:22
Alignment explanation
Indices: 43203744--43203787 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
43203734 AAAAATGATC
*
43203744 AAAATTAATAAAAATTAGATAT
1 AAAATTAATAAAAATTAAATAT
43203766 AAAATTAATAAAAATTAAATAT
1 AAAATTAATAAAAATTAAATAT
43203788 GTTAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATTAATAAAAATTAAATAT
Found at i:43213037 original size:13 final size:13
Alignment explanation
Indices: 43213019--43213043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43213009 AGTGACCAAA
43213019 AATGACCAAAATG
1 AATGACCAAAATG
43213032 AATGACCAAAAT
1 AATGACCAAAAT
43213044 AAAAAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (13 bp):
AATGACCAAAATG
Found at i:43214119 original size:15 final size:15
Alignment explanation
Indices: 43214092--43214138 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
43214082 CATAGTACTG
*
43214092 TATCTTAGGTTTCTT
1 TATCTTGGGTTTCTT
43214107 TAT-TCTGGGTTTCTT
1 TATCT-TGGGTTTCTT
*
43214122 TATCTTGGATTTCTT
1 TATCTTGGGTTTCTT
43214137 TA
1 TA
43214139 CTCGATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.60
Consensus pattern (15 bp):
TATCTTGGGTTTCTT
Found at i:43222548 original size:30 final size:30
Alignment explanation
Indices: 43222514--43222574 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
43222504 TCCTTAACTC
43222514 AAACTTTAT-AAAAATTACAATTTTGCCCCT
1 AAACTTT-TGAAAAATTACAATTTTGCCCCT
* * *
43222544 AAACTTTTGAATATTTACACTTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
43222574 A
1 A
43222575 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.39
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACAATTTTGCCCCT
Found at i:43225781 original size:30 final size:29
Alignment explanation
Indices: 43225745--43225804 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
43225735 AGAGCCTTGG
43225745 GGCAAAAGTGTAAATATGCAAAAGTTTAGA
1 GGCAAAAGTGTAAATATGCAAAAG-TTAGA
* * * *
43225775 GGCAAAATTGTAATTTTGCCAAAGTTAGA
1 GGCAAAAGTGTAAATATGCAAAAGTTAGA
43225804 G
1 G
43225805 TTAAGGAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (29 bp):
GGCAAAAGTGTAAATATGCAAAAGTTAGA
Found at i:43226335 original size:52 final size:53
Alignment explanation
Indices: 43226239--43226342 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 53
43226229 ATAAACTACT
* * * ** *
43226239 ATAAGGCAAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTC
1 ATAAGGCAAAGATACCACGTAAGACCATGCCAAGACATCACAATGGTAAGTTC
* *
43226292 ATAAGG-AAGGATACCACGTAAGACCATGTCAAGACATCACAATGGTAAGTT
1 ATAAGGCAAAGATACCACGTAAGACCATGCCAAGACATCACAATGGTAAGTT
43226343 TAAAAAGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
52 37 0.86
53 6 0.14
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (53 bp):
ATAAGGCAAAGATACCACGTAAGACCATGCCAAGACATCACAATGGTAAGTTC
Found at i:43232803 original size:34 final size:34
Alignment explanation
Indices: 43232765--43232836 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
43232755 GTAACAGTCC
43232765 AGTATCAGT-TAAGGCCTTAGCCCATTACAGTAAA
1 AGTATCAGTGT-AGGCCTTAGCCCATTACAGTAAA
* * *
43232799 AGTATCAGTGTGGGCCTTAGCCCATTTCAGTAAT
1 AGTATCAGTGTAGGCCTTAGCCCATTACAGTAAA
43232833 AGTA
1 AGTA
43232837 ACAAGACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 33 0.97
35 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (34 bp):
AGTATCAGTGTAGGCCTTAGCCCATTACAGTAAA
Found at i:43240940 original size:27 final size:26
Alignment explanation
Indices: 43240884--43240940 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
43240874 CAACCTTAAC
* * *
43240884 CCTAGTGGTATATTAGTAATTTTACT
1 CCTAGGGGTAAATTAGTAATTTTACA
* *
43240910 CCTAGGGGTAAATTTGTAAATTTTCCA
1 CCTAGGGGTAAATTAGT-AATTTTACA
43240937 CCTA
1 CCTA
43240941 TAAAGGTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (26 bp):
CCTAGGGGTAAATTAGTAATTTTACA
Found at i:43250368 original size:2 final size:2
Alignment explanation
Indices: 43250361--43250387 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43250351 TACCAGGTCA
43250361 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
43250388 GGTACTACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:43251460 original size:12 final size:12
Alignment explanation
Indices: 43251443--43251469 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43251433 CCTATGTTCC
43251443 ATGCCTTGTGCT
1 ATGCCTTGTGCT
43251455 ATGCCTTGTGCT
1 ATGCCTTGTGCT
43251467 ATG
1 ATG
43251470 TCGTTCCAAA
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:0.11, C:0.22, G:0.26, T:0.41
Consensus pattern (12 bp):
ATGCCTTGTGCT
Found at i:43254401 original size:47 final size:47
Alignment explanation
Indices: 43254327--43254680 Score: 315
Period size: 47 Copynumber: 7.6 Consensus size: 47
43254317 ATGCGAACGC
*
43254327 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
* * * * *
43254374 CCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAAC---GC--
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCAT
*
43254420 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
* * * * *
43254467 CCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAAC---GC--
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCAT
*
43254513 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
* * * * *
43254560 CCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAAC---GC--
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCAT
*
43254606 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
*
43254653 CCGAACTCGTTGAGTTGAGTTCGAGTTC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC
43254681 ACTTATGGAT
Statistics
Matches: 242, Mismatches: 38, Indels: 54
0.72 0.11 0.16
Matches are distributed among these distances:
42 9 0.04
43 9 0.04
45 12 0.05
46 78 0.32
47 104 0.43
48 12 0.05
50 9 0.04
51 9 0.04
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (47 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCAT
Found at i:43254436 original size:93 final size:93
Alignment explanation
Indices: 43254277--43254727 Score: 893
Period size: 93 Copynumber: 4.8 Consensus size: 93
43254267 GGATGGTTGA
*
43254277 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
43254342 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
43254370 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
43254435 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
43254463 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
43254528 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
43254556 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
43254621 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
43254649 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
43254714 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
43254728 CTTATGGGCG
Statistics
Matches: 357, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 357 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:43258682 original size:3 final size:3
Alignment explanation
Indices: 43258668--43258713 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
43258658 CGAATGTATT
43258668 TAA TAA -AA TAA TAA T-A TCAA -AA CTAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA -TAA TAA TAA TAA TAA TAA TAA
43258712 TA
1 TA
43258714 TAAATGTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 6 0.16
3 29 0.76
4 3 0.08
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:43258709 original size:15 final size:14
Alignment explanation
Indices: 43258668--43258717 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 14
43258658 CGAATGTATT
43258668 TAATAAAATAATAA
1 TAATAAAATAATAA
43258682 T-ATCAAAACTAATAA
1 TAAT-AAAA-TAATAA
43258697 TAATAATAATAATAA
1 TAATAA-AATAATAA
43258712 T-ATAAA
1 TAATAAA
43258718 TGTATACGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 3 0.09
14 9 0.28
15 16 0.50
16 4 0.12
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATAAAATAATAA
Found at i:43260377 original size:42 final size:42
Alignment explanation
Indices: 43260266--43260386 Score: 199
