Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 127 of 198
Found at i:40526175 original size:84 final size:84
Alignment explanation
Indices: 40526084--40526324 Score: 297
Period size: 84 Copynumber: 2.9 Consensus size: 84
40526074 CGAGAAATTA
* *
40526084 AAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGTCGCTTAACAATATTTGATTTGATTTTAT
1 AAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGCTTAACAAGATTTGATTTGATTTTAT
40526149 TTTGTTTCCAAATTAGAAT
66 TTTGTTTCCAAATTAGAAT
* * * * *
40526168 AAAATTAAGTAAAAGT-TGTTTGGGGATTTATTCCTGCCGTTTAACAAGATTTTATTTGATTTTA
1 AAAATTAAATAAAA-TCTGTTTCGGGATTTATTCCCGCCGCTTAACAAGATTTGATTTGATTTTA
*
40526232 TTTTGTTTTCAAATTAGAAT
65 TTTTGTTTCCAAATTAGAAT
* * * ** * * * *
40526252 CAAATTAAATAAAATCTATTTCGGGATTTTTTCCTACCGTTTAAC-AGATTTTATTTTGATATAA
1 AAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGCTTAACAAGATTTGA-TTTGATTTTA
40526316 TTTTGTTTC
65 TTTTGTTTC
40526325 GGGATTTAAT
Statistics
Matches: 137, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
83 9 0.07
84 127 0.93
85 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.46
Consensus pattern (84 bp):
AAAATTAAATAAAATCTGTTTCGGGATTTATTCCCGCCGCTTAACAAGATTTGATTTGATTTTAT
TTTGTTTCCAAATTAGAAT
Found at i:40533874 original size:37 final size:37
Alignment explanation
Indices: 40533824--40533898 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
40533814 CATATCACCG
40533824 CTTTCACTTTGAACAATAAACTTCTTTTTATAGCAAT
1 CTTTCACTTTGAACAATAAACTTCTTTTTATAGCAAT
40533861 CTTTCACTTTGAACAATAAACTTCTTTTTATAGCAAT
1 CTTTCACTTTGAACAATAAACTTCTTTTTATAGCAAT
40533898 C
1 C
40533899 CAGAATCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (37 bp):
CTTTCACTTTGAACAATAAACTTCTTTTTATAGCAAT
Found at i:40539720 original size:19 final size:18
Alignment explanation
Indices: 40539686--40539738 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
40539676 TCTTTCTAGT
40539686 TTATTTTTATTTATTAAA
1 TTATTTTTATTTATTAAA
*
40539704 TTATTTTTCTTTAATT-AA
1 TTATTTTTATTT-ATTAAA
40539722 -T-TTTTTATTT-TTAAA
1 TTATTTTTATTTATTAAA
40539737 TT
1 TT
40539739 TATTATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 2 0.07
15 2 0.07
16 9 0.30
17 1 0.03
18 13 0.43
19 3 0.10
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTTTTATTTATTAAA
Found at i:40540610 original size:22 final size:22
Alignment explanation
Indices: 40540585--40540640 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
40540575 TATATTGTCA
**
40540585 TATGTATTTTTATATACATTTT
1 TATGTATTTTTATATACATAAT
* * *
40540607 TATGGATATTTATATATATAAT
1 TATGTATTTTTATATACATAAT
40540629 TATGTATATTTT
1 TATGTAT-TTTT
40540641 TCTCATATAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (22 bp):
TATGTATTTTTATATACATAAT
Found at i:40551029 original size:4 final size:4
Alignment explanation
Indices: 40551020--40551050 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
40551010 CCTAAGTGCA
40551020 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
40551051 GCTAGAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:40552745 original size:25 final size:25
Alignment explanation
Indices: 40552719--40552766 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
40552709 TGAGTTGATG
*
40552719 GGGCT-TTTGGGTATTGGGTTTGTT
1 GGGCTGTTTGGGTATTGAGTTTGTT
40552743 GGGCTGTTTGGGTATTGAGTTTGT
1 GGGCTGTTTGGGTATTGAGTTTGT
40552767 AAAAAATTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.06, C:0.04, G:0.42, T:0.48
Consensus pattern (25 bp):
GGGCTGTTTGGGTATTGAGTTTGTT
Found at i:40554201 original size:6 final size:6
Alignment explanation
Indices: 40554191--40554235 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
40554181 AAATATTCAA
*
40554191 AAAAACT AAAAAT AAAAAAT AAAAAT AAAAAT AAGAAT AAAAAT A
1 AAAAA-T AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
40554236 GCTAAGATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
6 24 0.69
7 11 0.31
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:40555824 original size:44 final size:45
Alignment explanation
Indices: 40555742--40555855 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 45
40555732 AAGACTTGTA
** *
40555742 TCTTCGATCTACTTCACCACCAGTATGGGAAGTCAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAGTACAGGAAGACAAGATCTGCTT
* * *
40555787 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAGTACAGGAAGACAAGATCTGCTT
* *
40555831 TCTTCAATCTACTCCACCACCAGTA
1 TCTTCGATCTACTTCACCACCAGTA
40555856 TGGGGAGATA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 36 0.62
45 22 0.38
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (45 bp):
TCTTCGATCTACTTCACCACCAGTACAGGAAGACAAGATCTGCTT
Found at i:40556109 original size:44 final size:43
Alignment explanation
Indices: 40556061--40556190 Score: 120
Period size: 45 Copynumber: 2.9 Consensus size: 43
40556051 TGTCTTTGAT
* *
40556061 CTACTTCACGCCAGTACATGAAGACACGATTTGTTTTCTTCGAC
1 CTACTTCACGCCAGTACATGAAGACAAGATCTG-TTTCTTCGAC
* * * * *
40556105 CTACTCCACCACCAG--CATGGGGAGACAAGATCTGTTTCTTTGAT
1 CTACTTCA-CGCCAGTACAT--GAAGACAAGATCTGTTTCTTCGAC
40556149 CTACTTCACGCCAGTACATGAAGAGACAAGATCTGTTATCTT
1 CTACTTCACGCCAGTACATG-A-AGACAAGATCTGTT-TCTT
40556191 TCACCCTGCT
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
43 9 0.13
44 22 0.32
45 33 0.49
46 4 0.06
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (43 bp):
CTACTTCACGCCAGTACATGAAGACAAGATCTGTTTCTTCGAC
Found at i:40568308 original size:2 final size:2
Alignment explanation
Indices: 40568301--40568325 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40568291 TACGCGCCTT
40568301 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
40568326 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:40579394 original size:2 final size:2
Alignment explanation
Indices: 40579387--40579416 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40579377 CTCATAGCTT
40579387 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40579417 GAAAGTGGTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40587946 original size:17 final size:18
Alignment explanation
Indices: 40587913--40587946 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40587903 GTAGATCATC
*
40587913 AAACTATTTTTATGCTTG
1 AAACTATTTTGATGCTTG
40587931 AAACTA-TTTGATGCTT
1 AAACTATTTTGATGCTT
40587947 ACTATTCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (18 bp):
AAACTATTTTGATGCTTG
Found at i:40591827 original size:43 final size:43
Alignment explanation
Indices: 40591757--40591861 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
40591747 CTTCGAATGC
** * *
40591757 CCACACGGCCT-AAAACACGGGCGTGTCTCTTAATCGTGTGAG
1 CCACACGGCCTGATCACACGGGCATGTCTCTTAACCGTGTGAG
* *
40591799 TCACACGGCCTGATCACACGGGCATGTCTCTTGACCGTGTGAG
1 CCACACGGCCTGATCACACGGGCATGTCTCTTAACCGTGTGAG
*
40591842 CCACACAG-CTAGATCACACG
1 CCACACGGCCT-GATCACACG
40591862 AGTGTGTGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 12 0.23
43 41 0.77
ACGTcount: A:0.24, C:0.31, G:0.25, T:0.20
Consensus pattern (43 bp):
CCACACGGCCTGATCACACGGGCATGTCTCTTAACCGTGTGAG
Found at i:40594938 original size:27 final size:27
Alignment explanation
Indices: 40594907--40594961 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
40594897 TTTGAAATTG
40594907 AGAAGTTTGATGGTGTCACAAATTTCA
1 AGAAGTTTGATGGTGTCACAAATTTCA
40594934 AGAAGTTTGATGGTGTCACAAATTTCA
1 AGAAGTTTGATGGTGTCACAAATTTCA
40594961 A
1 A
40594962 TCTATGGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (27 bp):
AGAAGTTTGATGGTGTCACAAATTTCA
Found at i:40597773 original size:124 final size:124
Alignment explanation
Indices: 40597483--40597918 Score: 674
Period size: 124 Copynumber: 3.5 Consensus size: 124
40597473 AAATCAAAGT
* * * * *
40597483 AGGATGTTTTATCAAAAGAATTTCTAAAATCGCGCCCATGTGGACGTGCTTTTGCTACAGTAGCT
1 AGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
* * *
40597548 CTTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTCAAGC
66 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAACGCTTCAAGC
** * * * *
40597608 AAAATGCTTTATCAGAAGAATTTTTGAAATCGCGCTCACGTGGACACGCTTTTGCTACAGTAGGT
1 AGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
40597673 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGC
66 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGC
* *
40597732 AGGATGATTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCCACAGTAGGT
1 AGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
*
40597797 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAATGCTTCAAGC
66 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGC
* * * *
40597856 AGGATGCTTTATCAGAAGAATTTATGAAATCGTGCCCCCGTGGACGCGCTTTTGCTACAGTAG
1 AGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
40597919 CATGTTTGGC
Statistics
Matches: 282, Mismatches: 29, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
124 187 0.66
125 95 0.34
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (124 bp):
AGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGT
CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTCAAGC
Found at i:40601112 original size:112 final size:112
Alignment explanation
Indices: 40600915--40601128 Score: 383
Period size: 112 Copynumber: 1.9 Consensus size: 112
40600905 ATATTTTTTT
40600915 GTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTA
1 GTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTA
40600980 TTAATTGTTAATAAAATTATCAAATTATATCAAATTATTAATTGTTA
66 TTAATTGTTAATAAAATTATCAAATTATATCAAATTATTAATTGTTA
* *
40601027 GTACCAGTTAAAACATTTTGTAAAATCTAACATTTTGTTAGTCAAATTATTAATTGTTAATTGTA
1 GTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTA
* * *
40601092 TTAATTGTTAGTAAATTTATCAAATTATATCATATTA
