Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 75 of 187
Found at i:22001802 original size:12 final size:12
Alignment explanation
Indices: 22001785--22001810 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
22001775 AGTTTGAACT
22001785 TAAATACAAAAA
1 TAAATACAAAAA
22001797 TAAATACAAAAA
1 TAAATACAAAAA
22001809 TA
1 TA
22001811 CAAAAAGACA
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:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (12 bp):
TAAATACAAAAA
Found at i:22001809 original size:8 final size:8
Alignment explanation
Indices: 22001802--22001849 Score: 57
Period size: 7 Copynumber: 6.4 Consensus size: 8
22001792 AAAAATAAAT
*
22001802 ACAAAAAT
1 ACAAAAAG
22001810 ACAAAAAG
1 ACAAAAAG
22001818 AC-AAAAG
1 ACAAAAAG
22001825 AC-AAAAG
1 ACAAAAAG
*
22001832 ACAAAAAT
1 ACAAAAAG
22001840 AC-AAAAG
1 ACAAAAAG
22001847 ACA
1 ACA
22001850 TAATAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 20 0.57
8 15 0.43
ACGTcount: A:0.73, C:0.15, G:0.08, T:0.04
Consensus pattern (8 bp):
ACAAAAAG
Found at i:22001828 original size:15 final size:15
Alignment explanation
Indices: 22001802--22001849 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
22001792 AAAAATAAAT
22001802 ACAAAAATACAAAAAG
1 ACAAAAATAC-AAAAG
*
22001818 AC-AAAAGACAAAAG
1 ACAAAAATACAAAAG
22001832 ACAAAAATACAAAAG
1 ACAAAAATACAAAAG
22001847 ACA
1 ACA
22001850 TAATAGTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 7 0.24
15 20 0.69
16 2 0.07
ACGTcount: A:0.73, C:0.15, G:0.08, T:0.04
Consensus pattern (15 bp):
ACAAAAATACAAAAG
Found at i:22001835 original size:22 final size:22
Alignment explanation
Indices: 22001805--22001849 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
22001795 AATAAATACA
*
22001805 AAAATACAAAAAGACAAAAGAC
1 AAAAGACAAAAAGACAAAAGAC
*
22001827 AAAAGACAAAAATACAAAAGAC
1 AAAAGACAAAAAGACAAAAGAC
22001849 A
1 A
22001850 TAATAGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.73, C:0.13, G:0.09, T:0.04
Consensus pattern (22 bp):
AAAAGACAAAAAGACAAAAGAC
Found at i:22011168 original size:27 final size:27
Alignment explanation
Indices: 22011136--22011208 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
22011126 GAAAAGTTTG
22011136 TAAAATTACCAAATTACCCTCAAAGGA
1 TAAAATTACCAAATTACCCTCAAAGGA
* * * *
22011163 TAAAATTATCGAAA-TACCTTCGAAGGG
1 TAAAATTA-CCAAATTACCCTCAAAGGA
* *
22011190 TAAAATGACCGAATTACCC
1 TAAAATTACCAAATTACCC
22011209 CCTTAGGGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 3 0.08
27 29 0.81
28 4 0.11
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23
Consensus pattern (27 bp):
TAAAATTACCAAATTACCCTCAAAGGA
Found at i:22011271 original size:24 final size:24
Alignment explanation
Indices: 22011242--22011288 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
22011232 GGCCTCGAGG
22011242 TTAAATGATTGATTTT-TCTGTGAT
1 TTAAATGATTG-TTTTGTCTGTGAT
22011266 TTAAATGATTGTTTTGTCTGTGA
1 TTAAATGATTGTTTTGTCTGTGA
22011289 ATTGTATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.23, C:0.04, G:0.19, T:0.53
Consensus pattern (24 bp):
TTAAATGATTGTTTTGTCTGTGAT
Found at i:22011675 original size:28 final size:27
Alignment explanation
Indices: 22011626--22011680 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
22011616 ACATCTGATA
*
22011626 CTGGTTCTGTATTGGGCTTAGGTCCAG
1 CTGGTTCTGTATTGGGCTTAGGCCCAG
22011653 CTGGTTCTGT-TGATGGGCTTAGGCCCAG
1 CTGGTTCTGTAT--TGGGCTTAGGCCCAG
22011681 TCTTTTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 1 0.04
27 10 0.40
28 14 0.56
ACGTcount: A:0.11, C:0.20, G:0.35, T:0.35
Consensus pattern (27 bp):
CTGGTTCTGTATTGGGCTTAGGCCCAG
Found at i:22020834 original size:132 final size:132
Alignment explanation
Indices: 22020597--22020871 Score: 471
Period size: 132 Copynumber: 2.1 Consensus size: 132
22020587 CTTCGTTGCC
*
22020597 TAGGGAGATAAGATTTGTAATCTTCAATCTATTCCACTGCTGCCCAGGAAGATAGAATTACTAGC
1 TAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGAAGATAGAATTACTAGC
* * *
22020662 TTCAATGTACTCCACTGTAACCTCAGTGAGGTAAAATCTGCCAT-CTTCGATTTGCTCCACTACT
66 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCCCT-GATCTGCTCCACTACT
22020726 GCT
130 GCT
* *
22020729 TAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGC
1 TAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGAAGATAGAATTACTAGC
*
22020794 TTCAATGTACTCCGCTGTAACCTCAGGGAGGTAAAATCTGCCATCCCTGATCTGCTCCACTACTG
66 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCCCTGATCTGCTCCACTACTG
22020859 CT
131 CT
22020861 TAGGGAGATAA
1 TAGGGAGATAA
22020872 AATTACTGGC
Statistics
Matches: 135, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
132 133 0.99
133 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
TAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGAAGATAGAATTACTAGC
TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCCCTGATCTGCTCCACTACTG
CT
Found at i:22020879 original size:88 final size:88
Alignment explanation
Indices: 22020774--22020959 Score: 302
Period size: 88 Copynumber: 2.1 Consensus size: 88
22020764 ACTGCTGCCC
* *
22020774 AGGGAGATAGAATTACTGGCTTCAATGTACTCCGCTGTAACCTCAGGGAGGTAAAATCTGCCATC
1 AGGGAGATAAAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATC
*
22020839 C-CTGATCTGCTCCACTACTGCTT
66 CTC-AATCTGCTCCACTACTGCTT
*
22020862 AGGGAGATAAAATTACTGGCTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAATCTGCCATC
1 AGGGAGATAAAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATC
* *
22020927 TTCAATCTGCTCCACTATTGCTT
66 CTCAATCTGCTCCACTACTGCTT
22020950 AGGGAGATAA
1 AGGGAGATAA
22020960 GATCTGTAAT
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
88 90 0.99
89 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (88 bp):
AGGGAGATAAAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATC
CTCAATCTGCTCCACTACTGCTT
Found at i:22020954 original size:132 final size:132
Alignment explanation
Indices: 22020862--22021201 Score: 574
Period size: 132 Copynumber: 2.6 Consensus size: 132
22020852 ACTACTGCTT
* * *
22020862 AGGGAGATAAAATTACTGGCTTCAATGTACTCCACTGTAACCTTAGGGAGGTAAAATCTGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTTAGAGAGGTAAAATCCGCCATC
* *
22020927 TTCAATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
66 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
22020992 CC
131 CC
22020994 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTTAGAGAGGTAAAATCCGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTTAGAGAGGTAAAATCCGCCAT-
* * *
22021059 CTT-GATCTACTCCACTACTGTTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCTG
65 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTG
22021123 CCC
130 CCC
* *
22021126 AGGGAGATAGAATTACTGGCTTTAATGTACTCCACTGTAACCTCAGAGAGGTAAAATCCGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTTAGAGAGGTAAAATCCGCCATC
22021191 TTCGATCTGCT
66 TTCGATCTGCT
22021202 TCGCTGTCAA
Statistics
Matches: 195, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
131 3 0.02
132 189 0.97
133 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTTAGAGAGGTAAAATCCGCCATC
TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
CC
Found at i:22021034 original size:220 final size:220
Alignment explanation
Indices: 22020623--22021091 Score: 767
Period size: 220 Copynumber: 2.1 Consensus size: 220
22020613 GTAATCTTCA
* * ** * *
22020623 ATCTATTCCACTGCTGCCCAGGAAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCTCAG
1 ATCTACTCCACTACTGCTTAGGGAGATAAAATTACTAGCTTCAATGTACTCCACTGTAACCTCAG
* * *
22020688 TGAGGTAAAATCTGCCATCTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
66 GGAGGTAAAATCTGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
*
22020753 CAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCGCTGTAACCTC
131 CAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTC
* *
22020818 AGGGAGGTAAAATCTGCCATCCCTG
196 AGAGAGGTAAAATCCGCCATCCCTG
* * *
22020843 ATCTGCTCCACTACTGCTTAGGGAGATAAAATTACTGGCTTCAATGTACTCCACTGTAACCTTAG
1 ATCTACTCCACTACTGCTTAGGGAGATAAAATTACTAGCTTCAATGTACTCCACTGTAACCTCAG
*
22020908 GGAGGTAAAATCTGCCATCTTCAATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTT
66 GGAGGTAAAATCTGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
*
22020973 CAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTT
131 CAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTC
*
22021038 AGAGAGGTAAAATCCGCCATCCTTG
196 AGAGAGGTAAAATCCGCCATCCCTG
*
22021063 ATCTACTCCACTACTGTTTAGGGAGATAA
1 ATCTACTCCACTACTGCTTAGGGAGATAA
22021092 GATCTATAAT
Statistics
Matches: 229, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
220 229 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (220 bp):
ATCTACTCCACTACTGCTTAGGGAGATAAAATTACTAGCTTCAATGTACTCCACTGTAACCTCAG
GGAGGTAAAATCTGCCATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
CAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTC
AGAGAGGTAAAATCCGCCATCCCTG
Found at i:22052622 original size:27 final size:27
Alignment explanation
Indices: 22052592--22052648 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
22052582 GAATAGTGAC
*
22052592 TCGGGAAGTTAAATAACTAAGAAGTAA
1 TCGGGAAGTTAAAGAACTAAGAAGTAA
22052619 TCGGGAAGTTAAAGAACTAAGAAGTAA
1 TCGGGAAGTTAAAGAACTAAGAAGTAA
22052646 TCG
1 TCG
22052649 AGTGCCATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.09, G:0.25, T:0.21
Consensus pattern (27 bp):
TCGGGAAGTTAAAGAACTAAGAAGTAA
Found at i:22058723 original size:6 final size:6
Alignment explanation
Indices: 22058707--22058762 Score: 60
Period size: 7 Copynumber: 8.8 Consensus size: 6
22058697 TTCCACCATT
*
22058707 TTTTTA CTTTTTA TTTTTA -TTTTA TTTATTA TTTTTA CTTTTCTA TTTATA
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA -TTTT-TA TTTTTA
22058758 TTTTT
1 TTTTT
22058763 GTATATTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
5 5 0.12
6 17 0.40
7 19 0.44
8 2 0.05
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:22058738 original size:18 final size:19
Alignment explanation
Indices: 22058708--22058762 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
22058698 TCCACCATTT
22058708 TTTTACTTT-TTATTTTTA-
1 TTTTA-TTTATTATTTTTAC
22058726 TTTTATTTATTATTTTTAC
1 TTTTATTTATTATTTTTAC
22058745 TTTTCTATTTA-TATTTTT
1 -TTT-TATTTATTATTTTT
22058763 GTATATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.09
18 14 0.42
20 10 0.30
21 6 0.18
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTATTTATTATTTTTAC
Found at i:22058762 original size:14 final size:13
Alignment explanation
Indices: 22058706--22058780 Score: 64
Period size: 14 Copynumber: 5.6 Consensus size: 13
22058696 CTTCCACCAT
*
22058706 TTTTTTACTTTTTA
1 TTTTTTA-TTTATA
22058720 -TTTTTATTT-TA
1 TTTTTTATTTATA
* *
22058731 TTTATTATTTTTA
1 TTTTTTATTTATA
*
22058744 CTTTTCTATTTATA
1 -TTTTTTATTTATA
22058758 TTTTTGTATATTATA
1 TTTTT-TAT-TTATA
22058773 TTTTTTAT
1 TTTTTTAT
22058781 GCCTAATTCT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
11 2 0.04
12 11 0.22
13 12 0.24
14 16 0.31
15 10 0.20
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (13 bp):
TTTTTTATTTATA
Found at i:22063640 original size:21 final size:20
Alignment explanation
Indices: 22063582--22063640 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
22063572 ATCACATATC
*
22063582 TAATAATTTCTCAAT-TAAAT
1 TAATAATTT-TAAATATAAAT
* *
22063602 TAATTATTATTAATTATAAAT
1 TAATAATT-TTAAATATAAAT
22063623 TAATAATTTGTAAATATA
1 TAATAATTT-TAAATATA
22063641 CGAGGAGAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (20 bp):
TAATAATTTTAAATATAAAT
Found at i:22070412 original size:41 final size:41
Alignment explanation
Indices: 22070355--22070433 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