Period size: 41 Copynumber: 2.9 Consensus size: 42
43260256 AGACACGTGA
* *
43260266 CTTCAATCAATTCCACTGAAACTTCAAGGAGATCTACTGTAG
1 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAG
* *
43260308 CTTCGCTTAA-TCCACTGAAACTTCAAGGAGATCTGCTGTAG
1 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAG
43260349 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTGCT
1 CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTGCT
43260387 ATGGCTTTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
41 38 0.53
42 34 0.47
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (42 bp):
CTTCGATCAATTCCACTGAAACTTCAAGGAGATCTGCTGTAG
Found at i:43260587 original size:44 final size:43
Alignment explanation
Indices: 43260435--43260645 Score: 120
Period size: 44 Copynumber: 4.9 Consensus size: 43
43260425 ATATTTGATT
* * * **
43260435 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCA
1 TTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAAGC-TAT-AAAA
* * * * * * * * *
43260480 TTGATC-TGTTTCCCTACTACTTAGGGGTTTAGATCTGT-AAG
1 TTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTATAAAA
* * * * * *
43260521 CTCAACCTGTTATCCTACTGCTTAGGGGGTTAAAGGTTTGAAAA
1 TTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTAT-AAAA
** * * * * * *
43260565 TTTGGCTTGTTACCCTATTGCTTAGAGCGATAATATCTATAAAC
1 TTCAGCTTGTTACCCTACTGCTTAGGGGGTTAA-AGCTATAAAA
43260609 TTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCT
1 TTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCT
43260646 TGGTGGTTTG
Statistics
Matches: 118, Mismatches: 44, Indels: 10
0.69 0.26 0.06
Matches are distributed among these distances:
41 3 0.03
42 24 0.20
43 6 0.05
44 78 0.66
45 7 0.06
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (43 bp):
TTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTATAAAA
Found at i:43260985 original size:43 final size:44
Alignment explanation
Indices: 43260908--43261002 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 44
43260898 CTATACATTT
* *
43260908 AGTCTGCTCCACTGCGACTTCAAGGAGATGAGACTTGTAACTTC
1 AGTCTGCTCCACTGCGACTTCAAGGAGATAAGACTAGTAACTTC
* * *
43260952 AGTCTGCTCTACTGC-ACTTCAGGGAGATAAGACTAGTGACTTC
1 AGTCTGCTCCACTGCGACTTCAAGGAGATAAGACTAGTAACTTC
*
43260995 AATCTGCT
1 AGTCTGCT
43261003 TCGCTGAGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
43 31 0.69
44 14 0.31
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (44 bp):
AGTCTGCTCCACTGCGACTTCAAGGAGATAAGACTAGTAACTTC
Found at i:43263666 original size:24 final size:24
Alignment explanation
Indices: 43263639--43263689 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
43263629 TTCGGGGATA
*
43263639 CCAGGAATGCCCCGATTCCATTTC
1 CCAGGAATGCCCCGATTCCATTGC
43263663 CCAGGAATGCCCCGATTCCATTGC
1 CCAGGAATGCCCCGATTCCATTGC
43263687 CCA
1 CCA
43263690 CGGCATTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.39, G:0.18, T:0.22
Consensus pattern (24 bp):
CCAGGAATGCCCCGATTCCATTGC
Found at i:43269364 original size:22 final size:22
Alignment explanation
Indices: 43269312--43269376 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
43269302 TTAAAGCCTT
* *
43269312 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
43269334 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
43269356 CTGATTATGGTTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
43269377 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:43269587 original size:27 final size:27
Alignment explanation
Indices: 43269535--43269591 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
43269525 ATTCTGTTAA
* *
43269535 GTGGCTTTGCCACATTACCTGTTTCTG
1 GTGGCTATGCCACAATACCTGTTTCTG
*
43269562 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTATGCCAC-AATACCTGTTTCTG
43269589 GTG
1 GTG
43269592 ACTCTATCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.37
Consensus pattern (27 bp):
GTGGCTATGCCACAATACCTGTTTCTG
Found at i:43269784 original size:6 final size:6
Alignment explanation
Indices: 43269746--43269865 Score: 77
Period size: 6 Copynumber: 19.3 Consensus size: 6
43269736 TTGCATTCAC
* * *
43269746 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCT-
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
43269795 ATTACCTC ATACTG ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
43269846 ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
43269866 AATGTTTCTT
Statistics
Matches: 89, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
5 7 0.08
6 65 0.73
7 13 0.15
8 4 0.04
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:43269792 original size:31 final size:31
Alignment explanation
Indices: 43269746--43269856 Score: 150
Period size: 31 Copynumber: 3.5 Consensus size: 31
43269736 TTGCATTCAC
* *
43269746 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTCTGATTCTGTTACCTAATACTG
* * *
43269778 ATTCTGATTTTGATTCTATTACCTCATACTG
1 ATTCTGATTCTGATTCTGTTACCTAATACTG
* *
43269809 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACCTAATACTG
43269840 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
43269857 AGTTCTGATA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
31 65 0.90
32 7 0.10
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTAATACTG
Found at i:43270712 original size:28 final size:28
Alignment explanation
Indices: 43270652--43270706 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
43270642 AAAATATAAT
43270652 AATTA-TAAAATAATTAAATTTCAATCA
1 AATTATTAAAATAATTAAATTTCAATCA
*
43270679 AATTATTAAAAT-ATTAAATTTTAATCA
1 AATTATTAAAATAATTAAATTTCAATCA
43270706 A
1 A
43270707 TTTTATATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (28 bp):
AATTATTAAAATAATTAAATTTCAATCA
Found at i:43270719 original size:22 final size:22
Alignment explanation
Indices: 43270689--43270732 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43270679 AATTATTAAA
*
43270689 ATATTAAATTTTAATCAATTTT
1 ATATCAAATTTTAATCAATTTT
* *
43270711 ATATCAAATTTTTATTAATTTT
1 ATATCAAATTTTAATCAATTTT
43270733 GTTCATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATCAAATTTTAATCAATTTT
Found at i:43277330 original size:61 final size:63
Alignment explanation
Indices: 43277188--43277330 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 63
43277178 TCAAGCTCTA
*
43277188 CTGGGCC-TAAGCCCTATT-CAGAAATCAGAGTTAACTGAGCCTGAGCCCATATCAATATTAAT
1 CTGGGCCAT-AGCCCTATTACAGAAATCAGAGTTAACTGAGCCTGAGCCCATATCAATATCAAT
* * * *
43277250 CTGGGCCATAGCCC-CTTACAG-TATCAGAG-TATACTGAGCCT-AGCCCATATCAGTGTCAAT
1 CTGGGCCATAGCCCTATTACAGAAATCAGAGTTA-ACTGAGCCTGAGCCCATATCAATATCAAT
* *
43277310 CTGGGTCGTAGCCCTATTACA
1 CTGGGCCATAGCCCTATTACA
43277331 AGTCGAGATA
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
60 30 0.43
61 23 0.33
62 15 0.22
63 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (63 bp):
CTGGGCCATAGCCCTATTACAGAAATCAGAGTTAACTGAGCCTGAGCCCATATCAATATCAAT
Found at i:43288990 original size:24 final size:24
Alignment explanation
Indices: 43288958--43289012 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
43288948 GGACATGCTG
43288958 CTCAATAACATTATGGCCAAGCCA
1 CTCAATAACATTATGGCCAAGCCA
* *
43288982 CTCAATAACGTTGTGGCCAAGCCA
1 CTCAATAACATTATGGCCAAGCCA
43289006 CTCAATA
1 CTCAATA
43289013 TTGTAGCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.22
Consensus pattern (24 bp):
CTCAATAACATTATGGCCAAGCCA
Found at i:43291543 original size:39 final size:39
Alignment explanation
Indices: 43291481--43291559 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
43291471 GACAATATCT
* *
43291481 GGGATATGGCATCAATATGAGACTACGTGTAAGACTATA
1 GGGATATGGCATCAATATAAGACTACGTGTAAGACCATA
* *
43291520 GGGATATGGCATCGATATAAGACTTCGTGTAAGACCATA
1 GGGATATGGCATCAATATAAGACTACGTGTAAGACCATA
43291559 G
1 G
43291560 CTGGGCTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (39 bp):
GGGATATGGCATCAATATAAGACTACGTGTAAGACCATA
Found at i:43302317 original size:50 final size:49
Alignment explanation
Indices: 43302212--43302337 Score: 157
