Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 8 of 290
Found at i:2763129 original size:55 final size:54
Alignment explanation
Indices: 2763068--2763342 Score: 208
Period size: 54 Copynumber: 5.0 Consensus size: 54
2763058 ATACGAGTTT
*
2763068 TTAAAAAAAAATTCAAATTTTTTCGGTGCTAGCCTGTCAATGGCCGGCACCAGTA
1 TTAAAAAAAAATTCAAATTTTTT-GATGCTAGCCTGTCAATGGCCGGCACCAGTA
* *
2763123 TTAAAAAAAAAATTCAAATTTTTTTATGCTAGTCTGTCAATGGCCGGCACCAGAATACGA
1 TT-AAAAAAAAATTCAAATTTTTTGATGCTAGCCTGTCAATGGCCGGCACCAG--T---A
*** * * * *
2763183 GTTTTTTTAAAAAA---AAA---TTT-ATGCTGGCCAGTCAATGGCTGACACCAGTA
1 ---TTAAAAAAAAATTCAAATTTTTTGATGCTAGCCTGTCAATGGCCGGCACCAGTA
* * * * *
2763233 TT-AAAAAAAATTCAATTTTTTTTGGTGCTGGCCTGTCAATGCCCGGCACCAATA
1 TTAAAAAAAAATTCAA-ATTTTTTGATGCTAGCCTGTCAATGGCCGGCACCAGTA
* * * *
2763287 TTAAAAAAAAA-TCAATTTTTTTTGTTTCTAGCCGGTCAATGGCCGGCACCAGTA
1 TTAAAAAAAAATTCAA-ATTTTTTGATGCTAGCCTGTCAATGGCCGGCACCAGTA
2763341 TT
1 TT
2763343 TTAATTTTTT
Statistics
Matches: 176, Mismatches: 26, Indels: 37
0.74 0.11 0.15
Matches are distributed among these distances:
46 6 0.03
47 2 0.01
49 2 0.01
50 1 0.01
53 4 0.02
54 65 0.37
55 59 0.34
56 24 0.14
57 1 0.01
59 3 0.02
60 1 0.01
62 6 0.03
63 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (54 bp):
TTAAAAAAAAATTCAAATTTTTTGATGCTAGCCTGTCAATGGCCGGCACCAGTA
Found at i:2763178 original size:119 final size:118
Alignment explanation
Indices: 2762950--2763201 Score: 375
Period size: 117 Copynumber: 2.1 Consensus size: 118
2762940 CACACCAGTA
* ** * *
2762950 TTTAAAAAAAAATTCAATTTTTTTTTGTGCTGGCCTGTCAATGGTCGGCACCAGTATTAAAAAAA
1 TTTAAAAAAAAATTCAAATTTTTTCGGTGCTAGCCTGTCAATGGCCGGCACCAGTATTAAAAAAA
*
2763015 TTCAAATTTTTTTTGTGCTGGCTTGTCAATGGCCGGCACCAGAATACGAG-TT
66 TTCAAATTTTTTTTATGCTGGCTTGTCAATGGCCGGCACCAGAATACGAGTTT
2763067 TTTAAAAAAAAATTCAAATTTTTTCGGTGCTAGCCTGTCAATGGCCGGCACCAGTATTAAAAAAA
1 TTTAAAAAAAAATTCAAATTTTTTCGGTGCTAGCCTGTCAATGGCCGGCACCAGTATT---AAAA
*
2763132 AAATTCAAA-TTTTTTTATGCTAG-TCTGTCAATGGCCGGCACCAGAATACGAGTTTT
63 AAATTCAAATTTTTTTTATGCTGGCT-TGTCAATGGCCGGCACCAGAATACGAG-TTT
2763188 TTTAAAAAAAAATT
1 TTTAAAAAAAAATT
2763202 TATGCTGGCC
Statistics
Matches: 122, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
117 53 0.43
118 1 0.01
119 39 0.32
120 13 0.11
121 16 0.13
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (118 bp):
TTTAAAAAAAAATTCAAATTTTTTCGGTGCTAGCCTGTCAATGGCCGGCACCAGTATTAAAAAAA
TTCAAATTTTTTTTATGCTGGCTTGTCAATGGCCGGCACCAGAATACGAGTTT
Found at i:2766469 original size:27 final size:26
Alignment explanation
Indices: 2766411--2766527 Score: 112
Period size: 27 Copynumber: 4.3 Consensus size: 26
2766401 AATAGTACAA
* *
2766411 AATTTAAATGAAAATTGA-AAGAAAGATA
1 AATTTAAATG-AAA-TGAGAAGAAA-TTT
2766439 AATTTAAATGAAATGAGGAAGAAATTT
1 AATTTAAATGAAATGA-GAAGAAATTT
* * *
2766466 AATTGAAATGAAATGAGAAAAAAATT
1 AATTTAAATGAAATGAGAAGAAATTT
*
2766492 AAATTAAATGAAATGAG-AGAAACTTTT
1 AATTTAAATGAAATGAGAAGAAA--TTT
2766519 AATTTAAAT
1 AATTTAAAT
2766528 AGTATAAGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
25 4 0.05
26 26 0.35
27 29 0.39
28 16 0.21
ACGTcount: A:0.56, C:0.01, G:0.15, T:0.28
Consensus pattern (26 bp):
AATTTAAATGAAATGAGAAGAAATTT
Found at i:2766491 original size:22 final size:22
Alignment explanation
Indices: 2766384--2766502 Score: 62
Period size: 21 Copynumber: 5.0 Consensus size: 22
2766374 AATGGCAAAA
*
2766384 AAAATAAATTGGAATGAAAT-AG
1 AAAA-AAATTGAAATGAAATGAG
* * *
2766406 TACAAAATTTAAATGAAAATTGAAAG
1 AAAAAAATTGAAATG-AAA-TG--AG
*
2766432 AAAGATAAATTTAAATGAAATGAGG
1 AAA-A-AAATTGAAATGAAATGA-G
2766457 AAGAAATTTAATTGAAATGAAATGAG
1 AA-AAA---AATTGAAATGAAATGAG
*
2766483 AAAAAAATT-AAATTAAATGA
1 AAAAAAATTGAAATGAAATGA
2766503 AATGAGAGAA
Statistics
Matches: 77, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
21 19 0.25
22 9 0.12
23 1 0.01
24 2 0.03
25 7 0.09
26 9 0.12
27 19 0.25
28 11 0.14
ACGTcount: A:0.59, C:0.01, G:0.15, T:0.25
Consensus pattern (22 bp):
AAAAAAATTGAAATGAAATGAG
Found at i:2766520 original size:53 final size:53
Alignment explanation
Indices: 2766437--2766548 Score: 140
Period size: 53 Copynumber: 2.1 Consensus size: 53
2766427 GAAAGAAAGA
*
2766437 TAAATTTAAATGAAATGAGGAAGAAATTTAATTGAAAT-GAAATGAGAAAAAAAT
1 TAAA-TTAAATGAAATGAGGAAGAAATTTAATTGAAATAG-AATAAGAAAAAAAT
* *
2766491 TAAATTAAATGAAATGA-G-AGAAACTTTTAATTTAAATAGTATAAGAAAAAAAT
1 TAAATTAAATGAAATGAGGAAGAAA--TTTAATTGAAATAGAATAAGAAAAAAAT
2766544 TAAAT
1 TAAAT
2766549 GGAAAGATAG
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
51 5 0.10
52 1 0.02
53 41 0.79
54 5 0.10
ACGTcount: A:0.57, C:0.01, G:0.13, T:0.29
Consensus pattern (53 bp):
TAAATTAAATGAAATGAGGAAGAAATTTAATTGAAATAGAATAAGAAAAAAAT
Found at i:2766631 original size:48 final size:46
Alignment explanation
Indices: 2766562--2766695 Score: 130
Period size: 48 Copynumber: 2.9 Consensus size: 46
2766552 AAGATAGATA
* * *
2766562 ATTTAAAAGAAATGACAAAAAAATTAAATTTGCATTGAAAAATATAAT
1 ATTTAAATGAAATGA-GAAAAAATTAAATTTGAATTGAAAAA-ATAAT
* * * *
2766610 ATTTAAATGAAATGAGGAAAAATTTAAAATTAAATT-TAAAAATAAT
1 ATTTAAATGAAATGA-GAAAAAATTAAATTTGAATTGAAAAAATAAT
* * *
2766656 A--TAAATGAATTGAGAAAAAAATAAATTGGAATTGAAAAAA
1 ATTTAAATGAAATGAGAAAAAATTAAATTTGAATTGAAAAAA
2766696 ACATAATATG
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
43 15 0.21
44 16 0.23
46 6 0.09
47 4 0.06
48 29 0.41
ACGTcount: A:0.60, C:0.01, G:0.10, T:0.28
Consensus pattern (46 bp):
ATTTAAATGAAATGAGAAAAAATTAAATTTGAATTGAAAAAATAAT
Found at i:2766681 original size:20 final size:20
Alignment explanation
Indices: 2766642--2766706 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 20
2766632 TTTAAAATTA
* *
2766642 AATTTAAAAATAATATAAATG
1 AATTGAAAAA-AACATAAATG
2766663 AATTGAGAAAAAA-ATAAATTGG
1 AATTGA-AAAAAACATAAA-T-G
2766685 AATTGAAAAAAACATAATATG
1 AATTGAAAAAAACATAA-ATG
2766706 A
1 A
2766707 TTTAAATGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
20 5 0.13
21 16 0.42
22 16 0.42
23 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.26
Consensus pattern (20 bp):
AATTGAAAAAAACATAAATG
Found at i:2766747 original size:17 final size:16
Alignment explanation
Indices: 2766711--2766757 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
2766701 ATATGATTTA
2766711 AATGAAATGAAAATGTG
1 AATGAAAT-AAAATGTG
2766728 AATGGAAATAAAAT-TAG
1 AAT-GAAATAAAATGT-G
*
2766745 AATGAAATGAAAT
1 AATGAAATAAAAT
2766758 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 10 0.37
17 12 0.44
18 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.23
Consensus pattern (16 bp):
AATGAAATAAAATGTG
Found at i:2766756 original size:21 final size:21
Alignment explanation
Indices: 2766732--2766783 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
2766722 AATGTGAATG
* *
2766732 GAAATAAAATTAGAATGAAAT
1 GAAATAAAATTAAAATGAAAA
2766753 GAAATAAAATTAAAATGAAAA
1 GAAATAAAATTAAAATGAAAA
2766774 GAAATGAAAA
1 GAAAT-AAAA
2766784 AAAAATTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.19
Consensus pattern (21 bp):
GAAATAAAATTAAAATGAAAA
Found at i:2766788 original size:21 final size:21
Alignment explanation
Indices: 2766732--2766789 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
2766722 AATGTGAATG
* * *
2766732 GAAATAAAATTAGAATGAAAT
1 GAAATAAAATAAAAATGAAAA
*
2766753 GAAATAAAATTAAAATGAAAA
1 GAAATAAAATAAAAATGAAAA
2766774 GAAATGAAAA-AAAAAT
1 GAAAT-AAAATAAAAAT
2766790 TTGACAAGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (21 bp):
GAAATAAAATAAAAATGAAAA
Found at i:2767056 original size:22 final size:25
Alignment explanation
Indices: 2767031--2767088 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 25
2767021 ATTAAAATTT
*
2767031 AAAATAATATAAA-TG-AATTG-AG
1 AAAATAATATAAATTGAAATTGAAA
2767053 AAAA-AA-ATAAATTGAAATTGAAAA
1 AAAATAATATAAATTGAAATTG-AAA
2767077 AAAATAATATAA
1 AAAATAATATAA
2767089 TTTAAATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
20 5 0.17
21 4 0.14
22 9 0.31
24 5 0.17
25 2 0.07
26 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (25 bp):
AAAATAATATAAATTGAAATTGAAA
Found at i:2767074 original size:383 final size:383
Alignment explanation
Indices: 2766543--2767278 Score: 1284
Period size: 383 Copynumber: 1.9 Consensus size: 383
2766533 AAGAAAAAAA
* *
2766543 TTAAATGGAAAGATAGATAATTTAAAAGAAATGACAAAAAAATTAAATTTGCATTGAAAAATATA
1 TTAAATAGAAAGATAGATAATTTAAAAGAAATGACAAAAAAATTAAATTTGCATTGAAAAATAGA
* *
2766608 ATATTTAAATGAAATGAGGAAAAATTTAAAATTAAATTTAAAAATAATATAAATGAATTGAGAAA
66 ACATTTAAATGAAATGAGGAAAAAATTAAAATTAAATTTAAAAATAATATAAATGAATTGAGAAA
* *
2766673 AAAATAAATTGGAATTGAAAAAAACATAATATGATTTAAATGAAATGAAAATGTGAATGGAAATA
131 AAAATAAATTGAAATTGAAAAAAA-ATAATATAATTTAAATGAAATGAAAATGTGAATGGAAATA
*
2766738 AAATTAGAATGAAATGAAATAAAATTAAAATGAAAAGAAATG-AAAAAAAAA-TTTGACAAGACT
195 AAATTAGAATGAAATGAAATAAAATTAAAATGAAAAGAAATGAAAAAAAAAAGTTTCACAAGACT
* *
2766801 AATCTGCAGGCCTGGCCTGCATCACTTAAGTATAGGCCTGACAATGGCCTTGCAATGG-CCGGCT
260 AATCTACAGGCCTGGCCTGCATCACCTAAGTATAGGCCTGACAATGGCCTTGCAATGGCCCGGCT
2766865 TCAGCTTGCTTTTTAAAAGTCCAAATGATTTTTTATTAAGCCTGATAAATGAGAAAATT
325 TCAGCTTGCTTTTTAAAAGTCCAAATGATTTTTTATTAAGCCTGATAAATGAGAAAATT
2766924 TTAAATAGAAAGATAGATAATTTAAAAGAAATGACAAAAAAAAATTAAATTTGCATTGAAAAATA
1 TTAAATAGAAAGATAGATAATTTAAAAGAAATGAC--AAAAAAATTAAATTTGCATTGAAAAATA
