Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 130 of 135
Found at i:42227479 original size:27 final size:26
Alignment explanation
Indices: 42227365--42227483 Score: 96
Period size: 28 Copynumber: 4.3 Consensus size: 26
42227355 TAAAAGTTGA
*
42227365 TAAAAAAAATTTGGGCCCTT-AAAAT
1 TAAAAAAATTTTGGGCCCTTAAAAAT
*
42227390 CTAAAAAAAGTTTTGGGCCCTTTAAAAGT
1 -TAAAAAAA-TTTTGGGCCC-TTAAAAAT
** * * *
42227419 TAATAAATTTTTTTTGGCCTTTAAAAAG
1 TAA-AAA-AATTTTGGGCCCTTAAAAAT
*
42227447 AAAAAAATATTTTGGGCCCCTTAAAAAT
1 TAAAAAA-ATTTTGGG-CCCTTAAAAAT
42227475 TAAAAAAAT
1 TAAAAAAAT
42227484 AAAATTTTGG
Statistics
Matches: 71, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
26 8 0.11
27 20 0.28
28 28 0.39
29 15 0.21
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (26 bp):
TAAAAAAATTTTGGGCCCTTAAAAAT
Found at i:42232135 original size:22 final size:24
Alignment explanation
Indices: 42232087--42232136 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
42232077 AATTATTGGG
* *
42232087 TATTAAAATAAAATTTTATCATTA
1 TATTAAAATAAAATTTCATCATAA
*
42232111 TATTAATATAAAATTTCAT-A-AA
1 TATTAAAATAAAATTTCATCATAA
42232133 TATT
1 TATT
42232137 TAAGGGGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 1 0.04
24 17 0.74
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTAAAATAAAATTTCATCATAA
Found at i:42234984 original size:30 final size:30
Alignment explanation
Indices: 42234948--42235008 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
42234938 TAAATAGTAT
*
42234948 TAGTGTAGGGATCAATTTGTGTAATTGATG
1 TAGTGTAAGGATCAATTTGTGTAATTGATG
42234978 TAGTGTAAGGATCAATTTGTGTAATTGATG
1 TAGTGTAAGGATCAATTTGTGTAATTGATG
42235008 T
1 T
42235009 CAACTTTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.41
Consensus pattern (30 bp):
TAGTGTAAGGATCAATTTGTGTAATTGATG
Found at i:42237701 original size:20 final size:20
Alignment explanation
Indices: 42237664--42237703 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42237654 CAAAACTCTA
*
42237664 AATTTGATTACTTTTTTTTT
1 AATTTGATTACTTATTTTTT
42237684 AATTTGATT-CTTGATTTTTT
1 AATTTGATTACTT-ATTTTTT
42237704 TTAGTATCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (20 bp):
AATTTGATTACTTATTTTTT
Found at i:42245024 original size:2 final size:2
Alignment explanation
Indices: 42245017--42245041 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42245007 ATTTTAGAAG
42245017 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
42245042 GTGTGTCCCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42255643 original size:31 final size:31
Alignment explanation
Indices: 42255567--42255624 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
42255557 ATTATTTATT
42255567 TATTTAAA-ATTTTTATTTAAGTTATTGAAC
1 TATTTAAATATTTTTATTTAAGTTATTGAAC
42255597 TATTTAAATATTTTTATTTAAGTTATTG
1 TATTTAAATATTTTTATTTAAGTTATTG
42255625 GGTTATTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (31 bp):
TATTTAAATATTTTTATTTAAGTTATTGAAC
Found at i:42261428 original size:9 final size:9
Alignment explanation
Indices: 42261399--42261428 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
42261389 TGAATTTCAC
42261399 AATTCGAAT
1 AATTCGAAT
*
42261408 AACTCGAAT
1 AATTCGAAT
42261417 AATTCGAAT
1 AATTCGAAT
42261426 AAT
1 AAT
42261429 GTATTGATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42261561 original size:18 final size:19
Alignment explanation
Indices: 42261528--42261564 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
42261518 AATAAATTTT
42261528 AAAATTTAAAATATTTATA
1 AAAATTTAAAATATTTATA
*
42261547 AAAATTTTAAA-ATTTATA
1 AAAATTTAAAATATTTATA
42261565 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATTTAAAATATTTATA
Found at i:42261667 original size:10 final size:10
Alignment explanation
Indices: 42261614--42261663 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
42261604 AGTTAAGATT
42261614 TTAAAAAA-A
1 TTAAAAAATA
*
42261623 TTAAAACATA
1 TTAAAAAATA
42261633 TTAAAAAATA
1 TTAAAAAATA
42261643 TTCACAAAAA-A
1 TT-A-AAAAATA
*
42261654 ATAAAAAATA
1 TTAAAAAATA
42261664 ATAATTGTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 12 0.35
10 14 0.41
11 3 0.09
12 5 0.15
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (10 bp):
TTAAAAAATA
Found at i:42266198 original size:31 final size:31
Alignment explanation
Indices: 42266160--42266267 Score: 81
Period size: 31 Copynumber: 3.3 Consensus size: 31
42266150 TTTATTTGTT
*
42266160 AATTTTAGTCCTTAAATTTTTTGAATTGGTA
1 AATTTTAGTCCTTAAATTTTTTAAATTGGTA
* ** ** * *
42266191 AATTTTAGTTTCTGTACTTTTCAAATTTTTATTTGTT
1 AATTTTAG-TCCT-TAAATTT----TTTAAATTGGTA
*
42266228 AATTTTAGTCCTTAAATTTTTCAAATTGGTA
1 AATTTTAGTCCTTAAATTTTTTAAATTGGTA
42266259 AATTTTAGT
1 AATTTTAGT
42266268 TTCTGTACTT
Statistics
Matches: 56, Mismatches: 15, Indels: 12
0.67 0.18 0.14
Matches are distributed among these distances:
31 24 0.43
32 3 0.05
33 5 0.09
35 5 0.09
36 3 0.05
37 16 0.29
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (31 bp):
AATTTTAGTCCTTAAATTTTTTAAATTGGTA
Found at i:42266246 original size:68 final size:68
Alignment explanation
Indices: 42266137--42266287 Score: 284
Period size: 68 Copynumber: 2.2 Consensus size: 68
42266127 TAATTTAAGC
**
42266137 TACTTTTCAAATTTTTATTTGTTAATTTTAGTCCTTAAATTTTTTGAATTGGTAAATTTTAGTTT
1 TACTTTTCAAATTTTTATTTGTTAATTTTAGTCCTTAAATTTTTCAAATTGGTAAATTTTAGTTT
42266202 CTG
66 CTG
42266205 TACTTTTCAAATTTTTATTTGTTAATTTTAGTCCTTAAATTTTTCAAATTGGTAAATTTTAGTTT
1 TACTTTTCAAATTTTTATTTGTTAATTTTAGTCCTTAAATTTTTCAAATTGGTAAATTTTAGTTT
42266270 CTG
66 CTG
42266273 TACTTTTCAAATTTT
1 TACTTTTCAAATTTT
42266288 GAAAGTGTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 81 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (68 bp):
TACTTTTCAAATTTTTATTTGTTAATTTTAGTCCTTAAATTTTTCAAATTGGTAAATTTTAGTTT
CTG
Found at i:42266280 original size:31 final size:31
Alignment explanation
Indices: 42266183--42266285 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 31
42266173 AAATTTTTTG
42266183 AATTGGTAAATTTTAGTTTCTGTACTTTTCAA
1 AATTGGTAAATTTTAGTTTCTGTACTTTTC-A
* * * *
42266215 ATTTTTATTTGTTAATTTTAG-TCCT-TAAATTTTTCA
1 A-----ATTGGTAAATTTTAGTTTCTGT--ACTTTTCA
