Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 130 of 202
Found at i:40249855 original size:5 final size:5
Alignment explanation
Indices: 40249845--40249882 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
40249835 AACTTGGATA
40249845 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
40249883 TAAAATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:40250259 original size:51 final size:50
Alignment explanation
Indices: 40250134--40250430 Score: 312
Period size: 51 Copynumber: 5.9 Consensus size: 50
40250124 TTTATACACG
* *
40250134 TAGGTCACATGTGTAGTACTATGTGCGGGCTACTAAGTGTACCGGAAT-GA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACC-GAATAGA
* * *
40250184 TAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAATAG-A
* * *
40250235 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGAAT-GA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACC-GAATAGA
* ** * * *
40250285 TAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCATACTGGATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAATAG-A
* * * * * *
40250336 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGCATCGAAT-GAA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAATAG-A
* * *
40250386 AATGGTCACATGTGTAGTACTATGTGTAGGCTACTATGTGAACCG
1 TA-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
40250431 GTATCATTTA
Statistics
Matches: 200, Mismatches: 41, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
49 7 0.04
50 78 0.39
51 111 0.56
52 4 0.02
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAATAGA
Found at i:40250318 original size:101 final size:100
Alignment explanation
Indices: 40250138--40250423 Score: 428
Period size: 101 Copynumber: 2.8 Consensus size: 100
40250128 TACACGTAGG
* *
40250138 TCACATGTGTAGTACTATGTGCGGGCTACTAAGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTAAGTGTACC-GAATGATAGGTCGCATGTGTAGTAC
*
40250203 TATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
65 TATGTGCAGGCTACTATGCATACCGAATAGCTTCGA
*
40250239 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTAAGTGTACC-GAATGATAGGTCGCATGTGTAGTAC
* *
40250304 TATGTGCAGGCTACTATGCATACTGGATAGCTTCGA
65 TATGTGCAGGCTACTATGCATACCGAATAGCTTCGA
* * * * *
40250340 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGCATCGAATGAAAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTAAGTGTACCGAATG-ATA-GGTCGCATGTGTAGTA
*
40250405 CTATGTGTAGGCTACTATG
64 CTATGTGCAGGCTACTATG
40250424 TGAACCGGTA
Statistics
Matches: 170, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
100 5 0.03
101 132 0.78
102 33 0.19
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (100 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTAAGTGTACCGAATGATAGGTCGCATGTGTAGTACT
ATGTGCAGGCTACTATGCATACCGAATAGCTTCGA
Found at i:40250961 original size:21 final size:21
Alignment explanation
Indices: 40250937--40250977 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40250927 CTAACTTTGG
40250937 AAAATAATTAAAAATTATAAA
1 AAAATAATTAAAAATTATAAA
* *
40250958 AAAATAATTATAAGTTATAA
1 AAAATAATTAAAAATTATAA
40250978 TTTATATGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATAATTAAAAATTATAAA
Found at i:40257958 original size:23 final size:20
Alignment explanation
Indices: 40257894--40257972 Score: 74
Period size: 20 Copynumber: 3.9 Consensus size: 20
40257884 TAAAACTTGT
*
40257894 TAAAAATTAATTAAAAACCA
1 TAAAAATTTATTAAAAACCA
*
40257914 T-AAAA-TT-TTAAAAACTTTA
1 TAAAAATTTATTAAAAAC--CA
40257933 TAAAAACAATTTATTAAAAACCA
1 T--AAA-AATTTATTAAAAACCA
40257956 TAAAAATTTATTAAAAA
1 TAAAAATTTATTAAAAA
40257973 ATAAATTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
17 8 0.17
18 1 0.02
19 6 0.12
20 14 0.29
21 3 0.06
22 2 0.04
23 4 0.08
24 2 0.04
25 8 0.17
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAAATTTATTAAAAACCA
Found at i:40266781 original size:9 final size:10
Alignment explanation
Indices: 40266757--40266804 Score: 53
Period size: 9 Copynumber: 4.6 Consensus size: 10
40266747 GTATTTGACT
*
40266757 AAAATAATAC
1 AAAAAAATAC
40266767 AAAAAAATA-
1 AAAAAAATAC
40266776 AAAAAAATAC
1 AAAAAAATAC
40266786 TAAAATAATATAC
1 -AAAA-AA-ATAC
40266799 AAAAAA
1 AAAAAA
40266805 GTTTATTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
9 9 0.27
10 8 0.24
11 6 0.18
12 6 0.18
13 4 0.12
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:40266804 original size:22 final size:19
Alignment explanation
Indices: 40266757--40266795 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40266747 GTATTTGACT
*
40266757 AAAATAATACAAAAAAATA
1 AAAAAAATACAAAAAAATA
*
40266776 AAAAAAATACTAAAATAATA
1 AAAAAAATAC-AAAAAAATA
40266796 TACAAAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAAAATACAAAAAAATA
Found at i:40267312 original size:149 final size:152
Alignment explanation
Indices: 40267039--40267691 Score: 901
Period size: 149 Copynumber: 4.3 Consensus size: 152
40267029 TTAGTGTGTT
* *
40267039 TTTTTATTGAAAGTAAGAAAATCTGGGAAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTT
1 TTTTT-TT-AAAGTAATAAAATC-CGGAAAAAAATACGAACAAAGGGCCGAAATAAGG-TTTTTT
*
40267104 TAAAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTA
62 TTAAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTA
40267169 AAATAATAAAATTAGAAAATAGT-T-
127 AAATAATAAAATTAGAAAATAGTATA
*
40267193 TTTTTTTAAAGTAATAAAATCCGGAAAAAAATACGAACAAAGGACCGAAATAATGG-TTTTTTT-
1 TTTTTTTAAAGTAATAAAATCCGGAAAAAAATACGAACAAAGGGCCGAAATAA-GGTTTTTTTTA
* * * * *
40267256 AAATTTATTTAAAAAACACAGTAAGTTAATACATTTCAAACATGATTTACTAAAATAATGTAAAA
65 AAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
* * *
40267321 TAATAAAA-TACAAAAATAATATC
130 TAATAAAATTA-GAAAATAGTATA
* *
40267344 TTTTTATTGAAAGTAATAAAATTCGGAAAAAAATACGAACAAATGGCCGAAATAAGAGTTTTTTT
1 TTTTT-TT-AAAGTAATAAAATCCGGAAAAAAATACGAACAAAGGGCCGAAATAAG-G--TTTTT
** *
40267409 TTTAAAAATTTAAATAAAAAGCACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATG
61 TTT-AAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATG
40267474 TAAAATAATAAAATTAGAAAATAGTATA
125 TAAAATAATAAAATTAGAAAATAGTATA
* * * *
40267502 TTTTTTAAAAGTAATAAAATCCGAGGAAAAAATACGAACAAAGGGCTGAAATAAGG-ATTTTTT-
1 TTTTTTTAAAGTAATAAAATCCG-GAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTTA
* *
40267565 -AATTTATTTAAAAAACACGCTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
65 AAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
40267629 TAAT-AAATTAGAAAATAGTATA
130 TAATAAAATTAGAAAATAGTATA
* *
40267651 TTTTTTAAAAGTAATAAAATCCGGGAAAAAATACGAACAAA
1 TTTTTTTAAAGTAATAAAATCCGGAAAAAAATACGAACAAA
40267692 TGGTTGAAAT
Statistics
Matches: 449, Mismatches: 36, Indels: 34
0.87 0.07 0.07
Matches are distributed among these distances:
148 20 0.04
149 116 0.26
150 70 0.16
151 35 0.08
152 18 0.04
153 52 0.12
154 5 0.01
156 23 0.05
157 29 0.06
158 79 0.18
159 2 0.00
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.30
Consensus pattern (152 bp):
TTTTTTTAAAGTAATAAAATCCGGAAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTTAA
AATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT
AATAAAATTAGAAAATAGTATA
Found at i:40268291 original size:13 final size:13
Alignment explanation
Indices: 40268253--40268303 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
40268243 GGAAATAAAC
40268253 TTTTTTGTA-TAT
1 TTTTTTGTATTAT
* *
40268265 TATTTTG--GTAT
1 TTTTTTGTATTAT
40268276 TTTTTT-TATTAT
1 TTTTTTGTATTAT
40268288 TTTTTTGTATTAT
1 TTTTTTGTATTAT
40268301 TTT
1 TTT
40268304 AGTAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 8 0.25
12 15 0.47
13 9 0.28
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTTTGTATTAT
Found at i:40268292 original size:22 final size:22
Alignment explanation
Indices: 40268253--40268303 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
40268243 GGAAATAAAC
*
40268253 TTTTTTGTATATTATTTTGGTA
1 TTTTTTTTATATTATTTTGGTA
*
40268275 TTTTTTTTATTATT-TTTTTGTA
1 TTTTTTTTA-TATTATTTTGGTA
*
40268297 TTATTTT
1 TTTTTTT
40268304 AGTAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (22 bp):
TTTTTTTTATATTATTTTGGTA
Found at i:40268610 original size:10 final size:10
Alignment explanation
Indices: 40268581--40268689 Score: 71
Period size: 10 Copynumber: 11.1 Consensus size: 10
40268571 TTCATTCTAG
40268581 AATTATTAAA
1 AATTATTAAA
* *
40268591 AA-AATAAAA
1 AATTATTAAA
40268600 AATTATTAAA
1 AATTATTAAA
*
40268610 AATCATTAAA
1 AATTATTAAA
** *
40268620 TTTTACTAAA
1 AATTATTAAA
*
40268630 ATTTA-TAAA
1 AATTATTAAA
* *
40268639 ATTTATTAGA
1 AATTATTAAA
40268649 AATTATTCAAA
1 AATTATT-AAA
*
40268660 AATCA-TAAA
1 AATTATTAAA
* *
40268669 ATTTATAAAA
1 AATTATTAAA
*
40268679 AAATATTAAA
1 AATTATTAAA
40268689 A
1 A
40268690 CCATAAAAAT
Statistics
Matches: 75, Mismatches: 20, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
9 22 0.29
10 47 0.63
11 6 0.08
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.36
Consensus pattern (10 bp):
AATTATTAAA
Found at i:40268645 original size:39 final size:39
Alignment explanation
Indices: 40268597--40268689 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 39
40268587 TAAAAAAATA
** *
40268597 AAAAATTATTAAAAATCATT-AAATTTTACTAAAATTTAT
1 AAAAATTATTAAAAATCATTCAAAAATCA-TAAAATTTAT
* * *
40268636 AAAATTTATTAGAAATTATTCAAAAATCATAAAATTTAT
1 AAAAATTATTAAAAATCATTCAAAAATCATAAAATTTAT
*
40268675 AAAAAAATATTAAAA
1 -AAAAATTATTAAAA
40268690 CCATAAAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
39 27 0.63
40 16 0.37
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (39 bp):
AAAAATTATTAAAAATCATTCAAAAATCATAAAATTTAT
Found at i:40269501 original size:87 final size:88
Alignment explanation
Indices: 40269351--40269546 Score: 256
Period size: 87 Copynumber: 2.2 Consensus size: 88
40269341 ACTTTAAGAA
* * *
40269351 AAAAAAACAATTAAGCACTTCCT--TTTTCTTTGCACTTAATTGAGCATTTGAACTTTTAAAATG
1 AAAAAAACAATTAAGC-C--CCTAATTTTCTTTGCACTCAATTGAGCACTTGAACTTTCAAAATG
* * * *
40269414 CATTAAAAGGGCCCTCAAACTTTTTC
63 CATCAAAAAGACCCTCAAAATTTTTC
*
40269440 AAAAAAAGCAATTAAGCCCCTAATTTT-TTT-CACTCAATTGGGCACTTGAACTTTCAAAATGCA
1 AAAAAAA-CAATTAAGCCCCTAATTTTCTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGCA
40269503 TCAAAAAGACCCTCAAAATTTTTC
65 TCAAAAAGACCCTCAAAATTTTTC
40269527 AAAAAAACAATTAAGCCCCT
