Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 54 of 189
Found at i:15380659 original size:23 final size:24
Alignment explanation
Indices: 15380633--15380686 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
15380623 ATATTTGTTA
* *
15380633 TTAAAACAT-TATTATAAGTATT-T
1 TTAAAA-ATATATTAAAAATATTAT
*
15380656 TTAATAATATATTAAAAATATTAT
1 TTAAAAATATATTAAAAATATTAT
15380680 TTAAAAA
1 TTAAAAA
15380687 CTAAATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 2 0.08
23 16 0.64
24 7 0.28
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
TTAAAAATATATTAAAAATATTAT
Found at i:15387437 original size:33 final size:32
Alignment explanation
Indices: 15387365--15387441 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 32
15387355 TATATACATG
* **
15387365 TGTAAGACCATAACTGGGCTATGACATTCTGA
1 TGTAAGACCATAACTGGGCTATGACATACAAA
*
15387397 TGATAAGACCATAACTGGGTTATGGTAC-TACAAA
1 TG-TAAGACCATAACTGGGCTAT-G-ACATACAAA
15387431 TGTAAGACCAT
1 TGTAAGACCAT
15387442 GACAGGGCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
32 2 0.05
33 28 0.74
34 6 0.16
35 2 0.05
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGACATACAAA
Found at i:15387453 original size:105 final size:105
Alignment explanation
Indices: 15387260--15387456 Score: 270
Period size: 105 Copynumber: 1.9 Consensus size: 105
15387250 AATGTTTAAA
* * **
15387260 TGTAAGACCATAACTGGGCTATGACATTTTAATGAAAAGACTATAACTGGGTTATGGCACCTTGA
1 TGTAAGACCATAACTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGGCACCTCAA
***
15387325 ACGTAAGACCATGGTTGGACCATGGTAGTATATATACATG
66 ACGTAAGACCATGACAGGACCATGGTAGTATATATACATG
* * *
15387365 TGTAAGACCATAACTGGGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGTA-CTACA
1 TGTAAGACCATAACTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGGCACCT-CA
* *
15387429 AATGTAAGACCATGACAGGGCCATGGTA
65 AACGTAAGACCATGACAGGACCATGGTA
15387457 ATGCATGTGT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
104 2 0.03
105 77 0.97
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (105 bp):
TGTAAGACCATAACTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGGCACCTCAA
ACGTAAGACCATGACAGGACCATGGTAGTATATATACATG
Found at i:15387455 original size:33 final size:33
Alignment explanation
Indices: 15387400--15387475 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 33
15387390 ATTCTGATGA
* ** *
15387400 TAAGACCATAACTGGGTTATGGTACTACAAATG
1 TAAGACCATAACAGGGCCATGGTAATACAAATG
* * **
15387433 TAAGACCATGACAGGGCCATGGTAATGCATGTG
1 TAAGACCATAACAGGGCCATGGTAATACAAATG
15387466 TAAGACCATA
1 TAAGACCATA
15387476 GTTGGACTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (33 bp):
TAAGACCATAACAGGGCCATGGTAATACAAATG
Found at i:15415578 original size:9 final size:9
Alignment explanation
Indices: 15415566--15415744 Score: 69
Period size: 10 Copynumber: 18.8 Consensus size: 9
15415556 AAAAAGCATA
15415566 AAAAATTAT
1 AAAAATTAT
*
15415575 -AAAATAAT
1 AAAAATTAT
15415583 AAAAATATAT
1 AAAAAT-TAT
*
15415593 TAAAATTATT
1 AAAAATTA-T
15415603 AAAAA-T-T
1 AAAAATTAT
15415610 AAAAA-TAT
1 AAAAATTAT
*
15415618 TAAAATTGAT
1 AAAAATT-AT
15415628 AAAAAAATTAT
1 --AAAAATTAT
*
15415639 AAAAACTAT
1 AAAAATTAT
* *
15415648 AAAAACATAA
1 AAAAA-TTAT
* *
15415658 AAAAAATCT
1 AAAAATTAT
* *
15415667 AGCAAATTTT
1 A-AAAATTAT
**
15415677 AATGCATTAT
1 AA-AAATTAT
*
15415687 AAAAATTTT
1 AAAAATTAT
15415696 ATAAAATTAAT
1 A-AAAATT-AT
*
15415707 AAAACATATTT
1 AAAA-AT-TAT
*
15415718 AAAATTTTAT
1 AAAA-ATTAT
15415728 AAAAATGTAT
1 AAAAAT-TAT
15415738 AAAAATT
1 AAAAATT
15415745 CTTAGAAACT
Statistics
Matches: 127, Mismatches: 27, Indels: 32
0.68 0.15 0.17
Matches are distributed among these distances:
7 7 0.06
8 12 0.09
9 32 0.25
10 57 0.45
11 12 0.09
12 7 0.06
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:15415610 original size:16 final size:16
Alignment explanation
Indices: 15415566--15415622 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 16
15415556 AAAAAGCATA
*
15415566 AAAAATTATAAAATAAT
1 AAAAATTA-AAAATATT
15415583 AAAAATATATTAAAATTATT
1 AAAAAT-TA--AAAA-TATT
15415603 AAAAATTAAAAATATT
1 AAAAATTAAAAATATT
15415619 AAAA
1 AAAA
15415623 TTGATAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 8 0.22
17 10 0.28
18 2 0.06
19 7 0.19
20 9 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATTAAAAATATT
Found at i:15415633 original size:27 final size:26
Alignment explanation
Indices: 15415567--15415642 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 26
15415557 AAAAGCATAA
* *
15415567 AAAATTATAAAATAATAAAAATATATT
1 AAAATTATAAAAAAATTAAAA-ATATT
*
15415594 AAAATTAT-TAAAAATTAAAAATATT
1 AAAATTATAAAAAAATTAAAAATATT
15415619 AAAATTGATAAAAAAATTATAAAA
1 AAAATT-ATAAAAAAATTA-AAAA
15415643 ACTATAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.26
26 11 0.26
27 16 0.38
28 4 0.10
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (26 bp):
AAAATTATAAAAAAATTAAAAATATT
Found at i:15415635 original size:37 final size:35
Alignment explanation
Indices: 15415566--15415660 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 35
15415556 AAAAAGCATA
**
15415566 AAAAATTATAAAATAATAAAAATATATTAAAATTATT
1 AAAAATTA-AAAATAATAAAAATATAAAAAAATTA-T
* *
15415603 AAAAATTAAAAATATTAAAATTGATAAAAAAATTAT
1 AAAAATTAAAAATAATAAAAAT-ATAAAAAAATTAT
*
15415639 AAAAACTATAAAAA-CATAAAAA
1 AAAAA-T-TAAAAATAATAAAAA
15415661 AAATCTAGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
36 18 0.38
37 24 0.50
38 6 0.12
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.28
Consensus pattern (35 bp):
AAAAATTAAAAATAATAAAAATATAAAAAAATTAT
Found at i:15416331 original size:10 final size:10
Alignment explanation
Indices: 15416297--15416396 Score: 66
Period size: 10 Copynumber: 10.1 Consensus size: 10
15416287 AGTATGGTTC
15416297 AAGTTTTTAT
1 AAGTTTTTAT
*
15416307 AA-TTTTTTT
1 AAGTTTTTAT
15416316 ATAGTTTTTAT
1 A-AGTTTTTAT
*
15416327 AAGTTTATAT
1 AAGTTTTTAT
*
15416337 CAA-TTTTAAT
1 -AAGTTTTTAT
*
15416347 -ATTTTTTAT
1 AAGTTTTTAT
* *
15416356 GATTTTTTAT
1 AAGTTTTTAT
15416366 AAGTTTTTA-
1 AAGTTTTTAT
*
15416375 AGAATTTTTA-
1 A-AGTTTTTAT
15416385 AATGTTTTTAT
1 AA-GTTTTTAT
15416396 A
1 A
15416397 GAATTTATTT
Statistics
Matches: 72, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
8 1 0.01
9 15 0.21
10 46 0.64
11 10 0.14
ACGTcount: A:0.31, C:0.01, G:0.07, T:0.61
Consensus pattern (10 bp):
AAGTTTTTAT
Found at i:15416381 original size:39 final size:39
Alignment explanation
Indices: 15416301--15416397 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
15416291 TGGTTCAAGT
*
15416301 TTTTATAAT-TTTTTTATAGTTTTTATAAGTTTATATCAA
1 TTTT-TAATATTTTTTATAGTTTTTATAAGTTTATAACAA
* * *
15416340 -TTTTAATATTTTTTATGATTTTTTATAAGTTTTTAAGAA
1 TTTTTAATATTTTTTAT-AGTTTTTATAAGTTTATAACAA
15416379 TTTTTAA-ATGTTTTTATAG
1 TTTTTAATAT-TTTTTATAG
15416398 AATTTATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
37 4 0.08
38 11 0.22
39 21 0.43
40 13 0.27
ACGTcount: A:0.30, C:0.01, G:0.07, T:0.62
Consensus pattern (39 bp):
TTTTTAATATTTTTTATAGTTTTTATAAGTTTATAACAA
Found at i:15423410 original size:22 final size:22
Alignment explanation
Indices: 15423385--15423428 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
15423375 TAGTCATATA
15423385 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
15423407 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
15423429 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:15424278 original size:19 final size:19
Alignment explanation
Indices: 15424219--15424279 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 19
15424209 TATCAAGTCT
15424219 TAACAA-TTACCCAAATTTC
1 TAACAATTTA-CCAAATTTC
** * * *
15424238 TATGATTTTTCCAAAATATC
1 TAACAATTTACC-AAATTTC
15424258 TAACAATTTACCAAATTTC
1 TAACAATTTACCAAATTTC
15424277 TAA
1 TAA
15424280 GGACTTACCA
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.38
Consensus pattern (19 bp):
TAACAATTTACCAAATTTC
Found at i:15424386 original size:20 final size:19
Alignment explanation
Indices: 15424328--15424386 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
15424318 AAAGTTGAAC
* *
15424328 CAAAATTTCAAAGGATTTGC
1 CAAAATTTCTAAGGATTT-A
* *
15424348 CAAAATATCTAACGATTTA
1 CAAAATTTCTAAGGATTTA
15424367 CAAATATTTCTAAGGATTTA
1 CAAA-ATTTCTAAGGATTTA
15424387 TCGATATATC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (19 bp):
CAAAATTTCTAAGGATTTA
Found at i:15424914 original size:25 final size:26
Alignment explanation
Indices: 15424858--15424914 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
15424848 AAATATCCCT
*
15424858 AGAATAATCAGAGTCTAATTGGGAAA
1 AGAATAATCAGAGTCTAACTGGGAAA
* * * *
15424884 AAAATAA-CATAGTTTAACTGGGAGA
1 AGAATAATCAGAGTCTAACTGGGAAA
15424909 AGAATA
1 AGAATA
15424915 CGAGGCACAC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (26 bp):
AGAATAATCAGAGTCTAACTGGGAAA
Found at i:15430091 original size:40 final size:39
Alignment explanation
Indices: 15430031--15430136 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 39
15430021 GAGGCACACC
* *
15430031 TTACAAAATTGTTAAGGTTTTACCAAAACATCTAAC-AA
1 TTACAAAATTTTTAATGTTTTACCAAAACATCTAACGAA
* *
15430069 TTTACTAAAATTTTTAATGTTTTACGAAAATATCTAACGAA
1 -TTAC-AAAATTTTTAATGTTTTACCAAAACATCTAACGAA
* * *
15430110 TTACCAAAATTTCTATTGATTTACCAA
1 TTA-CAAAATTTTTAATGTTTTACCAA
15430137 TATTTATGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
39 4 0.07
40 49 0.88
41 3 0.05
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.38
Consensus pattern (39 bp):
TTACAAAATTTTTAATGTTTTACCAAAACATCTAACGAA
Found at i:15430133 original size:20 final size:20
Alignment explanation
Indices: 15430049--15430182 Score: 74
Period size: 20 Copynumber: 6.7 Consensus size: 20