66 TTAATTGTTAATAAAATTATCAAATTATATCAAATTA
40601129 GGGTTAGGTT
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 97 1.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44
Consensus pattern (112 bp):
GTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTA
TTAATTGTTAATAAAATTATCAAATTATATCAAATTATTAATTGTTA
Found at i:40601228 original size:22 final size:21
Alignment explanation
Indices: 40601195--40601268 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
40601185 TAAGGGTTAC
*
40601195 GGTTAGGGTTTTTAAGTTTAG
1 GGTTAGGGTTTTTAAGTTAAG
*
40601216 GGTTAGGCTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
40601237 GGTTTAGGGTTTTTAAGTTAAG
1 GG-TTAGGGTTTTTAAGTTAAG
40601259 GGTTAGGGTT
1 GGTTAGGGTT
40601269 AGGATTAGGG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
21 29 0.59
22 20 0.41
ACGTcount: A:0.20, C:0.01, G:0.34, T:0.45
Consensus pattern (21 bp):
GGTTAGGGTTTTTAAGTTAAG
Found at i:40601551 original size:21 final size:20
Alignment explanation
Indices: 40601519--40601557 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
40601509 AGCTTTCGGC
*
40601519 CGGGGTTATGGTTGCTCCGG
1 CGGGGTTATGGTTCCTCCGG
*
40601539 CGGGGATTCTGGTTCCTCC
1 CGGGG-TTATGGTTCCTCC
40601558 AGTAGGGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.05, C:0.26, G:0.38, T:0.31
Consensus pattern (20 bp):
CGGGGTTATGGTTCCTCCGG
Found at i:40602515 original size:7 final size:7
Alignment explanation
Indices: 40602505--40602530 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40602495 TTATATACGT
40602505 AATACTA
1 AATACTA
40602512 AATACTA
1 AATACTA
40602519 AATACTA
1 AATACTA
40602526 AATAC
1 AATAC
40602531 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:40603740 original size:51 final size:51
Alignment explanation
Indices: 40603656--40603753 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 51
40603646 AAATAATTAA
* *
40603656 AAATAGGGATTTAAGAGAAATTTAAGAGGAAATT-AAGAGTAAATTAAAATT
1 AAATAGGGATTTAAGAGAAATTTAAGAGCAAATTGAA-AGCAAATTAAAATT
* * *
40603707 AAATATGGATTTGAGAGAAATTT-GGAAGCAAATTGAAAGCAAATTAA
1 AAATAGGGATTTAAGAGAAATTTAAG-AGCAAATTGAAAGCAAATTAA
40603754 GAGCAAATTG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 1 0.03
51 37 0.93
52 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.20, T:0.27
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAAGAGCAAATTGAAAGCAAATTAAAATT
Found at i:40603742 original size:22 final size:21
Alignment explanation
Indices: 40603717--40603770 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
40603707 AAATATGGAT
**
40603717 TTGAGAGAAATTTGGAAGCAAA
1 TTGAGAGAAATTAAG-AGCAAA
*
40603739 TTGAAAGCAAATTAAGAGCAAA
1 TTGAGAG-AAATTAAGAGCAAA
40603761 TTGAGA-AAAT
1 TTGAGAGAAAT
40603771 AATTGAGAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 4 0.15
22 17 0.63
23 6 0.22
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (21 bp):
TTGAGAGAAATTAAGAGCAAA
Found at i:40603746 original size:11 final size:11
Alignment explanation
Indices: 40603732--40603764 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
40603722 AGAAATTTGG
40603732 AAGCAAATTGA
1 AAGCAAATTGA
40603743 AAGCAAATT-A
1 AAGCAAATTGA
40603753 AGAGCAAATTGA
1 A-AGCAAATTGA
40603765 GAAAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.10
11 17 0.85
12 1 0.05
ACGTcount: A:0.55, C:0.09, G:0.18, T:0.18
Consensus pattern (11 bp):
AAGCAAATTGA
Found at i:40603991 original size:40 final size:40
Alignment explanation
Indices: 40603913--40603991 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
40603903 CAGGGGCGCG
* *
40603913 CTACGTGGCAACAAAACGCGTCCACGTCAGCGTACTTTGC
1 CTACGTGGCAACAAAACGCGTCCACGTAAGCGCACTTTGC
* *
40603953 CTACGTGGCAACAAATCGCGT-CATCGTAAGCGCGCTTTG
1 CTACGTGGCAACAAAACGCGTCCA-CGTAAGCGCACTTTG
40603992 AGTCCATGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (40 bp):
CTACGTGGCAACAAAACGCGTCCACGTAAGCGCACTTTGC
Found at i:40610609 original size:15 final size:16
Alignment explanation
Indices: 40610589--40610621 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40610579 TTTATTAAAA
*
40610589 AAATTA-AATAATGTT
1 AAATTAGAATAAAGTT
40610604 AAATTAGAATAAAGTT
1 AAATTAGAATAAAGTT
40610620 AA
1 AA
40610622 TATTTAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (16 bp):
AAATTAGAATAAAGTT
Found at i:40615666 original size:22 final size:24
Alignment explanation
Indices: 40615641--40615699 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
40615631 CAAGTCTCAA
* *
40615641 TTTTAATAT-TTATACTTTAATTT
1 TTTTAATATCTCATACTTCAATTT
40615664 TTTTATATAATCTCATACTTCAATTT
1 TTTTA-AT-ATCTCATACTTCAATTT
*
40615690 TTATAATATC
1 TTTTAATATC
40615700 ATTGTTAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 5 0.17
24 5 0.17
25 4 0.13
26 16 0.53
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTAATATCTCATACTTCAATTT
Found at i:40615941 original size:38 final size:38
Alignment explanation
Indices: 40615899--40615974 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
40615889 CTTTATTCTG
40615899 ATTAAAATGTTGGTTTAACATAATTTGGTACTTCAACT
1 ATTAAAATGTTGGTTTAACATAATTTGGTACTTCAACT
40615937 ATTAAAATGTTGGTTTAACATAATTTGGTACTTCAACT
1 ATTAAAATGTTGGTTTAACATAATTTGGTACTTCAACT
40615975 TTAGCCCCTA
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:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (38 bp):
ATTAAAATGTTGGTTTAACATAATTTGGTACTTCAACT
Found at i:40616506 original size:17 final size:16
Alignment explanation
Indices: 40616465--40616506 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
40616455 AAAATATTTT
40616465 TAAAAATCAAAGATAA
1 TAAAAATCAAAGATAA
40616481 -AAATGAATCAAAAGATAA
1 TAAA--AATC-AAAGATAA
40616499 TAAAAATC
1 TAAAAATC
40616507 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
15 3 0.14
17 8 0.36
18 8 0.36
19 3 0.14
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (16 bp):
TAAAAATCAAAGATAA
Found at i:40620848 original size:2 final size:2
Alignment explanation
Indices: 40620841--40620878 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
40620831 TTTACATTTG
*
40620841 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40620879 AGAGATAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:40621498 original size:18 final size:18
Alignment explanation
Indices: 40621475--40621510 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40621465 AAGCAACTAG
40621475 TAAATTAGGGTTTAGTTC
1 TAAATTAGGGTTTAGTTC
40621493 TAAATTAGGGTTTAGTTC
1 TAAATTAGGGTTTAGTTC
40621511 ATACAAGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (18 bp):
TAAATTAGGGTTTAGTTC
Found at i:40625307 original size:14 final size:14
Alignment explanation
Indices: 40625272--40625310 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
40625262 AATGTTTGGG
* *
40625272 GTTTAGGATTTAGA
1 GTTTAGGGTTTAAA
40625286 GTTTAGGGTTTAAA
1 GTTTAGGGTTTAAA
40625300 GTTTAGGGTTT
1 GTTTAGGGTTT
40625311 GAGTCTGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
GTTTAGGGTTTAAA
Found at i:40632766 original size:32 final size:34
Alignment explanation
Indices: 40632700--40632780 Score: 103
Period size: 32 Copynumber: 2.4 Consensus size: 34
40632690 TACATTCAAC
40632700 ATTGCCTGGTGTCTTTGTTAAAAAAAAAACAAAAAA
1 ATTGCCTGGTGTCTTTGTT--AAAAAAAACAAAAAA
* *
40632736 ATTGCCTGGTGTCTTTG-T-AAAAAAAGAAAAAC
1 ATTGCCTGGTGTCTTTGTTAAAAAAAACAAAAAA
*
40632768 ATTGCTTGGTGTC
1 ATTGCCTGGTGTC
40632781 GGTAGCATTG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 24 0.57
35 1 0.02
36 17 0.40
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (34 bp):
ATTGCCTGGTGTCTTTGTTAAAAAAAACAAAAAA
Found at i:40638528 original size:27 final size:28
Alignment explanation
Indices: 40638476--40638528 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
40638466 ATAGATTTAA
*
40638476 TATTAAATTTAATTTAATAATTATTATT
1 TATTAAATTTAATTTAATAATGATTATT
*
40638504 TATT-AATTTAATATTAA-AGTGATTA
1 TATTAAATTTAAT-TTAATAATGATTA
40638529 AGTTTAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (28 bp):
TATTAAATTTAATTTAATAATGATTATT
Found at i:40639598 original size:12 final size:12
Alignment explanation
Indices: 40639579--40639609 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
40639569 CAACTATAAC
40639579 TATCATCATAGT
1 TATCATCATAGT
*
40639591 TCTCATCATAGT
1 TATCATCATAGT
40639603 TATCATC
1 TATCATC
40639610 TCTATCATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (12 bp):
TATCATCATAGT
Found at i:40640460 original size:24 final size:24
Alignment explanation
Indices: 40640433--40640483 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
40640423 AAGATTTAGT
*
40640433 ATTTATGAGTATAATATATTTAAC
1 ATTTATGAGCATAATATATTTAAC
* *
40640457 ATTTATTAGCATAATATATTTGAC
1 ATTTATGAGCATAATATATTTAAC
40640481 ATT
1 ATT
40640484 GATTAGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (24 bp):
ATTTATGAGCATAATATATTTAAC
Found at i:40640488 original size:24 final size:24
Alignment explanation
Indices: 40640443--40640489 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
40640433 ATTTATGAGT
*
40640443 ATAATATATTTAACATTTATTAGC
1 ATAATATATTTAACATTGATTAGC
*
40640467 ATAATATATTTGACATTGATTAG
1 ATAATATATTTAACATTGATTAG
40640490 AATTAGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (24 bp):
ATAATATATTTAACATTGATTAGC
Found at i:40644745 original size:24 final size:24
Alignment explanation
Indices: 40644682--40644733 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40644672 TTTCTAAAAG
* * *
40644682 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
40644706 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
40644730 ATTT
1 ATTT
40644734 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:40646381 original size:7 final size:7
Alignment explanation