1 AAAAAAACAATTAAGCCCCT
40269547 GTTCTTATTA
Statistics
Matches: 96, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
86 13 0.14
87 59 0.61
88 3 0.03
89 12 0.12
90 9 0.09
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (88 bp):
AAAAAAACAATTAAGCCCCTAATTTTCTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGCAT
CAAAAAGACCCTCAAAATTTTTC
Found at i:40269688 original size:16 final size:17
Alignment explanation
Indices: 40269667--40269699 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40269657 ACATGTGGCG
40269667 AAAAATGATA-AAAAAT
1 AAAAATGATAGAAAAAT
*
40269683 AAAAATTATAGAAAAAT
1 AAAAATGATAGAAAAAT
40269700 TATAAAATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAAATGATAGAAAAAT
Found at i:40273459 original size:10 final size:10
Alignment explanation
Indices: 40273444--40273471 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
40273434 TTTTTTTTTA
40273444 AATTAGTATT
1 AATTAGTATT
40273454 AATTAGTATT
1 AATTAGTATT
40273464 AATTAGTA
1 AATTAGTA
40273472 GGGTAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (10 bp):
AATTAGTATT
Found at i:40275651 original size:20 final size:20
Alignment explanation
Indices: 40275626--40275675 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
40275616 CATTCTCCTT
*
40275626 ATTTTTTGTACATATACATA-
1 ATTTTTTG-AAATATACATAC
40275646 ATTTTTATGAAATATACATAC
1 ATTTTT-TGAAATATACATAC
40275667 ATATTTTTG
1 AT-TTTTTG
40275676 GAGATTATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 16 0.62
21 6 0.23
22 4 0.15
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (20 bp):
ATTTTTTGAAATATACATAC
Found at i:40278326 original size:30 final size:31
Alignment explanation
Indices: 40278270--40278392 Score: 89
Period size: 30 Copynumber: 4.1 Consensus size: 31
40278260 TAAAAAATAT
* * * *
40278270 ATTTTAACCCCTATACTTTT-TGAAATTTAT
1 ATTTCAACCCCTAAACTTTTCTAAAATTTAC
*
40278300 ATTTCGA-CCCTAAACTTTTCTAAAA-TTAC
1 ATTTCAACCCCTAAACTTTTCTAAAATTTAC
* *
40278329 ATTTCAACCCCTAAGC-TTTCTCAAAA-TTGC
1 ATTTCAACCCCTAAACTTTTCT-AAAATTTAC
* * *
40278359 ACTTT-GACCCTTAAAC-TTTCTAAAAATTAC
1 A-TTTCAACCCCTAAACTTTTCTAAAATTTAC
40278389 ATTT
1 ATTT
40278393 TGGCCAATTA
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
29 32 0.42
30 41 0.54
31 3 0.04
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.41
Consensus pattern (31 bp):
ATTTCAACCCCTAAACTTTTCTAAAATTTAC
Found at i:40278332 original size:29 final size:29
Alignment explanation
Indices: 40278300--40278392 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 29
40278290 TGAAATTTAT
40278300 ATTTCGACCCTAAACTTTTCT-AAAATTAC
1 ATTTCGACCCTAAAC-TTTCTAAAAATTAC
* * * *
40278329 ATTTCAACCCCTAAGCTTTCTCAAAATTGC
1 ATTTCGA-CCCTAAACTTTCTAAAAATTAC
40278359 ACTTT-GACCCTTAAACTTTCTAAAAATTAC
1 A-TTTCGACCC-TAAACTTTCTAAAAATTAC
40278389 ATTT
1 ATTT
40278393 TGGCCAATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
29 17 0.32
30 33 0.62
31 3 0.06
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (29 bp):
ATTTCGACCCTAAACTTTCTAAAAATTAC
Found at i:40278949 original size:23 final size:23
Alignment explanation
Indices: 40278916--40278960 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40278906 GCAATCAAGC
*
40278916 AAAAAAACAAGCAAAACGAAAAT
1 AAAAAAACAAGCAAAAAGAAAAT
* *
40278939 AAAAAAGCAAGTAAAAAGAAAA
1 AAAAAAACAAGCAAAAAGAAAA
40278961 AACAGCAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.76, C:0.09, G:0.11, T:0.04
Consensus pattern (23 bp):
AAAAAAACAAGCAAAAAGAAAAT
Found at i:40279119 original size:13 final size:13
Alignment explanation
Indices: 40279103--40279160 Score: 80
Period size: 13 Copynumber: 4.4 Consensus size: 13
40279093 GAAGAAAAAT
40279103 AAAAAAGAGAAAG
1 AAAAAAGAGAAAG
40279116 AAAAAAGAAGAAAG
1 AAAAAAG-AGAAAG
* * *
40279130 AAAGAAGAAAAAT
1 AAAAAAGAGAAAG
40279143 AAAAAAGAGAAAG
1 AAAAAAGAGAAAG
40279156 AAAAA
1 AAAAA
40279161 GAGCAGACTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
13 26 0.68
14 12 0.32
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAAAAGAGAAAG
Found at i:40279122 original size:7 final size:7
Alignment explanation
Indices: 40279097--40279160 Score: 53
Period size: 7 Copynumber: 9.6 Consensus size: 7
40279087 CGGCCTGAAG
*
40279097 AAAAATA
1 AAAAAGA
40279104 AAAAAG-
1 AAAAAGA
*
40279110 AGAAAGA
1 AAAAAGA
40279117 AAAAAGA
1 AAAAAGA
*
40279124 AGAAAGA
1 AAAAAGA
*
40279131 AAGAAG-
1 AAAAAGA
*
40279137 AAAAATA
1 AAAAAGA
40279144 AAAAAG-
1 AAAAAGA
*
40279150 AGAAAGA
1 AAAAAGA
40279157 AAAA
1 AAAA
40279161 GAGCAGACTA
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
6 14 0.33
7 29 0.67
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (7 bp):
AAAAAGA
Found at i:40279127 original size:14 final size:14
Alignment explanation
Indices: 40279094--40279160 Score: 79
Period size: 13 Copynumber: 5.1 Consensus size: 14
40279084 GTTCGGCCTG
*
40279094 AAGAA-AAATAAAA
1 AAGAAGAAAGAAAA
40279107 AAG-AGAAAGAAAA
1 AAGAAGAAAGAAAA
*
40279120 AAGAAGAAAGAAAG
1 AAGAAGAAAGAAAA
*
40279134 AAGAA-AAATAAAA
1 AAGAAGAAAGAAAA
40279147 AAG-AGAAAGAAAA
1 AAGAAGAAAGAAAA
40279160 A
1 A
40279161 GAGCAGACTA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
12 2 0.04
13 30 0.65
14 14 0.30
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (14 bp):
AAGAAGAAAGAAAA
Found at i:40279904 original size:18 final size:17
Alignment explanation
Indices: 40279879--40279923 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
40279869 TAAAAGATCG
40279879 TGTTTCAAAAGTTT-TCA
1 TGTTTCAAAA-TTTCTCA
*
40279896 TGTTTTCAAAATTTCTCG
1 TG-TTTCAAAATTTCTCA
40279914 TGTTTCAAAA
1 TGTTTCAAAA
40279924 AATAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (17 bp):
TGTTTCAAAATTTCTCA
Found at i:40279936 original size:27 final size:27
Alignment explanation
Indices: 40279903--40279954 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
40279893 TCATGTTTTC
*
40279903 AAAATTTCTCGTGTTTCAAAAAATAAT
1 AAAATTTCCCGTGTTTCAAAAAATAAT
40279930 AAAATTTCCCGTGTTTCAAAAAATA
1 AAAATTTCCCGTGTTTCAAAAAATA
40279955 TATTCGTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (27 bp):
AAAATTTCCCGTGTTTCAAAAAATAAT
Found at i:40280016 original size:17 final size:17
Alignment explanation
Indices: 40279976--40280021 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
40279966 TTTAAAATAA
40279976 TTTC-AAATTTTCGTGT
1 TTTCAAAATTTTCGTGT
40279992 TTTCCAAAATTTCTCGTG-
1 TTT-CAAAATTT-TCGTGT
40280010 TTTCAAAATTTT
1 TTTCAAAATTTT
40280022 TTTCGACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.15
17 9 0.33
18 9 0.33
19 5 0.19
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (17 bp):
TTTCAAAATTTTCGTGT
Found at i:40280069 original size:19 final size:18
Alignment explanation
Indices: 40280030--40280085 Score: 76
Period size: 19 Copynumber: 3.0 Consensus size: 18
40280020 TTTTTCGACT
* *
40280030 TTTCGCGTTTTCAAAAAA
1 TTTCGTGTTTTAAAAAAA
40280048 TTTCGTGTTTTAAAACAAA
1 TTTCGTGTTTTAAAA-AAA
40280067 TTTCGTGTTTTCAAAAAAA
1 TTTCGTGTTTT-AAAAAAA
40280086 AGTTATTGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 13 0.38
19 17 0.50
20 4 0.12
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (18 bp):
TTTCGTGTTTTAAAAAAA
Found at i:40283560 original size:147 final size:147
Alignment explanation
Indices: 40283293--40283592 Score: 591
Period size: 147 Copynumber: 2.0 Consensus size: 147
40283283 CTCATCAGCA
40283293 ACATTTGGATGACCTTCTGAGAGCTTTAGAAGAGAAGAATGGTCAGCATGACAGAGACATTCGCG
1 ACATTTGGATGACCTTCTGAGAGCTTTAGAAGAGAAGAATGGTCAGCATGACAGAGACATTCGCG
40283358 CCTACGAAAGAGCCCTCCAAGAAAAGGATATGCATCTCGGCAGTTTGATCAATGAAATTCGTAAG
66 CCTACGAAAGAGCCCTCCAAGAAAAGGATATGCATCTCGGCAGTTTGATCAATGAAATTCGTAAG
40283423 GCGGCTGCGCATGTAGT
131 GCGGCTGCGCATGTAGT
40283440 ACATTTGGATGACCTTCTGAGAGCTTTAGAAGAGAAGAATGGTCAGCATGACAGAGACATTCGCG
1 ACATTTGGATGACCTTCTGAGAGCTTTAGAAGAGAAGAATGGTCAGCATGACAGAGACATTCGCG
*
40283505 CCTACGAAAGAGCCCTCCAAGAAAAGGATATGCATCTCGGTAGTTTGATCAATGAAATTCGTAAG
66 CCTACGAAAGAGCCCTCCAAGAAAAGGATATGCATCTCGGCAGTTTGATCAATGAAATTCGTAAG
40283570 GCGGCTGCGCATGTAGT
131 GCGGCTGCGCATGTAGT
40283587 ACATTT
1 ACATTT
40283593 ATCAGATGAA
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 152 1.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.23
Consensus pattern (147 bp):
ACATTTGGATGACCTTCTGAGAGCTTTAGAAGAGAAGAATGGTCAGCATGACAGAGACATTCGCG
CCTACGAAAGAGCCCTCCAAGAAAAGGATATGCATCTCGGCAGTTTGATCAATGAAATTCGTAAG
GCGGCTGCGCATGTAGT
Found at i:40283966 original size:9 final size:9
Alignment explanation
Indices: 40283952--40283976 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40283942 CAAACTCAAT
40283952 GAAAGGATG
1 GAAAGGATG
40283961 GAAAGGATG
1 GAAAGGATG
40283970 GAAAGGA
1 GAAAGGA
40283977 CCCAAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (9 bp):
GAAAGGATG
Found at i:40291258 original size:1 final size:1
Alignment explanation
Indices: 40291252--40291353 Score: 60
Period size: 1 Copynumber: 102.0 Consensus size: 1
40291242 TATTATGCCT
* * * * * * * * * *
40291252 AAAAAAAACAAAAAAACAAAAAAAAACAAAAACAAAAAACAAAAAACAAAAAACAGAGAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
40291317 AAAGAAAACAAAAAAAGAAAGAAAATAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
40291354 TCAAGATGAA
Statistics
Matches: 69, Mismatches: 32, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.01
Consensus pattern (1 bp):
A
Found at i:40291266 original size:8 final size:8
Alignment explanation
Indices: 40291253--40291347 Score: 81
Period size: 8 Copynumber: 11.6 Consensus size: 8
40291243 ATTATGCCTA
40291253 AAAAAAAC
1 AAAAAAAC
40291261 AAAAAAAC
1 AAAAAAAC
40291269 AAAAAAA-
1 AAAAAAAC
40291276 AACAAAAAC
1 AA-AAAAAC
40291285 -AAAAAAC
1 AAAAAAAC
40291292 -AAAAAAC
1 AAAAAAAC
40291299 -AAAAAAC
1 AAAAAAAC
*
40291306 AGAGAAACAAA
1 A-A-AAA-AAC
40291317 AAAGAAAAC
1 AAA-AAAAC
*
40291326 AAAAAAAG
1 AAAAAAAC
*
40291334 AAAGAAAAT
1 AAA-AAAAC
40291343 AAAAA
1 AAAAA
40291348 GAAAAATCAA
Statistics
Matches: 75, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
7 22 0.29
8 30 0.40
9 14 0.19
10 6 0.08
11 3 0.04
ACGTcount: A:0.84, C:0.09, G:0.05, T:0.01
Consensus pattern (8 bp):
AAAAAAAC
Found at i:40291331 original size:7 final size:7
Alignment explanation
Indices: 40291254--40291324 Score: 79