Period size: 50 Copynumber: 2.5 Consensus size: 49
43302202 GAGACTGATA
* * *
43302212 CCATGTCCCAGAAATGTTCTTACACTAGCTCTCATACCTACATGCTGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCT-ATACCTACATGCTAATG
* *
43302262 TCATGTCCCAGACATGGTCTTACACTAGCTCT-TGCCTATCCATG-TCAATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTATACCTA--CATGCT-AATG
43302312 CCATGTCCCAGACATGGTCTTACACT
1 CCATGTCCCAGACATGGTCTTACACT
43302338 GACATGTCTT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
48 5 0.07
49 1 0.01
50 61 0.91
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.30
Consensus pattern (49 bp):
CCATGTCCCAGACATGGTCTTACACTAGCTCTATACCTACATGCTAATG
Found at i:43302390 original size:45 final size:44
Alignment explanation
Indices: 43302316--43302475 Score: 144
Period size: 45 Copynumber: 3.5 Consensus size: 44
43302306 TCAATGCCAT
*
43302316 GTCCCAGACATGGTCTTACACTGACATGTCTTGTA-ACCGATGCAA
1 GTCCCAGACAT-GTCTTACACTGACATGTCTCG-AGACCGATGCAA
* * *
43302361 GTCTCAGACATGTCTTACACTG-CTTATGTCTCGAGGCCGATGCAT
1 GTCCCAGACATGTCTTACACTGAC--ATGTCTCGAGACCGATGCAA
* * * * *
43302406 GTCCCGGACATGTCTTACACTGGCACTTGTCTCAATACCGATGCCAT
1 GTCCCAGACATGTCTTACACT-G-ACATGTCTCGAGACCGATG-CAA
*
43302453 GTCCCGGACATGGTCTTACACTG
1 GTCCCAGACAT-GTCTTACACTG
43302476 GCAAACAAAT
Statistics
Matches: 97, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
43 1 0.01
44 12 0.12
45 44 0.45
46 14 0.14
47 15 0.15
48 11 0.11
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (44 bp):
GTCCCAGACATGTCTTACACTGACATGTCTCGAGACCGATGCAA
Found at i:43303469 original size:44 final size:44
Alignment explanation
Indices: 43303419--43303508 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
43303409 TCTCCCAAGC
43303419 CTTGTTTTTAATGTTCTTCGTAATTTTGAAGTCTCGGTAGCTTA
1 CTTGTTTTTAATGTTCTTCGTAATTTTGAAGTCTCGGTAGCTTA
43303463 CTTGTTTTTAATGTTCTTCGTAATTTTGAAGTCTCGGTAGCTTA
1 CTTGTTTTTAATGTTCTTCGTAATTTTGAAGTCTCGGTAGCTTA
43303507 CT
1 CT
43303509 CTCTCCATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (44 bp):
CTTGTTTTTAATGTTCTTCGTAATTTTGAAGTCTCGGTAGCTTA
Found at i:43308347 original size:24 final size:24
Alignment explanation
Indices: 43308320--43308369 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
43308310 CCAAATGAAA
*
43308320 ATATATTCATTAATCTTA-AATTCC
1 ATAT-TTCATTAATCATATAATTCC
*
43308344 ATATTTTATTAATCATATAATTCC
1 ATATTTCATTAATCATATAATTCC
43308368 AT
1 AT
43308370 CTCTACTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATTTCATTAATCATATAATTCC
Found at i:43309232 original size:93 final size:93
Alignment explanation
Indices: 43309088--43309299 Score: 343
Period size: 93 Copynumber: 2.3 Consensus size: 93
43309078 AGCAAACTCG
* * * *
43309088 GACTCAACTCAACGAGCTCAGATGCCTAGTTACATCTCACGAATTCAGACTCAACTCAACGAGTT
1 GACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACAAACTCAGACTCAACTCAACGAGCT
* *
43309153 CGGGCATTCGCATCCATAAGTGAAATCA
66 CAGACATTCGCATCCATAAGTGAAATCA
*
43309181 GACTCAATTCAACGAGCTCGGATGCCTAGTTACATCTCACAAACTCAGACTCAACTCAACGAGCT
1 GACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACAAACTCAGACTCAACTCAACGAGCT
*
43309246 CAGACATTCGCATCCATAAGTGAACTCA
66 CAGACATTCGCATCCATAAGTGAAATCA
*
43309274 GACTCGACTCAACGAGCTCGGATGCC
1 GACTCAACTCAACGAGCTCGGATGCC
43309300 CAAATATCCT
Statistics
Matches: 109, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 109 1.00
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (93 bp):
GACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACAAACTCAGACTCAACTCAACGAGCT
CAGACATTCGCATCCATAAGTGAAATCA
Found at i:43309233 original size:47 final size:47
Alignment explanation
Indices: 43309080--43309246 Score: 166
Period size: 47 Copynumber: 3.6 Consensus size: 47
43309070 CGCCCATAAG
* *
43309080 CAAACTCGGACTCAACTCAACGAGCTCAGATGCCTAGTTACATCTCA
1 CAAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCA
* * * *
43309127 CGAATTCAGACTCAACTCAACGAGTTCGG--G-C-A-TTCGCATC-CA
1 CAAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACATCTCA
* * *
43309169 TAAGTGAAATCAGACTCAATTCAACGAGCTCGGATGCCTAGTTACATCTCA
1 -CA---AACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCA
43309220 CAAACTCAGACTCAACTCAACGAGCTC
1 CAAACTCAGACTCAACTCAACGAGCTC
43309247 AGACATTCGC
Statistics
Matches: 94, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
42 4 0.04
43 5 0.05
44 1 0.01
45 1 0.01
46 24 0.26
47 47 0.50
48 1 0.01
49 1 0.01
50 6 0.06
51 4 0.04
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (47 bp):
CAAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:43309284 original size:46 final size:46
Alignment explanation
Indices: 43309132--43309292 Score: 152
Period size: 46 Copynumber: 3.5 Consensus size: 46
43309122 TCTCACGAAT
* * * *
43309132 TCAGACTCAACTCAACGAGTTCGGGCATTCGCATCCATAAGTGAAA
1 TCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAAC
* * * *
43309178 TCAGACTCAATTCAACGAGCTCGGATGCCTAGTT-ACATCTCA-CA---AAC
1 TCAGACTCAACTCAACGAGCTC--A-GAC-A-TTCGCATC-CATAAGTGAAC
43309225 TCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAAC
1 TCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAAC
*
43309271 TCAGACTCGACTCAACGAGCTC
1 TCAGACTCAACTCAACGAGCTC
43309293 GGATGCCCAA
Statistics
Matches: 92, Mismatches: 12, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
42 4 0.04
43 6 0.07
44 2 0.02
45 1 0.01
46 44 0.48
47 23 0.25
49 2 0.02
50 6 0.07
51 4 0.04
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (46 bp):
TCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAAC
Found at i:43315984 original size:47 final size:47
Alignment explanation
Indices: 43315039--43315976 Score: 1777
Period size: 47 Copynumber: 20.0 Consensus size: 47
43315029 TTAGGATTTT
** * * *
43315039 ATGTGATGAATGTGAATGTGTATATATGAGACAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315086 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315133 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315180 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315227 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315274 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315321 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315368 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315415 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315462 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315509 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315556 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315603 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315650 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315697 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315744 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315791 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
43315838 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
43315885 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
43315932 ATGTGATGAATATGAACATGCATATATGTGGTAAAGCTGAATGGC
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC
43315977 TAGTGTGAAA
Statistics
Matches: 878, Mismatches: 13, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 878 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:43316189 original size:37 final size:37
Alignment explanation
Indices: 43316139--43316210 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
43316129 GGAAATATAT
*
43316139 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
*
43316176 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTT
43316211 CGTCTGAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
Found at i:43320603 original size:46 final size:46
Alignment explanation
Indices: 43320550--43320846 Score: 594
Period size: 46 Copynumber: 6.5 Consensus size: 46
43320540 TGGGCATCCG
43320550 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
43320596 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
43320642 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