2766989 GAACATTTAAATGGAAA-GAGGAAAAAATTAAAATTAAAATTT-AAAATAATATAAATGAATTGA
64 GAACATTTAAAT-GAAATGAGGAAAAAATTAAAATT-AAATTTAAAAATAATATAAATGAATTGA
2767052 GAAAAAAATAAATTGAAATTGAAAAAAAATAATATAATTTAAATGAAATGAAAATGTGAATGGAA
127 GAAAAAAATAAATTGAAATTGAAAAAAAATAATATAATTTAAATGAAATGAAAATGTGAATGGAA
* *
2767117 ATGAAATTAGAATTAAATGAAATAAAATTAAAATGAAAAGAAATGAAAAAAAAAAGTTTCACAAG
192 ATAAAATTAGAATGAAATGAAATAAAATTAAAATGAAAAGAAATGAAAAAAAAAAGTTTCACAAG
2767182 ACTAATCTACAGGCCTGGCCTGCATCACCTAAGTATAGGCCTGACAATGGCCTTGCAATGGCCCG
257 ACTAATCTACAGGCCTGGCCTGCATCACCTAAGTATAGGCCTGACAATGGCCTTGCAATGGCCCG
*
2767247 GCTTCAGCTTGCTTTTTAAAAGTTCAAATGAT
322 GCTTCAGCTTGCTTTTTAAAAGTCCAAATGAT
2767279 CTCCAAATGA
Statistics
Matches: 336, Mismatches: 12, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
381 34 0.10
382 79 0.24
383 112 0.33
384 77 0.23
385 34 0.10
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (383 bp):
TTAAATAGAAAGATAGATAATTTAAAAGAAATGACAAAAAAATTAAATTTGCATTGAAAAATAGA
ACATTTAAATGAAATGAGGAAAAAATTAAAATTAAATTTAAAAATAATATAAATGAATTGAGAAA
AAAATAAATTGAAATTGAAAAAAAATAATATAATTTAAATGAAATGAAAATGTGAATGGAAATAA
AATTAGAATGAAATGAAATAAAATTAAAATGAAAAGAAATGAAAAAAAAAAGTTTCACAAGACTA
ATCTACAGGCCTGGCCTGCATCACCTAAGTATAGGCCTGACAATGGCCTTGCAATGGCCCGGCTT
CAGCTTGCTTTTTAAAAGTCCAAATGATTTTTTATTAAGCCTGATAAATGAGAAAATT
Found at i:2767077 original size:21 final size:21
Alignment explanation
Indices: 2767010--2767083 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
2767000 TGGAAAGAGG
* * *
2767010 AAAAAATTAAAATTAAAATTTA
1 AAAAAAAT-AAATTGAAATTGA
*
2767032 AAATAATATAAA-TG-AATTGA
1 AAA-AAAATAAATTGAAATTGA
2767052 GAAAAAAATAAATTGAAATTGA
1 -AAAAAAATAAATTGAAATTGA
2767074 AAAAAAATAA
1 AAAAAAATAA
2767084 TATAATTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
20 12 0.28
21 16 0.37
22 12 0.28
23 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.26
Consensus pattern (21 bp):
AAAAAAATAAATTGAAATTGA
Found at i:2767080 original size:24 final size:24
Alignment explanation
Indices: 2767053--2767099 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2767043 ATGAATTGAG
2767053 AAAAAAATA-AATTGAAATTGAAAA
1 AAAAAAATATAATTGAAA-TGAAAA
* *
2767077 AAAATAATATAATTTAAATGAAA
1 AAAAAAATATAATTGAAATGAAA
2767100 TGAAAATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (24 bp):
AAAAAAATATAATTGAAATGAAAA
Found at i:2767144 original size:21 final size:21
Alignment explanation
Indices: 2767114--2767165 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2767104 AATGTGAATG
* * * *
2767114 GAAATGAAATTAGAATTAAAT
1 GAAATAAAATTAAAATGAAAA
2767135 GAAATAAAATTAAAATGAAAA
1 GAAATAAAATTAAAATGAAAA
2767156 GAAATGAAAA
1 GAAAT-AAAA
2767166 AAAAAAGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.21
Consensus pattern (21 bp):
GAAATAAAATTAAAATGAAAA
Found at i:2767160 original size:16 final size:16
Alignment explanation
Indices: 2767115--2767154 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2767105 ATGTGAATGG
*
2767115 AAATGAAATTAGAATT-
1 AAATGAAA-TAAAATTA
2767131 AAATGAAATAAAATTA
1 AAATGAAATAAAATTA
2767147 AAATGAAA
1 AAATGAAA
2767155 AGAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (16 bp):
AAATGAAATAAAATTA
Found at i:2767442 original size:38 final size:37
Alignment explanation
Indices: 2767366--2767442 Score: 84
Period size: 38 Copynumber: 2.1 Consensus size: 37
2767356 TGAAAATATG
* ** *
2767366 AAATAAAATTAACAAATTTTAAATTTAAATTGACAAA
1 AAATAAAATTAAAAAATTTTAAAAATAAATTGAAAAA
*
2767403 AAATAAAATATAAAAAATTTTAAAAAATAGA-TGAAAAA
1 AAATAAAAT-TAAAAAATTTT-AAAAATAAATTGAAAAA
2767441 AA
1 AA
2767443 TTTAAATGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
37 9 0.27
38 18 0.55
39 6 0.18
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (37 bp):
AAATAAAATTAAAAAATTTTAAAAATAAATTGAAAAA
Found at i:2767516 original size:25 final size:25
Alignment explanation
Indices: 2767488--2767644 Score: 122
Period size: 25 Copynumber: 6.5 Consensus size: 25
2767478 AATTTGATAA
*
2767488 AATATAAAATGAATTGAAAAAAAAT
1 AATATGAAATGAATTGAAAAAAAAT
* *
2767513 AATATTAAATGAATTGAAAAAAAAAAC
1 AATATGAAATGAATTG--AAAAAAAAT
* * *
2767540 AATATGAAA--AATAGTATAAAAAT
1 AATATGAAATGAATTGAAAAAAAAT
2767563 AATATGAAAAAT-AATATGAAAAGAAAAT
1 AATATG--AAATGAAT-TGAAAA-AAAAT
2767591 -A-AT--AAT--A-TG-AAAAAAAT
1 AATATGAAATGAATTGAAAAAAAAT
2767608 AATATGAAATGAATTGAAAAAAAAT
1 AATATGAAATGAATTGAAAAAAAAT
2767633 AAT-TGAAATGAA
1 AATATGAAATGAA
2767645 ATAATTGAAA
Statistics
Matches: 107, Mismatches: 10, Indels: 31
0.72 0.07 0.21
Matches are distributed among these distances:
17 5 0.05
18 4 0.04
19 4 0.04
21 4 0.04
22 3 0.03
23 13 0.12
24 11 0.10
25 33 0.31
26 5 0.05
27 20 0.19
28 5 0.05
ACGTcount: A:0.66, C:0.01, G:0.10, T:0.24
Consensus pattern (25 bp):
AATATGAAATGAATTGAAAAAAAAT
Found at i:2767560 original size:11 final size:12
Alignment explanation
Indices: 2767534--2767584 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
2767524 AATTGAAAAA
*
2767534 AAAAACAATATG
1 AAAAATAATATG
*
2767546 AAAAATAGTAT-
1 AAAAATAATATG
2767557 AAAAATAATATG
1 AAAAATAATATG
2767569 AAAAATAATATG
1 AAAAATAATATG
2767581 AAAA
1 AAAA
2767585 GAAAATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
11 10 0.29
12 25 0.71
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (12 bp):
AAAAATAATATG
Found at i:2767561 original size:12 final size:11
Alignment explanation
Indices: 2767534--2767612 Score: 61
Period size: 11 Copynumber: 7.0 Consensus size: 11
2767524 AATTGAAAAA
*
2767534 AAAAACAATAT
1 AAAAATAATAT
*
2767545 GAAAAATAGTAT
1 -AAAAATAATAT
2767557 AAAAATAATAT
1 AAAAATAATAT
2767568 GAAAAATAATAT
1 -AAAAATAATAT
* * *
2767580 GAAAAGAAAAT
1 AAAAATAATAT
* *
2767591 AATAAT-ATGAA
1 AAAAATAAT-AT
2767602 AAAAATAATAT
1 AAAAATAATAT
2767613 GAAATGAATT
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
10 1 0.02
11 28 0.55
12 22 0.43
ACGTcount: A:0.68, C:0.01, G:0.08, T:0.23
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:2767566 original size:23 final size:22
Alignment explanation
Indices: 2767534--2767616 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
2767524 AATTGAAAAA
*
2767534 AAAAACAATATGAAAAATAGTAT
1 AAAAATAATATGAAAAATA-TAT
2767557 AAAAATAATATGAAAAATAATAT
1 AAAAATAATATGAAAAAT-ATAT
* * * * *
2767580 GAAAAGAAAAT-AATAATATGAA
1 AAAAATAATATGAAAAATAT-AT
2767602 AAAAATAATATGAAA
1 AAAAATAATATGAAA
2767617 TGAATTGAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
21 2 0.04
22 14 0.30
23 30 0.64
24 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.08, T:0.22
Consensus pattern (22 bp):
AAAAATAATATGAAAAATATAT
Found at i:2767596 original size:19 final size:17
Alignment explanation
Indices: 2767572--2767611 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 17
2767562 TAATATGAAA
2767572 AATAATATGAAAAGAAAAT
1 AATAATATG-AAA-AAAAT
2767591 AATAATATGAAAAAAAT
1 AATAATATGAAAAAAAT
2767608 AATA
1 AATA
2767612 TGAAATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.43
18 3 0.14
19 9 0.43
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
AATAATATGAAAAAAAT
Found at i:2767608 original size:14 final size:14
Alignment explanation
Indices: 2767557--2767616 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
2767547 AAAATAGTAT
2767557 AAAAATAATATGAA
1 AAAAATAATATGAA
* *
2767571 AAATAATATGAAAAGAA
1 AAA-AATA--ATATGAA
*
2767588 AATAATAATATGAA
1 AAAAATAATATGAA
2767602 AAAAATAATATGAA
1 AAAAATAATATGAA
2767616 A
1 A
2767617 TGAATTGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 22 0.59
15 4 0.11
16 4 0.11
17 7 0.19
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (14 bp):
AAAAATAATATGAA
Found at i:2767619 original size:19 final size:19
Alignment explanation
Indices: 2767569--2767645 Score: 63
Period size: 19 Copynumber: 4.1 Consensus size: 19
2767559 AAATAATATG
*
2767569 AAAAATAATATGAAAAGAA
1 AAAAATAATATGAAATGAA
*
2767588 AATAATAATATGAAA--AA
1 AAAAATAATATGAAATGAA
*
2767605 AATAATATGAA-ATGAATTGAAA
1 AA-AA-AT-AATATGAAATG-AA
2767627 AAAAATAAT-TGAAATGAA
1 AAAAATAATATGAAATGAA
2767645 A
1 A
2767646 TAATTGAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
17 4 0.09
18 4 0.09
19 29 0.62
20 4 0.09
21 2 0.04
22 4 0.09
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (19 bp):
AAAAATAATATGAAATGAA
Found at i:2767655 original size:14 final size:14
Alignment explanation
Indices: 2767611--2767660 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
2767601 AAAAAATAAT
2767611 ATGAAATGAATTGAA
1 ATGAAAT-AATTGAA
**
2767626 AAAAAATAATTGAA
1 ATGAAATAATTGAA
2767640 ATGAAATAATTGAA
1 ATGAAATAATTGAA
*
2767654 ATTAAAT
1 ATGAAAT
2767661 TAAATTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 25 0.83
15 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (14 bp):
ATGAAATAATTGAA
Found at i:2769665 original size:213 final size:213
Alignment explanation
Indices: 2769251--2769754 Score: 624
Period size: 214 Copynumber: 2.3 Consensus size: 213
2769241 ATCAAAGAAT
* * * *
2769251 CATTGATAGGCCAGCACCAAATTTTTTTTAAAAAAAACTCGTATTCTGGTGCCGGCCATTGACAA
1 CATTGACAGGCCAACACC-AATTTTTTTT---TAAAACTCGTATTCTGGTGCCGGCCATTGACAG
*
2769316 GCCAGCA-CAAAAAAAATTGAATTCTTTTTTTTAATACTGGTGCCGGCCATTGACTGGCCAGCAC
62 GCCAGCACCAAAAAAAATTGAA-T-TTTTTTTTAATACTGGTGCCGGCCATTGACTGACCAGCAC
* *