22070345 TATTCGCCCA
* * *
22070355 TTGTACTTTGTATTGAGTGATTTTAGATTATAGTTGGTATG
1 TTGTACTTTGTATTGAGTGATTCTACACTATAGTTGGTATG
*
22070396 TTGTACTTTGTTTTGAGTGATTCTACACTATAGTTGGT
1 TTGTACTTTGTATTGAGTGATTCTACACTATAGTTGGT
22070434 TAAACATACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.20, C:0.06, G:0.23, T:0.51
Consensus pattern (41 bp):
TTGTACTTTGTATTGAGTGATTCTACACTATAGTTGGTATG
Found at i:22075637 original size:121 final size:120
Alignment explanation
Indices: 22075449--22075682 Score: 423
Period size: 121 Copynumber: 1.9 Consensus size: 120
22075439 TTTTATAGTA
* *
22075449 TTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTAT
1 TTATAGTATTATATATTATGATTTTAGTAAATTAATATAAGAATATCTAATATTAAGAATTTTAT
22075514 TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATT
66 TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATT
* *
22075569 TTATAGTATTTTATATTATGATTTTAGTAATTTAATATTAAGAATATCTAATATTAAGAATTTTA
1 TTATAGTATTATATATTATGATTTTAGTAAATTAATA-TAAGAATATCTAATATTAAGAATTTTA
22075634 TTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
65 TTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
22075683 ATATGATTAA
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
120 34 0.31
121 75 0.69
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (120 bp):
TTATAGTATTATATATTATGATTTTAGTAAATTAATATAAGAATATCTAATATTAAGAATTTTAT
TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATT
Found at i:22080531 original size:107 final size:107
Alignment explanation
Indices: 22080345--22080557 Score: 408
Period size: 107 Copynumber: 2.0 Consensus size: 107
22080335 TTGGTTTGAA
*
22080345 TCGATAGATAAAGAGATACTCAAAAGGTCATTTTGTTTGAATAAATTTGTTTTAGTCATTCAATT
1 TCGATAGATAAAGAGATACTCAAAAGGTCATTTTGTTTGAATAAATTGGTTTTAGTCATTCAATT
*
22080410 GGAAATAACTTTTCCCTATACTCATATACAAATATGTATTTG
66 GGAAATAACTTTTCCCTATACTCATATACAAATATGCATTTG
22080452 TCGATAGATAAAGAGATACTCAAAAGGTCATTTTGTTTGAATAAATTGGTTTTAGTCATTCAATT
1 TCGATAGATAAAGAGATACTCAAAAGGTCATTTTGTTTGAATAAATTGGTTTTAGTCATTCAATT
22080517 GGAAATAACTTTTCCCTATACTCATATACAAATATGCATTT
66 GGAAATAACTTTTCCCTATACTCATATACAAATATGCATTT
22080558 ATAACAAATT
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (107 bp):
TCGATAGATAAAGAGATACTCAAAAGGTCATTTTGTTTGAATAAATTGGTTTTAGTCATTCAATT
GGAAATAACTTTTCCCTATACTCATATACAAATATGCATTTG
Found at i:22081191 original size:16 final size:16
Alignment explanation
Indices: 22081170--22081208 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
22081160 TTGCATTATT
* *
22081170 ATTACAGGTTTATTCC
1 ATTACAGATATATTCC
*
22081186 ATTACATATATATTCC
1 ATTACAGATATATTCC
22081202 ATTACAG
1 ATTACAG
22081209 CCCTATTTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (16 bp):
ATTACAGATATATTCC
Found at i:22081273 original size:20 final size:19
Alignment explanation
Indices: 22081250--22081288 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
22081240 CCAAACAAAT
22081250 AAAAAATAATATAATAACCC
1 AAAAAATAATATAA-AACCC
* *
22081270 AAAACATTATATAAAACCC
1 AAAAAATAATATAAAACCC
22081289 TTTTAGGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAAATAATATAAAACCC
Found at i:22081500 original size:19 final size:20
Alignment explanation
Indices: 22081458--22081501 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
22081448 TTATTTATAA
*
22081458 TATATATTTAAAATTTGATC
1 TATATATTTAAAATATGATC
* *
22081478 TATATATTT-TAATATGATT
1 TATATATTTAAAATATGATC
22081497 TATAT
1 TATAT
22081502 TAAATCAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (20 bp):
TATATATTTAAAATATGATC
Found at i:22082111 original size:19 final size:19
Alignment explanation
Indices: 22082087--22082123 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22082077 TAATAAACAT
*
22082087 TAAAAAATTATTTTAAAAA
1 TAAAAAAATATTTTAAAAA
22082106 TAAAAAAATATTTTAAAA
1 TAAAAAAATATTTTAAAA
22082124 GTATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAAAATATTTTAAAAA
Found at i:22099688 original size:30 final size:30
Alignment explanation
Indices: 22099626--22099688 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
22099616 ACTTATTTTA
**
22099626 TTGTTAATTTTATTATTATTTTAAAGGTAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
22099656 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
22099686 TTG
1 TTG
22099689 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:22099826 original size:11 final size:11
Alignment explanation
Indices: 22099810--22099840 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
22099800 TATATATATT
22099810 TAAAAATTATA
1 TAAAAATTATA
*
22099821 TAAAAATAATA
1 TAAAAATTATA
22099832 TAAAAATTA
1 TAAAAATTA
22099841 ATACGGGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:22103718 original size:579 final size:578
Alignment explanation
Indices: 22102122--22105018 Score: 4821
Period size: 579 Copynumber: 5.0 Consensus size: 578
22102112 ACCATGTGTG
* *
22102122 TATTCGAAGTTGGGTCATACGACAGTGTCGTAAGCCGTGTTTTAAACTGTGTAACAATCTATTTT
1 TATTCGAAGTTGGGTCATACGACAGTGTCGTAAGCCGTGTTCTAAACCGTGTAACAATCTATTTT
* * * *
22102187 GGCACACACGGTCGTGTCGTAGGCTATGTGCTAGGTCATGTGGATATGCACCTATAATCAATAAT
66 GGCACACACGGTCGTGTCGCAGGCTATGTGCTAGGCCGTGTAGATATGCACCTATAATCAATAAT
* *
22102252 TACACACGGTCGTACGTGGTGACTGTGTGTGGCACATGGTCGTGTGCACCCTTTTTGACCCCTTA
131 TACACACGGTCGTGCGTGGTGACTGTGTGTGGCACATGGCCGTGTGCACCCTTTTTGACCCC-TA
* *
22102317 AATCAAGCAATGTCATGCATTATTCCTTGCATAACAAGACATGCCATATCTAGATCAATTCCTAA
195 AATCAAGCAATGTCATGCATTATTCCTTGCACAACAAGACATGCCATATCTAGATCAATTCCTAG
* *
22102382 GTTCAAAAACACATTTAAATCATCAAGTACATGCTAAAATTTCATTCATTTCACTCCTAACCAAT
260 GTTCAAAAACACATTTAAATCATCAAATACATGCTAAAATTTCATTCATTTCACGCCTAACCAAT
*
22102447 ATGTCATTCAAATGTACCACAATTAAAGATCATTCAATTACTAATTTAGCTAAGTAAGCACATGA
325 ATGTCATTCAAATGCACCACAATTAAAGATCATTCAATTACTAATTTAGCTAAGTAAGCACATGA
22102512 CATTAAACATCTATTCATGCTCAACCATCAACCAAATTAACCAAAGTACAAACATATTCAAAACT
390 CATTAAACATCTATTCATGCTCAACCATCAACCAAATTAACCAAAGTACAAACATATTCAAAACT
22102577 TACCATTTCAAAGTATTACCACTTAGCTCTTGACCATTAAGAATCAATCCAACCAAAAACACTTT
455 TACCATTTCAAAGTATTACCACTTAGCTCTTGACCATTAAGAATCAATCCAACCAAAAACACTTT
*
22102642 AAACACATATTCAAAACCAAACATTTCACTAGGAACACCATTATAATATAACATTTACA
520 AAACACATATTCAAAACCAAACATTTCACTAGGAACACCATTATAGTATAACATTTACA
* *
22102701 TATTCGAAGTTGGGTCATACGACAGTGTCGTAGGCCGTATTCTAAACCGTGTAACAATCTATTTT
1 TATTCGAAGTTGGGTCATACGACAGTGTCGTAAGCCGTGTTCTAAACCGTGTAACAATCTATTTT
* *
22102766 GGCACACACGGTCGTGTCGTATGCTATGTGCTAGGCCGTGTAGATATGCACCTATAATCAATAAT
66 GGCACACACGGTCGTGTCGCAGGCTATGTGCTAGGCCGTGTAGATATGCACCTATAATCAATAAT
* *
22102831 TATACACGGTCGTGTGTGGTGACTGTGTGTGGCACATGGCCGTGTGCACCCTTTTTGACCCCTAA
131 TACACACGGTCGTGCGTGGTGACTGTGTGTGGCACATGGCCGTGTGCACCCTTTTTGACCCCTAA
* * *
22102896 ATCAAGTAATGTCATGCATTATTCCTTGCACAACAAGACATGACATATCTGGATCAATTCCTAGG
196 ATCAAGCAATGTCATGCATTATTCCTTGCACAACAAGACATGCCATATCTAGATCAATTCCTAGG
*
22102961 TTCAAAAACACATTTAAATCATCAAATACATG-TGAAAATTTCATTCATTTCACACCTAACCAAT
261 TTCAAAAACACATTTAAATCATCAAATACATGCT-AAAATTTCATTCATTTCACGCCTAACCAAT
22103025 ATGTCATTCAAATGCACCACAATTAAAGATCATTCAATTACTAATTTAGCTAAGTAAGCACATGA
325 ATGTCATTCAAATGCACCACAATTAAAGATCATTCAATTACTAATTTAGCTAAGTAAGCACATGA
**
22103090 CATTAAACATCTATTCATGCTCAACCATCAACCAAATTAACCAAAGTACAAGTATATTCAAAACT
390 CATTAAACATCTATTCATGCTCAACCATCAACCAAATTAACCAAAGTACAAACATATTCAAAACT
22103155 TACCATTTCAAAGTATTACCACTTAGCTCTTGACCATTAAGAATCAATCCAACCAAAAACACTTT
455 TACCATTTCAAAGTATTACCACTTAGCTCTTGACCATTAAGAATCAATCCAACCAAAAACACTTT
22103220 AAACACATATTCAAAACCAAACATTTCACTAGGAACACCATTATAGTATAACATTTACA
520 AAACACATATTCAAAACCAAACATTTCACTAGGAACACCATTATAGTATAACATTTACA
* * * * * *
22103279 TATTCGAAGTTGGGTCACACAACAGTGTCATAGGTCGTGTGCTAAACCGTGTAACAATCTATTTT
1 TATTCGAAGTTGGGTCATACGACAGTGTCGTAAGCCGTGTTCTAAACCGTGTAACAATCTATTTT
* * * * *
22103344 GGCTCACACAGTCATGTCGCAGGCCATGTGTTAGGCCGTGTAGATACTGCACCTATAATCAATAA
66 GGCACACACGGTCGTGTCGCAGGCTATGTGCTAGGCCGTGTAGATA-TGCACCTATAATCAATAA
* * * *
22103409 TTACACAAGGCCGTGCGTGGTGACTGTATGTGGCACATGGCCGTATGCACCCTTTTTGACCCCTA
130 TTACACACGGTCGTGCGTGGTGACTGTGTGTGGCACATGGCCGTGTGCACCCTTTTTGACCCCTA
* * * *
22103474 AATCAAGCAATGTCATGCATTATTCCTTGCACAATAAGACATTCCATATCTAGATGAAATCCTAG
195 AATCAAGCAATGTCATGCATTATTCCTTGCACAACAAGACATGCCATATCTAGATCAATTCCTAG
* * *
22103539 GTTCAAAAACACATTTAAATCATCAAATACATGCTAAATTTTAATTCATTTCACGTCTAACCAAT
260 GTTCAAAAACACATTTAAATCATCAAATACATGCTAAAATTTCATTCATTTCACGCCTAACCAAT
* * *
22103604 ATGCCATTCAAATGCACCACAATTAAAGATCATTCAATTACTAATTTAGTTAAGTAAGCACATGG
325 ATGTCATTCAAATGCACCACAATTAAAGATCATTCAATTACTAATTTAGCTAAGTAAGCACATGA
22103669 CATTAAACATCTATTCATGCTCAACCATCAACCAAATTAACCAAAGTACAAACATATTCAAAACT
390 CATTAAACATCTATTCATGCTCAACCATCAACCAAATTAACCAAAGTACAAACATATTCAAAACT
*
22103734 TACCATTTCAAAGTATTAACACTTAGCTCTTGACCATTAAGAATCAATCCAACCAAAAACACTTT
455 TACCATTTCAAAGTATTACCACTTAGCTCTTGACCATTAAGAATCAATCCAACCAAAAACACTTT
*
22103799 AAACACATATTCAAAACCAAACATTTCACTAGGAACACCATTATAGTATAACATTTATA
520 AAACACATATTCAAAACCAAACATTTCACTAGGAACACCATTATAGTATAACATTTACA
* * *** * * * *
22103858 TATTCGAAGTTGGGTCACACAACAGTGTTACAAGCCGTGTGCTAGACCGTCTAACAATCTGTTTT
1 TATTCGAAGTTGGGTCATACGACAGTGTCGTAAGCCGTGTTCTAAACCGTGTAACAATCTATTTT
* * * * * * *
22103923 GGCTCACATGGTCGTGTTGCAAGCCATGTGCTAGGCTGTGTGGATATTGCA-CTGATAATCAATA
66 GGCACACACGGTCGTGTCGCAGGCTATGTGCTAGGCCGTGTAGATA-TGCACCT-ATAATCAATA
*
22103987 ATTACACACGG-CTGTGCGTGGTGACTGTGTGTGGTACATGGCCGTGTGCACCCTTTTTGACCCC
129 ATTACACACGGTC-GTGCGTGGTGACTGTGTGTGGCACATGGCCGTGTGCACCCTTTTTGACCCC
* * *
22104051 TAAATCAAGTAATGTCATGCATTGTTCCTTGCACAACAAGACATGCCATATTTAGATCAATTCCT
193 TAAATCAAGCAATGTCATGCATTATTCCTTGCACAACAAGACATGCCATATCTAGATCAATTCCT
* * * *
22104116 AGGCTCAAAAACACATTTAAATCATCAAATACATGTTAAAATTTAATTCATTTCACGCCTAACTA
258 AGGTTCAAAAACACATTTAAATCATCAAATACATGCTAAAATTTCATTCATTTCACGCCTAACCA
* * * * *
22104181 ATATGCCATTCAAATGCACCACAATTAAATATCAGTAAATTACTAATTTAGCTAAGTAAACACAT
323 ATATGTCATTCAAATGCACCACAATTAAAGATCATTCAATTACTAATTTAGCTAAGTAAGCACAT
22104246 GACATTAAACATCTATTCATGCTCAACCATCAACCAAATTAACCAAAGTACAAACATATTCAAAA
388 GACATTAAACATCTATTCATGCTCAACCATCAACCAAATTAACCAAAGTACAAACATATTCAAAA
*
22104311 CTTACCATTTCAAAGTATTACCACTTGGCTCTTGACCATTAAGAATCAATCCAACCAAAAACACT
453 CTTACCATTTCAAAGTATTACCACTTAGCTCTTGACCATTAAGAATCAATCCAACCAAAAACACT
* *
22104376 TTAAACACATATTCAAAACCAAACATTTCACTAGAAACACCATTATAATATAACATTTACA
518 TTAAACACATATTCAAAACCAAACATTTCACTAGGAACACCATTATAGTATAACATTTACA
*
22104437 TATTCAAAGTTGGGTCATACGACAGTGTCGTAAGCCGTGTTCTAAACCGTGTAACAATCTATTTT
1 TATTCGAAGTTGGGTCATACGACAGTGTCGTAAGCCGTGTTCTAAACCGTGTAACAATCTATTTT
* *
22104502 GGCACACACGGTCGTGTCGCATGCTATGTGCTAGGCCGTGT-GCATATGCACCTATAACCAATAA
66 GGCACACACGGTCGTGTCGCAGGCTATGTGCTAGGCCGTGTAG-ATATGCACCTATAATCAATAA
* *
22104566 TTACACACGGTCGTGTGTGGTGACTGTGTGTGACACATGGCCGTGTGCACCCTTTTTGACCCCTA
130 TTACACACGGTCGTGCGTGGTGACTGTGTGTGGCACATGGCCGTGTGCACCCTTTTTGACCCCTA
* * *
22104631 AATCAAGCAATGTCATGTATTATTCCTTGCATAACAAGACATGGCATATCTAGATCAATTCCTAG
195 AATCAAGCAATGTCATGCATTATTCCTTGCACAACAAGACATGCCATATCTAGATCAATTCCTAG
22104696 GTTCAAAAACACATTTAAATCATCAAATACATGCTAAAATTTCATTCATTTCACGCCTAACCAAT
260 GTTCAAAAACACATTTAAATCATCAAATACATGCTAAAATTTCATTCATTTCACGCCTAACCAAT
*
22104761 ATGTCATTCAAATGTACCACAATTAAAGATCATTCAATTACTAATTTAGCTAAGTAAGCACATGA
325 ATGTCATTCAAATGCACCACAATTAAAGATCATTCAATTACTAATTTAGCTAAGTAAGCACATGA
22104826 CATTAAACATCTATTCATGCTCAACCATCAACCAAATTAACCAAAGTACAAACATATTCAAAACT
390 CATTAAACATCTATTCATGCTCAACCATCAACCAAATTAACCAAAGTACAAACATATTCAAAACT
* *
22104891 TACCATTTCAAAGTATTACCACTTAGCTCTTGACCATTAAGAATCAATCTAACCAAAAATACTTT
455 TACCATTTCAAAGTATTACCACTTAGCTCTTGACCATTAAGAATCAATCCAACCAAAAACACTTT