Indices: 40646371--40646401 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
40646361 CCTAAACCCT
40646371 AGGCCCA
1 AGGCCCA
40646378 AGGCCCA
1 AGGCCCA
40646385 AGGCCCA
1 AGGCCCA
*
40646392 AGGCCTA
1 AGGCCCA
40646399 AGG
1 AGG
40646402 TCTACGGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.29, C:0.35, G:0.32, T:0.03
Consensus pattern (7 bp):
AGGCCCA
Found at i:40647509 original size:4 final size:4
Alignment explanation
Indices: 40647500--40647528 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
40647490 CTCACCCGTA
40647500 ATTT ATTT ATTT ATTT ATTT ATTT -TTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
40647529 AATTGTGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:40653371 original size:19 final size:19
Alignment explanation
Indices: 40653344--40653392 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
40653334 AAATGATAAG
*
40653344 GATGAGAAATGGAAAATGA
1 GATGTGAAATGGAAAATGA
* *
40653363 GATGTGAAATTGAATATGA
1 GATGTGAAATGGAAAATGA
*
40653382 AATGGTGAAAT
1 GAT-GTGAAAT
40653393 TGGTTGTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (19 bp):
GATGTGAAATGGAAAATGA
Found at i:40656374 original size:16 final size:16
Alignment explanation
Indices: 40656353--40656386 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40656343 TAGTCCCTAT
*
40656353 AGTTTTGATTTATTTA
1 AGTTTTGATTTAGTTA
*
40656369 AGTTTTGTTTTAGTTA
1 AGTTTTGATTTAGTTA
40656385 AG
1 AG
40656387 AAATATGTTT
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:0.24, C:0.00, G:0.18, T:0.59
Consensus pattern (16 bp):
AGTTTTGATTTAGTTA
Found at i:40659276 original size:42 final size:44
Alignment explanation
Indices: 40659167--40659323 Score: 130
Period size: 42 Copynumber: 3.6 Consensus size: 44
40659157 AGCTTGTACA
** * *
40659167 ATGCC-ATCGTCCCAGACGCGGTCTTACATGT-AATC-AAATATCG
1 ATGCCAAT-GTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCG
* * * *
40659210 ATGCCACTGTCCCAGATA-GAGTCTTACACG--AA-GTCATATACG
1 ATGCCAATGTCCCAGACATG-GTCTTACACGTAAATCTCAAAT-CG
* *
40659252 GTGCCAATGTCCTAGACATGGTCTTACACGTAAATCTCAAATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAATCG
*
40659296 ATGCCAATGTCCCAGACGTGGTCTTACA
1 ATGCCAATGTCCCAGACATGGTCTTACA
40659324 TGAAATAACA
Statistics
Matches: 90, Mismatches: 16, Indels: 15
0.74 0.13 0.12
Matches are distributed among these distances:
41 2 0.02
42 30 0.33
43 23 0.26
44 30 0.33
45 5 0.06
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAATCG
Found at i:40664964 original size:28 final size:28
Alignment explanation
Indices: 40664919--40664990 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
40664909 TAAAGAGATT
* *
40664919 AGCATTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGTTTAATTATAA
* * *
40664947 AGTACTAAGTGTGCGAGTTTGATTATTA
1 AGCACTAAGTGTGCGAGTTTAATTATAA
40664975 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
40664991 ACTTATTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTAATTATAA
Found at i:40669726 original size:32 final size:31
Alignment explanation
Indices: 40669633--40669743 Score: 102
Period size: 30 Copynumber: 3.6 Consensus size: 31
40669623 CCATTTACTA
**
40669633 AAATGTGGAAGCCTTTGTGGTTGTTCTCTAAT
1 AAATGT-GAAGCCTTTGTGGTTGTTCTCTGTT
* * * **
40669665 ATATGTG-AGCCTTAGTGGTGGAAC-CTGTT
1 AAATGTGAAGCCTTTGTGGTTGTTCTCTGTT
*
40669694 AAATGTTGAAGCCTTTGCGGTTGTTCTCTGTT
1 AAATG-TGAAGCCTTTGTGGTTGTTCTCTGTT
*
40669726 ACATGT-AAGCCTTTGTGG
1 AAATGTGAAGCCTTTGTGG
40669744 CAAAATCGTC
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
29 7 0.11
30 26 0.43
31 14 0.23
32 14 0.23
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (31 bp):
AAATGTGAAGCCTTTGTGGTTGTTCTCTGTT
Found at i:40670705 original size:18 final size:20
Alignment explanation
Indices: 40670682--40670721 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
40670672 ATATCCATAT
40670682 AGAGG-AAGAATGAA-AGAA
1 AGAGGAAAGAATGAAGAGAA
*
40670700 AGAGGAAAGCATGAAGAGAA
1 AGAGGAAAGAATGAAGAGAA
40670720 AG
1 AG
40670722 CTATATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 8 0.42
20 6 0.32
ACGTcount: A:0.57, C:0.03, G:0.35, T:0.05
Consensus pattern (20 bp):
AGAGGAAAGAATGAAGAGAA
Found at i:40674838 original size:11 final size:11
Alignment explanation
Indices: 40674819--40674848 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
40674809 AACAGAAGAC
*
40674819 TTGGGAAAAAA
1 TTGGAAAAAAA
40674830 TTGGAAAAAAA
1 TTGGAAAAAAA
40674841 TTGGAAAA
1 TTGGAAAA
40674849 CAGGGGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (11 bp):
TTGGAAAAAAA
Found at i:40675777 original size:38 final size:38
Alignment explanation
Indices: 40675721--40675879 Score: 169
Period size: 38 Copynumber: 4.2 Consensus size: 38
40675711 CATCAGCTCA
* * * *
40675721 AAGCCTGCTAAGCACTAAGTCTGATTAACACCGGCA-T
1 AAGCCTGCTAGGCACTAAGCCTGAATAACACCGGAACT
*
40675758 CAAGCTTGCTAGGCACTAAGCCTGAATAACACCGGAACT
1 -AAGCCTGCTAGGCACTAAGCCTGAATAACACCGGAACT
* **
40675797 AATCCTGCTAGGCACTAAGCCTGAATAACA-CTAACACT
1 AAGCCTGCTAGGCACTAAGCCTGAATAACACCGGA-ACT
* * * * *
40675835 AAGCCTGCTAGGCACTTAGCCGGAATAGCACCAGCACT
1 AAGCCTGCTAGGCACTAAGCCTGAATAACACCGGAACT
40675873 AAGCCTG
1 AAGCCTG
40675880 AATAATACCC
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
37 2 0.02
38 98 0.96
39 2 0.02
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (38 bp):
AAGCCTGCTAGGCACTAAGCCTGAATAACACCGGAACT
Found at i:40677863 original size:27 final size:27
Alignment explanation
Indices: 40677833--40677884 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
40677823 GCAGGGTTTG
40677833 CCATAGAAGCTATCCCTTCATAATTTA
1 CCATAGAAGCTATCCCTTCATAATTTA
* *
40677860 CCATATAGGCTATCCCTTCATAATT
1 CCATAGAAGCTATCCCTTCATAATT
40677885 CGCCATAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (27 bp):
CCATAGAAGCTATCCCTTCATAATTTA
Found at i:40677890 original size:27 final size:27
Alignment explanation
Indices: 40677832--40677891 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
40677822 TGCAGGGTTT
*
40677832 GCCATAGAAGCTATCCCTTCATAATTT
1 GCCATAGAAGCTATCCCTTCATAATTC
* * *
40677859 ACCATATAGGCTATCCCTTCATAATTC
1 GCCATAGAAGCTATCCCTTCATAATTC
40677886 GCCATA
1 GCCATA
40677892 AAGTCTTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (27 bp):
GCCATAGAAGCTATCCCTTCATAATTC
Found at i:40677906 original size:27 final size:27
Alignment explanation
Indices: 40677876--40678120 Score: 203
Period size: 27 Copynumber: 9.1 Consensus size: 27
40677866 AGGCTATCCC
*
40677876 TTCATAATTCGCCATAAAGTCTTTTCT
1 TTCATAATTCGCCACAAAGTCTTTTCT
*
40677903 TTCATGATTCGCCACAAAGGT-TTTTCT
1 TTCATAATTCGCCACAAA-GTCTTTTCT
* * *
40677930 TTCAT-ATCTTGCCACAAAGACTTTTGT
1 TTCATAAT-TCGCCACAAAGTCTTTTCT
* * * *
40677957 TTCATATTTTGCCATAAA-TTTTTTCT
1 TTCATAATTCGCCACAAAGTCTTTTCT
* *
40677983 TTCATGATTCGCCACAAAGGT-TTTCCT
1 TTCATAATTCGCCACAAA-GTCTTTTCT
* * * *
40678010 TTCGTATTTCGCCATAAAAT-TTTTCCT
1 TTCATAATTCGCCACAAAGTCTTTT-CT
** * *
40678037 TTTGTATTTCGCCACAAAGGCTTTTCT
1 TTCATAATTCGCCACAAAGTCTTTTCT
* *
40678064 TTCATGATTCGCCACAAAGGCTTTTCT
1 TTCATAATTCGCCACAAAGTCTTTTCT
* * *
40678091 TTCATGATTCACCACAAAGGCTTTTCT
1 TTCATAATTCGCCACAAAGTCTTTTCT
40678118 TTC
1 TTC
40678121 TTGACGTATT
Statistics
Matches: 180, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
26 26 0.14
27 146 0.81
28 8 0.04
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (27 bp):
TTCATAATTCGCCACAAAGTCTTTTCT
Found at i:40677934 original size:54 final size:53
Alignment explanation
Indices: 40677876--40678120 Score: 237
Period size: 54 Copynumber: 4.6 Consensus size: 53
40677866 AGGCTATCCC
* *
40677876 TTCATAATTCGCCATAAAGTCTTTTCTTTCATGA-TTCGCCACAAAGGTTTTTCT
1 TTCATAATTCGCCACAAAGGCTTTTCTTTCAT-ATTTCGCCACAAA-GTTTTTCT
* * * * * *
40677930 TTCAT-ATCTTGCCACAAAGACTTTTGTTTCATATTTTGCCATAAATTTTTTCT
1 TTCATAAT-TCGCCACAAAGGCTTTTCTTTCATATTTCGCCACAAAGTTTTTCT
* * * *
40677983 TTCATGATTCGCCACAAAGG-TTTTCCTTTCGTATTTCGCCATAAAATTTTTCCT
1 TTCATAATTCGCCACAAAGGCTTTT-CTTTCATATTTCGCCACAAAGTTTTT-CT
** * *
40678037 TTTGTATTTCGCCACAAAGGCTTTTCTTTCATGA-TTCGCCACAAAGGCTTTTCT
1 TTCATAATTCGCCACAAAGGCTTTTCTTTCAT-ATTTCGCCACAAA-GTTTTTCT
* *
40678091 TTCATGATTCACCACAAAGGCTTTTCTTTC
1 TTCATAATTCGCCACAAAGGCTTTTCTTTC
40678121 TTGACGTATT
Statistics
Matches: 157, Mismatches: 26, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
52 4 0.03
53 47 0.30
54 97 0.62
55 9 0.06
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (53 bp):
TTCATAATTCGCCACAAAGGCTTTTCTTTCATATTTCGCCACAAAGTTTTTCT
Found at i:40679682 original size:24 final size:25
Alignment explanation
Indices: 40679645--40679743 Score: 105
Period size: 25 Copynumber: 4.0 Consensus size: 25
40679635 ACAATAAACA
* *
40679645 CGAATT-TCTAAAAAGTCTTTGTGG
1 CGAATTATCTGAAAAGACTTTGTGG
* *
40679669 CGAATTATCT-AAAACGGCTTTGTTG
1 CGAATTATCTGAAAA-GACTTTGTGG
*
40679694 CGAATTATCTGAAAAGACTTTATGG
1 CGAATTATCTGAAAAGACTTTGTGG
*
40679719 CGAATTCTCTGAAAA-ACCTTTGTGG
1 CGAATTATCTGAAAAGA-CTTTGTGG
40679744 TAAATTCTCT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
24 11 0.17
25 49 0.77
26 4 0.06
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (25 bp):
CGAATTATCTGAAAAGACTTTGTGG
Found at i:40679749 original size:25 final size:25
Alignment explanation
Indices: 40679721--40679834 Score: 81
Period size: 25 Copynumber: 4.5 Consensus size: 25
40679711 CTTTATGGCG
40679721 AATTCTCTGAAAAACCTTTGTGGTA
1 AATTCTCTGAAAAACCTTTGTGGTA
* *
40679746 AATTCTCT-AGAACATCTTTGTGGTA
1 AATTCTCTGA-AAAACCTTTGTGGTA
* * * *
40679771 AATCCTCT-AGAAAGCCTTTATGGTG
1 AATTCTCTGA-AAAACCTTTGTGGTA
* * * *
40679796 AATTCTCAGGAAAGCCTTTGCGGCT-
1 AATTCTCTGAAAAACCTTTGTGG-TA
40679821 AATTCTCTAGAAAA
1 AATTCTCT-GAAAA
40679835 TTCATATAGT