42266251 AATTGGTAAATTTTAGTTTCTGTACTTTTCA
1 AATTGGTAAATTTTAGTTTCTGTACTTTTCA
42266282 AATT
1 AATT
42266286 TTGAAAGTGT
Statistics
Matches: 54, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
31 24 0.44
32 4 0.07
33 1 0.02
35 1 0.02
36 5 0.09
37 19 0.35
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.54
Consensus pattern (31 bp):
AATTGGTAAATTTTAGTTTCTGTACTTTTCA
Found at i:42266764 original size:19 final size:17
Alignment explanation
Indices: 42266729--42266773 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
42266719 AATTATTTTT
*
42266729 AAAATATAAAAAGTTAA
1 AAAATATAAAAAATTAA
42266746 AAAAGTATAAAAATATTAAA
1 AAAA-TATAAAAA-ATT-AA
42266766 AAAATATA
1 AAAATATA
42266774 TTTTTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.17
18 8 0.33
19 6 0.25
20 6 0.25
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (17 bp):
AAAATATAAAAAATTAA
Found at i:42267941 original size:11 final size:11
Alignment explanation
Indices: 42267925--42267980 Score: 85
Period size: 11 Copynumber: 5.0 Consensus size: 11
42267915 TACTTTGAAA
*
42267925 TTAAATTTATT
1 TTAAATTTAAT
*
42267936 TTAAATTCAAT
1 TTAAATTTAAT
42267947 TTAAATTTAAAT
1 TTAAATTT-AAT
42267959 TTAAATTTAAT
1 TTAAATTTAAT
42267970 TTAAATTTAAT
1 TTAAATTTAAT
42267981 ATTATTATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
11 30 0.73
12 11 0.27
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:42267955 original size:6 final size:6
Alignment explanation
Indices: 42267925--42267979 Score: 71
Period size: 6 Copynumber: 9.7 Consensus size: 6
42267915 TACTTTGAAA
* *
42267925 TTAAAT TT-ATT TTAAA- TTCAAT TTAAAT TTAAAT TTAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
42267970 TTAAAT TTAA
1 TTAAAT TTAA
42267980 TATTATTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
5 13 0.31
6 29 0.69
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:42267998 original size:17 final size:16
Alignment explanation
Indices: 42267922--42267997 Score: 82
Period size: 17 Copynumber: 4.6 Consensus size: 16
42267912 TTCTACTTTG
*
42267922 AAATTAAATTTATTTT
1 AAATTAAATTTAATTT
*
42267938 AAATTCAATTTAAATTT
1 AAATTAAATTT-AATTT
42267955 AAATTTAAATTTAATTT
1 AAA-TTAAATTTAATTT
*
42267972 AAATTTAATATT-ATTAT
1 AAATTAAAT-TTAATT-T
42267989 AAATTAAAT
1 AAATTAAAT
42267998 AAAATGTTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
16 18 0.35
17 26 0.51
18 7 0.14
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTAAATTTAATTT
Found at i:42268757 original size:24 final size:22
Alignment explanation
Indices: 42268725--42268781 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
42268715 TAAATGGCAT
*
42268725 TAATAATAATACTTATTTACTAAA
1 TAATAATAATA-TT-TATACTAAA
*
42268749 TAATAATAATATTTATAGTAAA
1 TAATAATAATATTTATACTAAA
*
42268771 TAATAGTAATA
1 TAATAATAATA
42268782 AGTAGCATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 17 0.57
23 2 0.07
24 11 0.37
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
TAATAATAATATTTATACTAAA
Found at i:42268817 original size:21 final size:21
Alignment explanation
Indices: 42268791--42268831 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42268781 AAGTAGCATT
42268791 AATAATAATAAATATTTTTTA
1 AATAATAATAAATATTTTTTA
*
42268812 AATAATAATAAATGTTTTTT
1 AATAATAATAAATATTTTTT
42268832 GGTAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AATAATAATAAATATTTTTTA
Found at i:42270050 original size:29 final size:29
Alignment explanation
Indices: 42269996--42270082 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 29
42269986 CCCTGGAGGT
***
42269996 CCCT-AAACTGTCCAAAAATAGTATTTTGA
1 CCCTAAAACT-TCCAAAAATTCCATTTTGA
*
42270025 -CCTCAAAACTTCCAAAAATTCCATTTTTTA
1 CCCT-AAAACTTCCAAAAATTCCA-TTTTGA
*
42270055 CCCTGAAACTTCCCAAAAATTCCATTTT
1 CCCTAAAACTT-CCAAAAATTCCATTTT
42270083 TGACTCCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
28 3 0.06
29 10 0.21
30 20 0.42
31 15 0.31
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (29 bp):
CCCTAAAACTTCCAAAAATTCCATTTTGA
Found at i:42270098 original size:30 final size:31
Alignment explanation
Indices: 42270019--42270091 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
42270009 AAAAATAGTA
42270019 TTTTGACCTCA-AAACTT-CCAAAAATTCCAT
1 TTTTGACC-CAGAAACTTCCCAAAAATTCCAT
* *
42270049 TTTTTACCCTGAAACTTCCCAAAAATTCCAT
1 TTTTGACCCAGAAACTTCCCAAAAATTCCAT
42270080 TTTTGACTCCAG
1 TTTTGAC-CCAG
42270092 TATTCCCGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 1 0.03
30 13 0.36
31 19 0.53
32 3 0.08
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (31 bp):
TTTTGACCCAGAAACTTCCCAAAAATTCCAT
Found at i:42282118 original size:92 final size:92
Alignment explanation
Indices: 42281961--42283245 Score: 2405
Period size: 92 Copynumber: 14.0 Consensus size: 92
42281951 GTCATGATCA
*
42281961 ATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
42282026 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
* *
42282053 ATCAAACATCATTTTCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
* *
42282118 GAAGTTATAGTAAGAACAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
42282145 ATC-AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
*
42282209 GAAGTTGTAGTAAAAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
42282236 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
42282301 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
* * *
42282328 ATCAAACATTATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTTTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
42282393 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
*
42282420 ATC-AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTTTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
42282484 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
42282511 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
42282576 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
42282603 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
42282668 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
*
42282695 ATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