15430039 TTGTTAAGGT
** **
15430049 TTTACCAAAACATCTAACAA
1 TTTACCAAAATTTCTAATGA
* * *
15430069 TTTACTAAAATTTTTAATGT
1 TTTACCAAAATTTCTAATGA
* * *
15430089 TTTACGAAAATATCTAACGA
1 TTTACCAAAATTTCTAATGA
* *
15430109 ATTACCAAAATTTCTATTGA
1 TTTACCAAAATTTCTAATGA
* * *
15430129 TTTACCAATATTTATGA-GAA
1 TTTACCAAAATTTCTAATG-A
* *
15430149 TTTAACAAAATTTTTAA-GA
1 TTTACCAAAATTTCTAATGA
*
15430168 TTTAACCAATATTTC
1 TTT-ACCAAAATTTC
15430183 CAAATTTTCT
Statistics
Matches: 83, Mismatches: 29, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
19 5 0.06
20 78 0.94
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (20 bp):
TTTACCAAAATTTCTAATGA
Found at i:15430259 original size:20 final size:20
Alignment explanation
Indices: 15430236--15430386 Score: 83
Period size: 20 Copynumber: 7.5 Consensus size: 20
15430226 TTTGTATGAC
* * *
15430236 TTTACCAAAATATTTAAGGA
1 TTTACCAATATATCTAACGA
* *
15430256 TTTACTAATGTATCTAACGA
1 TTTACCAATATATCTAACGA
* *
15430276 TTTACTAATATATCTAACAA
1 TTTACCAATATATCTAACGA
* * * *
15430296 TTTTCTAATAT-TTTCAAGGA
1 TTTACCAATATATCT-AACGA
* * * *
15430316 CTTTTCCAAAATAT-TTACAA
1 -TTTACCAATATATCTAACGA
15430336 TTTACCAATATATCTAACGA
1 TTTACCAATATATCTAACGA
* * *
15430356 TTTATCAAAATTTCTATA-GA
1 TTTACCAATATATCTA-ACGA
*
15430376 TTTACTAATAT
1 TTTACCAATAT
15430387 TTATGAGGCT
Statistics
Matches: 100, Mismatches: 26, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
19 13 0.13
20 75 0.75
21 11 0.11
22 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTACCAATATATCTAACGA
Found at i:15430280 original size:40 final size:40
Alignment explanation
Indices: 15430236--15430386 Score: 123
Period size: 40 Copynumber: 3.8 Consensus size: 40
15430226 TTTGTATGAC
*
15430236 TTTACCAAAATATTTA-AGGATTTACTAATGTATCTAACGA
1 TTTACCAAAATATTTACA-GATTTACTAATATATCTAACGA
* * * * * *
15430276 TTTACTAATATATCTAACA-ATTTTCTAATAT-TTTCAAGGA
1 TTTACCAAAATAT-TTACAGATTTACTAATATATCT-AACGA
* *
15430316 CTTTTCCAAAATATTTACA-ATTTACCAATATATCTAACGA
1 -TTTACCAAAATATTTACAGATTTACTAATATATCTAACGA
* *
15430356 TTTATCAAAAT-TTCTATAGATTTACTAATAT
1 TTTACCAAAATATT-TACAGATTTACTAATAT
15430387 TTATGAGGCT
Statistics
Matches: 85, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
38 2 0.02
39 14 0.16
40 54 0.64
41 14 0.16
42 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (40 bp):
TTTACCAAAATATTTACAGATTTACTAATATATCTAACGA
Found at i:15430384 original size:80 final size:80
Alignment explanation
Indices: 15430233--15430422 Score: 194
Period size: 80 Copynumber: 2.4 Consensus size: 80
15430223 AAATTTGTAT
* * *
15430233 GACTTTACCAAAATATTTAAGGATTTACTAATGTATCTAACGATTTACTAATATATCTAACAATT
1 GACTTTACCAAAATATTTAA-GATTTACCAATATATCTAACGATTTACTAAAATATCTAACAATT
*
15430298 TTCTAATATTTTCAAG
65 TACTAATATTTTCAAG
* * *
15430314 GACTTTTCCAAAATATTTACA-ATTTACCAATATATCTAACGATTTA-TCAAAATTTCTATA-GA
1 GACTTTACCAAAATATTTA-AGATTTACCAATATATCTAACGATTTACT-AAAATATCTA-ACAA
*
15430376 TTTACTAATATTTAT-GAG
63 TTTACTAATATTT-TCAAG
*
15430394 G-CTTTACAAAAAT-TTCTAAGATTTTACCA
1 GACTTTACCAAAATATT-TAAGA-TTTACCA
15430423 TTATTTCCAA
Statistics
Matches: 92, Mismatches: 10, Indels: 15
0.79 0.09 0.13
Matches are distributed among these distances:
78 3 0.03
79 14 0.15
80 54 0.59
81 20 0.22
82 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (80 bp):
GACTTTACCAAAATATTTAAGATTTACCAATATATCTAACGATTTACTAAAATATCTAACAATTT
ACTAATATTTTCAAG
Found at i:15430627 original size:26 final size:25
Alignment explanation
Indices: 15430598--15430646 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
15430588 ATATCTAACA
15430598 ATTTACTAAAATAATA-AACATTTTGG
1 ATTTAC-AAAAT-ATAGAACATTTTGG
*
15430624 ATTTACCAAATATAGAACATTTT
1 ATTTACAAAATATAGAACATTTT
15430647 ACCAAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 12 0.57
26 6 0.29
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (25 bp):
ATTTACAAAATATAGAACATTTTGG
Found at i:15430810 original size:16 final size:16
Alignment explanation
Indices: 15430789--15430843 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
15430779 GTTTGGTTCG
15430789 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAA
* *
15430805 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAA
15430821 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAA
15430837 CTGTAAT
1 CTGTAAT
15430844 AGTAATTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAA
Found at i:15430918 original size:44 final size:45
Alignment explanation
Indices: 15430825--15430918 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 45
15430815 ATAGAGCTGT
* * * *
15430825 AATGGAATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGG
1 AATGAAATAGAACTGTAATAGTAATTCAATTGTTTGATTAAATAG
*
15430870 AATGAAATAGAACTGTAATAGT-ATTC-TTGTGTTTGATTAAATAG
1 AATGAAATAGAACTGTAATAGTAATTCAAT-TGTTTGATTAAATAG
15430914 AATGA
1 AATGA
15430919 TGTTGTAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.49
45 21 0.49
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.36
Consensus pattern (45 bp):
AATGAAATAGAACTGTAATAGTAATTCAATTGTTTGATTAAATAG
Found at i:15436538 original size:20 final size:20
Alignment explanation
Indices: 15436513--15436561 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
15436503 GACCAAAGAG
15436513 AAAATTTATAT-TGATATATA
1 AAAATTTATATAT-ATATATA
* *
15436533 AAAATTCAAATATATATATA
1 AAAATTTATATATATATATA
*
15436553 AATATTTAT
1 AAAATTTAT
15436562 GCAAGAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAATTTATATATATATATA
Found at i:15439784 original size:23 final size:23
Alignment explanation
Indices: 15439748--15439806 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
15439738 TTATCTCATT
15439748 TTTTATTTTA-TTTTTTATTTTA
1 TTTTATTTTATTTTTTTATTTTA
*
15439770 TTTTACTTTATTTTTTTATTTTA
1 TTTTATTTTATTTTTTTATTTTA
15439793 TTTTATTTTATTTT
1 TTTTATTTTATTTT
15439807 GTGGTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 9 0.26
23 25 0.74
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTATTTTATTTTTTTATTTTA
Found at i:15439786 original size:18 final size:17
Alignment explanation
Indices: 15439746--15439801 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 17
15439736 TATTATCTCA
15439746 TTTTTTATTTTATTT-T
1 TTTTTTATTTTATTTAT
15439762 TTATTTTATTTTACTTTAT
1 TT-TTTTATTTTA-TTTAT
15439781 TTTTTTATTTTATTTTAT
1 TTTTTTATTTTA-TTTAT
15439799 TTT
1 TTT
15439802 ATTTTGTGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
16 2 0.06
17 10 0.28
18 21 0.58
19 3 0.08
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTATTTTATTTAT
Found at i:15439793 original size:28 final size:27
Alignment explanation
Indices: 15439749--15439802 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
15439739 TATCTCATTT
15439749 TTTATTTTATTTTTTATTTTATTTTAC
1 TTTATTTTATTTTTTATTTTATTTTAC
*
15439776 TTTATTTTTTTATTTTATTTTATTTTA
1 TTTATTTTATT-TTTTATTTTATTTTA
15439803 TTTTGTGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTATTTTATTTTTTATTTTATTTTAC
Found at i:15439819 original size:5 final size:5
Alignment explanation
Indices: 15439748--15439806 Score: 77
Period size: 5 Copynumber: 11.8 Consensus size: 5
15439738 TTATCTCATT
*
15439748 TTTTA TTTTA TTTTTTA TTTTA TTTTA CTTTA -TTT- TTTTA TTTTA TTTTA
1 TTTTA TTTTA --TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
15439798 TTTTA TTTT
1 TTTTA TTTT
15439807 GTGGTATTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
4 6 0.12
5 38 0.78
7 5 0.10
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:15439822 original size:33 final size:34
Alignment explanation
Indices: 15439745--15439822 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 34
15439735 TTATTATCTC
*
15439745 ATTTT-TTATTTTATTTTTTATTTTATTTTACTTT
1 ATTTTATTATTTTA-TTTTTATTTTATTTTACTGT
* *
15439779 ATTTTTTTATTTTA-TTTTATTTTATTTT-GTGGT
1 ATTTTATTATTTTATTTTTATTTTATTTTACT-GT
15439812 ATTTTATTATT
1 ATTTTATTATT
15439823 CCTTTTATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 1 0.03
33 25 0.64
34 5 0.13
35 8 0.21
ACGTcount: A:0.18, C:0.01, G:0.04, T:0.77
Consensus pattern (34 bp):
ATTTTATTATTTTATTTTTATTTTATTTTACTGT
Found at i:15452878 original size:15 final size:15
Alignment explanation
Indices: 15452858--15452887 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15452848 GGATCCTGGT
15452858 ATTTCTGGGTTGAGA
1 ATTTCTGGGTTGAGA
15452873 ATTTCTGGGTTGAGA
1 ATTTCTGGGTTGAGA
15452888 TGCCTTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (15 bp):
ATTTCTGGGTTGAGA
Found at i:15453389 original size:26 final size:26
Alignment explanation
Indices: 15453362--15453412 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 26
15453352 AGTTAATAAA
15453362 TTCTCTTTGAGTTTTCTTTT-CAAGAAT
1 TTCTC-TTGAG-TTTCTTTTACAAGAAT
15453389 TTCTCTTGAGTTTCTTTTACAAGA
1 TTCTCTTGAGTTTCTTTTACAAGA
15453413 GTTTTAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.35
26 10 0.43
27 5 0.22
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.53
Consensus pattern (26 bp):
TTCTCTTGAGTTTCTTTTACAAGAAT
Found at i:15457326 original size:31 final size:30
Alignment explanation
Indices: 15457281--15457360 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
15457271 ACCCTCTCTT
*
15457281 TTTAAATCAAAATTAAAGTTTTAATTATATA
1 TTTAAATC-AAATTAAAGTTTTAAGTATATA
* * *
15457312 TTTAAATTATAATTAGAGTTTTACGTATATA
1 TTTAAATCA-AATTAAAGTTTTAAGTATATA
*
15457343 -TTACATCAAATTAAAGTT
1 TTTAAATCAAATTAAAGTT
15457361 CATGTGTATA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 9 0.22
30 7 0.17
31 25 0.61
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (30 bp):
TTTAAATCAAATTAAAGTTTTAAGTATATA
Found at i:15457644 original size:20 final size:21
Alignment explanation