Statistics
Matches: 70, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
24 1 0.01
25 64 0.91
26 5 0.07
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (25 bp):
AATTCTCTGAAAAACCTTTGTGGTA
Found at i:40681568 original size:11 final size:10
Alignment explanation
Indices: 40681542--40681566 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40681532 TCAAAAAAAA
40681542 TTAAATATTT
1 TTAAATATTT
40681552 TTAAATATTT
1 TTAAATATTT
40681562 TTAAA
1 TTAAA
40681567 ATTAATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAAATATTT
Found at i:40688147 original size:15 final size:15
Alignment explanation
Indices: 40688119--40688157 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
40688109 AATTGCAAAC
* *
40688119 CAAAAACAAAATCTA
1 CAAAAATAATATCTA
*
40688134 GAAAAATAATATCTA
1 CAAAAATAATATCTA
40688149 CAAAAATAA
1 CAAAAATAA
40688158 AGGCCCCTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.67, C:0.13, G:0.03, T:0.18
Consensus pattern (15 bp):
CAAAAATAATATCTA
Found at i:40692074 original size:13 final size:13
Alignment explanation
Indices: 40692056--40692081 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40692046 GAAGAAATTG
40692056 ATAAATTTAACAT
1 ATAAATTTAACAT
40692069 ATAAATTTAACAT
1 ATAAATTTAACAT
40692082 GGAAAAACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAAATTTAACAT
Found at i:40694492 original size:3 final size:3
Alignment explanation
Indices: 40694486--40694541 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
40694476 AAGGCAAGAA
*
40694486 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GGT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
40694534 GAT GAT GA
1 GAT GAT GA
40694542 AATAACAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:40695150 original size:42 final size:42
Alignment explanation
Indices: 40695091--40695213 Score: 201
Period size: 42 Copynumber: 2.9 Consensus size: 42
40695081 AATTTTTTTT
* *
40695091 ACCGTTACAATATCAAATAATTATCCAAATTAAAAACTATTG
1 ACCGTTATAATACCAAATAATTATCCAAATTAAAAACTATTG
*
40695133 ATCGTTATAATACCAAATAATTATCCAAATTAAAAACTATTG
1 ACCGTTATAATACCAAATAATTATCCAAATTAAAAACTATTG
* *
40695175 ACCGTTATAATACCAAATAATTACCCTAATTAAAAACTA
1 ACCGTTATAATACCAAATAATTATCCAAATTAAAAACTA
40695214 CTAATAATTT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (42 bp):
ACCGTTATAATACCAAATAATTATCCAAATTAAAAACTATTG
Found at i:40696912 original size:3 final size:3
Alignment explanation
Indices: 40696904--40696937 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
40696894 ATTATATATT
40696904 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
40696938 CAAAATAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40697326 original size:18 final size:19
Alignment explanation
Indices: 40697291--40697328 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
40697281 GTGAAAATTT
* *
40697291 TGAAACTTAGATATTTAAA
1 TGAAACTTAGAGAGTTAAA
40697310 TGAAA-TTAGAGAGTTAAA
1 TGAAACTTAGAGAGTTAAA
40697328 T
1 T
40697329 CTAGTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (19 bp):
TGAAACTTAGAGAGTTAAA
Found at i:40697707 original size:24 final size:24
Alignment explanation
Indices: 40697680--40697726 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40697670 ATTGAAATGG
40697680 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
40697704 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
40697727 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:40698004 original size:40 final size:40
Alignment explanation
Indices: 40697883--40698022 Score: 126
Period size: 40 Copynumber: 3.5 Consensus size: 40
40697873 GACTTCGAGT
* * * * * *
40697883 CGATGAGACACTAGGTGTCAATTTACTACTTTGGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATT-ATC
* * * *
40697924 CGATGAGGCACTGGGTG-CCAA-T-TTACTTC-AGTTTAAC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGA-ATTATC
40697961 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
* *
40698001 CGATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
40698023 CTGGTGTGTT
Statistics
Matches: 78, Mismatches: 16, Indels: 11
0.74 0.15 0.10
Matches are distributed among these distances:
37 17 0.22
38 10 0.13
39 2 0.03
40 33 0.42
41 16 0.21
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
Found at i:40704439 original size:49 final size:50
Alignment explanation
Indices: 40704386--40704517 Score: 130
Period size: 49 Copynumber: 2.7 Consensus size: 50
40704376 GGCTCTCACG
* * *
40704386 AGCTTCCCAATTAATGGCTCTT-TGGAGCTTCCTGATA-TTGGCTCGCATA
1 AGCTTCCCGATTAATGGCTCTTAT-GAGCTTCCCGATATTTGGCTCACATA
* *
40704435 AGCTTCCTGATTACA--GCTCTTATGAGCTTCCCGTTATTTGGCTCACATA
1 AGCTTCCCGATTA-ATGGCTCTTATGAGCTTCCCGATATTTGGCTCACATA
* * *
40704484 AGCTTCTCGATTAGTGGCTCTCT-TAAGCTTCCCG
1 AGCTTCCCGATTAATGGCTCT-TATGAGCTTCCCG
40704518 TTTATATGCT
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
48 17 0.25
49 34 0.50
50 16 0.24
51 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.36
Consensus pattern (50 bp):
AGCTTCCCGATTAATGGCTCTTATGAGCTTCCCGATATTTGGCTCACATA
Found at i:40704487 original size:25 final size:24
Alignment explanation
Indices: 40704459--40704519 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
40704449 AGCTCTTATG
*
40704459 AGCTTCCCGTTATTTGGCTCACATA
1 AGCTTCCCGTTA-GTGGCTCACATA
* * *
40704484 AGCTTCTCGATTAGTGGCTCTCTTA
1 AGCTTCCCG-TTAGTGGCTCACATA
40704509 AGCTTCCCGTT
1 AGCTTCCCGTT
40704520 TATATGCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 2 0.07
25 25 0.83
26 3 0.10
ACGTcount: A:0.16, C:0.28, G:0.18, T:0.38
Consensus pattern (24 bp):
AGCTTCCCGTTAGTGGCTCACATA
Found at i:40708156 original size:29 final size:30
Alignment explanation
Indices: 40708123--40708188 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
40708113 CAAAAATTTG
* *
40708123 TGTATATAATT-ACATAAAATCAAAGTTCA
1 TGTATACAATTCACATAAAACCAAAGTTCA
*
40708152 TGTATACAATTGCACATTAAACCAAAGTTCA
1 TGTATACAATT-CACATAAAACCAAAGTTCA
40708183 TGTATA
1 TGTATA
40708189 ATTTTGACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 10 0.31
31 22 0.69
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (30 bp):
TGTATACAATTCACATAAAACCAAAGTTCA
Found at i:40717605 original size:23 final size:24
Alignment explanation
Indices: 40717578--40717622 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
40717568 GAAAAATATT
*
40717578 AAATAT-ATATTTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
40717601 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
40717623 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:40717733 original size:9 final size:9
Alignment explanation
Indices: 40717719--40717746 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
40717709 TTTTGTTACA
40717719 ACAATTAAT
1 ACAATTAAT
40717728 ACAATTAAT
1 ACAATTAAT
40717737 ACAATTAAT
1 ACAATTAAT
40717746 A
1 A
40717747 ATTTGATAAA
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:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:40717768 original size:68 final size:68
Alignment explanation
Indices: 40717689--40717898 Score: 379
Period size: 68 Copynumber: 3.1 Consensus size: 68
40717679 TCAAGTTTGT
*
40717689 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
40717754 AAA
66 AAA
*
40717757 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAGTACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
40717822 AAA
66 AAA
40717825 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
40717888 AAT
66 AAA
40717891 TTTACTAA
1 TTTACTAA
40717899 CAATTAATTT
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
66 27 0.20
67 1 0.01
68 110 0.80
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:40717908 original size:16 final size:16
Alignment explanation
Indices: 40717887--40717928 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
40717877 AATAATTTGA
*
40717887 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
40717903 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
40717919 TAGTTTTAAT
1 TAATTTTAAT
40717929 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:40719075 original size:25 final size:25
Alignment explanation
Indices: 40719023--40719075 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
40719013 TTTCATTTTC
* *
40719023 TTTATTTTTTTTATTAATTAGTTTT
1 TTTATTTTTTTTATTAATTAATTAT
*
40719048 TTTATTCTTTTTTA-TATTTAATTAT
1 TTTATT-TTTTTTATTAATTAATTAT
40719073 TTT
1 TTT
40719076 TAAAAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTATTTTTTTTATTAATTAATTAT
Found at i:40719194 original size:23 final size:24
Alignment explanation
Indices: 40719142--40719200 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
40719132 TAATATAATT
*
40719142 ATTATTT-TTATTTATTTATATGTA
1 ATTATTTATT-TTTATCTATATGTA
40719166 ATTA-TTATTTTTATCTATATGT-
1 ATTATTTATTTTTATCTATATGTA
40719188 ATATATTTATTTT
1 AT-TATTTATTTT
40719201 AGTATACATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 2 0.06
23 16 0.52
24 13 0.42
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (24 bp):
ATTATTTATTTTTATCTATATGTA
Found at i:40719197 original size:27 final size:27
Alignment explanation
Indices: 40719116--40719198 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 27
40719106 ATACGCATAT
* *
40719116 TTATTTTTTTGTAGTATA-ATATAATTA
1 TTATTTTTATCTA-TATATATATAATTA
* * *
40719143 TTATTTTTATTTATTTATATGTAATTA
1 TTATTTTTATCTATATATATATAATTA
* *
40719170 TTATTTTTATCTATATGTATATATTTA
1 TTATTTTTATCTATATATATATAATTA
40719197 TT
1 TT
40719199 TTAGTATACA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
26 3 0.07
27 43 0.93
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (27 bp):
TTATTTTTATCTATATATATATAATTA
Found at i:40720168 original size:216 final size:218
