Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 14 of 259
Found at i:3957977 original size:40 final size:40
Alignment explanation
Indices: 3957879--3958141 Score: 318
Period size: 40 Copynumber: 6.6 Consensus size: 40
3957869 TCCTCGTTCA
* * * * *
3957879 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
3957918 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
3957958 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
3957998 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
3958038 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
3958077 ACAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 A-ATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
3958118 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3958142 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
39 38 0.19
40 153 0.76
41 9 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:3965296 original size:28 final size:28
Alignment explanation
Indices: 3965253--3965308 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3965243 GAAGAAGAAG
3965253 CTAAAATAGTGCTTTAAATTTTGGCACT
1 CTAAAATAGTGCTTTAAATTTTGGCACT
*
3965281 CTAAAATAGTGTTTTAAATTTTGGCACT
1 CTAAAATAGTGCTTTAAATTTTGGCACT
3965309 TCTCTAGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (28 bp):
CTAAAATAGTGCTTTAAATTTTGGCACT
Found at i:3965692 original size:43 final size:43
Alignment explanation
Indices: 3965599--3965722 Score: 119
Period size: 43 Copynumber: 2.9 Consensus size: 43
3965589 CGAGATGTGA
* * **
3965599 TTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTGC
1 TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATAATGC
*
3965642 TTACGTGTAAGACCATGTCTGGGATATTGGCATCGT-TAAT-C
1 TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATAATGC
* * * * *
3965683 AATTTCGTGTAAGACCCTATCTAGGACAGTGGCATC-TATA
1 --TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
3965723 TGTAATAACA
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 3 0.04
43 63 0.94
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATAATGC
Found at i:3972482 original size:21 final size:21
Alignment explanation
Indices: 3972448--3972490 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3972438 AGCTTGATTG
3972448 AGATTAAGAACGAAAGAAATC
1 AGATTAAGAACGAAAGAAATC
* * *
3972469 AGATTTAGATCGAAGGAAATC
1 AGATTAAGAACGAAAGAAATC
3972490 A
1 A
3972491 AAAGTTATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (21 bp):
AGATTAAGAACGAAAGAAATC
Found at i:3972768 original size:43 final size:42
Alignment explanation
Indices: 3972721--3972844 Score: 140
Period size: 43 Copynumber: 2.9 Consensus size: 42
3972711 TACCGAGATG
* * * *
3972721 TGATTACATGTAAGACCATGTCTAGGACATTGTCATTGTATTA
1 TGATTACGTGTAAGACCATGTCTAGGACATTGGCATCGT-TAA
* *
3972764 TGATTACGTGTAAGACCATGTCTGGGATATTGGCATCGTTAA
1 TGATTACGTGTAAGACCATGTCTAGGACATTGGCATCGTTAA
* * * *
3972806 TCAATTTCGTGTAAGACCTTGTCTAGGACAGTGGCATCG
1 T-GATTACGTGTAAGACCATGTCTAGGACATTGGCATCG
3972845 ATATGTAATA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 3 0.04
43 65 0.96
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (42 bp):
TGATTACGTGTAAGACCATGTCTAGGACATTGGCATCGTTAA
Found at i:3977733 original size:13 final size:13
Alignment explanation
Indices: 3977715--3977740 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3977705 ATGAAGGAGA
3977715 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
3977728 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
3977741 GGGGAAAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:3983989 original size:16 final size:16
Alignment explanation
Indices: 3983968--3984005 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3983958 TTGAAAGTGT
3983968 CTGATGGTTACATAGA
1 CTGATGGTTACATAGA
3983984 CTGATGGTTACATAGA
1 CTGATGGTTACATAGA
3984000 CT-ATGG
1 CTGATGG
3984006 AATGAGCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (16 bp):
CTGATGGTTACATAGA
Found at i:3990562 original size:55 final size:55
Alignment explanation
Indices: 3990503--3990685 Score: 143
Period size: 55 Copynumber: 3.1 Consensus size: 55
3990493 ATATAGACAT
3990503 TAAATATAATAACAATATATAGATGTTAGTTTATAGTAATTTACAAATTTAATAA
1 TAAATATAATAACAATATATAGATGTTAGTTTATAGTAATTTACAAATTTAATAA
* * * * * * * * *
3990558 TAAATAATGAAATAATATATAATAAAAGAAGGATAATATAGGGAATAATATATA-ATAATATAGA
1 TAAAT-AT--AATAACA-AT-AT-ATAG-ATGTTAGTTTA--TAGTAAT-T-TACA-AATTTA-A
* *
3990622 CAT
53 TAA
3990625 TAAATATAATAACAATATATAGATGTTAGTTTATAGTAATTTACAAATTTAATAA
1 TAAATATAATAACAATATATAGATGTTAGTTTATAGTAATTTACAAATTTAATAA
3990680 TAAATA
1 TAAATA
3990686 ATGAAATAAT
Statistics
Matches: 92, Mismatches: 22, Indels: 28
0.65 0.15 0.20
Matches are distributed among these distances:
55 13 0.14
56 9 0.10
57 2 0.02
58 11 0.12
59 2 0.02
60 9 0.10
61 6 0.07
62 9 0.10
63 2 0.02
64 11 0.12
65 2 0.02
66 9 0.10
67 7 0.08
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.36
Consensus pattern (55 bp):
TAAATATAATAACAATATATAGATGTTAGTTTATAGTAATTTACAAATTTAATAA
Found at i:3990620 original size:122 final size:122
Alignment explanation
Indices: 3990492--3990741 Score: 491
Period size: 122 Copynumber: 2.0 Consensus size: 122
3990482 ATAAATTTTG
3990492 AATATAGACATTAAATATAATAACAATATATAGATGTTAGTTTATAGTAATTTACAAATTTAATA
1 AATATAGACATTAAATATAATAACAATATATAGATGTTAGTTTATAGTAATTTACAAATTTAATA
*
3990557 ATAAATAATGAAATAATATATAATAAAAGAAGGATAATATAGGGAATAATATATAAT
66 ATAAATAATGAAATAATATATAATAAAAGAAAGATAATATAGGGAATAATATATAAT
3990614 AATATAGACATTAAATATAATAACAATATATAGATGTTAGTTTATAGTAATTTACAAATTTAATA
1 AATATAGACATTAAATATAATAACAATATATAGATGTTAGTTTATAGTAATTTACAAATTTAATA
3990679 ATAAATAATGAAATAATATATAATAAAAGAAAGATAATATAGGGAATAATATATAAT
66 ATAAATAATGAAATAATATATAATAAAAGAAAGATAATATAGGGAATAATATATAAT
3990736 AATATA
1 AATATA
3990742 TGATATGTAA
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 127 1.00
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (122 bp):
AATATAGACATTAAATATAATAACAATATATAGATGTTAGTTTATAGTAATTTACAAATTTAATA
ATAAATAATGAAATAATATATAATAAAAGAAAGATAATATAGGGAATAATATATAAT
Found at i:3990752 original size:17 final size:16
Alignment explanation
Indices: 3990723--3990777 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
3990713 TAATATAGGG
3990723 AATA-ATATATAATAA
1 AATATATATATAATAA
* *
3990738 TATATGATATGTAATAA
1 AATAT-ATATATAATAA
3990755 AATATATATATAAATAA
1 AATATATATAT-AATAA
3990772 AATATA
1 AATATA
3990778 ATGAAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.09
16 5 0.15
17 25 0.76
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (16 bp):
AATATATATATAATAA
Found at i:3990961 original size:18 final size:19
Alignment explanation
Indices: 3990928--3990965 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3990918 AAGGAATAAT
*
3990928 ATATATAGTAAAATTTATA
1 ATATATACTAAAATTTATA
3990947 ATATATACT-AAATTTATA
1 ATATATACTAAAATTTATA
3990965 A
1 A
3990966 ATAAAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
ATATATACTAAAATTTATA
Found at i:3990968 original size:19 final size:20
Alignment explanation
Indices: 3990923--3990968 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
3990913 AACACAAGGA
*
3990923 ATAATATATATAGTAAAATTT
1 ATAA-ATATATACTAAAATTT
3990944 AT-AATATATACT-AAATTT
1 ATAAATATATACTAAAATTT
3990962 ATAAATA
1 ATAAATA
3990969 AAATGTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 8 0.35
19 12 0.52
20 1 0.04
21 2 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
ATAAATATATACTAAAATTT
Found at i:4000647 original size:14 final size:15
Alignment explanation
Indices: 4000630--4000667 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
4000620 GCTTAGATAT
4000630 GATATG-CAATCTTA
1 GATATGACAATCTTA
4000644 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
4000661 GATATGA
1 GATATGA
4000668 TTGCAATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
17 14 0.67
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:4000706 original size:17 final size:19
Alignment explanation
Indices: 4000609--4000699 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
4000599 ATAATCTTCA
*
4000609 ATGATATGCAAGCTTAGAT
1 ATGATATGCAATCTTAGAT
4000628 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
4000647 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
4000664 ATGAT-TGCAATCTTATAT
1 ATGATATGCAATCTTAGAT
4000682 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
4000700 AGATATGATT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.24
18 15 0.23
19 35 0.53
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:4001010 original size:17 final size:18
Alignment explanation
Indices: 4000988--4001023 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
4000978 ATGTTTCCCG
*
4000988 AATTTTTTA-TATATTTT
1 AATTTTTTACTAAATTTT
4001005 AATTTTTTACTAAATTTT
1 AATTTTTTACTAAATTTT
4001023 A
1 A
4001024 GTATCATATC
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:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
AATTTTTTACTAAATTTT
Found at i:4009603 original size:44 final size:44
Alignment explanation
Indices: 4009467--4009742 Score: 306
Period size: 44 Copynumber: 6.3 Consensus size: 44
4009457 GATCCAAGAT
** * *
4009467 GATTTGGCATCTCTGTATTGTCAGAGAATAAATCAAAGA-AACA
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
* * * * *
4009510 GATTTGACATTTCTGTATTAGACAGGGAGCAGATCGAAGATAGCA
1 GATTTGGCATCTCTGTATT-GTCAGAGAGCAGATCAAAGATAGCA
* * * *
4009555 GATTTGGCGTCTCTGTATTGTTAGAGAGCTGATCGAAGATAGTC-
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAG-CA
*
4009599 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGTA
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
**
4009643 GATTTGGTGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
* * * * * *