Indices: 15457603--15457645 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
15457593 AATTCTTTAA
15457603 TTTATAATATTTTAAAAGGAT
1 TTTATAATATTTTAAAAGGAT
*
15457624 TTTATTATATTTTAAAA-GAT
1 TTTATAATATTTTAAAAGGAT
15457644 TT
1 TT
15457646 AAAACCCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTATAATATTTTAAAAGGAT
Found at i:15465515 original size:25 final size:25
Alignment explanation
Indices: 15465441--15465515 Score: 96
Period size: 26 Copynumber: 2.9 Consensus size: 25
15465431 ACGAATTTTC
*
15465441 TCAAAATTTTACCAGGAATAAAATCA
1 TCAAAATTTTACCAGG-GTAAAATCA
* *
15465467 TCAAAATTTTATCGAGGGTAAAATCG
1 TCAAAATTTTA-CCAGGGTAAAATCA
*
15465493 TCAAAATTTTACTAGGGTAAAAT
1 TCAAAATTTTACCAGGGTAAAAT
15465516 TGGGTGAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 11 0.25
26 29 0.66
27 4 0.09
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (25 bp):
TCAAAATTTTACCAGGGTAAAATCA
Found at i:15465800 original size:173 final size:173
Alignment explanation
Indices: 15465511--15465853 Score: 596
Period size: 173 Copynumber: 2.0 Consensus size: 173
15465501 TTACTAGGGT
* * *
15465511 AAAATTGGGTGAGAAAATTATTTAATATGTAGATATTAAAGTTTATTTTGGGAAATAAAAAAACT
1 AAAATTGAGTGAGAAAATTATTTAATATGTAGATATTAAAGTTTATTTTAGAAAATAAAAAAACT
* * *
15465576 AAATCGGGTTGGATCATATTACAGGTACTCGGTCAAAACGGTTCAAGAAGTACTCGTAATTGAAC
66 AAATCGGGTTGGATCATATTACAAGTACTCAGTCAAAAAGGTTCAAGAAGTACTCGTAATTGAAC
*
15465641 CCGATGTGAGAAAGGCCCAAAATCCCTCATATAACATGAAAGG
131 CCGATGTGAGAAAGGCCCAAAACCCCTCATATAACATGAAAGG
*
15465684 AAAATTGAGTGAGAAAATTATTTAATATGTAGATATTAAAGTTTATTTTAGAAAATAGAAAAACT
1 AAAATTGAGTGAGAAAATTATTTAATATGTAGATATTAAAGTTTATTTTAGAAAATAAAAAAACT
* *
15465749 AAATCGGGTTGGATCATATTACAAGTACTCAGTCAAAAATGTTCAAGAAGTACTTGTAATTGAAC
66 AAATCGGGTTGGATCATATTACAAGTACTCAGTCAAAAAGGTTCAAGAAGTACTCGTAATTGAAC
15465814 CCGATGTGAGAAAGGCCCAAAACCCCTCATATAACATGAA
131 CCGATGTGAGAAAGGCCCAAAACCCCTCATATAACATGAA
15465854 GGGGGCGGCA
Statistics
Matches: 160, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
173 160 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (173 bp):
AAAATTGAGTGAGAAAATTATTTAATATGTAGATATTAAAGTTTATTTTAGAAAATAAAAAAACT
AAATCGGGTTGGATCATATTACAAGTACTCAGTCAAAAAGGTTCAAGAAGTACTCGTAATTGAAC
CCGATGTGAGAAAGGCCCAAAACCCCTCATATAACATGAAAGG
Found at i:15467940 original size:40 final size:40
Alignment explanation
Indices: 15467884--15468094 Score: 226
Period size: 40 Copynumber: 5.3 Consensus size: 40
15467874 AGATCAACTG
* * * * *
15467884 AACACACTAGACAAAAGCTTATAAGAGCTTA-CCAAACCGA
1 AACACACCAAACAGAAGCTCATAAGAGCTGATCC-AACCGA
* * *
15467924 AACACACCAAATAAAAGCTCATAAGAGCTGATTCAACCGA
1 AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCGA
*** **
15467964 AACATGTCAAACAGAAGCTCATAAGAGCTGATCCAATTGA
1 AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCGA
* * * *
15468004 AACACACCAGACAGAAGCTTATAAGAGTTGATCCAACTGA
1 AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCGA
* *
15468044 AACACACCAGACAGAAGCTCATAAAAGCTGATCCAACCGA
1 AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCGA
*
15468084 AACACGCCAAA
1 AACACACCAAA
15468095 TAGAGAGTAT
Statistics
Matches: 143, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
40 142 0.99
41 1 0.01
ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15
Consensus pattern (40 bp):
AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCGA
Found at i:15470732 original size:16 final size:16
Alignment explanation
Indices: 15470663--15470735 Score: 55
Period size: 16 Copynumber: 4.7 Consensus size: 16
15470653 TTCAACTATG
*
15470663 ATTAAAT-TTA-ATCA
1 ATTAAATATTATATTA
* *
15470677 ATTTAATATTAAATTA
1 ATTAAATATTATATTA
* *
15470693 ATATAACAT-TTATCTTG
1 AT-TAA-ATATTATATTA
15470710 A-TAAATATTATATTA
1 ATTAAATATTATATTA
15470725 ATTAAATATTA
1 ATTAAATATTA
15470736 AATCTTATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
14 8 0.18
15 13 0.29
16 14 0.31
17 8 0.18
18 2 0.04
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (16 bp):
ATTAAATATTATATTA
Found at i:15472445 original size:16 final size:16
Alignment explanation
Indices: 15472424--15472454 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15472414 CTATGCATGC
*
15472424 AAAATATAAAAGACAA
1 AAAATAAAAAAGACAA
15472440 AAAATAAAAAAGACA
1 AAAATAAAAAAGACA
15472455 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATAAAAAAGACAA
Found at i:15473395 original size:902 final size:903
Alignment explanation
Indices: 15471651--15473452 Score: 2520
Period size: 902 Copynumber: 2.0 Consensus size: 903
15471641 ATCCAATGAC
* *
15471651 CTCGTCATGTGTGTGTTACCCTCATATGATATCATTGATTCCTTTGAATTAAATCCGTTCACTCA
1 CTCGTCATGTGTGTGTTACCCTCATATGACATCATTGATTCATTTGAATTAAATCCGTTCACTCA
* * * * ** *
15471716 ATACAATCCTATTTTATCTCATTGTAACCATTGTGTCTTCTTAATGATTGATATGGTCACTGTCA
66 ATACAATCCTATTTCATCTCATTATAACCATTGTGTCTTCTTAATAATTAATATAATCACTATCA
* * ** * *
15471781 ACAAATGACTGTGATAAATTGCTCGTTCGAGAACGAGCAACCCGTGGCCACGTTCCATATTTATT
131 ACAAATGACTGTGATAAATTGCTCGTTCGAGAACAAGCAACCCATCACCACGTTCAATATTTATC
* ** *
15471846 AATCCATACAATGCCAATGAGAGGATATCATTAACTCTTTAATTGAGTTATGAATTCCACTGTTG
196 AATCCACACAATGCCAATGAGAGGATATCATTAACTCTTTAATCAAGCTATGAATTCCACTGTTG
* *
15471911 CTAGTAAAGACATGCCATACACAAGTCATGTACCCAACATACCGGCAATGAGCTCGATCATCTTT
261 CTAGTAAAGACATGCCATACAAAAGTCATGTACCCAACATACCGGCAATGAGCTCAATCATCTTT
* ** * * * * *
15471976 AGAGTATAAGCCTTCACTTATATCAAAGCACATGAGTTGCACACGCATGGTCAGTGACTAACTCA
326 AGAGCATAAAACTTCACCTATATCAAAGCACATGAGTTACACACACATGGTCAATAACTAACTCA
* * *
15472041 GGATTTAGGTAAATTACACCATGAACATGACAAGTGAATTAATTCACAAACGGATTTAGAATTAA
391 GGATTTAGGTAAATAACACCATGAACATCACAAGTGAATTAATTCACAAACGGATTCAGAATTAA
* ** * *
15472106 TTCATCTTGTGTCTAGTCTTATGTATCATTCTAAAAATGAATGCATCAATGTCTCTACTCGTGGA
456 TTCATCTTGGGTCTAGTCCAATGTATCATTCTAAAAATGAATACATCAATGTCTCTACCCGTGGA
* * * * ** *
15472171 GTCAACTACTCGGATAGCCAAGACTAGTCATCTTTTCAATTGGGATTGTAGACGACATAATAATC
521 GTCAACTACTCAGATAACCAAGACTAGTCATCTCTCCAATTGAAATTGTAGACGACAAAATAATC
* ** * *
15472236 TTTCTCGGTATTTGAATCAAATACTCATTTTGATTCTTTTACGGGATTACGAACTCATTTAGATT
586 CTTCTAAGAATTTGAATCAAATACTCACTTTGATTCTTTTACGGGATTACGAACTCATTTAGATT
* * * * * *
15472301 ATCTATTGAAGTAAGTTGTCTTTTTCGTAATGTAAACATTTTTTACAATGCCACTTATGTTCAGT
651 ATCTACTAAAGTAAGTTATCTTTTTCGCAATATAAACATTTTTTACAATGCCACTTATCTTCAGT
15472366 TTAAACTTTAGACAATCAATGAGCTAATATTTGCTTGTCACAATTTCGCTATGCATGCAAAATAT
716 TTAAACTTTAGACAATCAATGAGCTAATATTTGCTTGTCACAATTTCGCTATGCATGCAAAATAT
15472431 AAAAGACAAAAAATAAAAAAGACATAATAGTGAAATGTGAAATTAAATTTATTTATTTATTTA-C
781 AAAAGACAAAAAATAAAAAAGACATAATAGTGAAATGTGAAATTAAA--TATTTATTTATTTATC
15472495 -CGTTCAAATAAATAGAAAACAATTACATGTTTACTACAATATGGGCACATTTTCTAGCA
844 ACGTTCAAATAAATAGAAAACAATTACATGTTTACTACAATATGGGCACATTTTCTAGCA
* * **
15472554 CTCGTCATGTGTGTGTTACCCTCATATGACATCCTTGATTCATTTGAGTTAAATTTGTTCACTCA
1 CTCGTCATGTGTGTGTTACCCTCATATGACATCATTGATTCATTTGAATTAAATCCGTTCACTCA
* * *
15472619 ATACAATCTTATTTCATCTCATTATCACCATTGTGTCTTCTTAATAATTAATATAATCATTATCA
66 ATACAATCCTATTTCATCTCATTATAACCATTGTGTCTTCTTAATAATTAATATAATCACTATCA
* * *
15472684 ACAAATGACTGTGATAAATTGCTTGTTTGAGAACAAGCAACCTATCACCACGTTCAATATTTATC
131 ACAAATGACTGTGATAAATTGCTCGTTCGAGAACAAGCAACCCATCACCACGTTCAATATTTATC
* * * * *
15472749 AATCCACATAATGCCAAT-AGGAGTATATCGTTAACTCTTTAATCAAGCTATGAATTCCATTTTT
196 AATCCACACAATGCCAATGA-GAGGATATCATTAACTCTTTAATCAAGCTATGAATTCCACTGTT
* * * * *
15472813 TCTAGTAAAGCCATGCCATACAAAAGTCATGTACCCAACATATCGGCTATGGGCTCAATCATCTT
260 GCTAGTAAAGACATGCCATACAAAAGTCATGTACCCAACATACCGGCAATGAGCTCAATCATCTT
* *
15472878 TAGAGCATAAAACTTC-CCTATATTAAAGCACATGAGTTACATACACATGGTCAATAACTAACTC
325 TAGAGCATAAAACTTCACCTATATCAAAGCACATGAGTTACACACACATGGTCAATAACTAACTC
* * * * *
15472942 TGGATTTAGGTAGATAATACCATTAACGTCACAAGTGAATTAATTCACAAACGGATTCAGAATTA
390 AGGATTTAGGTAAATAACACCATGAACATCACAAGTGAATTAATTCACAAACGGATTCAGAATTA
*** *
15473007 ATTCATCTTGGGTCTAGTCCAATGTATCATTCTTCCAATGAATACATCTATGTCTCTACCCGTGG
455 ATTCATCTTGGGTCTAGTCCAATGTATCATTCTAAAAATGAATACATCAATGTCTCTACCCGTGG
* * * *
15473072 AGTCAATTGCTCAGATAACTAAGACTAGTCATCTCTCCAATTGAAATTTTAGACGACAAAATAAT
520 AGTCAACTACTCAGATAACCAAGACTAGTCATCTCTCCAATTGAAATTGTAGACGACAAAATAAT
* *
15473137 CCTTCTAAGAATTTGAATCAAATGCTCACTTTGATTTTTTTACGGGATTAC-AGACTCATTTAGA
585 CCTTCTAAGAATTTGAATCAAATACTCACTTTGATTCTTTTACGGGATTACGA-ACTCATTTAGA
* ***
15473201 TTATCTACTAAAGTAAGTTATCTTTTTTGCAATATAATTGTTTTTTACAATGCCACTTATCTTCA
649 TTATCTACTAAAGTAAGTTATCTTTTTCGCAATATAAACATTTTTTACAATGCCACTTATCTTCA
* * *
15473266 GTTTGAACTTTAGACAATCAATGAGCTAATATTTGCTTGTCACAATTTCGCTATGCGTGTAAAAT
714 GTTTAAACTTTAGACAATCAATGAGCTAATATTTGCTTGTCACAATTTCGCTATGCATGCAAAAT
* *
15473331 ATAAAAGACAAAAAATAATAAAAAAATACATAATAGTGAAATGTGAAATT-AA-CTTTATTTATT
779 ATAAAAGAC--AAAA-AAT-AAAAAAGACATAATAGTGAAATGTGAAATTAAATATTTATTTATT
* * * *
15473394 TATTCATCGTTCAAATACATAGAAAATAATTACATGTTTACTACAATATGTGCATATTT
840 TA-TCA-CGTTCAAATAAATAGAAAACAATTACATGTTTACTACAATATGGGCACATTT
15473453 CCCAATAGTA
Statistics
Matches: 784, Mismatches: 105, Indels: 17
0.87 0.12 0.02
Matches are distributed among these distances:
901 1 0.00
902 402 0.51
903 294 0.38
904 5 0.01
905 5 0.01
906 77 0.10
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (903 bp):
CTCGTCATGTGTGTGTTACCCTCATATGACATCATTGATTCATTTGAATTAAATCCGTTCACTCA
ATACAATCCTATTTCATCTCATTATAACCATTGTGTCTTCTTAATAATTAATATAATCACTATCA
ACAAATGACTGTGATAAATTGCTCGTTCGAGAACAAGCAACCCATCACCACGTTCAATATTTATC
AATCCACACAATGCCAATGAGAGGATATCATTAACTCTTTAATCAAGCTATGAATTCCACTGTTG
CTAGTAAAGACATGCCATACAAAAGTCATGTACCCAACATACCGGCAATGAGCTCAATCATCTTT
AGAGCATAAAACTTCACCTATATCAAAGCACATGAGTTACACACACATGGTCAATAACTAACTCA
GGATTTAGGTAAATAACACCATGAACATCACAAGTGAATTAATTCACAAACGGATTCAGAATTAA
