Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 16 of 131
Found at i:5467881 original size:13 final size:13
Alignment explanation
Indices: 5467865--5467889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5467855 CCTCCTTTTT
5467865 TTTTGTTTTTGTG
1 TTTTGTTTTTGTG
5467878 TTTTGTTTTTGT
1 TTTTGTTTTTGT
5467890 TCTTTTTTTC
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:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (13 bp):
TTTTGTTTTTGTG
Found at i:5467919 original size:12 final size:10
Alignment explanation
Indices: 5467815--5467922 Score: 56
Period size: 11 Copynumber: 9.9 Consensus size: 10
5467805 CAGCGGGGTT
5467815 TTTTCTTTTTC
1 TTTT-TTTTTC
5467826 TCTTTTTTTTC
1 T-TTTTTTTTC
5467837 TGTTTTTTCTTC
1 T-TTTTTT-TTC
** *
5467849 TTTTTCCCTCC
1 TTTTT-TTTTC
*
5467860 TTTTTTTTTG
1 TTTTTTTTTC
5467870 TTTTTGTGTTT-
1 TTTTT-T-TTTC
*
5467881 TGTTTTTGTTC
1 T-TTTTTTTTC
5467892 TTTTTTTCTTTC
1 -TTTTTT-TTTC
**
5467904 TTTTTTCCTC
1 TTTTTTTTTC
5467914 TTTTTTTTT
1 TTTTTTTTT
5467923 TGAATTGAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
10 17 0.23
11 39 0.53
12 18 0.24
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.79
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:5473882 original size:9 final size:9
Alignment explanation
Indices: 5473870--5473900 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
5473860 AATTATAATA
5473870 ATAAACAAT
1 ATAAACAAT
5473879 ATAAACAAT
1 ATAAACAAT
5473888 ATAAACAAT
1 ATAAACAAT
5473897 ATAA
1 ATAA
5473901 TAAAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (9 bp):
ATAAACAAT
Found at i:5473909 original size:9 final size:10
Alignment explanation
Indices: 5473866--5473897 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
5473856 TAATAATTAT
5473866 AATAATAAAC
1 AATAATAAAC
5473876 AAT-ATAAAC
1 AATAATAAAC
5473885 AAT-ATAAAC
1 AATAATAAAC
5473894 AATA
1 AATA
5473898 TAATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 18 0.86
10 3 0.14
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (10 bp):
AATAATAAAC
Found at i:5473909 original size:18 final size:18
Alignment explanation
Indices: 5473864--5473911 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
5473854 TATAATAATT
*
5473864 ATAATAATAAACAATATA
1 ATAAAAATAAACAATATA
*
5473882 A-ACAATATAAACAATATA
1 ATA-AAAATAAACAATATA
5473900 ATAAAAATAAAC
1 ATAAAAATAAAC
5473912 TAAAAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAAAATAAACAATATA
Found at i:5477021 original size:21 final size:20
Alignment explanation
Indices: 5476993--5477048 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
5476983 GATCAACACT
5476993 TTTGAGCTTCTGTTAAGCTC
1 TTTGAGCTTCTGTTAAGCTC
* *
5477013 TTATGAGCTTTTGTTCAGCTC
1 TT-TGAGCTTCTGTTAAGCTC
5477034 TTTCGAGCTTCTGTT
1 TTT-GAGCTTCTGTT
5477049 GGCGTGTTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.10
21 28 0.90
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (20 bp):
TTTGAGCTTCTGTTAAGCTC
Found at i:5485412 original size:16 final size:17
Alignment explanation
Indices: 5485391--5485426 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
5485381 TCAGCTCCTA
5485391 TTTTAATTTCG-ATTAT
1 TTTTAATTTCGAATTAT
*
5485407 TTTTAATTTTGAATTAT
1 TTTTAATTTCGAATTAT
5485424 TTT
1 TTT
5485427 CAACCTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTAATTTCGAATTAT
Found at i:5486498 original size:98 final size:98
Alignment explanation
Indices: 5486396--5486592 Score: 376
Period size: 98 Copynumber: 2.0 Consensus size: 98
5486386 TCTAATTACC
5486396 TAAGTAGATTAAAAATTAGTATCTAATCACCTATCATATCAGCTTCCAGATCTGGTGGAATTTTC
1 TAAGTAGATTAAAAATTAGTATCTAATCACCTATCATATCAGCTTCCAGATCTGGTGGAATTTTC
*
5486461 TGTAATATTTAGATTTTCCCTGATTTTTTGTTT
66 TGTAATATTTAGATTTTCCCTGATTTTTGGTTT
5486494 TAAGTAGATTAAAAATTAGTATCTAATCACCTATCATATCAGCTTCCAGATCTGGTGGAATTTTC
1 TAAGTAGATTAAAAATTAGTATCTAATCACCTATCATATCAGCTTCCAGATCTGGTGGAATTTTC
*
5486559 TGTAATATTTGGATTTTCCCTGATTTTTGGTTT
66 TGTAATATTTAGATTTTCCCTGATTTTTGGTTT
5486592 T
1 T
5486593 TATAAAATAT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (98 bp):
TAAGTAGATTAAAAATTAGTATCTAATCACCTATCATATCAGCTTCCAGATCTGGTGGAATTTTC
TGTAATATTTAGATTTTCCCTGATTTTTGGTTT
Found at i:5486890 original size:54 final size:54
Alignment explanation
Indices: 5486802--5486968 Score: 309
Period size: 54 Copynumber: 3.1 Consensus size: 54
5486792 TATCATTGAC
*
5486802 CATTGGTCAACTAACTGCCACATCTAATTCTGATTTATTTGATAAAGATTAAAAG
1 CATTAGTCAACT-ACTGCCACATCTAATTCTGATTTATTTGATAAAGATTAAAAG
5486857 CATTAGTCAACTACTGCCACATCTAATTCTGATTTATTTGATAAAGATTAAAAG
1 CATTAGTCAACTACTGCCACATCTAATTCTGATTTATTTGATAAAGATTAAAAG
5486911 CATTAGTCAACTACTGCCACATCTAATTCTGATTTATTTGATAAAGATTAAAAG
1 CATTAGTCAACTACTGCCACATCTAATTCTGATTTATTTGATAAAGATTAAAAG
5486965 -ATTA
1 CATTA
5486969 AGGTGGCAAT
Statistics
Matches: 111, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
53 4 0.04
54 96 0.86
55 11 0.10
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (54 bp):
CATTAGTCAACTACTGCCACATCTAATTCTGATTTATTTGATAAAGATTAAAAG
Found at i:5496370 original size:127 final size:127
Alignment explanation
Indices: 5496144--5496405 Score: 497
Period size: 127 Copynumber: 2.1 Consensus size: 127
5496134 AGCCTGTTGT
*
5496144 TTAATTTGCAGAGCCTACAATTCGCTGGTCAAGTGCATAAAGAAGGCAGCATCATGCAAAATGGA
1 TTAATTTTCAGAGCCTACAATTCGCTGGTCAAGTGCATAAAGAAGGCAGCATCATGCAAAATGGA
*
5496209 GATAACATGCCATGTTACCAAGTAAACGCAGATCCGAAGGTGATTATCTGAGCATCCATGCC
66 GATAACATGCCATGTTACCAAGTAAACGCAGATCCGAAGGTGATTATCTGAGCACCCATGCC
5496271 TTAATTTTCAGAGCCTACAATTCGCTGGTCAAGTGCATAAAGAAGGCAGCATCATGCAAAATGGA
1 TTAATTTTCAGAGCCTACAATTCGCTGGTCAAGTGCATAAAGAAGGCAGCATCATGCAAAATGGA
5496336 GATAACATGCCATGTTACCAAGTAAACGCAGATCCGAAGGTGATTATCTGAGCACCCATGCC
66 GATAACATGCCATGTTACCAAGTAAACGCAGATCCGAAGGTGATTATCTGAGCACCCATGCC
*
5496398 TTATTTTT
1 TTAATTTT
5496406 TCTTGCTGGT
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 132 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (127 bp):
TTAATTTTCAGAGCCTACAATTCGCTGGTCAAGTGCATAAAGAAGGCAGCATCATGCAAAATGGA
GATAACATGCCATGTTACCAAGTAAACGCAGATCCGAAGGTGATTATCTGAGCACCCATGCC
Found at i:5500744 original size:10 final size:10
Alignment explanation
Indices: 5500731--5500757 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5500721 ATTAAATTTT
5500731 AAAAATATAG
1 AAAAATATAG
5500741 AAAAATATAG
1 AAAAATATAG
5500751 AAAAATA
1 AAAAATA
5500758 AAAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (10 bp):
AAAAATATAG
Found at i:5508982 original size:20 final size:20
Alignment explanation
Indices: 5508948--5508989 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5508938 AACCATCTAA
** *
5508948 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
5508968 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
5508988 AT
1 AT
5508990 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:5511035 original size:13 final size:14
Alignment explanation
Indices: 5511016--5511055 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
5511006 CAATGGCATA
5511016 GAAATAATATAAAC
1 GAAATAATATAAAC
5511030 -AAATAA-ATAAAC
1 GAAATAATATAAAC
5511042 GAAATTAATATAAA
1 GAAA-TAATATAAA
5511056 AAAACAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.26
13 9 0.39
14 3 0.13
15 5 0.22
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:5511373 original size:9 final size:9
Alignment explanation
Indices: 5511359--5511424 Score: 98
Period size: 9 Copynumber: 7.2 Consensus size: 9
5511349 TTGGGTAATT
5511359 TTCGGGTAA
1 TTCGGGTAA
5511368 TTCGGGTAA
1 TTCGGGTAA
5511377 TTTTCGGGTAA
1 --TTCGGGTAA
*
5511388 TTCGGTTAA
1 TTCGGGTAA
5511397 -TCGGGTAA
1 TTCGGGTAA
5511405 TTCGGGTAA
1 TTCGGGTAA
5511414 TTCGGGTAA
1 TTCGGGTAA
5511423 TT
1 TT
5511425 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
8 7 0.13
9 36 0.69
11 9 0.17
ACGTcount: A:0.21, C:0.11, G:0.30, T:0.38
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:5511376 original size:20 final size:18
Alignment explanation
Indices: 5511359--5511424 Score: 98
Period size: 20 Copynumber: 3.6 Consensus size: 18
5511349 TTGGGTAATT
5511359 TTCGGGTAATTCGGGTAA
1 TTCGGGTAATTCGGGTAA
*
5511377 TTTTCGGGTAATTCGGTTAA
1 --TTCGGGTAATTCGGGTAA
5511397 -TCGGGTAATTCGGGTAA
1 TTCGGGTAATTCGGGTAA
5511414 TTCGGGTAATT
1 TTCGGGTAATT
5511425 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.37
18 10 0.23
20 17 0.40
ACGTcount: A:0.21, C:0.11, G:0.30, T:0.38
Consensus pattern (18 bp):
TTCGGGTAATTCGGGTAA
Found at i:5512711 original size:22 final size:21
Alignment explanation
Indices: 5512676--5512961 Score: 143
Period size: 19 Copynumber: 14.7 Consensus size: 21
5512666 AAAAGGTATC
* *
5512676 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
5512697 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