4009687 AATTTGGCATCTCTGTACTGTCAGAGAACAAATCGAAGA-AACA
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
*
4009730 GATTTAGCATCTC
1 GATTTGGCATCTC
4009743 CATATTCGAC
Statistics
Matches: 195, Mismatches: 34, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
43 31 0.16
44 144 0.74
45 20 0.10
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (44 bp):
GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA
Found at i:4009758 original size:88 final size:88
Alignment explanation
Indices: 4009577--4009769 Score: 210
Period size: 88 Copynumber: 2.2 Consensus size: 88
4009567 CTGTATTGTT
* * * * **
4009577 AGAGAGCTGATCGAAGATAGTCGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGT
1 AGAGAGCTGATCGAAGATAGTCAATTTGGCATCTCTGTACTGTCAGAGAACAAATCAAAGATAAC
* ** ** *
4009642 AGATTTGGTGTCTCTGTATTGTC
66 AGATTTAGCATCTCCATATTGAC
* * *
4009665 AGAGAGCAGATCAAAGATAG-CAAATTTGGCATCTCTGTACTGTCAGAGAACAAATCGAAGA-AA
1 AGAGAGCTGATCGAAGATAGTC-AATTTGGCATCTCTGTACTGTCAGAGAACAAATCAAAGATAA
4009728 CAGATTTAGCATCTCCATATTCGAC
65 CAGATTTAGCATCTCCATATT-GAC
*
4009753 GGAGAGCTGATCGAAGA
1 AGAGAGCTGATCGAAGA
4009770 CATAGCAGAT
Statistics
Matches: 85, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
87 17 0.20
88 68 0.80
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (88 bp):
AGAGAGCTGATCGAAGATAGTCAATTTGGCATCTCTGTACTGTCAGAGAACAAATCAAAGATAAC
AGATTTAGCATCTCCATATTGAC
Found at i:4009758 original size:132 final size:133
Alignment explanation
Indices: 4009521--4009769 Score: 297
Period size: 132 Copynumber: 1.9 Consensus size: 133
4009511 ATTTGACATT
* * * * * * * **
4009521 TCTGTATTAGACAGGGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTTAGAGAGCTG
1 TCTGTATTAGACAGAGAGCAGATCAAAGATAGCAAATTTGGCATCTCTGTACTGTCAGAGAACAA
* * ** *
4009586 ATCGAAGATAGTCGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCAAAGATAGTAGATTTGGT
66 ATCGAAGATAGACGATTTAGCATCTCCATATTGACAGAGAGCAGATCAAAGATAGTAGATTTGGT
4009651 GTC
131 GTC
*
4009654 TCTGTATT-GTCAGAGAGCAGATCAAAGATAGCAAATTTGGCATCTCTGTACTGTCAGAGAACAA
1 TCTGTATTAGACAGAGAGCAGATCAAAGATAGCAAATTTGGCATCTCTGTACTGTCAGAGAACAA
* * *
4009718 ATCGAAGA-A-ACAGATTTAGCATCTCCATATTCGACGGAGAGCTGATCGAAGA
66 ATCGAAGATAGAC-GATTTAGCATCTCCATATT-GACAGAGAGCAGATCAAAGA
4009770 CATAGCAGAT
Statistics
Matches: 96, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
130 1 0.01
131 17 0.18
132 70 0.73
133 8 0.08
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (133 bp):
TCTGTATTAGACAGAGAGCAGATCAAAGATAGCAAATTTGGCATCTCTGTACTGTCAGAGAACAA
ATCGAAGATAGACGATTTAGCATCTCCATATTGACAGAGAGCAGATCAAAGATAGTAGATTTGGT
GTC
Found at i:4009865 original size:78 final size:78
Alignment explanation
Indices: 4009731--4010022 Score: 419
Period size: 78 Copynumber: 3.8 Consensus size: 78
4009721 GAAGAAACAG
* * * * *
4009731 ATTTAGCATCTCCATATTCGACGGAGAGCTGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
1 ATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
4009796 CAGATCCAAGATA
66 CAGATCCAAGATA
* * *
4009809 ATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACACAGCAGATTTAACCTTCATTGAAG
1 ATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
*
4009874 CAGATCCAAGATG
66 CAGATCCAAGATA
* * * *
4009887 ATTTGGCAT-TCTGTATTAGACGGGGGGCAGATCAAAGACATAACAGAT-TGGA-CTTCATTGAA
1 ATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGAA
4009949 GCAGATCCAAGATA
65 GCAGATCCAAGATA
* *
4009963 ATTTGGCATCTCTGTATTAGATGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
1 ATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
4010023 GTGTTTACAT
Statistics
Matches: 190, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
76 33 0.17
77 72 0.38
78 85 0.45
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (78 bp):
ATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
CAGATCCAAGATA
Found at i:4009977 original size:77 final size:77
Alignment explanation
Indices: 4009731--4010091 Score: 411
Period size: 78 Copynumber: 4.5 Consensus size: 77
4009721 GAAGAAACAG
* ** * * *
4009731 ATTTAGCATCTCCATATTCGACGGAGAGCTGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGAT-TGACCTTCATTGAAG
4009796 CAGATCCAAGATA
65 CAGATCCAAGATA
* * *
4009809 ATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACACAGCAGATTTAACCTTCATTGAAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGA-TTGACCTTCATTGAAG
*
4009874 CAGATCCAAGATG
65 CAGATCCAAGATA
* * *
4009887 ATTTGGCAT-TCTGTATTAGACGGGGGGCAGATCAAAGACATAACAGATTGGA-CTTCATTGAAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATT-GACCTTCATTGAAG
4009950 CAGATCCAAGATA
65 CAGATCCAAGATA
*
4009963 ATTTGGCATCTCTGTATTAGATGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATGTGTT
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGAT-TGACCTTCA------
*
4010028 TACATCGAAGTAGATCCAAGATGACA
59 T---T-GAAGCAGATCCAAGAT---A
4010054 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAA
1 -ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAA
4010092 TATAACAGAT
Statistics
Matches: 243, Mismatches: 21, Indels: 24
0.84 0.07 0.08
Matches are distributed among these distances:
76 34 0.14
77 71 0.29
78 83 0.34
79 1 0.00
84 1 0.00
87 1 0.00
88 15 0.06
91 1 0.00
92 36 0.15
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25
Consensus pattern (77 bp):
ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATTGACCTTCATTGAAGC
AGATCCAAGATA
Found at i:4010088 original size:45 final size:45
Alignment explanation
Indices: 4010039--4010146 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
4010029 ACATCGAAGT
* * *
4010039 AGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGC
1 AGATCAAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGA
* * * *
4010084 AGATCGAATATAACAGATTTGGCGTCTCTGTATTAGATGGGGAGA
1 AGATCAAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGA
*
4010129 AGATCAAAGATAGCAGAT
1 AGATCAAAGATAACAGAT
4010147 ATCATCTTCC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (45 bp):
AGATCAAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGA
Found at i:4010565 original size:18 final size:18
Alignment explanation
Indices: 4010498--4010641 Score: 229
Period size: 18 Copynumber: 7.9 Consensus size: 18
4010488 ATAATCTTCA
4010498 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
4010517 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
4010536 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
4010553 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
4010571 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
4010589 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
4010606 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
4010624 ATGATATGCAATCTTAGA
1 ATGAT-TGCAATCTTAGA
4010642 AGATATGATT
Statistics
Matches: 118, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
17 32 0.27
18 51 0.43
19 35 0.30
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:4010569 original size:35 final size:37
Alignment explanation
Indices: 4010498--4010641 Score: 242
Period size: 35 Copynumber: 4.0 Consensus size: 37
4010488 ATAATCTTCA
4010498 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGAT
*
4010536 ATGA-TACAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATATGCAATCTTAGAT
4010571 ATGATTGCAATCTTAGATATGATA--CAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATATGCAATCTTAGAT
4010606 ATGATTGCAATCTTAGATATGATATGCAATCTTAGA
1 ATGATTGCAATCTTAGATATGATATGCAATCTTAGA
4010642 AGATATGATT
Statistics
Matches: 100, Mismatches: 2, Indels: 9
0.90 0.02 0.08
Matches are distributed among these distances:
35 52 0.52
36 34 0.34
37 10 0.10
38 4 0.04
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (37 bp):
ATGATTGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:4010585 original size:53 final size:54
Alignment explanation
Indices: 4010498--4010641 Score: 272
Period size: 53 Copynumber: 2.7 Consensus size: 54
4010488 ATAATCTTCA
4010498 ATGATATGCAATCTTAGATATGATATGCAATCTTAGATATGATACAATCTTAGAT
1 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGATATGATACAATCTTAGAT
4010553 ATGATTGCAATCTTAGATATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATATGCAATCTTAGATATGATACAATCTTAGAT
4010606 ATGATTGCAATCTTAGATATGATATGCAATCTTAGA
1 ATGATTGCAATCTTAGATATGATATGCAATCTTAGA
4010642 AGATATGATT
Statistics
Matches: 88, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
53 53 0.60
54 30 0.34
55 5 0.06
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (54 bp):
ATGATTGCAATCTTAGATATGATATGCAATCTTAGATATGATACAATCTTAGAT
Found at i:4010667 original size:22 final size:22
Alignment explanation
Indices: 4010498--4010664 Score: 111
Period size: 18 Copynumber: 8.8 Consensus size: 22
4010488 ATAATCTTCA
4010498 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
4010517 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
4010536 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
4010553 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
4010571 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
4010589 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
4010606 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
4010624 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
4010646 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
4010665 GATTTAATTT
Statistics
Matches: 136, Mismatches: 2, Indels: 16
0.88 0.01 0.10
Matches are distributed among these distances:
17 32 0.24
18 50 0.37
19 34 0.25
22 8 0.06
23 12 0.09
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:4018988 original size:25 final size:26
Alignment explanation
Indices: 4018951--4019002 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
4018941 TCAAACATGC
4018951 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAA-TTAACTCCTAGGGGT