TTCATCTTGGGTCTAGTCCAATGTATCATTCTAAAAATGAATACATCAATGTCTCTACCCGTGGA
GTCAACTACTCAGATAACCAAGACTAGTCATCTCTCCAATTGAAATTGTAGACGACAAAATAATC
CTTCTAAGAATTTGAATCAAATACTCACTTTGATTCTTTTACGGGATTACGAACTCATTTAGATT
ATCTACTAAAGTAAGTTATCTTTTTCGCAATATAAACATTTTTTACAATGCCACTTATCTTCAGT
TTAAACTTTAGACAATCAATGAGCTAATATTTGCTTGTCACAATTTCGCTATGCATGCAAAATAT
AAAAGACAAAAAATAAAAAAGACATAATAGTGAAATGTGAAATTAAATATTTATTTATTTATCAC
GTTCAAATAAATAGAAAACAATTACATGTTTACTACAATATGGGCACATTTTCTAGCA
Found at i:15474561 original size:29 final size:30
Alignment explanation
Indices: 15474524--15474582 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
15474514 TTTCGTTTTT
*
15474524 TCGACCTAATTCGATAAATTT-TAAAAAAA
1 TCGACCTAATTCGACAAATTTCTAAAAAAA
*
15474553 TCGATCTAATTCGACAAATTTCTAAAAAAA
1 TCGACCTAATTCGACAAATTTCTAAAAAAA
15474583 ATTGGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (30 bp):
TCGACCTAATTCGACAAATTTCTAAAAAAA
Found at i:15475917 original size:3 final size:3
Alignment explanation
Indices: 15475909--15475936 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15475899 ACATGTAACT
15475909 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
15475937 CATTTCAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:15483696 original size:15 final size:15
Alignment explanation
Indices: 15483647--15483697 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
15483637 ATTTGTTTCA
*
15483647 TTACATTTTAGTAAT
1 TTACGTTTTAGTAAT
* *
15483662 TTATG-TTT-GAAAT
1 TTACGTTTTAGTAAT
15483675 ATTACGTTTTAGTAAT
1 -TTACGTTTTAGTAAT
15483691 TTACGTT
1 TTACGTT
15483698 ATCTTTTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 4 0.14
14 7 0.25
15 13 0.46
16 4 0.14
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (15 bp):
TTACGTTTTAGTAAT
Found at i:15494106 original size:17 final size:17
Alignment explanation
Indices: 15494080--15494116 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
15494070 ATAATTCAAC
*
15494080 AAATTTTAAAAAATAAA
1 AAATTCTAAAAAATAAA
15494097 AAATTCTAAAAAATAAA
1 AAATTCTAAAAAATAAA
15494114 AAA
1 AAA
15494117 AATTATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATTCTAAAAAATAAA
Found at i:15494116 original size:19 final size:19
Alignment explanation
Indices: 15494080--15494136 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 19
15494070 ATAATTCAAC
*
15494080 AAATTTTAAAAAAT--AAA
1 AAATTATAAAAAATAAAAA
*
15494097 AAATTCTAAAAAATAAAAA
1 AAATTATAAAAAATAAAAA
15494116 AAATTATATAAAAATTAAAAA
1 AAATTATA-AAAAA-TAAAAA
15494137 CAATGTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 13 0.38
19 10 0.29
20 5 0.15
21 6 0.18
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATTATAAAAAATAAAAA
Found at i:15496585 original size:25 final size:24
Alignment explanation
Indices: 15496518--15496594 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 24
15496508 AGCTTCGGAT
*
15496518 AGCCATATAACAGGAAGTTCA-AGAA-
1 AGCCATAT--CAGGAAGCTCACA-AAG
15496543 AGCCATATCAGGAAGCTCACAAAG
1 AGCCATATCAGGAAGCTCACAAAG
* * *
15496567 AGCCTATATCGGGACGCTCATAAAG
1 AGCC-ATATCAGGAAGCTCACAAAG
15496592 AGC
1 AGC
15496595 TGCGGTATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
23 12 0.27
24 5 0.11
25 28 0.62
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (24 bp):
AGCCATATCAGGAAGCTCACAAAG
Found at i:15496680 original size:64 final size:64
Alignment explanation
Indices: 15496578--15496762 Score: 246
Period size: 64 Copynumber: 2.9 Consensus size: 64
15496568 GCCTATATCG
* * * *
15496578 GGACGCTCATAAAGAGCTGCGGTATGTCCGCAATACATGCAGGATTAATACCGATCATATAACA
1 GGACGCTCACAAAGAGCTGCGGTATGTCCTCAACACATGCAGGATAAATACCGATCATATAACA
* *
15496642 GGACGCTCACAAAGAGTTGCGGTATGTCCTCAACACATGCAGGATAAATACTGATCATATAACA
1 GGACGCTCACAAAGAGCTGCGGTATGTCCTCAACACATGCAGGATAAATACCGATCATATAACA
* ** * * *
15496706 GGACGTTCACAAAGAGCAACGGTATATCCAT-AACACATGTAGGATAAATACCTATCA
1 GGACGCTCACAAAGAGCTGCGGTATGTCC-TCAACACATGCAGGATAAATACCGATCA
15496763 GGATGCTCGC
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 105 0.99
65 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (64 bp):
GGACGCTCACAAAGAGCTGCGGTATGTCCTCAACACATGCAGGATAAATACCGATCATATAACA
Found at i:15501730 original size:3 final size:3
Alignment explanation
Indices: 15501722--15501769 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
15501712 GTTACTTTCT
15501722 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
15501770 TGCTTTTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:15515989 original size:13 final size:13
Alignment explanation
Indices: 15515971--15515995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15515961 AAAAGTATTT
15515971 TAAAAATAAAAAA
1 TAAAAATAAAAAA
15515984 TAAAAATAAAAA
1 TAAAAATAAAAA
15515996 TATATATTTA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:15516467 original size:25 final size:25
Alignment explanation
Indices: 15516434--15516501 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
15516424 CTGTAAATGG
15516434 TAAGCTCCTCCGAGCTGAATAACGA
1 TAAGCTCCTCCGAGCTGAATAACGA
*
15516459 TAAGTTCCTCCGAGCTGAATAACGA
1 TAAGCTCCTCCGAGCTGAATAACGA
* *
15516484 TAAGCTCATACGAGCTGA
1 TAAGCTCCTCCGAGCTGA
15516502 GTATAGGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (25 bp):
TAAGCTCCTCCGAGCTGAATAACGA
Found at i:15517822 original size:23 final size:23
Alignment explanation
Indices: 15517792--15517843 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
15517782 TACGGTATTT
15517792 CTGTAATA-TCCCAAAAATTACTA
1 CTGTAATACT-CCAAAAATTACTA
*
15517815 CTGTAATACTCCGAAAATTACTA
1 CTGTAATACTCCAAAAATTACTA
*
15517838 CAGTAA
1 CTGTAA
15517844 GAAATTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (23 bp):
CTGTAATACTCCAAAAATTACTA
Found at i:15518026 original size:30 final size:31
Alignment explanation
Indices: 15517992--15518059 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
15517982 TTGCCCAAGA
** * **
15517992 GTAAATACTCAAAATTTGAGGGATTAA-AGT
1 GTAAATACAAAAAATTTGAAGGACCAATAGT
15518022 GTAAATACAAAAAATTTGAAGGACCAATAGT
1 GTAAATACAAAAAATTTGAAGGACCAATAGT
15518053 GTAAATA
1 GTAAATA
15518060 TTTTAATGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (31 bp):
GTAAATACAAAAAATTTGAAGGACCAATAGT
Found at i:15521990 original size:16 final size:17
Alignment explanation
Indices: 15521969--15522011 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
15521959 AAATAAATCT
*
15521969 TTAAAAATTTATAA-AA
1 TTAAAAATTTAAAATAA
15521985 TTAAAAATATTAAAATAA
1 TTAAAAAT-TTAAAATAA
15522003 TTAAAAATT
1 TTAAAAATT
15522012 GGTATAACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
17 6 0.25
18 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAAAATTTAAAATAA
Found at i:15522280 original size:16 final size:15
Alignment explanation
Indices: 15522255--15522289 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
15522245 TTGGTTAATT
15522255 CAAAATCTTAATTTC
1 CAAAATCTTAATTTC
*
15522270 CAAATATCTTAATTTT
1 CAAA-ATCTTAATTTC
15522286 CAAA
1 CAAA
15522290 CAAAGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (15 bp):
CAAAATCTTAATTTC
Found at i:15522320 original size:7 final size:7
Alignment explanation
Indices: 15522310--15522334 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
15522300 AGAAATAATA
15522310 AAATCAT
1 AAATCAT
15522317 AAATCAT
1 AAATCAT
15522324 AAATCAT
1 AAATCAT
15522331 AAAT
1 AAAT
15522335 TTCAAAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATCAT
Found at i:15528888 original size:14 final size:14
Alignment explanation
Indices: 15528869--15528904 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
15528859 TTGATTGCTA
*
15528869 GTAAAATGTTTTCT
1 GTAAAATGATTTCT
15528883 GTAAAATGATTTCT
1 GTAAAATGATTTCT
*
15528897 GGAAAATG
1 GTAAAATG
15528905 CTTTACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (14 bp):
GTAAAATGATTTCT
Found at i:15529623 original size:108 final size:108
Alignment explanation
Indices: 15529434--15529651 Score: 436
Period size: 108 Copynumber: 2.0 Consensus size: 108
15529424 GATGAAGTAT
15529434 TGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAAT
1 TGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAAT
15529499 GTCTGTACATATTAACAAACTTTAATACAACAATACAACTACA
66 GTCTGTACATATTAACAAACTTTAATACAACAATACAACTACA
15529542 TGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAAT
1 TGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAAT
15529607 GTCTGTACATATTAACAAACTTTAATACAACAATACAACTACA
66 GTCTGTACATATTAACAAACTTTAATACAACAATACAACTACA
15529650 TG
1 TG
15529652 CATGGTATTG
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 110 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (108 bp):
TGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAAT
GTCTGTACATATTAACAAACTTTAATACAACAATACAACTACA
Found at i:15530627 original size:2 final size:2
Alignment explanation
Indices: 15530593--15530618 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15530583 CCATGTATCA
15530593 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
15530619 CCAGAGAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15533992 original size:33 final size:31
Alignment explanation
Indices: 15533939--15534008 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 31
15533929 TTTTTAGAGT
*
15533939 TTTAAATTTTTTTAAAAAA-TTTAGATTATGATA
1 TTTAAACTTTTTTAAAAAATTTTA-A-TAT-ATA
**
15533972 TTTAAACTTTTTTATTAAATTTTAATATATA
1 TTTAAACTTTTTTAAAAAATTTTAATATATA
15534003 TTTAAA
1 TTTAAA
15534009 ATTATGACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 9 0.27
32 3 0.09
33 17 0.52
34 4 0.12
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTAAACTTTTTTAAAAAATTTTAATATATA
Found at i:15535370 original size:9 final size:9
Alignment explanation