43320688 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
43320734 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
43320780 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
43320826 AACTCGTTGAGTTGAGTCCGA
1 AACTCGTTGAGTTGAGTCCGA
43320847 AGGTAAAATT
Statistics
Matches: 251, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 251 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
Found at i:43320892 original size:21 final size:21
Alignment explanation
Indices: 43320867--43320910 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
43320857 CTACTCAAAT
43320867 GGAGGAATACTCGAGATGAAA
1 GGAGGAATACTCGAGATGAAA
43320888 GGAGGAATACTCGAGATGAAA
1 GGAGGAATACTCGAGATGAAA
43320909 GG
1 GG
43320911 GACATATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.36, T:0.14
Consensus pattern (21 bp):
GGAGGAATACTCGAGATGAAA
Found at i:43322214 original size:23 final size:23
Alignment explanation
Indices: 43322171--43322214 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
43322161 AACCCCTAAT
* *
43322171 ATGCATAATTGTTTGATTTATGA
1 ATGCATAATTGATTGAGTTATGA
43322194 ATGCATAA-TGATTGCAGTTAT
1 ATGCATAATTGATTG-AGTTAT
43322215 TATTGGCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (23 bp):
ATGCATAATTGATTGAGTTATGA
Found at i:43325156 original size:31 final size:30
Alignment explanation
Indices: 43325121--43325210 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 30
43325111 ATTTTAAAGG
*
43325121 GTTAAAGTGATAAATTTTGTAAATATTAAAA
1 GTTAAATTGATAAATTTT-TAAATATTAAAA
* * *
43325152 GTTAAATTTATTAAATTTTTTATATAATAAAA
1 GTTAAATTGA-TAAA-TTTTTAAATATTAAAA
*
43325184 -TTAAATTGATAGAATATTTAAATATTA
1 GTTAAATTGATA-AATTTTTAAATATTA
43325211 GAGGATTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
30 12 0.25
31 18 0.38
32 14 0.29
33 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (30 bp):
GTTAAATTGATAAATTTTTAAATATTAAAA
Found at i:43325167 original size:32 final size:31
Alignment explanation
Indices: 43325131--43325190 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
43325121 GTTAAAGTGA
*
43325131 TAAATTTTGTAAATATTAAAAGTTAAATTTAT
1 TAAATTTTGTAAATAATAAAA-TTAAATTTAT
* *
43325163 TAAATTTTTTATATAATAAAATTAAATT
1 TAAATTTTGTAAATAATAAAATTAAATT
43325191 GATAGAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (31 bp):
TAAATTTTGTAAATAATAAAATTAAATTTAT
Found at i:43325686 original size:48 final size:49
Alignment explanation
Indices: 43325634--43325728 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 49
43325624 TGTAATCAAT
* *
43325634 GCTTACTATCACTAAGTATTA-CTCTTCTCCATCTTTTATTGTCTGTAC
1 GCTTACTATCACCAAGTATTAGCTCTTCTCCATCTTTTATTGCCTGTAC
*
43325682 GCTTACTATCACCAGGTATTAGCTCTTCTCCATCTTTTATTGCCTGT
1 GCTTACTATCACCAAGTATTAGCTCTTCTCCATCTTTTATTGCCTGT
43325729 TTTGTTTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
48 19 0.44
49 24 0.56
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.44
Consensus pattern (49 bp):
GCTTACTATCACCAAGTATTAGCTCTTCTCCATCTTTTATTGCCTGTAC
Found at i:43330247 original size:24 final size:24
Alignment explanation
Indices: 43330220--43330326 Score: 85
Period size: 24 Copynumber: 4.3 Consensus size: 24
43330210 ATATAAATTT
43330220 TAAATACTTTTTA-AATAAATAATA
1 TAAATA-TTTTTATAATAAATAATA
* * * *
43330244 TAAATATATATACAAAAAATAA-A
1 TAAATATTTTTATAATAAATAATA
*
43330267 TAAATATTTAAATTATTTATAAAATAATA
1 TAAATATTT---TTA-TAAT-AAATAATA
43330296 TAAATACTTTTTA-AATAAATAATA
1 TAAATA-TTTTTATAATAAATAATA
43330320 TAAATAT
1 TAAATAT
43330327 ATATACAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
23 14 0.21
24 28 0.42
25 2 0.03
26 2 0.03
27 4 0.06
28 6 0.09
29 7 0.11
30 3 0.05
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAATATTTTTATAATAAATAATA
Found at i:43330305 original size:76 final size:73
Alignment explanation
Indices: 43330220--43330364 Score: 254
Period size: 76 Copynumber: 1.9 Consensus size: 73
43330210 ATATAAATTT
43330220 TAAATACTTTTTAAATAAATAATATAAATATATATACAAAAAATAAATAAATATTTAAATTATTT
1 TAAATACTTTTTAAATAAATAATATAAATATATATACAAAAAATAAAT-AATA--TAAATTATTT
43330285 ATAAAATAATA
63 ATAAAATAATA
*
43330296 TAAATACTTTTTAAATAAATAATATAAATATATATACAAAAAATAAATGATATAAATTATTTATA
1 TAAATACTTTTTAAATAAATAATATAAATATATATACAAAAAATAAATAATATAAATTATTTATA
43330361 AAAT
66 AAAT
43330365 TTAATTTAAA
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
73 17 0.25
75 3 0.04
76 48 0.71
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.38
Consensus pattern (73 bp):
TAAATACTTTTTAAATAAATAATATAAATATATATACAAAAAATAAATAATATAAATTATTTATA
AAATAATA
Found at i:43330339 original size:24 final size:24
Alignment explanation
Indices: 43330287--43330341 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
43330277 AATTATTTAT
* *
43330287 AAAATAATATAAATACTTTTTAAA
1 AAAATAATATAAATACTATATAAA
*
43330311 TAAATAATATAAATA-TATATACAA
1 AAAATAATATAAATACTATATA-AA
43330335 AAAATAA
1 AAAATAA
43330342 ATGATATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAATAATATAAATACTATATAAA
Found at i:43331315 original size:24 final size:25
Alignment explanation
Indices: 43331270--43331316 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
43331260 CTTGTACTTC
* * *
43331270 AATTTAGTCATTTTCAATTTTTATA
1 AATTTAGTAATTTTAAAATTTTATA
43331295 AATTTAG-AATTTTAAAATTTTA
1 AATTTAGTAATTTTAAAATTTTA
43331317 GTCTTGACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (25 bp):
AATTTAGTAATTTTAAAATTTTATA
Found at i:43331604 original size:36 final size:36
Alignment explanation
Indices: 43331557--43331631 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
43331547 ATTAGATAGC
43331557 ATTTGTCAATTTGTCTGTAATTTTAACATGAGCGAA
1 ATTTGTCAATTTGTCTGTAATTTTAACATGAGCGAA
43331593 ATTTGTCAATTTGTCTGTAATTTTAACATGAGCGAA
1 ATTTGTCAATTTGTCTGTAATTTTAACATGAGCGAA
43331629 ATT
1 ATT
43331632 AGTAAAGCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.43
Consensus pattern (36 bp):
ATTTGTCAATTTGTCTGTAATTTTAACATGAGCGAA
Found at i:43344186 original size:21 final size:20
Alignment explanation
Indices: 43344162--43344200 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
43344152 GAGTATTTTG
43344162 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
43344183 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
43344201 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:43344272 original size:25 final size:25
Alignment explanation
Indices: 43344244--43344293 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
43344234 CAAATTAGGG
*
43344244 ATTAAATTGTGCAATGTGGAAACTT
1 ATTAAATTGTGAAATGTGGAAACTT
43344269 ATTAAATTGTGAAATGTGGAAACTT
1 ATTAAATTGTGAAATGTGGAAACTT
43344294 TGTAGTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (25 bp):
ATTAAATTGTGAAATGTGGAAACTT
Found at i:43347455 original size:52 final size:50
Alignment explanation
Indices: 43347391--43347513 Score: 149
Period size: 50 Copynumber: 2.4 Consensus size: 50
43347381 ATGAACAAAT
* * * *
43347391 GAGTTACTTAATGCATGACTTAAAT-TAATGATGCAAACTTTAACTAACATGG
1 GAGTTACATAATGCATGACTT-AATGT-ATGATGAAAAC-TTAACTAACAAGA
* * *
43347443 GAGTTACATAATGCATGTCATAATGTATGGTGAAAACTTAACTAACAAGA
1 GAGTTACATAATGCATGACTTAATGTATGATGAAAACTTAACTAACAAGA
43347493 GAGTTACATAATGCATGACTT
1 GAGTTACATAATGCATGACTT
43347514 TTTTAAATGC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
50 30 0.49
51 12 0.20
52 19 0.31
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (50 bp):
GAGTTACATAATGCATGACTTAATGTATGATGAAAACTTAACTAACAAGA
Found at i:43349306 original size:39 final size:39
Alignment explanation
Indices: 43349248--43349443 Score: 202
Period size: 39 Copynumber: 5.0 Consensus size: 39
43349238 TTCAGTGATG
* *
43349248 TATATCCGGACTTAGGGTCCGCAGACTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
43349287 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * *
43349326 TATATCCGGACTTAAGGTCCGTAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
* * * * *
43349365 TATGTCCGGGC-TAAAGTCCCGCAGGCT-TCGAGCTGGTAT
1 TATATCCGGACTTAAGGT-CCGCAGGCTAT-GTGCTGGAAT