* *
22104956 AAACCCATATTCAGAACCAAACATTTCACTAGGAACACCATTATAGTATAACATTTACA
520 AAACACATATTCAAAACCAAACATTTCACTAGGAACACCATTATAGTATAACATTTACA
22105015 TATT
1 TATT
22105019 TACAACAAAA
Statistics
Matches: 2164, Mismatches: 146, Indels: 17
0.93 0.06 0.01
Matches are distributed among these distances:
577 1 0.00
578 914 0.42
579 1248 0.58
580 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.29
Consensus pattern (578 bp):
TATTCGAAGTTGGGTCATACGACAGTGTCGTAAGCCGTGTTCTAAACCGTGTAACAATCTATTTT
GGCACACACGGTCGTGTCGCAGGCTATGTGCTAGGCCGTGTAGATATGCACCTATAATCAATAAT
TACACACGGTCGTGCGTGGTGACTGTGTGTGGCACATGGCCGTGTGCACCCTTTTTGACCCCTAA
ATCAAGCAATGTCATGCATTATTCCTTGCACAACAAGACATGCCATATCTAGATCAATTCCTAGG
TTCAAAAACACATTTAAATCATCAAATACATGCTAAAATTTCATTCATTTCACGCCTAACCAATA
TGTCATTCAAATGCACCACAATTAAAGATCATTCAATTACTAATTTAGCTAAGTAAGCACATGAC
ATTAAACATCTATTCATGCTCAACCATCAACCAAATTAACCAAAGTACAAACATATTCAAAACTT
ACCATTTCAAAGTATTACCACTTAGCTCTTGACCATTAAGAATCAATCCAACCAAAAACACTTTA
AACACATATTCAAAACCAAACATTTCACTAGGAACACCATTATAGTATAACATTTACA
Found at i:22105610 original size:20 final size:20
Alignment explanation
Indices: 22105545--22105667 Score: 97
Period size: 20 Copynumber: 6.2 Consensus size: 20
22105535 GCATCATAGA
* *
22105545 TGCATAACAGAAGCATCGAAG
1 TGCA-AACAGAGGCACCGAAG
* *
22105566 TACAAACAGAGACA-CGAATG
1 TGCAAACAGAGGCACCGAA-G
* * *
22105586 TGCAATCAGCGGCACTGAAG
1 TGCAAACAGAGGCACCGAAG
**
22105606 TGCAAACAGAGATACCGAAG
1 TGCAAACAGAGGCACCGAAG
* * *
22105626 TG-TAATAGAGGCACCAAAG
1 TGCAAACAGAGGCACCGAAG
*
22105645 TGCAAACAGAGGCACTGAAG
1 TGCAAACAGAGGCACCGAAG
22105665 TGC
1 TGC
22105668 GCGCATACTG
Statistics
Matches: 77, Mismatches: 22, Indels: 7
0.73 0.21 0.07
Matches are distributed among these distances:
19 18 0.23
20 53 0.69
21 6 0.08
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.13
Consensus pattern (20 bp):
TGCAAACAGAGGCACCGAAG
Found at i:22105617 original size:40 final size:39
Alignment explanation
Indices: 22105561--22105667 Score: 117
Period size: 39 Copynumber: 2.7 Consensus size: 39
22105551 ACAGAAGCAT
* *
22105561 CGAAGTACAAACAGAGACA-CGAATGTGCAATCAGCGGCAC
1 CGAAGTGCAAACAGAGACACCGAA-GTGCAAT-AGAGGCAC
* * *
22105601 TGAAGTGCAAACAGAGATACCGAAGTGTAATAGAGGCAC
1 CGAAGTGCAAACAGAGACACCGAAGTGCAATAGAGGCAC
* * *
22105640 CAAAGTGCAAACAGAGGCACTGAAGTGC
1 CGAAGTGCAAACAGAGACACCGAAGTGC
22105668 GCGCATACTG
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
39 29 0.53
40 22 0.40
41 4 0.07
ACGTcount: A:0.40, C:0.21, G:0.27, T:0.12
Consensus pattern (39 bp):
CGAAGTGCAAACAGAGACACCGAAGTGCAATAGAGGCAC
Found at i:22111048 original size:92 final size:92
Alignment explanation
Indices: 22110889--22111056 Score: 273
Period size: 92 Copynumber: 1.8 Consensus size: 92
22110879 CACGCCATCC
* * * *
22110889 GAGGCTCCTCGTCTCGAGGCTTGACAAGCCCCTGCCGCCATTTCACCAAAATGGCAAGGGCATCC
1 GAGGCTCCTCGTCCCGAGGCCTGACAAGCCCCTGCCGCCATTTCACCAAAATGGCAAAGGCACCC
22110954 TTCTCTCCCCGCCATCTCACACCACCT
66 TTCTCTCCCCGCCATCTCACACCACCT
* * *
22110981 GAGGCTCCTTGTCCCGAGGCCTGACACGCCCCTGCCGCCATTTCACCAAAATGGCAAAGGCGCCC
1 GAGGCTCCTCGTCCCGAGGCCTGACAAGCCCCTGCCGCCATTTCACCAAAATGGCAAAGGCACCC
22111046 TTCTCTCCCCG
66 TTCTCTCCCCG
22111057 ACGTTGACCG
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 69 1.00
ACGTcount: A:0.18, C:0.42, G:0.20, T:0.20
Consensus pattern (92 bp):
GAGGCTCCTCGTCCCGAGGCCTGACAAGCCCCTGCCGCCATTTCACCAAAATGGCAAAGGCACCC
TTCTCTCCCCGCCATCTCACACCACCT
Found at i:22111345 original size:17 final size:18
Alignment explanation
Indices: 22111323--22111357 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22111313 TTTTTATTTT
22111323 AGAAAAA-AAAAGAATAA
1 AGAAAAAGAAAAGAATAA
*
22111340 AGAAAAAGAAAATAATAA
1 AGAAAAAGAAAAGAATAA
22111358 GTAAAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (18 bp):
AGAAAAAGAAAAGAATAA
Found at i:22112356 original size:3 final size:3
Alignment explanation
Indices: 22112329--22112403 Score: 57
Period size: 3 Copynumber: 25.3 Consensus size: 3
22112319 TGTATCCCTC
* * *
22112329 TTA TCA TTA TT- TTA TCTA CTTA TTA TTA TTA TTA -TA ATA TGA TTA
1 TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
22112374 TTA ATA TTA TTA TTA -CA TTA TTA TTG TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
22112404 AGTATTCCTT
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
2 5 0.09
3 46 0.82
4 4 0.07
5 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:22112363 original size:20 final size:19
Alignment explanation
Indices: 22112328--22112403 Score: 55
Period size: 20 Copynumber: 3.7 Consensus size: 19
22112318 TTGTATCCCT
*
22112328 CTTATCATTATT-TTATCTA
1 CTTATTATTATTATTAT-TA
22112347 CTTATTATTATTATTATAATA
1 CTTATTATTATTATTAT--TA
* *
22112368 TGATTATTAATATTATTATTA
1 --CTTATTATTATTATTATTA
*
22112389 CATTATTATTGTTAT
1 C-TTATTATTATTAT
22112404 AGTATTCCTT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
19 11 0.24
20 15 0.33
21 4 0.09
23 15 0.33
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.58
Consensus pattern (19 bp):
CTTATTATTATTATTATTA
Found at i:22112396 original size:23 final size:23
Alignment explanation
Indices: 22112348--22112398 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
22112338 TTTTATCTAC
* *
22112348 TTATTATTATTATTATAATATGA
1 TTATTAATATTATTATAACATGA
* *
22112371 TTATTAATATTATTATTACATTA
1 TTATTAATATTATTATAACATGA
22112394 TTATT
1 TTATT
22112399 GTTATAGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTATTAATATTATTATAACATGA
Found at i:22129287 original size:29 final size:29
Alignment explanation
Indices: 22129192--22130388 Score: 834
Period size: 29 Copynumber: 43.7 Consensus size: 29
22129182 GGTTTTTACA
*
22129192 TTAATTAAATTAGGTTAGGGTTAGGGATTT
1 TTAATTAAATTAAGTTAGGGTTAGGG-TTT
** * * * ** *
22129222 CAAATAAAATGATAAATCAAAGTAAGGGTTT
1 TTAATTAAAT--TAAGTTAGGGTTAGGGTTT
* * *
22129253 TCAATTAAATTAGGTTAGGGTTAGGGATT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* * *
22129282 TTAATTAAGA-TAGGTTAGAGTTTGGG-TT
1 TTAATTAA-ATTAAGTTAGGGTTAGGGTTT
* * *
22129310 TTCATGTAAAATAGGTTAGGGTTAGGGTTT
1 TTAAT-TAAATTAAGTTAGGGTTAGGGTTT
*
22129340 TTAACT-AA-T---TTA-GGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* *
22129363 TTAATTAAATTAGGTTAGGGTTAGGGATT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* * *
22129392 TTAGTTAAAATAGGTTAGGGTTAGGG-TT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* * *
22129420 TTCATGTAAAATAGGTTAGGGTTAGGGTTT
1 TTAAT-TAAATTAAGTTAGGGTTAGGGTTT
* *
22129450 TTAACT--A--AA-TTA-GGTTAGGTTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
** *
22129473 TTAATTAAATTAAAATAGGGTAAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22129502 TTAATTAAATTAAATTAGGTTAGGGTTAGGGATT
1 TTAATTAAATT--A--A-GTTAGGGTTAGGGTTT
* *
22129536 TTAATTAAAATAGGTTAGGGTTAGGG-TT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* *
22129564 TTCATGTAAAATAAGTTAGGGTTAGGGTTT
1 TTAAT-TAAATTAAGTTAGGGTTAGGGTTT
* *
22129594 TTAACT--A--AA-TTA-GGTTAGGTTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
** *
22129617 TTAATTAAATTAAAATAGGGTAAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22129646 TTAATTAAATTAAATTA-GGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
** *
22129674 TTAATTAAATTAAAATAGGGTAAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* * * *
22129703 TTAATTAAATTAGGTTAGGCTTAGGGATC
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* *
22129732 TTAA-TACAAATAGGTTAGGGTTAGGG-TT
1 TTAATTA-AATTAAGTTAGGGTTAGGGTTT
* *
22129760 TTCATGTAAAATAAGTTAGGGTTAGGGTTT
1 TTAAT-TAAATTAAGTTAGGGTTAGGGTTT
*
22129790 TTAACT--A--AA-TTA-GGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
** * *
22129813 TTAATTAAATTAAAATAGGGTAAGGGTCT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* * *
22129842 TTAATTAATTTAAATTA-AGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22129870 TTAATTAAATTAAATTA-GGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22129898 TTAATTAAATTAAATTA-GGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22129926 TTAATTAAGTTAAGTTA-GG--A---TTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* * *
22129949 TTAATTAAAATAGGTTAGGGTTAGAGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* *
22129978 TTAACT--A--AA-TTA-GGTTAGGGATT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* *
22130001 TTAATTAAATTAAATTA-GGTTAGAGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22130029 TTAATTAAATTAAATTA-GGTTAGGG--T
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* *
22130055 TT--TT-AATTAAGTTA-AGTTAGGGCTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* *
22130080 TTAATTAAAATAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* *
22130109 TTAACT--A--AA-TTA-GGTTAGGGATT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22130132 TTAATT-AA--A--TTA-GGTTAGGGATT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* * * *
22130155 TTAATTAAATTAAATTA-AGTTGGGGATT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22130183 TTAATTAAATTAAATTA-GGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22130211 TTAATTAAATTAAATTA-GGTTAGGG--T
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22130237 TT--TT-AATTAAGTTA-AGTTAGGG-TT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22130261 TTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
* *
22130290 TT-ATGTAAAATAGGTTAGGGTTAGGGTTT
1 TTAAT-TAAATTAAGTTAGGGTTAGGGTTT
*
22130319 TTAACT--A--AA-TTA-GGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22130342 TTAATTAAATTAAATTA-GGTTAGGGTTT
1 TTAATTAAATTAAGTTAGGGTTAGGGTTT
*
22130370 TTAATTAAATTAGGTTAGG
1 TTAATTAAATTAAGTTAGG
22130389 NNNNNNNNNN
Statistics
Matches: 963, Mismatches: 123, Indels: 163
0.77 0.10 0.13
Matches are distributed among these distances:
23 176 0.18
24 36 0.04
25 17 0.02
26 11 0.01
27 28 0.03
28 284 0.29
29 335 0.35
30 31 0.03
31 11 0.01
32 11 0.01
33 1 0.00
34 22 0.02
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.42
Consensus pattern (29 bp):
TTAATTAAATTAAGTTAGGGTTAGGGTTT
Found at i:22129342 original size:58 final size:57
Alignment explanation
Indices: 22129192--22130388 Score: 760
Period size: 52 Copynumber: 21.8 Consensus size: 57
22129182 GGTTTTTACA
* * * * ** *
22129192 TTAATTAAATTAGGTTAGGGTTAGGGATTTCAAATAAAAT-GATAAATCAAAGTAAGGGTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGT---T-AGGGTTAGGGTT
* * * *
22129252 TTCAATTAAATTAGGTTAGGGTTAGGGATTTTAATTAAGATAGGTTAGAGTTTGGGTT
1 TT-AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTT
* * *
22129310 TTCATGTAAAATAGGTTAGGGTTAGGGTTTTTAACT--AAT---TTA-GGTTAGGGTTT
1 TTAAT-TAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGG-TT
* *
22129363 TTAATTAAATTAGGTTAGGGTTAGGGATTTTAGTTAAAATAGGTTAGGGTTAGGGTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTT
* * * *
22129420 TTCATGTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAATTAGGTTA-GGTT----TT
1 TTAAT-TAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTT
*** *
22129473 TTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTAGGGATT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT--A--AAA-TAGGTTAGGGTTAGGG-TT
* * *
22129536 TTAATTAAAATAGGTTAGGGTTAGGG-TTTTCATGTAAAATAAGTTAGGGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAT-TAAAATAGGTTAGGGTTAGGG-TT
* * *** *
22129594 TTAACTAAATTAGGTTA-GG-T----TTTTTAATTAAATTAAAATAGGGTAAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGG-TT
** * *** *
22129646 TTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGG-TT
* * *
22129703 TTAATTAAATTAGGTTAGGCTTAGGGATCTTAA-TACAAATAGGTTAGGGTTAGGGTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA-AAATAGGTTAGGGTTAGGGTT
* * * * *