Indices: 15535356--15535383 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
15535346 TATAGTTTGA
15535356 TATTCGAAT
1 TATTCGAAT
15535365 TATTCGAAT
1 TATTCGAAT
15535374 TATTCGAAT
1 TATTCGAAT
15535383 T
1 T
15535384 CGAAAACTCA
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:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:15538092 original size:107 final size:107
Alignment explanation
Indices: 15537903--15538299 Score: 609
Period size: 107 Copynumber: 3.7 Consensus size: 107
15537893 TTTCTAATTG
* * *
15537903 AGGCAATGTTTTGCATTTGGAAATTCGAGGGACGTGCCCTAAGGTGCTGGGTTTCGATTTATCGT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGT
* *
15537968 TCAACCAAATGGGTTAATATCCTTTTCAAAAATTACAAAATA
66 TCAACCAAATGGCTTAATATCCTTTTCAAAAATTTCAAAATA
* *
15538010 AGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTAGGTTTTGATTTCTCGT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGT
*
15538075 TCGACCAAATGGCTTAATATCCTTTTCAAAAATTTCAAAATA
66 TCAACCAAATGGCTTAATATCCTTTTCAAAAATTTCAAAATA
* * *
15538117 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTTTCGA--TTTCT
* *
15538182 CGTTCAACCAAATAGCTAAATATCC-TTTC-AAAATTTCAAAATA
63 CGTTCAACCAAATGGCTTAATATCCTTTTCAAAAATTTCAAAATA
* *
15538225 AGGCAATGTTTTGCGTTTGGAAATTCGGGGAACGTGCCCTAGGGTGCTGGGTTTCGATTTCTCGT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGT
*
15538290 TTAACCAAAT
66 TCAACCAAAT
15538300 TGCCAAATAT
Statistics
Matches: 265, Mismatches: 22, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
105 17 0.06
107 152 0.57
108 65 0.25
109 4 0.02
110 27 0.10
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (107 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGT
TCAACCAAATGGCTTAATATCCTTTTCAAAAATTTCAAAATA
Found at i:15538286 original size:215 final size:214
Alignment explanation
Indices: 15537903--15538299 Score: 609
Period size: 215 Copynumber: 1.9 Consensus size: 214
15537893 TTTCTAATTG
** * *
15537903 AGGCAATGTTTTGCATTTGGAAATTCGAGGGACGTGCCCTAAGGTGCTGGGTTTCGATTTATCGT
1 AGGCAATGTTTTGCATTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGATTTATCGT
* * *
15537968 TCAACCAAATGGGTTAATATCCTTTTCAAAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAA
66 TCAACCAAATAGCTAAATATCCTTTTCAAAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAA
* *
15538033 TTCGAGGAACGTGCCCTAAGGTGCTAGGTTTTGATTTCTCGTTCGACCAAATGGCTTAATATCCT
131 TTCGAGGAACGTGCCCTAAGGTGCTAGGTTTCGATTTCTCGTTCAACCAAATGGCTTAATATCCT
15538098 TTTCAAAAATTTCAAAATA
196 TTTCAAAAATTTCAAAATA
* *
15538117 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCATTTGGAAATTCGAG-AAACATGCCCTAAGGTGCTGGGTGTCGA--TTTAT
*
15538182 CGTTCAACCAAATAGCTAAATATCC-TTTC-AAAATTTCAAAATAAGGCAATGTTTTGCGTTTGG
63 CGTTCAACCAAATAGCTAAATATCCTTTTCAAAAATTACAAAATAAGGCAATGTTTTGCGTTTGG
* * * *
15538245 AAATTCGGGGAACGTGCCCTAGGGTGCTGGGTTTCGATTTCTCGTTTAACCAAAT
128 AAATTCGAGGAACGTGCCCTAAGGTGCTAGGTTTCGATTTCTCGTTCAACCAAAT
15538300 TGCCAAATAT
Statistics
Matches: 164, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
214 28 0.17
215 106 0.65
216 4 0.02
217 26 0.16
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (214 bp):
AGGCAATGTTTTGCATTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGATTTATCGT
TCAACCAAATAGCTAAATATCCTTTTCAAAAATTACAAAATAAGGCAATGTTTTGCGTTTGGAAA
TTCGAGGAACGTGCCCTAAGGTGCTAGGTTTCGATTTCTCGTTCAACCAAATGGCTTAATATCCT
TTTCAAAAATTTCAAAATA
Found at i:15545981 original size:29 final size:30
Alignment explanation
Indices: 15545944--15546011 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
15545934 AAAAAAATTA
* *
15545944 TATTTAATT-ACATTGAATCAAAGTTCATG
1 TATTAAATTCACATTGAATCAAAATTCATG
* *
15545973 TATTAAATTGCACATTGGATCAAAATTTATG
1 TATTAAATT-CACATTGAATCAAAATTCATG
15546004 TA-TAAATT
1 TATTAAATT
15546012 TGAAATTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.24
30 6 0.18
31 19 0.58
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (30 bp):
TATTAAATTCACATTGAATCAAAATTCATG
Found at i:15545995 original size:31 final size:30
Alignment explanation
Indices: 15545953--15546011 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
15545943 ATATTTAATT
*
15545953 ACATTGAATCAAAGTTCATGTATTAAATTGC
1 ACATTGAATCAAAATTCATGTA-TAAATTGC
* *
15545984 ACATTGGATCAAAATTTATGTATAAATT
1 ACATTGAATCAAAATTCATGTATAAATT
15546012 TGAAATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (30 bp):
ACATTGAATCAAAATTCATGTATAAATTGC
Found at i:15546437 original size:21 final size:22
Alignment explanation
Indices: 15546411--15546463 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
15546401 CATTGTTTCT
*
15546411 AATCTCAAC-GCTACAGTATCC
1 AATCTCAACTGCTACAGTAACC
*
15546432 AATCTC-ACTGCTACAGTAACT
1 AATCTCAACTGCTACAGTAACC
15546453 AATCTC-ACTGC
1 AATCTCAACTGC
15546464 CACCGCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.26
Consensus pattern (22 bp):
AATCTCAACTGCTACAGTAACC
Found at i:15553587 original size:16 final size:16
Alignment explanation
Indices: 15553540--15553577 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
15553530 TATATATAAC
* *
15553540 ATATTTAATATAAGTA
1 ATATTTAAAATAAATA
15553556 ATATTTAAAATAAATA
1 ATATTTAAAATAAATA
15553572 ATATTT
1 ATATTT
15553578 TACAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
ATATTTAAAATAAATA
Found at i:15558343 original size:21 final size:21
Alignment explanation
Indices: 15558275--15558343 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
15558265 CATAGAAGCA
* * *
15558275 CATAAGTGCTAAACAGAAACC
1 CATAAGAGCTGAACGGAAACC
* * *
15558296 CATAAGGGTTGAA-GGAAAGCT
1 CATAAGAGCTGAACGGAAA-CC
*
15558317 CGTAAGAGCTGAACGGAAACC
1 CATAAGAGCTGAACGGAAACC
15558338 CATAAG
1 CATAAG
15558344 GGTTAAATTG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
20 4 0.11
21 27 0.75
22 5 0.14
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (21 bp):
CATAAGAGCTGAACGGAAACC
Found at i:15558366 original size:42 final size:42
Alignment explanation
Indices: 15558290--15558444 Score: 206
Period size: 42 Copynumber: 3.7 Consensus size: 42
15558280 GTGCTAAACA
* * **
15558290 GAAACCCATAAGGGTTGAA-GGAAAGCTCGTAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACTG-AAGCTCAAAAGAGCTGAACG
* * *
15558332 GAAACCCATAAGGGTTAAATTGAAGTTCAAAAGAGCTAAAC-
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
15558373 GATAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
1 GA-AACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
*
15558416 GAAACCCATAAGGGTTAAACTGAAACTCA
1 GAAACCCATAAGGGTTAAACTGAAGCTCA
15558445 TATGAGTGGA
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
41 2 0.02
42 95 0.95
43 3 0.03
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
Found at i:15558423 original size:84 final size:84
Alignment explanation
Indices: 15558282--15558439 Score: 239
Period size: 84 Copynumber: 1.9 Consensus size: 84
15558272 GCACATAAGT
* **
15558282 GCTAAACAGAAACCCATAAGGGTTGAAGGAAAGCTCGTAAGAGCTGAACGGAAACCCATAAGGGT
1 GCTAAACAGAAACCCATAAGGGTTAAAGGAAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGT
*
15558347 TAAATTGAAGTTCAAAAGA
66 TAAACTGAAGTTCAAAAGA
*
15558366 GCTAAAC-GATAACCCATAAGGGTTAAACTG-AAGCTCAAAAGAGCTGAACGGAAACCCATAAGG
1 GCTAAACAGA-AACCCATAAGGGTTAAA-GGAAAGCTCAAAAGAGCTGAACGGAAACCCATAAGG
15558429 GTTAAACTGAA
64 GTTAAACTGAA
15558440 ACTCATATGA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
83 2 0.03
84 64 0.96
85 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.16
Consensus pattern (84 bp):
GCTAAACAGAAACCCATAAGGGTTAAAGGAAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGT
TAAACTGAAGTTCAAAAGA
Found at i:15558446 original size:21 final size:21
Alignment explanation
Indices: 15558332--15558446 Score: 79
Period size: 21 Copynumber: 5.5 Consensus size: 21
15558322 GAGCTGAACG
*
15558332 GAAACCCATAAGGGTTAAATT
1 GAAACCCATAAGGGTTAAACT
*** * * *
15558353 GAAGTTCAAAAGAGCTAAAC-
1 GAAACCCATAAGGGTTAAACT
15558373 GATAACCCATAAGGGTTAAACT
1 GA-AACCCATAAGGGTTAAACT
* * * * * * *
15558395 GAAGCTCAAAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACT
15558416 GAAACCCATAAGGGTTAAACT
1 GAAACCCATAAGGGTTAAACT
*
15558437 GAAACTCATA
1 GAAACCCATA
15558447 TGAGTGGACT
Statistics
Matches: 64, Mismatches: 28, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
20 2 0.03
21 60 0.94
22 2 0.03
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.18
Consensus pattern (21 bp):
GAAACCCATAAGGGTTAAACT
Found at i:15564879 original size:14 final size:14
Alignment explanation
Indices: 15564860--15564899 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
15564850 TTGATTGCCA
15564860 GTAAAATGTTTTCT
1 GTAAAATGTTTTCT
*
15564874 GTAAAATGATTTCT
1 GTAAAATGTTTTCT
*
15564888 GGAAAATGTTTT
1 GTAAAATGTTTT
15564900 ATTTTTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (14 bp):
GTAAAATGTTTTCT
Found at i:15564908 original size:20 final size:20
Alignment explanation
Indices: 15564883--15564920 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15564873 TGTAAAATGA
*
15564883 TTTCTGGAAAATGTTTTATT
1 TTTCTGGAAAATGATTTATT
*
15564903 TTTCTGTAAAATGATTTA
1 TTTCTGGAAAATGATTTA
15564921 CTGGAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTATT
Found at i:15564911 original size:34 final size:35
Alignment explanation
Indices: 15564868--15564934 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
15564858 CAGTAAAATG
*
15564868 TTTTCTGTAAAATGATTT-CTGGAAAATGTTTTAT
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTTAT
15564902 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
15564935 CTGATGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.49
Consensus pattern (35 bp):
TTTTCTGTAAAATGATTTACTGGAAAATATTTTAT
Found at i:15564999 original size:32 final size:32