Period size: 7 Copynumber: 9.6 Consensus size: 7
40291244 TTATGCCTAA
40291254 AAAAAAC
1 AAAAAAC
40291261 AAAAAAAC
1 -AAAAAAC
*
40291269 AAAAAAAA
1 -AAAAAAC
40291277 ACAAAAAC
1 A-AAAAAC
40291285 AAAAAAC
1 AAAAAAC
40291292 AAAAAAC
1 AAAAAAC
40291299 AAAAAAC
1 AAAAAAC
*
40291306 AGAGAAAC
1 A-AAAAAC
*
40291314 AAAAAAG
1 AAAAAAC
40291321 AAAA
1 AAAA
40291325 CAAAAAAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
7 30 0.54
8 26 0.46
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:40291353 original size:29 final size:28
Alignment explanation
Indices: 40291252--40291353 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 28
40291242 TATTATGCCT
* *
40291252 AAAAAAAACAAAAAAACAAAAAAA-AACAA
1 AAAAAAAA-AGAAAAACAAAAAAAGAA-AG
*
40291281 AAACAAAAAACAAAAAACAAAAAACAG--AG
1 AAA-AAAAAA-GAAAAACAAAAAA-AGAAAG
40291310 AAACAAAAAAG-AAAACAAAAAAAGAAAG
1 AAA-AAAAAAGAAAAACAAAAAAAGAAAG
40291338 AAAATAAAAAGAAAAA
1 AAAA-AAAAAGAAAAA
40291354 TCAAGATGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
26 2 0.03
27 12 0.19
28 11 0.17
29 19 0.30
30 18 0.29
31 1 0.02
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.01
Consensus pattern (28 bp):
AAAAAAAAAGAAAAACAAAAAAAGAAAG
Found at i:40292597 original size:76 final size:76
Alignment explanation
Indices: 40292206--40292847 Score: 757
Period size: 76 Copynumber: 8.4 Consensus size: 76
40292196 TCAAGAATTA
* *
40292206 TATTTTTCAATTTCT-ATTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGG
1 TATTTTT-AATTTCTGTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
** *
40292268 GCCGCACGCCGAGG
65 G--TTACGCTGAGG
* * * * *
40292282 TATTTTCAATTTCTATTTTTTTTAAAAAAATCAACTCATAATGCGAGAAGTGAGTTAAGCCTCGG
1 TATTTTTAATTTCT-GTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
*
40292347 GTTACGCTGAGC
65 GTTACGCTGAGG
* *
40292359 TATTTTTAATTTCTGTTTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTTGG
1 TATTTTTAATTTCTG-TTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
* *
40292422 GTCATGCTGAGG
65 GTTACGCTGAGG
* * * *
40292434 TATTTTCAATTTCTATTTAAAAAAATAAT-AAAAAAATCAACTCATAATGCGAGAAGTGAGTTGA
1 TATTTTTAATTTCTGTTT-------T-TTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
40292498 GCCTCGGGTTACG-TAGAGG
58 GCCTCGGGTTACGCT-GAGG
*
40292517 TATTTTTAATTTCTGTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGG
1 TATTTTTAATTTCTGTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
*
40292582 TTACGCTGAGA
66 TTACGCTGAGG
40292593 TATTTTTAATTTCTG-TTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTGTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
40292656 TTACGCTGAGG
66 TTACGCTGAGG
* * * * *
40292667 TATTTCTAATTTCTGTTTTTTCAAAAAAAATCAACTCATAATACGAGAAGTGAGTTGAACCTCAG
1 TATTTTTAATTTCTGTTTTTTC-AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
*
40292732 GTTACACTGAGG
65 GTTACGCTGAGG
* * * * *
40292744 TATTTTTAATTTCTAGTTTTTACAAAAATA-CAACTCATAATGCGAGAGATGGGTTGAGCTTCGG
1 TATTTTTAATTTCT-GTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
*
40292808 GTCACGCTGAGG
65 GTTACGCTGAGG
*
40292820 TATTTTCAATTTCTG-TTTTTCAAAAAAA
1 TATTTTTAATTTCTGTTTTTTCAAAAAAA
40292848 AAAAAGAAAA
Statistics
Matches: 487, Mismatches: 57, Indels: 46
0.83 0.10 0.08
Matches are distributed among these distances:
74 79 0.16
75 79 0.16
76 121 0.25
77 99 0.20
78 7 0.01
79 38 0.08
81 1 0.00
82 2 0.00
83 61 0.13
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (76 bp):
TATTTTTAATTTCTGTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
TTACGCTGAGG
Found at i:40292785 original size:227 final size:228
Alignment explanation
Indices: 40292228--40292846 Score: 782
Period size: 227 Copynumber: 2.7 Consensus size: 228
40292218 TCTATTTTTC
* * ** * *
40292228 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGCCGCACGCCGAGGTATTTTCAATT
1 AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGG--TTAC-CTGAGGTATTTTTAATT
* * * * *
40292293 TCTATTTTTTTTAAAAAAAT-CAACTCATAATGCGAGAAGTGAGTTAAGCCTCGGGTTACGCTGA
63 TCTA--GTTTTTACAAAAATACAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTTACGCTGA
* * *
40292357 GCTATTTTTAATTTCTGTTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTTG
126 GATATTTTTAATTTCTG--TTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
*
40292421 GGTCATGCTGAGGTATTTTCAATTTCTATTTAAAAAAATAATAA
189 GGTCACGCTGAGGTATTTTCAATTTCTATTT----AAATAATAA
*
40292465 AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTTACGTAGAGGTATTTTTAATTTC
1 AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTTACCT-GAGGTATTTTTAATTTC
* *
40292530 T-GTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTTACGCTGAGAT
65 TAGTTTTTACAAAAATA-CAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTTACGCTGAGAT
*
40292594 ATTTTTAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTA
129 ATTTTTAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
* ** *
40292659 CGCTGAGGTA-TTTCTAATTTCTGTTT-TTTCA-AA
194 CGCTGAGGTATTTTC-AATTTCTATTTAAATAATAA
* * *
40292692 AAAAATCAACTCATAATACGAGAAGTGAGTTGAACCTCAGGTTACACTGAGGTATTTTTAATTTC
1 AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTTAC-CTGAGGTATTTTTAATTTC
* * * *
40292757 TAGTTTTTACAAAAATACAACTCATAATGCGAGAGATGGGTTGAGCTTCGGGTCACGCTGAGGTA
65 TAGTTTTTACAAAAATACAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTTACGCTGAGATA
*
40292822 TTTTCAATTTCTGTTTTTCAAAAAA
130 TTTTTAATTTCTGTTTTTCAAAAAA
40292847 AAAAAAGAAA
Statistics
Matches: 341, Mismatches: 34, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
227 130 0.38
228 16 0.05
232 20 0.06
233 60 0.18
234 57 0.17
235 19 0.06
237 39 0.11
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (228 bp):
AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTTACCTGAGGTATTTTTAATTTCT
AGTTTTTACAAAAATACAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTTACGCTGAGATAT
TTTTAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACG
CTGAGGTATTTTCAATTTCTATTTAAATAATAA
Found at i:40293318 original size:29 final size:30
Alignment explanation
Indices: 40293284--40293415 Score: 151
Period size: 30 Copynumber: 4.4 Consensus size: 30
40293274 ACAAAACATA
**
40293284 AAAATTACATTTTAACCCCTGTA-TTTTTT
1 AAAATTACATTTTAACCCCTAAACTTTTTT
* * *
40293313 GAAATTTACATTTTGA-CCCTAAACTTTTCT
1 -AAAATTACATTTTAACCCCTAAACTTTTTT
* *
40293343 AAAATTACATTTCAACCCCTAAACTTTCTT
1 AAAATTACATTTTAACCCCTAAACTTTTTT
* * *
40293373 AAAATTACACTTTAACCCCTAAACTTTCTA
1 AAAATTACATTTTAACCCCTAAACTTTTTT
40293403 AAAATTACATTTT
1 AAAATTACATTTT
40293416 GGCCCTATAT
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
29 17 0.20
30 69 0.80
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.41
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTTTT
Found at i:40293349 original size:59 final size:60
Alignment explanation
Indices: 40293282--40293415 Score: 166
Period size: 59 Copynumber: 2.2 Consensus size: 60
40293272 ATACAAAACA
** * * * *
40293282 TAAAAATTACATTTTAACCCCTGTA-TTTTTTGAAATTTACATTTTGA-CCCTAAACTTTTC
1 TAAAAATTACATTTTAACCCCTAAACTTTCTT-AAAATTACACTTTAACCCCTAAAC-TTTC
*
40293342 T-AAAATTACATTTCAACCCCTAAACTTTCTTAAAATTACACTTTAACCCCTAAACTTTC
1 TAAAAATTACATTTTAACCCCTAAACTTTCTTAAAATTACACTTTAACCCCTAAACTTTC
40293401 TAAAAATTACATTTT
1 TAAAAATTACATTTT
40293416 GGCCCTATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 37 0.59
60 26 0.41
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.41
Consensus pattern (60 bp):
TAAAAATTACATTTTAACCCCTAAACTTTCTTAAAATTACACTTTAACCCCTAAACTTTC
Found at i:40293421 original size:29 final size:29
Alignment explanation
Indices: 40293282--40293454 Score: 150
Period size: 30 Copynumber: 5.8 Consensus size: 29
40293272 ATACAAAACA
** * *
40293282 TAAAAATTACATTTTAACCCCTGTATTTTT
1 TAAAAATTACATTTTAA-CCCTAAACTTTC
* * *
40293312 TGAAATTTACATTTTGACCCTAAACTTTTC
1 TAAAAATTACATTTTAACCCTAAAC-TTTC
*
40293342 T-AAAATTACATTTCAACCCCTAAACTTTC
1 TAAAAATTACATTTTAA-CCCTAAACTTTC
* *
40293371 TTAAAATTACACTTTAACCCCTAAACTTTC
1 TAAAAATTACATTTTAA-CCCTAAACTTTC
** * *
40293401 TAAAAATTACATTTTGGCCCTATATTTTCC
1 TAAAAATTACATTTTAACCCTAAACTTT-C
* *
40293431 AAAAAATTACATTTTTACCCTAAA
1 TAAAAATTACATTTTAACCCTAAA
40293455 TATTTTACGT
Statistics
Matches: 117, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
29 31 0.26
30 86 0.74
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (29 bp):
TAAAAATTACATTTTAACCCTAAACTTTC
Found at i:40294143 original size:20 final size:21
Alignment explanation
Indices: 40294118--40294191 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 21
40294108 TGGCCTGAAG
40294118 AAAAATAAAA-A-ATAGAAAGA
1 AAAAATAAAAGAGA-AGAAAGA
40294138 AAAAATAAAAGAGAAGAAAGA
1 AAAAATAAAAGAGAAGAAAGA
* * *
40294159 AAGAAGAAAA-AGAAAAAAGA
1 AAAAATAAAAGAGAAGAAAGA
*
40294179 GAAAGA-AAAAGAG
1 -AAAAATAAAAGAG
40294192 CAAACCATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 23 0.51
21 21 0.47
22 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (21 bp):
AAAAATAAAAGAGAAGAAAGA
Found at i:40294147 original size:18 final size:18
Alignment explanation
Indices: 40294114--40294156 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
40294104 GGTTTGGCCT
*
40294114 GAAGAAAAATAAAAAATA
1 GAAGAAAAATAAAAAAGA
*
40294132 GAAAGAAAAA-ATAAAAGA
1 G-AAGAAAAATAAAAAAGA
40294150 GAAGAAA
1 GAAGAAA
40294157 GAAAGAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 8 0.36
19 8 0.36
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (18 bp):
GAAGAAAAATAAAAAAGA
Found at i:40294187 original size:13 final size:13
Alignment explanation
Indices: 40294152--40294188 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
40294142 ATAAAAGAGA
*
40294152 AGAAAGAAAGAAG
1 AGAAAGAAAAAAG
*
40294165 AAAAAGAAAAAAG
1 AGAAAGAAAAAAG
40294178 AGAAAGAAAAA
1 AGAAAGAAAAA
40294189 GAGCAAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAAAAG
Found at i:40294918 original size:18 final size:18
Alignment explanation
Indices: 40294895--40294938 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
40294885 AAAGATCGTG
40294895 TTTCAAAAGTTT-TCATGT
1 TTTCAAAA-TTTCTCATGT
*
40294913 TTTCAAAATTTCTCGTGT
1 TTTCAAAATTTCTCATGT
*
40294931 TTCCAAAA
1 TTTCAAAA
40294939 ATAATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (18 bp):
TTTCAAAATTTCTCATGT