2769380 CAAATTTTCTTTTTAAAAACTCGTATTCTGGTGCCGACCATTGACATACCAGCACAAAAAAATTA
125 CAAATTTTCTTTTTAAAAACTCATATTCTGGTGCCGACCATTGACAGACCAGCACAAAAAAATTA
* *
2769445 ATTTTTTTTAATATTGGTGCCATC
190 ATTTTTTTTAATACTGGTGCCAGC
* * * *
2769469 TATTGTCAGGCTAACACCAA-TTTTTTTTAAAACTCGTATTCTGGTGCTGGCCATTGACAGGCCA
1 CATTGACAGGCCAACACCAATTTTTTTTTAAAACTCGTATTCTGGTGCCGGCCATTGACAGGCCA
* * *
2769533 GCACCAAAAAAATTTGAA-TTTTTTTTAATACTGGTGTCGGCCATTGATTGACCAGCACC-AATT
66 GCACCAAAAAAAATTGAATTTTTTTTTAATACTGGTGCCGGCCATTGACTGACCAGCACCAAATT
** * *
2769596 TT-TTTTTTTAAATTCATATTCTGGTGTCTG-CCATTGACAGACCAGCACAAAAAAATTTTGAAT
131 TTCTTTTTAAAAACTCATATTCTGGTG-CCGACCATTGACAGACCAGCACAAAAAAA--TT-AAT
*
2769659 TTTTTTTAATACTGGTGCCGGC
192 TTTTTTTAATACTGGTGCCAGC
* * * * * *
2769681 CATTGACAGGCCAGCACTAATTTTTTTTTACAAACTCGTATTTTGGTGCCGACAATTGACTGGCC
1 CATTGACAGGCCAACACCAATTTTTTTTTA-AAACTCGTATTCTGGTGCCGGCCATTGACAGGCC
2769746 AGCACCAAA
65 AGCACCAAA
2769755 TTTTTTTTAA
Statistics
Matches: 248, Mismatches: 31, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
209 44 0.18
210 8 0.03
211 40 0.16
212 37 0.15
213 46 0.19
214 51 0.21
216 7 0.03
217 2 0.01
218 13 0.05
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (213 bp):
CATTGACAGGCCAACACCAATTTTTTTTTAAAACTCGTATTCTGGTGCCGGCCATTGACAGGCCA
GCACCAAAAAAAATTGAATTTTTTTTTAATACTGGTGCCGGCCATTGACTGACCAGCACCAAATT
TTCTTTTTAAAAACTCATATTCTGGTGCCGACCATTGACAGACCAGCACAAAAAAATTAATTTTT
TTTAATACTGGTGCCAGC
Found at i:2769739 original size:53 final size:52
Alignment explanation
Indices: 2769670--2769806 Score: 150
Period size: 53 Copynumber: 2.6 Consensus size: 52
2769660 TTTTTTAATA
* * * *
2769670 CTGGTGCCGGCCATTGACAGGCCAGCACTAATTTTTTTTTACAAACTCGTATT
1 CTGGTGCCGACAATTGACAGGCCAGCACCAAATTTTTTTTA-AAACTCGTATT
* * *
2769723 TTGGTGCCGACAATTGACTGGCCAGCACCAAATTTTTTTTAAAACTTGTATT
1 CTGGTGCCGACAATTGACAGGCCAGCACCAAATTTTTTTTAAAACTCGTATT
* * * *
2769775 CTGGTGAC-AGCCATTGATAGGCCAGCATCAAA
1 CTGGTGCCGA-CAATTGACAGGCCAGCACCAAA
2769807 AAAAATTGAA
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
51 1 0.01
52 34 0.49
53 35 0.50
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (52 bp):
CTGGTGCCGACAATTGACAGGCCAGCACCAAATTTTTTTTAAAACTCGTATT
Found at i:2769739 original size:107 final size:106
Alignment explanation
Indices: 2769251--2769750 Score: 553
Period size: 107 Copynumber: 4.7 Consensus size: 106
2769241 ATCAAAGAAT
* * *
2769251 CATTGATAGGCCAGCACCAAATTTTTTTTAAAAAAAACTCGTATTCTGGTGCCGGCCATTGACA-
1 CATTGACAGGCCAGCA-CAAATTTTTTTT--TAAAAACTCGTATTCTGGTGCCGACCATTGACAG
*
2769315 AGCCAGCACAAAAAAAATTGAATTCTTTTTTTTAATACTGGTGCCGGC
63 A-CCAGCACAAAAAAATTTGAA---TTTTTTTTAATACTGGTGCCGGC
* *
2769363 CATTGACTGGCCAGCACCAAATTTTCTTTTTAAAAACTCGTATTCTGGTGCCGACCATTGACATA
1 CATTGACAGGCCAGCA-CAAATTTT-TTTTTAAAAACTCGTATTCTGGTGCCGACCATTGACAGA
* **
2769428 CCAGCACAAAAAAA-TT-AATTTTTTTTAATATTGGTGCCATC
64 CCAGCACAAAAAAATTTGAATTTTTTTTAATACTGGTGCCGGC
* * * * * * * *
2769469 TATTGTCAGGCTAACACCAA-TTTTTTTT-AAAACTCGTATTCTGGTGCTGGCCATTGACAGGCC
1 CATTGACAGGCCAGCACAAATTTTTTTTTAAAAACTCGTATTCTGGTGCCGACCATTGACAGACC
*
2769532 AGCACCAAAAAAATTTGAATTTTTTTTAATACTGGTGTCGGC
66 AGCA-CAAAAAAATTTGAATTTTTTTTAATACTGGTGCCGGC
** * * ** * * *
2769574 CATTGATTGACCAGCACCAATTTTTTTTTTTAAATTCATATTCTGGTGTCTG-CCATTGACAGAC
1 CATTGACAGGCCAGCACAAATTTTTTTTTAAAAACTCGTATTCTGGTG-CCGACCATTGACAGAC
2769638 CAGCACAAAAAAATTTTGAATTTTTTTTAATACTGGTGCCGGC
65 CAGCACAAAAAAA-TTTGAATTTTTTTTAATACTGGTGCCGGC
* * * * * *
2769681 CATTGACAGGCCAGCACTAATTTTTTTTTACAAACTCGTATTTTGGTGCCGACAATTGACTGGCC
1 CATTGACAGGCCAGCACAAATTTTTTTTTAAAAACTCGTATTCTGGTGCCGACCATTGACAGACC
2769746 AGCAC
66 AGCAC
2769751 CAAATTTTTT
Statistics
Matches: 332, Mismatches: 46, Indels: 25
0.82 0.11 0.06
Matches are distributed among these distances:
102 35 0.11
103 13 0.04
104 5 0.02
105 37 0.11
106 49 0.15
107 113 0.34
108 3 0.01
109 2 0.01
110 2 0.01
111 45 0.14
112 24 0.07
113 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (106 bp):
CATTGACAGGCCAGCACAAATTTTTTTTTAAAAACTCGTATTCTGGTGCCGACCATTGACAGACC
AGCACAAAAAAATTTGAATTTTTTTTAATACTGGTGCCGGC
Found at i:2769790 original size:212 final size:211
Alignment explanation
Indices: 2769251--2769806 Score: 532
Period size: 212 Copynumber: 2.6 Consensus size: 211
2769241 ATCAAAGAAT
* * * * *
2769251 CATTGATAGGCCAGCACCAAATTTTTTTTAAAAAAAACTCGTATTCTGGTGCCGGCCATTGACAA
1 CATTGACAGGCCAACACC-AATTTTTTTT----AAAACTCGTATTCTGGTGCCGACAATTGACAG
* * * * *
2769316 GCCAGCA-CAAAAAAAATTGAAT-TCTTTTTTTTAATACTGGTGCCGGCCATTGACTGGCCAGCA
61 GCCAGCACCAAAAAAATTTGAATAAC----TTGTAATACTGGTGACGGCCATTGATTGGCCAGCA
* *
2769379 CCAAATTTTCTTTTTAAAAACTCGTATTCTGGTGCCGACCATTGACATACCAGCACAAAAAAATT
122 CCAAATTTTCTTTTTAAAAACTCATATTCTGGTGCCGACCATTGACAGACCAGCACAAAAAAATT
* *
2769444 AATTTTTTTTAATATTGGTGCCATC
187 AATTTTTTTTAATACTGGTGCCAGC
* * * * * *
2769469 TATTGTCAGGCTAACACCAATTTTTTTTAAAACTCGTATTCTGGTGCTGGCCATTGACAGGCCAG
1 CATTGACAGGCCAACACCAATTTTTTTTAAAACTCGTATTCTGGTGCCGACAATTGACAGGCCAG
*** * * *
2769534 CACCAAAAAAATTTGAATTTTTTTTAATACTGGTGTCGGCCATTGATTGACCAGCACC-AATTTT
66 CACCAAAAAAATTTGAATAACTTGTAATACTGGTGACGGCCATTGATTGGCCAGCACCAAATTTT
** * *
2769598 -TTTTTTTAAATTCATATTCTGGTGTCTG-CCATTGACAGACCAGCACAAAAAAATTTTGAATTT
131 CTTTTTAAAAACTCATATTCTGGTG-CCGACCATTGACAGACCAGCACAAAAAAA--TT-AATTT
*
2769661 TTTTTAATACTGGTGCCGGC
192 TTTTTAATACTGGTGCCAGC
* * * *
2769681 CATTGACAGGCCAGCACTAATTTTTTTTTACAAACTCGTATTTTGGTGCCGACAATTGACTGGCC
1 CATTGACAGGCCAACACCAA-TTTTTTTTA-AAACTCGTATTCTGGTGCCGACAATTGACAGGCC
**** * * * * *
2769746 AGCACCAAATTTTTTTTAA-AACTTGT-ATTCTGGTGACAGCCATTGATAGGCCAGCATCAAA
64 AGCACCAAAAAAATTTGAATAACTTGTAATACTGGTGACGGCCATTGATTGGCCAGCACCAAA
2769807 AAAAATTGAA
Statistics
Matches: 283, Mismatches: 46, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
209 44 0.16
210 8 0.03
211 36 0.13
212 63 0.22
213 51 0.18
214 57 0.20
215 1 0.00
217 10 0.04
218 13 0.05
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (211 bp):
CATTGACAGGCCAACACCAATTTTTTTTAAAACTCGTATTCTGGTGCCGACAATTGACAGGCCAG
CACCAAAAAAATTTGAATAACTTGTAATACTGGTGACGGCCATTGATTGGCCAGCACCAAATTTT
CTTTTTAAAAACTCATATTCTGGTGCCGACCATTGACAGACCAGCACAAAAAAATTAATTTTTTT
TAATACTGGTGCCAGC
Found at i:2769791 original size:52 final size:51
Alignment explanation
Indices: 2769483--2769918 Score: 183
Period size: 54 Copynumber: 8.1 Consensus size: 51
2769473 GTCAGGCTAA
* *
2769483 CACC-AATTTTTTTTAAAACTCGTATTCTGGTGCTGGCCATTGACAGGCCAG
1 CACCAAATTTTTTTTAAAACTTGTATTCTGGTGC-AGCCATTGACAGGCCAG
**** * *** * * * ** *
2769534 CACCAAAAAAATTTGAATTTTTTTTAATACTGGTGTCGGCCATTGATTGACCAG
1 CACCAAATTTTTTTTAA-AACTTGT-ATTCTGGTG-CAGCCATTGACAGGCCAG
* * * * *
2769588 CACCAATTTTTTTTTTTAAA-TTCATATTCTGGTGTCTGCCATTGACAGACCAG
1 CACCAA-ATTTTTTTTAAAACTT-GTATTCTGGTG-CAGCCATTGACAGGCCAG
* *** * *** * * *
2769641 CACAAAAAAATTTTGAATTTTTTTTAATACTGGTGCCGGCCATTGACAGGCCAG
1 CACCAAATTTTTTTTAA-AACTTGT-ATTCTGGTG-CAGCCATTGACAGGCCAG
* * * * * * *
2769695 CACTAATTTTTTTTTACAAACTCGTATTTTGGTGCCGACAATTGACTGGCCAG
1 CACCAAATTTTTTTTA-AAACTTGTATTCTGGTGCAG-CCATTGACAGGCCAG
*
2769748 CACCAAATTTTTTTTAAAACTTGTATTCTGGTGACAGCCATTGATAGGCCAG
1 CACCAAATTTTTTTTAAAACTTGTATTCTGGTG-CAGCCATTGACAGGCCAG
* ***** * ** * *
2769800 CATCAAAAAAAATTGAAATTTTTTTTAGTACTGGTGCAGGCCATTGACAGGCCAG
1 CACCAAATTTTTTTTAAA--ACTTGTA-TTCTGGTGCA-GCCATTGACAGGCCAG
*
2769855 CACCAAAAATTTATTTTTTAAAAACTTGTATTCTGGTGCCAGCTATTGACAGGCCAG
1 CACC--AAA-TT-TTTTTT-AAAACTTGTATTCTGGTG-CAGCCATTGACAGGCCAG
2769912 CACCAAA
1 CACCAAA
2769919 AAAATTTAAA
Statistics
Matches: 273, Mismatches: 90, Indels: 40
0.68 0.22 0.10
Matches are distributed among these distances:
51 4 0.01
52 52 0.19
53 70 0.26
54 73 0.27
55 34 0.12
57 29 0.11
58 6 0.02
59 2 0.01
60 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (51 bp):
CACCAAATTTTTTTTAAAACTTGTATTCTGGTGCAGCCATTGACAGGCCAG
Found at i:2769844 original size:160 final size:162
Alignment explanation
Indices: 2769575--2769918 Score: 430
Period size: 160 Copynumber: 2.1 Consensus size: 162
2769565 GGTGTCGGCC
* * * * * *
2769575 ATTGATTGACCAGCACCAATTTTTTTTTTTAAATTCATATTCTGGTGTCTGCCATTGACAGACCA
1 ATTGACTGGCCAGCACCAA-ATTTTTTTTAAAATTCATATTCTGGTGACAGCCATTGACAGACCA
* * *
2769640 GCACAAAAAAATTTTGAATTTTTTTTAATACTGGTGCCGGCCATTGACAGGCCAGCA-C-TAATT
65 GCACAAAAAAATATTGAATTTTTTTTAATACTGGTGCAGGCCATTGACAGGCCAGCACCAAAATT
* *
2769703 T-TTTTTTACAAACTCGTATTTTGGTGCC-GACA
130 TATTTTTTAAAAACTCGTATTCTGGTGCCAG-CA
* * *
2769735 ATTGACTGGCCAGCACCAAATTTTTTTTAAAACTT-GTATTCTGGTGACAGCCATTGATAGGCCA
1 ATTGACTGGCCAGCACCAAATTTTTTTTAAAA-TTCATATTCTGGTGACAGCCATTGACAGACCA
*
2769799 GCATCAAAAAAA-ATTGAAATTTTTTTTAGTACTGGTGCAGGCCATTGACAGGCCAGCACCAAAA
65 GCA-CAAAAAAATATTG-AATTTTTTTTAATACTGGTGCAGGCCATTGACAGGCCAGCACC-AAA
* *
2769863 ATTTATTTTTTAAAAACTTGTATTCTGGTGCCAGCT
127 ATTTATTTTTTAAAAACTCGTATTCTGGTGCCAGCA
*
2769899 ATTGACAGGCCAGCACCAAA
1 ATTGACTGGCCAGCACCAAA
2769919 AAAATTTAAA
Statistics
Matches: 158, Mismatches: 18, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
159 41 0.26
160 66 0.42
161 1 0.01
163 5 0.03
164 44 0.28
165 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (162 bp):
ATTGACTGGCCAGCACCAAATTTTTTTTAAAATTCATATTCTGGTGACAGCCATTGACAGACCAG
CACAAAAAAATATTGAATTTTTTTTAATACTGGTGCAGGCCATTGACAGGCCAGCACCAAAATTT
ATTTTTTAAAAACTCGTATTCTGGTGCCAGCA