* *
4018977 ATTTCGGT-AATTATCTCCTAGGGGT
1 ATTTAGGTCAATTAACTCCTAGGGGT
4019002 A
1 A
4019003 AAACTATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 4 0.17
25 12 0.52
26 7 0.30
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (26 bp):
ATTTAGGTCAATTAACTCCTAGGGGT
Found at i:4020522 original size:32 final size:32
Alignment explanation
Indices: 4020481--4020545 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
4020471 AATTCTTACC
*
4020481 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAAAGCTA
4020513 ATGCCCATCATCCATTAACTATTAAAAAGCTA
1 ATGCCCATCATCCATTAACTATTAAAAAGCTA
4020545 A
1 A
4020546 AATGCATACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.40, C:0.25, G:0.06, T:0.29
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAAAGCTA
Found at i:4023657 original size:15 final size:15
Alignment explanation
Indices: 4023637--4023668 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4023627 TATTGTGTAG
*
4023637 ATGTATTTTTTTCAC
1 ATGTATTTCTTTCAC
4023652 ATGTATTTCTTTCAC
1 ATGTATTTCTTTCAC
4023667 AT
1 AT
4023669 TTGCACCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (15 bp):
ATGTATTTCTTTCAC
Found at i:4024614 original size:5 final size:5
Alignment explanation
Indices: 4024604--4024645 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
4024594 TTGTGTGTTC
* *
4024604 TTTAT TTTA- TTTAT TTTAT TATAT TTTAT TATAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
4024646 TCACAAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:4024630 original size:10 final size:10
Alignment explanation
Indices: 4024606--4024643 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
4024596 GTGTGTTCTT
4024606 TATTTTATT-
1 TATTTTATTA
4024615 TATTTTATTA
1 TATTTTATTA
4024625 TATTTTATTA
1 TATTTTATTA
4024635 TATTTTATT
1 TATTTTATT
4024644 TTTCACAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TATTTTATTA
Found at i:4035930 original size:17 final size:17
Alignment explanation
Indices: 4035908--4036112 Score: 77
Period size: 17 Copynumber: 11.8 Consensus size: 17
4035898 TAAAATGATA
*
4035908 TATATATTATTTTTATT
1 TATATATTATTATTATT
*
4035925 TATATATTATCCATTATTT
1 TATATATTAT-TATTA-TT
4035944 TATATCTATTATTATTTATT
1 TATA--TATTATTA-TTATT
* * *
4035964 TTTAAATTA-TATGTAAT
1 TATATATTATTAT-TATT
* *
4035981 TAAATTTTATTA-TATT
1 TATATATTATTATTATT
4035997 ATATGATATTA-TATTATT
1 -TAT-ATATTATTATTATT
4036015 CTATATAGTATATGTATTA-T
1 -TATATA-T-TAT-TATTATT
*
4036035 TA-ATATT-TTATTAAT
1 TATATATTATTATTATT
* * * *
4036050 TAAATATT-TTCTAATG
1 TATATATTATTATTATT
*
4036066 TATGTATGTATTATTATT
1 TATATAT-TATTATTATT
* * *
4036084 T-TTTGTTATTAATA-T
1 TATATATTATTATTATT
4036099 TATTATATTATTAT
1 TA-TATATTATTAT
4036113 ATGCTTCCTA
Statistics
Matches: 139, Mismatches: 29, Indels: 40
0.67 0.14 0.19
Matches are distributed among these distances:
14 5 0.04
15 6 0.04
16 26 0.19
17 40 0.29
18 31 0.22
19 10 0.07
20 7 0.05
21 14 0.10
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
TATATATTATTATTATT
Found at i:4035942 original size:24 final size:24
Alignment explanation
Indices: 4035913--4035958 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4035903 TGATATATAT
*
4035913 ATTATTTT-TATTTATATATTATCC
1 ATTATTTTATATCTAT-TATTATCC
4035937 ATTATTTTATATCTATTATTAT
1 ATTATTTTATATCTATTATTAT
4035959 TTATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTATTTTATATCTATTATTATCC
Found at i:4035996 original size:5 final size:5
Alignment explanation
Indices: 4035905--4036013 Score: 57
Period size: 5 Copynumber: 21.4 Consensus size: 5
4035895 GTATAAAATG
* *
4035905 ATATAT ATATT AT-TT TTATT -TA-T ATATT ATCCATT ATTTT ATATCT
1 ATAT-T ATATT ATATT ATATT ATATT ATATT AT--ATT ATATT ATAT-T
* * * *
4035951 ATTATT AT-TT ATTTTT AAATT ATATGT A-ATT AAATT TTATT ATATT
1 A-TATT ATATT A-TATT ATATT ATAT-T ATATT ATATT ATATT ATATT
*
4035997 ATATG ATATT ATATT AT
1 ATATT ATATT ATATT AT
4036014 TCTATATAGT
Statistics
Matches: 81, Mismatches: 11, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
3 1 0.01
4 12 0.15
5 47 0.58
6 13 0.16
7 8 0.10
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:4060135 original size:40 final size:40
Alignment explanation
Indices: 4059964--4060174 Score: 221
Period size: 40 Copynumber: 5.3 Consensus size: 40
4059954 TCTTCGGAAT
* * * *
4059964 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* * * * * *
4060003 TTAACTCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
* * **
4060043 TTAGCCTGGAT-ATATCAACCCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
*
4060083 TTAGCCCGGATAAAATCACTAGCACAAACGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* * *
4060123 TTAACCCGGATAAAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
4060163 TTAGCCCGGATA
1 TTAGCCCGGATA
4060175 TCATTCAAAT
Statistics
Matches: 144, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 5 0.03
40 135 0.94
41 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
Found at i:4098032 original size:96 final size:96
Alignment explanation
Indices: 4097866--4098151 Score: 482
Period size: 96 Copynumber: 3.0 Consensus size: 96
4097856 GTGTCCGAGG
* * * * *
4097866 AAGTCTGTTATCGATGGGAATGATCGAGCAGACACGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
*
4097931 AAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
66 TAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
4097962 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
*
4098027 TAAAGCCGAAGCTAAGAGGGCAAAGAGGAGC
66 TAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
* *
4098058 AAGTCTATCATCGCAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
*
4098123 TAAAGCCGAAGCCAAGAGGGCTAAGAGGA
66 TAAAGCCGAAGCCAAGAGGGCAAAGAGGA
4098152 ATAAAAAGAA
Statistics
Matches: 179, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 179 1.00
ACGTcount: A:0.35, C:0.19, G:0.35, T:0.12
Consensus pattern (96 bp):
AAGTCTGTCATCGAAGGGAACGATGGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
TAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
Found at i:4099854 original size:56 final size:55
Alignment explanation
Indices: 4099792--4099902 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 55
4099782 AATAAAATAC
4099792 AATCTAACTCTTAGTACAAAGGTCTTCATGATATTTTTACTACTTTTTTTATGTAT
1 AATCTAACTCTTAGTACAAAGGTCTTCATGATATTTTTACTA-TTTTTTTATGTAT
4099848 AATCTAACTCTTAGTACAAAGGTCTTCATGATATTTTTACTATTTTTTTATGTAT
1 AATCTAACTCTTAGTACAAAGGTCTTCATGATATTTTTACTATTTTTTTATGTAT
4099903 TCAAAACGGT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 13 0.24
56 42 0.76
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.49
Consensus pattern (55 bp):
AATCTAACTCTTAGTACAAAGGTCTTCATGATATTTTTACTATTTTTTTATGTAT
Found at i:4103004 original size:28 final size:29
Alignment explanation
Indices: 4102973--4103028 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
4102963 TTAGTCATAA
*
4102973 TTTTTAAAAAAAATTAACCCTTAACTTAT
1 TTTTTAAAAAAAATTAACCCTCAACTTAT
* * *
4103002 TTTTTTAACAAATTTAACCCTCAACTT
1 TTTTTAAAAAAAATTAACCCTCAACTT
4103029 TTATATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (29 bp):
TTTTTAAAAAAAATTAACCCTCAACTTAT
Found at i:4103181 original size:118 final size:122
Alignment explanation
Indices: 4103013--4103265 Score: 302
Period size: 130 Copynumber: 2.0 Consensus size: 122
4103003 TTTTTAACAA
* * *
4103013 ATTTAACCCTCAACTTTTATATAAATATATTTTTTTTAATTTTTAATTT-A-ATT-TT-TA-AAA
1 ATTTGACCCTCAACTTTTACATAAATATATTTTTTTTAATTATT-ATTTAATATTCTTGTATAAA
4103073 TATTTATGTATTATATATATTTCTTTGAATCTTTTAGAATTAGAATCAAATTGAGAAC
65 TATTTATGTATTATATATATTTCTTTGAATCTTTTAGAATTAGAATCAAATTGAGAAC
* * *
4103131 ATTTGACCCTCAACTTTTACATATATATTTTTTATTTTTATATATT-TTTAAATTTATTCTTGTA
1 ATTTGACCCTCAACTTTTACATAAATATATTTT-TTTTAAT-TATTATTT-AA--TATTCTTGTA
* *
4103195 TTTTTAAATATTTATGTATTTTATATATTTCTTTGAATCTTTTAGCATTAGAATCAAATTGAGAA
61 ----TAAATATTTATGTATTATATATATTTCTTTGAATCTTTTAGAATTAGAATCAAATTGAGAA
4103260 C
122 C
4103261 ATTTG
1 ATTTG
4103266 TGAATTTTGA
Statistics
Matches: 113, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
118 32 0.28
119 6 0.05
120 4 0.04
123 3 0.03
124 2 0.02
125 2 0.02
130 64 0.57
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (122 bp):
ATTTGACCCTCAACTTTTACATAAATATATTTTTTTTAATTATTATTTAATATTCTTGTATAAAT
ATTTATGTATTATATATATTTCTTTGAATCTTTTAGAATTAGAATCAAATTGAGAAC
Found at i:4103185 original size:18 final size:18
Alignment explanation
Indices: 4103152--4103216 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 18
4103142 AACTTTTACA
*
4103152 TATATATTTTT-TATTTT
1 TATATATTTTTAAATTTT
4103169 TATATATTTTTAAATTTAT
1 TATATATTTTTAAATTT-T
* * *
4103188 TCTTGTATTTTTAAATATT
1 T-ATATATTTTTAAATTTT
*
4103207 TATGTATTTT
1 TATATATTTT
4103217 ATATATTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 11 0.28
18 12 0.30
19 4 0.10
20 13 0.32
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.68
Consensus pattern (18 bp):
TATATATTTTTAAATTTT
Found at i:4106262 original size:20 final size:17
Alignment explanation
Indices: 4106246--4106280 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4106236 ATAAAATATG
4106246 TATAATAAAATTAAAATA
1 TATAA-AAAATTAAAATA
*
4106264 TATAAAATATTAAAATA
1 TATAAAAAATTAAAATA
4106281 AAACTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TATAAAAAATTAAAATA
Found at i:4109656 original size:33 final size:33
Alignment explanation
Indices: 4109611--4109733 Score: 112
Period size: 33 Copynumber: 3.8 Consensus size: 33
4109601 GTGAATAGCA
* *
4109611 CAGTATCAGTACAATCTGGGCCAAAGCCTTATT
1 CAGTAACAGTACAATCTGGGCCTAAGCCTTATT
* * * * *
4109644 CAGTAACGGTACAGTCTGGGCTTTAGCC--CTT
1 CAGTAACAGTACAATCTGGGCCTAAGCCTTATT
*
4109675 -A--AACAGTAGCAATATGGGCCTAAGCCTTATT