42282760 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
42282787 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
42282852 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
*
42282879 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTTTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
*
42282944 GAAGTTGTAGTAAGAGCAATATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
42282971 ATC-AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
42283035 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
42283062 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
*
42283127 GAAGTTGTAGTAAGAGTAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
* *
42283154 ATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTACCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
42283219 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
42283246 CTCGACATCA
Statistics
Matches: 1163, Mismatches: 27, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
91 262 0.23
92 901 0.77
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (92 bp):
ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
GAAGTTGTAGTAAGAGCAAGATGAAGC
Found at i:42282452 original size:275 final size:275
Alignment explanation
Indices: 42281961--42283256 Score: 2430
Period size: 275 Copynumber: 4.7 Consensus size: 275
42281951 GTCATGATCA
*
42281961 ATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
*
42282026 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCATTTTCTATCCTCTTGAAGTTGTAGTAA
66 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAA
* *
42282091 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTATAGTAAGAACAAGATGAAGCATCAACATCAA
131 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAACATCAA
42282156 TTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTA
196 TTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTA
*
42282221 AAAGCAAGATGAAGC
261 AGAGCAAGATGAAGC
42282236 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
*
42282301 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATTATTTCCTATCCTCTTGAAGTTGTAGTAA
66 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAA
*
42282366 AGTTGGATAGCAAGTCTTTATCTTTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAACATCAA
131 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAACATCAA
*
42282431 TTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTTTTTATCTCTCTGAAGTTGTAGTA
196 TTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTA
42282496 AGAGCAAGATGAAGC
261 AGAGCAAGATGAAGC
42282511 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
*
42282576 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAA
66 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAA
42282641 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCA
131 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATC-AACATCA
*
42282706 TTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
195 ATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
42282771 AAGAGCAAGATGAAGC
260 AAGAGCAAGATGAAGC
42282787 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
*
42282852 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAA
66 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAA
* *
42282917 AGTTGGATAGCAAGTCTTTATCTTTCTGAAGTTGTAGTAAGAGCAATATGAAGCATCAACATCAA
131 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAACATCAA
42282982 TTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTA
196 TTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTA
42283047 AGAGCAAGATGAAGC
261 AGAGCAAGATGAAGC
42283062 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
*
42283127 GAAGTTGTAGTAAGAGTAAGATGAAGCATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAA
66 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAA
* * *
42283192 AGTTGGATAGCAAGTCTTTACCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCCTCGACATCAA
131 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAACATCAA
42283257 ACCCTACTTT
Statistics
Matches: 997, Mismatches: 23, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
275 726 0.73
276 271 0.27
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (275 bp):
ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAA
AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAACATCAA
TTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTA
AGAGCAAGATGAAGC
Found at i:42282634 original size:367 final size:368
Alignment explanation
Indices: 42281961--42283245 Score: 2423
Period size: 367 Copynumber: 3.5 Consensus size: 368
42281951 GTCATGATCA
42281961 ATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
* *
42282026 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCATTTTCTATCCTCTTGAAGTTGTAGTAA
66 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAA
* *
42282091 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTATAGTAAGAACAAGATGAAGCATC-AACATCA
131 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCA
42282155 ATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
196 ATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
*
42282220 AAAAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGC
261 AAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGC
42282285 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
326 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
* *
42282328 ATCAAACATTATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTTTCT
1 ATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
42282393 GAAGTTGTAGTAAGAGCAAGATGAAGCATC-AACATCAATTCCTATCCTCTTGAAGTTGTAGTAA
66 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAA
*
42282457 AGTTGGATAGCAAGTTTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCA
131 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCA
42282522 ATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
196 ATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
42282587 AAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGC
261 AAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGC
42282652 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