Alignment explanation
Indices: 40719793--40720226 Score: 809
Period size: 217 Copynumber: 2.0 Consensus size: 218
40719783 ACTTATTATT
*
40719793 GGGAATTCAACACGTTGTGTCCTAACGTATTGGATGTGACGCATTGATTTCTCGAAATGAATATT
1 GGGAATTCAACACGTTGTGCCCTAACGTATTGGATGTGACGCATTGATTTCTCGAAATGAATATT
40719858 TTAAAAAAAATAATAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATTGTGCCCTAACGTAT
66 TTAAAAAAAATAATAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATTGTGCCCTAACGTAT
40719923 TAGGCCGCGATTTCTTAAATCTTGAATAAA-GGATATTCTTTTAAATTTTTATTACACTAGTATT
131 TAGGCCGCGATTTCTTAAATCTTGAATAAATGGATATTCTTTTAAATTTTTATTACACTAGTATT
*
40719987 TTGGCCTAATTTCTTTTTGGGGA
196 TTGGCCTAATTCCTTTTTGGGGA
40720010 GGGAATTCAACACGTTGTGCCCTAACGTATTGGATGTGACGCATTGATTTCTCGAAATGAATATT
1 GGGAATTCAACACGTTGTGCCCTAACGTATTGGATGTGACGCATTGATTTCTCGAAATGAATATT
*
40720075 TT-TAAAAAATAATAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATTGTGCCCTAACGTAT
66 TTAAAAAAAATAATAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATTGTGCCCTAACGTAT
* *
40720139 TGGGCCGCGATTTCTTAAATCTTGAATAAATGGATATTCTTTTAAATTTTTATTACATTAGTATT
131 TAGGCCGCGATTTCTTAAATCTTGAATAAATGGATATTCTTTTAAATTTTTATTACACTAGTATT
40720204 TTGGCCTAATTCCTTTTTGGGGA
196 TTGGCCTAATTCCTTTTTGGGGA
40720227 AAATTAAAGT
Statistics
Matches: 211, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
216 90 0.43
217 121 0.57
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (218 bp):
GGGAATTCAACACGTTGTGCCCTAACGTATTGGATGTGACGCATTGATTTCTCGAAATGAATATT
TTAAAAAAAATAATAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATTGTGCCCTAACGTAT
TAGGCCGCGATTTCTTAAATCTTGAATAAATGGATATTCTTTTAAATTTTTATTACACTAGTATT
TTGGCCTAATTCCTTTTTGGGGA
Found at i:40721367 original size:17 final size:17
Alignment explanation
Indices: 40721345--40721377 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40721335 CACTCAGCAT
40721345 CTTTCTTCCCAAACTTC
1 CTTTCTTCCCAAACTTC
*
40721362 CTTTCTTGCCAAACTT
1 CTTTCTTCCCAAACTT
40721378 TCTCCAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.36, G:0.03, T:0.42
Consensus pattern (17 bp):
CTTTCTTCCCAAACTTC
Found at i:40725106 original size:22 final size:23
Alignment explanation
Indices: 40725078--40725125 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
40725068 TAAGGTTAGA
40725078 GTTTTTAAT-TTTAAG-GGATAAG
1 GTTTTTAATATTTAAGAGG-TAAG
*
40725100 GTTTTTAATATTTTAGAGGTAAG
1 GTTTTTAATATTTAAGAGGTAAG
40725123 GTT
1 GTT
40725126 AGGGTTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 9 0.39
23 12 0.52
24 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (23 bp):
GTTTTTAATATTTAAGAGGTAAG
Found at i:40730292 original size:19 final size:20
Alignment explanation
Indices: 40730253--40730293 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
40730243 CTATTTGTTT
*
40730253 TTTACATTTTTTTACATCAAA
1 TTTACATTCTTTTA-ATCAAA
40730274 TTTACATTCTTTT-ATCAAA
1 TTTACATTCTTTTAATCAAA
40730293 T
1 T
40730294 CAACTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTACATTCTTTTAATCAAA
Found at i:40733880 original size:21 final size:21
Alignment explanation
Indices: 40733854--40733941 Score: 131
Period size: 21 Copynumber: 4.2 Consensus size: 21
40733844 GAAGCTCGAA
40733854 AGCTGAACAGAAGCTCATAAG
1 AGCTGAACAGAAGCTCATAAG
*
40733875 AGCTGAACAGAAGCTCGTAAG
1 AGCTGAACAGAAGCTCATAAG
* * *
40733896 GGCTGAATAGAAGCTCGTAAG
1 AGCTGAACAGAAGCTCATAAG
*
40733917 AGCTGAACAGAAACTCATAAG
1 AGCTGAACAGAAGCTCATAAG
40733938 AGCT
1 AGCT
40733942 AATCCATCCA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.16
Consensus pattern (21 bp):
AGCTGAACAGAAGCTCATAAG
Found at i:40733908 original size:42 final size:42
Alignment explanation
Indices: 40733843--40733941 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
40733833 ATAAGTCAAT
40733843 AGAAGCTCG-AA-AGCTGAACAGAAGCTCATAAGAGCTGAAC
1 AGAAGCTCGTAAGAGCTGAACAGAAGCTCATAAGAGCTGAAC
* * *
40733883 AGAAGCTCGTAAGGGCTGAATAGAAGCTCGTAAGAGCTGAAC
1 AGAAGCTCGTAAGAGCTGAACAGAAGCTCATAAGAGCTGAAC
* *
40733925 AGAAACTCATAAGAGCT
1 AGAAGCTCGTAAGAGCT
40733942 AATCCATCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
40 9 0.18
41 2 0.04
42 40 0.78
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.15
Consensus pattern (42 bp):
AGAAGCTCGTAAGAGCTGAACAGAAGCTCATAAGAGCTGAAC
Found at i:40734133 original size:19 final size:18
Alignment explanation
Indices: 40734111--40734153 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
40734101 CCATTTCAAT
40734111 ATTATAATTCCAACAATAA
1 ATTAT-ATTCCAACAATAA
*
40734130 ATTAT-TTCTAACAATAA
1 ATTATATTCCAACAATAA
*
40734147 AATATAT
1 ATTATAT
40734154 ATATATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 15 0.71
18 1 0.05
19 5 0.24
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTATATTCCAACAATAA
Found at i:40734666 original size:22 final size:21
Alignment explanation
Indices: 40734640--40734686 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
40734630 TTATTCATCA
* *
40734640 AAAACATCTAATATTTATTAAT
1 AAAACATCCAAAATTT-TTAAT
*
40734662 AAAACTTCCAAAATTTTTAAT
1 AAAACATCCAAAATTTTTAAT
40734683 AAAA
1 AAAA
40734687 TAAAAAACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAACATCCAAAATTTTTAAT
Found at i:40740214 original size:68 final size:71
Alignment explanation
Indices: 40740083--40740218 Score: 188
Period size: 68 Copynumber: 1.9 Consensus size: 71
40740073 AATTAAACCT
* * * *
40740083 AATCATTTTAATATTAAATTAATATAATATTTATCTAAAAGATAAACATTAAATTAAATTTAATA
1 AATCACTTTAATATTAAATTAATAAAATATCTATCT-AAAGATAAACATTAAATTAAAGTTAATA
40740148 TTAAGAC
65 TTAAGAC
* *
40740155 AATCACTTTAATATTAATTTAATAAAATA-CTAT-T-AAGATAAATATTAAATTAAAGTTAATAT
1 AATCACTTTAATATTAAATTAATAAAATATCTATCTAAAGATAAACATTAAATTAAAGTTAATAT
40740217 TA
66 TA
40740219 GATCTATTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
68 28 0.48
70 1 0.02
71 3 0.05
72 26 0.45
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.40
Consensus pattern (71 bp):
AATCACTTTAATATTAAATTAATAAAATATCTATCTAAAGATAAACATTAAATTAAAGTTAATAT
TAAGAC
Found at i:40751417 original size:36 final size:36
Alignment explanation
Indices: 40751369--40751439 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
40751359 ATCAAAGGCT
*
40751369 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
*
40751405 ATAATTAGAAGCTGTATACAATTAAAACTCTAAGA
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGA
40751440 TTAAATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (36 bp):
ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:40762521 original size:13 final size:13
Alignment explanation
Indices: 40762503--40762531 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40762493 GAAGTACTGT
40762503 GCATGGGTTTAAG
1 GCATGGGTTTAAG
40762516 GCATGGGTTTAAG
1 GCATGGGTTTAAG
40762529 GCA
1 GCA
40762532 GTTTAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.10, G:0.38, T:0.28
Consensus pattern (13 bp):
GCATGGGTTTAAG
Found at i:40768802 original size:24 final size:26
Alignment explanation
Indices: 40768775--40768825 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
40768765 CTACCAAGCT
40768775 TTAAGCTAAAC-A-CATACCAAAACA
1 TTAAGCTAAACTATCATACCAAAACA
*
40768799 TTAAGCTAAGCTATCATACCAAAACA
1 TTAAGCTAAACTATCATACCAAAACA
40768825 T
1 T
40768826 GTACAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
25 1 0.04
26 13 0.54
ACGTcount: A:0.49, C:0.24, G:0.06, T:0.22
Consensus pattern (26 bp):
TTAAGCTAAACTATCATACCAAAACA
Found at i:40771198 original size:17 final size:17
Alignment explanation
Indices: 40771176--40771209 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40771166 TAGACCAATT
40771176 TTATACAATTATATATA
1 TTATACAATTATATATA
*
40771193 TTATACAATTTTATATA
1 TTATACAATTATATATA
40771210 CAAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATACAATTATATATA
Found at i:40772543 original size:24 final size:24
Alignment explanation
Indices: 40772514--40772565 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40772504 TTTCTAGAAG
* *
40772514 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
40772538 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
40772562 ATTT
1 ATTT
40772566 GACCTACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:40773998 original size:24 final size:24
Alignment explanation
Indices: 40773971--40774064 Score: 71
Period size: 24 Copynumber: 3.9 Consensus size: 24
40773961 CAACTCACAA
* *
40773971 GAGCGTCCCGTTATTAGCTCTCAT
1 GAGCTTCCCGATATTAGCTCTCAT
* * * *
40773995 GAGCATCCCAATATTGGCTCTCTT
1 GAGCTTCCCGATATTAGCTCTCAT
* * * *
40774019 CAGCTTCCTGATATATGGCTCTCAC
1 GAGCTTCCCGATAT-TAGCTCTCAT
* *
40774044 GAGCTTCCCGTTAATAGCTCT
1 GAGCTTCCCGATATTAGCTCT
40774065 TTTGAGTATC
Statistics
Matches: 53, Mismatches: 16, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
24 35 0.66
25 18 0.34
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.33
Consensus pattern (24 bp):
GAGCTTCCCGATATTAGCTCTCAT
Found at i:40774157 original size:25 final size:25
Alignment explanation
Indices: 40774129--40774272 Score: 123
Period size: 27 Copynumber: 5.6 Consensus size: 25
40774119 TTTATGAGTG
*
40774129 TCCCGA-TATATGGCTCTTTGGAGCT
1 TCCCGATTA-ATGGCTCTTTTGAGCT
*
40774154 TCCCGATTAAAGGCTCTTTCATGAGCT
1 TCCCGATTAATGGCTCTTT--TGAGCT
*
40774181 TCCCGATTAAAGGCTCTTTAATGAGCT
1 TCCCGATTAATGGCTCTTT--TGAGCT
***
40774208 TCCCGATTAATGGCTCTCCAGAGCT
1 TCCCGATTAATGGCTCTTTTGAGCT
* ***
40774233 ACCCGA-TAATGGCTCACATGAGCT
1 TCCCGATTAATGGCTCTTTTGAGCT
40774257 TCCCG-TTATATGGCTC
1 TCCCGATTA-ATGGCTC
40774273 GAGAGAGAGC
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
24 21 0.21
25 32 0.31
26 2 0.02
27 47 0.46
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (25 bp):