1 CAGTAACAGTA-CAATCTGGGCCTAAGCCTTATT
* *
4109706 CAGTAACAGTACAGTCTGGGCCTTAGCC
1 CAGTAACAGTACAATCTGGGCCTAAGCC
4109734 CTTAAACAGT
Statistics
Matches: 68, Mismatches: 16, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
28 6 0.09
29 13 0.19
30 1 0.01
31 4 0.06
32 1 0.01
33 36 0.53
34 7 0.10
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (33 bp):
CAGTAACAGTACAATCTGGGCCTAAGCCTTATT
Found at i:4109682 original size:34 final size:33
Alignment explanation
Indices: 4109644--4109744 Score: 95
Period size: 34 Copynumber: 3.2 Consensus size: 33
4109634 AAGCCTTATT
*
4109644 CAGTAACGGTACAGTCTGGGCTTTAGCCCTTAAA
1 CAGTAAC-GTACAGTCTGGGCCTTAGCCCTTAAA
* * * **
4109678 CAGT-A-G--CAATATGGGCCTAAG-CCTTATT
1 CAGTAACGTACAGTCTGGGCCTTAGCCCTTAAA
4109706 CAGTAACAGTACAGTCTGGGCCTTAGCCCTTAAA
1 CAGTAAC-GTACAGTCTGGGCCTTAGCCCTTAAA
4109740 CAGTA
1 CAGTA
4109745 GCAATATGGG
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
28 9 0.18
29 12 0.24
31 2 0.04
33 13 0.26
34 14 0.28
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.26
Consensus pattern (33 bp):
CAGTAACGTACAGTCTGGGCCTTAGCCCTTAAA
Found at i:4109724 original size:62 final size:62
Alignment explanation
Indices: 4109617--4109762 Score: 240
Period size: 62 Copynumber: 2.4 Consensus size: 62
4109607 AGCACAGTAT
* * * *
4109617 CAGTA-CAATCTGGGCCAAAGCCTTATTCAGTAACGGTACAGTCTGGGCTTTAGCCCTTAAA
1 CAGTAGCAATATGGGCCTAAGCCTTATTCAGTAACAGTACAGTCTGGGCCTTAGCCCTTAAA
4109678 CAGTAGCAATATGGGCCTAAGCCTTATTCAGTAACAGTACAGTCTGGGCCTTAGCCCTTAAA
1 CAGTAGCAATATGGGCCTAAGCCTTATTCAGTAACAGTACAGTCTGGGCCTTAGCCCTTAAA
*
4109740 CAGTAGCAATATGGGCTTAAGCC
1 CAGTAGCAATATGGGCCTAAGCC
4109763 CAAATTCAGT
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
61 5 0.06
62 74 0.94
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (62 bp):
CAGTAGCAATATGGGCCTAAGCCTTATTCAGTAACAGTACAGTCTGGGCCTTAGCCCTTAAA
Found at i:4109743 original size:28 final size:28
Alignment explanation
Indices: 4109652--4109744 Score: 87
Period size: 33 Copynumber: 3.1 Consensus size: 28
4109642 TTCAGTAACG
*
4109652 GTACAGTCTGGGCTTTAGCCCTTAAACA
1 GTACAGTCTGGGCCTTAGCCCTTAAACA
* * * *
4109680 GTAGCAATATGGGCCTAAGCCTTATTCAGTAACA
1 GTA-CAGTCTGGGCCTTAGCC--CTT-A--AACA
4109714 GTACAGTCTGGGCCTTAGCCCTTAAACA
1 GTACAGTCTGGGCCTTAGCCCTTAAACA
4109742 GTA
1 GTA
4109745 GCAATATGGG
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 10 0.20
29 13 0.26
30 1 0.02
31 4 0.08
32 1 0.02
33 14 0.28
34 7 0.14
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.27
Consensus pattern (28 bp):
GTACAGTCTGGGCCTTAGCCCTTAAACA
Found at i:4109758 original size:28 final size:29
Alignment explanation
Indices: 4109660--4109763 Score: 95
Period size: 29 Copynumber: 3.4 Consensus size: 29
4109650 CGGTACAGTC
*
4109660 TGGGCTTTAGCCCTTAAACAGTAGCAATA
1 TGGGCCTTAGCCCTTAAACAGTAGCAATA
* * * *
4109689 TGGGCCTAAGCCTTATTCAGTAACAGTA-CAGTC
1 TGGGCCTTAGCC--CTT-A--AACAGTAGCAATA
4109722 TGGGCCTTAGCCCTTAAACAGTAGCAATA
1 TGGGCCTTAGCCCTTAAACAGTAGCAATA
4109751 TGGG-CTTAAGCCC
1 TGGGCCTT-AGCCC
4109764 AAATTCAGTC
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
28 10 0.17
29 22 0.37
30 1 0.02
31 4 0.07
32 1 0.02
33 14 0.24
34 7 0.12
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (29 bp):
TGGGCCTTAGCCCTTAAACAGTAGCAATA
Found at i:4110088 original size:25 final size:25
Alignment explanation
Indices: 4110051--4110120 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
4110041 CTCTTTTAAT
*
4110051 AACTAGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTTGATA
* *
4110076 AACTGGGGTAAAGCCCTTTTTGGTA
1 AACTGGGGCAAAGCCCTTTTTGATA
*
4110101 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
4110121 AGCACTTCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTTGATA
Found at i:4111083 original size:27 final size:27
Alignment explanation
Indices: 4111053--4111159 Score: 92
Period size: 27 Copynumber: 3.9 Consensus size: 27
4111043 GTAAATCTAC
4111053 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTGT
***
4111080 AAACCATTTGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTT-TAGTAATTTTGT
* *
4111106 AGAAAGTCAAGGGTATTTTTGTAATTTTGT
1 --AAA-CCAAGGGTATTTTAGTAATTTTGT
* * *
4111136 AAATCAGGGGTATTTTGGTAATTT
1 AAACCAAGGGTATTTTAGTAATTT
4111160 AACAAATTGA
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
26 1 0.02
27 38 0.59
28 9 0.14
29 15 0.23
30 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.45
Consensus pattern (27 bp):
AAACCAAGGGTATTTTAGTAATTTTGT
Found at i:4111166 original size:27 final size:27
Alignment explanation
Indices: 4111116--4111272 Score: 140
Period size: 27 Copynumber: 5.8 Consensus size: 27
4111106 AGAAAGTCAA
* ***
4111116 GGGTATTTTTGTAATTTTGTAAATCAG
1 GGGTATTTTGGTAATTTAACAAATCAG
*
4111143 GGGTATTTTGGTAATTTAACAAAT-TG
1 GGGTATTTTGGTAATTTAACAAATCAG
* * *
4111169 AGGGTATTTCGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTAACAAATCAG
* *
4111197 TGGTATTTTGGTAATTTTACAAA-CTAG
1 GGGTATTTTGGTAATTTAACAAATC-AG
* *
4111224 GGGTATTTTGGTAATTCTACCATAT-AG
1 GGGTATTTTGGTAATT-TAACAAATCAG
* *
4111251 GGGTATTTTAGTAATTTCACAA
1 GGGTATTTTGGTAATTTAACAA
4111273 TCGAGGGTAA
Statistics
Matches: 105, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
26 5 0.05
27 95 0.90
28 5 0.05
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTAACAAATCAG
Found at i:4111234 original size:81 final size:81
Alignment explanation
Indices: 4111117--4111272 Score: 208
Period size: 81 Copynumber: 1.9 Consensus size: 81
4111107 GAAAGTCAAG
* ** * *
4111117 GGTATTTTTGTAATTTTGTAAATCAGGGGTATTTTGGTAATT-TAACAAATTGAGGGTATTTCGG
1 GGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTCTAACAAATAG-GGGTATTTCAG
4111181 TAATTTCACAAACCAGT
65 TAATTTCACAAACCAGT
* * *
4111198 GGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTCTACCATATAGGGGTATTTTAG
1 GGTATTTTGGTAATTTTACAAATC-AGGGGTATTTTGGTAATTCTAACAAATAGGGGTATTTCAG
4111262 TAATTTCACAA
65 TAATTTCACAA
4111273 TCGAGGGTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
80 1 0.02
81 57 0.88
82 7 0.11
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (81 bp):
GGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTCTAACAAATAGGGGTATTTCAGT
AATTTCACAAACCAGT
Found at i:4111614 original size:27 final size:27
Alignment explanation
Indices: 4111271--4111603 Score: 393
Period size: 27 Copynumber: 12.4 Consensus size: 27
4111261 GTAATTTCAC
*
4111271 AATCGAGGGTAAAACGATAATTC-GTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * * **
4111297 ACTTGA-GGTAAAACGATAATTCCATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
** *
4111323 AATCGAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
4111350 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
4111377 AATCGATGGTAAAACGATAATT-TCGTA
1 AATCGAGGGTAAAACGGTAATTCT-GTA
** *
4111404 AATCGAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
4111431 AATTGAGGGTAAAAGGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
4111458 AATCGAGGGTAAAACGGCAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * * *
4111485 AATCAATGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
4111512 AATCAAGGGTAAAACGATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
4111539 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
4111566 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
4111593 AATCGAGGGTA
1 AATCGAGGGTA
4111604 CTTTGGTAAT
Statistics
Matches: 263, Mismatches: 40, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
25 16 0.06
26 11 0.04
27 235 0.89
28 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:4111627 original size:81 final size:81
Alignment explanation
Indices: 4111271--4111603 Score: 447
Period size: 81 Copynumber: 4.1 Consensus size: 81
4111261 GTAATTTCAC
* * **
4111271 AATCGAGGGTAAAACGATAATTC-GTAACTTGA-GGTAAAACGATAATTCCATAAATCGAGGGTA
1 AATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTA
*
4111334 AAATAGTAATTCTATA
66 AAACAGTAATTCTATA
* *
4111350 AATCGAGGGTAAAACGATAATTTTGTAAATCGATGGTAAAACGATAATT-TCGTAAATCGAGGGT
1 AATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACGATAATTCT-GTAAATCGAGGGT
*
4111414 AAAATAGTAATTCTATA
65 AAAACAGTAATTCTATA
* * * ** * * *
4111431 AATTGAGGGTAAAAGGGTAATTCTGTAAATCGAGGGTAAAACGGCAATTTTGTAAATCAATGGTA
1 AATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTA
4111496 AAACAGTAATTCTATA
66 AAACAGTAATTCTATA
* * *
4111512 AATCAAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTA
1 AATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTA
* *
4111577 AAACGGTAATTCTGTA
66 AAACAGTAATTCTATA
4111593 AATCGAGGGTA
1 AATCGAGGGTA
4111604 CTTTGGTAAT
Statistics
Matches: 223, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
79 22 0.10
80 7 0.03
81 193 0.87
82 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.27
Consensus pattern (81 bp):
AATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAACGATAATTCTGTAAATCGAGGGTA
AAACAGTAATTCTATA
Found at i:4114804 original size:39 final size:38
Alignment explanation
Indices: 4114714--4114813 Score: 103
Period size: 39 Copynumber: 2.6 Consensus size: 38
4114704 ACACTGGCAT
* *
4114714 GAAGCCTACTAGGCATCAAGCCCGATAAACACCGACAC
1 GAAGCCTACTAGGCTTAAAGCCCGATAAACACCGACAC
** * *
4114752 GAAGCCTGTTAGGCTTAAAGCCTGATAAGTCACC-AGCAC
1 GAAGCCTACTAGGCTTAAAGCCCGATAA-ACACCGA-CAC
* *
4114791 GAGGCCTACTAGGCTTAAGGCCC
1 GAAGCCTACTAGGCTTAAAGCCC
4114814 AATACAATAC
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
38 24 0.49
39 25 0.51
ACGTcount: A:0.31, C:0.30, G:0.23, T:0.16
Consensus pattern (38 bp):
GAAGCCTACTAGGCTTAAAGCCCGATAAACACCGACAC
Found at i:4120022 original size:37 final size:37
Alignment explanation
Indices: 4119972--4120045 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
4119962 GACGTTAGCT