5512720 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5512739 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5512758 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5512777 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5512796 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5512815 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5512834 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5512853 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5512872 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5512891 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5512910 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
5512929 TACATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
5512948 TGCATATCATATCT
1 TACAAATCATATCT
5512962 AAGATTGCAT
Statistics
Matches: 255, Mismatches: 6, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
19 226 0.89
21 4 0.02
22 15 0.06
23 10 0.04
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:5512719 original size:23 final size:22
Alignment explanation
Indices: 5512676--5512733 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
5512666 AAAAGGTATC
* *
5512676 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
5512697 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
5512720 TGCATATCATATCT
1 TACAAATCATATCT
5512734 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:5512736 original size:19 final size:19
Alignment explanation
Indices: 5512712--5512974 Score: 517
Period size: 19 Copynumber: 13.8 Consensus size: 19
5512702 AATCATATCT
5512712 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5512731 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5512750 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5512769 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5512788 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5512807 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5512826 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5512845 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5512864 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5512883 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5512902 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
5512921 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
5512940 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5512959 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
5512975 CTTGAAGATT
Statistics
Matches: 242, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
19 242 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:5516594 original size:144 final size:144
Alignment explanation
Indices: 5516369--5516652 Score: 498
Period size: 144 Copynumber: 2.0 Consensus size: 144
5516359 TAAGGTAGAT
**
5516369 TAGTAATAATGTGTAACCCTATATAGTATATACAACTATGTTACTATAATGTACATTTGTATATT
1 TAGTAATAATGTGTAACCCTATATAGTATATACAACTATGCCACTATAATGTACATTTGTATATT
* *
5516434 AATGATACGTAACCTTAAAC-CTTAAATGTGCAACTAACCTTATCGTATATTATTGTTATACTTA
66 AATGATACGCAACCTTAAACTC-TAAATGTGCAACTAACCTTATCATATATTATTGTTATACTTA
*
5516498 TATCCTTACCTTATA
130 TACCCTTACCTTATA
5516513 TAGTAATAATGTGTAACCCTATATAGTATATACAACTATGCCACTATAATGTACATTTGTATATT
1 TAGTAATAATGTGTAACCCTATATAGTATATACAACTATGCCACTATAATGTACATTTGTATATT
*
5516578 AATGATACGCAACCTTAAACTCTAAATGTGCAGCTAACCTTATCATATATTATTGTTATACTTAT
66 AATGATACGCAACCTTAAACTCTAAATGTGCAACTAACCTTATCATATATTATTGTTATACTTAT
5516643 ACCCTTACCT
131 ACCCTTACCT
5516653 CAATTTAGAC
Statistics
Matches: 133, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
144 132 0.99
145 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (144 bp):
TAGTAATAATGTGTAACCCTATATAGTATATACAACTATGCCACTATAATGTACATTTGTATATT
AATGATACGCAACCTTAAACTCTAAATGTGCAACTAACCTTATCATATATTATTGTTATACTTAT
ACCCTTACCTTATA
Found at i:5522296 original size:119 final size:119
Alignment explanation
Indices: 5522085--5522323 Score: 390
Period size: 119 Copynumber: 2.0 Consensus size: 119
5522075 TGGCTCAGCC
5522085 AGAATCTGCCGTACCATATGTTGTTTATAGTGATGCGTCTTTAAATGGTTTGGGTTGTGTACTGA
1 AGAATCTGCCGTACCATATGTTGTTTATAGTGATGCGTCTTTAAATGGTTTGGGTTGTGTACTGA
* * * *
5522150 TGTAGTCAGGAAAGATAGTAGCTTATGCTTCTTGATAATTAATGCGGCATGAGA
66 TGCAGTCAGGAAAGATAGTAGCCTATGCTTCTTGAAAATTAATACGGCATGAGA
*
5522204 AGAATCTAG-CGTACCGTATGTTGTTTATAGTGATGCGTCTTTAAATGGTTTGGGTTGTGTACTG
1 AGAATCT-GCCGTACCATATGTTGTTTATAGTGATGCGTCTTTAAATGGTTTGGGTTGTGTACTG
* * *
5522268 ATGCAGTCAGGAAAGGTAGTAGCCTATGCTTTTTGAAAATTAATACTGCATGAGA
65 ATGCAGTCAGGAAAGATAGTAGCCTATGCTTCTTGAAAATTAATACGGCATGAGA
5522323 A
1 A
5522324 AATTTATTCT
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
119 110 0.99
120 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.36
Consensus pattern (119 bp):
AGAATCTGCCGTACCATATGTTGTTTATAGTGATGCGTCTTTAAATGGTTTGGGTTGTGTACTGA
TGCAGTCAGGAAAGATAGTAGCCTATGCTTCTTGAAAATTAATACGGCATGAGA
Found at i:5522960 original size:19 final size:21
Alignment explanation
Indices: 5522926--5522966 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
5522916 ATGAAACGGG
*
5522926 AAATTTTTGAATTTG-TAGCA
1 AAATGTTTGAATTTGTTAGCA
5522946 AAATGTTTG-ATTTGTTAGCA
1 AAATGTTTGAATTTGTTAGCA
5522966 A
1 A
5522967 GTGAAAGCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (21 bp):
AAATGTTTGAATTTGTTAGCA
Found at i:5525026 original size:41 final size:42
Alignment explanation
Indices: 5524950--5525043 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 42
5524940 TCAACTCTCG
*
5524950 CGAGCTTCTGTTTAACTCATATGAGTTTCCGTTCAGCTC-TA
1 CGAGCTTCTATTTAACTCATATGAGTTTCCGTTCAGCTCTTA
* *
5524991 TTGAGCTTCTATTTAAC-CTTATGAGTTTCCGTTCAGCTCTTA
1 -CGAGCTTCTATTTAACTCATATGAGTTTCCGTTCAGCTCTTA
5525033 CGAGCTTCTAT
1 CGAGCTTCTAT
5525044 GCAGCTCTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
41 31 0.66
42 16 0.34
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.41
Consensus pattern (42 bp):
CGAGCTTCTATTTAACTCATATGAGTTTCCGTTCAGCTCTTA
Found at i:5525032 original size:21 final size:21
Alignment explanation
Indices: 5524969--5525032 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
5524959 GTTTAACTCA
5524969 TATGAGTTTCCGTTCAGCTC-
1 TATGAGTTTCCGTTCAGCTCT
* ** * *
5524989 TATTGAGCTTCTATTTAAC-CT
1 TA-TGAGTTTCCGTTCAGCTCT
5525010 TATGAGTTTCCGTTCAGCTCT
1 TATGAGTTTCCGTTCAGCTCT
5525031 TA
1 TA
5525033 CGAGCTTCTA
Statistics
Matches: 31, Mismatches: 10, Indels: 5
0.67 0.22 0.11
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.44
Consensus pattern (21 bp):
TATGAGTTTCCGTTCAGCTCT
Found at i:5525048 original size:21 final size:21
Alignment explanation
Indices: 5525024--5525064 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
5525014 AGTTTCCGTT
5525024 CAGCTCTTACGAGCTTCTATG
1 CAGCTCTTACGAGCTTCTATG
5525045 CAGCTCTTACGAGCTTCTAT
1 CAGCTCTTACGAGCTTCTAT
5525065 TCAACCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (21 bp):
CAGCTCTTACGAGCTTCTATG
Found at i:5528963 original size:3 final size:3
Alignment explanation
Indices: 5528950--5529007 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
5528940 ATTACTTAAC
* * * * * * *
5528950 TAT TTT TAT TAT TAT TGT TAT TAT TAT TAA TGT TAC TAT AAT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5528998 TAT TAT TAT T
1 TAT TAT TAT T
5529008 TGTATTAGTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5534806 original size:19 final size:17
Alignment explanation
Indices: 5534773--5534813 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
5534763 ATTATTTGAA
*
5534773 TTTTATATTTTATAATT
1 TTTTATATTTTATAACT
5534790 TTTTATGATTCTTATAACT
1 TTTTAT-ATT-TTATAACT
5534809 TTTTA
1 TTTTA
5534814 ATAATCAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 3 0.14
19 12 0.57
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTTATATTTTATAACT
Found at i:5534912 original size:19 final size:20
Alignment explanation
Indices: 5534890--5534938 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5534880 TTTCTTGGAA
5534890 TTTTTAATAAT-TCTATA-AT
1 TTTTTAATAATAT-TATATAT
* *
5534909 TTTTTAAAAATATTTTATAT
1 TTTTTAATAATATTATATAT
5534929 TTTTTAATAA
1 TTTTTAATAA
5534939 CAACTTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTAATAATATTATATAT
Found at i:5550242 original size:132 final size:133
Alignment explanation
Indices: 5550081--5550346 Score: 525
Period size: 132 Copynumber: 2.0 Consensus size: 133
5550071 TAAATGTAAA
5550081 ATTGTACTTTTTCCCCCTAAAATGATAAAATTTTGATTTAATCCTTTAAAAATTATCTTTTTACT
1 ATTGTACTTTTTCCCCCTAAAATGATAAAATTTTGATTTAATCCTTTAAAAATTATCTTTTTACT
5550146 ATTATAAAAATTACAATTTAATTTCGGTCTTCTTAAAAAAATTTCTTAGCTTCACCCCTGATTGT
66 ATTATAAAAATTACAATTTAATTTCGGTCTTCTTAAAAAAATTTCTTAGCTTCACCCCTGATTGT
5550211 ACT
131 ACT
5550214 ATTGTAC-TTTTCCCCCTAAAATGATAAAATTTTGATTTAATCCTTTAAAAATTATCTTTTTACT
1 ATTGTACTTTTTCCCCCTAAAATGATAAAATTTTGATTTAATCCTTTAAAAATTATCTTTTTACT
5550278 ATTATAAAAATTACAATTTAATTTCGGTCTTCTTAAAAAAATTTCTTAGCTTCACCCCTGATTGT
66 ATTATAAAAATTACAATTTAATTTCGGTCTTCTTAAAAAAATTTCTTAGCTTCACCCCTGATTGT
5550343 ACT
131 ACT
5550346 A
1 A
5550347 ACTATTTTTT
Statistics
Matches: 133, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
132 126 0.95
133 7 0.05
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (133 bp):
ATTGTACTTTTTCCCCCTAAAATGATAAAATTTTGATTTAATCCTTTAAAAATTATCTTTTTACT
ATTATAAAAATTACAATTTAATTTCGGTCTTCTTAAAAAAATTTCTTAGCTTCACCCCTGATTGT
ACT
Found at i:5553444 original size:20 final size:20