22129760 TTCATGTAAAATAAGTTAGGGTTAGGGTTTTTAACTAAATTAGGTTAGGG-T----TT
1 TTAAT-TAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTT
*** * * ** ** *
22129813 TTAATTAAATTAAAATAGGGTAAGGGTCTTTAATTAATTTAAATTA-AGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGG-TT
** * **
22129870 TTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGG-T
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTT
* * * *
22129924 TT--TT-AATTAAGTTA-AGTTAGGATTTTTAATTAAAATAGGTTAGGGTTAGAGTTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAG-GGTT
* * ** *
22129978 TTAACTAAATTAGGTTAGGG--A----TTTTAATTAAATTAAATTA-GGTTAGAGTTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAG-GGTT
** *
22130029 TTAATTAAATTAAATTA-GGTTAGGGTTTTTAATT---A-A-GTTA-AGTTAGGGCTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGG-TT
* * *
22130080 TTAATTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAATTAGGTTAGGG--A---TT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTT
* ** * *
22130132 TTAATTAAATTAGGTTAGGG--A----TTTTAATTAAATTAAATTA-AGTTGGGGATT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGG-TT
** * **
22130183 TTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGG-T
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTT
* * *
22130237 TT--TT-AATTAAGTTA-AGTTAGGG-TTTTAATTAAATTAGGTTAGGGTTAGGGTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTT
* * * *
22130289 TTTATGTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAATTAGGTTAGGG-T----TT
1 TTAAT-TAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTT
** *
22130342 TTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGG
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGG
22130389 NNNNNNNNNN
Statistics
Matches: 924, Mismatches: 133, Indels: 169
0.75 0.11 0.14
Matches are distributed among these distances:
45 1 0.00
46 16 0.02
50 23 0.02
51 152 0.16
52 203 0.22
53 35 0.04
54 14 0.02
55 1 0.00
56 82 0.09
57 119 0.13
58 202 0.22
59 6 0.01
60 2 0.00
61 36 0.04
62 8 0.01
63 24 0.03
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.42
Consensus pattern (57 bp):
TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTT
Found at i:22129356 original size:23 final size:23
Alignment explanation
Indices: 22129329--22129384 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
22129319 AATAGGTTAG
*
22129329 GGTTAGGGTTTTTAACTAATTTA
1 GGTTAGGGTTTTTAACTAAATTA
*
22129352 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAACTAAATTA
22129375 GGTTAGGGTT
1 GGTTAGGGTT
22129385 AGGGATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.25, C:0.02, G:0.27, T:0.46
Consensus pattern (23 bp):
GGTTAGGGTTTTTAACTAAATTA
Found at i:22129466 original size:23 final size:23
Alignment explanation
Indices: 22129439--22129484 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
22129429 AATAGGTTAG
22129439 GGTTAGGGTTTTTAACTAAATTA
1 GGTTAGGGTTTTTAACTAAATTA
* *
22129462 GGTTAGGTTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAACTAAATTA
22129485 AAATAGGGTA
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:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (23 bp):
GGTTAGGGTTTTTAACTAAATTA
Found at i:22129486 original size:28 final size:28
Alignment explanation
Indices: 22129246--22130381 Score: 805
Period size: 28 Copynumber: 41.7 Consensus size: 28
22129236 AATCAAAGTA
* **
22129246 AGGGTTTTCAATTAAATTAGGTTAGGGTT
1 AGGGTTTTTAATTAAATTAAATTA-GGTT
* **
22129275 AGGGATTTTAATTAAGA-TAGGTTAGAGTT
1 AGGGTTTTTAATTAA-ATTAAATTAG-GTT
* * * **
22129304 TGGG-TTTTCATGTAAAATAGGTTAGGGTT
1 AGGGTTTTTAAT-TAAATTAAATTA-GGTT
*
22129333 AGGGTTTTTAACT-AA-T---TTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
**
22129356 AGGGTTTTTAATTAAATTAGGTTAGGGTT
1 AGGGTTTTTAATTAAATTAAATTA-GGTT
* * * **
22129385 AGGGATTTTAGTTAAAATAGGTTAGGGTT
1 AGGGTTTTTAATTAAATTAAATTA-GGTT
* * **
22129414 AGGG-TTTTCATGTAAAATAGGTTAGGGTT
1 AGGGTTTTTAAT-TAAATTAAATTA-GGTT
*
22129443 AGGG--TTT--TT-AACTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
* * *
22129466 AGGTTTTTTAATTAAATTAAAATAGGGTA
1 AGGGTTTTTAATTAAATTAAATTA-GGTT
22129495 AGGGTTTTTAATTAAATTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
* **
22129523 AGGGTTAGGGATTTTAATTAAAATAGGTTAGGGTT
1 AGGG-T-----TTTTAATTAAATTAAATTA-GGTT
* * *
22129558 AGGG-TTTTCATGTAAAATAAGTTAGGGTT
1 AGGGTTTTTAAT-TAAATTAAATTA-GGTT
*
22129587 AGGG--TTT--TT-AACTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
* * *
22129610 AGGTTTTTTAATTAAATTAAAATAGGGTA
1 AGGGTTTTTAATTAAATTAAATTA-GGTT
22129639 AGGGTTTTTAATTAAATTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
* *
22129667 AGGGTTTTTAATTAAATTAAAATAGGGTA
1 AGGGTTTTTAATTAAATTAAATTA-GGTT
**
22129696 AGGGTTTTTAATTAAATTAGGTTAGGCTT
1 AGGGTTTTTAATTAAATTAAATTAGG-TT
* * * **
22129725 AGGGATCTTAA-TACAAATAGGTTAGGGTT
1 AGGGTTTTTAATTA-AATTAAATTA-GGTT
* * *
22129754 AGGG-TTTTCATGTAAAATAAGTTAGGGTT
1 AGGGTTTTTAAT-TAAATTAAATTA-GGTT
*
22129783 AGGG--TTT--TT-AACTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
* *
22129806 AGGGTTTTTAATTAAATTAAAATAGGGTA
1 AGGGTTTTTAATTAAATTAAATTA-GGTT
* * *
22129835 AGGGTCTTTAATTAATTTAAATTAAGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
22129863 AGGGTTTTTAATTAAATTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
22129891 AGGGTTTTTAATTAAATTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
*
22129919 AGGGTTTTTAATTAAGTT--A--A-GTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
* * **
22129942 AGGATTTTTAATTAAAATAGGTTAGGGTT
1 AGGGTTTTTAATTAAATTAAATTA-GGTT
* *
22129971 AGAG--TTT--TT-AACTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
*
22129994 AGGGATTTTAATTAAATTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
*
22130022 AGAGTTTTTAATTAAATTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
*
22130050 AGGGTTTTTAATTAAGTT--A--A-GTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
* * **
22130073 AGGGCTTTTAATTAAAATAGGTTAGGGTT
1 AGGGTTTTTAATTAAATTAAATTA-GGTT
*
22130102 AGGG--TTT--TT-AACTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
*
22130125 AGGGATTTTAATT--A---AATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
* *
22130148 AGGGATTTTAATTAAATTAAATTAAGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
* *
22130176 GGGGATTTTAATTAAATTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
22130204 AGGGTTTTTAATTAAATTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
*
22130232 AGGGTTTTTAATTAAGTT--A--A-GTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
**
22130255 AGGG-TTTTAATTAAATTAGGTTAGGGTT
1 AGGGTTTTTAATTAAATTAAATTA-GGTT
* **
22130283 AGGGTTTTT-ATGTAAAATAGGTTAGGGTT
1 AGGGTTTTTAAT-TAAATTAAATTA-GGTT
*
22130312 AGGG--TTT--TT-AACTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
22130335 AGGGTTTTTAATTAAATTAAATTAGGTT
1 AGGGTTTTTAATTAAATTAAATTAGGTT
22130363 AGGGTTTTTAATTAAATTA
1 AGGGTTTTTAATTAAATTA
22130382 GGTTAGGNNN
Statistics
Matches: 925, Mismatches: 98, Indels: 169
0.78 0.08 0.14
Matches are distributed among these distances:
22 12 0.01
23 126 0.14
24 52 0.06
25 28 0.03
26 9 0.01
27 24 0.03
28 343 0.37
29 296 0.32
30 11 0.01
34 16 0.02
35 8 0.01
ACGTcount: A:0.33, C:0.01, G:0.23, T:0.43
Consensus pattern (28 bp):
AGGGTTTTTAATTAAATTAAATTAGGTT
Found at i:22129491 original size:23 final size:23
Alignment explanation
Indices: 22129442--22129493 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
22129432 AGGTTAGGGT
***
22129442 TAGGGTTTTTAACTAAATTAGGT
1 TAGGGTTTTTAACTAAATTAAAA
* *
22129465 TAGGTTTTTTAATTAAATTAAAA
1 TAGGGTTTTTAACTAAATTAAAA
22129488 TAGGGT
1 TAGGGT
22129494 AAGGGTTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (23 bp):
TAGGGTTTTTAACTAAATTAAAA
Found at i:22129515 original size:34 final size:34
Alignment explanation
Indices: 22129475--22129544 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
22129465 TAGGTTTTTT
*
22129475 AATTAAATTAAAATAGGGTAAGGGTTTTTAATTA
1 AATTAAATTAAAATAGGGTAAGGGATTTTAATTA
*** *
22129509 AATTAAATTAGGTTAGGGTTAGGGATTTTAATTA
1 AATTAAATTAAAATAGGGTAAGGGATTTTAATTA
22129543 AA
1 AA
22129545 ATAGGTTAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (34 bp):
AATTAAATTAAAATAGGGTAAGGGATTTTAATTA
Found at i:22129554 original size:34 final size:35
Alignment explanation
Indices: 22129488--22129592 Score: 100
Period size: 34 Copynumber: 3.2 Consensus size: 35
22129478 TAAATTAAAA
* * *
22129488 TAGGGTAAGGGTTTTTAATTAAATTAAATTA-GGT
1 TAGGGTTAGGGATTTTAATTAAAATAAATTAGGGT
22129522 TAGGGTTAGGGATTTTAATT---A-AAA-TA-GGT
1 TAGGGTTAGGGATTTTAATTAAAATAAATTAGGGT
* *
22129551 TAGGGTTAGGG-TTTTCATGTAAAATAAGTTAGGGT
1 TAGGGTTAGGGATTTTAAT-TAAAATAAATTAGGGT
22129586 TAGGGTT
1 TAGGGTT
22129593 TTTAACTAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
28 6 0.10
29 17 0.29
30 3 0.05
32 1 0.02
33 2 0.03
34 20 0.34
35 10 0.17
ACGTcount: A:0.31, C:0.01, G:0.29, T:0.39
Consensus pattern (35 bp):
TAGGGTTAGGGATTTTAATTAAAATAAATTAGGGT
Found at i:22129610 original size:23 final size:23
Alignment explanation
Indices: 22129583--22129628 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
22129573 AATAAGTTAG
22129583 GGTTAGGGTTTTTAACTAAATTA
1 GGTTAGGGTTTTTAACTAAATTA
* *
22129606 GGTTAGGTTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAACTAAATTA
22129629 AAATAGGGTA
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:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (23 bp):
GGTTAGGGTTTTTAACTAAATTA
Found at i:22130006 original size:131 final size:132
Alignment explanation
Indices: 22129599--22130388 Score: 843
Period size: 131 Copynumber: 5.9 Consensus size: 132
22129589 GGTTTTTAAC
* * *
22129599 TAAATTAGGTTAGGTTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAAATTAG
1 TAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATT--A--A-
* *
22129664 GTTAGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTTTTTAATTAAATTAGGTTAGGCTTAGGG
61 GTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATT-AA--A--TTAGG-TTAGGG
* *
22129729 ATCTTAA-TACAAA
120 ATTTTAATTA-AAT
** * * * * *
22129742 TAGGTTAGGGTTAGGG-TTTTCATGTAAAATAAGTTAGGGTTAGGGTTTTTAACTAAATTAGGTT
1 TAAATTA-GGTTAGGGTTTTTAAT-TAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAGTT
* * * *
22129806 AGGGTTTTTAATTAAATTAAAATAGGGTAAGGGTCTTTAATTAATTTAAATTAAGTTAGGGTTTT
64 AGGGTTTTTAATTAAATTAAATTAGGGTTAGGG--TTT--TTAA-TTAAATTAGGTTAGGGATTT
22129871 TAATTAAAT
124 TAATTAAAT
*
22129880 TAAATTAGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAGTTAAGTTAG
1 TAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAGTTAG
* * ** * *
22129944 GATTTTTAATTAAAATAGGTTAGGGTTAGAGTTTTTAACTAAATTAGGTTAGGGATTTTAATTAA
66 GGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGATTTTAATTAA
22130009 AT
131 AT
* *
22130011 TAAATTAGGTTAGAGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAGTTAAGTTAG
1 TAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAGTTAG
* * ** *
22130075 GGCTTTTAATTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAATTAGGTTAGGGA--TT--TT-A
66 GGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGATTTTAATTAA
22130135 AT
131 AT
* * * *
22130137 TAAATTAGGTTAGGGATTTTAATTAAATTAAATTA-AGTTGGGGATTTTAATTAAATTAAATTAG
1 TAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGG--TTT--TT-AATTAAATTAA
* *
22130201 GTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAGTTAAGTTAGGG-TTTTA
61 GTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGATTTTA
22130264 ATTAAAT
126 ATTAAAT
** * ** * *
22130271 TAGGTTAGGGTTAGGGTTTTT-ATGTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAATTAGGTT
1 TAAATTA-GGTTAGGGTTTTTAAT-TAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAGTT
22130335 AGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGG
64 AGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
22130389 NNNNNNNNNN
Statistics
Matches: 565, Mismatches: 60, Indels: 56
0.83 0.09 0.08
Matches are distributed among these distances:
126 42 0.07
127 2 0.00
128 3 0.01
129 2 0.00
130 30 0.05
131 240 0.42
132 6 0.01
133 2 0.00
134 16 0.03
135 21 0.04
136 56 0.10
137 18 0.03
138 24 0.04
139 42 0.07
141 4 0.01
142 1 0.00
143 17 0.03
144 39 0.07
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.43
Consensus pattern (132 bp):
TAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAGTTAG
GGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGATTTTAATTAA
AT
Found at i:22130137 original size:18 final size:21
Alignment explanation
Indices: 22130114--22130166 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 21
22130104 GGTTTTTAAC
22130114 TAAATTAGGTTAGGGATTTTAAT
1 TAAATTAGGTTAGGGA-TTT-AT
22130137 TAAATTAGGTTAGGGATTTTAAT
1 TAAATTAGGTTAGGGA-TTT-AT
22130160 TAAATTA
1 TAAATTA
22130167 AATTAAGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (21 bp):
TAAATTAGGTTAGGGATTTAT
Found at i:22132398 original size:14 final size:15
Alignment explanation
Indices: 22132381--22132414 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
22132371 AATAAATATC
22132381 TAAAAATAT-ATAAA
1 TAAAAATATCATAAA
*
22132395 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
22132410 TAAAA
1 TAAAA
22132415 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:22132641 original size:22 final size:22
Alignment explanation
Indices: 22132611--22132652 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
22132601 ATTTGGAGAT
*
22132611 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
22132633 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
22132653 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:22132660 original size:30 final size:30
Alignment explanation
Indices: 22132624--22132682 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
22132614 TTGAAGGAAA
*
22132624 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAATTTGAGAGT
22132654 TTGAGAGAATTTTGGAAGGAATTTGAGAG
1 TTGAGAGAATTTTGGAAGGAATTTGAGAG
22132683 AATTTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAATTTGAGAGT
Found at i:22132673 original size:52 final size:51
Alignment explanation
Indices: 22132602--22132704 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
22132592 TTAATATGGA
* * *
22132602 TTTGGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAA-TTGAGAG
* *
22132653 TTTGAGAGAATTTTGGAAGGAATTTGAGAGAATTTTTGAACGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAATTGAGAG
22132705 AATTTTTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 37 0.82
53 4 0.09
ACGTcount: A:0.33, C:0.01, G:0.32, T:0.34
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAACGGAATTGAGAG
Found at i:22132678 original size:22 final size:22
Alignment explanation
Indices: 22132653--22132723 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
22132643 AATTTGAGAG
*
22132653 TTTGAGAGAATTTTGGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
22132675 TTTGAGAGAATTTTTGAACGGAA
1 TTTGAGAGAATTTTTGAA-GGAA
22132698 -TTGAGAGAATTTTTGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
*
22132719 ATTGA
1 TTTGA
22132724 TATTGAATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 4 0.09
22 38 0.83
23 4 0.09
ACGTcount: A:0.37, C:0.01, G:0.28, T:0.34
Consensus pattern (22 bp):
TTTGAGAGAATTTTTGAAGGAA
Found at i:22136897 original size:25 final size:24
Alignment explanation
Indices: 22136865--22136932 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 24
22136855 ATATAATAAG
**
22136865 ATAATTAAATTAATTATTATGTA-
1 ATAATTAAATTAATTAAAATGTAC
22136888 ATATGATTAAATTGAATTAAAATGTAC
1 ATA--ATTAAATT-AATTAAAATGTAC
22136915 ATAATTAAATTAAGTTAA
1 ATAATTAAATTAA-TTAA
22136933 GTTAATAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
23 3 0.08
24 2 0.05
25 20 0.53
26 10 0.26
27 3 0.08
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.41
Consensus pattern (24 bp):
ATAATTAAATTAATTAAAATGTAC
Found at i:22141343 original size:6 final size:6
Alignment explanation
Indices: 22141332--22141358 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
22141322 CATTTTTCTG
22141332 TTTTGA TTTTGA TTTTGA TTTTGA TTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTT
22141359 ATTAAGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTTGA
Found at i:22145976 original size:77 final size:77
Alignment explanation
Indices: 22145845--22145998 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 77
22145835 AGCTGGAGCT
*
22145845 CGAGGAACCACAAAGCAAGGCATGACTTATCACGGGCTCGTCTTCGTGCTATTGAGAGTTCATTG
1 CGAGGAACCACAAAGCAAGGCATGACTTATCACGGGCTCGTCTTCGTGCAATTGAGAGTTCATTG
22145910 GAGAATGGGCAA
66 GAGAATGGGCAA
*
22145922 CGAGGAACCACAGAGCAAGGCATGACTTATCACGGGCTCGTCTTCGTGCAATTGAGAGTTCATTG
1 CGAGGAACCACAAAGCAAGGCATGACTTATCACGGGCTCGTCTTCGTGCAATTGAGAGTTCATTG
22145987 GAGAATGGGCAA
66 GAGAATGGGCAA
22145999 GTCTGGGTGC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (77 bp):
CGAGGAACCACAAAGCAAGGCATGACTTATCACGGGCTCGTCTTCGTGCAATTGAGAGTTCATTG
GAGAATGGGCAA
Found at i:22152925 original size:26 final size:24
Alignment explanation
Indices: 22152880--22152927 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
22152870 ATATTATTGG
22152880 TATATAAAAATTGAATTAAAATTT
1 TATATAAAAATTGAATTAAAATTT
* *
22152904 TATATATACAATTGTATATAAAAT
1 TATATA-AAAATTGAAT-TAAAAT
22152928 CAAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 8 0.40
26 6 0.30
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
TATATAAAAATTGAATTAAAATTT
Found at i:22166234 original size:33 final size:33
Alignment explanation
Indices: 22166194--22166328 Score: 254
Period size: 33 Copynumber: 4.1 Consensus size: 33
22166184 GAAACACCAT
22166194 CACCACCCACAAATACTGAACCACATATTGAAC
1 CACCACCCACAAATACTGAACCACATATTGAAC
22166227 CACCACCCACAAATACTGAACCACATATTGAAC
1 CACCACCCACAAATACTGAACCACATATTGAAC
22166260 CACCACCCACAAATACTGAACCACATATTGAAC
1 CACCACCCACAAATACTGAACCACATATTGAAC
22166293 CACCACCCACAAATACTGAACCACATGA-TGAAC
1 CACCACCCACAAATACTGAACCACAT-ATTGAAC
22166326 CAC
1 CAC
22166329 ATATTGAACC
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
33 100 0.99
34 1 0.01
ACGTcount: A:0.42, C:0.37, G:0.07, T:0.14
Consensus pattern (33 bp):
CACCACCCACAAATACTGAACCACATATTGAAC
Found at i:22167671 original size:224 final size:224
Alignment explanation
Indices: 22167281--22167726 Score: 847
Period size: 224 Copynumber: 2.0 Consensus size: 224
22167271 GGAAGTATTG
*
22167281 TCTTGAGATTTTGACTGATAGTGGCTTCATGGAATGTAAACCAGCAAAAACTCCAATGGCAACCA
1 TCTTGAGATTTTAACTGATAGTGGCTTCATGGAATGTAAACCAGCAAAAACTCCAATGGCAACCA
22167346 AATCAAGCTCAAAATTGCGAAGTGATGACAGTGAATTACTTGCTGATAATACACTCTATAGACAG
66 AATCAAGCTCAAAATTGCGAAGTGATGACAGTGAATTACTTGCTGATAATACACTCTATAGACAG
* *
22167411 CTGGTTGGTCGACTCGTTTATCTTACATCAACACGACTAGACATTTCATTTGCAGTTCAACAGCT
131 CTGGTTGGTCGACTCATTTATCTTACATCAACACGACCAGACATTTCATTTGCAGTTCAACAGCT
22167476 AAGTCAATTCTTGGATAAACCAACTGTTA
196 AAGTCAATTCTTGGATAAACCAACTGTTA
*
22167505 TCTTGAGATTTTAACTGATAGTGGCTTCATGGAATGTAAACCAGTAAAAACTCCAATGGCAACCA
1 TCTTGAGATTTTAACTGATAGTGGCTTCATGGAATGTAAACCAGCAAAAACTCCAATGGCAACCA
22167570 AATCAAGCTCAAAATTGCGAAGTGATGACAGTGAATTACTTGCTGATAATACACTCTATAGACAG
66 AATCAAGCTCAAAATTGCGAAGTGATGACAGTGAATTACTTGCTGATAATACACTCTATAGACAG
*
22167635 CTGGTTGGTCGACTCATTTATCTTACATCAACACGACCAGACATTTCATTTGCAGTTCAGCAGCT
131 CTGGTTGGTCGACTCATTTATCTTACATCAACACGACCAGACATTTCATTTGCAGTTCAACAGCT
22167700 AAGTCAATTCTTGGATAAACCAACTGT
196 AAGTCAATTCTTGGATAAACCAACTGT
22167727 GTTGCATCTT
Statistics
Matches: 217, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
224 217 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (224 bp):
TCTTGAGATTTTAACTGATAGTGGCTTCATGGAATGTAAACCAGCAAAAACTCCAATGGCAACCA
AATCAAGCTCAAAATTGCGAAGTGATGACAGTGAATTACTTGCTGATAATACACTCTATAGACAG
CTGGTTGGTCGACTCATTTATCTTACATCAACACGACCAGACATTTCATTTGCAGTTCAACAGCT
AAGTCAATTCTTGGATAAACCAACTGTTA
Found at i:22168701 original size:21 final size:20
Alignment explanation
Indices: 22168673--22168711 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
22168663 TTTTTTTTTG
*
22168673 AATTGAGTCGAGTAAAATAA
1 AATTGAGTCAAGTAAAATAA
*
22168693 AATTCGAGTCAAGTTAAAT
1 AATT-GAGTCAAGTAAAAT
22168712 CGAGTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (20 bp):
AATTGAGTCAAGTAAAATAA
Found at i:22168726 original size:16 final size:16
Alignment explanation
Indices: 22168680--22168722 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
22168670 TTGAATTGAG
*
22168680 TCGAGTAAAATAAAAT
1 TCGAGTAAAATTAAAT
* *
22168696 TCGAGTCAAGTTAAA-
1 TCGAGTAAAATTAAAT
22168711 TCGAGTAAAATT
1 TCGAGTAAAATT
22168723 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (16 bp):
TCGAGTAAAATTAAAT
Found at i:22168886 original size:15 final size:17
Alignment explanation
Indices: 22168858--22168893 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
22168848 TTTAGGCCCT
22168858 AAAATTATTATTTTA-A
1 AAAATTATTATTTTATA
22168874 AAAATTATT-TTTTATA
1 AAAATTATTATTTTATA
22168890 AAAA
1 AAAA
22168894 GAAAAGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATTATTATTTTATA
Found at i:22176150 original size:9 final size:9
Alignment explanation
Indices: 22176136--22176168 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
22176126 AAGTGTTATG
22176136 ATAAACTAT
1 ATAAACTAT
22176145 ATAAACTAT
1 ATAAACTAT
22176154 ATAAA-TAT
1 ATAAACTAT
22176162 ACTAAAC
1 A-TAAAC
22176169 CTTTAGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (9 bp):
ATAAACTAT
Found at i:22179477 original size:9 final size:9
Alignment explanation
Indices: 22179456--22179484 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
22179446 GTATATTTAA
22179456 AAATAAA-T
1 AAATAAAGT
22179464 AAATAAAGT
1 AAATAAAGT
22179473 AAATAAAGT
1 AAATAAAGT
22179482 AAA
1 AAA
22179485 AAAAAAAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.35
9 13 0.65
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (9 bp):
AAATAAAGT
Found at i:22180942 original size:9 final size:9
Alignment explanation
Indices: 22180930--22180964 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
22180920 CAAAATATAT
22180930 AAAAAAAAC
1 AAAAAAAAC
22180939 -AAAAAAAC
1 AAAAAAAAC
22180947 AAAAAAAAC
1 AAAAAAAAC
22180956 AGAAAAAAA
1 A-AAAAAAA
22180965 AACCTGGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 9 0.38
10 7 0.29
ACGTcount: A:0.89, C:0.09, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:22180952 original size:17 final size:18
Alignment explanation
Indices: 22180930--22180963 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
22180920 CAAAATATAT
22180930 AAAAAAAACA-AAAAAAC
1 AAAAAAAACAGAAAAAAC
22180947 AAAAAAAACAGAAAAAA
1 AAAAAAAACAGAAAAAA
22180964 AAACCTGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAAAAAACAGAAAAAAC
Found at i:22181037 original size:27 final size:27
Alignment explanation
Indices: 22181005--22181073 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
22180995 GGAGGGAATA
22181005 CTGTTGGCGGCACCAAACAAAGGAACC
1 CTGTTGGCGGCACCAAACAAAGGAACC
* * **
22181032 CTGTTGGCGGCACCAACCAAGGGTTCC
1 CTGTTGGCGGCACCAAACAAAGGAACC
22181059 CTGTTGGCGGCACCA
1 CTGTTGGCGGCACCA
22181074 CTCGTGTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.23, C:0.32, G:0.29, T:0.16
Consensus pattern (27 bp):
CTGTTGGCGGCACCAAACAAAGGAACC
Found at i:22181379 original size:17 final size:16
Alignment explanation
Indices: 22181348--22181383 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