** **
43349404 TATA-CCGGGTTTAAATTCCCGCAGGCT-TGTGCTGGTAAT
1 TATATCCGGACTTAAGGT-CCGCAGGCTATGTGCTGG-AAT
43349443 T
1 T
43349444 GGTTTCAAGT
Statistics
Matches: 135, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
38 16 0.12
39 119 0.88
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:43367863 original size:46 final size:46
Alignment explanation
Indices: 43367813--43368714 Score: 1719
Period size: 46 Copynumber: 19.8 Consensus size: 46
43367803 ATGGTTGAGC
43367813 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43367859 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43367905 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43367951 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43367997 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43368043 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43368089 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43368135 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43368181 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43368227 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43368273 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43368319 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43368365 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43368411 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43368457 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43368503 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
* *
43368549 ATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GAT--G--T
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
*
43368588 AACCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
43368634 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
*
43368680 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
43368715 GGGGCGAGTT
Statistics
Matches: 842, Mismatches: 7, Indels: 14
0.98 0.01 0.02
Matches are distributed among these distances:
39 30 0.04
40 2 0.00
41 1 0.00
42 3 0.00
43 3 0.00
44 1 0.00
45 2 0.00
46 800 0.95
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (46 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
Found at i:43368580 original size:20 final size:20
Alignment explanation
Indices: 43368557--43368617 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
43368547 ATATCCGAAC
43368557 TCGTTGAGTTGAGTCCGAGT
1 TCGTTGAGTTGAGTCCGAGT
* * **
43368577 TCG-TGAGATGTA-ACCGAAC
1 TCGTTGAGTTG-AGTCCGAGT
43368596 TCGTTGAGTTGAGTCCGAGT
1 TCGTTGAGTTGAGTCCGAGT
43368616 TC
1 TC
43368618 ACTTATGGAT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (20 bp):
TCGTTGAGTTGAGTCCGAGT
Found at i:43375352 original size:16 final size:16
Alignment explanation
Indices: 43375331--43375375 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
43375321 CTTAAATTCC
43375331 AAAATTATTTAAACCT
1 AAAATTATTTAAACCT
* *
43375347 AAAATTATTTTAACTT
1 AAAATTATTTAAACCT
* *
43375363 GAAATAATTTAAA
1 AAAATTATTTAAA
43375376 TCACAATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAATTATTTAAACCT
Found at i:43376687 original size:10 final size:9
Alignment explanation
Indices: 43376637--43376688 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
43376627 TTTTAAATTG
*
43376637 TTATAAAAT
1 TTATAAAAA
43376646 TTATAAAAA
1 TTATAAAAA
43376655 TATATATAAAA
1 T-TATA-AAAA
*
43376666 TTATTAAGAA
1 TTA-TAAAAA
43376676 TTATAAGAAA
1 TTATAA-AAA
43376686 TTA
1 TTA
43376689 ATTTTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
9 12 0.33
10 17 0.47
11 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (9 bp):
TTATAAAAA
Found at i:43376786 original size:28 final size:28
Alignment explanation
Indices: 43376728--43376786 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
43376718 ACCATTATAA
* *
43376728 ATAATTTTAAAATAAATTTCTATATTTT
1 ATAAATTTAAAATAAATTTCTATATTAT
* *
43376756 ATAAATTTATAAT-AATTTTTATAATTAT
1 ATAAATTTAAAATAAATTTCTAT-ATTAT
43376784 ATA
1 ATA
43376787 GAAAACAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
ATAAATTTAAAATAAATTTCTATATTAT
Found at i:43379761 original size:16 final size:16
Alignment explanation
Indices: 43379740--43379794 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
43379730 GTTTGGTTCC
*
43379740 CTGTAATTGAATAGGG
1 CTGTAATTGAATAGAG
43379756 CTGTAATTGAATAGAG
1 CTGTAATTGAATAGAG
*
43379772 CTGTAATGGAATAGAG
1 CTGTAATTGAATAGAG
*
43379788 CTATAAT
1 CTGTAAT
43379795 CAATAATTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.31
Consensus pattern (16 bp):
CTGTAATTGAATAGAG
Found at i:43384656 original size:68 final size:68
Alignment explanation
Indices: 43384506--43384663 Score: 160
Period size: 68 Copynumber: 2.3 Consensus size: 68
43384496 CTAGCCAATT
* **
43384506 TATCTCATAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCATAGCTCTCTTGTCTACATGGTGT-CTACACTCCGAATCACACATGCGACCTAGCTACA
**
43384571 TTTA
65 CATA
* * * *
43384575 TCTCTCCCGTAGCTCTCTTGTCTACATGG-GT-TACA-TCCCGTATCACACATGTGACCTAGCTA
1 TATCT--CATAGCTCTCTTGTCTACATGGTGTCTACACT-CCGAATCACACATGCGACCTAGCTA
43384637 CTACATA
63 C-ACATA
43384644 GTATCTCATAGCTCTCTTGT
1 -TATCTCATAGCTCTCTTGT
43384664 ACACATGATG
Statistics
Matches: 73, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
67 1 0.01
68 38 0.52
69 7 0.10
70 6 0.08
71 21 0.29
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.35
Consensus pattern (68 bp):
TATCTCATAGCTCTCTTGTCTACATGGTGTCTACACTCCGAATCACACATGCGACCTAGCTACAC
ATA
Found at i:43392236 original size:43 final size:43
Alignment explanation
Indices: 43392100--43392240 Score: 130
Period size: 43 Copynumber: 3.3 Consensus size: 43
43392090 ACATAGGATC
* * *
43392100 TGATATGTGTTTTCGTGTAAGACCACGTCTGGGACA-TTGGCAT
1 TGATATTTGATTTCGTGTAAGACC-CATCTGGGACAGTTGGCAT
* * *
43392143 TGACT-TATGATTTACGTTTAAGACTACATCTGGGAC-GTTGGCAT
1 TGA-TATTTGATTT-CGTGTAAGAC-CCATCTGGGACAGTTGGCAT
* *
43392187 CG-TATTTGATTTCGTGTAAGACCCTATCTGGGACAGTT-GTAT
1 TGATATTTGATTTCGTGTAAGACCC-ATCTGGGACAGTTGGCAT
43392229 TGATATTTGATT
1 TGATATTTGATT
43392241 ACATGTAATA
Statistics
Matches: 79, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
41 1 0.01
42 23 0.29
43 28 0.35
44 27 0.34
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.38
Consensus pattern (43 bp):
TGATATTTGATTTCGTGTAAGACCCATCTGGGACAGTTGGCAT
Found at i:43397391 original size:39 final size:39
Alignment explanation
Indices: 43397324--43397499 Score: 237
Period size: 39 Copynumber: 4.5 Consensus size: 39
43397314 ACAAAGCATG
* * *
43397324 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
43397364 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
* * * *
43397404 TGGGGCTTAACCCAGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
43397443 CGAGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
43397482 CAGGACTTAGCCCGGATA
1 CGGGACTTAGCCCGGATA
43397500 ATTCTCCATT
Statistics
Matches: 121, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 102 0.84
40 19 0.16
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:43403922 original size:40 final size:39
Alignment explanation
Indices: 43403872--43403994 Score: 131
Period size: 39 Copynumber: 3.1 Consensus size: 39
43403862 CAAATCCAAT
43403872 CACCACCACAAAGCAAGCGGGACTTTAAGCCCGGATATAA
1 CACCACCACAAAGCAAGCGGGACTTTAA-CCCGGATATAA
* * **
43403912 TACCATCACAAAGCCTGCGGGACTTTAACCCGGATATAA
1 CACCACCACAAAGCAAGCGGGACTTTAACCCGGATATAA
* * *** *
43403951 CACCAGCACGAATGCCTTCGGGGC-TTAACCCGGATATAA
1 CACCACCAC-AAAGCAAGCGGGACTTTAACCCGGATATAA
43403990 CACCA
1 CACCA
43403995 GTACGAATGC
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
39 38 0.52
40 35 0.48
ACGTcount: A:0.33, C:0.31, G:0.20, T:0.16
Consensus pattern (39 bp):
CACCACCACAAAGCAAGCGGGACTTTAACCCGGATATAA
Found at i:43403979 original size:39 final size:39
Alignment explanation
Indices: 43403889--43404067 Score: 225
Period size: 39 Copynumber: 4.5 Consensus size: 39
43403879 ACAAAGCAAG
* * * *
43403889 CGGGACTTTAAGCCCGGATATAATACCATCAC-AAAGCCTG