Alignment explanation
Indices: 5553410--5553451 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5553400 AACTATTTAA
** *
5553410 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
5553430 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
5553450 AT
1 AT
5553452 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:5557806 original size:22 final size:22
Alignment explanation
Indices: 5557778--5557819 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5557768 TATAAAGAAT
5557778 ATATAAAAGAAAAACT-TAAAAA
1 ATATAAAA-AAAAACTCTAAAAA
5557800 ATATAAAAAAAAACTCTAAA
1 ATATAAAAAAAAACTCTAAA
5557820 CTTTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.19
Consensus pattern (22 bp):
ATATAAAAAAAAACTCTAAAAA
Found at i:5560304 original size:2 final size:2
Alignment explanation
Indices: 5560297--5560326 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5560287 TGGCTTGTAT
5560297 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5560327 TCGCTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5567615 original size:23 final size:23
Alignment explanation
Indices: 5567570--5567615 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5567560 AATGCAACAA
* *
5567570 GAGACCAGCAACAGTTCAGCATG
1 GAGACCAGCAACAGCTCAACATG
*
5567593 GAGACCAGCAGCAGCTCAACATG
1 GAGACCAGCAACAGCTCAACATG
5567616 AAGATCGGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.28, G:0.26, T:0.11
Consensus pattern (23 bp):
GAGACCAGCAACAGCTCAACATG
Found at i:5572086 original size:23 final size:23
Alignment explanation
Indices: 5572056--5572101 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5572046 AATGCAACAA
* *
5572056 GAGACCAGCAGCAGTTCAGCATG
1 GAGACCAGCAGCAGCTCAACATG
5572079 GAGACCAGCAGCAGCTCAACATG
1 GAGACCAGCAGCAGCTCAACATG
5572102 AAGATTGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.11
Consensus pattern (23 bp):
GAGACCAGCAGCAGCTCAACATG
Found at i:5575423 original size:19 final size:20
Alignment explanation
Indices: 5575390--5575443 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
5575380 AAAAAATATA
5575390 AATTTTAATATTTTT-ATAAAT
1 AATTTTAA-ATTTTTGA-AAAT
5575411 -ATTTTAAATTTTTGAAAAT
1 AATTTTAAATTTTTGAAAAT
*
5575430 AATTTTGAATTTTT
1 AATTTTAAATTTTT
5575444 TTTTTTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
AATTTTAAATTTTTGAAAAT
Found at i:5590196 original size:24 final size:24
Alignment explanation
Indices: 5590159--5590222 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
5590149 CCAAACACTC
* *
5590159 ACACTCAGTTCTCTGCGCAGCCAA
1 ACACTCAGTCCTCTGCCCAGCCAA
*
5590183 ACACTCAATCCTCTGCCCAGCCAA
1 ACACTCAGTCCTCTGCCCAGCCAA
5590207 ACACTCAGTCCT-TGCC
1 ACACTCAGTCCTCTGCC
5590223 TGCCAACCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 4 0.11
24 32 0.89
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.20
Consensus pattern (24 bp):
ACACTCAGTCCTCTGCCCAGCCAA
Found at i:5591246 original size:15 final size:15
Alignment explanation
Indices: 5591226--5591260 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
5591216 GGAGAATTTA
5591226 AAAGAATTTGAAGTC
1 AAAGAATTTGAAGTC
5591241 AAAGAATTTGAAGTC
1 AAAGAATTTGAAGTC
5591256 AAAGA
1 AAAGA
5591261 GCTCGGTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (15 bp):
AAAGAATTTGAAGTC
Found at i:5603835 original size:23 final size:24
Alignment explanation
Indices: 5603809--5603854 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5603799 TTCTAACATA
*
5603809 TGAGTATTGA-AAAAACAAATGTG
1 TGAGAATTGAGAAAAACAAATGTG
*
5603832 TGAGAATTGAGAAATACAAATGT
1 TGAGAATTGAGAAAAACAAATGT
5603855 TTGTTTCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (24 bp):
TGAGAATTGAGAAAAACAAATGTG
Found at i:5604082 original size:36 final size:36
Alignment explanation
Indices: 5604031--5604150 Score: 195
Period size: 36 Copynumber: 3.3 Consensus size: 36
5604021 GTTAGCCATG
* *
5604031 TATACCAGCAGCCATGTATAACAACATAAGCAACAA
1 TATACCAGCAACCATGTATACCAACATAAGCAACAA
*
5604067 TATACCAGCAACCATGTATACCAACATAAGTAACAA
1 TATACCAGCAACCATGTATACCAACATAAGCAACAA
**
5604103 TATACCAGCAGTCATGTATACCAACATAAGCAACAA
1 TATACCAGCAACCATGTATACCAACATAAGCAACAA
5604139 TATACCAGCAAC
1 TATACCAGCAAC
5604151 AATATTACAA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 76 1.00
ACGTcount: A:0.46, C:0.26, G:0.10, T:0.18
Consensus pattern (36 bp):
TATACCAGCAACCATGTATACCAACATAAGCAACAA
Found at i:5604108 original size:20 final size:20
Alignment explanation
Indices: 5604083--5604145 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
5604073 AGCAACCATG
5604083 TATACCAACATAAGTAACAA
1 TATACCAACATAAGTAACAA
* *
5604103 TATACCAGC---AGT--CATG
1 TATACCAACATAAGTAACA-A
*
5604119 TATACCAACATAAGCAACAA
1 TATACCAACATAAGTAACAA
5604139 TATACCA
1 TATACCA
5604146 GCAACAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 12
0.65 0.10 0.24
Matches are distributed among these distances:
15 2 0.06
16 8 0.25
17 3 0.09
19 2 0.06
20 15 0.47
21 2 0.06
ACGTcount: A:0.48, C:0.24, G:0.08, T:0.21
Consensus pattern (20 bp):
TATACCAACATAAGTAACAA
Found at i:5607456 original size:42 final size:41
Alignment explanation
Indices: 5607397--5607482 Score: 145
Period size: 42 Copynumber: 2.1 Consensus size: 41
5607387 TTTAGGCAGT
*
5607397 GTTTCTCTGTTATCAATCGCTGCTGATAAATGTCATCATGGG
1 GTTTCTCTGTTATCAATCACTGCTGAT-AATGTCATCATGGG
*
5607439 GTTTCTCTGTTATCAATCACTGCTGATAATGTCATCATGTG
1 GTTTCTCTGTTATCAATCACTGCTGATAATGTCATCATGGG
5607480 GTT
1 GTT
5607483 ACTTCTGGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
41 16 0.38
42 26 0.62
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (41 bp):
GTTTCTCTGTTATCAATCACTGCTGATAATGTCATCATGGG
Found at i:5611658 original size:9 final size:9
Alignment explanation
Indices: 5611644--5611673 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5611634 TCGAACTAGC
5611644 ATTAATCGA
1 ATTAATCGA
5611653 ATTAATCGA
1 ATTAATCGA
*
5611662 ATTATTCGA
1 ATTAATCGA
5611671 ATT
1 ATT
5611674 GTATAATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (9 bp):
ATTAATCGA
Found at i:5626687 original size:25 final size:25
Alignment explanation
Indices: 5626603--5626672 Score: 68
Period size: 27 Copynumber: 2.7 Consensus size: 25
5626593 CCAATATCGA
* * * *
5626603 GAAGCTTCGAAGAGCCATTAATTAG
1 GAAGCTCCGGAGAGCCTTTAATCAG
* *
5626628 GAAGCTCATGAAAGAGCCTTTAATCAG
1 GAAGCTC-CG-GAGAGCCTTTAATCAG
5626655 GAAGCTCCGGAGAGCCTT
1 GAAGCTCCGGAGAGCCTT
5626673 ATATCGGGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
25 14 0.38
26 2 0.05
27 21 0.57
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (25 bp):
GAAGCTCCGGAGAGCCTTTAATCAG
Found at i:5626693 original size:25 final size:25
Alignment explanation
Indices: 5626603--5626694 Score: 78
Period size: 25 Copynumber: 3.6 Consensus size: 25
5626593 CCAATATCGA
* * *
5626603 GAAGCTTCGAAGAGCCATTAATTAG
1 GAAGCTCCGAAGAGCCTTTAATCAG
*
5626628 GAAGCTCATGAAAGAGCCTTTAATCAG
1 GAAGCTC-CG-AAGAGCCTTTAATCAG
* *
5626655 GAAGCTCCGGAGAGCC-TTATATCGG
1 GAAGCTCCGAAGAGCCTTTA-ATCAG
* *
5626680 GATGCTCCTAAGAGC
1 GAAGCTCCGAAGAGC
5626695 TACGACGTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 3 0.06
25 28 0.52
26 2 0.04
27 21 0.39
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.22
Consensus pattern (25 bp):
GAAGCTCCGAAGAGCCTTTAATCAG
Found at i:5626767 original size:24 final size:25
Alignment explanation
Indices: 5626734--5626794 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
5626724 ACAACCAAAT
* *
5626734 CGGGATGCTCATAAGAACTAT-TAA
1 CGGGAAGCTCATAAGAACCATATAA
**
5626758 CGGGAAGCTCGCAAGAACCATATAA
1 CGGGAAGCTCATAAGAACCATATAA
5626783 CGGGAAGCTCAT
1 CGGGAAGCTCAT
5626795 GAGAGCCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 17 0.57
25 13 0.43
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (25 bp):
CGGGAAGCTCATAAGAACCATATAA
Found at i:5626789 original size:25 final size:24
Alignment explanation
Indices: 5626746--5626792 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
5626736 GGATGCTCAT
*
5626746 AAGAACTATTAACGGGAAGCTCGC
1 AAGAACCATTAACGGGAAGCTCGC
5626770 AAGAACCATATAACGGGAAGCTC
1 AAGAACCAT-TAACGGGAAGCTC
5626793 ATGAGAGCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.15
Consensus pattern (24 bp):
AAGAACCATTAACGGGAAGCTCGC
Found at i:5628970 original size:26 final size:26
Alignment explanation
Indices: 5628941--5629016 Score: 91
Period size: 26 Copynumber: 2.9 Consensus size: 26
5628931 TTTCATCCCT
* * *
5628941 ATTTTACCCCCAGCAAAATTTTGATG
1 ATTTTACCCCTAGTAAAATTTTGACG
*
5628967 ATTTTA-CCCTTGATAAAATTTTGACG
1 ATTTTACCCCTAG-TAAAATTTTGACG
*
5628993 ATTTTACCCCTGGTAAAATTTTGA
1 ATTTTACCCCTAGTAAAATTTTGA
5629017 GAAAATATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
25 4 0.09
26 34 0.79
27 5 0.12
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTTTGACG
Found at i:5631788 original size:18 final size:15
Alignment explanation
Indices: 5631751--5631780 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5631741 TCTAAGTTTA
5631751 AAAAAATAATTACAT
1 AAAAAATAATTACAT
5631766 AAAAAATAATTACAT
1 AAAAAATAATTACAT
5631781 CATTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAAATAATTACAT
Found at i:5632946 original size:14 final size:15
Alignment explanation
Indices: 5632927--5632960 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5632917 CTGAATCTAT
5632927 TTTGGGCCACTGTA-
1 TTTGGGCCACTGTAG
*
5632941 TTTGGGCCTCTGTAG
1 TTTGGGCCACTGTAG
5632956 TTTGG
1 TTTGG
5632961 TTTATTTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.09, C:0.18, G:0.32, T:0.41
Consensus pattern (15 bp):
TTTGGGCCACTGTAG
Found at i:5633842 original size:267 final size:267
Alignment explanation
Indices: 5633296--5633813 Score: 743
Period size: 267 Copynumber: 1.9 Consensus size: 267
5633286 ATATTCAGTC
5633296 TTTTAAATTGCAATGTTAGGGAAACAAGATTCGCCATCGTAGCTTCAATATGTTCTACTACACCG
1 TTTTAAATTGCAATGTTAGGGAAACAAGATTCGCCATCGTAGCTTCAATATGTTCTACTACACCG
* * * *
5633361 CCAGGGGAGTAAGAGTCGCCGTTGTGGCTTTAATCTGCTCCACCGTAATGCCAAAGAGATAGAAT
66 CCAGGGAAGTAAGAGTCACCGTCGTGGCTTTAATCTGCTCCACCATAATGCCAAAGAGATAGAAT
* *
5633426 TCACTGCCCACAGCTTCAATCCGCTTCACTTCAGCTAATCCAAGCCTTAACGCTAGGGAGATAAG
131 TCACTGCCCACAGCTTCAATCCGCTTCACTTCAGCTAATCCAAGCCTTAACGCCAAGGAGATAAG
* * * * * *
5633491 ATTCACCGCCGTGGCTTCAATTTGCTCCGCTACAATGCTAGGGAAGTAAGATTCGTCGTTATGGT
196 ATTCACCGCCGTGGCTTCAATCTGCTCCACTACAACGCCAGGGAAGTAAAATTCATCGTTATGGT
5633556 TTCAATA
261 TTCAATA
* * * *
5633563 TTTTAAATTGCAATGTT-GGAGAAACGAGATTTGCCGTCGTAGCTTCAATCTGTT-TCACTACAC
1 TTTTAAATTGCAATGTTAGG-GAAACAAGATTCGCCATCGTAGCTTCAATATGTTCT-ACTACAC
* * * * *
5633626 CGCTAGGGAAGTAAGATTCACCGTCGTGGTTTTAATCTGCTCCACTATAATGCCAAAGAGATAGG
64 CGCCAGGGAAGTAAGAGTCACCGTCGTGGCTTTAATCTGCTCCACCATAATGCCAAAGAGATAGA
* *
5633691 ATTCGCTGCCCACAGCTTCAATCCGCTTCACTTCAGCTAATCCAAGCCTTAATGCCAAGGAGATA
129 ATTCACTGCCCACAGCTTCAATCCGCTTCACTTCAGCTAATCCAAGCCTTAACGCCAAGGAGATA
* * * * * *
5633756 AGATTCACTGTCGTGGTTTCAATCTGCTCTACTATAACGCCAGGGGAGTAAAATTCAT
194 AGATTCACCGCCGTGGCTTCAATCTGCTCCACTACAACGCCAGGGAAGTAAAATTCAT
5633814 TGTTGTGGCT
Statistics
Matches: 220, Mismatches: 29, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
266 3 0.01
267 217 0.99
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (267 bp):
TTTTAAATTGCAATGTTAGGGAAACAAGATTCGCCATCGTAGCTTCAATATGTTCTACTACACCG
CCAGGGAAGTAAGAGTCACCGTCGTGGCTTTAATCTGCTCCACCATAATGCCAAAGAGATAGAAT
TCACTGCCCACAGCTTCAATCCGCTTCACTTCAGCTAATCCAAGCCTTAACGCCAAGGAGATAAG
ATTCACCGCCGTGGCTTCAATCTGCTCCACTACAACGCCAGGGAAGTAAAATTCATCGTTATGGT
TTCAATA
Found at i:5633957 original size:43 final size:44
Alignment explanation
Indices: 5633890--5634025 Score: 134
Period size: 44 Copynumber: 3.1 Consensus size: 44
5633880 ATTGCCAGCA
5633890 CAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCT
1 CAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCT
* * * * * **
5633934 CAGGGAGACAAG-GCTGGTATCTTCGATCTACTTGACTG-T-CAAT
1 CAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGC--T
* * *
5633977 ACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTACTGCT
1 -CAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCT
5634022 CAGG
1 CAGG
5634026 GAGATAAGTC
Statistics
Matches: 70, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 21 0.30
44 26 0.37
45 19 0.27
46 1 0.01
47 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (44 bp):
CAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCT
Found at i:5638931 original size:29 final size:29
Alignment explanation
Indices: 5638889--5638946 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
5638879 TCTAGGCTAA
5638889 AACAACAAGTTTGTTCTGAATATTACTCT
1 AACAACAAGTTTGTTCTGAATATTACTCT
*
5638918 AACAACAAGTTTGTTTTGAATATTACTCT
1 AACAACAAGTTTGTTCTGAATATTACTCT
5638947 GAGATAGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (29 bp):
AACAACAAGTTTGTTCTGAATATTACTCT
Found at i:5646040 original size:12 final size:13
Alignment explanation
Indices: 5646016--5646064 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
5646006 AATGGCATAT
5646016 AAATAATATAAAC
1 AAATAATATAAAC
5646029 AAATAA-ATAAAC
1 AAATAATATAAAC
*
5646041 AAAATGAATATATAAA
1 -AAAT-AATATA-AAC
5646057 AAATAATA
1 AAATAATA
5646065 ATCCATGGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.19
13 10 0.32
14 6 0.19
15 7 0.23
16 2 0.06
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (13 bp):
AAATAATATAAAC
Found at i:5646646 original size:19 final size:16
Alignment explanation
Indices: 5646606--5646638 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5646596 ATATATAAGT
5646606 TAAAAAAATAATTACA
1 TAAAAAAATAATTACA
5646622 TAAAAAAATAATTACA
1 TAAAAAAATAATTACA
5646638 T
1 T
5646639 CATTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAAAATAATTACA
Found at i:5647807 original size:14 final size:15
Alignment explanation
Indices: 5647788--5647821 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5647778 CTGAATCTTT
5647788 TTTGGGCCACTGTA-
1 TTTGGGCCACTGTAG
*
5647802 TTTGGGCCTCTGTAG
1 TTTGGGCCACTGTAG
5647817 TTTGG
1 TTTGG
5647822 TTTATTGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.09, C:0.18, G:0.32, T:0.41
Consensus pattern (15 bp):
TTTGGGCCACTGTAG
Found at i:5655313 original size:16 final size:17
Alignment explanation
Indices: 5655281--5655313 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5655271 ATTTTATATG
*
5655281 TTAATTAATAGAAGCAT
1 TTAATTAATAAAAGCAT
5655298 TTAATT-ATAAAAGCAT
1 TTAATTAATAAAAGCAT
5655314 GAAGAAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (17 bp):
TTAATTAATAAAAGCAT
Found at i:5668473 original size:20 final size:20
Alignment explanation
Indices: 5668448--5668485 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5668438 ATGCTAACAA
5668448 AGGCACCAAAGTGCAATCAG
1 AGGCACCAAAGTGCAATCAG
*
5668468 AGGCACCGAAGTGCAATC
1 AGGCACCAAAGTGCAATC
5668486 CCGTACAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.26, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGCACCAAAGTGCAATCAG
Found at i:5669307 original size:18 final size:18
Alignment explanation
Indices: 5669264--5669326 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 18
5669254 TTTAAATGTT
5669264 AAAAATAATTAAAAT-AAG
1 AAAAA-AATTAAAATAAAG
*
5669282 TAATAAAATTAAAATAAAAG
1 -AAAAAAATTAAAAT-AAAG
5669302 AAAAAAAGGTTAAAATATAAG
1 AAAAAAA--TTAAAATA-AAG
5669323 AAAA
1 AAAA
5669327 CATAATGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 9 0.24
19 10 0.27
20 4 0.11
21 14 0.38
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (18 bp):
AAAAAAATTAAAATAAAG
Found at i:5670309 original size:39 final size:39
Alignment explanation
Indices: 5670252--5670370 Score: 139
Period size: 39 Copynumber: 3.0 Consensus size: 39
5670242 TACTTTCTAT
* *
5670252 TTGGCATGATTCGAGTGGATCAGCTCTTATGAGCTTCTG
1 TTGGCATGTTTCGGGTGGATCAGCTCTTATGAGCTTCTG
*
5670291 TTGGCATGTTTCGGGTGGACCAGCTCTTATGAGCTTCTG
1 TTGGCATGTTTCGGGTGGATCAGCTCTTATGAGCTTCTG
** * * * **
5670330 TTTGGTGTATTTCAGTTGGATCAAATCTTATGAGCTTCTG
1 -TTGGCATGTTTCGGGTGGATCAGCTCTTATGAGCTTCTG
5670370 T
1 T
5670371 CTAGTTTGTT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 37 0.54
40 31 0.46
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (39 bp):
TTGGCATGTTTCGGGTGGATCAGCTCTTATGAGCTTCTG
Found at i:5674609 original size:122 final size:122
Alignment explanation
Indices: 5674390--5674635 Score: 467
Period size: 122 Copynumber: 2.0 Consensus size: 122
5674380 TTATTTTAGT
5674390 AAAAGGTTAATAAATTATTATATGCTAAAATTTAACTAAAAGAAAGCCATGTTCATCTTTGTGAT
1 AAAAGGTTAATAAATTATTATATGCTAAAATTTAACTAAAAGAAAGCCATGTTCATCTTTGTGAT
5674455 TGCCGAAACTCAAAGAAAAGAAATAGGAAAAAAATTTAGGAACATTCGGTCACTTGG
66 TGCCGAAACTCAAAGAAAAGAAATAGGAAAAAAATTTAGGAACATTCGGTCACTTGG
5674512 AAAAGGTTAAT-AATTATTATATGCTAAAAATTTAACTAAAAGAAAGCCATGTTCATCTTTGTGA
1 AAAAGGTTAATAAATTATTATATGCT-AAAATTTAACTAAAAGAAAGCCATGTTCATCTTTGTGA
*
5674576 TTGCCGAAACTCAAAGAAAAGAAATAGGGAAAAAATTTAGGAACATTCGGTCACTTGG
65 TTGCCGAAACTCAAAGAAAAGAAATAGGAAAAAAATTTAGGAACATTCGGTCACTTGG
5674634 AA
1 AA
5674636 GCTCAAATTC
Statistics
Matches: 122, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
121 14 0.11
122 108 0.89
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (122 bp):
AAAAGGTTAATAAATTATTATATGCTAAAATTTAACTAAAAGAAAGCCATGTTCATCTTTGTGAT
TGCCGAAACTCAAAGAAAAGAAATAGGAAAAAAATTTAGGAACATTCGGTCACTTGG
Found at i:5674842 original size:29 final size:30
Alignment explanation
Indices: 5674790--5674850 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 30
5674780 GTGATGTTTG
5674790 ATAATGAATAATGAAAGATATGTTTTAGATT
1 ATAATGAATAA-GAAAGATATGTTTTAGATT
5674821 ATAATGAATAA-AAAGATATGTTTTAGATT
1 ATAATGAATAAGAAAGATATGTTTTAGATT
5674850 A
1 A
5674851 ATATGTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 19 0.63
31 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.38
Consensus pattern (30 bp):
ATAATGAATAAGAAAGATATGTTTTAGATT
Found at i:5681824 original size:11 final size:11
Alignment explanation
Indices: 5681808--5681890 Score: 96
Period size: 11 Copynumber: 7.5 Consensus size: 11
5681798 AGCATGAAGA
5681808 TGGTGTTGTTT
1 TGGTGTTGTTT
5681819 TGGTGTTGTTT
1 TGGTGTTGTTT
*
5681830 GTGATGTTGTTTT
1 -TGGTGTTG-TTT
*
5681843 TTGTGTTGTTT
1 TGGTGTTGTTT
* *
5681854 TGATGCTG-TT
1 TGGTGTTGTTT