Found at i:2769903 original size:112 final size:108
Alignment explanation
Indices: 2769735--2769985 Score: 326
Period size: 112 Copynumber: 2.3 Consensus size: 108
2769725 GGTGCCGACA
* *
2769735 ATTGACTGGCCAGCACCAAATTTTTTTTAAAACTTGTATTCTGGTGACAGCCATTGATAGGCCAG
1 ATTGACAGGCCAGCACCAAATTTTTTTTAAAACTTGTATTCTGGTGACAGCCATTGACAGGCCAG
* *
2769800 CATCAAAAAAAATTGAAA-TTTTTTTT-AGTACTGGTGCAGGCC
66 CA-CAAAAAAAATTGAAATTTTTTTTTAAATACTAGTGCAGGCC
* *
2769842 ATTGACAGGCCAGCACCAAAAATTTATTTTTTAAAAACTTGTATTCTGGTGCCAGCTATTGACAG
1 ATTGACAGGCCAGCACC--AAA-TT-TTTTTT-AAAACTTGTATTCTGGTGACAGCCATTGACAG
* * *
2769907 GCCAGCACCAAAAAAATTTAAATTTTTTTTTAAATACTAGTGCCGGCC
61 GCCAGCACAAAAAAAATTGAAATTTTTTTTTAAATACTAGTGCAGGCC
* * *
2769955 ATTGACAGGCCAACACTAATTTTTTTTTAAA
1 ATTGACAGGCCAGCACCAAATTTTTTTTAAA
2769986 TACTGGTGTT
Statistics
Matches: 125, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
107 16 0.13
108 3 0.02
109 9 0.07
110 4 0.03
111 21 0.17
112 44 0.35
113 28 0.22
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (108 bp):
ATTGACAGGCCAGCACCAAATTTTTTTTAAAACTTGTATTCTGGTGACAGCCATTGACAGGCCAG
CACAAAAAAAATTGAAATTTTTTTTTAAATACTAGTGCAGGCC
Found at i:2772133 original size:31 final size:29
Alignment explanation
Indices: 2772097--2772169 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
2772087 TTCCAAAATT
2772097 TAAAAAATATAAAAACTAAAATTGACCAAA
1 TAAAAAATATAAAAACTAAAA-TGACCAAA
* * *
2772127 TAAAAAAGTACAATAACTAAAATGACTAAA
1 TAAAAAA-TATAAAAACTAAAATGACCAAA
*
2772157 T-TAAAATATAAAA
1 TAAAAAATATAAAA
2772170 CGCATAACAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 5 0.14
29 4 0.11
30 15 0.42
31 12 0.33
ACGTcount: A:0.66, C:0.08, G:0.04, T:0.22
Consensus pattern (29 bp):
TAAAAAATATAAAAACTAAAATGACCAAA
Found at i:2774349 original size:23 final size:25
Alignment explanation
Indices: 2774323--2774369 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2774313 TATCATTCAT
*
2774323 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
2774346 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
2774370 TATATTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:2774690 original size:46 final size:46
Alignment explanation
Indices: 2774630--2774941 Score: 417
Period size: 46 Copynumber: 7.0 Consensus size: 46
2774620 TTTGACGTGA
* * * * * *
2774630 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* ** * * *
2774676 TGCCATGATATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
2774722 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
2774768 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
2774814 TGTCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
2774860 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
2774898 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
2774942 ATAGCACACT
Statistics
Matches: 239, Mismatches: 18, Indels: 18
0.87 0.07 0.07
Matches are distributed among these distances:
38 33 0.14
39 1 0.00
40 3 0.01
41 1 0.00
43 1 0.00
44 3 0.01
45 5 0.02
46 192 0.80
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:2774906 original size:38 final size:38
Alignment explanation
Indices: 2774855--2774930 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2774845 CATCTCATAT
2774855 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
2774893 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
2774931 TTTCATATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:2781038 original size:153 final size:149
Alignment explanation
Indices: 2780824--2781104 Score: 445
Period size: 152 Copynumber: 1.9 Consensus size: 149
2780814 CTGCGGACAC
* *
2780824 TAGAGCTTTTGGTTAATTTTCAATTTTGAGTAAGAAATGCATTTTAGAAAGTTTCAAGTTCTGTT
1 TAGAGCTTTTGGTTAATTTTCAATTCTGAGTAAGAAATGCATTTTAGAAAGGTTCAAGTTCTG-T
* *
2780889 TTCAGTTTTGAGCTAAGAGTACCTCATTTGAGACCGAGTAACACTCTTAGAAGGTAAATCCGAGC
65 TTCAG-TTTGAGCTAAGAGTACCTCATTTGAGACC-AGGAACACTCTTAGAAGATAAATCCGAGC
2780954 TGCGGAGGCTAGAGAACATGAT
128 TGCGGAGGCTAGAGAACATGAT
*
2780976 TAGAGCTTTTGGTTAATTTTCAATTCTGAGTTAAGAGATGCATTTTAGAAAGGTTCAAGTTCTGT
1 TAGAGCTTTTGGTTAATTTTCAATTCTGAG-TAAGAAATGCATTTTAGAAAGGTTCAAGTTCTGT
* * * *
2781041 TTCAGTTTGAGCTAAGAGTACCTCTTTTGGGACCAGGAACACTCTTAGAATATTAATCCGAGCT
65 TTCAGTTTGAGCTAAGAGTACCTCATTTGAGACCAGGAACACTCTTAGAAGATAAATCCGAGCT
2781105 CTGAAACAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
150 26 0.22
151 27 0.23
152 35 0.29
153 31 0.26
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (149 bp):
TAGAGCTTTTGGTTAATTTTCAATTCTGAGTAAGAAATGCATTTTAGAAAGGTTCAAGTTCTGTT
TCAGTTTGAGCTAAGAGTACCTCATTTGAGACCAGGAACACTCTTAGAAGATAAATCCGAGCTGC
GGAGGCTAGAGAACATGAT
Found at i:2788058 original size:65 final size:65
Alignment explanation
Indices: 2787954--2788076 Score: 219
Period size: 65 Copynumber: 1.9 Consensus size: 65
2787944 ACTCCCAATA
2787954 GTTAACGGTTGCAAATTGGAGGAGGATTATTATTGAACAGAACAGGTAAATTTCTGATTATGTTT
1 GTTAACGGTTGCAAATTGGAGGAGGATTATTATTGAACAGAACAGGTAAATTTCTGATTATGTTT
* * *
2788019 GTTAACGGTTGCAAATTGGAGGAGGATTATTATTGAACAGAATAGGTAATTTTTTGAT
1 GTTAACGGTTGCAAATTGGAGGAGGATTATTATTGAACAGAACAGGTAAATTTCTGAT
2788077 CATTTTTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.36
Consensus pattern (65 bp):
GTTAACGGTTGCAAATTGGAGGAGGATTATTATTGAACAGAACAGGTAAATTTCTGATTATGTTT
Found at i:2788970 original size:16 final size:16
Alignment explanation
Indices: 2788949--2789019 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
2788939 TGAATTACTT
*
2788949 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
2788965 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
*
2788981 AATACAGCTCTATTCA
1 ATTACAGCTCTATTCA
* *
2788997 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCA
2789013 ATTACAG
1 ATTACAG
2789020 TGAACCAAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:2789622 original size:13 final size:13
Alignment explanation
Indices: 2789604--2789643 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
2789594 CCCGTTCTTC
2789604 ATTGCTTTTGAAA
1 ATTGCTTTTGAAA
2789617 ATTGCTTTTGAAA
1 ATTGCTTTTGAAA
* *
2789630 AGTGCTTTGGAAA
1 ATTGCTTTTGAAA
2789643 A
1 A
2789644 ATTTAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (13 bp):
ATTGCTTTTGAAA
Found at i:2791239 original size:15 final size:15
Alignment explanation
Indices: 2791205--2791245 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2791195 TGAATTCAAT
* *
2791205 AAATAAATTAATTTTT
1 AAATTAATT-ATTTTA
2791221 AAATTAATTATTTTA
1 AAATTAATTATTTTA
2791236 AAATTAATTA
1 AAATTAATTA
2791246 AGTCAGACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTAATTATTTTA
Found at i:2811624 original size:2 final size:2
Alignment explanation
Indices: 2811617--2811646 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2811607 TCGATCTTTC
2811617 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2811647 GTTCTTCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2818316 original size:28 final size:27
Alignment explanation
Indices: 2818284--2818339 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
2818274 AAAAATAATA
2818284 AATATTAATATAAAATATTATAATT-TTT
1 AATATTAATAT-AAATATT-TAATTATTT
* *
2818312 AATATTATTATACATATTTAATTATTT
1 AATATTAATATAAATATTTAATTATTT
2818339 A
1 A
2818340 TATCTAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 10 0.40
28 10 0.40
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
AATATTAATATAAATATTTAATTATTT
Found at i:2818384 original size:22 final size:20
Alignment explanation
Indices: 2818359--2818399 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 20
2818349 ATATAATATA
2818359 TTATTAATATAACTTATTATTT
1 TTATTAATATAA-TT-TTATTT
2818381 TTA-TAA-ATAATTTTATTT
1 TTATTAATATAATTTTATTT
2818399 T
1 T
2818400 ATTTTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 4 0.21
21 3 0.16
22 3 0.16
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATTAATATAATTTTATTT
Found at i:2818418 original size:23 final size:23
Alignment explanation
Indices: 2818375--2818418 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2818365 ATATAACTTA
* *
2818375 TTATTTTTATAAATAATTTTATT
1 TTATTTTAATAAATAAATTTATT
2818398 TTATTTTAAT-AATAAAATTTA
1 TTATTTTAATAAAT-AAATTTA
2818419 AAAATAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTATTTTAATAAATAAATTTATT
Found at i:2824814 original size:31 final size:29
Alignment explanation
Indices: 2824771--2824848 Score: 102
Period size: 31 Copynumber: 2.6 Consensus size: 29
2824761 AAGGCAACAC
*
2824771 TATTAACTTAATTTAATTACATTATATAACA
1 TATTAATTTAATTTAATTACATTATAT-A-A
* *
2824802 TTTTAATTTAATTTAATCACATTATATAA
1 TATTAATTTAATTTAATTACATTATATAA
*
2824831 TATTAATTTATTTTAATT
1 TATTAATTTAATTTAATT
2824849 GTCATATTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 16 0.39
30 1 0.02
31 24 0.59
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (29 bp):
TATTAATTTAATTTAATTACATTATATAA
Found at i:2829288 original size:23 final size:22
Alignment explanation
Indices: 2829247--2829294 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
2829237 TCTTTGTATT
2829247 TTTTATTTTTAAAAATTTAATAA
1 TTTTATTTTTAAAAATTTAA-AA
*
2829270 TTTTACTTTTT-AAATTTTAAAA
1 TTTTA-TTTTTAAAAATTTAAAA
2829292 TTT
1 TTT
2829295 ATGTCCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 13 0.57
24 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATTTTTAAAAATTTAAAA
Found at i:2834225 original size:22 final size:23
Alignment explanation
Indices: 2834200--2834244 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2834190 AATATGATAG
*
2834200 CAAAACGACA-CAAAAACAGTGA
1 CAAAACAACAGCAAAAACAGTGA
*
2834222 CAAAACAACAGCAAAAATAGTGA
1 CAAAACAACAGCAAAAACAGTGA
2834245 AAACAGGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.60, C:0.20, G:0.13, T:0.07
Consensus pattern (23 bp):
CAAAACAACAGCAAAAACAGTGA
Found at i:2834681 original size:20 final size:20
Alignment explanation
Indices: 2834670--2834707 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2834660 TTTTATTTTT
2834670 TATTTGTTTTTTTGTTTTAA
1 TATTTGTTTTTTTGTTTTAA
*
2834690 TATTTGTTTTTATGTTTT
1 TATTTGTTTTTTTGTTTT
2834708 TAAATGTATT
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:0.13, C:0.00, G:0.11, T:0.76
Consensus pattern (20 bp):
TATTTGTTTTTTTGTTTTAA
Found at i:2839331 original size:17 final size:18
Alignment explanation
Indices: 2839289--2839331 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2839279 AAAGAGGTAA
2839289 AAAATTAAATAATTAATT
1 AAAATTAAATAATTAATT
**
2839307 AAAA-TAAATTTTTAA-T
1 AAAATTAAATAATTAATT
2839323 AAAATTAAA
1 AAAATTAAA
2839332 GGACCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 13 0.59
18 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTAAATAATTAATT
Found at i:2840351 original size:29 final size:31
Alignment explanation
Indices: 2840306--2840366 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 31
2840296 TTGATAGTTC
2840306 ATGTACCACATTAGATAT-TT-TCAAAGTAT
1 ATGTACCACATTAGATATCTTATCAAAGTAT
* *
2840335 ATGTACCGA-ATTGGATATCTTATGAAAGTAT
1 ATGTACC-ACATTAGATATCTTATCAAAGTAT
2840366 A
1 A
2840367 GGTATCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 15 0.56
30 3 0.11
31 9 0.33
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (31 bp):
ATGTACCACATTAGATATCTTATCAAAGTAT
Found at i:2840397 original size:92 final size:92
Alignment explanation
Indices: 2840281--2840459 Score: 227
Period size: 92 Copynumber: 1.9 Consensus size: 92
2840271 ATCAAATAAA
** * *
2840281 ATAATAAAACACATATTGATAGTTCATGTACCACATT-AGATATTTTCAAAGTATATGTACCGA-
1 ATAATAAAACACATATTGATAGTTCAAATACCACATTGA-ACATTTTCAAAGTACATGTACC-AC
* *
2840344 ATTGGATATCTTATGAAAGTATAGGTATC
64 ATTGAACATCTTATGAAAGTATAGGTATC
** *
2840373 ATAATAAAATGCATATTGATAGTTCAAATATCACATTGAACATTTTCAAAGTACATGTACCACAT
1 ATAATAAAACACATATTGATAGTTCAAATACCACATTGAACATTTTCAAAGTACATGTACCACAT
* *
2840438 TGAACATTTTTTGAAAGTATAG
66 TGAACATCTTATGAAAGTATAG
2840460 ATGCTAAATG
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
91 1 0.01
92 72 0.97
93 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (92 bp):
ATAATAAAACACATATTGATAGTTCAAATACCACATTGAACATTTTCAAAGTACATGTACCACAT
TGAACATCTTATGAAAGTATAGGTATC
Found at i:2840828 original size:23 final size:21
Alignment explanation
Indices: 2840797--2840838 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
2840787 CAACTCAATT
2840797 AAACACATATATTATATAAATAA
1 AAACACATATA--ATATAAATAA
*
2840820 AAACTCATATAATATAAAT
1 AAACACATATAATATAAAT
2840839 TTTTTATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (21 bp):
AAACACATATAATATAAATAA
Found at i:2850580 original size:20 final size:20
Alignment explanation
Indices: 2850555--2850592 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2850545 AGGGAAATAT
2850555 ATATATACATGTATGCATGC
1 ATATATACATGTATGCATGC
*
2850575 ATATATATATGTATGCAT
1 ATATATACATGTATGCAT
2850593 ATGAAACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (20 bp):
ATATATACATGTATGCATGC
Found at i:2851845 original size:20 final size:20
Alignment explanation
Indices: 2851820--2851858 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2851810 TATAAAGTCT
2851820 ATAATGTATATATTATAAAA
1 ATAATGTATATATTATAAAA
* *
2851840 ATAATGTGTATTTTATAAA
1 ATAATGTATATATTATAAA
2851859 GTTATAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (20 bp):
ATAATGTATATATTATAAAA
Found at i:2852147 original size:16 final size:14
Alignment explanation
Indices: 2852126--2852159 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
2852116 TATAATTTTT
2852126 TTATAAATATTATATA
1 TTATAAA-ATT-TATA
2852142 TTATAAAATTTATA
1 TTATAAAATTTATA
2852156 TTAT
1 TTAT
2852160 TTTTTGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 3 0.17
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATAAAATTTATA
Found at i:2855883 original size:16 final size:16
Alignment explanation
Indices: 2855864--2855894 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2855854 TAAATAAATT
2855864 ATTAAAAATAAAAAAA
1 ATTAAAAATAAAAAAA
2855880 ATTAAAAATAAAAAA
1 ATTAAAAATAAAAAA
2855895 TAAATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
ATTAAAAATAAAAAAA
Found at i:2859587 original size:38 final size:38
Alignment explanation
Indices: 2859545--2859621 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2859535 GCCTGGAAGT
2859545 AAGTTGGTTTATTTTTCAGAAAAATTACTAAAGCTGAA
1 AAGTTGGTTTATTTTTCAGAAAAATTACTAAAGCTGAA
2859583 AAGTTGGTTTATTTTTCAGAAAAATTACTAAAGCTGAA
1 AAGTTGGTTTATTTTTCAGAAAAATTACTAAAGCTGAA
2859621 A
1 A
2859622 TATGAATTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (38 bp):
AAGTTGGTTTATTTTTCAGAAAAATTACTAAAGCTGAA
Found at i:2862951 original size:136 final size:136
Alignment explanation
Indices: 2862707--2862978 Score: 438
Period size: 136 Copynumber: 2.0 Consensus size: 136
2862697 CTTCATTGAG
* * * *
2862707 CAATAAAATCAGTAGATGAGTAAGAGCTATTCACAACTATGTTTGACGTATATTACTAAGGGGCT
1 CAATAAAATCAGTAGATGAGTAAGAGCTATTCACAACTATGTTCGACATATATTAATAAGGAGCT
*
2862772 TTTGGTTCAAGGAGTGTAAGATTAACTTTGGTAATAGAATTACCAAAAAGCAAAATGACTTGGCA
66 TTTGGTCCAAGGAGTGTAAGATTAACTTTGGTAATAGAATTACCAAAAAGCAAAATGACTTGGCA
2862837 CATTAC
131 CATTAC
**
2862843 CAATAAAATTGGTAGATGAGTAAGAGCTATTCACAACTATGTTCGACATATATTAATAAGGAG-T
1 CAATAAAATCAGTAGATGAGTAAGAGCTATTCACAACTATGTTCGACATATATTAATAAGGAGCT
* *
2862907 GTTTGGTCCAAGGAGTGTAAGATTCACTTTGGTAATAGAATTACCGAAAAGCAAAATGACTTGGC
66 -TTTGGTCCAAGGAGTGTAAGATTAACTTTGGTAATAGAATTACCAAAAAGCAAAATGACTTGGC
*
2862972 CCATTAC
130 ACATTAC
2862979 GGGATATGTT
Statistics
Matches: 125, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
135 1 0.01
136 124 0.99
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (136 bp):
CAATAAAATCAGTAGATGAGTAAGAGCTATTCACAACTATGTTCGACATATATTAATAAGGAGCT
TTTGGTCCAAGGAGTGTAAGATTAACTTTGGTAATAGAATTACCAAAAAGCAAAATGACTTGGCA
CATTAC
Found at i:2868748 original size:24 final size:27
Alignment explanation
Indices: 2868719--2868771 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 27
2868709 ATCTTCTTAA
*
2868719 TTTAATTACTCT-CA-TT-AAATAAAT
1 TTTAATCACTCTACAGTTAAAATAAAT
*
2868743 TTTAATCACTTTACAGTTAAAATAAAT
1 TTTAATCACTCTACAGTTAAAATAAAT
2868770 TT
1 TT
2868772 ATTTATTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.42
25 2 0.08
26 2 0.08
27 10 0.42
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (27 bp):
TTTAATCACTCTACAGTTAAAATAAAT
Found at i:2876414 original size:33 final size:34
Alignment explanation
Indices: 2876374--2876444 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 34
2876364 AAATAATTAT
2876374 AAATTTATA-AAATAGAAATTAT-TTAAAATA-AAA
1 AAATTTATAGAAAT--AAATTATATTAAAATATAAA
*
2876407 AAATTTATAGAAATAATTTATATTAAAATATAAA
1 AAATTTATAGAAATAAATTATATTAAAATATAAA
2876441 AAAT
1 AAAT
2876445 AAAAACATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
32 6 0.18
33 17 0.50
34 11 0.32
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (34 bp):
AAATTTATAGAAATAAATTATATTAAAATATAAA
Found at i:2876736 original size:17 final size:18
Alignment explanation
Indices: 2876714--2876764 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
2876704 GTAATTTTTT
2876714 TTAATATTTTATAA-ATA
1 TTAATATTTTATAATATA
*
2876731 TTAATAATTTTATAATATT
1 TTAAT-ATTTTATAATATA
*
2876750 TTTATATTTTTATAA
1 TTAATA-TTTTATAA
2876765 CTTTCAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 5 0.17
18 10 0.34
19 14 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATATTTTATAATATA
Found at i:2878323 original size:20 final size:19
Alignment explanation
Indices: 2878292--2878329 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
2878282 TTTACAAAAT
2878292 AAATTATATTATTATTATG
1 AAATTATATTATTATTATG
2878311 AAATTATTATTATTATTAT
1 AAATTA-TATTATTATTAT
2878330 TATATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
AAATTATATTATTATTATG
Found at i:2878335 original size:17 final size:17
Alignment explanation
Indices: 2878294--2878339 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2878284 TACAAAATAA
2878294 ATTATATTATTATTATG
1 ATTATATTATTATTATG
* *
2878311 A-AATTATTATTATTATT
1 ATTA-TATTATTATTATG
2878328 ATTATATT-TTAT
1 ATTATATTATTAT
2878340 ATAAAACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 5 0.21
17 18 0.75
18 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
ATTATATTATTATTATG
Found at i:2886567 original size:14 final size:14
Alignment explanation
Indices: 2886548--2886576 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2886538 TTCAAGGGAT
2886548 ACAAAATCCTAATC
1 ACAAAATCCTAATC
2886562 ACAAAATCCTAATC
1 ACAAAATCCTAATC
2886576 A
1 A
2886577 TCTATATATC
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:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