Found at i:40295026 original size:18 final size:18
Alignment explanation
Indices: 40295005--40295046 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40294995 TCCGTTTATC
*
40295005 AAATTTTCTTGT-TTTCA
1 AAATTTTCTCGTGTTTCA
*
40295022 AAAATTTCTCGTGTTTCA
1 AAATTTTCTCGTGTTTCA
40295040 AAATTTT
1 AAATTTT
40295047 TTTTTGACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (18 bp):
AAATTTTCTCGTGTTTCA
Found at i:40295043 original size:17 final size:16
Alignment explanation
Indices: 40294991--40295045 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
40294981 TTTTTAAAAT
40294991 AATTTC-CGTTTATCAA
1 AATTTCTCGTTT-TCAA
* *
40295007 ATTTTCTTGTTTTCAAA
1 AATTTCTCGTTTTC-AA
40295024 AATTTCTCGTGTTTCAA
1 AATTTCTCGT-TTTCAA
40295041 AATTT
1 AATTT
40295046 TTTTTTGACT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 7 0.22
17 21 0.66
18 4 0.12
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (16 bp):
AATTTCTCGTTTTCAA
Found at i:40295093 original size:20 final size:20
Alignment explanation
Indices: 40295068--40295128 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
40295058 TCGCATTTTC
40295068 AAAAATTTTCGTGTTTT-AAA
1 AAAAATTTT-GTGTTTTCAAA
40295088 AAAAATTTTGTGTTTTCAAA
1 AAAAATTTTGTGTTTTCAAA
*
40295108 AAAAGTTATTGTG-TTTCAAA
1 AAAAATT-TTGTGTTTTCAAA
40295128 A
1 A
40295129 TTCTTGTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
19 7 0.18
20 26 0.68
21 5 0.13
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (20 bp):
AAAAATTTTGTGTTTTCAAA
Found at i:40295635 original size:13 final size:13
Alignment explanation
Indices: 40295613--40295677 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
40295603 TTCTTCATTG
40295613 CTTTTGAAAAGTT
1 CTTTTGAAAAGTT
* *
40295626 CTTTTTAAAAGTG
1 CTTTTGAAAAGTT
** * *
40295639 CAGTGGAAAAGTG
1 CTTTTGAAAAGTT
*
40295652 CTTTTGAGAAGTT
1 CTTTTGAAAAGTT
40295665 CTTTTGAAAAGTT
1 CTTTTGAAAAGTT
40295678 TGGTTTAAAA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.40
Consensus pattern (13 bp):
CTTTTGAAAAGTT
Found at i:40300934 original size:16 final size:17
Alignment explanation
Indices: 40300913--40300949 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
40300903 ACTAAATAAT
*
40300913 TAAAATAAATAAACAA-
1 TAAAATAAACAAACAAC
40300929 TAAAATAAACAAACAAC
1 TAAAATAAACAAACAAC
40300946 TAAA
1 TAAA
40300950 CTGATTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.73, C:0.11, G:0.00, T:0.16
Consensus pattern (17 bp):
TAAAATAAACAAACAAC
Found at i:40315184 original size:20 final size:21
Alignment explanation
Indices: 40315132--40315184 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
40315122 ATTCACAGCG
40315132 AAATATGTAATACTTTATAAAA
1 AAATATGTAA-ACTTTATAAAA
* * *
40315154 AAACATTTAAA-TTTATATAA
1 AAATATGTAAACTTTATAAAA
*
40315174 GAATATGTAAA
1 AAATATGTAAA
40315185 ACAAATTAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 16 0.64
21 1 0.04
22 8 0.32
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.36
Consensus pattern (21 bp):
AAATATGTAAACTTTATAAAA
Found at i:40316867 original size:37 final size:35
Alignment explanation
Indices: 40316795--40316867 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 35
40316785 GAATAATATT
* * *
40316795 TTTTTGAAATAGAAAAAAGAAAAGATAATAGGTTA
1 TTTTCGAAATAGAAAAAAGAAAAGAAAAAAGGTTA
40316830 TTTTCGAAAT-GAAGAAAAGAAAAGAGAAAAAGAGTTA
1 TTTTCGAAATAGAA-AAAAGAAAAGA-AAAAAG-GTTA
40316867 T
1 T
40316868 GGACGAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 3 0.09
35 20 0.62
36 4 0.12
37 5 0.16
ACGTcount: A:0.55, C:0.01, G:0.19, T:0.25
Consensus pattern (35 bp):
TTTTCGAAATAGAAAAAAGAAAAGAAAAAAGGTTA
Found at i:40318697 original size:29 final size:28
Alignment explanation
Indices: 40318654--40318950 Score: 292
Period size: 28 Copynumber: 10.5 Consensus size: 28
40318644 ACGCGCCGGA
* * *
40318654 GAAAAGAAAGCCTTTGTGGCAAACCTAT
1 GAAAGGAAAGCCTTTGTGGAAAACCTCT
* **
40318682 GCAAAGAAAAGCCTTTGTGGTGAACCTCT
1 G-AAAGGAAAGCCTTTGTGGAAAACCTCT
* * ** *
40318711 GAAAGGAAATCCTTTATGGTGAACCTTT
1 GAAAGGAAAGCCTTTGTGGAAAACCTCT
* * **
40318739 AAAATGAAAGCCTTTGTGGTGAACCTCT
1 GAAAGGAAAGCCTTTGTGGAAAACCTCT
*
40318767 GCAAAGGAAAGCCTTTATGGAAAACCTCT
1 G-AAAGGAAAGCCTTTGTGGAAAACCTCT
40318796 GCAAAGGAAAGCCTTTGTGGAAAACCT-T
1 G-AAAGGAAAGCCTTTGTGGAAAACCTCT
** *
40318824 CGTAAAGGAGGGCCTTTGTGGCAAACCTCT
1 -G-AAAGGAAAGCCTTTGTGGAAAACCTCT
* * *
40318854 TAATGGAAAGCCTTTGTGAAAAACCTCT
1 GAAAGGAAAGCCTTTGTGGAAAACCTCT
* * **
40318882 GAAAGGAAAGTCTTTTTGGTGAACCTCT
1 GAAAGGAAAGCCTTTGTGGAAAACCTCT
40318910 GAAAGGAAAGCCTTTGTGGAAAACCTCT
1 GAAAGGAAAGCCTTTGTGGAAAACCTCT
40318938 GTAAAGG-AAGCCT
1 G-AAAGGAAAGCCT
40318951 CGTGGCAATC
Statistics
Matches: 223, Mismatches: 41, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
28 122 0.55
29 100 0.45
30 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (28 bp):
GAAAGGAAAGCCTTTGTGGAAAACCTCT
Found at i:40326639 original size:29 final size:29
Alignment explanation
Indices: 40326599--40326683 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
40326589 ACACCTTTTT
40326599 AAGGAAAGTCTTTATGACAAACCTCTGTA
1 AAGGAAAGTCTTTATGACAAACCTCTGTA
* *
40326628 AAGGAGAA-TCTTTGTGGCAAACCTCTGTA
1 AAGGA-AAGTCTTTATGACAAACCTCTGTA
* * * *
40326657 AAGGATAGCCTTTGTGGCAAACCTCTG
1 AAGGAAAGTCTTTATGACAAACCTCTG
40326684 CAAATGATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.02
29 47 0.94
30 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (29 bp):
AAGGAAAGTCTTTATGACAAACCTCTGTA
Found at i:40326692 original size:29 final size:28
Alignment explanation
Indices: 40326616--40326709 Score: 116
Period size: 29 Copynumber: 3.2 Consensus size: 28
40326606 GTCTTTATGA
* *
40326616 CAAACCTCTGTAAAGGAGAATCTTTGTGG
1 CAAACCTCTGCAAAGGATAA-CTTTGTGG
* *
40326645 CAAACCTCTGTAAAGGATAGCCTTTGTGG
1 CAAACCTCTGCAAAGGATA-ACTTTGTGG
*
40326674 CAAACCTCTGCAAATGATAACTTTCGTGG
1 CAAACCTCTGCAAAGGATAACTTT-GTGG
40326703 CAAACCT
1 CAAACCT
40326710 ATAAAAAGTA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
28 4 0.07
29 54 0.93
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (28 bp):
CAAACCTCTGCAAAGGATAACTTTGTGG
Found at i:40326802 original size:29 final size:28
Alignment explanation
Indices: 40326753--40326807 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
40326743 GCGAAAAGCA
*
40326753 TTTGTCGCGAACCTCTGAAAGGAAAAAT
1 TTTGTCGCAAACCTCTGAAAGGAAAAAT
* *
40326781 TTTGTGGCAAACCTTTGCAAAGGAAAA
1 TTTGTCGCAAACCTCTG-AAAGGAAAA
40326808 CCGTTATGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (28 bp):
TTTGTCGCAAACCTCTGAAAGGAAAAAT
Found at i:40326851 original size:28 final size:27
Alignment explanation
Indices: 40326819--40326954 Score: 101
Period size: 28 Copynumber: 4.8 Consensus size: 27
40326809 CGTTATGGTG
*
40326819 AACCTCTAAAAGTAAGGCCTTTGTAGCA
1 AACCTCTAAAAGTAA-GCCTTTGTAGAA
* * *
40326847 TACCTCTAAACAGAAAGCCTTTGTGGAA
1 AACCTCTAAA-AGTAAGCCTTTGTAGAA
* * *
40326875 AACCTCTACAAAGGTAAGCCTTTATGGTA
1 AACCTCTA-AAA-GTAAGCCTTTGTAGAA
* * *
40326904 AACCTCTGAAATGAAAGCCTTTGTGGAA
1 AACCTCT-AAAAGTAAGCCTTTGTAGAA
* *
40326932 AACCTTCAAAAAGGAAAGCCTTT
1 AACC-TCTAAAA-GTAAGCCTTT
40326955 ATGGCAACCT
Statistics
Matches: 88, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
28 47 0.53
29 40 0.45
30 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (27 bp):
AACCTCTAAAAGTAAGCCTTTGTAGAA
Found at i:40326896 original size:57 final size:55
Alignment explanation
Indices: 40326819--40326978 Score: 187
Period size: 57 Copynumber: 2.8 Consensus size: 55
40326809 CGTTATGGTG
* * *
40326819 AACCTCTAAAA-GTAAGGCCTTTGTAGCATACCTCTAAACAGAAAGCCTTTGTGGAA
1 AACCTCTAAAAGGTAA-GCCTTTATGGCA-ACCTCTAAAAAGAAAGCCTTTGTGGAA
* * *
40326875 AACCTCTACAAAGGTAAGCCTTTATGGTAAACCTCTGAAATGAAAGCCTTTGTGGAA
1 AACCTCTA-AAAGGTAAGCCTTTATGG-CAACCTCTAAAAAGAAAGCCTTTGTGGAA
* *
40326932 AACCTTCAAAAAGGAAAGCCTTTATGGCAACCTCTAAAAAAGAAAGC
1 AACC-TCTAAAAGGTAAGCCTTTATGGCAACCTCT-AAAAAGAAAGC
40326979 ATCGTGGCAA
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
56 15 0.17
57 65 0.74
58 8 0.09
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (55 bp):
AACCTCTAAAAGGTAAGCCTTTATGGCAACCTCTAAAAAGAAAGCCTTTGTGGAA
Found at i:40326963 original size:28 final size:28
Alignment explanation
Indices: 40326859--40326978 Score: 116
Period size: 29 Copynumber: 4.2 Consensus size: 28
40326849 CCTCTAAACA
* *
40326859 GAAAGCCTTTGTGGAAAACCTCTACAAAG
1 GAAAGCCTTTATGGAAAACCTC-AAAAAG
* * ** *
40326888 GTAAGCCTTTATGGTAAACCTCTGAAAT
1 GAAAGCCTTTATGGAAAACCTCAAAAAG
*
40326916 GAAAGCCTTTGTGGAAAACCTTCAAAAAG
1 GAAAGCCTTTATGGAAAACC-TCAAAAAG
* *
40326945 GAAAGCCTTTATGG-CAACCTCTAAAAAA
1 GAAAGCCTTTATGGAAAACCTC-AAAAAG
40326973 GAAAGC
1 GAAAGC
40326979 ATCGTGGCAA
Statistics
Matches: 74, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
27 2 0.03
28 35 0.47
29 37 0.50
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (28 bp):
GAAAGCCTTTATGGAAAACCTCAAAAAG
Found at i:40329697 original size:3 final size:3
Alignment explanation
Indices: 40329689--40329728 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
40329679 TCAATTGGCA
40329689 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
40329729 AAGAACTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:40330053 original size:3 final size:3
Alignment explanation
Indices: 40330045--40330090 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
40330035 TGAATTGGCA
40330045 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
40330091 AAGAACTAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:40330319 original size:362 final size:355
Alignment explanation
Indices: 40329660--40330361 Score: 1269
Period size: 362 Copynumber: 2.0 Consensus size: 355
40329650 GGAAAATCAG
40329660 TTGCACATTGAGCCTTAGCTCAATTGGCATTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTG
1 TTGCACATTGAGCCTTAGCTCAATTGGCATTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTG
* *
40329725 TTGTAAGAACTAGGAAGACGTGGGTTCATGCACACTTAAGCGCACATTTTCCTAAGATTTAATGA
66 TTGTAAGAACTAGGAAGACATGGGTTCATGCACACTTAAGCGCACATTTTCCTAAAATTTAATGA
*
40329790 TGGGGAGAGGTTATGAGCATAGATAGACTTTGCATAAACAATGGGGTAAACTACATCTAAGACCA
131 TGGGGAGAGGTTATGAGCATAGATAGACTTTGCATAAACAATGGAGTAAACTACATCTAAGACCA
40329855 CTAAATTATTAGTAAGTTGACATTTTGGTCACTCAACTTTAAAAAGTTACAAAATAACCCCTGAA