5681864 TGGTGTTGTTT
1 TGGTGTTGTTT
*
5681875 TGATGTTGTTT
1 TGGTGTTGTTT
5681886 TGGTG
1 TGGTG
5681891 CTACTTTTGT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
10 8 0.14
11 35 0.59
12 13 0.22
13 3 0.05
ACGTcount: A:0.04, C:0.01, G:0.34, T:0.61
Consensus pattern (11 bp):
TGGTGTTGTTT
Found at i:5681864 original size:35 final size:31
Alignment explanation
Indices: 5681810--5681892 Score: 103
Period size: 35 Copynumber: 2.5 Consensus size: 31
5681800 CATGAAGATG
*
5681810 GTGTTGTTTTGGTGTTGTTTGTGATGTTGTTTTTT
1 GTGTTGTTTTGGTGCTGTTTG-G-TGTTG--TTTT
*
5681845 GTGTTGTTTTGATGCTGTTTGGTGTTGTTTT
1 GTGTTGTTTTGGTGCTGTTTGGTGTTGTTTT
5681876 GATGTTGTTTTGGTGCT
1 G-TGTTGTTTTGGTGCT
5681893 ACTTTTGTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
31 5 0.11
32 14 0.32
33 5 0.11
34 1 0.02
35 19 0.43
ACGTcount: A:0.04, C:0.02, G:0.33, T:0.61
Consensus pattern (31 bp):
GTGTTGTTTTGGTGCTGTTTGGTGTTGTTTT
Found at i:5681869 original size:21 final size:22
Alignment explanation
Indices: 5681811--5681890 Score: 117
Period size: 21 Copynumber: 3.6 Consensus size: 22
5681801 ATGAAGATGG
5681811 TGTTGTTTTGGTGTTGTTTGTGA
1 TGTTGTTTTGGTGTTGTTT-TGA
*
5681834 TGTTGTTTTTTGTGTTGTTTTGA
1 TGTTG-TTTTGGTGTTGTTTTGA
*
5681857 TGCTG-TTTGGTGTTGTTTTGA
1 TGTTGTTTTGGTGTTGTTTTGA
5681878 TGTTGTTTTGGTG
1 TGTTGTTTTGGTG
5681891 CTACTTTTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
21 19 0.37
22 7 0.14
23 12 0.24
24 13 0.25
ACGTcount: A:0.04, C:0.01, G:0.33, T:0.62
Consensus pattern (22 bp):
TGTTGTTTTGGTGTTGTTTTGA
Found at i:5681976 original size:41 final size:42
Alignment explanation
Indices: 5681931--5682021 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 42
5681921 CAGCTCTTTA
5681931 TGTTTTTATTAT-ATTTTTAATTTGTGTATTGTTTTAAGAAT
1 TGTTTTTATTATCATTTTTAATTTGTGTATTGTTTTAAGAAT
* * * * * * *
5681972 TG-TTTTAGTGTCATTTTTTATTTGTTTCTTGTTTTAATATT
1 TGTTTTTATTATCATTTTTAATTTGTGTATTGTTTTAAGAAT
5682013 TGTTTTTAT
1 TGTTTTTAT
5682022 GTTTTTAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
40 7 0.17
41 28 0.70
42 5 0.12
ACGTcount: A:0.19, C:0.02, G:0.12, T:0.67
Consensus pattern (42 bp):
TGTTTTTATTATCATTTTTAATTTGTGTATTGTTTTAAGAAT
Found at i:5682384 original size:22 final size:22
Alignment explanation
Indices: 5682342--5682384 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5682332 ATACTCTTCG
*
5682342 TACTTTTAAATTTTAGTATTTT
1 TACTTTTAAATTTTAGAATTTT
5682364 TACTTTT-AATTTTAAGAATTT
1 TACTTTTAAATTTT-AGAATTT
5682385 AACCCCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (22 bp):
TACTTTTAAATTTTAGAATTTT
Found at i:5686262 original size:49 final size:49
Alignment explanation
Indices: 5686195--5686293 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
5686185 CATAAAACCG
5686195 AAATAAGTAATAACAAAAAAAAATGGCATATGATTAGGTATCCAGAAAT
1 AAATAAGTAATAACAAAAAAAAATGGCATATGATTAGGTATCCAGAAAT
5686244 AAATAAGTAATAACAAAAAAAAATGGCATATGATTAGGTATCCAGAAAT
1 AAATAAGTAATAACAAAAAAAAATGGCATATGATTAGGTATCCAGAAAT
5686293 A
1 A
5686294 GTTAAGACAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.56, C:0.08, G:0.14, T:0.22
Consensus pattern (49 bp):
AAATAAGTAATAACAAAAAAAAATGGCATATGATTAGGTATCCAGAAAT
Found at i:5690365 original size:71 final size:71
Alignment explanation
Indices: 5690249--5690405 Score: 287
Period size: 71 Copynumber: 2.2 Consensus size: 71
5690239 TAACACTCAA
5690249 AATTTATCAATATCACTTTAACAGTAGGCATGATTAATATCACATGTTTACTCATAGCATCGTAA
1 AATTTATCAATATCACTTTAACAGTAGGCATGATTAATATCACATGTTTACTCATAGCATCGTAA
5690314 CAATTC
66 CAATTC
*
5690320 AATTTATCAATATCACTTTAACAGTAGGCATGATTAATATCACATGTTTACTCATAGCATTGTAA
1 AATTTATCAATATCACTTTAACAGTAGGCATGATTAATATCACATGTTTACTCATAGCATCGTAA
**
5690385 TGATTC
66 CAATTC
5690391 AATTTATCAATATCA
1 AATTTATCAATATCA
5690406 ATAAACACAT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 83 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (71 bp):
AATTTATCAATATCACTTTAACAGTAGGCATGATTAATATCACATGTTTACTCATAGCATCGTAA
CAATTC
Found at i:5704015 original size:14 final size:14
Alignment explanation
Indices: 5703996--5704022 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5703986 ATTTGCCTAC
5703996 TTATTTTTTTATTG
1 TTATTTTTTTATTG
5704010 TTATTTTTTTATT
1 TTATTTTTTTATT
5704023 TATTTTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (14 bp):
TTATTTTTTTATTG
Found at i:5712371 original size:2 final size:2
Alignment explanation
Indices: 5712364--5712388 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5712354 TTTGCAAGAT
5712364 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5712389 GTGTGTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5714639 original size:2 final size:2
Alignment explanation
Indices: 5714632--5714663 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5714622 GTGTAACTGG
*
5714632 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5714664 GAACTGTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5716504 original size:2 final size:2
Alignment explanation
Indices: 5716497--5716526 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5716487 GCAACAATTA
*
5716497 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5716527 GTAATGCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5719201 original size:2 final size:2
Alignment explanation
Indices: 5719194--5719229 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5719184 TTAAATAACT
5719194 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5719230 CATCATCACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5719322 original size:2 final size:2
Alignment explanation
Indices: 5719315--5719350 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5719305 TTAAATAACT
5719315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5719351 CATCATCACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5737347 original size:102 final size:100
Alignment explanation
Indices: 5737140--5737473 Score: 379
Period size: 100 Copynumber: 3.3 Consensus size: 100
5737130 TATCGATGAA
*
5737140 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACGTGTAGTACTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACGTGTAGTACTA
* *
5737205 AGTGAAGGCTACAATGTGTACCGAGAAGCTTTGAT
66 AGTGAAGGCTACAATATGTACCGAAAAGCTTTGAT
* * *
5737240 CACGTGTGCAGTACTGTGTGAAGGCTACCACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCAC--GTGTAGTAC
* * *
5737305 TAAGTGTAGGCTACTATATGTACCGAAAAGCTTTGGT
64 TAAGTGAAGGCTACAATATGTACCGAAAAGCTTTGAT
* * * * * * *
5737342 CACGTGTGTAGTACTCTATGAAGGCTACTACGTAAACCG-TAAA-ACTTGATCACGTGTGCAGTG
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACGTGT--AGTA
* * ** * *
5737405 CTATGTGAAGGCTACTACGTGAACCCTAAAA-C-TTGAT
63 CTAAGTGAAGGCTACAATATGTA-CCGAAAAGCTTTGAT
*
5737442 CACGTGTGTAGTACTATGTGAAGGCTACTACG
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACG
5737474 CGTATCGAAT
Statistics
Matches: 200, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
99 4 0.02
100 84 0.42
101 32 0.16
102 80 0.40
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (100 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACGTGTAGTACTA
AGTGAAGGCTACAATATGTACCGAAAAGCTTTGAT
Found at i:5737414 original size:50 final size:50
Alignment explanation
Indices: 5737140--5737473 Score: 291
Period size: 51 Copynumber: 6.6 Consensus size: 50
5737130 TATCGATGAA
* * * * *
5737140 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGAT
* * * * *
5737191 CAC--GTGTAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGAT
* * * * *** *
5737240 CACGTGTGCAGTACTGTGTGAAGGCTACCACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGAT
* * * ** * *
5737291 CACATGTGTAGTACTAAGTGTAGGCTACTATATGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGAT
* * *
5737342 CACGTGTGTAGTACTCTATGAAGGCTACTACGTAAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
* * *
5737392 CACGTGTGCAGTGCTATGTGAAGGCTACTACGTGAACCCTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
5737442 CACGTGTGTAGTACTATGTGAAGGCTACTACG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACG
5737474 CGTATCGAAT
Statistics
Matches: 223, Mismatches: 50, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
47 1 0.00
48 2 0.01
49 38 0.17
50 78 0.35
51 97 0.43
52 6 0.03
53 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
Found at i:5737506 original size:202 final size:202
Alignment explanation
Indices: 5737140--5737507 Score: 431
Period size: 202 Copynumber: 1.8 Consensus size: 202
5737130 TATCGATGAA
* * ** * *
5737140 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACGTGTAGTACTA
1 CACGTGTGTAGTACTCTATGAAGGCTACTACGTAAACCGATAAATAATGATCACGTGTAGTACTA
* * * *
5737205 AGTGAAGGCTACAATGTGTACCGAGAAGCTTTGATCACGTGTGCAGTACTGTGTGAAGGCTACCA
66 AGTGAAGGCTACAACGTGAACCGAGAAACTTTGATCACGTGTGCAGTACTATGTGAAGGCTACCA
* * ** * *
5737270 CGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGTAGGCTACTATATGTACCGAAAAG
131 CGCGAATCGATAAATAAAAGTAACATGGGTAGTACTAAGTGTAGGCTACTATATGTACCGAAAAG
5737335 CTTTGGT
196 CTTTGGT
* *
5737342 CACGTGTGTAGTACTCTATGAAGGCTACTACGTAAACCG-TAAA-ACTTGATCACGTGTGCAGTG
1 CACGTGTGTAGTACTCTATGAAGGCTACTACGTAAACCGATAAATA-ATGATCACGTGT--AGTA