ACAAAATCCTAATC
Found at i:2893002 original size:20 final size:21
Alignment explanation
Indices: 2892959--2893009 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2892949 TCTTTCAAAA
2892959 AAAATAAAATTATTGTTGTTT
1 AAAATAAAATTATTGTTGTTT
*
2892980 AAAATTAAATT-TT-TTGCTTT
1 AAAATAAAATTATTGTTG-TTT
2893000 AAAATAAAAT
1 AAAATAAAAT
2893010 GTTTATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 14 0.52
21 10 0.37
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (21 bp):
AAAATAAAATTATTGTTGTTT
Found at i:2901949 original size:4 final size:4
Alignment explanation
Indices: 2901940--2901966 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2901930 AAGTTGCATA
2901940 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
2901967 ACCTCCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2906071 original size:16 final size:16
Alignment explanation
Indices: 2906050--2906087 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
2906040 TATAAAAAAA
*
2906050 GTATTTTTATAATTAT
1 GTATTTTTAAAATTAT
2906066 GTA-TTTTAAAATTAT
1 GTATTTTTAAAATTAT
2906081 GTATTTT
1 GTATTTT
2906088 GATTGTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (16 bp):
GTATTTTTAAAATTAT
Found at i:2907325 original size:20 final size:19
Alignment explanation
Indices: 2907291--2907340 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
2907281 TCTCTCTCAA
*
2907291 CAAAAATTTAAAAAAAATT
1 CAAAAATTTATAAAAAATT
2907310 CAAAATATTTAT-AAAAATT
1 CAAAA-ATTTATAAAAAATT
*
2907329 CCAAAATTTATA
1 CAAAAATTTATA
2907341 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.22
19 16 0.59
20 5 0.19
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
CAAAAATTTATAAAAAATT
Found at i:2909430 original size:12 final size:12
Alignment explanation
Indices: 2909413--2909437 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2909403 AAAATTCGAA
2909413 TTTTAGTAATTT
1 TTTTAGTAATTT
2909425 TTTTAGTAATTT
1 TTTTAGTAATTT
2909437 T
1 T
2909438 GATTTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTAGTAATTT
Found at i:2913348 original size:28 final size:30
Alignment explanation
Indices: 2913287--2913348 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 30
2913277 CAATCACCAA
* *
2913287 ATTTTAATTTAAATGTAAATTTTAATTAAT
1 ATTTTAATTTAAATGTAAATATTAATAAAT
2913317 -TTTTAATTT-AATG-AAATAATTAA-AAAT
1 ATTTTAATTTAAATGTAAAT-ATTAATAAAT
2913344 ATTTT
1 ATTTT
2913349 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
27 7 0.25
28 12 0.43
29 9 0.32
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
ATTTTAATTTAAATGTAAATATTAATAAAT
Found at i:2914501 original size:20 final size:19
Alignment explanation
Indices: 2914478--2914530 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
2914468 TTTTTATTTA
2914478 AATATTATAATTTCAAAAAT
1 AATATTAT-ATTTCAAAAAT
*
2914498 AATA-TAT-TTATTAAAAAT
1 AATATTATATT-TCAAAAAT
2914516 -ATATTATATTTCAAA
1 AATATTATATTTCAAA
2914531 TTGTATTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 5 0.18
18 14 0.50
19 5 0.18
20 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATTATATTTCAAAAAT
Found at i:2918279 original size:14 final size:16
Alignment explanation
Indices: 2918249--2918290 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
2918239 TTAAGTAAAA
* *
2918249 AAATTATTAAAATTAT
1 AAATTATAAAAAGTAT
2918265 -AATTA-AAAAAGTAT
1 AAATTATAAAAAGTAT
2918279 AAATTATAAAAA
1 AAATTATAAAAA
2918291 TCATAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 7 0.32
15 10 0.45
16 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AAATTATAAAAAGTAT
Found at i:2918360 original size:42 final size:41
Alignment explanation
Indices: 2918281--2918360 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 41
2918271 AAAAGTATAA
* *
2918281 ATTATAAAAATCATAAAAAAAATATTAGAAATTTATAAGTT
1 ATTATAAAAATCATAAAAAAAATATTAAAAATATATAAGTT
* *
2918322 ATTATAAACAATTATATAAAAAAT-TTAAAAGATATATAA
1 ATTATAAA-AATCATAAAAAAAATATTAAAA-ATATATAA
2918361 ATTTATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 13 0.39
42 20 0.61
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.34
Consensus pattern (41 bp):
ATTATAAAAATCATAAAAAAAATATTAAAAATATATAAGTT
Found at i:2918392 original size:20 final size:20
Alignment explanation
Indices: 2918321--2918395 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
2918311 ATTTATAAGT
*
2918321 TATTATAAACAATTATATAAAA
1 TATTATAAA-AATTAT-TTAAA
* *
2918343 AATT-TAAAAGA-TATATAAA
1 TATTATAAAA-ATTATTTAAA
**
2918362 T-TTATTTAAATTATTTAAA
1 TATTATAAAAATTATTTAAA
2918381 TATTATAAAAATTAT
1 TATTATAAAAATTAT
2918396 AAAATCATAA
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
18 3 0.08
19 14 0.35
20 15 0.38
21 5 0.12
22 3 0.08
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (20 bp):
TATTATAAAAATTATTTAAA
Found at i:2919183 original size:30 final size:30
Alignment explanation
Indices: 2919114--2919184 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
2919104 TAAATTATCG
* *
2919114 ATTAAACCCTTGTAAAATAAAAAAAAATCA
1 ATTAAACTCTCGTAAAATAAAAAAAAATCA
* *
2919144 ATTAAACTCTCGTAAAATAATAAAATATCA
1 ATTAAACTCTCGTAAAATAAAAAAAAATCA
*
2919174 ATTACACTCTC
1 ATTAAACTCTC
2919185 CACTTATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (30 bp):
ATTAAACTCTCGTAAAATAAAAAAAAATCA
Found at i:2919836 original size:28 final size:26
Alignment explanation
Indices: 2919804--2919869 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
2919794 ATCTTAAACT
2919804 TTAAAATTTTTAATCCT-AAATTTAAGG
1 TTAAAATTTTTAAT-CTAAAATTT-AGG
**
2919831 TCTAAAATTTAGAATCTAAAATTTAGG
1 T-TAAAATTTTTAATCTAAAATTTAGG
*
2919858 TTAAAAATTTTA
1 TTAAAATTTTTA
2919870 TAAAATAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
26 8 0.25
27 7 0.22
28 17 0.53
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (26 bp):
TTAAAATTTTTAATCTAAAATTTAGG
Found at i:2919838 original size:14 final size:13
Alignment explanation
Indices: 2919821--2919863 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
2919811 TTTTAATCCT
2919821 AAATTTAAGGTCTA
1 AAATTT-AGGTCTA
*
2919835 AAATTTAGAATCTA
1 AAATTTAG-GTCTA
2919849 AAATTTAGGT-TA
1 AAATTTAGGTCTA
2919861 AAA
1 AAA
2919864 ATTTTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 5 0.19
13 3 0.12
14 18 0.69
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.35
Consensus pattern (13 bp):
AAATTTAGGTCTA
Found at i:2921085 original size:8 final size:8
Alignment explanation
Indices: 2921074--2921115 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
2921064 AAAATACCAC
2921074 TAAAATTA
1 TAAAATTA
2921082 TAAAGA-TA
1 TAAA-ATTA
2921090 TAAAA-TA
1 TAAAATTA
2921097 TTAAAATTA
1 -TAAAATTA
2921106 TAAAATTA
1 TAAAATTA
2921114 TA
1 TA
2921116 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 3 0.10
8 25 0.81
9 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (8 bp):
TAAAATTA
Found at i:2927181 original size:16 final size:16
Alignment explanation
Indices: 2927160--2927193 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2927150 TTTATTTTTA
*
2927160 TTTTATATTTAAATAT
1 TTTTATATTTAAAAAT
*
2927176 TTTTATTTTTAAAAAT
1 TTTTATATTTAAAAAT
2927192 TT
1 TT
2927194 AGTTCCTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATATTTAAAAAT
Found at i:2932345 original size:27 final size:28
Alignment explanation
Indices: 2932281--2932349 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 28
2932271 GAATGTCCAA
*
2932281 CCCAAACACACCCGGAATATTATAAATCCT
1 CCCAAACACA-CCGG-ATATAATAAATCCT
*
2932311 -CCATAACACACCGG-TATAATATATCCT
1 CCCA-AACACACCGGATATAATAAATCCT
2932338 CCCAAACACACC
1 CCCAAACACACC
2932350 AATAAGGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 19 0.54
28 3 0.09
29 7 0.20
30 6 0.17
ACGTcount: A:0.39, C:0.36, G:0.06, T:0.19
Consensus pattern (28 bp):
CCCAAACACACCGGATATAATAAATCCT
Found at i:2933434 original size:25 final size:24
Alignment explanation
Indices: 2933398--2933446 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
2933388 TTGTCTTTCT
*
2933398 TTTTATTCTTTATTATT-TCATTTA
1 TTTTATTATTTATT-TTATCATTTA
2933422 TTTTACTTATTTATTTTATCATTTA
1 TTTTA-TTATTTATTTTATCATTTA
2933447 ACTAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTATTATTTATTTTATCATTTA
Found at i:2935588 original size:9 final size:9
Alignment explanation
Indices: 2935574--2935617 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
2935564 TTATTTATTC
*
2935574 AATTAATTT
1 AATTAATTA
2935583 AATTAATTA
1 AATTAATTA
*
2935592 AACTAATTA
1 AATTAATTA
*
2935601 AATTAAATA
1 AATTAATTA
2935610 AATTAATT
1 AATTAATT
2935618 TCTCAATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (9 bp):
AATTAATTA
Found at i:2935634 original size:16 final size:18
Alignment explanation
Indices: 2935608--2935640 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2935598 TTAAATTAAA
2935608 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
2935625 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
2935641 CTCAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:2936648 original size:21 final size:21
Alignment explanation
Indices: 2936624--2936688 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
2936614 AAATCTAACT
2936624 GAAGCACAAAAGTGCTAAACG
1 GAAGCACAAAAGTGCTAAACG
** *
2936645 GAAGC-CTGAAG-GCT-AACT
1 GAAGCACAAAAGTGCTAAACG
*