Alignment explanation
Indices: 15564915--15565000 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 32
15564905 TCTGTAAAAT
* **
15564915 GATTTACTGGAAAATATTTTCTGATGTTTGATT
1 GATTT-CTTGAAAATATTTTCTGATGTTTGACA
* *
15564948 GA-ATCTGTGTAAAATATTTTCTGCTGTTTGACA
1 GATTTCT-TG-AAAATATTTTCTGATGTTTGACA
15564981 GATTTCTTGAAAATATTTTC
1 GATTTCTTGAAAATATTTTC
15565001 CGGAAAAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
31 2 0.05
32 13 0.30
33 26 0.59
34 3 0.07
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (32 bp):
GATTTCTTGAAAATATTTTCTGATGTTTGACA
Found at i:15565425 original size:41 final size:41
Alignment explanation
Indices: 15565380--15565463 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
15565370 ATGGTAATCG
15565380 AACATCTCTCTTAAGATCATCAAATGTTTTGTGAGAGTCAA
1 AACATCTCTCTTAAGATCATCAAATGTTTTGTGAGAGTCAA
15565421 AACATCTCTCTTAAGATCATCAAATGTTTTGTGAGAGTCAA
1 AACATCTCTCTTAAGATCATCAAATGTTTTGTGAGAGTCAA
15565462 AA
1 AA
15565464 TTTCTAATGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (41 bp):
AACATCTCTCTTAAGATCATCAAATGTTTTGTGAGAGTCAA
Found at i:15565693 original size:111 final size:111
Alignment explanation
Indices: 15565499--15565720 Score: 435
Period size: 111 Copynumber: 2.0 Consensus size: 111
15565489 TGATGAAGTA
15565499 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCAAATAAACATACACTACTTTTTCTAAA
1 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCAAATAAACATACACTACTTTTTCTAAA
15565564 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
66 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
*
15565610 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCATATAAACATACACTACTTTTTCTAAA
1 TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCAAATAAACATACACTACTTTTTCTAAA
15565675 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
66 TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
15565721 CATGGTATTG
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (111 bp):
TTGTTGTCTAAGAGAGAGAGTAGTGATATATGTATACCAAATAAACATACACTACTTTTTCTAAA
TGTCTGTACATATTAACAAACTTTAATACAACAATACAACTACATG
Found at i:15574108 original size:18 final size:19
Alignment explanation
Indices: 15574087--15574122 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15574077 CTATTTTTCT
15574087 GAATTTT-CATAATATTTA
1 GAATTTTACATAATATTTA
*
15574105 GAATTTTATATAATATTT
1 GAATTTTACATAATATTT
15574123 TTATTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (19 bp):
GAATTTTACATAATATTTA
Found at i:15575397 original size:14 final size:15
Alignment explanation
Indices: 15575378--15575408 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
15575368 AACACAAAGG
15575378 TTAATACTC-AATAC
1 TTAATACTCAAATAC
15575392 TTAATACTCAAATAC
1 TTAATACTCAAATAC
15575407 TT
1 TT
15575409 TCTATCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAATACTCAAATAC
Found at i:15588163 original size:32 final size:32
Alignment explanation
Indices: 15588094--15588168 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
15588084 AAAAAGTGAC
*
15588094 TTGTCATTTAACCAGCCACGTTGGAGTCCTTA
1 TTGTCATTTAACCAGCCACGTTGGAGGCCTTA
* * * ** *
15588126 CTGTCATTTAATCGGCCACGTTGGAGGGTTTG
1 TTGTCATTTAACCAGCCACGTTGGAGGCCTTA
15588158 TTGTCATTTAA
1 TTGTCATTTAA
15588169 ACAATAGTAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (32 bp):
TTGTCATTTAACCAGCCACGTTGGAGGCCTTA
Found at i:15590576 original size:17 final size:18
Alignment explanation
Indices: 15590556--15590591 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15590546 TTTTTAAAAA
15590556 TATAAAT-TTTAAATTTT
1 TATAAATATTTAAATTTT
*
15590573 TATAAATATTTTAATTTT
1 TATAAATATTTAAATTTT
15590591 T
1 T
15590592 TGAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATAAATATTTAAATTTT
Found at i:15590602 original size:20 final size:19
Alignment explanation
Indices: 15590561--15590613 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
15590551 AAAAATATAA
*
15590561 ATTTTAAATTTTTATAAAT
1 ATTTTAATTTTTTATAAAT
15590580 ATTTTAATTTTTTGA-AAATT
1 ATTTTAATTTTTT-ATAAA-T
15590600 ATTTTGAATTTTTT
1 ATTTT-AATTTTTT
15590614 TTGTAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 15 0.50
20 7 0.23
21 8 0.27
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
ATTTTAATTTTTTATAAAT
Found at i:15591871 original size:311 final size:303
Alignment explanation
Indices: 15591312--15591871 Score: 703
Period size: 311 Copynumber: 1.8 Consensus size: 303
15591302 TCAATCAAGA
* * * * * * * *
15591312 TTCATTTTGATGCGTTTTATACATTTTTTGTTTTAATATGCACATTTTATTATCTCCGTCTGTAT
1 TTCATTTTAATGCATTTTATACAGTTTTTATTTTAATATGCACAATTCAGTATCTCCATCTGTAT
* * *
15591377 ATCTATACTTATATATTATTATTAAAGCCCTTGACTGAATTGGTGTAATGAGTCAACCGCGCACC
66 ATCTATACTTATATATTATTATTAAAGCCCATGACTGAATTGGTGTAACGAGTCAACCGAGCACC
* *
15591442 AACTTGATAGAGAAATTATGAAAATGCCATTTCATATTTAAAATAAGTTATATTATTTGATGGCA
131 AACTTGATAGAGAAATTATAAAAATGCC--TTCATATTTAAAATAAGTTATATTATTTGAAGGCA
15591507 CTTAGTCTTTTTATTTTAACAACCACCAATAAAAATAAAAATATGTATACATATGGTGAAATTTG
194 CTTAGTCTTTTTATTTTAACAACCACCAATAAAAATAAAAATATG-ATACATATGGTGAAATTTG
15591572 AACTCATCGCAATTAGCTTGATAAAACTTCACCATTCAACCAAAGC
258 AACTCATCGCAATTAGCTTGATAAAACTTCACCATTCAACCAAAGC
* *
15591618 TTCATTTTAATGTATTTTATAC-GTTTTTATTTTAATATGCATAATTCAGTATCTCCATCAGTTG
1 TTCATTTTAATGCATTTTATACAGTTTTTATTTTAATATGCACAATTCAGTATCTCCATC---TG
* * * * **
15591682 TATATCTATACTTCTATACTATATTATTTAAGCCCATGATTGAGTTGGTGTAACGAGTCAATTGA
63 TATATCTATACTTATATA-T-TATTATTAAAGCCCATGACTGAATTGGTGTAACGAGTCAACCGA
* * *
15591747 GCACCAACTTGGTTAGAGAAATTATAAAAATGTCC-TCCTGTGCTTAAAATAAGTTATATTATTT
126 GCACCAACTT-GATAGAGAAATTATAAAAATG-CCTTCATAT--TTAAAATAAGTTATATTATTT
* * * ** *
15591811 GAAGGTCACTTAATTTTTTTTATTTTAGCAATGACCAATAAAAATAGAAATATG-TACATAT
187 GAAGG-CACTT-AGTCTTTTTATTTTAACAACCACCAATAAAAATAAAAATATGATACATAT
15591872 ATGTTCGGAT
Statistics
Matches: 213, Mismatches: 30, Indels: 17
0.82 0.12 0.07
Matches are distributed among these distances:
305 30 0.14
306 19 0.09
308 19 0.09
309 5 0.02
310 46 0.22
311 51 0.24
312 7 0.03
313 36 0.17
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (303 bp):
TTCATTTTAATGCATTTTATACAGTTTTTATTTTAATATGCACAATTCAGTATCTCCATCTGTAT
ATCTATACTTATATATTATTATTAAAGCCCATGACTGAATTGGTGTAACGAGTCAACCGAGCACC
AACTTGATAGAGAAATTATAAAAATGCCTTCATATTTAAAATAAGTTATATTATTTGAAGGCACT
TAGTCTTTTTATTTTAACAACCACCAATAAAAATAAAAATATGATACATATGGTGAAATTTGAAC
TCATCGCAATTAGCTTGATAAAACTTCACCATTCAACCAAAGC
Found at i:15592823 original size:28 final size:27
Alignment explanation
Indices: 15592773--15592828 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
15592763 ATACTTTTCT
*
15592773 AATAATATTTTTTTATTTTTTAAATGA
1 AATAATATTTTTTTATTTCTTAAATGA
*
15592800 AATAA-ATTTTTAGTTATTTCTTAATTGA
1 AATAATATTTTT--TTATTTCTTAAATGA
15592828 A
1 A
15592829 TTAGAGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 14 0.56
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (27 bp):
AATAATATTTTTTTATTTCTTAAATGA
Found at i:15603064 original size:35 final size:35
Alignment explanation
Indices: 15603025--15603092 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
15603015 AAATTCTTTT
15603025 TTTTAACTATTATTCATA-AT-TTTATCATTTTAGGA
1 TTTT-ACTATTATT-ATATATATTTATCATTTTAGGA
*
15603060 TTTTATTATTATTATATATATTTATCATTTTAG
1 TTTTACTATTATTATATATATTTATCATTTTAG
15603093 AGAGAGAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 3 0.10
34 10 0.33
35 17 0.57
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (35 bp):
TTTTACTATTATTATATATATTTATCATTTTAGGA
Found at i:15608301 original size:25 final size:26
Alignment explanation
Indices: 15608273--15608383 Score: 81
Period size: 25 Copynumber: 4.4 Consensus size: 26
15608263 ACAGCTCTCT
*
15608273 TGAGCTTCCCGATACTTGGCTC-TAA
1 TGAGCTTCCCGATACTTAGCTCGTAA
* * * *
15608298 TGAGCTTTCCGATAATTGGCTCGCAA
1 TGAGCTTCCCGATACTTAGCTCGTAA
* *
15608324 -AAGCTTCCCGATA-TACAGCTCGT-A
1 TGAGCTTCCCGATACT-TAGCTCGTAA
* *
15608348 TGAGTTTCCCGTTACTTAGCTC--ACA
1 TGAGCTTCCCGATACTTAGCTCGTA-A
15608373 TGAGCTTCCCG
1 TGAGCTTCCCG
15608384 TTATATGCCC
Statistics
Matches: 67, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
24 2 0.03
25 62 0.93
26 3 0.04
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.31
Consensus pattern (26 bp):
TGAGCTTCCCGATACTTAGCTCGTAA
Found at i:15612198 original size:10 final size:10
Alignment explanation
Indices: 15612180--15612212 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
15612170 AAACTAACGT
15612180 GTGGGAAAAA
1 GTGGGAAAAA
15612190 GT-GGAAAAA
1 GTGGGAAAAA
15612199 GTGGGAAAAA
1 GTGGGAAAAA
15612209 -TGGG
1 GTGGG
15612213 GAAAGTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.12
Consensus pattern (10 bp):
GTGGGAAAAA
Found at i:15614009 original size:30 final size:30
Alignment explanation
Indices: 15613973--15614029 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
15613963 TGGGAGGGGA
* * *
15613973 AAGGAGTAAAGGTTTTGGGGGGAAAGTGGG
1 AAGGAGTAAAAGTTTTGAGGGAAAAGTGGG
15614003 AAGGAGTAAAAGTTTTGAGGGAAAAGT
1 AAGGAGTAAAAGTTTTGAGGGAAAAGT
15614030 AAAAAGGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.42, T:0.21
Consensus pattern (30 bp):
AAGGAGTAAAAGTTTTGAGGGAAAAGTGGG
Found at i:15614556 original size:5 final size:5
Alignment explanation
Indices: 15614546--15614586 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
15614536 CAACTTTTTT
15614546 GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC G
1 GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC G
15614587 AATATAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.00, C:0.59, G:0.41, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:15614665 original size:14 final size:14