196 CTAAATTATTAGTAAGTTGACATTTTGGTCACTCAACTTTAAAAAGTTACAAAATAACCCCTGAA
40329920 CTATTTAAAAGTTTTCATTTAAATCACTAAGTTGTTAAGTCTTTTTTTTTAAGTCCAACTGACAA
261 CTATTTAAAAGTTTTCATTTAAATCACTAAGTTGTTAAGTC-TTTTTTTTAAGTCCAACTGACAA
*
40329985 ACTCCAAGTGATGATTAGTTGTAAGAACTAA
325 ACTCCAAGCGATGATTAGTTGTAAGAACTAA
*
40330016 TTGCACATTGAGCCTTAGCTGAATTGGCATTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTG
1 TTGCACATTGAGCCTTAGCTCAATTGGCA------TTGTTGTTGTTGTTGTTGTTGTTGTTGTTG
40330081 TTGTTGTTGTAAGAACTAGGAAGACATGGGTTCATGCACACTTAAGCGCACATTTTCCTAAAATT
60 TTGTTGTTGTAAGAACTAGGAAGACATGGGTTCATGCACACTTAAGCGCACATTTTCCTAAAATT
*
40330146 TAATGATGGGGAGAGGTTATGAGCATAGATAGACTTTGCATAAACAATGGAGTAAACTACATTTA
125 TAATGATGGGGAGAGGTTATGAGCATAGATAGACTTTGCATAAACAATGGAGTAAACTACATCTA
* *
40330211 AGACCACTAAATTATTAGTAAGTTTACATTTTGGTCACTCAACTTTAAAAAGTTAGAAAATAACC
190 AGACCACTAAATTATTAGTAAGTTGACATTTTGGTCACTCAACTTTAAAAAGTTACAAAATAACC
40330276 CCTGAACTATTTAAAAGTTTTCATTTAAATCACTAAGTTGTTAAGTCTTTTTTTTAAGTCCAACT
255 CCTGAACTATTTAAAAGTTTTCATTTAAATCACTAAGTTGTTAAGTCTTTTTTTTAAGTCCAACT
40330341 GACAAACTCCAAGCGATGATT
320 GACAAACTCCAAGCGATGATT
40330362 CGACAAACGA
Statistics
Matches: 332, Mismatches: 8, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
356 28 0.08
361 38 0.11
362 266 0.80
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (355 bp):
TTGCACATTGAGCCTTAGCTCAATTGGCATTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTG
TTGTAAGAACTAGGAAGACATGGGTTCATGCACACTTAAGCGCACATTTTCCTAAAATTTAATGA
TGGGGAGAGGTTATGAGCATAGATAGACTTTGCATAAACAATGGAGTAAACTACATCTAAGACCA
CTAAATTATTAGTAAGTTGACATTTTGGTCACTCAACTTTAAAAAGTTACAAAATAACCCCTGAA
CTATTTAAAAGTTTTCATTTAAATCACTAAGTTGTTAAGTCTTTTTTTTAAGTCCAACTGACAAA
CTCCAAGCGATGATTAGTTGTAAGAACTAA
Found at i:40338274 original size:26 final size:26
Alignment explanation
Indices: 40338245--40338301 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
40338235 AACAGGTATC
*
40338245 AGGATAATGATGATGATGGAAAACAT
1 AGGACAATGATGATGATGGAAAACAT
40338271 AGGACAATGATGATGATGGAAAACAT
1 AGGACAATGATGATGATGGAAAACAT
40338297 AGGAC
1 AGGAC
40338302 TACTTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.28, T:0.19
Consensus pattern (26 bp):
AGGACAATGATGATGATGGAAAACAT
Found at i:40345743 original size:25 final size:24
Alignment explanation
Indices: 40345706--40345798 Score: 75
Period size: 25 Copynumber: 3.8 Consensus size: 24
40345696 AATTTATATT
40345706 CGGGAATGCTCATACGAGCACTTAAA
1 CGGGAA-GCTCATACGAGCACTT-AA
**
40345732 CGGGAAGCTCATGTGAGGCA-TGTAA
1 CGGGAAGCTCATACGA-GCACT-TAA
**
40345757 CGGGAAGCTCCGGA-GAGC-CATTAA
1 CGGGAAGCT-CATACGAGCAC-TTAA
40345781 CGGGAAGCTCATACGAGC
1 CGGGAAGCTCATACGAGC
40345799 CAATATCGGT
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
23 2 0.04
24 18 0.33
25 23 0.43
26 11 0.20
ACGTcount: A:0.30, C:0.23, G:0.31, T:0.16
Consensus pattern (24 bp):
CGGGAAGCTCATACGAGCACTTAA
Found at i:40345786 original size:24 final size:24
Alignment explanation
Indices: 40345730--40345865 Score: 87
Period size: 25 Copynumber: 5.5 Consensus size: 24
40345720 CGAGCACTTA
* *
40345730 AACGGGAAGCT-CATGTGAGGCATGT
1 AACGGGAAGCTCCA-GAGAGCCAT-T
*
40345755 AACGGGAAGCTCCGGAGAGCCATT
1 AACGGGAAGCTCCAGAGAGCCATT
* *
40345779 AACGGGAAGCT-CATACGAGCCAAT
1 AACGGGAAGCTCCAGA-GAGCCATT
* * * * * *
40345803 ATCGGTAAGGTTCAAGTGAGCCAAT
1 AACGGGAA-GCTCCAGAGAGCCATT
* *
40345828 ATCGGGAAGCTCCGGAGAGCCAATT
1 AACGGGAAGCTCCAGAGAGCC-ATT
40345853 AATCGGGAAGCTC
1 AA-CGGGAAGCTC
40345866 ATGAAAGAGC
Statistics
Matches: 86, Mismatches: 19, Indels: 11
0.74 0.16 0.09
Matches are distributed among these distances:
23 2 0.02
24 34 0.40
25 38 0.44
26 12 0.14
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.17
Consensus pattern (24 bp):
AACGGGAAGCTCCAGAGAGCCATT
Found at i:40346003 original size:24 final size:25
Alignment explanation
Indices: 40345976--40346023 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
40345966 GGATGCTCCG
*
40345976 AAGAGCTAT-TAACGGGAAGCTCGC
1 AAGAACTATATAACGGGAAGCTCGC
*
40346000 AAGAACTATATAATGGGAAGCTCG
1 AAGAACTATATAACGGGAAGCTCG
40346024 AGAGGGCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.19
Consensus pattern (25 bp):
AAGAACTATATAACGGGAAGCTCGC
Found at i:40366734 original size:39 final size:37
Alignment explanation
Indices: 40366685--40366784 Score: 110
Period size: 39 Copynumber: 2.6 Consensus size: 37
40366675 CTAATATAAT
*
40366685 AATTATAATTACTATAATTATAATAATGTTTGACCAAAA
1 AATTATAATTAC-ATAATTATAATAATATTTGACC-AAA
* * * **
40366724 AATTACAATTACAGTATTTATAATAATATTTGATCTTA
1 AATTATAATTACA-TAATTATAATAATATTTGACCAAA
40366762 AATTATAATTACAATAATTATAA
1 AATTATAATTAC-ATAATTATAA
40366785 CAAGGATTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
38 21 0.41
39 30 0.59
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (37 bp):
AATTATAATTACATAATTATAATAATATTTGACCAAA
Found at i:40372629 original size:19 final size:19
Alignment explanation
Indices: 40372593--40372628 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
40372583 ACCAAAAATT
40372593 TATTTTAAAAATAAAAAAG
1 TATTTTAAAAATAAAAAAG
40372612 TATTTT-AAAATAAAAAA
1 TATTTTAAAAATAAAAAA
40372629 ATAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
TATTTTAAAAATAAAAAAG
Found at i:40387808 original size:9 final size:9
Alignment explanation
Indices: 40387794--40387877 Score: 116
Period size: 9 Copynumber: 9.4 Consensus size: 9
40387784 TTTGGTTAAA
40387794 AATTAACCG
1 AATTAACCG
40387803 AATTAACCG
1 AATTAACCG
*
40387812 AATTACCCG
1 AATTAACCG
40387821 AATTAACCG
1 AATTAACCG
* *
40387830 GATTACCCG
1 AATTAACCG
40387839 AATTAACCG
1 AATTAACCG
* *
40387848 GATTACCCG
1 AATTAACCG
40387857 AATT-ACCG
1 AATTAACCG
40387865 AATTAACCG
1 AATTAACCG
40387874 AATT
1 AATT
40387878 GAATCACTAC
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
8 7 0.11
9 57 0.89
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:40387914 original size:8 final size:7
Alignment explanation
Indices: 40387901--40387952 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 7
40387891 ATTAAATTAT
40387901 TTTTAGA
1 TTTTAGA
40387908 CTTTTAGA
1 -TTTTAGA
40387916 TTTTAG-
1 TTTTAGA
40387922 TTTTAG-
1 TTTTAGA
40387928 TTTTAG-
1 TTTTAGA
40387934 TTTTAG-
1 TTTTAGA
40387940 TTTTAGAA
1 TTTTAG-A
40387948 TTTTA
1 TTTTA
40387953 TTTTTATTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 24 0.57
7 6 0.14
8 12 0.29
ACGTcount: A:0.23, C:0.02, G:0.13, T:0.62
Consensus pattern (7 bp):
TTTTAGA
Found at i:40387927 original size:6 final size:6
Alignment explanation
Indices: 40387909--40387945 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
40387899 ATTTTTAGAC
40387909 TTTTAG ATTTTAG TTTTAG TTTTAG TTTTAG TTTTAG
1 TTTTAG -TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG
40387946 AATTTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (6 bp):
TTTTAG
Found at i:40387969 original size:20 final size:20
Alignment explanation
Indices: 40387901--40387958 Score: 75
Period size: 18 Copynumber: 3.0 Consensus size: 20
40387891 ATTAAATTAT
*
40387901 TTTTAGACTTTTAGATTTTAG
1 TTTTAGAATTTTAG-TTTTAG
40387922 TTTTAG--TTTTAGTTTTAG
1 TTTTAGAATTTTAGTTTTAG
*
40387940 TTTTAGAATTTTATTTTTA
1 TTTTAGAATTTTAGTTTTA
40387959 TTTATTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 12 0.35
19 6 0.18
20 10 0.29
21 6 0.18
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.64
Consensus pattern (20 bp):
TTTTAGAATTTTAGTTTTAG
Found at i:40390575 original size:30 final size:30
Alignment explanation
Indices: 40390509--40390581 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
40390499 GACGACGACG
40390509 CAGGCCCATCAACGAGGCCCAGAAATTCAT
1 CAGGCCCATCAACGAGGCCCAGAAATTCAT
* * * * *
40390539 CCGGCCCATCATC-AGCGCCCATAACTTTAT
1 CAGGCCCATCAACGAG-GCCCAGAAATTCAT
*
40390569 CAGGCCCAGCAAC
1 CAGGCCCATCAAC
40390582 AGCACCGACA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 2 0.06
30 32 0.94
ACGTcount: A:0.29, C:0.38, G:0.18, T:0.15
Consensus pattern (30 bp):
CAGGCCCATCAACGAGGCCCAGAAATTCAT
Found at i:40390690 original size:18 final size:18
Alignment explanation
Indices: 40390663--40390697 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40390653 CATGTGCGTA
* *
40390663 TCCTAGCCCTTTTATGTG
1 TCCTAACCCTTATATGTG
40390681 TCCTAACCCTTATATGT
1 TCCTAACCCTTATATGT
40390698 TTCTTTTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.29, G:0.11, T:0.43
Consensus pattern (18 bp):
TCCTAACCCTTATATGTG
Found at i:40391165 original size:49 final size:49
Alignment explanation
Indices: 40391111--40391332 Score: 390
Period size: 49 Copynumber: 4.5 Consensus size: 49
40391101 GTTTATATTA
* *
40391111 ATGTAATAAAAGACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
40391160 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
* *
40391209 ATTTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTA
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
40391258 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
* *
40391307 ATTTAATAAAATATAAAATAGTTTAT
1 ATGTAATAAAATACAAAATAGTTTAT
40391333 ATAAAATAGT
Statistics
Matches: 165, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 165 1.00
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
Found at i:40391283 original size:98 final size:98
Alignment explanation
Indices: 40391114--40391480 Score: 527
Period size: 98 Copynumber: 3.6 Consensus size: 98
40391104 TATATTAATG
*
40391114 TAATAAAAGACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATGTAATAAAATACAAAAT
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATGTAATAAAATACAAAAT
40391179 AGTTTATTTTGAATATTTTGATATTATTTCATT
66 AGTTTATTTTGAATATTTTGATATTATTTCATT
*
40391212 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTAATGTAATAAAATACAAAAT
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATGTAATAAAATACAAAAT
40391277 AGTTTATTTTGAATATTTTGATATTATTTCATT
66 AGTTTATTTTGAATATTTTGATATTATTTCATT
* *
40391310 TAATAAAATATAAAATAGTTTATATAAAATAGTTTACTTTTAATATTTTGATATTATTTGATGTA
1 TAATAAAATACAAAATAG----T-T----TA---T--TTTGAATATTTTGATATTATTTGATGTA
* *
40391375 ATAAAATACAAAATAGTTTATTTTGAATTTTTTAATATTATTTCATT
52 ATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
* * *