326 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
42282695 ATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
42282760 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAA
66 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAA
42282825 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCA
131 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCA
*
42282890 ATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTTTCTGAAGTTGTAGT
196 ATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
*
42282955 AAGAGCAATATGAAGCATC-AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGC
261 AAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGC
42283019 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
326 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
*
42283062 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
* *
42283127 GAAGTTGTAGTAAGAGTAAGATGAAGCATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAA
66 GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAA
*
42283192 AGTTGGATAGCAAGTCTTTACCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
131 AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
42283246 CTCGACATCA
Statistics
Matches: 899, Mismatches: 17, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
366 86 0.10
367 633 0.70
368 180 0.20
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (368 bp):
ATCAAACATCATTTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
GAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAA
AGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCA
ATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGT
AAGAGCAAGATGAAGCATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGC
AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
Found at i:42283529 original size:6 final size:6
Alignment explanation
Indices: 42283518--42283579 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
42283508 AATTAAATTT
* * *
42283518 ATTTTA ATTTTA AATTT- ATTTTA AATTCA ATTTTA ATTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
*
42283565 A-TTTA ATTTAA ATTT
1 ATTTTA ATTTTA ATTT
42283580 AATAAAATGT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
5 9 0.19
6 38 0.81
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (6 bp):
ATTTTA
Found at i:42283532 original size:17 final size:17
Alignment explanation
Indices: 42283510--42283581 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
42283500 TACTTTGAAA
*
42283510 TTAAATTTATTTTAATT
1 TTAAATTTATTTTAAAT
42283527 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
* *
42283544 TCAATTTTAATTTT-AAT
1 TTAAATTT-ATTTTAAAT
* *
42283561 TTTAATTTAATTTAAAT
1 TTAAATTTATTTTAAAT
42283578 TTAA
1 TTAA
42283582 TAAAATGTCC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.09
17 36 0.80
18 5 0.11
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:42283553 original size:23 final size:22
Alignment explanation
Indices: 42283523--42283580 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
42283513 AATTTATTTT
42283523 AATTTTAAATTTATTTTAAATTC
1 AATTTTAAATTTATTTT-AATTC
* *
42283546 AATTTTAATTTTAATTTTAATTT
1 AATTTTAAATTT-ATTTTAATTC
42283569 AA-TTTAAATTTA
1 AATTTTAAATTTA
42283581 ATAAAATGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 8 0.26
23 17 0.55
24 5 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
AATTTTAAATTTATTTTAATTC
Found at i:42283580 original size:6 final size:6
Alignment explanation
Indices: 42283510--42283581 Score: 53
Period size: 6 Copynumber: 12.7 Consensus size: 6
42283500 TACTTTGAAA
* * * * *
42283510 TTAAAT TT-ATT TTAATT TTAAAT TT-ATT TTAAA- TTCAAT TTTAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
42283555 TTTAAT TTTAAT TT-AAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAA
42283582 TAAAATGTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
5 17 0.30
6 39 0.70
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (6 bp):
TTAAAT
Found at i:42283580 original size:11 final size:11
Alignment explanation
Indices: 42283507--42283582 Score: 73
Period size: 11 Copynumber: 6.8 Consensus size: 11
42283497 TTCTACTTTG
*
42283507 AAATTAAATTT
1 AAATTTAATTT
*
42283518 -ATTTTAATTTT
1 AAATTTAA-TTT
*
42283529 AAATTTATTTT
1 AAATTTAATTT
*
42283540 AAATTCAATTTT
1 AAATTTAA-TTT
*
42283552 AATTTTAATTT
1 AAATTTAATTT
*
42283563 TAATTTAATTT
1 AAATTTAATTT
42283574 AAATTTAAT
1 AAATTTAAT
42283583 AAAATGTCCA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
10 5 0.10
11 32 0.63
12 14 0.27
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:42284333 original size:24 final size:22
Alignment explanation
Indices: 42284301--42284357 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
42284291 TAAATGACAT
*
42284301 TAATAATAATACTTATTTACTAAA
1 TAATAATAATA-TT-TATACTAAA
*
42284325 TAATAATAATATTTATAGTAAA
1 TAATAATAATATTTATACTAAA
*
42284347 TAATAGTAATA
1 TAATAATAATA
42284358 AGTAGCATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 17 0.57
23 2 0.07
24 11 0.37
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
TAATAATAATATTTATACTAAA
Found at i:42284986 original size:8 final size:8
Alignment explanation
Indices: 42284973--42285003 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
42284963 ACATGGAGGT
42284973 GAGAAAGA
1 GAGAAAGA
42284981 GAGAAAGA
1 GAGAAAGA
42284989 GAGAAAAGA
1 GAG-AAAGA
42284998 GAGAAA
1 GAGAAA
42285004 AAAAGGGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (8 bp):
GAGAAAGA
Found at i:42284998 original size:9 final size:9
Alignment explanation
Indices: 42284976--42285004 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
42284966 TGGAGGTGAG
42284976 AAAGAGAG-
1 AAAGAGAGA
42284984 AAAGAGAGA
1 AAAGAGAGA
42284993 AAAGAGAGA
1 AAAGAGAGA
42285002 AAA
1 AAA
42285005 AAAGGGGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (9 bp):
AAAGAGAGA
Found at i:42285604 original size:29 final size:30
Alignment explanation
Indices: 42285580--42285840 Score: 245
Period size: 29 Copynumber: 8.9 Consensus size: 30
42285570 AGAAATTGTA
*
42285580 TTTTGACCTCGAAACTTCCAAAAATTCCAT
1 TTTTGACCTCGAAACTTCCAAAAATTACAT