TCCCGATTAATGGCTCTTTTGAGCT
Found at i:40774185 original size:27 final size:26
Alignment explanation
Indices: 40774149--40774261 Score: 133
Period size: 27 Copynumber: 4.4 Consensus size: 26
40774139 TGGCTCTTTG
40774149 GAGCTTCCCGATTAAAGGCTCTTTCAT
1 GAGCTTCCCGATTAAAGGCTC-TTCAT
*
40774176 GAGCTTCCCGATTAAAGGCTCTTTAAT
1 GAGCTTCCCGATTAAAGGCTC-TTCAT
* *
40774203 GAGCTTCCCGATTAATGGCTCTCCA-
1 GAGCTTCCCGATTAAAGGCTCTTCAT
* * *
40774228 GAGCTACCCGA-TAATGGCTC-ACAT
1 GAGCTTCCCGATTAAAGGCTCTTCAT
40774252 GAGCTTCCCG
1 GAGCTTCCCG
40774262 TTATATGGCT
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
23 2 0.03
24 18 0.23
25 10 0.13
26 2 0.03
27 46 0.59
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (26 bp):
GAGCTTCCCGATTAAAGGCTCTTCAT
Found at i:40774185 original size:52 final size:51
Alignment explanation
Indices: 40774129--40774247 Score: 136
Period size: 52 Copynumber: 2.3 Consensus size: 51
40774119 TTTATGAGTG
*
40774129 TCCCGATATATGGCTCTTT-GGAGCTTCCCGATTAAAGGCTCTTTCATGAGCT
1 TCCCGATATATGGCTCTTTAGGAGCTTCCCGATTAAAGGCTC-TCCA-GAGCT
* * *
40774181 TCCCGAT-TAAAGGCTCTTTAATGAGCTTCCCGATTAATGGCTCTCCAGAGCT
1 TCCCGATAT-ATGGCTCTTT-AGGAGCTTCCCGATTAAAGGCTCTCCAGAGCT
*
40774233 ACCCGATA-ATGGCTC
1 TCCCGATATATGGCTC
40774248 ACATGAGCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
51 7 0.12
52 27 0.47
53 3 0.05
54 20 0.35
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (51 bp):
TCCCGATATATGGCTCTTTAGGAGCTTCCCGATTAAAGGCTCTCCAGAGCT
Found at i:40774358 original size:39 final size:39
Alignment explanation
Indices: 40774304--40774382 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 39
40774294 GTGCTCGTAA
40774304 AAGCATTCCCGAATATGAATTGATAGG-TTACAGATTTAT
1 AAGCATTCCCGAATATGAATTGA-AGGATTACAGATTTAT
*
40774343 AAGCATTCCCGAATATGAATTGACGGATTACAGATTTAT
1 AAGCATTCCCGAATATGAATTGAAGGATTACAGATTTAT
40774382 A
1 A
40774383 CACTTCATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 2 0.05
39 36 0.95
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (39 bp):
AAGCATTCCCGAATATGAATTGAAGGATTACAGATTTAT
Found at i:40779414 original size:12 final size:12
Alignment explanation
Indices: 40779384--40779416 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
40779374 AGATAATGTA
*
40779384 GGAGATCAAGAT
1 GGAGATGAAGAT
40779396 GGAGATGAAGAT
1 GGAGATGAAGAT
40779408 GGAGATGAA
1 GGAGATGAA
40779417 TATGAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.39, T:0.15
Consensus pattern (12 bp):
GGAGATGAAGAT
Found at i:40779649 original size:4 final size:4
Alignment explanation
Indices: 40779640--40779681 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
40779630 TATCAAAATA
*
40779640 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT ATGT TT
1 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TT
40779682 ATAAAAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.02, C:0.00, G:0.24, T:0.74
Consensus pattern (4 bp):
TTGT
Found at i:40779836 original size:74 final size:75
Alignment explanation
Indices: 40779684--40779875 Score: 260
Period size: 74 Copynumber: 2.5 Consensus size: 75
40779674 GTATGTTTAT
** * * *
40779684 AAAAAATGAATAAATTGTTTGCGTGCATTGTATTGTATTGTTACATCAATAATCTACTTATTTAC
1 AAAAAATGAATAAATTGTTTGTTTGTATTGTATTGTATTGTTAAATCAATAATATACTTATTTAC
**
40779749 ATTTTAT-CG
66 ATTTTATAAA
*
40779758 AAAAAATGAATAAATTGTTTGTTTGTATTGTATTGTATTTTTAAATCAATAATATACTTATTTAC
1 AAAAAATGAATAAATTGTTTGTTTGTATTGTATTGTATTGTTAAATCAATAATATACTTATTTAC
40779823 ATTTTATAAAA
66 ATTTTAT-AAA
* * *
40779834 AAAAAAGAGAATAGATTGTTTGTTTATATTGTATTGTATTGT
1 AAAAAA-TGAATAAATTGTTTGTTTGTATTGTATTGTATTGT
40779876 ATCCTGATCA
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
74 66 0.64
76 6 0.06
77 31 0.30
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (75 bp):
AAAAAATGAATAAATTGTTTGTTTGTATTGTATTGTATTGTTAAATCAATAATATACTTATTTAC
ATTTTATAAA
Found at i:40780216 original size:30 final size:31
Alignment explanation
Indices: 40780182--40780245 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
40780172 ACTTATTTTA
*
40780182 TTGTTAA-TTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTTATTATTATTTTAAAGGCAT
*
40780212 TTGTTAATTTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTTATTATTATTTTAAAGGCAT
40780243 TTG
1 TTG
40780246 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (31 bp):
TTGTTAATTTTTATTATTATTTTAAAGGCAT
Found at i:40782397 original size:20 final size:20
Alignment explanation
Indices: 40782356--40782401 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
40782346 ATTTCCCAAG
**
40782356 GTATCAATACATAGGTTGAA
1 GTATCAATACATACCTTGAA
40782376 GTATCAATACATACCTCT-AA
1 GTATCAATACATACCT-TGAA
40782396 GTATCA
1 GTATCA
40782402 GTACTTAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (20 bp):
GTATCAATACATACCTTGAA
Found at i:40787095 original size:72 final size:72
Alignment explanation
Indices: 40786978--40787130 Score: 252
Period size: 72 Copynumber: 2.1 Consensus size: 72
40786968 AACTAGCTTT
** * *
40786978 CTCGACATTGACAAATTTGACATATAACTCTAGTATAACATTTCCAATAGAGCAATGTGTATATA
1 CTCGACATCAACAAATTTGAAATATAACTCTAGTATAACATTTCCAATAGAGCAATGTGTATAGA
40787043 GCATTAA
66 GCATTAA
* *
40787050 CTCGACATCAACAAATTTGAAATATAGCTCTAGTATAACATTTCCAATAGAGCAATGTGTATCGA
1 CTCGACATCAACAAATTTGAAATATAACTCTAGTATAACATTTCCAATAGAGCAATGTGTATAGA
40787115 GCATTAA
66 GCATTAA
40787122 CTCGACATC
1 CTCGACATC
40787131 CATTGTAACA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 75 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (72 bp):
CTCGACATCAACAAATTTGAAATATAACTCTAGTATAACATTTCCAATAGAGCAATGTGTATAGA
GCATTAA
Found at i:40788592 original size:11 final size:13
Alignment explanation
Indices: 40788576--40788609 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
40788566 AATTTTAGGG
40788576 AAAAATTTCG-T-
1 AAAAATTTCGTTC
40788587 AAAAATTTCGTTC
1 AAAAATTTCGTTC
40788600 AAAAATTTCG
1 AAAAATTTCG
40788610 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:40789917 original size:76 final size:76
Alignment explanation
Indices: 40789791--40789987 Score: 295
Period size: 76 Copynumber: 2.6 Consensus size: 76
40789781 NNNNNNNNNN
* * * *
40789791 GCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATTTGAAGGG
1 GCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATCTTTAAATGTGAAAGG
40789856 GGTTGCTAAGT
66 GGTTGCTAAGT
* * * * *
40789867 GCTGATTCCTCGAATGATTGGTGGTTGCTACGTGTTGATTCCACCATATCTTTGAATGTGAAAGG
1 GCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATCTTTAAATGTGAAAGG
40789932 GGTTGCTAAGT
66 GGTTGCTAAGT
* *
40789943 GCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACC
1 GCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACC
40789988 GATAACGGTT
Statistics
Matches: 106, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 106 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (76 bp):
GCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATCTTTAAATGTGAAAGG
GGTTGCTAAGT
Found at i:40796756 original size:39 final size:39
Alignment explanation
Indices: 40796685--40796814 Score: 188
Period size: 39 Copynumber: 3.3 Consensus size: 39
40796675 ATAGAATATC
* * *
40796685 GATTATACTGAATGTTTGCTCAAATGAGCATTATCCACT
1 GATTATACTAAATGCTTGCTCAAACGAGCATTATCCACT
* * *
40796724 GATTGTACTAAATGCTTGCTCAAACAAACATTATCCACT
1 GATTATACTAAATGCTTGCTCAAACGAGCATTATCCACT
*
40796763 GATTATACTAAATGCTTGCTCAAACGAGTATTATCCACT
1 GATTATACTAAATGCTTGCTCAAACGAGCATTATCCACT
*
40796802 AATTATACTAAAT
1 GATTATACTAAAT
40796815 AAGATTTTCT
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (39 bp):
GATTATACTAAATGCTTGCTCAAACGAGCATTATCCACT
Found at i:40800031 original size:31 final size:31
Alignment explanation
Indices: 40799985--40800055 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
40799975 GACTCTCGAA
* *
40799985 TTTTCAAAAACTTTATCCTAAAATTCTCAGG
1 TTTTCAGAAATTTTATCCTAAAATTCTCAGG
* * * * *
40800016 TTTTTAGAAATTTTATCTTGAGATTCTCGGG
1 TTTTCAGAAATTTTATCCTAAAATTCTCAGG
40800047 TTTTCAGAA
1 TTTTCAGAA
40800056 TTCAATCTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.44
Consensus pattern (31 bp):
TTTTCAGAAATTTTATCCTAAAATTCTCAGG
Found at i:40811284 original size:652 final size:652
Alignment explanation
Indices: 40810034--40811333 Score: 2271
Period size: 652 Copynumber: 2.0 Consensus size: 652
40810024 TTGATACAAC
* *
40810034 AAGAGAATGGTTATTTTACTTACCCCTCGGTTCTATTACAACGTGAGATGACTTATTTTGTGTAT
1 AAGAGAATAGTTATTTTACTTACCCCTCGGTTCTATTACAACGTGAGATGACTTATCTTGTGTAT
* *
40810099 TTCTTGACAGATTTTTCCCAGCATCGCAAGCAGCTGAACTTAAAAGAGACATAGTGGGAATTTGC
66 TTCTTGACAAATTTTTCCCAACATCGCAAGCAGCTGAACTTAAAAGAGACATAGTGGGAATTTGC
40810164 CAAATGGAGAGTGAATCGCTCTATGACTATTGGGAGCGGTACAAAAATCTGTGTGCAAGTTGTCC
131 CAAATGGAGAGTGAATCGCTCTATGACTATTGGGAGCGGTACAAAAATCTGTGTGCAAGTTGTCC
40810229 TCAACACAGTTTGACCGAACAATCACTTCTACAGTATTTCTACGAGGGTTTGCTCCCTATGAAAA
196 TCAACACAGTTTGACCGAACAATCACTTCTACAGTATTTCTACGAGGGTTTGCTCCCTATGAAAA
40810294 TGAAGATGATTGACGCTGCTAATGGAGGGGCACTTGTCAATATGACTCCTCAAAGGGCAAGAGAA
261 TGAAGATGATTGACGCTGCTAATGGAGGGGCACTTGTCAATATGACTCCTCAAAGGGCAAGAGAA
* * * ** *
40810359 TTGATATCCACCATGGCGGCAAATTTTCAATAGTATCGACCGAATTCGGAACCCATAAGACGAGT
326 TTGATATCCACCATGGCGGCAAATTCTCAACAGTATCGACCAAATTCAAAACCCACAAGACGAGT
* * *
40810424 TAATGGGGTAAACGTTTCATTCTTAGAAGATAAATTGGATAGGCTTACTAATATTGTTCAATCTT
391 TAATGGGGTAAACGTTTCATCCTTAAAAGATAAATTAGATAGGCTTACTAATATTGTTCAATCTT
* *
40810489 TACTTACAGAAAAGAAGAATCTGACCCAACTGTGTGGAATTTGTACTATGTTTGAACATCCGATG
456 TACTTACAGAAAAGAAGAATCTGACCCAACTGTGTGGAATTTGTACTACGTTTGAACATCCAATG
40810554 GATTTGTGCCCAATCATTAACGACAATTCAATGGCACATGTTGATGCTGTTGGAGGTTTTCTAGG
521 GATTTGTGCCCAATCATTAACGACAATTCAATGGCACATGTTGATGCTGTTGGAGGTTTTCTAGG