22181338 AAAAATAAAA
22181348 ATTTTATAGTATTATT
1 ATTTTATAGTATTATT
*
22181364 ATTTTATTATTATTATT
1 ATTTTA-TAGTATTATT
22181381 ATT
1 ATT
22181384 AAGATGTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTTATAGTATTATT
Found at i:22182142 original size:18 final size:18
Alignment explanation
Indices: 22182114--22182158 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
22182104 TTGATATGGT
* *
22182114 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
*
22182132 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
22182150 TGGTGGCGA
1 TGGTGGCGA
22182159 TCATTGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:22184556 original size:14 final size:14
Alignment explanation
Indices: 22184537--22184565 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
22184527 TAACTGAAAC
22184537 TAGAATAATTAAAT
1 TAGAATAATTAAAT
22184551 TAGAATAATTAAAT
1 TAGAATAATTAAAT
22184565 T
1 T
22184566 GATACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAGAATAATTAAAT
Found at i:22185690 original size:27 final size:28
Alignment explanation
Indices: 22185658--22185722 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
22185648 TTTTTGATAC
22185658 ATTTTGGTAAAT-AAAAAAA-TTATATAT
1 ATTTTGGTAAATAAAAAAAAGTTATA-AT
*
22185685 TTTTTGGTAAATAAAAAAAAGTTATAAT
1 ATTTTGGTAAATAAAAAAAAGTTATAAT
22185713 ATTTTGGTAA
1 ATTTTGGTAA
22185723 TTTTTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 11 0.32
28 18 0.53
29 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.42
Consensus pattern (28 bp):
ATTTTGGTAAATAAAAAAAAGTTATAAT
Found at i:22185782 original size:19 final size:19
Alignment explanation
Indices: 22185758--22185798 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
22185748 TATAAAACCC
*
22185758 ATAATAAAACATTACAAAA
1 ATAATAAAACATTAAAAAA
*
22185777 ATAATAAAATATTAAAAAA
1 ATAATAAAACATTAAAAAA
22185796 ATA
1 ATA
22185799 CCAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
ATAATAAAACATTAAAAAA
Found at i:22185804 original size:19 final size:19
Alignment explanation
Indices: 22185758--22185809 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
22185748 TATAAAACCC
* * *
22185758 ATAATAAAACATTACAAAA
1 ATAACAAAATATTAAAAAA
*
22185777 ATAATAAAATATTAAAAAA
1 ATAACAAAATATTAAAAAA
*
22185796 ATACCAAAATATTA
1 ATAACAAAATATTA
22185810 TATATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (19 bp):
ATAACAAAATATTAAAAAA
Found at i:22186545 original size:22 final size:22
Alignment explanation
Indices: 22186513--22186633 Score: 86
Period size: 22 Copynumber: 6.0 Consensus size: 22
22186503 CCTTTCCTCT
* * *
22186513 TCTTCTTCTTTCTTTTTTTTTC
1 TCTTCTCCTTTCCTTTTCTTTC
22186535 TCTTCTCCTTTCCTTTTCTTTC
1 TCTTCTCCTTTCCTTTTCTTTC
* *
22186557 -CTTAT--TTTTC-TTTCTTTC
1 TCTTCTCCTTTCCTTTTCTTTC
*
22186575 -C-TCCCCTTTCCTTTTCTTTC
1 TCTTCTCCTTTCCTTTTCTTTC
*
22186595 -CTTCT--TTTTC-TTTCTTTC
1 TCTTCTCCTTTCCTTTTCTTTC
*
22186613 -C-TCTCCTTTCCTTTTCCTTC
1 TCTTCTCCTTTCCTTTTCTTTC
22186633 T
1 T
22186634 TTTTCTTTCT
Statistics
Matches: 79, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
17 4 0.05
18 18 0.23
19 16 0.20
20 16 0.20
21 6 0.08
22 19 0.24
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (22 bp):
TCTTCTCCTTTCCTTTTCTTTC
Found at i:22186557 original size:10 final size:10
Alignment explanation
Indices: 22186486--22186642 Score: 87
Period size: 10 Copynumber: 15.9 Consensus size: 10
22186476 AATTACCTTA
*
22186486 TTTTCTTT-T
1 TTTTCTTTCC
*
22186495 TTTTCCTTCC
1 TTTTCTTTCC
*
22186505 TTTCCTCTT-C
1 TTTTCT-TTCC
*
22186515 TTCTTCTTTCT
1 TT-TTCTTTCC
*
22186526 TTTTTTTTCTC
1 TTTTCTTTC-C
*
22186537 TTCTCCTTTCC
1 TT-TTCTTTCC
22186548 TTTTCTTTCC
1 TTTTCTTTCC
22186558 TTATT-TTT-C
1 TT-TTCTTTCC
22186567 -TTTCTTTCC
1 TTTTCTTTCC
***
22186576 TCCCCTTTCC
1 TTTTCTTTCC
22186586 TTTTCTTTCC
1 TTTTCTTTCC
22186596 TTCTT-TTT-C
1 TT-TTCTTTCC
22186605 -TTTCTTTCC
1 TTTTCTTTCC
* *
22186614 TCTCCTTTCC
1 TTTTCTTTCC
* *
22186624 TTTTCCTTCT
1 TTTTCTTTCC
22186634 TTTTCTTTC
1 TTTTCTTTC
22186643 TTCCTTTCTT
Statistics
Matches: 110, Mismatches: 24, Indels: 27
0.68 0.15 0.17
Matches are distributed among these distances:
7 4 0.04
8 8 0.07
9 11 0.10
10 66 0.60
11 16 0.15
12 5 0.05
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTCTTTCC
Found at i:22186603 original size:14 final size:14
Alignment explanation
Indices: 22186586--22186659 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
22186576 TCCCCTTTCC
22186586 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
22186600 TTTTCTTTCTTTCCT
1 TTTTCTTTCCTT-CT
22186615 CTCCTTTCCTTTTCCTTCT
1 -T--TTT-C-TTTCCTTCT
22186634 TTTTCTTT-CTTC-
1 TTTTCTTTCCTTCT
*
22186646 CTTTCTTT-CTTCT
1 TTTTCTTTCCTTCT
22186659 T
1 T
22186660 CTTCCCCTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
12 11 0.22
13 4 0.08
14 14 0.29
15 3 0.06
16 4 0.08
18 4 0.08
19 3 0.06
20 6 0.12
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:22186611 original size:28 final size:28
Alignment explanation
Indices: 22186542--22186656 Score: 67
Period size: 28 Copynumber: 4.1 Consensus size: 28
22186532 TTCTCTTCTC
*
22186542 CTTTCCTTTTCTTTCCTTATTTTTCTTT
1 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
*** *
22186570 CTTTCCTCCCCTTTCCTT-TTCTTTCCTT
1 CTTTCCTTTTCTTTCCTTCTT-TTTCTTT
* * *
22186598 CTTT-TTCTTTCTTTCCTCTCCTTTCCTTTT
1 CTTTCCT-TTTCTTTCCT-TCTTTTTC-TTT
* * *
22186628 CCTTCTTTTTCTTT-CTTC-CTTTCTTT
1 CTTTCCTTTTCTTTCCTTCTTTTTCTTT
22186654 CTT
1 CTT
22186657 CTTCTTCCCC
Statistics
Matches: 66, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
26 5 0.08
27 6 0.09
28 34 0.52
29 6 0.09
30 13 0.20
31 2 0.03
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (28 bp):
CTTTCCTTTTCTTTCCTTCTTTTTCTTT
Found at i:22186618 original size:76 final size:75
Alignment explanation
Indices: 22186481--22186650 Score: 188
Period size: 76 Copynumber: 2.3 Consensus size: 75
22186471 ATAAAAATTA
* * *
22186481 CCTTA-TTTTCTTTTTTTTCCTTCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTTCTCTTCTCCTT
1 CCTTATTTTTC-TTTCTTTCCTCCCTTTCCTCTTCTTCTTCTTTCTTTTTCTTTCTCTTCTCCTT
*
22186545 TCCTTTTCTTT
65 TCCTTTTCCTT
*
22186556 CCTTATTTTTCTTTCTTTCCTCCCCTTTCCTTTTCTTTCCTTCTTT-TTCTTTCTTTC-C-TCTC
1 CCTTATTTTTCTTTCTTTCCT-CCCTTTCCTCTTC-TT-CTTCTTTCTT-TTTCTTTCTCTTCTC
22186618 CTTTCCTTTTCCTT
62 CTTTCCTTTTCCTT
* *
22186632 -CTTTTTCTTTCTTCCTTTC
1 CCTTATT-TTTCTTTCTTTC
22186651 TTTCTTCTTC
Statistics
Matches: 82, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
75 19 0.23
76 44 0.54
77 5 0.06
78 14 0.17
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (75 bp):
CCTTATTTTTCTTTCTTTCCTCCCTTTCCTCTTCTTCTTCTTTCTTTTTCTTTCTCTTCTCCTTT
CCTTTTCCTT
Found at i:22186643 original size:10 final size:10
Alignment explanation
Indices: 22186486--22186662 Score: 63
Period size: 10 Copynumber: 16.7 Consensus size: 10
22186476 AATTACCTTA
22186486 TTTTCTTT-T
1 TTTTCTTTCT
* *
22186495 TTTTCCTTCC
1 TTTTCTTTCT
*
22186505 TTTCCTCTTCT
1 TTTTCT-TTCT
*
22186516 TCTTCTTTCT
1 TTTTCTTTCT
*
22186526 TTTTTTTTCT
1 TTTTCTTTCT
* *
22186536 CTTCTCCTTTCC
1 -TT-TTCTTTCT
22186548 TTTTCTTTCCTTAT
1 TTTTCTTT-C---T
22186562 TTTTCTTTC-
1 TTTTCTTTCT
* ** *
22186571 TTTCCTCCCC
1 TTTTCTTTCT
*
22186581 TTTCCTTT-T
1 TTTTCTTTCT
* *
22186590 CTTTCCTTCT
1 TTTTCTTTCT
22186600 TTTTCTTTCT
1 TTTTCTTTCT
*
22186610 TTCCTCTCCTTTCC
1 TT--T-T-CTTTCT
*
22186624 TTTTCCTTCT
1 TTTTCTTTCT
22186634 TTTTCTTTCT
1 TTTTCTTTCT
22186644 TCCTTTCTTTCT
1 T--TTTCTTTCT
*
22186656 TCTTCTT
1 TTTTCTT
22186663 CCCCTCTCCT
Statistics
Matches: 122, Mismatches: 30, Indels: 31
0.67 0.16 0.17
Matches are distributed among these distances:
9 18 0.15
10 57 0.47
11 13 0.11
12 17 0.14
13 2 0.02
14 15 0.12
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:22186643 original size:38 final size:38
Alignment explanation
Indices: 22186486--22186650 Score: 162
Period size: 38 Copynumber: 4.3 Consensus size: 38
22186476 AATTACCTTA
* *
22186486 TTTTCTTTTTTTTCCT-TCCTTTCCTCTT-CTT-CTTCTT
1 TTTTC-TTTCTTTCCTCTCCTTTCCTTTTCCTTCCTT-TT
* *
22186523 TCTTT-TTT-TTTCTCTTCTCCTTTCCTTTTCTTTCCTTAT
1 T-TTTCTTTCTTTC-C-TCTCCTTTCCTTTTCCTTCCTTTT
* * *
22186562 TTTTCTTTCTTTCCTCCCCTTTCCTTTTCTTTCCTTCT
1 TTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCCTTTT
22186600 TTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTT-CTTTT
1 TTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCCTTTT
*
22186637 TCTTTCTTCCTTTC
1 T-TTTCTTTCTTTC
22186651 TTTCTTCTTC
Statistics
Matches: 110, Mismatches: 9, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
35 4 0.04
36 4 0.04
37 7 0.06
38 80 0.73
39 8 0.07
40 7 0.06
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (38 bp):
TTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCCTTTT
Found at i:22186655 original size:22 final size:23
Alignment explanation
Indices: 22186620--22186662 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
22186610 TTCCTCTCCT
*
22186620 TTCCTTTTCCTTCTTTTTCTTTC
1 TTCCTTTTCCTTCTTCTTCTTTC
*
22186643 TTCC-TTTCTTTCTTCTTCTT
1 TTCCTTTTCCTTCTTCTTCTT
22186663 CCCCTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (23 bp):
TTCCTTTTCCTTCTTCTTCTTTC
Found at i:22186660 original size:28 final size:30
Alignment explanation
Indices: 22186582--22186663 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 30
22186572 TTCCTCCCCT
*
22186582 TTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCC
1 TTCC-TTTCTTT-CTTCTTCTTCTTTCTTTCC
*
22186614 TCTCCTTTCCTTT-TCCTTCTT-TTTCTTT-C
1 T-TCCTTT-CTTTCTTCTTCTTCTTTCTTTCC
22186643 TTCCTTTCTTTCTTCTTCTTC
1 TTCCTTTCTTTCTTCTTCTTC
22186664 CCCTCTCCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
27 4 0.09
28 13 0.30
29 2 0.05
30 7 0.16
31 6 0.14
32 4 0.09
33 7 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (30 bp):
TTCCTTTCTTTCTTCTTCTTCTTTCTTTCC
Found at i:22186673 original size:42 final size:40
Alignment explanation
Indices: 22186561--22186676 Score: 105
Period size: 42 Copynumber: 2.9 Consensus size: 40
22186551 TCTTTCCTTA
* *
22186561 TTTTTCTTTCTTTCCTCCCCTT-TCCT-T--TTCTTTCCTTC
1 TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTT--TTC
* * *
22186599 TTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTC
1 TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTTTC
* *
22186639 TTTCTTCCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTT
1 TTT-TT-CTTTCTTTCCTCTCCTTCCCCTCTCCTTCTT
22186677 CCCCCCACCA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
38 21 0.33
39 2 0.03
40 7 0.11
41 2 0.03
42 32 0.50
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTTTC
Found at i:22186784 original size:27 final size:27
Alignment explanation
Indices: 22186711--22186787 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
22186701 AATTCAAGGG
** * *
22186711 TGGTGCCGCCAACAGGGAACCTTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTATT
22186738 TGGTGCCGCCAACAGGGTTCCCTTATT
1 TGGTGCCGCCAACAGGGTTCCCTTATT
* *
22186765 TGGTGCCGCCAATAGTGTTCCCT
1 TGGTGCCGCCAACAGGGTTCCCT
22186788 CCACCCAGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.29
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTATT
Found at i:22192666 original size:3 final size:3
Alignment explanation
Indices: 22192658--22192704 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
22192648 TACAAAACAA
22192658 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
22192705 AGTAATGGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:22199663 original size:96 final size:96
Alignment explanation
Indices: 22199544--22199719 Score: 280
Period size: 96 Copynumber: 1.8 Consensus size: 96