* * *
42285610 TTTTGACC-CTAAAACATCC-AAAATTCCAT
1 TTTTGACCTC-GAAACTTCCAAAAATTACAT
*
42285639 TTTTGACC-CTGAAACTTCCCAAAATTACAT
1 TTTTGACCTC-GAAACTTCCAAAAATTACAT
* *
42285669 TTTT-ACCTTGAAAATTCCAAAAATTACAT
1 TTTTGACCTCGAAACTTCCAAAAATTACAT
* * *
42285698 TTTT-ACCCCTAAACTTCCAAAAATTCCAT
1 TTTTGACCTCGAAACTTCCAAAAATTACAT
* **
42285727 TTTTAACCTTAAAACTTCCAAAAATTACA-
1 TTTTGACCTCGAAACTTCCAAAAATTACAT
* *
42285756 TTTTG--CTCCCAAACTTCCAAAAATTTCAT
1 TTTTGACCT-CGAAACTTCCAAAAATTACAT
* ** *
42285785 TTTTGACCCCG-GGCTTCCAAAAATTTCAT
1 TTTTGACCTCGAAACTTCCAAAAATTACAT
*
42285814 TTTTGACCTCGAAAATTCC-AAAATTAC
1 TTTTGACCTCGAAACTTCCAAAAATTAC
42285841 CATTATGTCC
Statistics
Matches: 192, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
27 2 0.01
28 17 0.09
29 119 0.62
30 53 0.28
31 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.34
Consensus pattern (30 bp):
TTTTGACCTCGAAACTTCCAAAAATTACAT
Found at i:42285653 original size:59 final size:60
Alignment explanation
Indices: 42285556--42285844 Score: 262
Period size: 59 Copynumber: 4.9 Consensus size: 60
42285546 CCTTGGAGGT
* **
42285556 CCCTAAAACTGTCCAGAAATTGTA-TTTTGA-CCTCGAAACTTCCAAAAATTCCATTTTTGA
1 CCCTAAAACT-TCCAAAAATTACATTTTTGACCCT-GAAACTTCCAAAAATTCCATTTTTGA
* * * *
42285616 CCCTAAAACATCC-AAAATTCCATTTTTGACCCTGAAACTTCCCAAAATTACATTTTT-A
1 CCCTAAAACTTCCAAAAATTACATTTTTGACCCTGAAACTTCCAAAAATTCCATTTTTGA
* *
42285674 CCTTGAAAA-TTCCAAAAATTACATTTTT-ACCCCT-AAACTTCCAAAAATTCCATTTTTAA
1 CCCT-AAAACTTCCAAAAATTACATTTTTGA-CCCTGAAACTTCCAAAAATTCCATTTTTGA
* * *
42285733 CCTTAAAACTTCCAAAAATTACA-TTTTG-CTCC-CAAACTTCCAAAAATTTCATTTTTGA
1 CCCTAAAACTTCCAAAAATTACATTTTTGAC-CCTGAAACTTCCAAAAATTCCATTTTTGA
**** * *
42285791 CCC-CGGGCTTCCAAAAATTTCATTTTTGA-CCTCGAAAATTCC-AAAATTACCATT
1 CCCTAAAACTTCCAAAAATTACATTTTTGACCCT-GAAACTTCCAAAAATT-CCATT
42285845 ATGTCCAAAA
Statistics
Matches: 192, Mismatches: 22, Indels: 31
0.78 0.09 0.13
Matches are distributed among these distances:
57 17 0.09
58 81 0.42
59 82 0.43
60 12 0.06
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (60 bp):
CCCTAAAACTTCCAAAAATTACATTTTTGACCCTGAAACTTCCAAAAATTCCATTTTTGA
Found at i:42285721 original size:88 final size:88
Alignment explanation
Indices: 42285579--42285840 Score: 279
Period size: 88 Copynumber: 3.0 Consensus size: 88
42285569 CAGAAATTGT
* * *
42285579 ATTTTGACCTCGAAACTTCCAAAAATTCCATTTTTGA-CCCTAAAACATCC-AAAATTCCATTTT
1 ATTTTTACCT-GAAACTTCCAAAAATTACATTTTTGACCCCT-AAACTTCCAAAAATTCCATTTT
42285642 TGACCCTGAAACTTCCCAAAATTAC
64 TGACCCTGAAACTTCCCAAAATTAC
*
42285667 ATTTTTACCTTGAAAATTCCAAAAATTACATTTTT-ACCCCTAAACTTCCAAAAATTCCATTTTT
1 ATTTTTACC-TGAAACTTCCAAAAATTACATTTTTGACCCCTAAACTTCCAAAAATTCCATTTTT
* * * *
42285731 AACCTTAAAACTTCCAAAAATTAC
65 GACCCTGAAACTTCCCAAAATTAC
* * *** *
42285755 ATTTTGCT-CC-CAAACTTCCAAAAATTTCATTTTTGACCCC-GGGCTTCCAAAAATTTCATTTT
1 ATTTT--TACCTGAAACTTCCAAAAATTACATTTTTGACCCCTAAACTTCCAAAAATTCCATTTT
*
42285817 TGA-CCTCGAAAATT-CCAAAATTAC
64 TGACCCT-GAAACTTCCCAAAATTAC
42285841 CATTATGTCC
Statistics
Matches: 147, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
86 11 0.07
87 54 0.37
88 78 0.53
89 3 0.02
90 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.34
Consensus pattern (88 bp):
ATTTTTACCTGAAACTTCCAAAAATTACATTTTTGACCCCTAAACTTCCAAAAATTCCATTTTTG
ACCCTGAAACTTCCCAAAATTAC
Found at i:42287662 original size:30 final size:30
Alignment explanation
Indices: 42287626--42287720 Score: 108
Period size: 29 Copynumber: 3.2 Consensus size: 30
42287616 ACCCGGGGGC
**
42287626 AAAATGGTAATTTTGGTGTAATCGGGGTTA
1 AAAATGGTAATTTTGGTAAAATCGGGGTTA
*
42287656 AAAATGG-AATTTTAG-AAAATTCGAGGG-T-
1 AAAATGGTAATTTTGGTAAAA-TCG-GGGTTA
*
42287684 AAAATGGTAATTTTGGTAAAATCAGGGTTA
1 AAAATGGTAATTTTGGTAAAATCGGGGTTA
42287714 AAAATGG
1 AAAATGG
42287721 GATTTAGGGA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
28 12 0.22
29 21 0.39
30 21 0.39
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTAAAATCGGGGTTA
Found at i:42287725 original size:29 final size:30
Alignment explanation
Indices: 42287626--42287720 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
42287616 ACCCGGGGGC
** *
42287626 AAAATGGTAATTTTGGTGTAATCGGGGTTA
1 AAAATGGTAATTTTGGTAAAATCAGGGTTA
*
42287656 AAAATGG-AATTTTAG-AAAATTCGAGGG-T-
1 AAAATGGTAATTTTGGTAAAA-TC-AGGGTTA
42287684 AAAATGGTAATTTTGGTAAAATCAGGGTTA
1 AAAATGGTAATTTTGGTAAAATCAGGGTTA
42287714 AAAATGG
1 AAAATGG
42287721 GATTTAGGGA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
28 13 0.24
29 20 0.37
30 21 0.39
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTAAAATCAGGGTTA
Found at i:42287777 original size:30 final size:30
Alignment explanation
Indices: 42287737--42287908 Score: 247
Period size: 30 Copynumber: 5.7 Consensus size: 30
42287727 GGGAAGTTTG
*
42287737 GGGTTAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
42287767 GGGTCAAAATGTAATTTTGGAAAAGTTTT-
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
* * *
42287796 GGTATCAAAATATAATTTTGGAAAAGTTTTG
1 GG-GTCAAAATGTAATTTTGGAAAAGTTTTA
42287827 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
* *
42287857 GGGTCAAAATGTAATTTCGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
**
42287887 GGGTTGAAATGTAATTTCTGGA
1 GGGTCAAAATGTAATTT-TGGA
42287909 CAATTTAGGG
Statistics
Matches: 128, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
29 2 0.02
30 121 0.95
31 5 0.04
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTTA
Found at i:42287902 original size:90 final size:91
Alignment explanation
Indices: 42287733--42287908 Score: 282
Period size: 90 Copynumber: 1.9 Consensus size: 91
42287723 TTTAGGGAAG
* *
42287733 TTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGG
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTCGGAAAAGTTTTGG
*
42287798 TATCAAAATATAATTT-TGGAAAAGT
66 GATCAAAATATAATTTCTGGAAAAGT
42287823 TTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTCGGAAAAGTTTTGG
1 TTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTCGGAAAAGTTTTGG
* ** *
42287888 GGTTGAAATGTAATTTCTGGA
66 GATCAAAATATAATTTCTGGA
42287909 CAATTTAGGG
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 74 0.95