4119972 ACGGAATAAAACAATTAAATCACATTAATATTACATA
1 ACGGAATAAAACAATTAAATCACATTAATATTACATA
4120009 ACGGAATAAAACAATTAAATCACATTAATATTACATA
1 ACGGAATAAAACAATTAAATCACATTAATATTACATA
4120046 TTTTAATTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27
Consensus pattern (37 bp):
ACGGAATAAAACAATTAAATCACATTAATATTACATA
Found at i:4120085 original size:19 final size:18
Alignment explanation
Indices: 4120043--4120085 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
4120033 TTAATATTAC
* *
4120043 ATATTTTAATTTCACATT
1 ATATTTCAATTTCACACT
*
4120061 AAATTTCAATTTTCACACT
1 ATATTTCAA-TTTCACACT
4120080 ATATTT
1 ATATTT
4120086 TGCTTATTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTTCAATTTCACACT
Found at i:4123862 original size:42 final size:42
Alignment explanation
Indices: 4123762--4123892 Score: 167
Period size: 42 Copynumber: 3.1 Consensus size: 42
4123752 GGATTACCGA
*
4123762 GATATGAGATTTGTGTACGACCATGTCTGGGACATTGGCATC
1 GATATGAGATTTGTGTAAGACCATGTCTGGGACATTGGCATC
* ** * *
4123804 AACCTAATATTTGTGTAAGACCATGTCTGGGACATTGGCATC
1 GATATGAGATTTGTGTAAGACCATGTCTGGGACATTGGCATC
*
4123846 GATATGAGATTCGTGTAAGACCATAG-CTGGG-CTATTGGCATC
1 GATATGAGATTTGTGTAAGACCAT-GTCTGGGAC-ATTGGCATC
4123888 GATAT
1 GATAT
4123893 ATGATAACAT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
41 1 0.01
42 73 0.97
43 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (42 bp):
GATATGAGATTTGTGTAAGACCATGTCTGGGACATTGGCATC
Found at i:4123927 original size:42 final size:42
Alignment explanation
Indices: 4123817--4123928 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
4123807 CTAATATTTG
* * * *
4123817 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTCG
1 TGTAAGACCATATCTGGGATATTGGCATCGATATGAGATACA
* *
4123859 TGTAAGACCATAGCTGGGCTATTGGCATCGATAT-ATGATAACA
1 TGTAAGACCATATCTGGGATATTGGCATCGATATGA-GAT-ACA
*
4123902 TGTAAGACCATATATGGGATA-TGGCAT
1 TGTAAGACCATATCTGGGATATTGGCAT
4123929 TGTACGAGTT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.02
42 39 0.66
43 19 0.32
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATTGGCATCGATATGAGATACA
Found at i:4125954 original size:69 final size:70
Alignment explanation
Indices: 4125843--4126015 Score: 199
Period size: 69 Copynumber: 2.5 Consensus size: 70
4125833 GTGTGCCTAG
* ** ** * * *
4125843 CACTAGTCGAACGAATCAACAAATTATTATGCCTGGTTCTAGTCGGATAATCGATGATAG-TTGT
1 CACTAGTCGAACAAATTGACAAATTATTATGCCCAGTACTAGTCGGATAACCGACGATAGCTT-T
4125907 GCCCAA
65 GCCCAA
* *
4125913 TACTAGTCTAA-AAATTGACAAATTATTATGCCCAGTACTAGTCGGATAACCGACGATAGCTTTG
1 CACTAGTCGAACAAATTGACAAATTATTATGCCCAGTACTAGTCGGATAACCGACGATAGCTTTG
4125977 CCCAA
66 CCCAA
* * *
4125982 CATTAGTCGAACAAATTG-TAAATTATTACGCCCA
1 CACTAGTCGAACAAATTGACAAATTATTATGCCCA
4126016 ACGCTAATTA
Statistics
Matches: 86, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
69 69 0.80
70 17 0.20
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (70 bp):
CACTAGTCGAACAAATTGACAAATTATTATGCCCAGTACTAGTCGGATAACCGACGATAGCTTTG
CCCAA
Found at i:4127880 original size:13 final size:13
Alignment explanation
Indices: 4127862--4127901 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 13
4127852 TAGATTTTCC
4127862 CTAAATATTATCA
1 CTAAATATTATCA
4127875 CTAAATA--ATC-
1 CTAAATATTATCA
4127885 CTAAATATTATCA
1 CTAAATATTATCA
4127898 -TAAA
1 CTAAA
4127902 ATAATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
10 7 0.29
11 3 0.12
12 7 0.29
13 7 0.29
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:4127891 original size:23 final size:23
Alignment explanation
Indices: 4127861--4127906 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4127851 ATAGATTTTC
4127861 CCTAAATATTATCACT-AAATAAT
1 CCTAAATATTATCA-TAAAATAAT
4127884 CCTAAATATTATCATAAAATAAT
1 CCTAAATATTATCATAAAATAAT
4127907 TCAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (23 bp):
CCTAAATATTATCATAAAATAAT
Found at i:4127913 original size:23 final size:23
Alignment explanation
Indices: 4127864--4127913 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
4127854 GATTTTCCCT
*
4127864 AAATATTATCACTAAATAATCCT
1 AAATATTATCACTAAATAATCCA
*
4127887 AAATATTATCA-TAAAATAATTCA
1 AAATATTATCACT-AAATAATCCA
4127910 AAAT
1 AAAT
4127914 TAAAAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATATTATCACTAAATAATCCA
Found at i:4130755 original size:8 final size:8
Alignment explanation
Indices: 4130737--4130774 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
4130727 TATATTGTTA
4130737 TTTTTATTT
1 TTTTTA-TT
4130746 TTTTTATT
1 TTTTTATT
*
4130754 TTTTTATA
1 TTTTTATT
4130762 TTTTTATT
1 TTTTTATT
4130770 TTTTT
1 TTTTT
4130775 CAAACGTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTATT
Found at i:4135486 original size:43 final size:44
Alignment explanation
Indices: 4135438--4135596 Score: 191
Period size: 43 Copynumber: 3.7 Consensus size: 44
4135428 GATTACCGAG
* *
4135438 ATGTGATTACATGAAAGACCATGTCTGGGACATTGAAATTGTAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGACATTGTAT
*
4135482 -TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGT-T
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGACATTGTAT
* * * * *
4135524 ATATGATTTCGTGTAATACCATGTCTGGGACATT-AGCATCG-AT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGA-CATTGTAT
* *
4135567 ATGTGATAACATGTAAGACCATATCTGGGA
1 ATGTGATTACATGTAAGACCATGTCTGGGA
4135597 TATGGCGTTG
Statistics
Matches: 97, Mismatches: 15, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
42 1 0.01
43 96 0.99
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGACATTGTAT
Found at i:4136453 original size:20 final size:20
Alignment explanation
Indices: 4136430--4136474 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
4136420 TAGGGGTTGA
*
4136430 ATGAATGGTTTAT-AAATGGC
1 ATGAAT-GTTTATGAAATAGC
4136450 ATGAAATGTTTATGAAATAGC
1 ATG-AATGTTTATGAAATAGC
4136471 ATGA
1 ATGA
4136475 TTTGGTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.33
Consensus pattern (20 bp):
ATGAATGTTTATGAAATAGC
Found at i:4146930 original size:22 final size:23
Alignment explanation
Indices: 4146876--4146957 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 23
4146866 CAAGTTGATG
* *
4146876 AACAGTAAGCTCTATATTGACCTGA
1 AACAGTAAGCTC--TATCGAGCTGA
*
4146901 AACGGTAAGCTCTATCGAGCT-A
1 AACAGTAAGCTCTATCGAGCTGA
4146923 AACAGTAAGCTC-ATACGAGCTGA
1 AACAGTAAGCTCTAT-CGAGCTGA
4146946 AAC-GATAAGCTC
1 AACAG-TAAGCTC
4146958 CAAAGAGCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.04
22 19 0.38
23 18 0.36
25 11 0.22
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (23 bp):
AACAGTAAGCTCTATCGAGCTGA
Found at i:4146965 original size:23 final size:23
Alignment explanation
Indices: 4146897--4146966 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
4146887 CTATATTGAC
* * *
4146897 CTGAAACGGTAAGCTCTATCGAG
1 CTGAAACGATAAGCTCCAACGAG
4146920 CT-AAAC-AGTAAGCT-CATACGAG
1 CTGAAACGA-TAAGCTCCA-ACGAG
*
4146942 CTGAAACGATAAGCTCCAAAGAG
1 CTGAAACGATAAGCTCCAACGAG
4146965 CT
1 CT
4146967 AAAAATAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 16 0.42
23 18 0.47
24 3 0.08
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (23 bp):
CTGAAACGATAAGCTCCAACGAG
Found at i:4146966 original size:45 final size:47
Alignment explanation
Indices: 4146876--4146969 Score: 120
Period size: 45 Copynumber: 2.0 Consensus size: 47
4146866 CAAGTTGATG
* * * **
4146876 AACAGTAAGCTCTATATTGACCTGAAACGGTAAGCTCTATCGAGCTA
1 AACAGTAAGCTCTATATCGACCTGAAACGATAAGCTCCAAAGAGCTA
*
4146923 AACAGTAAGCTC-ATA-CGAGCTGAAACGATAAGCTCCAAAGAGCTA
1 AACAGTAAGCTCTATATCGACCTGAAACGATAAGCTCCAAAGAGCTA
4146968 AA
1 AA
4146970 AATAGTAAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 26 0.63
46 3 0.07
47 12 0.29
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (47 bp):
AACAGTAAGCTCTATATCGACCTGAAACGATAAGCTCCAAAGAGCTA
Found at i:4149780 original size:92 final size:93
Alignment explanation
Indices: 4149667--4149841 Score: 228
Period size: 92 Copynumber: 1.9 Consensus size: 93
4149657 CATATCTGTG
* **
4149667 CCGATGCCATGTGCCAAACATGGTCTTACACTGACACATC-TCGTA-GCCGATGCATATCCCAGA
1 CCGATGCCATGTCCCAAACATGGTCTTACACTGACAC-TCATAATAGGCCGATGCATATCCCAGA
*
4149730 CATGTCTTAAACTAGCTCTCGTCTCAACA
65 CATGTCTTAAACAAGCTCTCGTCTCAACA
** * * *
4149759 CCGATGCCATGTCCCGGACATGGTCTTACACTGGCTCTCATAATATGGCCGATGCATGTCCCAGA
1 CCGATGCCATGTCCCAAACATGGTCTTACACTGACACTCATAATA-GGCCGATGCATATCCCAGA
*
4149824 CATGTCTTACACAAGCTC
65 CATGTCTTAAACAAGCTC
4149842 ACACAAGTGA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
91 2 0.03
92 35 0.50
94 33 0.47
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (93 bp):
CCGATGCCATGTCCCAAACATGGTCTTACACTGACACTCATAATAGGCCGATGCATATCCCAGAC
ATGTCTTAAACAAGCTCTCGTCTCAACA
Found at i:4154566 original size:13 final size:13
Alignment explanation
Indices: 4154548--4154576 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4154538 GATATAAATG
4154548 AAATCAACTCATT
1 AAATCAACTCATT
4154561 AAATCAACTCATT
1 AAATCAACTCATT
4154574 AAA
1 AAA
4154577 CTTGAGAATC
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:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATCAACTCATT
Found at i:4156337 original size:46 final size:45
Alignment explanation
Indices: 4156279--4156451 Score: 147
Period size: 46 Copynumber: 3.7 Consensus size: 45
4156269 TTTGGGTTGT
* * *
4156279 GAGCTAGTGTAAGACATGTTTGAGACATGCATCGGCCATATTATGA
1 GAGCCAGTGTAAGACATGTTTGGGACATGCATC-GCCATATGATGA
* * *
4156325 GAGCCAGTGTAAGACCATGTCTGGGAAATTGCATCGACAT-TGAGATGA
1 GAGCCAGTGTAAGA-CATGTTTGGGACA-TGCATCGCCATAT--GATGA
* * *
4156373 GTGCTAGCGTAAGACATGTTTGGGACATGCATCAGCC-TCGA-GATGTA
1 GAGCCAGTGTAAGACATGTTTGGGACATGCATC-GCCAT--ATGATG-A
*
4156420 -AGCCAGTGGAAGACATGTTTGGGACATGCATC