1 CGGGAC-TTAA-CCCGGATATAACACCAGCACGAATGCCTT
43403929 CGGGACTTTAACCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAACCCGGATATAACACCAGCACGAATGCCTT
* *
43403969 CGGGGCTTAACCCGGATATAACACCAGTACGAATGCCTT
1 CGGGACTTAACCCGGATATAACACCAGCACGAATGCCTT
* **
43404008 CGGGACTTAGCCTAGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAACCCGGATATAACACCAGCACGAATGCCTT
* *
43404047 CAGGACTTAGCCCGGATATAA
1 CGGGACTTAACCCGGATATAA
43404068 TGCTCCATTA
Statistics
Matches: 124, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 102 0.82
40 22 0.18
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (39 bp):
CGGGACTTAACCCGGATATAACACCAGCACGAATGCCTT
Found at i:43405362 original size:75 final size:75
Alignment explanation
Indices: 43405239--43405387 Score: 280
Period size: 75 Copynumber: 2.0 Consensus size: 75
43405229 GCATTTGTTC
43405239 AAGACATTAAGCAAAACCATGTTCGGCTAGTACACATATGAGTATTAGCAATTTATATTTTTAAA
1 AAGACATTAAGCAAAACCATGTTCGGCTAGTACACATATGAGTATTAGCAATTTATATTTTTAAA
43405304 AAGATCAACT
66 AAGATCAACT
*
43405314 AAGACATTAAGCAAAACCATGTTCGGCTAGTACACATATGAGTATTAGCAATTTATATTTTTAAC
1 AAGACATTAAGCAAAACCATGTTCGGCTAGTACACATATGAGTATTAGCAATTTATATTTTTAAA
*
43405379 ATGATCAAC
66 AAGATCAAC
43405388 GTCATTCATC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (75 bp):
AAGACATTAAGCAAAACCATGTTCGGCTAGTACACATATGAGTATTAGCAATTTATATTTTTAAA
AAGATCAACT
Found at i:43410161 original size:43 final size:42
Alignment explanation
Indices: 43410014--43410165 Score: 137
Period size: 43 Copynumber: 3.5 Consensus size: 42
43410004 TGTGTTTTCG
* * * *
43410014 TGTAAGACTACATCTGGGACGTTGGCATCGACT-TATAATTTACA
1 TGTAAGACCATATCTGGGACGTTGGCATC-A-TATTTGA-TTACA
** * *
43410058 TGTAAGACCACGTCTGGGACGTTGGCATCATATTTGATTTCG
1 TGTAAGACCATATCTGGGACGTTGGCATCATATTTGATTACA
* *
43410100 TGTAAGACCCTATCTGGGACAGTT-GTATCGATATTTGATTACA
1 TGTAAGACCATATCTGGGAC-GTTGGCATC-ATATTTGATTACA
* *
43410143 TGTAATACCATATTTGGGACGTT
1 TGTAAGACCATATCTGGGACGTT
43410166 TGGGGTTTGG
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
42 28 0.31
43 35 0.39
44 27 0.30
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGACGTTGGCATCATATTTGATTACA
Found at i:43412922 original size:46 final size:47
Alignment explanation
Indices: 43412832--43412943 Score: 183
Period size: 46 Copynumber: 2.4 Consensus size: 47
43412822 AGTAGCTCCT
*
43412832 TTAATGCTGTCCATGCATGCTTTTTCTTTAAGGCTTCAGCAGCATCA
1 TTAATGCCGTCCATGCATGCTTTTTCTTTAAGGCTTCAGCAGCATCA
*
43412879 TTAATGCCGTCCATGCTTGC-TTTTCTTTAAGGCTTCA-CTAGCATCA
1 TTAATGCCGTCCATGCATGCTTTTTCTTTAAGGCTTCAGC-AGCATCA
43412925 TTAATGCCGTCCATGCATG
1 TTAATGCCGTCCATGCATG
43412944 TTAGCTGCAC
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
45 1 0.02
46 42 0.69
47 18 0.30
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (47 bp):
TTAATGCCGTCCATGCATGCTTTTTCTTTAAGGCTTCAGCAGCATCA
Found at i:43422616 original size:46 final size:46
Alignment explanation
Indices: 43422549--43422815 Score: 534
Period size: 46 Copynumber: 5.8 Consensus size: 46
43422539 TGTAACCCGC
43422549 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
43422595 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
43422641 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
43422687 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
43422733 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
43422779 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
43422816 TGCTCAACCA
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 221 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:43431495 original size:29 final size:29
Alignment explanation
Indices: 43431432--43431499 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
43431422 TAATCAACCG
43431432 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
43431461 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
43431490 CGCACACTTA
1 CGCACACTTA
43431500 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:43433351 original size:47 final size:47
Alignment explanation
Indices: 43433282--43433543 Score: 270
Period size: 47 Copynumber: 5.6 Consensus size: 47
43433272 GCCCATAAGT
*
43433282 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
* * * ***
43433329 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGC-A--TCCATAAGT-
1 GAACTCAGACTCAACTCAACGAGCTCGG--ATGC-CTAGTTACATCTCTC
*
43433375 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
* * * ***
43433422 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGC-A--TCCATAAGT-
1 GAACTCAGACTCAACTCAACGAGCTCGG--ATGC-CTAGTTACATCTCTC
*
43433468 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
*
43433515 GAACTCAGACTCAACTCAACGAGTTCGGA
1 GAACTCAGACTCAACTCAACGAGCTCGGA
43433544 CATTCGCATC
Statistics
Matches: 171, Mismatches: 30, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
43 2 0.01
44 8 0.05
46 62 0.36
47 89 0.52
49 8 0.05
50 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (47 bp):
GAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:43433396 original size:46 final size:46
Alignment explanation
Indices: 43433329--43433589 Score: 273
Period size: 46 Copynumber: 5.6 Consensus size: 46
43433319 TACATCTCTC
43433329 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
* * * * ***
43433375 GAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTTACATCTCT
1 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGC-A--TCCATAAGT
43433421 CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 -GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
* * * * ***
43433468 GAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTTACATCTCT
1 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGC-A--TCCATAAGT
43433514 CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 -GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
*
43433561 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCAGACTCAACTCAACGAGTTCGGA
43433590 TGCTCAACCA
Statistics
Matches: 172, Mismatches: 29, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
43 2 0.01
44 8 0.05
46 90 0.52
47 62 0.36
49 8 0.05
50 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (46 bp):
GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
Found at i:43433433 original size:93 final size:93
Alignment explanation
Indices: 43433274--43433592 Score: 629
Period size: 93 Copynumber: 3.4 Consensus size: 93
43433264 TGTAACCCGC
43433274 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCAGAC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCAGAC
43433339 TCAACTCAACGAGTTCGGACATTCGCAT
66 TCAACTCAACGAGTTCGGACATTCGCAT
43433367 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCAGAC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCAGAC
43433432 TCAACTCAACGAGTTCGGACATTCGCAT
66 TCAACTCAACGAGTTCGGACATTCGCAT
43433460 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCAGAC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCAGAC
43433525 TCAACTCAACGAGTTCGGACATTCGCAT
66 TCAACTCAACGAGTTCGGACATTCGCAT
*
43433553 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGC
43433593 TCAACCATCC
Statistics
Matches: 225, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 225 1.00
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (93 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCAGAC
TCAACTCAACGAGTTCGGACATTCGCAT
Found at i:43433608 original size:46 final size:45
Alignment explanation
Indices: 43433279--43433608 Score: 174
Period size: 46 Copynumber: 7.1 Consensus size: 45
43433269 CCCGCCCATA
*
43433279 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTA-CATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATC-CT
* * *
43433328 --CGAACTCAGACTCAACTCAACGAGTTCGGA---CATTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCA-AC-CATCC-T
*
43433371 AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTA-CATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATC-CT
* * *