* * * *
5737405 CTATGTGAAGGCTACTACGTGAACCCTA-AAAC-TTGATCACGTGTGTAGTACTATGTGAAGGCT
63 CTAAGTGAAGGCTACAACGTGAA-CCGAGAAACTTTGATCACGTGTGCAGTACTATGTGAAGGCT
* * *
5737468 ACTACGCGTATCGA-ATGATAAAAGTAACATGGGTAGTACT
127 ACCACGCGAATCGATA-AATAAAAGTAACATGGGTAGTACT
5737508 GTGTGAAAAA
Statistics
Matches: 136, Mismatches: 25, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
200 1 0.01
201 15 0.11
202 92 0.68
203 25 0.18
204 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (202 bp):
CACGTGTGTAGTACTCTATGAAGGCTACTACGTAAACCGATAAATAATGATCACGTGTAGTACTA
AGTGAAGGCTACAACGTGAACCGAGAAACTTTGATCACGTGTGCAGTACTATGTGAAGGCTACCA
CGCGAATCGATAAATAAAAGTAACATGGGTAGTACTAAGTGTAGGCTACTATATGTACCGAAAAG
CTTTGGT
Found at i:5740470 original size:56 final size:50
Alignment explanation
Indices: 5740180--5740476 Score: 240
Period size: 50 Copynumber: 5.8 Consensus size: 50
5740170 GATAATAACA
* ** ** * *
5740180 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAAATGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * * ** *
5740229 TGCCAATGTCATATCCCAGATATGGTCTTACATGAGAATTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
5740279 TGCCCATGCCATGTCCCAGACATGGTCTTA-AGGGGGACCTTTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCGG
* **
5740329 TGTCAACGCCATGTCTTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* **
5740379 TGCCAACGCCATGTCCCAGACATAGTCTTGTATGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* * * *
5740434 ATGCCAATGCCTTGTCCCAGACATGGTTTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5740477 TTACCCAAAT
Statistics
Matches: 199, Mismatches: 39, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 39 0.20
50 116 0.58
51 1 0.01
53 5 0.03
55 2 0.01
56 35 0.18
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:5744104 original size:18 final size:18
Alignment explanation
Indices: 5744070--5744104 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5744060 ACATGCTCAC
*
5744070 ATAATCACTTATCACATA
1 ATAATCACTTATAACATA
*
5744088 ATAATCACTTTTAACAT
1 ATAATCACTTATAACAT
5744105 GTTTAACATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATCACTTATAACATA
Found at i:5746356 original size:29 final size:29
Alignment explanation
Indices: 5746316--5746407 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
5746306 CTGGGCATAC
* * *
5746316 GCCCGTATGCTTCACACGGTCATGTGATA
1 GCCCGTGTGCTTCACACAGCCATGTGATA
*
5746345 GCCTGTGTGCTTCACACAGCCATGTGATA
1 GCCCGTGTGCTTCACACAGCCATGTGATA
* *
5746374 GCCCGTGT-CCTCTACAC-GACTATGTGATA
1 GCCCGTGTGCTTC-ACACAG-CCATGTGATA
5746403 GCCCG
1 GCCCG
5746408 AGTCCTAGGC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.07
29 50 0.93
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (29 bp):
GCCCGTGTGCTTCACACAGCCATGTGATA
Found at i:5747359 original size:36 final size:36
Alignment explanation
Indices: 5747292--5747360 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
5747282 AATATATCAA
* *
5747292 TGGATAACGCTCATTTGAGCTTCTTCAGTATATTGG
1 TGGATAACGCTCAGTTGAACTTCTTCAGTATATTGG
* *
5747328 TGGATATCGCTC-GTTGAACTTCATTCGGTATAT
1 TGGATAACGCTCAGTTGAACTTC-TTCAGTATAT
5747361 GTAATATAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 8 0.29
36 20 0.71
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (36 bp):
TGGATAACGCTCAGTTGAACTTCTTCAGTATATTGG
Found at i:5751062 original size:30 final size:30
Alignment explanation
Indices: 5750996--5751075 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
5750986 AAACTAAGAT
*
5750996 ATATAAAATTATTTAAATAATTATGTTGTA
1 ATATAAAATTATATAAATAATTATGTTGTA
* *
5751026 ATATAAAATTATATAATTATGTTATGATT-TA
1 ATATAAAATTATATAAATA-ATTATG-TTGTA
5751057 A-ATAAAATTACTTATAAAT
1 ATATAAAATTA--TATAAAT
5751076 CCGTGTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 26 0.62
31 8 0.19
32 8 0.19
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (30 bp):
ATATAAAATTATATAAATAATTATGTTGTA
Found at i:5774606 original size:20 final size:21
Alignment explanation
Indices: 5774568--5774606 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5774558 CACCAAAAAG
*
5774568 AACAAGCAACAAACGGAGAAA
1 AACAAGCAACAAACCGAGAAA
*
5774589 AACAA-CAAGAAACCGAGA
1 AACAAGCAACAAACCGAGA
5774607 TCCAAAGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.62, C:0.21, G:0.18, T:0.00
Consensus pattern (21 bp):
AACAAGCAACAAACCGAGAAA
Found at i:5776994 original size:12 final size:12
Alignment explanation
Indices: 5776979--5777004 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5776969 AAAATTAATA
5776979 AAATATTAAATT
1 AAATATTAAATT
5776991 AAATATTAAATT
1 AAATATTAAATT
5777003 AA
1 AA
5777005 TATAATAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATATTAAATT
Found at i:5779962 original size:15 final size:15
Alignment explanation
Indices: 5779942--5779972 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5779932 GTTCATATTG
*
5779942 TCCAACCTCTTTAGA
1 TCCAACATCTTTAGA
5779957 TCCAACATCTTTAGA
1 TCCAACATCTTTAGA
5779972 T
1 T
5779973 TTTCCAATCT
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:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (15 bp):
TCCAACATCTTTAGA
Found at i:5780717 original size:72 final size:68
Alignment explanation
Indices: 5780595--5780733 Score: 215
Period size: 72 Copynumber: 2.0 Consensus size: 68
5780585 AATTTTATAT
* *
5780595 TATATATATATATACCATTCCTCCTTTTAGATTGTGTGTCTTAAAACAATTTCTGAAAAAATAGA
1 TATATATATATATACCATCCCTCCGTTTAGATTGTGTGTCTTAAAACAATTTCTGAAAAAATAGA
5780660 TTA
66 TTA
*
5780663 TATATATATATATACATCATCCCTCCGTTTAGATTGTGTTTGTCTTAAAACAATTTTTGAAAAAA
1 TATATATATATATAC--CATCCCTCCGTTTAGATTGTG--TGTCTTAAAACAATTTCTGAAAAAA
5780728 TAGATT
62 TAGATT
5780734 GGTTTTTTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
68 15 0.23
70 19 0.30
72 30 0.47
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (68 bp):
TATATATATATATACCATCCCTCCGTTTAGATTGTGTGTCTTAAAACAATTTCTGAAAAAATAGA
TTA
Found at i:5785600 original size:10 final size:10
Alignment explanation
Indices: 5785569--5785627 Score: 54
Period size: 10 Copynumber: 6.3 Consensus size: 10
5785559 TTTGAAAATT
5785569 AAAATATATA
1 AAAATATATA
*
5785579 AACAT-T-TA
1 AAAATATATA
5785587 AAAATATAT-
1 AAAATATATA
*
5785596 AAAA-ACATA
1 AAAATATATA
*
5785605 AAAATATTTA
1 AAAATATATA
*
5785615 AAAATATTTA
1 AAAATATATA
5785625 AAA
1 AAA
5785628 TAAAAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
8 9 0.22
9 10 0.25
10 21 0.52
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATATATA
Found at i:5785606 original size:18 final size:18
Alignment explanation
Indices: 5785569--5785618 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
5785559 TTTGAAAATT
* **
5785569 AAAATATATAAACATTTA
1 AAAATATATAAAAACATA
5785587 AAAATATATAAAAACATA
1 AAAATATATAAAAACATA
*
5785605 AAAATATTTAAAAA
1 AAAATATATAAAAA
5785619 TATTTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATATATAAAAACATA
Found at i:5785635 original size:28 final size:28
Alignment explanation
Indices: 5785582--5785637 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
5785572 ATATATAAAC
*
5785582 ATTTAAAAATATATAAAAACATAAAAAT
1 ATTTAAAAATATATAAAAACAAAAAAAT
* *
5785610 ATTTAAAAATATTTAAAATAAAAAAAAA
1 ATTTAAAAATATATAAAA-ACAAAAAAA
5785638 AACTATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (28 bp):
ATTTAAAAATATATAAAAACAAAAAAAT
Found at i:5785756 original size:11 final size:11
Alignment explanation
Indices: 5785740--5785769 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5785730 TTAAAAAAAA
5785740 ATAGATTTTTT
1 ATAGATTTTTT
*
5785751 ATAGATTATTT
1 ATAGATTTTTT
5785762 ATAGATTT
1 ATAGATTT
5785770 AAAAAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (11 bp):
ATAGATTTTTT
Found at i:5788268 original size:22 final size:23
Alignment explanation
Indices: 5788232--5788274 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
5788222 ACTCTTTTTC
*
5788232 AAAAGGTTGATGGTCAAATTTGA
1 AAAAGATTGATGGTCAAATTTGA
5788255 AAAAGATTGA-GGTCAAATTT
1 AAAAGATTGATGGTCAAATTT
5788275 AACTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (23 bp):
AAAAGATTGATGGTCAAATTTGA
Found at i:5788692 original size:29 final size:29
Alignment explanation
Indices: 5788660--5788720 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
5788650 TAAAAAACAT
*
5788660 ATAAAATTA-TTAAATGTTAA-AATAGAATA
1 ATAAAATTATTTAAA-ATTAATAATA-AATA
5788689 ATAAAATTATTTAAAATTAATAATAAATA
1 ATAAAATTATTTAAAATTAATAATAAATA
5788718 ATA
1 ATA
5788721 TGACAGGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
ATAAAATTATTTAAAATTAATAATAAATA
Found at i:5792552 original size:9 final size:9
Alignment explanation
Indices: 5792523--5792598 Score: 89
Period size: 9 Copynumber: 8.4 Consensus size: 9
5792513 GTAGTGATTC
5792523 AATTCGGTT
1 AATTCGGTT
*
5792532 AATTCAGTT
1 AATTCGGTT
*
5792541 AATTCGGGT
1 AATTCGGTT
* *
5792550 AATCCGATT
1 AATTCGGTT
*
5792559 AACTCGGTT
1 AATTCGGTT
*
5792568 AATTCGGGT
1 AATTCGGTT
*
5792577 AATCCGGTT
1 AATTCGGTT
5792586 AATTCGGTT
1 AATTCGGTT
5792595 AATT
1 AATT
5792599 TTTAACCAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (9 bp):
AATTCGGTT