Alignment explanation
Indices: 15614646--15614672 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
15614636 TTTAAAAATA
15614646 TTTTTATTTTTAAT
1 TTTTTATTTTTAAT
15614660 TTTTTATTTTTAA
1 TTTTTATTTTTAA
15614673 AATATATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTATTTTTAAT
Found at i:15615548 original size:34 final size:34
Alignment explanation
Indices: 15615505--15615685 Score: 254
Period size: 34 Copynumber: 5.3 Consensus size: 34
15615495 GTAAACCCCA
*
15615505 TATGACATAGTATGCGAACCCTCATGTTATGTAG
1 TATGACATAGTATGCGAACCCTCATGTTATATAG
* *
15615539 TATGACATAGTATGCAAACCTTCATGTTATATAG
1 TATGACATAGTATGCGAACCCTCATGTTATATAG
* * *
15615573 AATGACATAATATGCGAACCCTCACGTTATATAG
1 TATGACATAGTATGCGAACCCTCATGTTATATAG
* * *
15615607 TAAGACATAGTATGGGAACCCTTATGTTATATAG
1 TATGACATAGTATGCGAACCCTCATGTTATATAG
* * *
15615641 TAAGACATAGTATGTGAACCCTCATGTTATATGG
1 TATGACATAGTATGCGAACCCTCATGTTATATAG
15615675 TATGACATAGT
1 TATGACATAGT
15615686 GAACTGTTAG
Statistics
Matches: 129, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 129 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (34 bp):
TATGACATAGTATGCGAACCCTCATGTTATATAG
Found at i:15615867 original size:15 final size:15
Alignment explanation
Indices: 15615843--15615885 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
15615833 GTGAATTAGC
* *
15615843 ATGTGTGAACCTTAT
1 ATGTGCGAACCCTAT
15615858 ATGTGCGAACCCTAT
1 ATGTGCGAACCCTAT
**
15615873 ACATGCGAACCCT
1 ATGTGCGAACCCT
15615886 GTATACAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (15 bp):
ATGTGCGAACCCTAT
Found at i:15621280 original size:3 final size:3
Alignment explanation
Indices: 15621272--15621302 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
15621262 CCTGGCCCCC
15621272 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
15621303 TTGCCTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:15622798 original size:3 final size:3
Alignment explanation
Indices: 15622792--15622840 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
15622782 AGAAATAGTA
* * *
15622792 GAT GAT GAT GAT GAT GAT GGT GAT GAT GAT GGA- GAT GAA GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT -GAT GAT GAT GAT GAT
15622837 GAT G
1 GAT G
15622841 GCTTGAGCCA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.39, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:15624411 original size:22 final size:22
Alignment explanation
Indices: 15624344--15624414 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 22
15624334 TAAACAATTC
15624344 ATATATAATATATATAATTTTAAA
1 ATATATAAT-TATA-AATTTTAAA
* ** *
15624368 AAATATTTTTTATAAAACTTTAAA
1 ATATA-TAATTAT-AAATTTTAAA
15624392 ATATATAATTATAAATTTTAAA
1 ATATATAATTATAAATTTTAAA
15624414 A
1 A
15624415 AGTTAAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
22 10 0.27
23 5 0.14
24 19 0.51
25 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATATAATTATAAATTTTAAA
Found at i:15624443 original size:10 final size:10
Alignment explanation
Indices: 15624404--15624453 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 10
15624394 ATATAATTAT
15624404 AAATTT-TAA
1 AAATTTATAA
*
15624413 AAAGTTA-AA
1 AAATTTATAA
*
15624422 ATAATATATAA
1 A-AATTTATAA
15624433 AAATTTAT-A
1 AAATTTATAA
15624442 AAATTTATAA
1 AAATTTATAA
15624452 AA
1 AA
15624454 TAAAAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
9 17 0.52
10 13 0.39
11 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
AAATTTATAA
Found at i:15624446 original size:9 final size:9
Alignment explanation
Indices: 15624376--15624454 Score: 51
Period size: 9 Copynumber: 9.1 Consensus size: 9
15624366 AAAAATATTT
15624376 TTTATAAAA
1 TTTATAAAA
*
15624385 CTT-TAAAA
1 TTTATAAAA
*
15624393 --TATATAA
1 TTTATAAAA
*
15624400 -TTATAAAT
1 TTTATAAAA
15624408 TTTA-AAAA
1 TTTATAAAA
* *
15624416 GTTAAAATAA
1 TTTATAA-AA
*
15624426 TATATAAAAA
1 TTTAT-AAAA
15624436 TTTATAAAA
1 TTTATAAAA
15624445 TTTATAAAA
1 TTTATAAAA
15624454 T
1 T
15624455 AAAAAATATA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
6 1 0.02
7 4 0.07
8 16 0.30
9 21 0.39
10 10 0.19
11 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (9 bp):
TTTATAAAA
Found at i:15624453 original size:31 final size:32
Alignment explanation
Indices: 15624376--15624456 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 32
15624366 AAAAATATTT
* *
15624376 TTTATAAAACTTTAAAAT-ATATAATTATAAA
1 TTTATAAAAATTTAAAATAATATAATTAAAAA
*
15624407 TTT-TAAAAAGTTAAAATAATAT-A-TAAAAA
1 TTTATAAAAATTTAAAATAATATAATTAAAAA
*
15624436 TTTATAAAATTTATAAAATAA
1 TTTATAAAAATT-TAAAATAA
15624457 AAAATATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
29 8 0.19
30 19 0.45
31 15 0.36
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (32 bp):
TTTATAAAAATTTAAAATAATATAATTAAAAA
Found at i:15624653 original size:20 final size:21
Alignment explanation
Indices: 15624630--15624673 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
15624620 TTTTTCTAGG
15624630 TTTTATATA-TATTTGAATTT
1 TTTTATATATTATTTGAATTT
15624650 TTTTATATATTTATTTGAATTT
1 TTTTATATA-TTATTTGAATTT
15624672 TT
1 TT
15624674 ATATTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 9 0.41
22 13 0.59
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTATATATTATTTGAATTT
Found at i:15624674 original size:20 final size:21
Alignment explanation
Indices: 15624630--15624682 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
15624620 TTTTTCTAGG
15624630 TTTTATATA--TATTTGAATTT
1 TTTTATATATTTATTTGAA-TT
15624650 TTTTATATATTTATTTGAA-T
1 TTTTATATATTTATTTGAATT
*
15624670 TTTTATATTTTTA
1 TTTTATATATTTA
15624683 ATGTGTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 22 0.73
22 8 0.27
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTTATATATTTATTTGAATT
Found at i:15624678 original size:18 final size:19
Alignment explanation
Indices: 15624630--15624679 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 19
15624620 TTTTTCTAGG
*
15624630 TTTTATATATATTTGAATTTT
1 TTTTATATTTATTTGAA--TT
15624651 TTTATATATTTATTTGAA-T
1 TTT-TATATTTATTTGAATT
15624670 TTTTATATTT
1 TTTTATATTT
15624680 TTAATGTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.26
19 4 0.15
21 3 0.11
22 13 0.48
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (19 bp):
TTTTATATTTATTTGAATT
Found at i:15625483 original size:18 final size:16
Alignment explanation
Indices: 15625454--15625506 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 16
15625444 AGTTTTATTC
*
15625454 TAAAAATCCAAAAATAT
1 TAAAAATTCAAAAA-AT
15625471 TAAAAATTACAAAAAAAT
1 TAAAAATT-C-AAAAAAT
*
15625489 AAAAAATTCAAAAAAT
1 TAAAAATTCAAAAAAT
15625505 TA
1 TA
15625507 TAATATATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 8 0.26
17 8 0.26
18 10 0.32
19 5 0.16
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAATTCAAAAAAT
Found at i:15625509 original size:19 final size:18
Alignment explanation
Indices: 15625463--15625519 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
15625453 CTAAAAATCC
*
15625463 AAAAATATTAAAAATTACA
1 AAAAATATAAAAAATT-CA
15625482 AAAAA-ATAAAAAATTCA
1 AAAAATATAAAAAATTCA
* *
15625499 AAAAATTATAATATATTCA
1 AAAAA-TATAAAAAATTCA
15625518 AA
1 AA
15625520 TTATTATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 7 0.21
18 9 0.27
19 17 0.52
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATATAAAAAATTCA
Found at i:15627415 original size:18 final size:19
Alignment explanation
Indices: 15627392--15627427 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15627382 CATCTTTCCA
*
15627392 TTTA-TTCTTTTTTTTTAT
1 TTTATTTCTCTTTTTTTAT
15627410 TTTATTTCTCTTTTTTTA
1 TTTATTTCTCTTTTTTTA
15627428 CACCATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTATTTCTCTTTTTTTAT
Found at i:15628389 original size:34 final size:34
Alignment explanation
Indices: 15628335--15628461 Score: 130
Period size: 34 Copynumber: 3.7 Consensus size: 34
15628325 ACATGTCTTT
* * *
15628335 TGCTACTAAATTGAAT-TGTTATAAGCATAATAAT
1 TGCTACTATATT-AATCTGTTATAAGCATATTAAA
* *
15628369 TGCTATTATATTAATCTGTTATGAGCATATTAAA
1 TGCTACTATATTAATCTGTTATAAGCATATTAAA
* * *
15628403 TGCTACTGTATTGATATGTTATAAGCATATTAAA
1 TGCTACTATATTAATCTGTTATAAGCATATTAAA
* * * *
15628437 TGTTATTGTATTGATCTGTTATAAG
1 TGCTACTATATTAATCTGTTATAAG
15628462 TATGTCACAT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
33 3 0.04
34 76 0.96
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (34 bp):
TGCTACTATATTAATCTGTTATAAGCATATTAAA
Found at i:15632210 original size:26 final size:26
Alignment explanation
Indices: 15632166--15632281 Score: 144
Period size: 26 Copynumber: 4.5 Consensus size: 26
15632156 CACGGTGTTG
* *
15632166 ATCGAAATACACTCAATGGGTAAATT
1 ATCGAAATACCCTCGATGGGTAAATT
15632192 ATCGAAATACCCTCGATGGGTAAATT
1 ATCGAAATACCCTCGATGGGTAAATT
* * *
15632218 ACCAAAATACCTTCGATGGGTAAATT
1 ATCGAAATACCCTCGATGGGTAAATT
* *
15632244 ACCAAAATATCCC-CGATGGGTAAATT
1 ATCGAAATA-CCCTCGATGGGTAAATT
*
15632270 ATTGAAATACCC
1 ATCGAAATACCC
15632282 CCGTAGGGTA
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
25 3 0.04
26 75 0.94
27 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (26 bp):
ATCGAAATACCCTCGATGGGTAAATT
Found at i:15632283 original size:26 final size:26
Alignment explanation
Indices: 15632181--15632304 Score: 133
Period size: 26 Copynumber: 4.7 Consensus size: 26
15632171 AATACACTCA
* *
15632181 ATGGGTAAATTATCGAAATACCCTCG
1 ATGGGTAAATTACCGAAATACCCCCG
* **
15632207 ATGGGTAAATTACCAAAATACCTTCG
1 ATGGGTAAATTACCGAAATACCCCCG
* *
15632233 ATGGGTAAATTACCAAAATATCCCCG
1 ATGGGTAAATTACCGAAATACCCCCG
**
15632259 ATGGGTAAATTATTGAAATACCCCCG
1 ATGGGTAAATTACCGAAATACCCCCG