43433421 --CGAACTCAGACTCAACTCAACGAGTTCGGA---CATTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCA-AC-CATCC-T
*
43433464 AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTA-CATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATC-CT
* * *
43433514 --CGAACTCAGACTCAACTCAACGAGTTCGGA---CATTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCA-AC-CATCC-T
43433557 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCATCCT
43433604 AGTGA
1 AGTGA
43433609 CATGTCACTT
Statistics
Matches: 222, Mismatches: 23, Indels: 75
0.69 0.07 0.23
Matches are distributed among these distances:
41 3 0.01
42 3 0.01
43 18 0.08
44 3 0.01
46 87 0.39
47 82 0.37
48 5 0.02
49 3 0.01
50 14 0.06
51 2 0.01
52 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCCT
Found at i:43436782 original size:15 final size:15
Alignment explanation
Indices: 43436743--43436775 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
43436733 TAAAAAATTC
43436743 AAAGACAACACATAT
1 AAAGACAACACATAT
43436758 AAAGACAACACATAT
1 AAAGACAACACATAT
43436773 AAA
1 AAA
43436776 TCCAACATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.64, C:0.18, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAGACAACACATAT
Found at i:43448661 original size:27 final size:26
Alignment explanation
Indices: 43448623--43448682 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
43448613 CCACATATAT
* *
43448623 ATATATGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
43448649 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
43448676 ATATCTG
1 ATATCTG
43448683 GCAGCCTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:43455714 original size:19 final size:19
Alignment explanation
Indices: 43455690--43455733 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
43455680 AGGCTTAATA
43455690 GGCCAAAAACGGGCCAATG
1 GGCCAAAAACGGGCCAATG
43455709 GGCCAAAAACGGGCCAATG
1 GGCCAAAAACGGGCCAATG
43455728 GGCCAA
1 GGCCAA
43455734 GGGCCCACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.27, G:0.32, T:0.05
Consensus pattern (19 bp):
GGCCAAAAACGGGCCAATG
Found at i:43468659 original size:43 final size:42
Alignment explanation
Indices: 43468611--43468753 Score: 139
Period size: 43 Copynumber: 3.3 Consensus size: 42
43468601 ATCGAGATAT
*
43468611 GATTACATGTAAGACCATGTTTGGGACATTGGCATTGTATTG
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTG
* * *
43468653 AGATTACGTGTAAGGCCATGTCTGGGACATTGGCATCGTTAATT-
1 -GATTACATGTAAGACCATGTCTGGGACATTGGCATTG-T-ATTG
* * *
43468697 GATTTCGTGTAAGACCCA-GTCTGGGACAGTGGCATT-TATATG
1 GATTACATGTAAGA-CCATGTCTGGGACATTGGCATTGTAT-TG
*
43468739 TGATAACATGTAAGA
1 -GATTACATGTAAGA
43468754 TGATATTTGG
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
40 2 0.02
41 2 0.02
43 72 0.87
44 4 0.05
45 3 0.04
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (42 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTG
Found at i:43470147 original size:21 final size:21
Alignment explanation
Indices: 43470122--43470177 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
43470112 TGTGGTCCAA
*
43470122 GGGACACGCCCGTGTGACCTT
1 GGGACACGCCCGTGTAACCTT
* *
43470143 GGGACATGCTCGTGTAACCTT
1 GGGACACGCCCGTGTAACCTT
*
43470164 GGGACACGTCCGTG
1 GGGACACGCCCGTG
43470178 CTACAGGCCG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGACACGCCCGTGTAACCTT
Found at i:43473456 original size:40 final size:40
Alignment explanation
Indices: 43473401--43473582 Score: 305
Period size: 40 Copynumber: 4.6 Consensus size: 40
43473391 TATTCGAATG
43473401 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
43473441 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTAACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
43473481 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
43473521 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
43473561 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
43473583 TACTTGGGTT
Statistics
Matches: 135, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 14 0.10
40 119 0.88
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:43477822 original size:48 final size:48
Alignment explanation
Indices: 43477740--43478027 Score: 256
Period size: 48 Copynumber: 6.0 Consensus size: 48
43477730 ACTAGGGTTA
** *
43477740 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCAT
1 TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGGCATCGGCATCAT
** * * **
43477788 TATGTGAGCCAGTGTAAGACCACATTTGAAACATGGCCTCGACATTGT
1 TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGGCATCGGCATCAT
* * * * *
43477836 TATGAGAGCTAGTGTAAGACCATGTCT-AGGACATGGCATCGGCCTCGA-
1 TATGTGAGCCAGTGTAAGACCATGTTTGA-AACATGGCATCGGCATC-AT
* *
43477884 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTAT
1 TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGGCATCGGCATCAT
* * * * * * *
43477932 TGTATGAGCCAGTATAAGACCATGTCTGGAACATGGCATTGGCACCGAT
1 TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGGCATCGGCATC-AT
* * * * ** *
43477981 ATATGAGAGCTAGTGTAAGAACATGTCTGGGACATGACATCGGCATC
1 -TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGGCATCGGCATC
43478028 TTACCCTTTT
Statistics
Matches: 190, Mismatches: 44, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
47 2 0.01
48 150 0.79
49 2 0.01
50 36 0.19
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (48 bp):
TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGGCATCGGCATCAT
Found at i:43477917 original size:96 final size:95
Alignment explanation
Indices: 43477740--43478022 Score: 311
Period size: 96 Copynumber: 2.9 Consensus size: 95
43477730 ACTAGGGTTA
* *
43477740 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTC-ATTATGTGAGCCAGTGTA
1 TATGAGAGCCAGTGTAAGACCATGTCT-GGACATGGCATCGGCCTCGA-TATGTGAGCCAGTGTA
** * * *
43477804 AGACCACATTTGAAACATGGCCTCGACATTGT
64 AGACCATGTTTGGAACATGGCATCGACATTAT
*
43477836 TATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGATATGTGAGCCAGTGTAA
1 TATGAGAGCCAGTGTAAGACCATGTCT-GGACATGGCATCGGCCTCGATATGTGAGCCAGTGTAA
*
43477901 GACCATGTTTGGAACATGGCATCGGCATTAT
65 GACCATGTTTGGAACATGGCATCGACATTAT
* * * * *
43477932 TGT-ATGAGCCAGTATAAGACCATGTCTGGAACATGGCATTGGCAC-CGATATATGAGAGCTAGT
1 TATGA-GAGCCAGTGTAAGACCATGTCTGG-ACATGGCATCGGC-CTCG--ATATGTGAGCCAGT
* * * *
43477995 GTAAGAACATGTCTGGGACATGACATCG
61 GTAAGACCATGTTTGGAACATGGCATCG
43478023 GCATCTTACC
Statistics
Matches: 161, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
95 3 0.02
96 120 0.75
97 2 0.01
98 36 0.22
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (95 bp):
TATGAGAGCCAGTGTAAGACCATGTCTGGACATGGCATCGGCCTCGATATGTGAGCCAGTGTAAG
ACCATGTTTGGAACATGGCATCGACATTAT
Found at i:43489600 original size:21 final size:21
Alignment explanation
Indices: 43489571--43489611 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43489561 CATATAAATA
*
43489571 AAAAATTATAATTAATTTTTT
1 AAAAATTATAATGAATTTTTT
* *
43489592 AAAATTTATTATGAATTTTT
1 AAAAATTATAATGAATTTTT
43489612 AAAGTCAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AAAAATTATAATGAATTTTTT
Found at i:43490592 original size:93 final size:93
Alignment explanation
Indices: 43490484--43490654 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
43490474 GCCCCTAAGT
* * *
43490484 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTAAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTAAGACTCAACTCAA
43490549 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* **
43490577 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTAAGACTCAACTCAA
43490642 CGAGTTCGGATGC
66 CGAGTTCGGATGC
43490655 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTAAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:43490644 original size:46 final size:46
Alignment explanation
Indices: 43490479--43490651 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
43490469 AACCTGCCCC
* * * *
43490479 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
** * *
43490525 TAAGTGAACTAAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