22199534 AATTGATCTC
* *
22199544 TCACCTGTTGTGAAATATTATTGGTATAGTTCAAAAGATCATGAGGGTTTTCGATGTCCAATTAA
1 TCACCTGTTGTGAAATATTATTGGTATAGTTCAAAAGATCATAAGGGTTTTCAATGTCCAATTAA
22199609 ATATCCAAATAGAGAGAATACGATTAAGCTA
66 ATATCCAAATAGAGAGAATACGATTAAGCTA
* * * **
22199640 TCACCTTTTGTGCAATGTTATTGGTATAGTTCAAAAGATCATAAGGGTTTTCAATGTCCTTTTAA
1 TCACCTGTTGTGAAATATTATTGGTATAGTTCAAAAGATCATAAGGGTTTTCAATGTCCAATTAA
*
22199705 ATATCCAACTAGAGA
66 ATATCCAAATAGAGA
22199720 AGAAAGTAAG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 72 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (96 bp):
TCACCTGTTGTGAAATATTATTGGTATAGTTCAAAAGATCATAAGGGTTTTCAATGTCCAATTAA
ATATCCAAATAGAGAGAATACGATTAAGCTA
Found at i:22207606 original size:30 final size:32
Alignment explanation
Indices: 22207546--22207609 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
22207536 CACTTATTTT
22207546 CACCTATGCCGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
22207579 CACCTATGCCGAATGCAACATATATATATAT
1 CACCTATGCCGAATGCAACACATAAATATAT
22207610 ACATATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Found at i:22207869 original size:41 final size:41
Alignment explanation
Indices: 22207824--22208348 Score: 973
Period size: 41 Copynumber: 12.8 Consensus size: 41
22207814 ACCGGCTCTT
*
22207824 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
22207865 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
22207906 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
22207947 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
22207988 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
22208029 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
22208070 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
22208111 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
22208152 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
22208193 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
22208234 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
22208275 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
22208316 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
22208349 TAACGATAAA
Statistics
Matches: 476, Mismatches: 4, Indels: 8
0.98 0.01 0.02
Matches are distributed among these distances:
39 2 0.00
40 2 0.00
41 467 0.98
42 2 0.00
43 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:22215743 original size:41 final size:41
Alignment explanation
Indices: 22215682--22215795 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 41
22215672 TTAATTTAAA
* * *
22215682 CAGATTCAACGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
22215724 CAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
22215765 CAGATCACCGGCACGTAGCCTGCTAGACTTA
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTA
22215796 AAGTCTGAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
41 62 0.94
42 4 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (41 bp):
CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
Found at i:22217611 original size:13 final size:13
Alignment explanation
Indices: 22217593--22217617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22217583 CCATCCAATG
22217593 CACACAAAATAAA
1 CACACAAAATAAA
22217606 CACACAAAATAA
1 CACACAAAATAA
22217618 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:22220776 original size:39 final size:39
Alignment explanation
Indices: 22220727--22220804 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
22220717 GGAACGAAGG
*
22220727 AAAAGAAGAAAAAGAAAAGAAAAGAA-AAGAATGAGAAAA
1 AAAAGAAGAAAAAG-AAAGAAAAGAAGAAGAAGGAGAAAA
* **
22220766 AAAATAAGAAAAAGAAAGAAGGGAAGAAGAAGGAGAAAA
1 AAAAGAAGAAAAAGAAAGAAAAGAAGAAGAAGGAGAAAA
22220805 GAAACATCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 9 0.26
39 25 0.74
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (39 bp):
AAAAGAAGAAAAAGAAAGAAAAGAAGAAGAAGGAGAAAA
Found at i:22238072 original size:21 final size:22
Alignment explanation
Indices: 22238031--22238073 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
22238021 TAAATAAATG
22238031 TGTAATAAATATATGTATACATT
1 TGTAATAAATATATG-ATACATT
*
22238054 TGTAATTAATATATG-TACAT
1 TGTAATAAATATATGATACAT
22238074 ACTTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (22 bp):
TGTAATAAATATATGATACATT
Found at i:22238217 original size:26 final size:27
Alignment explanation
Indices: 22238155--22238225 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
22238145 AAAAGAGAAT
* *
22238155 AGAAACAGAATGACAAAACGAAAACAGGGG
1 AGAAA-AGAAAGA-AAAA-GAAAACAGGGA
22238185 AGAAAAGAAAGAAAAAGAAAA-AGGGA
1 AGAAAAGAAAGAAAAAGAAAACAGGGA
*
22238211 AGGAAAGAAAGAAAA
1 AGAAAAGAAAGAAAA
22238226 TTTGGGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 18 0.47
27 5 0.13
28 4 0.11
29 6 0.16
30 5 0.13
ACGTcount: A:0.66, C:0.06, G:0.27, T:0.01
Consensus pattern (27 bp):
AGAAAAGAAAGAAAAAGAAAACAGGGA
Found at i:22239106 original size:25 final size:25
Alignment explanation
Indices: 22239078--22239157 Score: 112
Period size: 25 Copynumber: 3.3 Consensus size: 25
22239068 ACTTTAGCGC
22239078 GCTCTCTGATTATTAGCACATCAGT
1 GCTCTCTGATTATTAGCACATCAGT
* *
22239103 GCTCTCTGATTACTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACATCAGT
*
22239128 GCTCTCTG--T-TTAGCACATCTGT
1 GCTCTCTGATTATTAGCACATCAGT
22239150 GCTCTCTG
1 GCTCTCTG
22239158 TATCACACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
22 18 0.36
23 1 0.02
25 31 0.62
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACATCAGT
Found at i:22239151 original size:22 final size:22
Alignment explanation
Indices: 22239090--22239181 Score: 96
Period size: 22 Copynumber: 4.0 Consensus size: 22
22239080 TCTCTGATTA
22239090 TTAGCACATCAGTGCTCTCTGAT
1 TTAGCACATCAGTGCTCTCTG-T
*
22239113 TACTAGCACGTCAGTGCTCTCTGT
1 T--TAGCACATCAGTGCTCTCTGT
*
22239137 TTAGCACATCTGTGCTCTCTGT
1 TTAGCACATCAGTGCTCTCTGT
* * *
22239159 ATCA-CACTTTAGTGCTCTCTGT
1 -TTAGCACATCAGTGCTCTCTGT
22239181 T
1 T
22239182 CATTAGTGCA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.02
22 34 0.58
23 3 0.05
24 2 0.03
25 19 0.32
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.38
Consensus pattern (22 bp):
TTAGCACATCAGTGCTCTCTGT
Found at i:22240770 original size:20 final size:21
Alignment explanation
Indices: 22240735--22240792 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
22240725 GAACAAAAAT
*
22240735 CAAAGGTATCGATACCTTTC-A
1 CAAA-GTATCAATACCTTTCTA
* *
22240756 TAAAGTATCAGTACC-TTCTA
1 CAAAGTATCAATACCTTTCTA
22240776 CAAAGTATCAATACCTT
1 CAAAGTATCAATACCTT
22240793 ACCCCTGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.10
20 23 0.77
21 4 0.13
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (21 bp):
CAAAGTATCAATACCTTTCTA
Found at i:22243005 original size:17 final size:17
Alignment explanation
Indices: 22242983--22243015 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22242973 AGTTTACTTT
22242983 TATAATTTATAA-TTTAA
1 TATAA-TTATAAGTTTAA
22243000 TATAATTATAAGTTTA
1 TATAATTATAAGTTTA
22243016 TTATTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TATAATTATAAGTTTAA
Found at i:22244322 original size:32 final size:32
Alignment explanation
Indices: 22244286--22244354 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
22244276 TTTGGGTAGA
* *
22244286 GGTTGCTTGATTCTCTCTATGGCTGATTCAGT
1 GGTTGCTTGATTCTCTCAATGACTGATTCAGT
22244318 GGTTGCTTGATTCTCTCAATGACTGATTCAGT
1 GGTTGCTTGATTCTCTCAATGACTGATTCAGT
22244350 GGTTG
1 GGTTG
22244355 AGGTAGGTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.42
Consensus pattern (32 bp):
GGTTGCTTGATTCTCTCAATGACTGATTCAGT
Found at i:22249180 original size:29 final size:29
Alignment explanation
Indices: 22249125--22249181 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
22249115 GGCTGTCGAT
* * *
22249125 ACCACACGGCCGTTTTTCAGGCCGTGTGA
1 ACCACACGACCGTTTGTCAAGCCGTGTGA
* *
22249154 ACCACTCGACCGTTTGTCAAGCTGTGTG
1 ACCACACGACCGTTTGTCAAGCCGTGTG
22249182 GGTCGTGTGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.18, C:0.30, G:0.26, T:0.26
Consensus pattern (29 bp):
ACCACACGACCGTTTGTCAAGCCGTGTGA
Found at i:22249348 original size:63 final size:63
Alignment explanation
Indices: 22249269--22249393 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 63
22249259 CACGGGTCAG
* *
22249269 GGACACAGGCGCGTGTCCAGACCTTGTGACTCACTGTTCACCAATTAGAGACATATAGGCCAA
1 GGACACAGGCGCGTGTCCAGACCTTGTGACTCACTATTCAACAATTAGAGACATATAGGCCAA
* * * * *
22249332 GGACACGGGCGCGTGTCCGGGCCTTGTGACTCACTATTCAAGAATTAGAGGCATATAGGCCA
1 GGACACAGGCGCGTGTCCAGACCTTGTGACTCACTATTCAACAATTAGAGACATATAGGCCA
22249394 GACACCCGGG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.21
Consensus pattern (63 bp):
GGACACAGGCGCGTGTCCAGACCTTGTGACTCACTATTCAACAATTAGAGACATATAGGCCAA
Found at i:22249412 original size:63 final size:63
Alignment explanation
Indices: 22249269--22249417 Score: 176
Period size: 63 Copynumber: 2.4 Consensus size: 63
22249259 CACGGGTCAG
* * * * *
22249269 GGACACAGGCGCGTGTCCAGACCTTGTGACTCACTGTTCACCAATTAGAGACATATAGGCCAA
1 GGACACGGGCGCATGTCCAGGCCTTGTGACTCACTATTCAACAATTAGAGACATATAGGCCAA
* * * *
22249332 GGACACGGGCGCGTGTCCGGGCCTTGTGACTCACTATTCAAGAATTAGAGGCATATAGGCC-A
1 GGACACGGGCGCATGTCCAGGCCTTGTGACTCACTATTCAACAATTAGAGACATATAGGCCAA
*
22249394 -GACACCCGGGTGCATGTCCAGGCC
1 GGACA--CGGGCGCATGTCCAGGCC
22249418 GCGTGACTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
61 4 0.05
62 1 0.01
63 69 0.93
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (63 bp):
GGACACGGGCGCATGTCCAGGCCTTGTGACTCACTATTCAACAATTAGAGACATATAGGCCAA
Found at i:22254996 original size:9 final size:9
Alignment explanation
Indices: 22254982--22255012 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
22254972 GTTAAACGAA
22254982 TCGAGTTAT
1 TCGAGTTAT
*
22254991 TCGAGTTAA
1 TCGAGTTAT
22255000 TCGAGTTAT
1 TCGAGTTAT
22255009 TCGA
1 TCGA
22255013 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:22259601 original size:21 final size:21
Alignment explanation
Indices: 22259572--22259630 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
22259562 TACTAAACAA
22259572 AAACCCATAAGGGTTAAATAG
1 AAACCCATAAGGGTTAAATAG
* *
22259593 AAGCTCAT-AGGAGATT-AATAG
1 AAACCCATAAGG-G-TTAAATAG
22259614 AAACCCATAAGGGTTAA
1 AAACCCATAAGGGTTAA
22259631 TATAATGCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
20 5 0.17
21 20 0.67
22 5 0.17
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (21 bp):
AAACCCATAAGGGTTAAATAG
Found at i:22259717 original size:42 final size:41
Alignment explanation
Indices: 22259572--22259715 Score: 153
Period size: 42 Copynumber: 3.4 Consensus size: 41
22259562 TACTAAACAA
* * * * *
22259572 AAACCCATAAGGGTTAAATAGAAGCTCATAGGAGATTAATAG
1 AAACCCATAAGGGTTAAATA-AAGCTCAAAAGAGCTAAATTG
* * *
22259614 AAACCCATAAGGGTTAATATAATGCTCAGAAGAGCTAAACTG
1 AAACCCATAAGGGTTAA-ATAAAGCTCAAAAGAGCTAAATTG
* *
22259656 AAACCCATTAGGGTTAAACTAAAGCTCAAAAGAGCTGAATTG
1 AAACCCATAAGGGTTAAA-TAAAGCTCAAAAGAGCTAAATTG
* *
22259698 AAACCCAGAATGGTTAAA
1 AAACCCATAAGGGTTAAA
22259716 CTGAAACTCA
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.01
42 81 0.95
43 3 0.04
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.21
Consensus pattern (41 bp):
AAACCCATAAGGGTTAAATAAAGCTCAAAAGAGCTAAATTG
Found at i:22261622 original size:28 final size:28
Alignment explanation
Indices: 22261558--22261631 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
22261548 GAGGCTCTAA
* *
22261558 AAGGAAAGCATTTGTAGCAATTTTTGGAT
1 AAGG-AAGCCTTTGTGGCAATTTTTGGAT
**
22261587 AATAAAGCCTTTGTGGCAATTTTTGGAT
1 AAGGAAGCCTTTGTGGCAATTTTTGGAT
22261615 AAGGAAGCCTTTGTGGC