*
40810619 ACCTCCACAAAGACGCTATGATCCTTTCTCCAACACTTATAATCCCGAGTGGAATGATCATCCTT
586 ACCTCCACAAAGACGCTATGATCCTTTCTCCAACACTTATAATCCCGAGTGGAAGGATCATCCTT
40810684 AG
651 AG
40810686 AAGAGAATAGTTATTTTACTTACCCC-CTGGTTCTATTACAACGTGAGATGACTTATCTTGTGTA
1 AAGAGAATAGTTATTTTACTTACCCCTC-GGTTCTATTACAACGTGAGATGACTTATCTTGTGTA
* ** *
40810750 TTTCTTGACAAATTTTTCCCAACATTGTGAGTAGCTGAACTTAAAAGAGACATAGTGGGAATTTG
65 TTTCTTGACAAATTTTTCCCAACATCGCAAGCAGCTGAACTTAAAAGAGACATAGTGGGAATTTG
40810815 CCAAATGGAGAGTGAATCGCTCTATGACTATTGGGAGCGGTACAAAAATCTGTGTGCAAGTTGTC
130 CCAAATGGAGAGTGAATCGCTCTATGACTATTGGGAGCGGTACAAAAATCTGTGTGCAAGTTGTC
* * * * *
40810880 CTCAACACAGTTTGACCGAGCAATCACTTCTTCAGTATTTCTATGAGGGTTTGCTCCTTATGGAA
195 CTCAACACAGTTTGACCGAACAATCACTTCTACAGTATTTCTACGAGGGTTTGCTCCCTATGAAA
* *
40810945 ATGAAGATGATTGACGCTGCTAGTGGATGGGCACTTGTCAATATGACTCCTCAAAGGGCAAGAGA
260 ATGAAGATGATTGACGCTGCTAATGGAGGGGCACTTGTCAATATGACTCCTCAAAGGGCAAGAGA
*
40811010 ATTGATATCCACCATGGCGGCAAATTCTCAACAGTATCGACCAAATTCAAAACCCACAAGACGGG
325 ATTGATATCCACCATGGCGGCAAATTCTCAACAGTATCGACCAAATTCAAAACCCACAAGACGAG
40811075 TTAATGGGGTAAACGTTTCATCCTTAAAAGATAAATTAGATAGGCTTACTAATATTGTTCAATCT
390 TTAATGGGGTAAACGTTTCATCCTTAAAAGATAAATTAGATAGGCTTACTAATATTGTTCAATCT
*
40811140 TTGCTTACAGAAAAGAAGAATCTGACCCAACTGTGTGGAATTTGTACTACGTTTGAACATCCAAT
455 TTACTTACAGAAAAGAAGAATCTGACCCAACTGTGTGGAATTTGTACTACGTTTGAACATCCAAT
* *
40811205 GGATTTGTGCCCAATCCTTAACGACAATTCAATGGCACATGTTGATGCTGTTGGAGGTTTT-TCG
520 GGATTTGTGCCCAATCATTAACGACAATTCAATGGCACATGTTGATGCTGTTGGAGGTTTTCT-A
* *
40811269 GGACCTCCGCAAAGACGCTATGATCCTTTCTCCAACACTTATAATCCCGGGTGGAAGGATCATCC
584 GGACCTCCACAAAGACGCTATGATCCTTTCTCCAACACTTATAATCCCGAGTGGAAGGATCATCC
40811334 CAACTTGAAT
Statistics
Matches: 613, Mismatches: 33, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
651 2 0.00
652 611 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (652 bp):
AAGAGAATAGTTATTTTACTTACCCCTCGGTTCTATTACAACGTGAGATGACTTATCTTGTGTAT
TTCTTGACAAATTTTTCCCAACATCGCAAGCAGCTGAACTTAAAAGAGACATAGTGGGAATTTGC
CAAATGGAGAGTGAATCGCTCTATGACTATTGGGAGCGGTACAAAAATCTGTGTGCAAGTTGTCC
TCAACACAGTTTGACCGAACAATCACTTCTACAGTATTTCTACGAGGGTTTGCTCCCTATGAAAA
TGAAGATGATTGACGCTGCTAATGGAGGGGCACTTGTCAATATGACTCCTCAAAGGGCAAGAGAA
TTGATATCCACCATGGCGGCAAATTCTCAACAGTATCGACCAAATTCAAAACCCACAAGACGAGT
TAATGGGGTAAACGTTTCATCCTTAAAAGATAAATTAGATAGGCTTACTAATATTGTTCAATCTT
TACTTACAGAAAAGAAGAATCTGACCCAACTGTGTGGAATTTGTACTACGTTTGAACATCCAATG
GATTTGTGCCCAATCATTAACGACAATTCAATGGCACATGTTGATGCTGTTGGAGGTTTTCTAGG
ACCTCCACAAAGACGCTATGATCCTTTCTCCAACACTTATAATCCCGAGTGGAAGGATCATCCTT
AG
Found at i:40812309 original size:28 final size:26
Alignment explanation
Indices: 40812278--40812336 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
40812268 TTAAGATGAC
**
40812278 TATATA-AAAATTTTAATAAATAAAAA
1 TATATATAAAATTAAAAT-AATAAAAA
* *
40812304 TATATATTAAATTAAAATAATATAAA
1 TATATATAAAATTAAAATAATAAAAA
40812330 TATATAT
1 TATATAT
40812337 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TATATATAAAATTAAAATAATAAAAA
Found at i:40812326 original size:18 final size:17
Alignment explanation
Indices: 40812281--40812331 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
40812271 AGATGACTAT
* *
40812281 ATAAAAAT-TTTAATAA
1 ATAAAAATATATATTAA
40812297 ATAAAAATATATATTAA
1 ATAAAAATATATATTAA
*
40812314 ATTAAAATA-ATA-TAA
1 ATAAAAATATATATTAA
40812329 ATA
1 ATA
40812332 TATATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 5 0.17
16 11 0.37
17 14 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAAAATATATATTAA
Found at i:40813943 original size:16 final size:16
Alignment explanation
Indices: 40813899--40813945 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
40813889 TATTATAAAA
*
40813899 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
40813915 TATTATT-AAATATAT
1 TATAATTAAAATATAT
40813930 TATAATTAAAATATAT
1 TATAATTAAAATATAT
40813946 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:40813946 original size:61 final size:60
Alignment explanation
Indices: 40813881--40814067 Score: 174
Period size: 61 Copynumber: 3.1 Consensus size: 60
40813871 TCAAATCATA
40813881 ATATATGATATTATAAAATATAATTTAACATAATTATTATTAAATATATTATAATTAAAAT
1 ATATATGATATTATAAAATATAATTTAACATAATTATTATTAAATATATT-TAATTAAAAT
* * * * * *
40813942 ATATA--AT-TTAATAAAAT-T--CTT-A-ATAATTAATATTCGTATATAAATTTACTCAAATCA
1 ATATATGATATT-ATAAAATATAATTTAACATAATTATTA-T--TAAATATATTTAATTAAA--A
40813999 T
60 T
*
40814000 AATATATGATACTATAAAATATAATTTAACATAATTATTATTAAATATATTTTAATTAAAAT
1 -ATATATGATATTATAAAATATAATTTAACATAATTATTATTAAATATA-TTTAATTAAAAT
40814062 ATATAT
1 ATATAT
40814068 TTTAATAAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
54 9 0.09
55 2 0.02
56 8 0.08
57 8 0.08
58 5 0.05
59 14 0.14
61 20 0.21
62 4 0.04
63 6 0.06
64 10 0.10
65 2 0.02
66 9 0.09
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (60 bp):
ATATATGATATTATAAAATATAATTTAACATAATTATTATTAAATATATTTAATTAAAAT
Found at i:40813997 original size:120 final size:120
Alignment explanation
Indices: 40813784--40814096 Score: 563
Period size: 120 Copynumber: 2.6 Consensus size: 120
40813774 TTAATCATAT
*
40813784 TTTAACATAATTATTATTAAATATATTATAATTAAAATATACAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * *
40813849 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATATTATAAAATATAA
66 CAATATTCGTATATAAATTTACTCAAATCATAATATATGATACTATAAAATATAA
40813904 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
*
40813969 TAATATTCGTATATAAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCGTATATAAATTTACTCAAATCATAATATATGATACTATAAAATATAA
* *
40814024 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATATTTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
40814089 CAATATTC
66 CAATATTC
40814097 TTANNNNNNN
Statistics
Matches: 185, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 185 1.00
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
CAATATTCGTATATAAATTTACTCAAATCATAATATATGATACTATAAAATATAA
Found at i:40814065 original size:18 final size:17
Alignment explanation
Indices: 40814044--40814078 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
40814034 TTATTATTAA
40814044 ATATATTTTAATTAAAAT
1 ATATATTTTAA-TAAAAT
40814062 ATATATTTTAATAAAAT
1 ATATATTTTAATAAAAT
40814079 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATTTTAATAAAAT
Found at i:40818357 original size:23 final size:23
Alignment explanation
Indices: 40818297--40818371 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
40818287 TCTACTCACT
40818297 AACAAATCAAGAACAATTTCCAG
1 AACAAATCAAGAACAATTTCCAG
*
40818320 CAGAC-TATCAA-AACAATTTCCAG
1 -A-ACAAATCAAGAACAATTTCCAG
*
40818343 AACAAATCAAGAACAATAT-CAG
1 AACAAATCAAGAACAATTTCCAG
40818365 AACAAAT
1 AACAAAT
40818372 GCAACAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
21 2 0.04
22 16 0.36
23 19 0.42
24 6 0.13
25 2 0.04
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.17
Consensus pattern (23 bp):
AACAAATCAAGAACAATTTCCAG
Found at i:40818493 original size:18 final size:18
Alignment explanation
Indices: 40818470--40818504 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40818460 GTAAACTCTT
40818470 TCAAAAAACAACAGACTA
1 TCAAAAAACAACAGACTA
40818488 TCAAAAAACAACAGACT
1 TCAAAAAACAACAGACT
40818505 CTAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.60, C:0.23, G:0.06, T:0.11
Consensus pattern (18 bp):
TCAAAAAACAACAGACTA
Found at i:40821813 original size:21 final size:21
Alignment explanation
Indices: 40821787--40821830 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40821777 CATTTTTCCT
40821787 ATATTCCCAAAGTATTGTAAA
1 ATATTCCCAAAGTATTGTAAA
40821808 ATATTCCCAAAGTATTGTAAA
1 ATATTCCCAAAGTATTGTAAA
40821829 AT
1 AT
40821831 CATCTGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (21 bp):
ATATTCCCAAAGTATTGTAAA
Found at i:40834365 original size:28 final size:28
Alignment explanation
Indices: 40834329--40834425 Score: 106
Period size: 28 Copynumber: 3.4 Consensus size: 28
40834319 ACAAAGTGCA
*
40834329 AATAACGATAAGCACTGAAGTGCAAAAT
1 AATAACGATAAGCACAGAAGTGCAAAAT
* *
40834357 AATAACGATAAGCACAAAAGTGCAAATTTT
1 AATAACGATAAGCACAGAAGTGCAAA--AT
* * * *
40834387 TACAACGATAAGCACCGAAGTGCGAAAT
1 AATAACGATAAGCACAGAAGTGCAAAAT
40834415 AAT-ACGATAAG
1 AATAACGATAAG
40834426 AGCGCTAATT
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
27 8 0.14
28 26 0.46
30 22 0.39
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (28 bp):
AATAACGATAAGCACAGAAGTGCAAAAT
Found at i:40852739 original size:22 final size:23
Alignment explanation
Indices: 40852697--40852739 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
40852687 AAGGTTATAA
*
40852697 TAAAATTTTATTATATTTTAATT
1 TAAAATTTTATTAAATTTTAATT
40852720 TAAAATTTTA-TAAATTTTAA
1 TAAAATTTTATTAAATTTTAA
40852740 AAATAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TAAAATTTTATTAAATTTTAATT
Found at i:40852746 original size:23 final size:23
Alignment explanation
Indices: 40852695--40852747 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
40852685 TGAAGGTTAT
*
40852695 AATAAAATTTTATTATATTTTAA
1 AATAAAATTTTATTAAATTTTAA
**
40852718 TTTAAAATTTTA-TAAATTTTAAA
1 AATAAAATTTTATTAAATTTT-AA
40852741 AATAAAA
1 AATAAAA
40852748 AGTTGAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAAAATTTTATTAAATTTTAA
Found at i:40858411 original size:19 final size:19
Alignment explanation
Indices: 40858350--40858416 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
40858340 TTGAAGGTGG
*
40858350 TTCTCTTTTC-TT-TTTCT
1 TTCTATTTTCTTTGTTTCT
* *
40858367 TTCTCTTTCTCTTCG-TTCT
1 TTCTATTT-TCTTTGTTTCT
40858386 TTACTATTTTCTTTGTTTCT
1 TT-CTATTTTCTTTGTTTCT