*
15632285 -TAGGGTAAAATTACTGAAAT
1 AT-GGGT-AAATTACCGAAAT
15632305 GATTGATATG
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
25 1 0.01
26 72 0.85
27 12 0.14
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (26 bp):
ATGGGTAAATTACCGAAATACCCCCG
Found at i:15633020 original size:12 final size:12
Alignment explanation
Indices: 15633003--15633029 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15632993 TTAACAGGTA
15633003 CAAATAAGTTTT
1 CAAATAAGTTTT
15633015 CAAATAAGTTTT
1 CAAATAAGTTTT
15633027 CAA
1 CAA
15633030 TACAAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (12 bp):
CAAATAAGTTTT
Found at i:15639708 original size:26 final size:27
Alignment explanation
Indices: 15639679--15639801 Score: 146
Period size: 26 Copynumber: 4.6 Consensus size: 27
15639669 TACCAAGCTA
15639679 CCCTCGATGGGTAAATTATTGAAAT-C
1 CCCTCGATGGGTAAATTATTGAAATAC
15639705 CCCTCGATGGGTAAATTATTGAAATAC
1 CCCTCGATGGGTAAATTATTGAAATAC
* *
15639732 CCCT-GATAGGTAAATTATCGAAATA-
1 CCCTCGATGGGTAAATTATTGAAATAC
*
15639757 CCCTCG-TAGGGTAAAATTACTGAAATAC
1 CCCTCGAT-GGGT-AAATTATTGAAATAC
* * *
15639785 TCCTAGAAGGGTAAATT
1 CCCTCGATGGGTAAATT
15639802 GACCGATATA
Statistics
Matches: 83, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
25 5 0.06
26 48 0.58
27 22 0.27
28 8 0.10
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (27 bp):
CCCTCGATGGGTAAATTATTGAAATAC
Found at i:15639733 original size:52 final size:53
Alignment explanation
Indices: 15639677--15639815 Score: 149
Period size: 52 Copynumber: 2.6 Consensus size: 53
15639667 ATTACCAAGC
* * *
15639677 TACCCTCGATGGGTAAATTATTGAAATCCCCTCG-ATGGGT-AAATTATTGAAA
1 TACCCTCGATGGGTAAATTATCGAAATACCCTCGTA-GGGTAAAATTACTGAAA
*
15639729 TACCC-CTGATAGGTAAATTATCGAAATACCCTCGTAGGGTAAAATTACTGAAA
1 TACCCTC-GATGGGTAAATTATCGAAATACCCTCGTAGGGTAAAATTACTGAAA
* * * *
15639782 TACTCCTAGAAGGGTAAATTGACCGATATACCCT
1 TAC-CCTCGATGGGTAAATT-ATCGAAATACCCT
15639816 TAGTAGATGA
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
51 1 0.01
52 33 0.46
53 15 0.21
54 12 0.17
55 11 0.15
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (53 bp):
TACCCTCGATGGGTAAATTATCGAAATACCCTCGTAGGGTAAAATTACTGAAA
Found at i:15642525 original size:21 final size:21
Alignment explanation
Indices: 15642479--15642526 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
15642469 ACTTAAAGTG
*
15642479 GAGGCAGCAGTAAGGGAAACA
1 GAGGCAGCAGCAAGGGAAACA
* * *
15642500 AAGGCAGCAGCAAGGGCAGCA
1 GAGGCAGCAGCAAGGGAAACA
15642521 GAGGCA
1 GAGGCA
15642527 ACAAGAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.40, T:0.02
Consensus pattern (21 bp):
GAGGCAGCAGCAAGGGAAACA
Found at i:15643837 original size:32 final size:32
Alignment explanation
Indices: 15643772--15643830 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
15643762 AATTTTAGAA
*
15643772 ATTTTAATAAATTTTGATTTGTTTTTATATAT
1 ATTTTAATAAATTTTGAATTGTTTTTATATAT
*
15643804 ATTTTTAT-AATTTTGAATT-TTTTTATA
1 ATTTTAATAAATTTTGAATTGTTTTTATA
15643831 AGTATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.32
31 10 0.40
32 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (32 bp):
ATTTTAATAAATTTTGAATTGTTTTTATATAT
Found at i:15644252 original size:6 final size:6
Alignment explanation
Indices: 15644241--15644273 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
15644231 TCATATAAGT
*
15644241 AATGCA AATGCA AATGCA AATGCA AATTCA AAT
1 AATGCA AATGCA AATGCA AATGCA AATGCA AAT
15644274 ATGAATATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (6 bp):
AATGCA
Found at i:15646994 original size:27 final size:27
Alignment explanation
Indices: 15646964--15647018 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
15646954 ATTTGTGTTA
*
15646964 ATAAACTATAAGATAACAGAGTAATTT
1 ATAAACTATAAGATAACAAAGTAATTT
*
15646991 ATAAACTATAAGATGACAAAGTAATTT
1 ATAAACTATAAGATAACAAAGTAATTT
15647018 A
1 A
15647019 ATCTTTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (27 bp):
ATAAACTATAAGATAACAAAGTAATTT
Found at i:15661942 original size:21 final size:19
Alignment explanation
Indices: 15661919--15661957 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
15661909 GAAAACCAAA
15661919 ACAA-AAAAAAAACATGGG
1 ACAACAAAAAAAACATGGG
15661937 ACAACAAAAAAAACATGGG
1 ACAACAAAAAAAACATGGG
15661956 AC
1 AC
15661958 TTCTTCACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.64, C:0.15, G:0.15, T:0.05
Consensus pattern (19 bp):
ACAACAAAAAAAACATGGG
Found at i:15667751 original size:33 final size:31
Alignment explanation
Indices: 15667697--15667763 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 31
15667687 TAATTCAATA
*
15667697 ACAGTTCAGTTCAGTTGGGCCTTAGCCCATT
1 ACAGTTCAGTTCAGTTGGGCCTAAGCCCATT
15667728 ACAGTATCAGTATCAG-TGTGGCCTAAGCCCATT
1 ACAGT-TCAGT-TCAGTTG-GGCCTAAGCCCATT
15667761 ACA
1 ACA
15667764 ATGACAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 5 0.16
32 7 0.22
33 20 0.62
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (31 bp):
ACAGTTCAGTTCAGTTGGGCCTAAGCCCATT
Found at i:15671694 original size:130 final size:130
Alignment explanation
Indices: 15671398--15671846 Score: 615
Period size: 130 Copynumber: 3.5 Consensus size: 130
15671388 TAAATTTACA
*
15671398 ATTTACGATCACAACCTAAGTTCATTGATTTATGATCATGAACAATTTCTTCTGAGTTAGCTAAT
1 ATTTACGATCACAGCCTAAGTTCATTGATTTATGATCATGAACAATTTCTTCTGAGTTAGCTAAT
15671463 TTACGATCGTAACTCCAAACAGCTC-TTGATTTATGATCAC-GATTGATATTATTAAGGCTCATT
66 TTACGATCGTAACTCCAAACAGCTCGTTGATTTATGATCACAG-TTGATATTATTAAGGCTCATT
15671526 G
130 G
* * *
15671527 ATTTACAATCACAGCCTAAGTTCATTAATTTATGATCATGAACCATTTCTTCTGAGTTAGCTGAA
1 ATTTACGATCACAGCCTAAGTTCATTGATTTATGATCATGAACAATTTCTTCTGAGTTAGCT-AA
* * * *
15671592 -TTACGATCGTAACTCCAAATAGCTCGTTGGTTTACGATCACAGTTGATATTATT-AGTGCTCAC
65 TTTACGATCGTAACTCCAAACAGCTCGTTGATTTATGATCACAGTTGATATTATTAAG-GCTCAT
15671655 TG
129 TG
* * *
15671657 ATTTACGATTACAGCCTAAGTTCATTGATTTATGATCATGAATAATTTCTTCTTAGTTAGCTAAT
1 ATTTACGATCACAGCCTAAGTTCATTGATTTATGATCATGAACAATTTCTTCTGAGTTAGCTAAT
* * * **
15671722 TTACGA-CTGCAACTCTAAACAACTCG-TGTATTTATGATCACAACTGATATTATTAAGGCT-AG
66 TTACGATC-GTAACTCCAAACAGCTCGTTG-ATTTATGATCACAGTTGATATTATTAAGGCTCA-
*
15671784 TTA
128 TTG
* * *
15671787 ATTTACGATCATAGCCTAAGTTCATTGATTTACGATCATGAACAATTTCTTCTAAGTTAG
1 ATTTACGATCACAGCCTAAGTTCATTGATTTATGATCATGAACAATTTCTTCTGAGTTAG
15671847 TTGATTTGTT
Statistics
Matches: 282, Mismatches: 29, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
129 90 0.32
130 189 0.67
131 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (130 bp):
ATTTACGATCACAGCCTAAGTTCATTGATTTATGATCATGAACAATTTCTTCTGAGTTAGCTAAT
TTACGATCGTAACTCCAAACAGCTCGTTGATTTATGATCACAGTTGATATTATTAAGGCTCATTG
Found at i:15671859 original size:8 final size:8
Alignment explanation
Indices: 15671846--15671871 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
15671836 TTCTAAGTTA
15671846 GTTGATTT
1 GTTGATTT
15671854 GTTGATTT
1 GTTGATTT
15671862 GTTGATTT
1 GTTGATTT
15671870 GT
1 GT
15671872 GATAACAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.27, T:0.62
Consensus pattern (8 bp):
GTTGATTT
Found at i:15673027 original size:24 final size:24
Alignment explanation
Indices: 15672999--15673047 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
15672989 CAGTAGACAT
*
15672999 AAACTTCAATGAACCCTCAATAGG
1 AAACTTCAATGAACCCCCAATAGG
15673023 AAACTTCAATGAACCCCCAATAGG
1 AAACTTCAATGAACCCCCAATAGG
15673047 A
1 A
15673048 CCATGTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (24 bp):
AAACTTCAATGAACCCCCAATAGG
Found at i:15673694 original size:39 final size:39
Alignment explanation
Indices: 15673640--15673719 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
15673630 AAAACTAACA
15673640 TAATGTCCACACCATTCTTGTCATCAATTGGCCGCCACC
1 TAATGTCCACACCATTCTTGTCATCAATTGGCCGCCACC
15673679 TAATGTCCACACCATTCTTGTCATCAATTGGCCGCCACC
1 TAATGTCCACACCATTCTTGTCATCAATTGGCCGCCACC
15673718 TA
1 TA
15673720 TTAGGGCTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.24, C:0.35, G:0.12, T:0.29
Consensus pattern (39 bp):
TAATGTCCACACCATTCTTGTCATCAATTGGCCGCCACC
Found at i:15686029 original size:38 final size:40
Alignment explanation
Indices: 15685978--15686054 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
15685968 ATTATTTAAT
15685978 ATAATTAAGAATAT-AAA-ATATGTTTTGTACTAAACTAA
1 ATAATTAAGAATATAAAATATATGTTTTGTACTAAACTAA
15686016 ATAATTAAGAATATAAAATATATGTTTTGTACTAAACTA
1 ATAATTAAGAATATAAAATATATGTTTTGTACTAAACTA
15686055 GCATTGGCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 14 0.38
39 3 0.08
40 20 0.54
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (40 bp):
ATAATTAAGAATATAAAATATATGTTTTGTACTAAACTAA
Found at i:15686223 original size:21 final size:22
Alignment explanation
Indices: 15686170--15686212 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
15686160 TGGTGGTTGT
*
15686170 TGTTTGTGGTTTACGGGTTTAA
1 TGTTTATGGTTTACGGGTTTAA
15686192 TGTTTATGGTTTA-GGGTTTAA
1 TGTTTATGGTTTACGGGTTTAA
15686213 GATTTTCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.16, C:0.02, G:0.30, T:0.51
Consensus pattern (22 bp):
TGTTTATGGTTTACGGGTTTAA
Found at i:15686295 original size:7 final size:7
Alignment explanation
Indices: 15686283--15686329 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
15686273 GTTAATTGAC
15686283 GGGTTTA
1 GGGTTTA
15686290 GGGTTTA
1 GGGTTTA
*
15686297 AGGTTTA
1 GGGTTTA
*
15686304 AGGTTTA
1 GGGTTTA
*
15686311 CGGTTT-
1 GGGTTTA
15686317 GAGGTTTA
1 G-GGTTTA
15686325 GGGTT
1 GGGTT
15686330 CATAGTTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 34 0.97
8 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.38, T:0.43
Consensus pattern (7 bp):
GGGTTTA
Done.