40391422 TAATAAAATATAAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAATA
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATGTAATAAAATA
40391481 ATGAATAATT
Statistics
Matches: 245, Mismatches: 10, Indels: 28
0.87 0.04 0.10
Matches are distributed among these distances:
98 146 0.60
100 1 0.00
102 1 0.00
103 3 0.01
107 3 0.01
108 1 0.00
110 1 0.00
112 89 0.36
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (98 bp):
TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATGTAATAAAATACAAAAT
AGTTTATTTTGAATATTTTGATATTATTTCATT
Found at i:40391336 original size:14 final size:14
Alignment explanation
Indices: 40391317--40391345 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40391307 ATTTAATAAA
40391317 ATATAAAATAGTTT
1 ATATAAAATAGTTT
40391331 ATATAAAATAGTTT
1 ATATAAAATAGTTT
40391345 A
1 A
40391346 CTTTTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATAAAATAGTTT
Found at i:40391342 original size:63 final size:63
Alignment explanation
Indices: 40391272--40391395 Score: 205
Period size: 63 Copynumber: 2.0 Consensus size: 63
40391262 AATAAAATAC
* *
40391272 AAAATAGTTTA-TTTTGAATATTTTGATATTATTTCATTTAATAAAATATAAAATAGTTTATAT
1 AAAATAGTTTACTTTT-AATATTTTGATATTATTTCATGTAATAAAATACAAAATAGTTTATAT
*
40391335 AAAATAGTTTACTTTTAATATTTTGATATTATTTGATGTAATAAAATACAAAATAGTTTAT
1 AAAATAGTTTACTTTTAATATTTTGATATTATTTCATGTAATAAAATACAAAATAGTTTAT
40391396 TTTGAATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 53 0.93
64 4 0.07
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (63 bp):
AAAATAGTTTACTTTTAATATTTTGATATTATTTCATGTAATAAAATACAAAATAGTTTATAT
Found at i:40391355 original size:112 final size:112
Alignment explanation
Indices: 40391223--40391444 Score: 401
Period size: 112 Copynumber: 2.0 Consensus size: 112
40391213 AATAAAATAC
40391223 AAAATAGTTTATTTTGAATATTTTGATATTATTTAATGTAATAAAATACAAAATAGTTTATTTTG
1 AAAATAGTTTATTTTGAATATTTTGATATTATTTAATGTAATAAAATACAAAATAGTTTATTTTG
*
40391288 AATATTTTGATATTATTTCATTTAATAAAATATAAAATAGTTTATAT
66 AATATTTTAATATTATTTCATTTAATAAAATATAAAATAGTTTATAT
*
40391335 AAAATAGTTTACTTTT-AATATTTTGATATTATTTGATGTAATAAAATACAAAATAGTTTATTTT
1 AAAATAGTTTA-TTTTGAATATTTTGATATTATTTAATGTAATAAAATACAAAATAGTTTATTTT
*
40391399 GAATTTTTTAATATTATTTCATTTAATAAAATATAAAATAGTTTAT
65 GAATATTTTAATATTATTTCATTTAATAAAATATAAAATAGTTTAT
40391445 TTTGAATATT
Statistics
Matches: 106, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
112 102 0.96
113 4 0.04
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (112 bp):
AAAATAGTTTATTTTGAATATTTTGATATTATTTAATGTAATAAAATACAAAATAGTTTATTTTG
AATATTTTAATATTATTTCATTTAATAAAATATAAAATAGTTTATAT
Found at i:40391357 original size:161 final size:161
Alignment explanation
Indices: 40391174--40391480 Score: 535
Period size: 161 Copynumber: 1.9 Consensus size: 161
40391164 AATAAAATAC
*
40391174 AAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAATACAAAATAGTTTATTTTG
1 AAAATAGTTTATTTTGAATATTTTGATATTATTTCATGTAATAAAATACAAAATAGTTTATTTTG
*
40391239 AATATTTTGATATTATTTAATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTAT
66 AATATTTTAATATTATTTAATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTAT
40391304 TTCATTTAATAAAATATAAAATAGTTTATAT
131 TTCATTTAATAAAATATAAAATAGTTTATAT
*
40391335 AAAATAGTTTACTTTT-AATATTTTGATATTATTTGATGTAATAAAATACAAAATAGTTTATTTT
1 AAAATAGTTTA-TTTTGAATATTTTGATATTATTTCATGTAATAAAATACAAAATAGTTTATTTT
* * * *
40391399 GAATTTTTTAATATTATTTCATTTAATAAAATATAAAATAGTTTATTTTGAATATTTTGATATTA
65 GAATATTTTAATATTATTTAATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTA
40391464 TTTCATTTAATAAAATA
130 TTTCATTTAATAAAATA
40391481 ATGAATAATT
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
161 134 0.97
162 4 0.03
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.49
Consensus pattern (161 bp):
AAAATAGTTTATTTTGAATATTTTGATATTATTTCATGTAATAAAATACAAAATAGTTTATTTTG
AATATTTTAATATTATTTAATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTAT
TTCATTTAATAAAATATAAAATAGTTTATAT
Found at i:40391392 original size:49 final size:49
Alignment explanation
Indices: 40391335--40391480 Score: 231
Period size: 49 Copynumber: 3.0 Consensus size: 49
40391325 TAGTTTATAT
* *
40391335 AAAATAGTTTACTTTT-AATATTTTGATATTATTTGATGTAATAAAATAC
1 AAAATAGTTTA-TTTTGAATATTTTGATATTATTTCATTTAATAAAATAC
* * *
40391384 AAAATAGTTTATTTTGAATTTTTTAATATTATTTCATTTAATAAAATAT
1 AAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAATAC
40391433 AAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAATA
1 AAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAATA
40391481 ATGAATAATT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
48 4 0.04
49 85 0.96
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (49 bp):
AAAATAGTTTATTTTGAATATTTTGATATTATTTCATTTAATAAAATAC
Found at i:40394677 original size:124 final size:124
Alignment explanation
Indices: 40394436--40394845 Score: 682
Period size: 124 Copynumber: 3.3 Consensus size: 124
40394426 CCCAAACATG
* *
40394436 CTACTGTAGCAAAAACGCGTCCATGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* * *
40394501 TTGAATCG-TTTTTATACTATTTACTTAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTT-AGGAC
*
40394560 CTACTGTAGCAAAAGCGCGTCCACATGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
40394625 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACT-AGAAATTATTTTTTAGGAC
66 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCA-AAATTATTTTTTAGGAC
* *
40394684 CTACTGTAGCAAAAGCGCTTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* *
40394749 TTGAAGTGTTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAA-AATTTTTTAGGAC
66 TTGAAGCG-TTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTAGGAC
40394808 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
40394846 CTTAATAAAT
Statistics
Matches: 270, Mismatches: 12, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
124 193 0.71
125 76 0.28
126 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTAGGAC
Found at i:40396619 original size:11 final size:11
Alignment explanation
Indices: 40396596--40396630 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
40396586 TTTTTTTATT
40396596 TTTTAAAA-A-
1 TTTTAAAATAC
40396605 TTTTAAAATAC
1 TTTTAAAATAC
40396616 TTTTAAAATAC
1 TTTTAAAATAC
40396627 TTTT
1 TTTT
40396631 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.33
10 1 0.04
11 15 0.62
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:40396632 original size:40 final size:39
Alignment explanation
Indices: 40396587--40396711 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 39
40396577 ATATTTTAAT
*
40396587 TTTTTTATTTTTTAAAAATTTTAAAATACTTTTAAAATAC
1 TTTTTTATTTTTT-AAAATTTTAAAATATTTTTAAAATAC
*
40396627 -----T-TTTTTTAAAATTTT-AAATTTTTTTAAAATAC
1 TTTTTTATTTTTTAAAATTTTAAAATATTTTTAAAATAC
**
40396659 TTTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTT-ATTTTTTAAAATTTTAAAATATTTTTAAAATAC
40396699 TTTTTTATTTTTT
1 TTTTTTATTTTTT
40396712 GTTTTAATTT
Statistics
Matches: 72, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
32 15 0.21
33 8 0.11
34 6 0.08
35 1 0.01
37 1 0.01
39 19 0.26
40 22 0.31
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (39 bp):
TTTTTTATTTTTTAAAATTTTAAAATATTTTTAAAATAC
Found at i:40396702 original size:29 final size:29
Alignment explanation
Indices: 40396648--40396709 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
40396638 TTTTAAATTT
* **
40396648 TTTTAAAATACTTTTTTAATTTTTTTTAA
1 TTTTAAAATACTTTTTAAATACTTTTTAA
*
40396677 TTTTAAAATA-TTTTTAAAATACTTTTTTA
1 TTTTAAAATACTTTTT-AAATACTTTTTAA
40396706 TTTT
1 TTTT
40396710 TTGTTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTAAAATACTTTTTAAATACTTTTTAA
Found at i:40404109 original size:2 final size:2
Alignment explanation
Indices: 40404102--40404126 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40404092 TGAAAATTAA
40404102 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
40404127 CATAATGCTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40411914 original size:12 final size:13
Alignment explanation
Indices: 40411888--40411915 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40411878 ACTTTTCCAC
40411888 AATACTTTTTAAA
1 AATACTTTTTAAA
40411901 AATACTTTTTAAA
1 AATACTTTTTAAA
40411914 AA
1 AA
40411916 CAATGCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
AATACTTTTTAAA
Found at i:40413962 original size:11 final size:11
Alignment explanation
Indices: 40413930--40413975 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
40413920 GGTTGAATTG
40413930 ATATTTTAAAA
1 ATATTTTAAAA
* *
40413941 A-ATAATAAAAA
1 ATAT-TTTAAAA
40413952 ATATTTTAAAA
1 ATATTTTAAAA
40413963 ATATTTTAAAA
1 ATATTTTAAAA
40413974 AT
1 AT
40413976 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 2 0.07
11 25 0.86
12 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATTTTAAAA
Found at i:40417403 original size:15 final size:15
Alignment explanation
Indices: 40417383--40417413 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40417373 CATTGCATAT
40417383 AAATGTTAAGTTATG
1 AAATGTTAAGTTATG
40417398 AAATGTTAAGTTATG
1 AAATGTTAAGTTATG
40417413 A
1 A
40417414 GATTGCATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (15 bp):
AAATGTTAAGTTATG
Found at i:40419327 original size:6 final size:6
Alignment explanation
Indices: 40419316--40419364 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
40419306 ATTAGTAGCA
*
40419316 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAAGG GGGAGG GA-AGG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAG-AGG GAGAGG GAGAGG
40419364 G
1 G
40419365 GGATGGGGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
5 4 0.10
6 31 0.77
7 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:40431685 original size:30 final size:31
Alignment explanation
Indices: 40431646--40431705 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
40431636 GGAGGTGGGA
* *
40431646 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAACTTTGAGGGGAAAAG
* *
40431677 TGGG-AGGGAGTAAAACTTTGGGGGGAAAA
1 TGGGAAGGGAATAAAACTTTGAGGGGAAAA
40431706 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.38, C:0.02, G:0.42, T:0.18
Consensus pattern (31 bp):
TGGGAAGGGAATAAAACTTTGAGGGGAAAAG