40858406 TTCTATTTTCT
1 TTCTATTTTCT
40858417 ATACGAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
17 8 0.19
18 2 0.05
19 21 0.50
20 11 0.26
ACGTcount: A:0.04, C:0.22, G:0.03, T:0.70
Consensus pattern (19 bp):
TTCTATTTTCTTTGTTTCT
Found at i:40861979 original size:113 final size:114
Alignment explanation
Indices: 40861728--40862022 Score: 321
Period size: 113 Copynumber: 2.6 Consensus size: 114
40861718 TTTTGGTTAT
* * ** *
40861728 GCGCCGCAAAATCTCA-AGACCAAAACGCATCGTTTTTGTATTGATGTATACAATAATTAGTGGC
1 GCGCCGCAAAATATCATA-ACCAAAACGCATCGTTTTGGTATTGATGTATATTAGAATTAGTGGC
* ** * * * **
40861792 GATTATGATAAAACGCCGCTAAAGCAAGTAATAGCGGCGCATTGTGGGAA
65 GCTTACAAAAAAACGCCGCTAAAACAAGTAATAGCGGCGCATTCTGAAAA
* * *
40861842 GCGCCGCAAAA-ATCTTAACGAAAACGCATCGTTTTGGTATCGATGTATATTAGAATTAGTGGCG
1 GCGCCGCAAAATATCATAACCAAAACGCATCGTTTTGGTATTGATGTATATTAGAATTAGTGGCG
* *
40861906 CTTACAAAAAAACGCCAG-TAAAACAAGTATTAGCGGCG-TTTACT-AAAA
66 CTTACAAAAAAACGCC-GCTAAAACAAGTAATAGCGGCGCATT-CTGAAAA
* ** * *
40861954 GCGCCGCAAAATATGATAACCAAAACGCAGAGTTTTGATCTTGATGTATATTAGAATTAGTGGCG
1 GCGCCGCAAAATATCATAACCAAAACGCATCGTTTTGGTATTGATGTATATTAGAATTAGTGGCG
40862019 CTTA
66 CTTA
40862023 ATAGAAGTGC
Statistics
Matches: 151, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
112 15 0.10
113 123 0.81
114 13 0.09
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (114 bp):
GCGCCGCAAAATATCATAACCAAAACGCATCGTTTTGGTATTGATGTATATTAGAATTAGTGGCG
CTTACAAAAAAACGCCGCTAAAACAAGTAATAGCGGCGCATTCTGAAAA
Found at i:40862110 original size:75 final size:75
Alignment explanation
Indices: 40861934--40862090 Score: 183
Period size: 75 Copynumber: 2.1 Consensus size: 75
40861924 TAAAACAAGT
* * * * *
40861934 ATTAGCGGCGTTTACTAAAAGCGCCGCAAAATATGATAACCAAAACGCAGAGTTTTGATCTTGAT
1 ATTAGTGGCGCTTAATAAAAGCGCCGCAAAATATGATAACCAAAACGCAGAGGTTTGATCTCGAT
* *
40861999 GTATATTAGA
66 GTATAATACA
* * * *
40862009 ATTAGTGGCGCTTAATAGAAGTGCCGCAAAA-AGTGTTAACCAAAACGCA-ACGGTTTGGTCTCG
1 ATTAGTGGCGCTTAATAAAAGCGCCGCAAAATA-TGATAACCAAAACGCAGA-GGTTTGATCTCG
40862072 ATGTATAATACA
64 ATGTATAATACA
40862084 ATTAGTG
1 ATTAGTG
40862091 TCGTTAGTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
74 2 0.03
75 67 0.97
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (75 bp):
ATTAGTGGCGCTTAATAAAAGCGCCGCAAAATATGATAACCAAAACGCAGAGGTTTGATCTCGAT
GTATAATACA
Found at i:40862193 original size:188 final size:187
Alignment explanation
Indices: 40861839--40862210 Score: 448
Period size: 188 Copynumber: 2.0 Consensus size: 187
40861829 CGCATTGTGG
* * * * *
40861839 GAAGCGCCGCAAAAATCTTAACGAAAACGCATCGTTTTGGTATCGATGTATATTAGAATTAGTGG
1 GAAGCGCCGCAAAAATCTTAACCAAAACGCAACGGTTTGGTATCGATGTATAATACAATTAGTGG
*
40861904 CGCTTACAAAAAAACGCCAGTAAAACAAGTATTAGCGGCGTTTACTAAAAGCGCCGCAAAATATG
66 CGCTTACAAAAAAACGCCAGTAAAACAAGAATTAGCGGCGTTTACTAAAAGCGCCGCAAAATATG
*
40861969 ATAACCAAAACGCAGAGTTTTGATCTTGATGTATATTAGAATTAGTGGCGCTTAATA
131 ATAACCAAAACGCAGAGTTTTGATCTTGAGGTATATTAGAATTAGTGGCGCTTAATA
* * *
40862026 GAAGTGCCGCAAAAAGTGTTAACCAAAACGCAACGGTTTGGTCTCGATGTATAATACAATTAGTG
1 GAAGCGCCGCAAAAA-TCTTAACCAAAACGCAACGGTTTGGTATCGATGTATAATACAATTAGTG
* *** * ** * * *
40862091 TCG-TTAGTTAAAAACGCC-GCTAAAGTATAA-AATTAGCGGCGATTTTTTAGAATCGCCGCAAG
65 GCGCTTACAAAAAAACGCCAG-TAAA--ACAAGAATTAGCGGCG-TTTACTAAAAGCGCCGCAAA
* * *
40862153 ATATGCA-CACCAAAACGCAGAG-TTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTA
126 ATATG-ATAACCAAAACGCAGAGTTTTGATCTTGAGGTATATTAGAATTAGTGGCGCTTA
40862211 CGGAAAAACG
Statistics
Matches: 156, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
186 1 0.01
187 30 0.19
188 87 0.56
189 37 0.24
190 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (187 bp):
GAAGCGCCGCAAAAATCTTAACCAAAACGCAACGGTTTGGTATCGATGTATAATACAATTAGTGG
CGCTTACAAAAAAACGCCAGTAAAACAAGAATTAGCGGCGTTTACTAAAAGCGCCGCAAAATATG
ATAACCAAAACGCAGAGTTTTGATCTTGAGGTATATTAGAATTAGTGGCGCTTAATA
Found at i:40862218 original size:114 final size:114
Alignment explanation
Indices: 40862047--40862609 Score: 429
Period size: 114 Copynumber: 4.9 Consensus size: 114
40862037 AAAAGTGTTA
* * * * * *
40862047 ACCAAAACGCA-ACGGTTTGGTCTCGATGTATAATACAATTAGTGTCG-TTA-GTTAAAAACGCC
1 ACCAAAACGCAGA--GTTTGGTCTTGAGGTATATTAAAATTAGTGGCGCTTACG-GAAAAACGCC
** * * *
40862109 GCTAAAGTATAAAATTAGCGGCGATTTTTTAGAATCGCCGCAAGATATGCAC
63 GCTAAAGTATACTATTAGCGGCGCTTTTTTAGAAGCGCCGCAAGATATACAC
** *
40862161 ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTACGGAAAAACGCCGTT
1 ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAAAATTAGTGGCGCTTACGGAAAAACGCCGCT
* * ** * * *
40862226 AAAG-AGTACTATTAGCGGGGCGTTTGGAGAAGCGCCGCTATAT-TTCTTA-
66 AAAGTA-TACTATTAGCGGCGCTTTTTTAGAAGCGCCGCAAGATATAC--AC
** * * * *
40862275 ACCAAAACTTA-ACGTTTTGGTCTTGATGTATAATATAATTAGTGGCGCTTAC-AATAAAACGCC
1 ACCAAAACGCAGA-G-TTTGGTCTTGAGGTATATTAAAATTAGTGGCGCTTACGGA-AAAACGCC
*
40862338 GCTAAA-TATCAGTATTAGCGGCGC--TTTTAGTTAAGCGCCGCAAGATATACAC
63 GCTAAAGTAT-ACTATTAGCGGCGCTTTTTTAG--AAGCGCCGCAAGATATACAC
* * *
40862390 ACCAAAACGCAGAGTTTGGTATTGAGGTATATTAAAATTAGTGGCGCTTATTGG-AAAACGCCAC
1 ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAAAATTAGTGGCGCTTA-CGGAAAAACGCCGC
* *
40862454 TAAAGTATACTATTAGCGGCGCTTTCTTAGAAGCGCCGCAAGATATATTA-
65 TAAAGTATACTATTAGCGGCGCTTTTTTAGAAGCGCCGCAAGATATA-CAC
* * * ** * * ** * *
40862504 ACCGAAACGCTGCGTTTAAATCTTGATGTATACTGGAATCAGTGGCG-TTCAC-GAGAAATCGCC
1 ACCAAAACGCAGAGTTT-GGTCTTGAGGTATATTAAAATTAGTGGCGCTT-ACGGA-AAAACGCC
* * *
40862567 GCTAAA-TCATATTATTAGCAGCGCTTTTTTATAAGCGCCGCAA
63 GCTAAAGT-ATACTATTAGCGGCGCTTTTTTAGAAGCGCCGCAA
40862610 AAGATCTTTA
Statistics
Matches: 358, Mismatches: 64, Indels: 53
0.75 0.13 0.11
Matches are distributed among these distances:
113 36 0.10
114 161 0.45
115 153 0.43
116 8 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (114 bp):
ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAAAATTAGTGGCGCTTACGGAAAAACGCCGCT
AAAGTATACTATTAGCGGCGCTTTTTTAGAAGCGCCGCAAGATATACAC
Found at i:40862450 original size:229 final size:227
Alignment explanation
Indices: 40862044--40862472 Score: 580
Period size: 229 Copynumber: 1.9 Consensus size: 227
40862034 GCAAAAAGTG
* **
40862044 TTAACCAAAACGCAACGGTTTGGTCTCGATGTATAATACAATTAGTGTCGTTAGTTAAAAACGCC
1 TTAACCAAAACGCAACGGTTTGGTCTCGATGTATAATACAATTAGTGGCGTTAAATAAAAACGCC
* *
40862109 GCTAAAGTATAAAATTAGCGGCGATTTTTTAGAATCGCCGCAAGATATGCACACCAAAACGCAGA
66 GCTAAAGTATAAAATTAGCGGCGATTTTTTA-AAGCGCCGCAAGATATACACACCAAAACGCAGA
* ** **
40862174 GTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTACGGAAAAACGCCGTTAAAG-AGTACTAT
130 GTTTGGTATTGAGGTATATTAAAATTAGTGGCGCTTACGGAAAAACGCCACTAAAGTA-TACTAT
40862238 TAGCGGGGCGTTTGGAGAAGCGCCGCTATATTTC
194 TAGCGGGGCGTTTGGAGAAGCGCCGCTATATTTC
** * * *
40862272 TTAACCAAAACTTAACGTTTTGGTCTTGATGTATAATATAATTAGTGGCGCTTACAAT-AAAACG
1 TTAACCAAAACGCAACGGTTTGGTCTCGATGTATAATACAATTAGTGGCG-TTA-AATAAAAACG
** *
40862336 CCGCTAAA-TATCAGTATTAGCGGCGCTTTTAGTT-AAGCGCCGCAAGATATACACACCAAAACG
64 CCGCTAAAGTAT-AAAATTAGCGGCGATTTT--TTAAAGCGCCGCAAGATATACACACCAAAACG
*
40862399 CAGAGTTTGGTATTGAGGTATATTAAAATTAGTGGCGCTTATTGG-AAAACGCCACTAAAGTATA
126 CAGAGTTTGGTATTGAGGTATATTAAAATTAGTGGCGCTTA-CGGAAAAACGCCACTAAAGTATA
40862463 CTATTAGCGG
190 CTATTAGCGG
40862473 CGCTTTCTTA
Statistics
Matches: 175, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
228 47 0.27
229 122 0.70
230 4 0.02
231 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (227 bp):
TTAACCAAAACGCAACGGTTTGGTCTCGATGTATAATACAATTAGTGGCGTTAAATAAAAACGCC
GCTAAAGTATAAAATTAGCGGCGATTTTTTAAAGCGCCGCAAGATATACACACCAAAACGCAGAG
TTTGGTATTGAGGTATATTAAAATTAGTGGCGCTTACGGAAAAACGCCACTAAAGTATACTATTA
GCGGGGCGTTTGGAGAAGCGCCGCTATATTTC
Found at i:40862530 original size:229 final size:225
Alignment explanation
Indices: 40862071--40862609 Score: 575
Period size: 229 Copynumber: 2.3 Consensus size: 225
40862061 GTTTGGTCTC
* * * *
40862071 GATGTATAATACAATTAGTGTCGTTA-GTTAAAAACGCCGCTAAAGTATAAAATTAGCGGCGATT
1 GATGTATAATACAATTAGTGGCGTTACGAT-AAAACGCCGCTAAA-TATAATATTAGCGGCGCTT
* * * **
40862135 TTTTAGAATCGCCGCAAGATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATT
64 TTTT--AAGCGCCGCAAGATATACACACCAAAACGCAGAGTTTGGTATTGAGGTATATTAAAATT
** * *
40862200 AGTGGCGCTTACGGAAAAACGCCGTTAAAGAGTACTATTAGCGGGGCGTTTGGAGAAGCGCCGCT
127 AGTGGCGCTTACGGAAAAACGCCACTAAAGAGTACTATTAGCGGCGCGTTTGGAGAAGCGCCGCA
* * * * ***
40862265 ATATTTCTTAACCAAAACTTAACGTTTTGGTCTT
192 AGATATATTAACCAAAACCTAACGTTTAAATCTT
* * *
40862299 GATGTATAATATAATTAGTGGCGCTTACAATAAAACGCCGCTAAATATCAGTATTAGCGGCGCTT
1 GATGTATAATACAATTAGTGGCG-TTACGATAAAACGCCGCTAAATAT-AATATTAGCGGCGCTT
40862364 TTAGTTAAGCGCCGCAAGATATACACACCAAAACGCAGAGTTTGGTATTGAGGTATATTAAAATT
64 TT--TTAAGCGCCGCAAGATATACACACCAAAACGCAGAGTTTGGTATTGAGGTATATTAAAATT
* **
40862429 AGTGGCGCTTATTGG-AAAACGCCACTAAAGTA-TACTATTAGCGGCGC-TTTCTTAGAAGCGCC
127 AGTGGCGCTTA-CGGAAAAACGCCACTAAAG-AGTACTATTAGCGGCGCGTTT-GGAGAAGCGCC
* *
40862491 GCAAGATATATTAACCGAAACGCT-GCGTTTAAATCTT
189 GCAAGATATATTAACCAAAAC-CTAACGTTTAAATCTT
* ** * * * * *
40862528 GATGTATACTGGAATCAGTGGCGTTCACGAGAAATCGCCGCTAAATCATATTATTAGCAGCGCTT
1 GATGTATAATACAATTAGTGGCGTT-ACGATAAAACGCCGCTAAAT-ATAATATTAGCGGCGC-T
40862593 TTTTATAAGCGCCGCAA
63 TTTT-TAAGCGCCGCAA
40862610 AAGATCTTTA
Statistics
Matches: 261, Mismatches: 37, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
228 30 0.11
229 218 0.84
230 11 0.04
231 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (225 bp):
GATGTATAATACAATTAGTGGCGTTACGATAAAACGCCGCTAAATATAATATTAGCGGCGCTTTT
TTAAGCGCCGCAAGATATACACACCAAAACGCAGAGTTTGGTATTGAGGTATATTAAAATTAGTG
GCGCTTACGGAAAAACGCCACTAAAGAGTACTATTAGCGGCGCGTTTGGAGAAGCGCCGCAAGAT
ATATTAACCAAAACCTAACGTTTAAATCTT
Done.