1 AAGGAAGCCTTTGTGGC
22261632 TATCTCTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.34
Consensus pattern (28 bp):
AAGGAAGCCTTTGTGGCAATTTTTGGAT
Found at i:22263138 original size:13 final size:12
Alignment explanation
Indices: 22263109--22263157 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
22263099 TTCAAAACTT
22263109 ATAAAAAT--AA
1 ATAAAAATAAAA
*
22263119 A-AAAAATCAAA
1 ATAAAAATAAAA
22263130 ATCAAAAATAAAA
1 AT-AAAAATAAAA
22263143 ATAAAAATATAAA
1 ATAAAAATA-AAA
22263156 AT
1 AT
22263158 GTTTATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
9 6 0.18
10 1 0.03
11 3 0.09
12 7 0.21
13 16 0.48
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:22263156 original size:7 final size:6
Alignment explanation
Indices: 22263109--22263157 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
22263099 TTCAAAACTT
*
22263109 ATAAAA AT--AA A-AAAA ATCAAA ATCAAAA ATAAAA ATAAAA ATATAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA AT-AAAA ATAAAA ATAAAA ATA-AAA
22263156 AT
1 AT
22263158 GTTTATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
4 3 0.08
5 3 0.08
6 20 0.56
7 10 0.28
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:22263327 original size:31 final size:32
Alignment explanation
Indices: 22263268--22263329 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
22263258 AATCATTTCT
* *
22263268 ACTCTTTTTCAAAAGGTTGGTGGTCAAATTTG
1 ACTCTTTTTCAAAAGGTCGGTGGCCAAATTTG
22263300 ACTCTTTTT-AAAAGGTCGAG-GGCCAAATTT
1 ACTCTTTTTCAAAAGGTCG-GTGGCCAAATTT
22263330 AGCTCCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (32 bp):
ACTCTTTTTCAAAAGGTCGGTGGCCAAATTTG
Found at i:22265124 original size:21 final size:21
Alignment explanation
Indices: 22265100--22265139 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
22265090 GTTTTGATAT
22265100 GGAAAATGGAGAAA-AAGTGAA
1 GGAAAAT-GAGAAACAAGTGAA
*
22265121 GGAAAGTGAGAAACAAGTG
1 GGAAAATGAGAAACAAGTG
22265140 GAGAGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.10
Consensus pattern (21 bp):
GGAAAATGAGAAACAAGTGAA
Found at i:22265174 original size:3 final size:3
Alignment explanation
Indices: 22265168--22265227 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
22265158 GGAGCCAAAG
22265168 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
22265216 GAA AAA GAA GAA
1 GAA GAA GAA GAA
22265228 AGCTCAACTC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:22265464 original size:19 final size:18
Alignment explanation
Indices: 22265440--22265494 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
22265430 TATGTAATAG
22265440 AGAAAATAAAAGAAAAGTA
1 AGAAAA-AAAAGAAAAGTA
*
22265459 AGAAAAAAAGATTAAAAGTA
1 AGAAAAAAA-A-GAAAAGTA
22265479 A-AAAAAAAAGAGAAAG
1 AGAAAAAAAAGA-AAAG
22265495 ACTAAAGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 1 0.03
18 8 0.26
19 14 0.45
20 8 0.26
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (18 bp):
AGAAAAAAAAGAAAAGTA
Found at i:22265475 original size:20 final size:20
Alignment explanation
Indices: 22265452--22265489 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
22265442 AAAATAAAAG
*
22265452 AAAAGTAAGAAAAAAAGATT
1 AAAAGTAAAAAAAAAAGATT
22265472 AAAAGTAAAAAAAAAAGA
1 AAAAGTAAAAAAAAAAGA
22265490 GAAAGACTAA
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:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (20 bp):
AAAAGTAAAAAAAAAAGATT
Found at i:22267879 original size:19 final size:19
Alignment explanation
Indices: 22267844--22267925 Score: 50
Period size: 18 Copynumber: 4.4 Consensus size: 19
22267834 TAACCATTTT
22267844 TTTCAATATCTTATGTT-AA
1 TTTCAA-ATCTTATGTTCAA
* *
22267863 TTTCAAATCGTTTTGTTCAT
1 TTTCAAATC-TTATGTTCAA
*
22267883 TTTCAAAACATTA--TTC-A
1 TTTCAAATC-TTATGTTCAA
22267900 TTTACAAATCATTA--TTCAA
1 TTT-CAAATC-TTATGTTCAA
22267919 TTTCAAA
1 TTTCAAA
22267926 ATGTTTTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
17 3 0.06
18 22 0.42
19 16 0.31
20 11 0.21
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.48
Consensus pattern (19 bp):
TTTCAAATCTTATGTTCAA
Found at i:22267901 original size:18 final size:18
Alignment explanation
Indices: 22267878--22267926 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
22267868 AATCGTTTTG
22267878 TTCATTTTCAAAACATTA
1 TTCATTTTCAAAACATTA
* *
22267896 TTCATTTACAAATCATTA
1 TTCATTTTCAAAACATTA
*
22267914 TTCAATTTCAAAA
1 TTCATTTTCAAAA
22267927 TGTTTTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (18 bp):
TTCATTTTCAAAACATTA
Found at i:22275524 original size:24 final size:24
Alignment explanation
Indices: 22275493--22275540 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
22275483 GATTCTGAGG
22275493 ACATTTTGCACATTATTCAAGATT
1 ACATTTTGCACATTATTCAAGATT
*
22275517 ACATTTTGCACATTATTCGAGATT
1 ACATTTTGCACATTATTCAAGATT
22275541 GCACTTTAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (24 bp):
ACATTTTGCACATTATTCAAGATT
Found at i:22280893 original size:22 final size:21
Alignment explanation
Indices: 22280865--22280961 Score: 72
Period size: 22 Copynumber: 4.4 Consensus size: 21
22280855 ATTTTTACTA
22280865 CGGTGCCTATTGTTCTGCACTT
1 CGGTGCCTATTGTT-TGCACTT
*
22280887 CGGTGCCTATTAATTTGCACTAT
1 CGGTGCCTATT-GTTTGCACT-T
* *
22280910 -GCTGCCTACTGCTTTGCACTT
1 CGGTGCCTATTG-TTTGCACTT
* *
22280931 TGGTGCCTACTAGTTAT-CACTT
1 CGGTGCCTA-TTGTT-TGCACTT
*
22280953 CGATGCCTA
1 CGGTGCCTA
22280962 CTGGTGTGGT
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
21 1 0.02
22 54 0.90
23 5 0.08
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.38
Consensus pattern (21 bp):
CGGTGCCTATTGTTTGCACTT
Found at i:22283357 original size:15 final size:16
Alignment explanation
Indices: 22283337--22283366 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
22283327 TTAAAAAATA
22283337 ATTTTTA-ATTATTTT
1 ATTTTTACATTATTTT
22283352 ATTTTTACATTATTT
1 ATTTTTACATTATTT
22283367 CTCTCTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTTACATTATTTT
Found at i:22283721 original size:16 final size:16
Alignment explanation
Indices: 22283700--22283733 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
22283690 CGGTTTTCTC
22283700 TATTTTTAAAAATTTT
1 TATTTTTAAAAATTTT
*
22283716 TATTTTTAATAATTTT
1 TATTTTTAAAAATTTT
22283732 TA
1 TA
22283734 AATAGATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTAAAAATTTT
Found at i:22286754 original size:32 final size:32
Alignment explanation
Indices: 22286689--22286756 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
22286679 TGGAAGTTTG
* * *
22286689 TATTTGTTTTTTCCAAAAAAATTGGAAGTTTA
1 TATTTGCTTTTTCCAAAAAAATTAGAAGCTTA
** *
22286721 TATTTGCTTTTTCCTCAAAATTTAGAAGCTTA
1 TATTTGCTTTTTCCAAAAAAATTAGAAGCTTA
22286753 TATT
1 TATT
22286757 CAATAAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (32 bp):
TATTTGCTTTTTCCAAAAAAATTAGAAGCTTA
Found at i:22286997 original size:24 final size:24
Alignment explanation
Indices: 22286963--22287014 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
22286953 TTTCTAGAAG
* **
22286963 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
22286987 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
22287011 ATTT
1 ATTT
22287015 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:22292098 original size:26 final size:26
Alignment explanation
Indices: 22292062--22292113 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
22292052 TAGAAGAAGA
22292062 AAAAAAAACTAAGATTTCTTTTGGTT
1 AAAAAAAACTAAGATTTCTTTTGGTT
22292088 AAAAAAAACTAAGATTTCTTTTGGTT
1 AAAAAAAACTAAGATTTCTTTTGGTT
22292114 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (26 bp):
AAAAAAAACTAAGATTTCTTTTGGTT
Found at i:22295122 original size:21 final size:22
Alignment explanation
Indices: 22295096--22295136 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
22295086 GCTTACTAAC
22295096 TACC-TTGTATCGGTAGAAGTA
1 TACCTTTGTATCGGTAGAAGTA
*
22295117 TACCTTTGTGTCGGTAGAAG
1 TACCTTTGTATCGGTAGAAG
22295137 CCAAGTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (22 bp):
TACCTTTGTATCGGTAGAAGTA
Found at i:22295755 original size:20 final size:20
Alignment explanation
Indices: 22295713--22295772 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
22295703 TACCCAGAGA
*
22295713 TCAAAGTATC-GATACCCTAC
1 TCAAAGTATCAG-TACCTTAC
*
22295733 TCAAAGTATCAGTACCTTTC
1 TCAAAGTATCAGTACCTTAC
** *
22295753 TCATTGTATCAATACCTTAC
1 TCAAAGTATCAGTACCTTAC
22295773 CCCTAGTATC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.33
Consensus pattern (20 bp):
TCAAAGTATCAGTACCTTAC
Found at i:22299235 original size:18 final size:18
Alignment explanation
Indices: 22299212--22299895 Score: 216
Period size: 18 Copynumber: 42.3 Consensus size: 18
22299202 TTAACCCTAA
22299212 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
* ****
22299230 CCTAACCCTAA-CCCTAAC
1 CCTAA-CTTAATTAAAAAC
* *
22299248 CCTAATTTAATTAAAACC
1 CCTAACTTAATTAAAAAC
22299266 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
* **
22299284 TCTAAC---CCT---AA-
1 CCTAACTTAATTAAAAAC
*
22299295 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
* ****
22299313 CCTAACCCTAA-CCCTAAC
1 CCTAA-CTTAATTAAAAAC
* *
22299331 CCTAATTTAATTAAAACC
1 CCTAACTTAATTAAAAAC
22299349 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
* **
22299367 TCTAAC---CCT---AA-
1 CCTAACTTAATTAAAAAC
*
22299378 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
*
22299396 TCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
**
22299414 CCTAAC---CCT---AA-
1 CCTAACTTAATTAAAAAC
22299425 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
22299443 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
* **
22299461 TCTAAC---CCT---AA-
1 CCTAACTTAATTAAAAAC
*
22299472 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
22299490 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
* **
22299508 TCTAAC---CCT---AA-
1 CCTAACTTAATTAAAAAC
*
22299519 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
* ****
22299537 CCTAACCCTAA-CCCTAA-
1 CCTAA-CTTAATTAAAAAC
*
22299554 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
22299572 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
22299590 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
* **
22299608 ACTAAC---CCT---AA-
1 CCTAACTTAATTAAAAAC
22299619 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
*
22299637 CCCAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
**
22299655 CCTAAC---CCT---AA-
1 CCTAACTTAATTAAAAAC
* *
22299666 CCTAATTTAATTAAAGAC
1 CCTAACTTAATTAAAAAC
**
22299684 CCTAAC---CCT---AA-
1 CCTAACTTAATTAAAAAC
*
22299695 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
*
22299713 CCTAACTAAATTAAAAAC
1 CCTAACTTAATTAAAAAC
**
22299731 CCTAAC---CCT---AA-
1 CCTAACTTAATTAAAAAC
*
22299742 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
22299760 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
**
22299778 CCTAAC---CCT---AA-
1 CCTAACTTAATTAAAAAC
*
22299789 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
*
22299807 TCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
22299825 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
**
22299843 CCTAAC---CCT---AA-
1 CCTAACTTAATTAAAAAC
* *
22299854 CCTAATTTAATTAAAAAT
1 CCTAACTTAATTAAAAAC
22299872 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
22299890 CCTAAC
1 CCTAAC
22299896 CCTAACATAA
Statistics
Matches: 460, Mismatches: 122, Indels: 168
0.61 0.16 0.22
Matches are distributed among these distances:
11 52 0.11
12 21 0.05
14 11 0.02
15 11 0.02
16 3 0.01
17 34 0.07
18 318 0.69
19 10 0.02
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (18 bp):
CCTAACTTAATTAAAAAC
Done.