Found at i:40431933 original size:9 final size:9
Alignment explanation
Indices: 40431919--40431956 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
40431909 TATAGTTTGA
40431919 TATTCGAAT
1 TATTCGAAT
40431928 TATTCGAAT
1 TATTCGAAT
*
40431937 TATTCGAGT
1 TATTCGAAT
40431946 TATTCGAAT
1 TATTCGAAT
40431955 TA
1 TA
40431957 GAAAACTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40435573 original size:18 final size:18
Alignment explanation
Indices: 40435522--40435573 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
40435512 GGTTTTTTTA
40435522 ATTTTGTT-AGGTTTAAGG
1 ATTTTGTTAAGGTTT-AGG
*
40435540 TTTTTGTTAAGG-TTAGG
1 ATTTTGTTAAGGTTTAGG
40435557 ATTTT-TTAAGGGTTTAG
1 ATTTTGTTAA-GGTTTAG
40435574 TGTTTGGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 4 0.14
17 9 0.31
18 13 0.45
19 3 0.10
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (18 bp):
ATTTTGTTAAGGTTTAGG
Found at i:40441084 original size:18 final size:18
Alignment explanation
Indices: 40441036--40441085 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
40441026 CTAAGGTTGT
* *
40441036 TTTATATTCTGTTATTTA
1 TTTATATACTATTATTTA
* * *
40441054 TTTATCTATTATTATTTG
1 TTTATATACTATTATTTA
40441072 TTTATATACTATTA
1 TTTATATACTATTA
40441086 ATAAATAAGG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTATATACTATTATTTA
Found at i:40441885 original size:28 final size:26
Alignment explanation
Indices: 40441859--40441932 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 26
40441849 AAGTTTATAC
40441859 ATGTAATTATTATTTTTATGATTTAT
1 ATGTAATTATTATTTTTATGATTTAT
* *
40441885 A--TATTTATTA-TCTTAT-A--TAT
1 ATGTAATTATTATTTTTATGATTTAT
40441905 ATGTAATTATTATTTTTATGATTTAT
1 ATGTAATTATTATTTTTATGATTTAT
40441931 AT
1 AT
40441933 ATTTATTACC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 4 0.11
22 9 0.24
23 10 0.26
24 9 0.24
26 6 0.16
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.61
Consensus pattern (26 bp):
ATGTAATTATTATTTTTATGATTTAT
Found at i:40441892 original size:8 final size:8
Alignment explanation
Indices: 40441865--40441938 Score: 50
Period size: 8 Copynumber: 9.5 Consensus size: 8
40441855 ATACATGTAA
40441865 TTAT-TAT
1 TTATATAT
*
40441872 TTTTATGAT
1 TTATAT-AT
40441881 TTATATAT
1 TTATATAT
40441889 TTAT-TAT
1 TTATATAT
40441896 CTTATATA-
1 -TTATATAT
* *
40441904 -TATGTAA
1 TTATATAT
40441911 TTAT-TAT
1 TTATATAT
*
40441918 TTTTATGAT
1 TTATAT-AT
40441927 TTATATAT
1 TTATATAT
40441935 TTAT
1 TTAT
40441939 TACCTTATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
6 5 0.09
7 11 0.21
8 21 0.40
9 16 0.30
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (8 bp):
TTATATAT
Found at i:40441900 original size:16 final size:15
Alignment explanation
Indices: 40441873--40441950 Score: 63
Period size: 16 Copynumber: 5.1 Consensus size: 15
40441863 AATTATTATT
*
40441873 TTTATGATTTATATA
1 TTTATTATTTATATA
40441888 TTTATTATCTTATATA
1 TTTATTAT-TTATATA
40441904 TATGTAATTA-TTAT-T-
1 T-T-T-ATTATTTATATA
*
40441919 TTTATGATTTATATA
1 TTTATTATTTATATA
*
40441934 TTTATTACCTTATATA
1 TTTATTA-TTTATATA
40441950 T
1 T
40441951 ATATGTACGT
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
12 3 0.06
13 5 0.10
14 2 0.04
15 14 0.27
16 17 0.33
17 5 0.10
18 1 0.02
19 4 0.08
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (15 bp):
TTTATTATTTATATA
Found at i:40441909 original size:46 final size:46
Alignment explanation
Indices: 40441854--40441952 Score: 180
Period size: 46 Copynumber: 2.2 Consensus size: 46
40441844 ATTTTAAGTT
* *
40441854 TATACATGTAATTATTATTTTTATGATTTATATATTTATTATCTTA
1 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTA
40441900 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTA
1 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTA
40441946 TATATAT
1 TATATAT
40441953 ATGTACGTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (46 bp):
TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTA
Found at i:40442006 original size:20 final size:20
Alignment explanation
Indices: 40441960--40442008 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
40441950 TATATGTACG
*
40441960 TATATATATTATACTTTCTA
1 TATATATATTATAATTTCTA
** *
40441980 TCCATATTTTATAATTTCTA
1 TATATATATTATAATTTCTA
40442000 TATATATAT
1 TATATATAT
40442009 ATATTTTTTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATATTATAATTTCTA
Found at i:40443975 original size:44 final size:45
Alignment explanation
Indices: 40443883--40443999 Score: 148
Period size: 44 Copynumber: 2.6 Consensus size: 45
40443873 CCACTAAATA
40443883 TTTAATTAAATTACATAGTATCTATTATAAATTATTAAAACGAAT
1 TTTAATTAAATTACATAGTATCTATTATAAATTATTAAAACGAAT
* * * * * *
40443928 TTTAACTAAATTACATAGTATTTGTTAT-AATTATTCATACTAAT
1 TTTAATTAAATTACATAGTATCTATTATAAATTATTAAAACGAAT
*
40443972 TTTAATTAAATTATATAGTA-CTCATTAT
1 TTTAATTAAATTACATAGTATCT-ATTAT
40444000 TTATTAAGAC
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
43 1 0.02
44 35 0.57
45 25 0.41
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (45 bp):
TTTAATTAAATTACATAGTATCTATTATAAATTATTAAAACGAAT
Found at i:40447838 original size:40 final size:39
Alignment explanation
Indices: 40447790--40447904 Score: 162
Period size: 40 Copynumber: 2.9 Consensus size: 39
40447780 GTTTGGATAA
40447790 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTTTGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCG-TTTTTGG
*
40447830 AAAACGCCGCTAAAGATCGAG-ATTTAGCGGCGGTTTATGG
1 AAAACGCCGCTAAAGATCGAGCA-TTAGCGGC-GTTTTTGG
* *
40447870 AAAACGCCGCTAAAAAT-AAGCATTAGCGGCGTTTT
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGTTTT
40447905 CAATAAAGCG
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
38 4 0.06
39 11 0.16
40 52 0.76
41 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (39 bp):
AAAACGCCGCTAAAGATCGAGCATTAGCGGCGTTTTTGG
Found at i:40448007 original size:41 final size:41
Alignment explanation
Indices: 40447962--40448072 Score: 204
Period size: 41 Copynumber: 2.7 Consensus size: 41
40447952 CTTTCGGGGA
* *
40447962 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGTCCAGGCC
1 TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCCCAGGCC
40448003 TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCCCAGGCC
1 TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCCCAGGCC
40448044 TTTAGCGGCGTTTTTGTGAAAGCGCCGCT
1 TTTAGCGGCGTTTTTGTGAAAGCGCCGCT
40448073 GAAAGCGCCG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCCCAGGCC
Found at i:40448077 original size:12 final size:12
Alignment explanation
Indices: 40448060--40448084 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40448050 GGCGTTTTTG
40448060 TGAAAGCGCCGC
1 TGAAAGCGCCGC
40448072 TGAAAGCGCCGC
1 TGAAAGCGCCGC
40448084 T
1 T
40448085 AATGCCAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.32, T:0.12
Consensus pattern (12 bp):
TGAAAGCGCCGC
Found at i:40448100 original size:53 final size:53
Alignment explanation
Indices: 40448019--40448125 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
40448009 GGCGTTTTTG
* *
40448019 TGAAAGCGCCGCTAATGCCCAGGCCTTTAGCGGCGTTTTTGTGAAAGCGCCGC
1 TGAAAGCGCCGCTAATGCCAAGGCCTTTAGCGGCGTTTTTGGGAAAGCGCCGC
*
40448072 TGAAAGCGCCGCTAATGCCAAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGC
1 TGAAAGCGCCGCTAATGCCAAGGCCTTTAGCGGCGTTTTTGGGAAAGCGCCGC
40448125 T
1 T
40448126 AATAATGCTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.20, C:0.26, G:0.32, T:0.22
Consensus pattern (53 bp):
TGAAAGCGCCGCTAATGCCAAGGCCTTTAGCGGCGTTTTTGGGAAAGCGCCGC
Found at i:40448319 original size:66 final size:67
Alignment explanation
Indices: 40448248--40448383 Score: 247
Period size: 66 Copynumber: 2.0 Consensus size: 67
40448238 ATTTATATAT
*
40448248 TAAATAATTTCTTATATAATTGTAAAAGAGATAGTATTAATTTT-AAAATATTGAATTAATTATC
1 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTTAAAAATATTGAATTAATTATC
40448312 AC
66 AC
40448314 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTTAAAAAATATTGAATTAATTAT
1 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTT-AAAAATATTGAATTAATTAT
40448379 CAC
65 CAC
40448382 TA
1 TA
40448384 TAGTTTAGGG
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
66 43 0.64
68 24 0.36
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (67 bp):
TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTTAAAAATATTGAATTAATTATC
AC
Found at i:40448460 original size:61 final size:65
Alignment explanation
Indices: 40448386--40448537 Score: 172
Period size: 68 Copynumber: 2.4 Consensus size: 65
40448376 TATCACTATA
* *
40448386 GTTTAGGGTTTTTGGGTTTAGGGT-ATATGGTTTA-A-AT-A-GGTTTAGGTGTTACCATTTTAA
1 GTTTATGGATTTTGGGTTTAGGGTCAT-TGGTTTAGATATCATGGTTTAGGTGTTACCATTTTAA
40448446 G
65 G
* *
40448447 GTTTATGGATTTTGGGTTTA-GGTCCTTGGTTTAGGGTATATGCATGGTTTAGGTGTTGCCATTT
1 GTTTATGGATTTTGGGTTTAGGGTCATTGGTTTA--G-ATAT-CATGGTTTAGGTGTTACCATTT
40448511 TAAG
62 TAAG
*
40448515 GTTTATGGATTATGGGTTTAGGG
1 GTTTATGGATTTTGGGTTTAGGG
40448538 ATTATGGGTT
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
60 10 0.13
61 19 0.25
64 1 0.01
65 2 0.03
67 1 0.01
68 41 0.54
69 2 0.03
ACGTcount: A:0.18, C:0.05, G:0.32, T:0.45
Consensus pattern (65 bp):
GTTTATGGATTTTGGGTTTAGGGTCATTGGTTTAGATATCATGGTTTAGGTGTTACCATTTTAAG
Found at i:40448527 original size:7 final size:7
Alignment explanation
Indices: 40448509--40448576 Score: 73
Period size: 7 Copynumber: 9.6 Consensus size: 7
40448499 GTGTTGCCAT
*
40448509 TTTAAGG
1 TTTATGG
40448516 TTTATGG
1 TTTATGG
*
40448523 ATTATGGG
1 TTTAT-GG
*
40448531 TTTAGGG
1 TTTATGG
*
40448538 ATTATGG
1 TTTATGG
*
40448545 GTTATGG
1 TTTATGG
*
40448552 GTTATGG
1 TTTATGG
40448559 TTTATGG
1 TTTATGG
40448566 TTTATGG
1 TTTATGG
40448573 TTTA
1 TTTA
40448577 AAGGTTGGGG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
7 47 0.90
8 5 0.10
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (7 bp):
TTTATGG
Found at i:40448573 original size:14 final size:14
Alignment explanation
Indices: 40448514--40448576 Score: 81
Period size: 14 Copynumber: 4.4 Consensus size: 14
40448504 GCCATTTTAA
40448514 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
40448528 GGGTTTAGGGATTAT
1 -GGTTTATGGATTAT
* *
40448543 GGGTTATGGGTTAT
1 GGTTTATGGATTAT
*
40448557 GGTTTATGGTTTAT