1 GAGCCAGTGTAAGACATGTTTGGGACATGCATC
4156452 AGCTACGAGA
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
46 53 0.52
47 28 0.27
48 21 0.21
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (45 bp):
GAGCCAGTGTAAGACATGTTTGGGACATGCATCGCCATATGATGA
Found at i:4158263 original size:147 final size:147
Alignment explanation
Indices: 4158083--4158447 Score: 419
Period size: 147 Copynumber: 2.5 Consensus size: 147
4158073 TAATAGCATA
* * * ** *
4158083 GAACTACAAGTGTTAATGGATCCCATCCATTTAAAGCTCCAAGTGGGTCAAAGAGACGATCACTG
1 GAACTACAAGGGTTGATGAATCCCATCTGTTTAAAGCTACAAGTGGGTCAAAGAGACGATCACTG
* ** *
4158148 AGTGGGCTACCAAGTTATAATTGAGCTAGAAATAGCTTAGTGACTTAGTTGTCGGAACATGAAAC
66 AGTGGACTACCAAGTTATAATTGAAATAGAAATAGCTTAGTGACTTAGTTGTCAGAACATGAAAC
* * **
4158213 TCCACATTAGTTGTTTG
131 TCCACAATAGTCGCCTG
* * * * *
4158230 TAACTATC-AGGGTTGATGAATCCCATTTGTTTAAAGCTACAAGTAGGT-AAGTGAGATGATCAC
1 GAACTA-CAAGGGTTGATGAATCCCATCTGTTTAAAGCTACAAGTGGGTCAA-AGAGACGATCAC
* * * * * * *
4158293 TAAGTGGACTACCGAGTTATAGTTGAAATAGACATAGGTTAGTGACTTAGTTGTTAGAACATGCA
64 TGAGTGGACTACCAAGTTATAATTGAAATAGAAATAGCTTAGTGACTTAGTTGTCAGAACATGAA
4158358 ACTCCACAATAGTCGCCTG
129 ACTCCACAATAGTCGCCTG
* * * * *
4158377 GAACTACAAGTGTTGATGCATCTCATCTGTTTAAATCTTCAAGTGGGTCAAAGAGACGATCACTG
1 GAACTACAAGGGTTGATGAATCCCATCTGTTTAAAGCTACAAGTGGGTCAAAGAGACGATCACTG
4158442 AGTGGA
66 AGTGGA
4158448 TGATAACTCT
Statistics
Matches: 177, Mismatches: 37, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
146 3 0.02
147 171 0.97
148 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (147 bp):
GAACTACAAGGGTTGATGAATCCCATCTGTTTAAAGCTACAAGTGGGTCAAAGAGACGATCACTG
AGTGGACTACCAAGTTATAATTGAAATAGAAATAGCTTAGTGACTTAGTTGTCAGAACATGAAAC
TCCACAATAGTCGCCTG
Found at i:4168322 original size:12 final size:12
Alignment explanation
Indices: 4168305--4168334 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4168295 CTGTGTGTCG
*
4168305 CACACGGCCTAC
1 CACACGGCCAAC
4168317 CACACGGCCAAC
1 CACACGGCCAAC
4168329 CACACG
1 CACACG
4168335 ACCGTGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.50, G:0.17, T:0.03
Consensus pattern (12 bp):
CACACGGCCAAC
Found at i:4170608 original size:28 final size:27
Alignment explanation
Indices: 4170470--4170651 Score: 156
Period size: 27 Copynumber: 6.7 Consensus size: 27
4170460 AAATTGTACA
* *
4170470 GCACTAAGTGTGCGATTCT-ACTTTGTT
1 GCACTAAGTGTGCGATT-TGACTATGTG
** *
4170497 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATG-TG
**
4170524 GCACTAAGTGTGCGAAATGA-TATGAT-
1 GCACTAAGTGTGCGATTTGACTATG-TG
* * *
4170550 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTG
* *
4170577 GCACTAAGTGTGCGGGTTTGACTATGTA
1 GCACTAAGTGTGC-GATTTGACTATGTG
* *
4170605 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGATTTGACTATGTG
* *
4170632 GCACTAAATGTGCGAGTTGA
1 GCACTAAGTGTGCGATTTGA
4170652 TTATATNNNN
Statistics
Matches: 132, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
26 26 0.20
27 83 0.63
28 23 0.17
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTG
Found at i:4170635 original size:55 final size:54
Alignment explanation
Indices: 4170470--4170651 Score: 174
Period size: 53 Copynumber: 3.4 Consensus size: 54
4170460 AAATTGTACA
* * *
4170470 GCACTAAGTGTGCGATTCT-ACTTTGTTGCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGATT-TGACTATGTAGCACTAAGTGTGCGAATTGAATATG-TG
** ** *
4170524 GCACTAAGTGTGCGAAATGA-TATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTA-GCACTAAGTGTGCGAATTGAATATGTG
* * * *
4170577 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGC-GATTTGACTATGTAGCACTAAGTGTGCGAATTGAATATGTG
* *
4170632 GCACTAAATGTGCGAGTTGA
1 GCACTAAGTGTGCGATTTGA
4170652 TTATATNNNN
Statistics
Matches: 103, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
53 39 0.38
54 25 0.24
55 38 0.37
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (54 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAATTGAATATGTG
Found at i:4181824 original size:47 final size:48
Alignment explanation
Indices: 4181770--4181901 Score: 176
Period size: 47 Copynumber: 2.8 Consensus size: 48
4181760 CAAAATCGAT
* * *
4181770 AAGTACCTATACCATGGTCTGTAGCCAAATCAAGGTAACTTATCTC-G
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCTG
* * * *
4181817 GAGTACCTATACCATGGCCCATAGCCAAATTAAGGTAACTCCTCTCTG
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCTG
* *
4181865 AAATAACTATACCATGGCCCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
4181902 TCACTCGCAC
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
47 39 0.54
48 33 0.46
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCTG
Found at i:4185901 original size:23 final size:23
Alignment explanation
Indices: 4185850--4185894 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
4185840 TGTTAACTCA
*
4185850 TAAG-TTT-TTCTGAAAATAAGT
1 TAAGTTTTCTTCTGAAAATAAAT
4185871 TAAGTTTTCTTCT-AAAATAAAT
1 TAAGTTTTCTTCTGAAAATAAAT
4185893 TA
1 TA
4185895 TTGTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 13 0.62
23 4 0.19
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (23 bp):
TAAGTTTTCTTCTGAAAATAAAT
Found at i:4187182 original size:30 final size:30
Alignment explanation
Indices: 4187100--4187187 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
4187090 TTTTTTTATT
* *
4187100 AAAATAATATAAAA-ATAAATTTAATTT-TC
1 AAAATAATATAAAAGATAAAATT-ATTTACC
* *
4187129 AAAATAATGT--AAGTTATAAATTATTTACC
1 AAAATAATATAAAAGATA-AAATTATTTACC
*
4187158 AAAATAATATAAAAGCTAAAATTATTTACC
1 AAAATAATATAAAAGATAAAATTATTTACC
4187188 GACATTCCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.04
28 6 0.12
29 23 0.48
30 12 0.25
31 5 0.10
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATAATATAAAAGATAAAATTATTTACC
Found at i:4204218 original size:21 final size:21
Alignment explanation
Indices: 4204175--4204228 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
4204165 GCATGTGCCC
* * **
4204175 CCTCCACACTGGCTTGTGGGG
1 CCTCCACACGGGCATGTAAGG
4204196 CCTCCACACGGGCATGTAAGG
1 CCTCCACACGGGCATGTAAGG
*
4204217 CCTTCACACGGG
1 CCTCCACACGGG
4204229 TGTGTGTGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.17, C:0.35, G:0.30, T:0.19
Consensus pattern (21 bp):
CCTCCACACGGGCATGTAAGG
Found at i:4206209 original size:59 final size:59
Alignment explanation
Indices: 4206143--4206260 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
4206133 GTTCAAGAAA
4206143 GATAGGAATGATCAATTGCGGTTTAAATGGCTTTCTTGAATCCCAAGTAAAATGATTGG
1 GATAGGAATGATCAATTGCGGTTTAAATGGCTTTCTTGAATCCCAAGTAAAATGATTGG
4206202 GATAGGAATGATCAATTGCGGTTTAAATGGCTTTCTTGAATCCCAAGTAAAATGATTGG
1 GATAGGAATGATCAATTGCGGTTTAAATGGCTTTCTTGAATCCCAAGTAAAATGATTGG
4206261 TGACTTGAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (59 bp):
GATAGGAATGATCAATTGCGGTTTAAATGGCTTTCTTGAATCCCAAGTAAAATGATTGG
Found at i:4208602 original size:15 final size:16
Alignment explanation
Indices: 4208561--4208604 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
4208551 GTACACTACC
*
4208561 ATATATTTCAATTTTTTT
1 ATATATTT--ATTTTTTA
4208579 ATATATTTATTTTTTA
1 ATATATTTATTTTTTA
4208595 ATAT-TTTATT
1 ATATATTTATT
4208605 ATACTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 6 0.24
16 11 0.44
18 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATATTTATTTTTTA
Found at i:4208886 original size:21 final size:21
Alignment explanation
Indices: 4208849--4208888 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4208839 AAAAATTCCA
4208849 ATATCTTTTAAAGTTTTATAT
1 ATATCTTTTAAAGTTTTATAT
*
4208870 ATAT-TTTTACAATTTTTAT
1 ATATCTTTTA-AAGTTTTAT
4208889 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (21 bp):
ATATCTTTTAAAGTTTTATAT
Found at i:4208926 original size:17 final size:17
Alignment explanation
Indices: 4208913--4208963 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
4208903 TTGTTTTTTC
*
4208913 ATTTTTATACTTTTACA
1 ATTTTTATATTTTTACA
*
4208930 ATTTTTATATTTTTAATA
1 ATTTTTATATTTTT-ACA
4208948 ATTTCTTATAGTTTTT
1 ATTT-TTATA-TTTTT
4208964 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 13 0.45
18 6 0.21
19 5 0.17
20 5 0.17
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTTTATATTTTTACA
Found at i:4211452 original size:51 final size:51
Alignment explanation
Indices: 4211396--4211505 Score: 141
Period size: 51 Copynumber: 2.2 Consensus size: 51
4211386 ACCCTTAAAG
* * *
4211396 TTTACATATTCTGTCAATTTGGTTTTGTTTTAACAAATTCAGTCTT-CAACA
1 TTTACATATTCTATCAATTTGATTTTGATTTAACAAATTCAG-CTTGCAACA
* * * *
4211447 TTTACATATTCTATCATTTTGATTTTGATTTAGCAAATTTAGCTTGTAACA
1 TTTACATATTCTATCAATTTGATTTTGATTTAACAAATTCAGCTTGCAACA
4211498 TTTACATA
1 TTTACATA
4211506 GAATATATAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 3 0.06
51 48 0.94
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (51 bp):
TTTACATATTCTATCAATTTGATTTTGATTTAACAAATTCAGCTTGCAACA
Found at i:4213668 original size:29 final size:30
Alignment explanation
Indices: 4213635--4213695 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
4213625 TTTCACGTAC
*
4213635 ATAATT-ACATCAAATTAAAATTTATTTAT
1 ATAATTAACATCAAATCAAAATTTATTTAT
* *
4213664 ATAATTACACATTAAATCAAAGTTTATTTAT
1 ATAATTA-ACATCAAATCAAAATTTATTTAT
4213695 A
1 A
4213696 ATTTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 6 0.22
31 21 0.78
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43
Consensus pattern (30 bp):
ATAATTAACATCAAATCAAAATTTATTTAT
Found at i:4219365 original size:29 final size:28
Alignment explanation
Indices: 4219332--4219399 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
4219322 AAAGTTTCAC
* *
4219332 ATATATAATTAT-ATTAATTTAAAATTT
1 ATATATAATTATAATTAAATCAAAATTT
4219359 ATGTATATAATTATACATTAAATCAAAATTT
1 A--TATATAATTATA-ATTAAATCAAAATTT
4219390 ATATATAATT
1 ATATATAATT