91 4 0.05
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (91 bp):
TTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTCGGAAAAGTTTTGG
GATCAAAATATAATTTCTGGAAAAGT
Found at i:42288312 original size:10 final size:10
Alignment explanation
Indices: 42288297--42288321 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42288287 CTGATGCGGG
42288297 TCGGGTCGGA
1 TCGGGTCGGA
42288307 TCGGGTCGGA
1 TCGGGTCGGA
42288317 TCGGG
1 TCGGG
42288322 GGTTAGTATA
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:0.08, C:0.20, G:0.52, T:0.20
Consensus pattern (10 bp):
TCGGGTCGGA
Found at i:42289617 original size:20 final size:20
Alignment explanation
Indices: 42289589--42289650 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
42289579 GGGCATGGTG
*
42289589 GAGCAGGTGGTCAGCAGATA
1 GAGCTGGTGGTCAGCAGATA
*
42289609 GAGCTGGTGGTCAGCAGATG
1 GAGCTGGTGGTCAGCAGATA
*
42289629 GAGCTGGTGGCCAGCAGCATA
1 GAGCTGGTGGTCAGCAG-ATA
42289650 G
1 G
42289651 GCACGTGGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 34 0.92
21 3 0.08
ACGTcount: A:0.24, C:0.18, G:0.42, T:0.16
Consensus pattern (20 bp):
GAGCTGGTGGTCAGCAGATA
Found at i:42289880 original size:28 final size:27
Alignment explanation
Indices: 42289849--42289933 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 27
42289839 GGACTTTTCT
*
42289849 AATTAAATTTATAA-TAATATTGAATTTA
1 AATTAAATTTA-AATTAA-ATTAAATTTA
*
42289877 AATTAAATTCAAATTTAAATTAAATTTA
1 AATTAAATTTAAA-TTAAATTAAATTTA
* *
42289905 AAATAAATTTAAGATTAAAATAAATTTA
1 AATTAAATTTAA-ATTAAATTAAATTTA
42289933 A
1 A
42289934 TTTTCAAATG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.04
28 43 0.88
29 4 0.08
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (27 bp):
AATTAAATTTAAATTAAATTAAATTTA
Found at i:42289890 original size:6 final size:5
Alignment explanation
Indices: 42289874--42289935 Score: 52
Period size: 5 Copynumber: 11.4 Consensus size: 5
42289864 AATATTGAAT
*
42289874 TTAAA TTAAA TTCAAA TTTAAA TTAAA TTTAAA ATAAA TTTAAGA TTAAA
1 TTAAA TTAAA TT-AAA -TTAAA TTAAA -TTAAA TTAAA -TTAA-A TTAAA
* *
42289924 ATAAA TTTAA TT
1 TTAAA TTAAA TT
42289936 TTCAAATGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
5 26 0.55
6 18 0.38
7 3 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:42289903 original size:11 final size:11
Alignment explanation
Indices: 42289849--42289936 Score: 74
Period size: 11 Copynumber: 7.9 Consensus size: 11
42289839 GGACTTTTCT
42289849 AATTAAATTTA
1 AATTAAATTTA
*
42289860 TAA-TAATATTGA
1 -AATTAA-ATTTA
*
42289872 ATTTAAA-TTA
1 AATTAAATTTA
42289882 AATTCAAATTTA
1 AATT-AAATTTA
42289894 AATTAAATTTA
1 AATTAAATTTA
*
42289905 AAATAAATTTA
1 AATTAAATTTA
*
42289916 AGATTAAA-ATA
1 A-ATTAAATTTA
*
42289927 AATTTAATTT
1 AATTAAATTT
42289937 TCAAATGGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
10 10 0.16
11 30 0.49
12 21 0.34
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:42289942 original size:17 final size:17
Alignment explanation
Indices: 42289892--42289933 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
42289882 AATTCAAATT
42289892 TAAA-TTAAATTTAAAA
1 TAAATTTAAATTTAAAA
42289908 TAAATTTAAGA-TTAAAA
1 TAAATTTAA-ATTTAAAA
42289925 TAAATTTAA
1 TAAATTTAA
42289934 TTTTCAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.17
17 19 0.79
18 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:42290352 original size:31 final size:30
Alignment explanation
Indices: 42290308--42290703 Score: 103
Period size: 31 Copynumber: 11.5 Consensus size: 30
42290298 GTGTTATCCA
*
42290308 CTCTATTTCAATTTCAAGAGGATGACGTTG
1 CTCTACTTCAATTTCAAGAGGATGACGTTG
* * * *
42290338 CTGCTACTTCAATTTCAGAGATGAAGTCTTGTTATCCAA
1 CT-CTACTTCAATTTCA-AGAGGATGAC--G-T-T---G
42290377 CTCTACTTCAATTTCAAGAGGATGACGTTG
1 CTCTACTTCAATTTCAAGAGGATGACGTTG
** * *
42290407 CTCTTACTTCAATTTCAGAGATAAGGACGTGTTATCCA
1 CTC-TACTTCAATTTCA-AGAGGATGAC--G-T-T--G
42290445 CTCTACTTCAATTTCAAGAGGATAGGA-GATGATG
1 CTCTACTTCAATTTCAAGAGGAT--GACG-T--TG
* *
42290479 TCACTCTTACTTCAATTTC-AGAGCTGAGGACGTGTTATCCA
1 ---CTC-TACTTCAATTTCAAGAG--GATGAC--G-T-T--G
* * *
42290520 CTCTACTTCAATTTCAAGCGGGTGGCGTTG
1 CTCTACTTCAATTTCAAGAGGATGACGTTG
* * * *
42290550 CTCTTACTTCAATTTCAGAGATGAAGTCTTGTTATC
1 CTC-TACTTCAATTTCA-AGAGGATGAC--G-T-TG
42290586 CAACTCTACTTCAATTTCAAGAGGATGACGTTG
1 C---TCTACTTCAATTTCAAGAGGATGACGTTG
** * *
42290619 CTCTTACTTCAATTTCAGAGATAAGGACGTATTATCCA
1 CTC-TACTTCAATTTCA-AGAGGATGACG---T-T--G
*
42290657 CTCTACTTCAATTTCAAGGGGATGACGTTG
1 CTCTACTTCAATTTCAAGAGGATGACGTTG
42290687 CTCTTACTTCAATTTCA
1 CTC-TACTTCAATTTCA
42290704 GAGATAAAGA
Statistics
Matches: 271, Mismatches: 45, Indels: 99
0.65 0.11 0.24
Matches are distributed among these distances:
30 13 0.05
31 65 0.24
32 29 0.11
33 5 0.02
34 6 0.02
35 8 0.03
36 21 0.08
37 61 0.23
38 53 0.20
39 8 0.03
40 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (30 bp):
CTCTACTTCAATTTCAAGAGGATGACGTTG
Found at i:42290444 original size:137 final size:136
Alignment explanation
Indices: 42290274--42290754 Score: 682
Period size: 137 Copynumber: 3.5 Consensus size: 136
42290264 ATGTTACTCC
*
42290274 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTATTTCAATTTCAAGAGGATGACGTTGC
1 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
* *
42290339 TGC-TACTTCAATTTCAGAGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
66 T-CTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGAC
42290403 GTTGCTCT
129 GTTGCTCT
42290411 TACTTCAATTTCAGAGAT-AAGGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATAGGA-GA
1 TACTTCAATTTCAGAGATGAA-GACGTGTTATCCACTCTACTTCAATTTCAAGAGGAT--GACG-
* * *
42290474 TGATGTCACTCTTACTTCAATTTCAGAGCTGAGGACGTGTTATCCACTCTACTTCAATTTCAAGC
62 T--TG---CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGA
* *
42290539 GGGTGGCGTTGCTCT
122 GGATGACGTTGCTCT
* *
42290554 TACTTCAATTTCAGAGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGACGTTG
* *
42290619 CTCTTACTTCAATTTCAGAGAT-AAGGACGTATTATCCACTCTACTTCAATTTCAAGGGGATGAC
65 CTCTTACTTCAATTTCAGAGATGAA-GACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGAC
42290683 GTTGCTCT