43490573 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
43490618 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
43490652 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 58 0.57
47 27 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:43491109 original size:30 final size:30
Alignment explanation
Indices: 43491075--43491134 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
43491065 ATTTAATACG
43491075 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * * *
43491105 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
43491135 GGATCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:43497279 original size:46 final size:47
Alignment explanation
Indices: 43497159--43497282 Score: 198
Period size: 46 Copynumber: 2.7 Consensus size: 47
43497149 AACCCGCCCC
* *
43497159 TAAGTGAACTCGGACTCAACTCAACGAGCTC-AGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAGACATTCGCATCCA
*
43497205 TAAGTGACCTCGGACTCAACTCAACGAGTTCGA-ACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAGACATTCGCATCCA
*
43497251 TAAGTGAACTCTGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
43497283 GATGCTCAAC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
46 71 0.99
47 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGAGACATTCGCATCCA
Found at i:43497737 original size:30 final size:30
Alignment explanation
Indices: 43497703--43497763 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
43497693 CATTTAATAC
*
43497703 AAACTTTGGAAAAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTACCCCT
* * *
43497733 AAACTTTTGCATAATTACACTTTTACCCCT
1 AAACTTTGGAAAAATTACACTTTTACCCCT
43497763 A
1 A
43497764 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTACCCCT
Found at i:43503118 original size:15 final size:15
Alignment explanation
Indices: 43503079--43503111 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
43503069 TAAAAAATTC
*
43503079 AAAGACAACATATAT
1 AAAGACAACACATAT
43503094 AAAGACAACACATAT
1 AAAGACAACACATAT
43503109 AAA
1 AAA
43503112 TCCAACATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.15, G:0.06, T:0.15
Consensus pattern (15 bp):
AAAGACAACACATAT
Found at i:43511807 original size:262 final size:262
Alignment explanation
Indices: 43511336--43512122 Score: 1493
Period size: 262 Copynumber: 3.0 Consensus size: 262
43511326 ATAGGACCGG
*
43511336 TTGCTTATAGATTGGTTCGGCCACATGAACTCGCAAAGATTCATAATGTATTCCATGTATCGATG
1 TTGCTTATAGATTGGTTCTGCCACATGAACTCGCAAAGA-T--T--T-TATTCCATGTATCGATG
*
43511401 CTTAGACGGTATAGATCTGATCCTTCACATGTGGTTAGTCCATCTGAAATTGAGATTCAATCAGA
60 CTTAGACGGTATAGATCTGATCCTTCACATGTGGTTAGTCCATCTGAAATTGAGATTCAATCGGA
*
43511466 TTTGAGCTATGAAGAAGAACCAATCCGTATCTTAGCTCAGGAAGTGAAAGAAATGCGGAATAAGA
125 TTTGAGCTATGAAGAAGAACCGATCCGTATCTTAGCTCAGGAAGTGAAAGAAATGCGGAATAAGA
43511531 AGATTTCTTTAGTAAAAGTATTATGGGTCAAACATGGAGTAGAAGAGGCTACTTGGGAGCTAGAA
190 AGATTTCTTTAGTAAAAGTATTATGGGTCAAACATGGAGTAGAAGAGGCTACTTGGGAGCTAGAA
43511596 GACTCTTT
255 GACTCTTT
43511604 TTGCTTATAGATTGGTTCTGCCACATGAACTCGCAAAGATTTTATTCCATGTATCGATGCTTAGA
1 TTGCTTATAGATTGGTTCTGCCACATGAACTCGCAAAGATTTTATTCCATGTATCGATGCTTAGA
43511669 CGGTATAGATCTGATCCTTCACATGTGGTTAGTCCATCTGAAATTGAGATTCAATCGGATTTGAG
66 CGGTATAGATCTGATCCTTCACATGTGGTTAGTCCATCTGAAATTGAGATTCAATCGGATTTGAG
43511734 CTATGAAGAAGAACCGATCCGTATCTTAGCTCAGGAAGTGAAAGAAATGCGGAATAAGAAGATTT
131 CTATGAAGAAGAACCGATCCGTATCTTAGCTCAGGAAGTGAAAGAAATGCGGAATAAGAAGATTT
43511799 CTTTAGTAAAAGTATTATGGGTCAAACATGGAGTAGAAGAGGCTACTTGGGAGCTAGAAGACTCT
196 CTTTAGTAAAAGTATTATGGGTCAAACATGGAGTAGAAGAGGCTACTTGGGAGCTAGAAGACTCT
43511864 TT
261 TT
43511866 TTGCTTATAGATTGGTTCTGCCACATGAACTCGCAAAGATTTTATTCCATGTATCGATGCTTAGA
1 TTGCTTATAGATTGGTTCTGCCACATGAACTCGCAAAGATTTTATTCCATGTATCGATGCTTAGA
43511931 CGGTATAGATCTGATCCTTCACATGTGGTTAGTCCATCTGAAATTGAGATTCAATCGGATTTGAG
66 CGGTATAGATCTGATCCTTCACATGTGGTTAGTCCATCTGAAATTGAGATTCAATCGGATTTGAG
43511996 CTATGAAGAAGAACCGATCCGTATCTTAGCTCAGGAAGTGAAAGAAATGCGGAATAAGAAGATTT
131 CTATGAAGAAGAACCGATCCGTATCTTAGCTCAGGAAGTGAAAGAAATGCGGAATAAGAAGATTT
43512061 CTTTAGTAAAAGTATTATGGGTCAAACATGGAGTAGAAGAGGCTACTTGGGAGCTAGAAGAC
196 CTTTAGTAAAAGTATTATGGGTCAAACATGGAGTAGAAGAGGCTACTTGGGAGCTAGAAGAC
43512123 AAGAGTGTTA
Statistics
Matches: 516, Mismatches: 3, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
262 475 0.92
263 1 0.00
265 1 0.00
267 1 0.00
268 38 0.07
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (262 bp):
TTGCTTATAGATTGGTTCTGCCACATGAACTCGCAAAGATTTTATTCCATGTATCGATGCTTAGA
CGGTATAGATCTGATCCTTCACATGTGGTTAGTCCATCTGAAATTGAGATTCAATCGGATTTGAG
CTATGAAGAAGAACCGATCCGTATCTTAGCTCAGGAAGTGAAAGAAATGCGGAATAAGAAGATTT
CTTTAGTAAAAGTATTATGGGTCAAACATGGAGTAGAAGAGGCTACTTGGGAGCTAGAAGACTCT
TT
Found at i:43516249 original size:209 final size:209
Alignment explanation
Indices: 43515889--43516311 Score: 747
Period size: 209 Copynumber: 2.0 Consensus size: 209
43515879 CCTCTATCAG
* **
43515889 TCAATTCTTGCAACTGAGACTTTAATTCTTTCAGTTCGGTCGAAGCCATTCTATACAGAGCTATT
1 TCAATTCTTGCAACTGAGACTTTAATTCTATCAGTTCAATCGAAGCCATTCTATACAGAGCTATT
* *
43515954 GAAATCAGAGTAGTACCATGTACCAATTCAATGTCAAACTCTACTTCTCTAATCGGAGGTAAACC
66 GAAACCAGAGTAGTACCAGGTACCAATTCAATGTCAAACTCTACTTCTCTAATCGGAGGTAAACC
* *
43516019 CAGAAGTTCTTCAGGATATACATCAGGGAACTCACAGACAATAAGCACTGATTCAACTTTCTTTT
131 CAGAAGTTCTTCAGGATATACATCAGGGAACTCACACACAATAAGCACTAATTCAACTTTCTTTT
43516084 CTGACACTCTCGAA
196 CTGACACTCTCGAA
43516098 TCAATTCTTGCAACTGAGACTTTAATTCTATCAGTTCAATCGAAGCCATTCTATACAGAGCTATT
1 TCAATTCTTGCAACTGAGACTTTAATTCTATCAGTTCAATCGAAGCCATTCTATACAGAGCTATT
43516163 GAAACCAGAGTAGTACCAGGTACCAATTCAATGTCAAACTCTACTTCTCTAATCGGAGGTAAACC
66 GAAACCAGAGTAGTACCAGGTACCAATTCAATGTCAAACTCTACTTCTCTAATCGGAGGTAAACC
* * * *
43516228 CAGAAGTTCTTCAGGATATACATTAGGGAACTCACACACAATAGGGACTAATTCAATTTTCTTTT
131 CAGAAGTTCTTCAGGATATACATCAGGGAACTCACACACAATAAGCACTAATTCAACTTTCTTTT
43516293 CTGACACTCTCGAA
196 CTGACACTCTCGAA
43516307 TCAAT
1 TCAAT
43516312 CACATATGCA
Statistics
Matches: 203, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
209 203 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (209 bp):
TCAATTCTTGCAACTGAGACTTTAATTCTATCAGTTCAATCGAAGCCATTCTATACAGAGCTATT
GAAACCAGAGTAGTACCAGGTACCAATTCAATGTCAAACTCTACTTCTCTAATCGGAGGTAAACC
CAGAAGTTCTTCAGGATATACATCAGGGAACTCACACACAATAAGCACTAATTCAACTTTCTTTT
CTGACACTCTCGAA
Found at i:43522012 original size:47 final size:47
Alignment explanation
Indices: 43521941--43522117 Score: 157
Period size: 47 Copynumber: 3.8 Consensus size: 47
43521931 GGTAAGGTGC
* *
43521941 CGATGCCATGTCCTAGACACGGTCTTACACTAGCTCATATCTCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCAAGT
* * * * *
43521988 CGATGCCATGTCCCATACATGGTCTTAC-TTTGACT-ATTATCTCGTAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCA-TATCTC-AAGT
* * * *
43522036 CGATG-CATGTCCCAAACAT-GTCTTACACTAGC-CCTCGTCTCAATT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCAT-ATCTCAAGT
* *
43522081 CCAATGCCATGTCCTAGACATGGTCTTACACTAGCTC
1 -CGATGCCATGTCCCAGACATGGTCTTACACTAGCTC
43522118 TAACAAATGA
Statistics
Matches: 102, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
45 2 0.02
46 19 0.19
47 60 0.59
48 20 0.20
49 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.30
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCAAGT
Found at i:43525818 original size:25 final size:25
Alignment explanation
Indices: 43525765--43525880 Score: 108
Period size: 25 Copynumber: 4.6 Consensus size: 25
43525755 ATTCATGAAT
* * ** *
43525765 GCTCATACGAGCTATGAATTGATAT
1 GCTCATACGAGCTGTGAATCGGGAA
*
43525790 GCTC-TCACGAGCTGTGAATCGGTAA
1 GCTCAT-ACGAGCTGTGAATCGGGAA
* **
43525815 GCTCATAAGAGCTGCAAATCGGGAA
1 GCTCATACGAGCTGTGAATCGGGAA
* *
43525840 GCTCATACGACCTGTCAATCGGGAA
1 GCTCATACGAGCTGTGAATCGGGAA
*
43525865 GCTTATACGAGCTGTG
1 GCTCATACGAGCTGTG
43525881 GTGTGTCTGC
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
24 1 0.01
25 72 0.97
26 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTGTGAATCGGGAA
Done.