4219400 TTAAGATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 1 0.03
29 20 0.57
31 14 0.40
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (28 bp):
ATATATAATTATAATTAAATCAAAATTT
Found at i:4223861 original size:49 final size:49
Alignment explanation
Indices: 4223808--4223914 Score: 128
Period size: 49 Copynumber: 2.2 Consensus size: 49
4223798 CCACCCGGTC
* * * * *
4223808 GTGTGAAATCGTGCAGACCT-TGTGGGTAGA-TAGTGTGTACCACATGATT
1 GTGTGAAATCGTACAG-CCTGTGCGGGTAGACT-GTGTGGACCACACGACT
*
4223857 GTGTGAAATCGTACAGGCTGTGCGGGTAGACTGTGTGGACCACACGACT
1 GTGTGAAATCGTACAGCCTGTGCGGGTAGACTGTGTGGACCACACGACT
4223906 GTGTGAAAT
1 GTGTGAAAT
4223915 AGTGTAGTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 2 0.04
49 47 0.94
50 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (49 bp):
GTGTGAAATCGTACAGCCTGTGCGGGTAGACTGTGTGGACCACACGACT
Found at i:4223950 original size:80 final size:80
Alignment explanation
Indices: 4223853--4224009 Score: 233
Period size: 80 Copynumber: 2.0 Consensus size: 80
4223843 TGTACCACAT
* * * *
4223853 GATTGTGTGAAATCGTACAGGCTGTGCGGGTAGACTGTGTGGACCACACGACTGTGTGAAATAGT
1 GATTGCGTGAAATCGTACAGACCGTGCGGGTAGACTGTGTGGACCACACAACTGTGTGAAATAGT
* *
4223918 GTAGTCTGTGTAGGA
66 GCAGACTGTGTAGGA
* * *
4223933 GATTGCGTGAAATCGTACAGACCGTGTGGGTAGACTGTGTGGACCACATAACTGTGTGAAATCGT
1 GATTGCGTGAAATCGTACAGACCGTGCGGGTAGACTGTGTGGACCACACAACTGTGTGAAATAGT
4223998 GCAGACTGTGTA
66 GCAGACTGTGTA
4224010 AACCACACAA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (80 bp):
GATTGCGTGAAATCGTACAGACCGTGCGGGTAGACTGTGTGGACCACACAACTGTGTGAAATAGT
GCAGACTGTGTAGGA
Found at i:4225518 original size:22 final size:24
Alignment explanation
Indices: 4225474--4225521 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
4225464 CATGTTAGTT
*
4225474 TAATTTTATATTTTATAAATTTAA
1 TAATTTTATATTATATAAATTTAA
4225498 TAATTTTA-ATTATA-AAATTTAA
1 TAATTTTATATTATATAAATTTAA
4225520 TA
1 TA
4225522 TTATTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.43
23 5 0.22
24 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TAATTTTATATTATATAAATTTAA
Found at i:4228021 original size:22 final size:21
Alignment explanation
Indices: 4227989--4228035 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
4227979 AAAAGAAGCT
*
4227989 TTGTATCAAGACATGGAGACCA
1 TTGTATCAAGAAATGGAGA-CA
* *
4228011 TTGTATTAAGAAATGGTGACA
1 TTGTATCAAGAAATGGAGACA
4228032 TTGT
1 TTGT
4228036 CTCGAGACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (21 bp):
TTGTATCAAGAAATGGAGACA
Found at i:4232002 original size:19 final size:19
Alignment explanation
Indices: 4231978--4232015 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4231968 TTGAGATTGC
*
4231978 CAACCTATTTGCTTGAAAT
1 CAACCTATTTGCCTGAAAT
4231997 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
4232016 TATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:4236925 original size:123 final size:123
Alignment explanation
Indices: 4236706--4236944 Score: 324
Period size: 123 Copynumber: 1.9 Consensus size: 123
4236696 TTAAACAGAT
** * *
4236706 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTGATTCAGTACACCGGCACTTAGCCTGCTAGAC
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGCCTGATTCACTACACCGGCACTTAGCCTGCTAGAC
* *
4236771 ATATAGTCTGAAATGTATCACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA
66 ATAAAGTCTGAAATGTATCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATGTA
* *
4236829 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATT-ACTTCACCGGCA-TTAAGCCTGCTAG
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGCCTG-ATTCACTACACCGGCACTT-AGCCTGCTAG
* *
4236892 ACTTAAAGTCTG-AAT-TACTTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTG
64 ACATAAAGTCTGAAATGTA--TCACCGGCATTAAGCCTGCTAGACATAAAGTCTG
4236945 TATTACATTC
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
121 2 0.02
122 5 0.05
123 92 0.90
124 3 0.03
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (123 bp):
TCACCGGCATTAAGCCTGCTAGACTTAAAGCCTGATTCACTACACCGGCACTTAGCCTGCTAGAC
ATAAAGTCTGAAATGTATCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATGTA
Found at i:4236950 original size:41 final size:41
Alignment explanation
Indices: 4236705--4236955 Score: 289
Period size: 41 Copynumber: 6.1 Consensus size: 41
4236695 TTTAAACAGA
** * * *
4236705 TTCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTG-ATTCAG
1 TTCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATT-AC
* * *
4236746 TACACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTA-
1 TTCACCGGCA-TTAAGCCTGCTAGACTTAAAGTCTG-AAT-TAC
* *
4236788 -TCACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA-
1 TTCACCGGCATTAAGCCTGCTAGACTTAAAGTCTG-AAT-TAC
4236829 -TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTAC
1 TTCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTAC
4236869 TTCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTAC
1 TTCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTAC
* *
4236910 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGTATTAC
1 TTCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTAC
4236951 ATTCA
1 -TTCA
4236956 ATCACTTTAT
Statistics
Matches: 191, Mismatches: 11, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
39 2 0.01
40 5 0.03
41 174 0.91
42 6 0.03
43 3 0.02
44 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (41 bp):
TTCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTAC
Found at i:4245078 original size:25 final size:28
Alignment explanation
Indices: 4245028--4245079 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 28
4245018 CAATATTTTT
*
4245028 GTATGAAAATTGATATGATAGGAAAATC
1 GTATGAAAATTGATATGATAGAAAAATC
4245056 GTATGAAAA-T-AT-TGATAGAAAAAT
1 GTATGAAAATTGATATGATAGAAAAAT
4245080 TTTAACGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 2 0.09
27 1 0.04
28 9 0.39
ACGTcount: A:0.50, C:0.02, G:0.19, T:0.29
Consensus pattern (28 bp):
GTATGAAAATTGATATGATAGAAAAATC
Found at i:4246675 original size:23 final size:23
Alignment explanation
Indices: 4246649--4246693 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4246639 TGGGTATGTG
*
4246649 ATGACTTTATCTT-ATAAATATGC
1 ATGAATTTATCTTGA-AAATATGC
4246672 ATGAATTTATCTTGAAAATATG
1 ATGAATTTATCTTGAAAATATG
4246694 TTGAATTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (23 bp):
ATGAATTTATCTTGAAAATATGC
Found at i:4253579 original size:30 final size:30
Alignment explanation
Indices: 4253543--4253619 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
4253533 GTCTTCTCAA
* *
4253543 TCCCAAGATCTTGAATGAGATATCGAGTTT
1 TCCCAAGATCCTGAATGAGATATCAAGTTT
* **
4253573 TCCCAAGCTCCTGAACAAGATATCAAGTTT
1 TCCCAAGATCCTGAATGAGATATCAAGTTT
* *
4253603 TCTCAAGTTCCTGAATG
1 TCCCAAGATCCTGAATG
4253620 TCCTCATAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCCAAGATCCTGAATGAGATATCAAGTTT
Found at i:4256026 original size:26 final size:26
Alignment explanation
Indices: 4255997--4256047 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
4255987 AAATTACAAG
*
4255997 TTATTAGCAATTAATATTAATTAATA
1 TTATTAGCAATTAATATTAAGTAATA
* **
4256023 TTATTTGTTATTAATATTAAGTAAT
1 TTATTAGCAATTAATATTAAGTAAT
4256048 TAATAATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (26 bp):
TTATTAGCAATTAATATTAAGTAATA
Found at i:4256113 original size:12 final size:13
Alignment explanation
Indices: 4256096--4256146 Score: 61
Period size: 12 Copynumber: 3.9 Consensus size: 13
4256086 TATATTACTA
4256096 TATTATT-TATTT
1 TATTATTCTATTT
4256108 TATTATTCTA-TT
1 TATTATTCTATTT
4256120 TATTATTCTATTAT
1 TATTATTCTATT-T
*
4256134 CTATTATTATATT
1 -TATTATTCTATT
4256147 ATTCTTACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
12 19 0.56
13 3 0.09
14 1 0.03
15 11 0.32
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTATTCTATTT
Found at i:4256114 original size:15 final size:15
Alignment explanation
Indices: 4256088--4256149 Score: 63
Period size: 15 Copynumber: 4.0 Consensus size: 15
4256078 TATAAATCTA
*
4256088 TATTACTATATTATT
1 TATTATTATATTATT
4256103 TATT-TTATTATTCTATT
1 TATTATTA-TA-T-TATT
* *
4256120 TATTATTCTATTATC
1 TATTATTATATTATT
4256135 TATTATTATATTATT
1 TATTATTATATTATT
4256150 CTTACAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
14 2 0.05
15 22 0.58
16 2 0.05
17 10 0.26
18 2 0.05
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTATTATATTATT
Found at i:4256167 original size:8 final size:8
Alignment explanation
Indices: 4256086--4256149 Score: 53
Period size: 8 Copynumber: 8.1 Consensus size: 8
4256076 TTTATAAATC
*
4256086 TATATTAC
1 TATATTAT
4256094 TATATTATT
1 TATATTA-T
*
4256103 TATTTTAT
1 TATATTAT
4256111 TAT-TCTAT
1 TATAT-TAT
4256119 T-TATTAT
1 TATATTAT
*
4256126 TCTATTA-
1 TATATTAT
*
4256133 TCTATTAT
1 TATATTAT
4256141 TATATTAT
1 TATATTAT
4256149 T
1 T
4256150 CTTACAATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
7 13 0.27
8 29 0.60
9 6 0.12
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (8 bp):
TATATTAT
Found at i:4256173 original size:12 final size:12
Alignment explanation
Indices: 4256094--4256177 Score: 57
Period size: 12 Copynumber: 6.9 Consensus size: 12
4256084 TCTATATTAC
4256094 TATATTATT-TA
1 TATATTATTATA
* *
4256105 TTTTATTATTCTA
1 -TATATTATTATA
* *
4256118 TTTATTATTCTA
1 TATATTATTATA
4256130 T-TATCTATTAT-
1 TATAT-TATTATA
*
4256141 TATATTATTCTTA
1 TATATTATT-ATA
*
4256154 CAATATTATTATA
1 -TATATTATTATA
4256167 TATATTATTAT
1 TATATTATTAT
4256178 TTCTATTTAG
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
11 8 0.13
12 40 0.67
13 4 0.07
14 8 0.13
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATTATTATA
Found at i:4256247 original size:32 final size:33
Alignment explanation