Found at i:5792568 original size:27 final size:27
Alignment explanation
Indices: 5792538--5792598 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
5792528 GGTTAATTCA
5792538 GTTAATTCGGGTAATCCGATTAACTCG
1 GTTAATTCGGGTAATCCGATTAACTCG
* *
5792565 GTTAATTCGGGTAATCCGGTTAATTCG
1 GTTAATTCGGGTAATCCGATTAACTCG
5792592 GTTAATT
1 GTTAATT
5792599 TTTAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
GTTAATTCGGGTAATCCGATTAACTCG
Found at i:5794229 original size:25 final size:27
Alignment explanation
Indices: 5794199--5794266 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
5794189 AAAATTGGTA
5794199 AGACATTTTCCATTCT-TCTCTAAGCA-
1 AGACATTTTCCATTCTCT-TCTAAGCAC
5794225 A-ACATTTTCCATTCTCTTCTAAGCAGC
1 AGACATTTTCCATTCTCTTCTAAGCA-C
5794252 AGACATTTTCCATTC
1 AGACATTTTCCATTC
5794267 CTCAAAGCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
25 22 0.58
26 2 0.05
27 1 0.03
28 13 0.34
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.38
Consensus pattern (27 bp):
AGACATTTTCCATTCTCTTCTAAGCAC
Found at i:5800258 original size:72 final size:72
Alignment explanation
Indices: 5800137--5800280 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 72
5800127 TTGATACATT
* *
5800137 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGATGTAATATTATGCACTTGGACAATGTTATTACTATGTGGTGTACCATTAATTATGTAT
5800202 TTGGATA
66 TTGGATA
* * *
5800209 TATGTGATGTAATATTATTCACTTGGACAATGTTATTATTATGTTGTGTACCATTAATTATGTAT
1 TATGTGATGTAATATTATGCACTTGGACAATGTTATTACTATGTGGTGTACCATTAATTATGTAT
5800274 TTGGATA
66 TTGGATA
5800281 ATATTATTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.45
Consensus pattern (72 bp):
TATGTGATGTAATATTATGCACTTGGACAATGTTATTACTATGTGGTGTACCATTAATTATGTAT
TTGGATA
Found at i:5800371 original size:32 final size:33
Alignment explanation
Indices: 5800330--5800414 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
5800320 AACTTTTCCG
* * *
5800330 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
5800362 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
5800394 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
5800415 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:5800413 original size:14 final size:15
Alignment explanation
Indices: 5800391--5800467 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
5800381 TTACCAAACA
5800391 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
5800405 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
5800420 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
5800440 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
5800454 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
5800468 ACTGCCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:5800432 original size:20 final size:20
Alignment explanation
Indices: 5800407--5800446 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5800397 AATATTTTCC
*
5800407 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
5800427 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
5800447 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:5800452 original size:34 final size:35
Alignment explanation
Indices: 5800395--5800461 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
5800385 CAAACACCAG
*
5800395 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
5800430 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
5800462 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:5800468 original size:14 final size:14
Alignment explanation
Indices: 5800430--5800469 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5800420 ACAGAAAAGT
*
5800430 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
5800444 AAATCATTTTACGG
1 AAAACATTTTACAG
5800458 AAAACATTTTAC
1 AAAACATTTTAC
5800470 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:5817342 original size:20 final size:21
Alignment explanation
Indices: 5817296--5817342 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
5817286 CAAGATAAAT
*
5817296 ATTAATTTAATTTAATATTAAG
1 ATTAA-TTAATTTAATAGTAAG
*
5817318 A-TAATTACTTTAATAGTAA-
1 ATTAATTAATTTAATAGTAAG
5817337 ATTAAT
1 ATTAAT
5817343 AAAATACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.05
20 17 0.77
21 3 0.14
22 1 0.05
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
ATTAATTAATTTAATAGTAAG
Found at i:5825648 original size:35 final size:35
Alignment explanation
Indices: 5825588--5825671 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 35
5825578 TACACGGTTA
* * *
5825588 ACCATCCAGCACACCAGATGTTCATAAGAGCTAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
* *
5825623 ACCACCCAACACACTAGATGCTCATAAGAGCCAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
*
5825658 ACCATCCAATACAC
1 ACCATCCAACACAC
5825672 AAGAAACAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (35 bp):
ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
Found at i:5827953 original size:50 final size:50
Alignment explanation
Indices: 5827894--5827997 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 50
5827884 TTCTGGCACC
*
5827894 CAAGCAACATGCTTCGGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
1 CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
* *
5827944 CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGGAACTAAGAAGG
1 CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
5827994 CAAG
1 CAAG
5827998 TTAAGGACTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (50 bp):
CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
Found at i:5835125 original size:44 final size:44
Alignment explanation
Indices: 5835075--5835732 Score: 855
Period size: 44 Copynumber: 15.0 Consensus size: 44
5835065 GATCTGTTAC
* *
5835075 CTTCGATCTACTTCATGTCAATACATGGAGATAAGATCCAATAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
**
5835119 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTGCTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* *
5835163 C-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTAT
1 CTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* *
5835207 CTTCGATCTACTCCATGTCAATACATGAAGATAAGATCCGCT-T
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
*
5835250 C-T-GATCTACTTCATGTCAATACATGAAGACAAGATCCATCATTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCA-C--TAT
* **
5835295 CTTCGATCTACTTCACGTCAATACATGAAGATAAGATCTGCTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* *
5835339 C-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTAT
1 CTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* *
5835383 CTTCGATCTACTCCATGTCAATACATGAAGATAAGATCCGCTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* *
5835427 CTTTGATCTACTTCATGTCAATACATGAAGATAAGATCCATTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* * * **
5835471 CCTCGATCTACTTCACGTCAATACATGAAGATAATATCTGCTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* *
5835515 C-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTAT
1 CTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* **
5835559 CTTCGATCTACTCCATGTCAATACATGAAGATAAGATCTGCTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* * *
5835603 C-TCTGATCTACTTAATGTCAATACATGAAGACAAGATCCATTAT
1 CTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* * ***
5835647 CTTTGATCTACTCCATGTCAATACATGAAGATAAGATTTGCTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
*
5835691 C-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCACT
1 CTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCCACT
5835733 GCTTTTCAAC
Statistics
Matches: 529, Mismatches: 70, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
41 33 0.06
42 2 0.00
43 11 0.02
44 440 0.83
45 9 0.02
46 2 0.00
47 32 0.06
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.32
Consensus pattern (44 bp):
CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
Found at i:5835173 original size:88 final size:88
Alignment explanation
Indices: 5835079--5835730 Score: 1103
Period size: 88 Copynumber: 7.4 Consensus size: 88
5835069 TGTTACCTTC
* * * *
5835079 GATCTACTTCATGTCAATACATGGAGATAAGATCCAATATCTTCGATCTACTTCATGTCAATACA
1 GATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACA
5835144 TGAAGATAAGATCTGCTATCTCT
66 TGAAGATAAGATCTGCTATCTCT
5835167 GATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACA
1 GATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACA
*
5835232 TGAAGATAAGATCCGC--T-TCT
66 TGAAGATAAGATCTGCTATCTCT
* *
5835252 GATCTACTTCATGTCAATACATGAAGACAAGATCCATCATTATCTTCGATCTACTTCACGTCAAT
1 GATCTACTTCATGTCAATACATGAAGACAAGAT-C--CATTATCTTCGATCTACTCCATGTCAAT
5835317 ACATGAAGATAAGATCTGCTATCTCT
63 ACATGAAGATAAGATCTGCTATCTCT
5835343 GATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACA
1 GATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACA
* *
5835408 TGAAGATAAGATCCGCTATCTTT
66 TGAAGATAAGATCTGCTATCTCT
* * * *
5835431 GATCTACTTCATGTCAATACATGAAGATAAGATCCATTATCCTCGATCTACTTCACGTCAATACA
1 GATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACA
*
5835496 TGAAGATAATATCTGCTATCTCT
66 TGAAGATAAGATCTGCTATCTCT
5835519 GATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACA
1 GATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACA
5835584 TGAAGATAAGATCTGCTATCTCT
66 TGAAGATAAGATCTGCTATCTCT
* *
5835607 GATCTACTTAATGTCAATACATGAAGACAAGATCCATTATCTTTGATCTACTCCATGTCAATACA
1 GATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACA
*
5835672 TGAAGATAAGATTTGCTATCTCT
66 TGAAGATAAGATCTGCTATCTCT
5835695 GATCTACTTCATGTCAATACATGAAGACAAGATCCA
1 GATCTACTTCATGTCAATACATGAAGACAAGATCCA
5835731 CTGCTTTTCA
Statistics
Matches: 530, Mismatches: 28, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
85 36 0.07
86 2 0.00
88 454 0.86
90 2 0.00
91 36 0.07
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (88 bp):
GATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACA
TGAAGATAAGATCTGCTATCTCT
Found at i:5837006 original size:21 final size:21
Alignment explanation
Indices: 5836980--5837028 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
5836970 TTAGCCTCTC
*
5836980 CATTTTTACTTTTTCAT-TTTT
1 CATTTTT-CATTTTCATCTTTT
5837001 CATTTTTCATTTTCATCTTTT
1 CATTTTTCATTTTCATCTTTT
5837022 CATTTTT
1 CATTTTT
5837029 TCACATCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.69
Consensus pattern (21 bp):
CATTTTTCATTTTCATCTTTT
Found at i:5837031 original size:8 final size:7
Alignment explanation
Indices: 5836980--5837028 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
5836970 TTAGCCTCTC
5836980 CATTTTT
1 CATTTTT
5836987 -ACTTTTT
1 CA-TTTTT
5836994 CATTTTT
1 CATTTTT
5837001 CATTTTT
1 CATTTTT
5837008 CA-TTTT
1 CATTTTT
5837014 CATCTTTT
1 CAT-TTTT
5837022 CATTTTT
1 CATTTTT
5837029 TCACATCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.18
7 23 0.61
8 8 0.21
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:5839956 original size:19 final size:20
Alignment explanation
Indices: 5839932--5839975 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
5839922 TACCAGTGTT
* *
5839932 TAATGCATATG-ATGTAATG
1 TAATGCAGATGCATGAAATG
5839951 TAATGCAGATGCATGAAATG
1 TAATGCAGATGCATGAAATG
5839971 -AATGC
1 TAATGC
5839976 CTAAAGAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (20 bp):
TAATGCAGATGCATGAAATG
Found at i:5844960 original size:15 final size:15
Alignment explanation
Indices: 5844936--5844965 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5844926 AATGTTATTT
5844936 TTTAGAATTTTTTAA
1 TTTAGAATTTTTTAA
*
5844951 TTTAGTATTTTTTAA
1 TTTAGAATTTTTTAA
5844966 GAGTTATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
TTTAGAATTTTTTAA
Found at i:5845706 original size:22 final size:24
Alignment explanation
Indices: 5845675--5845733 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 24
5845665 TTAATATTAA
5845675 TATAAAAATTTTATTTA-AA-TTT
1 TATAAAAATTTTATTTATAATTTT
*
5845697 TATAACAA--TTATTTATAATTTT
1 TATAAAAATTTTATTTATAATTTT
*
5845719 TATAATACATTTTAT
1 TATAA-AAATTTTAT
5845734 ATTTTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 7 0.24
21 2 0.07
22 15 0.52
23 1 0.03
25 4 0.14
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (24 bp):
TATAAAAATTTTATTTATAATTTT
Found at i:5846920 original size:131 final size:132
Alignment explanation
Indices: 5846761--5847023 Score: 519
Period size: 131 Copynumber: 2.0 Consensus size: 132
5846751 TTTCCTTTTA
5846761 AATTATAATTATTATAACATTTTTGCCTTTTTATATTATTTTTAAATAAAGAGATAATGGTCAAA
1 AATTATAATTATTATAACATTTTTGCCTTTTTATATTATTTTTAAATAAAGAGATAATGGTCAAA
5846826 AAAAACCTATACTTTGATAAAATTGTCACTTTTAATTTGTCTATTATATTACTTTAACTTTTCTA
66 AAAAACCTATACTTTGATAAAATTGTCACTTTTAATTTGTCTATTATATTACTTTAACTTTTCTA
5846891 TG
131 TG
5846893 AATTATAATT-TTATAACATTTTTGCCTTTTTATATTATTTTTAAATAAAGAGATAATGGTCAAA
1 AATTATAATTATTATAACATTTTTGCCTTTTTATATTATTTTTAAATAAAGAGATAATGGTCAAA
5846957 AAAAACCTATACTTTGATAAAATTGTCACTTTTAATTTGTCTATTATATTACTTTAACTTTTCTA
66 AAAAACCTATACTTTGATAAAATTGTCACTTTTAATTTGTCTATTATATTACTTTAACTTTTCTA
5847022 TG
131 TG
5847024 GTCTAGCATC
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
131 121 0.92
132 10 0.08
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (132 bp):
AATTATAATTATTATAACATTTTTGCCTTTTTATATTATTTTTAAATAAAGAGATAATGGTCAAA
AAAAACCTATACTTTGATAAAATTGTCACTTTTAATTTGTCTATTATATTACTTTAACTTTTCTA
TG
Found at i:5849610 original size:27 final size:28
Alignment explanation
Indices: 5849579--5849637 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
5849569 TGACAAATCT
*
5849579 AATA-TTTTTTAATATG-TTTATAAAGGA
1 AATATTTTTTTAA-ATGTTTTATAAAGAA
*
5849606 AATATTTTTTTGAATGTTTTATAAAGAA
1 AATATTTTTTTAAATGTTTTATAAAGAA
5849634 AATA
1 AATA
5849638 ATTACTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (28 bp):
AATATTTTTTTAAATGTTTTATAAAGAA
Found at i:5849652 original size:28 final size:28
Alignment explanation
Indices: 5849579--5849653 Score: 68
Period size: 28 Copynumber: 2.7 Consensus size: 28
5849569 TGACAAATCT
* *
5849579 AATATT-TTTT-AATATGTTTATAAAGGA
1 AATATTCTTTTGAATGT-TTTATAAAGAA
*
5849606 AATATTTTTTTGAATGTTTTATAAAGAA
1 AATATTCTTTTGAATGTTTTATAAAGAA
5849634 AATAATTACTTTT-AA-GTTTT
1 AAT-ATT-CTTTTGAATGTTTT
5849654 TTCCTTCCGC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 6 0.15
28 22 0.54
29 9 0.22
30 4 0.10
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (28 bp):
AATATTCTTTTGAATGTTTTATAAAGAA
Found at i:5850414 original size:20 final size:20
Alignment explanation
Indices: 5850389--5850429 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5850379 AAATGTGAAA
5850389 ACCTAAGATGTATACTTTCT
1 ACCTAAGATGTATACTTTCT
5850409 ACCTAAGATGTATACTTTCT
1 ACCTAAGATGTATACTTTCT
5850429 A
1 A
5850430 TCTTCCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (20 bp):
ACCTAAGATGTATACTTTCT
Found at i:5851582 original size:10 final size:11
Alignment explanation
Indices: 5851565--5851616 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
5851555 GGCCCATTTT
5851565 TATTTTAAAAA
1 TATTTTAAAAA
5851576 T-TTTT-AAAA
1 TATTTTAAAAA
**
5851585 -ATTAAAAAAA
1 TATTTTAAAAA
5851595 GTATTTTAAAAA
1 -TATTTTAAAAA
5851607 TATTTTAAAA
1 TATTTTAAAA
5851617 TCAAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 6 0.18
10 8 0.24
11 11 0.33
12 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:5851603 original size:31 final size:31
Alignment explanation
Indices: 5851565--5851646 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
5851555 GGCCCATTTT
*
5851565 TATTTTAAAAAT-TTTTAAAAATTAAAAAAAG
1 TATTTTAAAAATATTTT-AAAATCAAAAAAAG
5851596 TATTTTAAAAATATTTTAAAATCAAAAAAA-
1 TATTTTAAAAATATTTTAAAATCAAAAAAAG
**
5851626 T-TTAAAAAAAGTATTTTAAAA
1 TATTTTAAAAA-TATTTTAAAA
5851647 ATATATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.15
30 11 0.24
31 24 0.52
32 4 0.09
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (31 bp):
TATTTTAAAAATATTTTAAAATCAAAAAAAG
Found at i:5851657 original size:14 final size:14
Alignment explanation
Indices: 5851586--5851647 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
5851576 TTTTTAAAAA
5851586 TTAAAAAAAGTATT
1 TTAAAAAAAGTATT
5851600 TT--AAAAA-TATT
1 TTAAAAAAAGTATT
** *
5851611 TTAAAATCAAAAAAAT
1 TTAAAA--AAAGTATT
5851627 TTAAAAAAAGTATT
1 TTAAAAAAAGTATT
5851641 TTAAAAA
1 TTAAAAA
5851648 TATATTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
11 6 0.16
12 5 0.13
13 2 0.05
14 14 0.37
15 3 0.08
16 8 0.21
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (14 bp):
TTAAAAAAAGTATT
Found at i:5851857 original size:46 final size:46
Alignment explanation
Indices: 5851790--5851881 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
5851780 TTACGATTTG
*
5851790 GTCCCCACTTTTATATTTCAAATACATACCAAGAAATTTCTTATTA
1 GTCCCCACTTTTATATTTCAAATACAAACCAAGAAATTTCTTATTA
5851836 GTCCCCACTTTTATATTTCAAATACAAACCAAGAAATTTCTTATTA
1 GTCCCCACTTTTATATTTCAAATACAAACCAAGAAATTTCTTATTA
5851882 TTCCGATTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (46 bp):
GTCCCCACTTTTATATTTCAAATACAAACCAAGAAATTTCTTATTA
Found at i:5852072 original size:2 final size:2
Alignment explanation
Indices: 5852067--5852106 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5852057 TATACGTATT
*
5852067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5852107 CATCTCTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5861803 original size:43 final size:45
Alignment explanation
Indices: 5861637--5861807 Score: 151
Period size: 44 Copynumber: 3.9 Consensus size: 45
5861627 GCATTACATG
* * *
5861637 ATTTCGTATAAGACCATAACTGGGCTA-TGGCATTGATATATG-A
1 ATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATATATGTA
* * * * *
5861680 GTCTTTGTGTAAGACCATATCT-GG-TATATAGCATCGATATATGTG
1 AT-TTCGTGTAAGACCATAGCTGGGCTAT-TGGCATCGATATATGTA
* * *
5861725 ATTACGTGTAAGACCAT-GTCTAGGAC-ATTGACATCG-T-TATGTA
1 ATTTCGTGTAAGACCATAG-CT-GGGCTATTGGCATCGATATATGTA
5861768 ATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATAT
1 ATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATAT
5861808 GTGATAACAT
Statistics
Matches: 98, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
42 5 0.05
43 35 0.36
44 47 0.48
45 8 0.08
46 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (45 bp):
ATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATATATGTA
Done.