2936663 GAAGCACATAAGTGCTAAACG
1 GAAGCACAAAAGTGCTAAACG
2936684 GAAGC
1 GAAGC
2936689 CCGAAGGCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 7 0.20
21 13 0.37
ACGTcount: A:0.42, C:0.20, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAGCACAAAAGTGCTAAACG
Found at i:2936676 original size:39 final size:39
Alignment explanation
Indices: 2936618--2936706 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
2936608 AACCCGAAAT
*
2936618 CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCTGAAGG
1 CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
*
2936657 CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGG
1 CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
2936696 CTAACTGAAGC
1 CTAACTGAAGC
2936707 TCATCAGAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.13
Consensus pattern (39 bp):
CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
Found at i:2943478 original size:23 final size:23
Alignment explanation
Indices: 2943441--2943488 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2943431 TAGTCCAAAG
*
2943441 ATTTTGTTTAAAAAATTAT-CAA
1 ATTTTGTTTAAAAAATCATACAA
*
2943463 ATTTTTTTTAACAAAATCATACAA
1 ATTTTGTTTAA-AAAATCATACAA
2943487 AT
1 AT
2943489 CAGAAAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.45
23 7 0.32
24 5 0.23
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTTTGTTTAAAAAATCATACAA
Found at i:2949276 original size:15 final size:16
Alignment explanation
Indices: 2949256--2949290 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2949246 AATAATTTAT
*
2949256 TAAAAATATT-TAAAA
1 TAAAAATATTAGAAAA
2949271 TAAAAATATTAGAAAA
1 TAAAAATATTAGAAAA
2949287 TAAA
1 TAAA
2949291 GAAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAATATTAGAAAA
Found at i:2951561 original size:16 final size:16
Alignment explanation
Indices: 2951522--2951562 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2951512 TAATTAGAAT
*
2951522 GATGGAAAATTAAAGG
1 GATGGAAAATTAAAAG
* *
2951538 GGTAGAAAATTAAAAG
1 GATGGAAAATTAAAAG
2951554 GATGGAAAA
1 GATGGAAAA
2951563 CATAATTTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (16 bp):
GATGGAAAATTAAAAG
Found at i:2953554 original size:13 final size:14
Alignment explanation
Indices: 2953526--2953558 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2953516 ATTACAAAAT
2953526 AAATTTAATGTTTTA
1 AAATTTAA-GTTTTA
2953541 AAATTTAA-TTTTA
1 AAATTTAAGTTTTA
2953554 AAATT
1 AAATT
2953559 AATAGTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
15 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (14 bp):
AAATTTAAGTTTTA
Found at i:2953864 original size:23 final size:22
Alignment explanation
Indices: 2953823--2953868 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
2953813 ATTGCTTTAA
2953823 ATTATTTTTTATTTAAAACCAAT
1 ATTATTTTTTATTTAAAA-CAAT
*
2953846 ATTA-TTTTTATTATGAAACAAT
1 ATTATTTTTTATT-TAAAACAAT
2953868 A
1 A
2953869 AAAACACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTATTTTTTATTTAAAACAAT
Found at i:2955605 original size:67 final size:69
Alignment explanation
Indices: 2955526--2955661 Score: 206
Period size: 68 Copynumber: 2.0 Consensus size: 69
2955516 AAAGATACAT
* *
2955526 TTAATTAATTTTTA-TTTTTATATATAAAATATTTACCCATAATAGAAA-TTAGTGCATATATA-
1 TTAATTAATTTTTATTTTTTATATATAAAATATTTAACCATAATA-AAATTTAATGCATATATAT
2955588 AAAAA
65 AAAAA
* *
2955593 TTAATTATTTTTTATTTTTTATATATAAAATATTTAAGCATAATAAAATTTAATGCATATATATA
1 TTAATTAATTTTTATTTTTTATATATAAAATATTTAACCATAATAAAATTTAATGCATATATATA
2955658 AAAA
66 AAAA
2955662 AAATTACACA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
67 16 0.26
68 41 0.66
69 5 0.08
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (69 bp):
TTAATTAATTTTTATTTTTTATATATAAAATATTTAACCATAATAAAATTTAATGCATATATATA
AAAA
Found at i:2955997 original size:20 final size:19
Alignment explanation
Indices: 2955955--2955997 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
2955945 TCAAATTTTT
* *
2955955 TAAAATATATTAATTAATT
1 TAAAATATAATAATTAATA
*
2955974 TAAAATATGAATAATTGATA
1 TAAAATAT-AATAATTAATA
2955994 TAAA
1 TAAA
2955998 GGCATTTGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
TAAAATATAATAATTAATA
Found at i:2959003 original size:11 final size:9
Alignment explanation
Indices: 2958976--2959003 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2958966 GAATCAAGAT
2958976 TAAAATATA
1 TAAAATATA
2958985 TAAAATATA
1 TAAAATATA
2958994 TAAAATATA
1 TAAAATATA
2959003 T
1 T
2959004 CAAAGCAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TAAAATATA
Found at i:2962801 original size:31 final size:29
Alignment explanation
Indices: 2962766--2962825 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 29
2962756 TTTTCAAAAA
2962766 TAAAAAAATATTTATTTA-ATAATTTTATTTT
1 TAAAAAAATATTT-TTTATAT-ATTTT-TTTT
2962797 TAAAAAAATATTTTTTATATATTTTTTTT
1 TAAAAAAATATTTTTTATATATTTTTTTT
2962826 GAAATTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 4 0.14
30 9 0.32
31 15 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TAAAAAAATATTTTTTATATATTTTTTTT
Found at i:2964436 original size:20 final size:21
Alignment explanation
Indices: 2964400--2964441 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
2964390 AATGCCAGTC
*
2964400 AAATTTAAATGAGAATT-TTG
1 AAATTTAAATGAAAATTATTG
2964420 AAATTTAGAAT-AAAATTATTG
1 AAATTTA-AATGAAAATTATTG
2964441 A
1 A
2964442 TATAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (21 bp):
AAATTTAAATGAAAATTATTG
Found at i:2967623 original size:13 final size:13
Alignment explanation
Indices: 2967591--2967624 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2967581 CATATGTGCA
2967591 ATATTATTTTTAT
1 ATATTATTTTTAT
* *
2967604 TTGTTATTTTTAT
1 ATATTATTTTTAT
2967617 ATATTATT
1 ATATTATT
2967625 CACAAAAAAT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
ATATTATTTTTAT
Found at i:2969270 original size:8 final size:8
Alignment explanation
Indices: 2969259--2969289 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
2969249 TTCTTTTTTT
2969259 TTTTTTAC
1 TTTTTTAC
2969267 TTTTTTTAC
1 -TTTTTTAC
2969276 TTTTTTAC
1 TTTTTTAC
2969284 TTTTTT
1 TTTTTT
2969290 CTTATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTAC
Found at i:2969270 original size:9 final size:9
Alignment explanation
Indices: 2969258--2969289 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
2969248 GTTCTTTTTT
2969258 TTTTTTTAC
1 TTTTTTTAC
2969267 TTTTTTTAC
1 TTTTTTTAC
2969276 -TTTTTTAC
1 TTTTTTTAC
2969284 TTTTTT
1 TTTTTT
2969290 CTTATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:2969279 original size:17 final size:15
Alignment explanation
Indices: 2969251--2969289 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
2969241 TTGTTAGGTT
2969251 CTTTTTTTTTTTTTA
1 CTTTTTTTTTTTTTA
2969266 CTTTTTTTACTTTTTTA
1 CTTTTTTT--TTTTTTA
2969283 CTTTTTT
1 CTTTTTT
2969290 CTTATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.36
17 14 0.64
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (15 bp):
CTTTTTTTTTTTTTA
Found at i:2969416 original size:21 final size:20
Alignment explanation
Indices: 2969387--2969454 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 20
2969377 TTAATTTTAA
* *
2969387 AAAAATTTTAATATATATTT
1 AAAATTTTTAATATATTTTT
2969407 AAAATGTTTT-ATAATATTTTTT
1 AAAAT-TTTTAAT-ATA-TTTTT
2969429 AAAATTTTTAATTATTATTTTT
1 AAAATTTTTAA-TA-TATTTTT
2969451 AAAA
1 AAAA
2969455 ATATTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
20 6 0.15
21 11 0.28
22 20 0.50
23 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (20 bp):
AAAATTTTTAATATATTTTT
Found at i:2969429 original size:22 final size:23
Alignment explanation
Indices: 2969394--2969461 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
2969384 TAAAAAAATT
*
2969394 TTAATATATATTTAAAATGTTTT-A
1 TTAATAT-TTTTTAAAAT-TTTTAA
2969418 -TAATATTTTTTAAAATTTTTAA
1 TTAATATTTTTTAAAATTTTTAA
* *
2969440 TTATTATTTTTAAAAATATTTT
1 TTAATATTTTTTAAAAT-TTTT
2969462 TTATCTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.11
22 10 0.26
23 20 0.53
24 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (23 bp):
TTAATATTTTTTAAAATTTTTAA
Found at i:2969455 original size:23 final size:23
Alignment explanation
Indices: 2969375--2969461 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 23
2969365 TAATTTATAT
* *
2969375 TATTAATTTTAAAAAAATTTTAA
1 TATTATTTTTAAAAATATTTTAA
* *
2969398 TA-TATATTT-AAAATGTTTT-A
1 TATTATTTTTAAAAATATTTTAA
* *
2969418 TAATATTTTTTAAAAT-TTTTAA
1 TATTATTTTTAAAAATATTTTAA
2969440 TTATTATTTTTAAAAATATTTT
1 -TATTATTTTTAAAAATATTTT
2969462 TTATCTTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
20 3 0.06
21 18 0.35
22 11 0.21
23 16 0.31
24 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (23 bp):
TATTATTTTTAAAAATATTTTAA
Found at i:2969465 original size:22 final size:22
Alignment explanation
Indices: 2969374--2969465 Score: 64
Period size: 22 Copynumber: 4.2 Consensus size: 22
2969364 TTAATTTATA
* *
2969374 TTATTAATTTTAAAAA-AATTT
1 TTATTATTTTTAAAAATATTTT
* * *
2969395 TAATATATATTT-AAAATGTTTT
1 TTAT-TATTTTTAAAAATATTTT
* * *
2969417 ATAATATTTTTTAAAAT-TTTT
1 TTATTATTTTTAAAAATATTTT
2969438 AATTATTATTTTTAAAAATATTTT
1 --TTATTATTTTTAAAAATATTTT
2969462 TTAT
1 TTAT
2969466 CTTTATATAT
Statistics