Indices: 4256211--4256284 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
4256201 TATTATTATT
*
4256211 TAATTTAAGTTAAAGT-TAAATAGAA-AAATTAA
1 TAATTTAA-TTAAAGTATAAATAAAATAAATTAA
* * *
4256243 TAATTTAATTTAAGTATAATTAAAATAAATTAT
1 TAATTTAATTAAAGTATAAATAAAATAAATTAA
4256276 TAATTTAAT
1 TAATTTAAT
4256285 AATTTAGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 6 0.17
32 15 0.42
33 15 0.42
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (33 bp):
TAATTTAATTAAAGTATAAATAAAATAAATTAA
Found at i:4256280 original size:33 final size:31
Alignment explanation
Indices: 4256205--4256284 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 31
4256195 AGAATTTATT
*
4256205 ATTATTTAATTTAAGTTAAAGTTAAATAGAAAA
1 ATTA-TTAATTTAA-TTAAAGTTAAATAAAAAA
* * *
4256238 ATTAATAATTTAATTTAAGTATAATTAAAATAA
1 ATTATTAATTTAATTAAAGT-TAAATAAAA-AA
4256271 ATTATTAATTTAAT
1 ATTATTAATTTAAT
4256285 AATTTAGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 15 0.38
33 19 0.47
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTAATTTAATTAAAGTTAAATAAAAAA
Found at i:4257379 original size:21 final size:22
Alignment explanation
Indices: 4257338--4257385 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
4257328 ATAGGTAGAT
*
4257338 TAAATTAATTGTTTGTTAATAA
1 TAAATTAATTGTTTGTAAATAA
4257360 TAAATTAATT-TTTGTAAATAA
1 TAAATTAATTGTTTGTAAATAA
4257381 TAAAT
1 TAAAT
4257386 ATCACTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (22 bp):
TAAATTAATTGTTTGTAAATAA
Found at i:4257446 original size:45 final size:46
Alignment explanation
Indices: 4257350--4257447 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 46
4257340 AATTAATTGT
*
4257350 TTGTTAATAATAAATTAATTTTTGTAAATAATAAATATCACTAAAA
1 TTGTTAATAATAAACTAATTTTTGTAAATAATAAATATCACTAAAA
* *
4257396 TTGTTAATAATAAACTAACTTTTT-T-TATAATAAATATCATTGAAAA
1 TTGTTAATAATAAACTAA-TTTTTGTAAATAATAAATATCACT-AAAA
4257442 -TGTTAA
1 TTGTTAA
4257448 AATTAATCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
45 20 0.43
46 22 0.47
47 5 0.11
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (46 bp):
TTGTTAATAATAAACTAATTTTTGTAAATAATAAATATCACTAAAA
Found at i:4259161 original size:22 final size:23
Alignment explanation
Indices: 4259136--4259191 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
4259126 CACTTAACTG
*
4259136 TTAATTTTTTTAATTTAAAT-TC
1 TTAATTTTTTTAAATTAAATATC
* * *
4259158 TTAAATTTTTAAAATTAAATATT
1 TTAATTTTTTTAAATTAAATATC
*
4259181 TTAATTATTTT
1 TTAATTTTTTT
4259192 CCGTTAGTTG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTAATTTTTTTAAATTAAATATC
Found at i:4261592 original size:4 final size:4
Alignment explanation
Indices: 4261583--4261617 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
4261573 TGTTTAACAA
4261583 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
4261618 AAGAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:4261622 original size:6 final size:7
Alignment explanation
Indices: 4261584--4261632 Score: 57
Period size: 8 Copynumber: 6.9 Consensus size: 7
4261574 GTTTAACAAA
4261584 AAGAAAG
1 AAGAAAG
4261591 AAAGAAAG
1 -AAGAAAG
4261599 AAAGAAAG
1 -AAGAAAG
4261607 AAAGAAAG
1 -AAGAAAG
4261615 AA-AAAG
1 AAGAAAG
4261621 AAGAAA-
1 AAGAAAG
4261627 AAGAAA
1 AAGAAA
4261633 CCTTGTACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.30
7 5 0.12
8 23 0.57
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:4262322 original size:21 final size:21
Alignment explanation
Indices: 4262298--4262338 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4262288 TTAACAGGTA
4262298 TTATAATAAAATTAA-AAAAAT
1 TTATAATAAAA-TAATAAAAAT
4262319 TTATAATAAAATAATAAAAA
1 TTATAATAAAATAATAAAAA
4262339 CAAAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TTATAATAAAATAATAAAAAT
Found at i:4265458 original size:18 final size:18
Alignment explanation
Indices: 4265397--4265458 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 18
4265387 ACTTTAGCCA
4265397 TTTATTTTATTAC--AAT
1 TTTATTTTATTACTAAAT
*
4265413 TTAAATTTTATT--TAAAT
1 TT-TATTTTATTACTAAAT
4265430 TTT-TTTATATTACTAAAT
1 TTTATTT-TATTACTAAAT
4265448 TTTATTTTATT
1 TTTATTTTATT
4265459 TACTTCTGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
15 3 0.08
16 6 0.16
17 13 0.35
18 12 0.32
19 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATTTTATTACTAAAT
Found at i:4276484 original size:23 final size:22
Alignment explanation
Indices: 4276438--4276487 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
4276428 GTTGTAAATA
4276438 TATATTTTATGCATTATTAATT
1 TATATTTTATGCATTATTAATT
*
4276460 TATATTTTTTGACA-TATTAATT
1 TATATTTTATG-CATTATTAATT
4276482 T-TATTT
1 TATATTT
4276488 ATGTTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 5 0.19
22 19 0.73
23 2 0.08
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (22 bp):
TATATTTTATGCATTATTAATT
Found at i:4277156 original size:20 final size:20
Alignment explanation
Indices: 4277131--4277169 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
4277121 CAAAGTGAAT
4277131 AAAACGAATCATTTTCAAAG
1 AAAACGAATCATTTTCAAAG
4277151 AAAACGAATCATTTTCAAA
1 AAAACGAATCATTTTCAAA
4277170 TGACAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (20 bp):
AAAACGAATCATTTTCAAAG
Found at i:4282348 original size:30 final size:31
Alignment explanation
Indices: 4282312--4282371 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
4282302 TAATAGCTAG
4282312 TGACTTAAAT-AAAACTTTTAAATAATTTAA
1 TGACTTAAATGAAAACTTTTAAATAATTTAA
* *
4282342 TGACTTAAATGAAAATTTTTGAATAATTTA
1 TGACTTAAATGAAAACTTTTAAATAATTTA
4282372 GTGATCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTTAAATAATTTAA
Found at i:4284386 original size:37 final size:37
Alignment explanation
Indices: 4284336--4284410 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
4284326 AAATTAGACT
*
4284336 CGGGTTAGTTTTGATTTGAAACTGTACAAGTCGAAGG
1 CGGGTTAGTTTTGATTTGAAACTGTACAAGTCAAAGG
*
4284373 CGGGTTAGTTTTGATTTGAAAGTGTACAAGTCAAAGG
1 CGGGTTAGTTTTGATTTGAAACTGTACAAGTCAAAGG
4284410 C
1 C
4284411 TAGAAGTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.28, C:0.11, G:0.29, T:0.32
Consensus pattern (37 bp):
CGGGTTAGTTTTGATTTGAAACTGTACAAGTCAAAGG
Found at i:4285161 original size:21 final size:21
Alignment explanation
Indices: 4285136--4285204 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
4285126 TATAATGATT
4285136 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
4285157 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
4285177 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
4285197 ATTATTAT
1 ATTATTAT
4285205 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:4285217 original size:15 final size:14
Alignment explanation
Indices: 4285191--4285221 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4285181 TATGGTTTTA
4285191 TATTAGATTATTAT
1 TATTAGATTATTAT
4285205 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
4285220 TA
1 TA
4285222 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:4292640 original size:21 final size:21
Alignment explanation
Indices: 4292615--4292683 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
4292605 TATAATGATT
4292615 ATTATTATAGTTTTATATTAA
1 ATTATTATAGTTTTATATTAA
*
4292636 ATTATTATAATTATTA-ATT-A
1 ATTATTATAGTT-TTATATTAA
* * *
4292656 A-CATTATGGTTTTATATTAG
1 ATTATTATAGTTTTATATTAA
4292676 ATTATTAT
1 ATTATTAT
4292684 TAGCATTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.26
20 3 0.08
21 19 0.50
22 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTATTATAGTTTTATATTAA
Found at i:4296290 original size:16 final size:16
Alignment explanation
Indices: 4296254--4296292 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4296244 ATTAAGATTG
*
4296254 TATGCAAGCTATATTA
1 TATGCAAGCTATATCA
* *
4296270 CATGCGAGCTATATCA
1 TATGCAAGCTATATCA
4296286 TATGCAA
1 TATGCAA
4296293 ACCATGATAT
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (16 bp):
TATGCAAGCTATATCA
Found at i:4302599 original size:20 final size:19
Alignment explanation
Indices: 4302565--4302607 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
4302555 TTAAAAACTT
4302565 ATATAATAATATATATACC
1 ATATAATAATATATATACC
* *
4302584 ATATAATGATTATATATATC
1 ATATAAT-AATATATATACC
4302604 ATAT
1 ATAT
4302608 GGTAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATAATAATATATATACC
Found at i:4305103 original size:20 final size:22
Alignment explanation
Indices: 4305060--4305109 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
4305050 ATTCTACTTT
*
4305060 TTTC-ATAAAAATTACATTTAA
1 TTTCAATAAAAATTACATATAA
4305081 TTTCAATAAAAATTA-A-ATAA
1 TTTCAATAAAAATTACATATAA
*
4305101 TTTAAATAA
1 TTTCAATAA
4305110 TATTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 11 0.42
21 5 0.19
22 10 0.38
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTCAATAAAAATTACATATAA
Found at i:4324474 original size:25 final size:25
Alignment explanation
Indices: 4324446--4324496 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
4324436 AAAATTTGGT
4324446 TACTTATTGCAAAGTTCGAAAGCGA
1 TACTTATTGCAAAGTTCGAAAGCGA
4324471 TACTTATTGCAAAGTTCGAAAGCGA
1 TACTTATTGCAAAGTTCGAAAGCGA
4324496 T
1 T
4324497 CACCACGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (25 bp):
TACTTATTGCAAAGTTCGAAAGCGA
Found at i:4324744 original size:31 final size:31
Alignment explanation
Indices: 4324698--4324772 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
4324688 ACAGTTACTA
* *
4324698 GGCCGAAGCCATTTCATAAATCATACCACTG
1 GGCCGAAGCCTTTTCATAAATCATACAACTG
*
4324729 GGCTGAAGCCTTTTCATAAATCATACAACTG
1 GGCCGAAGCCTTTTCATAAATCATACAACTG
*
4324760 GGCCAAAGCCTTT
1 GGCCGAAGCCTTT
4324773 ACTGTAAACG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (31 bp):
GGCCGAAGCCTTTTCATAAATCATACAACTG
Done.