129 GTTGCTCT
* * *
42290691 TACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTG
42290755 AGACCTGCAG
Statistics
Matches: 309, Mismatches: 21, Indels: 29
0.86 0.06 0.08
Matches are distributed among these distances:
136 33 0.11
137 146 0.47
138 1 0.00
139 3 0.01
140 2 0.01
141 2 0.01
142 3 0.01
143 62 0.20
144 57 0.18
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (136 bp):
TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
TCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGT
TGCTCT
Found at i:42290603 original size:212 final size:210
Alignment explanation
Indices: 42290226--42290754 Score: 811
Period size: 212 Copynumber: 2.5 Consensus size: 210
42290216 AAGACTTTGC
* * * *
42290226 TATCCTACTTTACTTCAATTTCTAGAGGATAGGAAATAATGTTACTCCTACTTCAATTTCAGAGA
1 TATCC-ACTCTACTTCAATTTCAAGAGGATAGGAGAT-ATG-TACTCTTACTTCAATTTCAGAGA
*
42290291 TGAAGACGTGTTATCCACTCTATTTCAATTTCAAGAGGATGACGTTGCTGCTACTTCAATTTCAG
63 TGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTGCTACTTCAATTTCAG
42290356 AGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATT
128 AGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATT
*
42290421 TCAGAGATAAGGACGTGT
193 TCAGAGATAAGGACGTAT
*
42290439 TATCCACTCTACTTCAATTTCAAGAGGATAGGAGATGATGTCACTCTTACTTCAATTTCAGAGCT
1 TATCCACTCTACTTCAATTTCAAGAGGATAGGAGAT-ATGT-ACTCTTACTTCAATTTCAGAGAT
* * * *
42290504 GAGGACGTGTTATCCACTCTACTTCAATTTCAAGCGGGTGGCGTTGCT-CTTACTTCAATTTCAG
64 GAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTGC-TACTTCAATTTCAG
42290568 AGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATT
128 AGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATT
42290633 TCAGAGATAAGGACGTAT
193 TCAGAGATAAGGACGTAT
* *
42290651 TATCCACTCTACTTCAATTTCAAGGGGAT--GACG-T-TG--CTCTTACTTCAATTTCAGAGATA
1 TATCCACTCTACTTCAATTTCAAGAGGATAGGA-GATATGTACTCTTACTTCAATTTCAGAGATG
* *
42290710 AAGACGTATTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
65 AAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTG
42290755 AGACCTGCAG
Statistics
Matches: 293, Mismatches: 20, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
205 61 0.21
208 2 0.01
210 3 0.01
211 3 0.01
212 219 0.75
213 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (210 bp):
TATCCACTCTACTTCAATTTCAAGAGGATAGGAGATATGTACTCTTACTTCAATTTCAGAGATGA
AGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCTGCTACTTCAATTTCAGAGA
TGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTCTTACTTCAATTTCA
GAGATAAGGACGTAT
Found at i:42290664 original size:106 final size:105
Alignment explanation
Indices: 42290341--42290672 Score: 346
Period size: 106 Copynumber: 3.1 Consensus size: 105
42290331 GACGTTGCTG
42290341 CTACTTCAATTTCAGAGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTT
1 CTACTTCAATTTCAGAGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTT
42290406 GCTCTTACTTCAATTTCAGAGATAAGGACGTGTTATCCACT
66 GCTCTTACTTCAATTTCAGAGATAAGGACGT-TTATCCACT
* * * * *
42290447 CTACTTCAATTTCAAGAGGATAGGAG--ATGATGT-C-ACTCTTACTTCAATTTC-AGAGCTGAG
1 CTACTTCAATTTC-AGA-GAT-GAAGTCTTGTTATCCAACTC-TACTTCAATTTCAAGAG--GAT
* * * * * *
42290507 GACGTGTTATCCACTCTACTTCAATTTCAAGCGGGT--GG-CG--T-TGCTCT
60 GAC--G-T-TGCTCT-TACTTCAATTTC-AG-AGATAAGGACGTTTATCCACT
42290554 -TACTTCAATTTCAGAGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTT
1 CTACTTCAATTTCAGAGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTT
42290618 GCTCTTACTTCAATTTCAGAGATAAGGACGTATTATCCACT
66 GCTCTTACTTCAATTTCAGAGATAAGGACGT-TTATCCACT
42290659 CTACTTCAATTTCA
1 CTACTTCAATTTCA
42290673 AGGGGATGAC
Statistics
Matches: 178, Mismatches: 22, Indels: 52
0.71 0.09 0.21
Matches are distributed among these distances:
98 2 0.01
99 2 0.01
100 14 0.08
101 6 0.03
102 1 0.01
103 4 0.02
104 4 0.02
105 24 0.13
106 64 0.36
107 24 0.13
108 4 0.02
109 4 0.02
110 1 0.01
111 6 0.03
112 14 0.08
113 2 0.01
114 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (105 bp):
CTACTTCAATTTCAGAGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTT
GCTCTTACTTCAATTTCAGAGATAAGGACGTTTATCCACT
Found at i:42290690 original size:68 final size:67
Alignment explanation
Indices: 42290274--42290754 Score: 660
Period size: 68 Copynumber: 6.9 Consensus size: 67
42290264 ATGTTACTCC
*
42290274 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTATTTCAATTTCAAGAGGATGACGTTGC
1 TACTTCAATTTCAGAGAT-AAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
42290339 TGC-
65 T-CT
* *
42290342 TACTTCAATTTCAGAGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTCAGAGAT-AAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGACGTTG
42290407 CTCT
64 CTCT
42290411 TACTTCAATTTCAGAGATAAGGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATAGGA-GAT
1 TACTTCAATTTCAGAGATAA-GACGTGTTATCCACTCTACTTCAATTTCAAGAGGAT--GACG-T
42290475 GATGTCACTCT
62 --TG---CTCT
* * * * *
42290486 TACTTCAATTTCAGAGCTGAGGACGTGTTATCCACTCTACTTCAATTTCAAGCGGGTGGCGTTGC
1 TACTTCAATTTCAGAGAT-AAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
42290551 TCT
65 TCT
* *
42290554 TACTTCAATTTCAGAGATGAAGTCTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTCAGAGAT-AAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGACGTTG
42290619 CTCT
64 CTCT
* *
42290623 TACTTCAATTTCAGAGATAAGGACGTATTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGC
1 TACTTCAATTTCAGAGATAA-GACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
42290688 TCT
65 TCT
* *
42290691 TACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 TACTTCAATTTCAGAGAT-AAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTG
42290755 AGACCTGCAG
Statistics
Matches: 376, Mismatches: 21, Indels: 32
0.88 0.05 0.07
Matches are distributed among these distances:
68 188 0.50
69 122 0.32
70 3 0.01
71 2 0.01
72 2 0.01
73 2 0.01
74 1 0.00
75 55 0.15
76 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (67 bp):
TACTTCAATTTCAGAGATAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGCT
CT
Found at i:42302724 original size:58 final size:59
Alignment explanation
Indices: 42302659--42302797 Score: 156
Period size: 58 Copynumber: 2.4 Consensus size: 59
42302649 TGATAAATGA
* * * *