Matches: 53, Mismatches: 12, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
21 17 0.32
22 18 0.34
23 14 0.26
24 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (22 bp):
TTATTATTTTTAAAAATATTTT
Found at i:2969631 original size:22 final size:22
Alignment explanation
Indices: 2969596--2969637 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2969586 TTTTTCTTAT
*
2969596 TTTATTTTGTTTATATATTTTA
1 TTTATTTTGTTTATACATTTTA
2969618 TTTATTTT-TATTATACATTT
1 TTTATTTTGT-TTATACATTT
2969638 CAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTATTTTGTTTATACATTTTA
Found at i:2969691 original size:13 final size:13
Alignment explanation
Indices: 2969673--2969697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2969663 CATAGATTTT
2969673 ATTTTTTTCTTTA
1 ATTTTTTTCTTTA
2969686 ATTTTTTTCTTT
1 ATTTTTTTCTTT
2969698 TTTAAGTTTT
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
ATTTTTTTCTTTA
Found at i:2970234 original size:10 final size:9
Alignment explanation
Indices: 2970216--2970314 Score: 65
Period size: 10 Copynumber: 10.4 Consensus size: 9
2970206 TAAAATTTAA
2970216 AAAATATTT
1 AAAATATTT
2970225 AAAATCATTT
1 AAAAT-ATTT
*
2970235 AAAATATTAA
1 AAAATATT-T
2970245 AAAATATTT
1 AAAATATTT
*
2970254 TAAATCATTT
1 AAAAT-ATTT
*
2970264 TAAATCATTT
1 AAAAT-ATTT
* *
2970274 TAAATGTTTT
1 AAAAT-ATTT
* *
2970284 ATAATATTA
1 AAAATATTT
2970293 AAAATATATT
1 AAAATAT-TT
*
2970303 -TAATATTT
1 AAAATATTT
2970311 AAAA
1 AAAA
2970315 AATAATTTGA
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
8 2 0.03
9 27 0.38
10 43 0.60
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (9 bp):
AAAATATTT
Found at i:2970278 original size:29 final size:29
Alignment explanation
Indices: 2970206--2970268 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
2970196 AAATTCTATG
*
2970206 TAAAAT-TTAAAAAATATTTAAAATCATT
1 TAAAATATTAAAAAATATTTTAAATCATT
2970234 TAAAATATTAAAAAATATTTTAAATCATT
1 TAAAATATTAAAAAATATTTTAAATCATT
*
2970263 TTAAAT
1 TAAAAT
2970269 CATTTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAAATATTAAAAAATATTTTAAATCATT
Found at i:2970305 original size:39 final size:39
Alignment explanation
Indices: 2970207--2970314 Score: 100
Period size: 39 Copynumber: 2.8 Consensus size: 39
2970197 AATTCTATGT
2970207 AAAAT-TTAAAAA-ATATTTAAAATCATTTAAAATATTAA
1 AAAATATTAAAAATATATTT-AAATCATTTAAAATATTAA
** * * **
2970245 AAAATATTTTAAATCAT-TTTAAATCATTTTAAATGTTTT
1 AAAATATTAAAAAT-ATATTTAAATCATTTAAAATATTAA
*
2970284 ATAATATTAAAAATATATTT-AAT-ATTTAAAA
1 AAAATATTAAAAATATATTTAAATCATTTAAAA
2970315 AATAATTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
37 7 0.12
38 10 0.18
39 34 0.61
40 3 0.05
41 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (39 bp):
AAAATATTAAAAATATATTTAAATCATTTAAAATATTAA
Found at i:2970509 original size:85 final size:87
Alignment explanation
Indices: 2970419--2970584 Score: 309
Period size: 87 Copynumber: 1.9 Consensus size: 87
2970409 ATAAGGACTT
2970419 AAAAAAGAAAAAAGAAAGTC-AAACTTT-AAAAAAAAAAGACTGAAACAAATAAGTTGGCTGTCA
1 AAAAAAGAAAAAAGAAAGTCAAAACTTTAAAAAAAAAAAGACTGAAACAAATAAGTTGGCTGTCA
2970482 GACTTGAAAACTGGTATAGCCA
66 GACTTGAAAACTGGTATAGCCA
*
2970504 AAAAAAGAAAAAAGAAAGTCAAAACTTTAAAAAAAAAAAGGCTGAAACAAATAAGTTGGCTGTCA
1 AAAAAAGAAAAAAGAAAGTCAAAACTTTAAAAAAAAAAAGACTGAAACAAATAAGTTGGCTGTCA
2970569 GACTTGAAAACTGGTA
66 GACTTGAAAACTGGTA
2970585 GCGCCAAATT
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
85 20 0.26
86 7 0.09
87 51 0.65
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (87 bp):
AAAAAAGAAAAAAGAAAGTCAAAACTTTAAAAAAAAAAAGACTGAAACAAATAAGTTGGCTGTCA
GACTTGAAAACTGGTATAGCCA
Found at i:2973326 original size:51 final size:51
Alignment explanation
Indices: 2973244--2973361 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
2973234 CTCAAACTTA
* * *
2973244 CTTCATACTTCATCCGGAATTATTAGCTTGTTGCTCTAACTTTAACAAGAG
1 CTTCATATTTCATCCGAAATAATTAGCTTGTTGCTCTAACTTTAACAAGAG
*
2973295 CTTCATATTTCATCCGAAATAATTA-CTTTGTTGCTCTAGCTTTAACAAGAG
1 CTTCATATTTCATCCGAAATAATTAGC-TTGTTGCTCTAACTTTAACAAGAG
*
2973346 CTTCATATTTTATCCG
1 CTTCATATTTCATCCG
2973362 GATAACTTAG
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 1 0.02
51 60 0.98
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (51 bp):
CTTCATATTTCATCCGAAATAATTAGCTTGTTGCTCTAACTTTAACAAGAG
Found at i:2974240 original size:31 final size:32
Alignment explanation
Indices: 2974205--2974270 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
2974195 ATTTTATTTC
2974205 ATCAT-TCTAAACTATTACACAACCTTTAAAA
1 ATCATATCTAAACTATTACACAACCTTTAAAA
* *
2974236 ATCATAATTTCAACTATTACACAACCTTTAAAA
1 ATCAT-ATCTAAACTATTACACAACCTTTAAAA
2974269 AT
1 AT
2974271 AATAATTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 5 0.16
33 26 0.84
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (32 bp):
ATCATATCTAAACTATTACACAACCTTTAAAA
Found at i:2974251 original size:33 final size:33
Alignment explanation
Indices: 2974214--2974282 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
2974204 CATCATTCTA
*
2974214 AACTATTACACAACCTTTAAAAATCATAATTTC
1 AACTATTACACAACCTTTAAAAATAATAATTTC
2974247 AACTATTACACAACCTTTAAAAATAATAATTTC
1 AACTATTACACAACCTTTAAAAATAATAATTTC
2974280 AAC
1 AAC
2974283 ACTAAACCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (33 bp):
AACTATTACACAACCTTTAAAAATAATAATTTC
Found at i:2976763 original size:30 final size:30
Alignment explanation
Indices: 2976689--2976776 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 30
2976679 AAATGGACTT
* * * *
2976689 GAACCTCCTATATCCAGGTGAGATGAACTC
1 GAACCACCTATGTCCGGGTGATATGAACTC
* *
2976719 AAACCATC-ATGTCCGGGTGATATGAACTC
1 GAACCACCTATGTCCGGGTGATATGAACTC
*
2976748 GAACCACCTATGTCCGGGTTATATGAACT
1 GAACCACCTATGTCCGGGTGATATGAACT
2976777 GCTCTGGAAC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
29 24 0.50
30 24 0.50
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (30 bp):
GAACCACCTATGTCCGGGTGATATGAACTC
Found at i:2978661 original size:20 final size:20
Alignment explanation
Indices: 2978624--2978661 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2978614 TGATGGGGAG
*
2978624 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
2978644 CAAGAA-ATCAAAGCTGGA
1 CAAGAATATC-AAGCTGGA
2978662 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:2980614 original size:46 final size:46
Alignment explanation
Indices: 2980562--2980928 Score: 556
Period size: 46 Copynumber: 8.0 Consensus size: 46
2980552 GAGTGTGCTC
2980562 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
*
2980608 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAG
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* *
2980654 CCTGATATGAAATGTGTAAGACCGTGGTTGAAAGATACCATGGCAG
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
**
2980700 CCTGATATGAAATGTGTAAGACTGTGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
*
2980746 CCTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
*
2980792 CCTGATATGAAATGTGTAAGACTATGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* *** *
2980838 CGTGATATGAAATGAACAAGACCGTGGTTGAAAGATACCATGGCAA
1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* * * * * *
2980884 CATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CCTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
2980929 TCATGTCAAA
Statistics
Matches: 297, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.00
46 296 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (46 bp):
CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
Found at i:2983524 original size:46 final size:44
Alignment explanation
Indices: 2983465--2983579 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
2983455 ACAGGACAGA
* *
2983465 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
2983511 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
2983555 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
2983580 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:2983560 original size:44 final size:45
Alignment explanation
Indices: 2983465--2983598 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
2983455 ACAGGACAGA
* *
2983465 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
2983511 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
2983555 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2983599 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2986048 original size:18 final size:19
Alignment explanation
Indices: 2986005--2986055 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
2985995 AATAAAAAAA
*
2986005 TATATTTAATATATATATAT
1 TATATTTAA-ATTTATATAT
2986025 T-T-TTTAAATTTATAT-T
1 TATATTTAAATTTATATAT
2986041 TATATTTAAATTTAT
1 TATATTTAAATTTAT
2986056 TAATGGTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 2 0.07
17 8 0.29
18 16 0.57
19 1 0.04
20 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATTTAAATTTATATAT
Found at i:2986185 original size:21 final size:21
Alignment explanation
Indices: 2986157--2986200 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2986147 TTAAAAAAAG
2986157 AATTT-AAAAATAATATT-TAA
1 AATTTAAAAAAT-ATATTATAA
2986177 AATTGTAAAAAATATATTATAA
1 AATT-TAAAAAATATATTATAA
2986199 AA
1 AA
2986201 CATTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AATTTAAAAAATATATTATAA
Done.