1 GGTTTATGGATTAT
40448571 GGTTTA
1 GGTTTA
40448577 AAGGTTGGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 29 0.69
15 13 0.31
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:40448588 original size:21 final size:21
Alignment explanation
Indices: 40448564--40448603 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40448554 TATGGTTTAT
*
40448564 GGTTTATGGTTTAAAGGTTGG
1 GGTTTAAGGTTTAAAGGTTGG
*
40448585 GGTTTAAGGTTTAGAGGTT
1 GGTTTAAGGTTTAAAGGTT
40448604 ATGTGTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (21 bp):
GGTTTAAGGTTTAAAGGTTGG
Found at i:40449333 original size:29 final size:29
Alignment explanation
Indices: 40449302--40449372 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
40449292 TTTTTCGTGA
40449302 TTTAAAATTTTAAGATCAATTTT-AAAAGAT
1 TTTAAAATTTTAAGA--AATTTTAAAAAGAT
* *
40449332 TTTAAATTTTTTAGAAATTTTAAAAAGAT
1 TTTAAAATTTTAAGAAATTTTAAAAAGAT
*
40449361 TTTAAACTTTTA
1 TTTAAAATTTTA
40449373 TTTTTATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 6 0.17
29 17 0.47
30 13 0.36
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (29 bp):
TTTAAAATTTTAAGAAATTTTAAAAAGAT
Found at i:40452878 original size:24 final size:25
Alignment explanation
Indices: 40452833--40452885 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 25
40452823 TAATATTTTT
*
40452833 TATTTATCCTTAAAACATAATATAA
1 TATTTATCCATAAAACATAATATAA
*
40452858 TATTTAT-CATAAAA-ATAA-ATAT
1 TATTTATCCATAAAACATAATATAA
40452880 TATTTA
1 TATTTA
40452886 AAAAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.35
23 4 0.15
24 6 0.23
25 7 0.27
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (25 bp):
TATTTATCCATAAAACATAATATAA
Found at i:40453020 original size:43 final size:43
Alignment explanation
Indices: 40452916--40453261 Score: 515
Period size: 42 Copynumber: 8.2 Consensus size: 43
40452906 GATATGTTTT
* *
40452916 TAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGT-CTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
40452958 TAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
40453001 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-CTGCTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* *
40453043 TAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * * * *
40453086 TAGTGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCTTGAGCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
40453129 TAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
40453171 TAGCGGCGTTTGTAGGG--AAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* *
40453213 TAGCGGCATTTGTGGG-GAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
40453255 TAGCGGC
1 TAGCGGC
40453262 ATTAGCAACA
Statistics
Matches: 282, Mismatches: 17, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
41 3 0.01
42 181 0.64
43 96 0.34
44 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
Found at i:40453062 original size:85 final size:85
Alignment explanation
Indices: 40452916--40453261 Score: 520
Period size: 85 Copynumber: 4.1 Consensus size: 85
40452906 GATATGTTTT
* * *
40452916 TAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTGTTCTATAGCGGCGTTTGTGTGAAAAGCG
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTATAGCGGCGTTTGTGGGAAAAGCG
40452981 CCGCTAAAGGTCCTGATCTA
66 CCGCTAAAGGTCCTGATCTA
* *
40453001 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGCTCTATAGCGGCGTTTGTGGGAAAAGTG
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTATAGCGGCGTTTGTGGGAAAAGCG
*
40453066 CCGCTAAAGGTCTTGATCTA
66 CCGCTAAAGGTCCTGATCTA
* * * *
40453086 TAGTGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCTTGAGCTATAGCGGCGTTTGT-GGAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-TGATCTATAGCGGCGTTTGTGGGAAAAGC
*
40453150 GCCGCTAAAGGTCTTGATCTA
65 GCCGCTAAAGGTCCTGATCTA
* *
40453171 TAGCGGCGTTTGTAGGG--AAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGG-GAAG
1 TAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGGT-CTGATCTATAGCGGCGTTTGTGGGAAAAG
40453233 CGCCGCTAAAGGTCCTGATCTA
64 CGCCGCTAAAGGTCCTGATCTA
40453255 TAGCGGC
1 TAGCGGC
40453262 ATTAGCAACA
Statistics
Matches: 240, Mismatches: 17, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
84 64 0.27
85 155 0.65
86 21 0.09
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.25
Consensus pattern (85 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTATAGCGGCGTTTGTGGGAAAAGCG
CCGCTAAAGGTCCTGATCTA
Found at i:40461374 original size:9 final size:9
Alignment explanation
Indices: 40461360--40461390 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40461350 GTTAAACGAA
40461360 TCGAGTTAT
1 TCGAGTTAT
*
40461369 TCGAGTTAA
1 TCGAGTTAT
40461378 TCGAGTTAT
1 TCGAGTTAT
40461387 TCGA
1 TCGA
40461391 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:40467215 original size:69 final size:67
Alignment explanation
Indices: 40467118--40467249 Score: 185
Period size: 69 Copynumber: 1.9 Consensus size: 67
40467108 TCCGAATAAG
** *
40467118 AAAAGACAAAACTACATCGTTTTGATAAATGTTCACCTTTTCTAAATTAAAAGTCAAAATCATTA
1 AAAAGACAAAACTACATCGTTTTGATAAATGTTCA-CTCAT-TAAATTAAAAGGCAAAATCATTA
40467183 AGTT
64 AGTT
* *
40467187 AAAAGACAAAACTACGA-CGTTTTGATAAATGTTTACTCATTAAGTTAAAAGGCAAAATCATTA
1 AAAAGACAAAACTAC-ATCGTTTTGATAAATGTTCACTCATTAAATTAAAAGGCAAAATCATTA
40467250 TATTGTTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 21 0.37
68 3 0.05
69 32 0.56
70 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.31
Consensus pattern (67 bp):
AAAAGACAAAACTACATCGTTTTGATAAATGTTCACTCATTAAATTAAAAGGCAAAATCATTAAG
TT
Found at i:40470746 original size:2 final size:2
Alignment explanation
Indices: 40470739--40470769 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40470729 TCAATTCTCA
40470739 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40470770 AGATATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40484078 original size:104 final size:103
Alignment explanation
Indices: 40483898--40484268 Score: 618
Period size: 104 Copynumber: 3.6 Consensus size: 103
40483888 TAACCGTTAT
** *
40483898 TGGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
40483963 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
40484001 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
40484066 GAATCAGAACATAGCAACCCCCTTTTCATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
40484105 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
40484170 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * **
40484210 TGGTGGATCA-CGCACATAGCACCACCCATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
40484269 TTTATATACA
Statistics
Matches: 255, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
103 27 0.11
104 188 0.74
105 39 0.15
106 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:40493281 original size:16 final size:17
Alignment explanation
Indices: 40493256--40493293 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
40493246 TCTTGTCCTT
* *
40493256 ATCCCCATCC-ACTTCC
1 ATCCCAATCCAACTACC
40493272 ATCCCAATCCAACTACC
1 ATCCCAATCCAACTACC
40493289 ATCCC
1 ATCCC
40493294 TATAGTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.26, C:0.53, G:0.00, T:0.21
Consensus pattern (17 bp):
ATCCCAATCCAACTACC
Found at i:40495178 original size:17 final size:18
Alignment explanation
Indices: 40495147--40495180 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40495137 AATTTAATTT
40495147 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
40495165 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
40495181 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:40495389 original size:7 final size:7
Alignment explanation
Indices: 40495373--40495407 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
40495363 AATCCCAAAT
40495373 CTTGAA-
1 CTTGAAC
40495379 CTTGAAC
1 CTTGAAC
40495386 CTTGAAC
1 CTTGAAC
40495393 CTTGAAC
1 CTTGAAC
*
40495400 CTTAAAC
1 CTTGAAC
40495407 C
1 C
40495408 CTAAGGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (7 bp):
CTTGAAC
Found at i:40495471 original size:33 final size:34
Alignment explanation
Indices: 40495413--40495484 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 34
40495403 AAACCCTAAG
*
40495413 GTTTAGGGTTTGGGATTTAAGGTTTAAGG-TTCAA
1 GTTTAGGGTTCGGGATTTAAGGTTT-AGGATTCAA
* * *
40495447 GTTTA-GGTTCGGGGTTTGAGGTTTAGGATTTAA
1 GTTTAGGGTTCGGGATTTAAGGTTTAGGATTCAA
40495480 GTTTA
1 GTTTA
40495485 AGATTTTAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 3 0.09
33 25 0.76
34 5 0.15
ACGTcount: A:0.21, C:0.03, G:0.33, T:0.43
Consensus pattern (34 bp):
GTTTAGGGTTCGGGATTTAAGGTTTAGGATTCAA
Found at i:40495544 original size:7 final size:7
Alignment explanation
Indices: 40495534--40495580 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
40495524 TTTAAAGATA
*
40495534 GGGTTAT
1 GGGTTTT
40495541 GGG-TTT
1 GGGTTTT
*
40495547 AGGTTTT
1 GGGTTTT
*
40495554 GGATTTT
1 GGGTTTT
40495561 GGGTTTT
1 GGGTTTT
*
40495568 GGGTTTA
1 GGGTTTT
40495575 GGGTTT
1 GGGTTT
40495581 GAGATTTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 4 0.12
7 29 0.88
ACGTcount: A:0.09, C:0.00, G:0.40, T:0.51
Consensus pattern (7 bp):
GGGTTTT
Found at i:40495564 original size:27 final size:28
Alignment explanation
Indices: 40495534--40495588 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
40495524 TTTAAAGATA
*
40495534 GGGTTATGGGTTTAGGTTTTG-GATTTT
1 GGGTTATGGGTTTAGGGTTTGAGATTTT
*
40495561 GGGTTTTGGGTTTAGGGTTTGAGATTTT
1 GGGTTATGGGTTTAGGGTTTGAGATTTT
40495589 ATATTTAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.11, C:0.00, G:0.38, T:0.51
Consensus pattern (28 bp):
GGGTTATGGGTTTAGGGTTTGAGATTTT
Found at i:40495588 original size:28 final size:27
Alignment explanation
Indices: 40495534--40495606 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 27
40495524 TTTAAAGATA
* *
40495534 GGGTTATGGGTTTAGGTTTTGGATTTT
1 GGGTTTTGGGTTTAGGGTTTGGATTTT
40495561 GGGTTTTGGGTTTAGGGTTTGAGATTTT
1 GGGTTTTGGGTTTAGGGTTTG-GATTTT
*** *
40495589 ATATTTAGGGTTTAGGGT
1 GGGTTTTGGGTTTAGGGT
40495607 AAAAAATACC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 19 0.49
28 20 0.51
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (27 bp):
GGGTTTTGGGTTTAGGGTTTGGATTTT
Done.