42302659 TGAAATCGGGGTGAAAAATGGGACTTAT-GGATACCCGGGGGCAAAATGGTAATTTTGG
1 TGAAATCGGGGTTAAAAATGGGAATTATAGAAAACCCGGGGGCAAAATGGTAATTTTGG
* * * ** * *
42302717 TGTAATCGGGATTAAAAAT-GGAATTTTAGAAAATTCGGGGGTACAATGGTAATTTTGG
1 TGAAATCGGGGTTAAAAATGGGAATTATAGAAAACCCGGGGGCAAAATGGTAATTTTGG
*
42302775 TGAAATCGAGGTTAAAAATGGGA
1 TGAAATCGGGGTTAAAAATGGGA
42302798 TTTAGGGAAG
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
57 6 0.09
58 56 0.86
59 3 0.05
ACGTcount: A:0.35, C:0.07, G:0.31, T:0.27
Consensus pattern (59 bp):
TGAAATCGGGGTTAAAAATGGGAATTATAGAAAACCCGGGGGCAAAATGGTAATTTTGG
Found at i:42302737 original size:30 final size:29
Alignment explanation
Indices: 42302701--42302795 Score: 88
Period size: 29 Copynumber: 3.2 Consensus size: 29
42302691 ACCCGGGGGC
*
42302701 AAAATGGTAATTTTGGTGTAATCGGGATTA
1 AAAATGGTAATTTTGGTGAAATCGGG-TTA
* * *
42302731 AAAATGG-AATTTTAG-AAAATTCGGGGGT-
1 AAAATGGTAATTTTGGTGAAA-TC-GGGTTA
*
42302759 ACAATGGTAATTTTGGTGAAATCGAGGTTA
1 AAAATGGTAATTTTGGTGAAATCG-GGTTA
42302789 AAAATGG
1 AAAATGG
42302796 GATTTAGGGA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 9 0.18
29 22 0.44
30 19 0.38
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTGAAATCGGGTTA
Found at i:42302815 original size:58 final size:58
Alignment explanation
Indices: 42302694--42302830 Score: 170
Period size: 58 Copynumber: 2.4 Consensus size: 58
42302684 TATGGATACC
* *
42302694 CGGGGGCAAAATGGTAATTTTGGTGTAATCGGGATTAAAAATGGAATTTTAGAAAATT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGATTAAAAATGGAATTTTAGAAAATT
* * * *
42302752 CGGGGGTACAATGGTAATTTTGGTGAAATCGAGG-TTAAAAATGGGA-TTTAGGGAAGTT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCG-GGATTAAAAATGGAATTTTA-GAAAATT
* *
42302810 TGGGGGTAAAATGATAATTTT
1 CGGGGGTAAAATGGTAATTTT
42302831 TGAAAGTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 4 0.06
58 62 0.91
59 2 0.03
ACGTcount: A:0.34, C:0.04, G:0.31, T:0.31
Consensus pattern (58 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGATTAAAAATGGAATTTTAGAAAATT
Found at i:42302891 original size:19 final size:19
Alignment explanation
Indices: 42302867--42302921 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
42302857 TTTGGAAAAG
42302867 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
42302886 TTTT--GG--AAAA-G---
1 TTTTGGGGTCAAAATGTAA
42302897 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
42302916 TTTTGG
1 TTTTGG
42302922 AAAAGTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
13 2 0.07
14 1 0.04
15 8 0.29
16 1 0.04
17 2 0.07
19 10 0.36
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (19 bp):
TTTTGGGGTCAAAATGTAA
Found at i:42302995 original size:30 final size:30
Alignment explanation
Indices: 42302805--42302983 Score: 263
Period size: 30 Copynumber: 6.0 Consensus size: 30
42302795 GGATTTAGGG
* *
42302805 AAGTTTGGGGGT-AAAATGATAATTTTTG-A
1 AAGTTTTGGGGTCAAAATG-TAATTTTGGAA
*
42302834 AAGTTTTGGGGTTAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
42302864 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
42302894 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* * *
42302924 AAGTTTTAGGGTCGAAATGTAATTTCGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
42302954 AAGTTTTGGGGTCGAAATGTAATTTCTGGA
1 AAGTTTTGGGGTCAAAATGTAATTT-TGGA
42302984 CAATTTAGGG
Statistics
Matches: 139, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
29 19 0.14
30 117 0.84
31 3 0.02
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.37
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAA
Found at i:42304676 original size:20 final size:20
Alignment explanation
Indices: 42304651--42304689 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42304641 CAGGGCATGG
*
42304651 TGGAGCAGGTGGTCAGCAGA
1 TGGAGCAGGTGGCCAGCAGA
*
42304671 TGGAGCTGGTGGCCAGCAG
1 TGGAGCAGGTGGCCAGCAG
42304690 CATAGGCACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.46, T:0.15
Consensus pattern (20 bp):
TGGAGCAGGTGGCCAGCAGA
Found at i:42304924 original size:28 final size:27
Alignment explanation
Indices: 42304893--42304977 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 27
42304883 GGACTTTTCT
42304893 AATTAAATTTATAA-TAATATTGAATTTA
1 AATTAAATTTA-AATTAA-ATTGAATTTA
*
42304921 AATTAAATTCAAATTTAAATTGAATTTA
1 AATTAAATTTAAA-TTAAATTGAATTTA
* * *
42304949 AAATAAATTTAAGATTAAAATAAATTTA
1 AATTAAATTTAA-ATTAAATTGAATTTA
42304977 A
1 A
42304978 TTTTCAAATG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.04
28 43 0.88
29 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (27 bp):
AATTAAATTTAAATTAAATTGAATTTA
Found at i:42304940 original size:12 final size:11
Alignment explanation
Indices: 42304893--42304980 Score: 65
Period size: 11 Copynumber: 7.9 Consensus size: 11
42304883 GGACTTTTCT
42304893 AATTAAATTTA
1 AATTAAATTTA
*
42304904 TAA-TAATATTGA
1 -AATTAA-ATTTA
*
42304916 ATTTAAA-TTA
1 AATTAAATTTA
42304926 AATTCAAATTTA
1 AATT-AAATTTA
*
42304938 AATTGAATTTA
1 AATTAAATTTA
*
42304949 AAATAAATTTA
1 AATTAAATTTA
*
42304960 AGATTAAA-ATA
1 A-ATTAAATTTA
*
42304971 AATTTAATTT
1 AATTAAATTT
42304981 TCAAATGGTT
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
10 10 0.17
11 28 0.47
12 21 0.36
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:42304986 original size:17 final size:16
Alignment explanation
Indices: 42304936--42304980 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
42304926 AATTCAAATT
*
42304936 TAAATTGAATTTAAAA
1 TAAATTTAATTTAAAA
*
42304952 TAAATTTAAGATTAAAA
1 TAAATTTAA-TTTAAAA
42304969 TAAATTTAATTT
1 TAAATTTAATTT
42304981 TCAAATGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
TAAATTTAATTTAAAA
Found at i:42309413 original size:1 final size:1
Alignment explanation
Indices: 42309407--42309434 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
42309397 TTTCCAATTT
42309407 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
42309435 AAGGCTGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:42309854 original size:15 final size:15
Alignment explanation
Indices: 42309834--42309885 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
42309824 CGAATGAAAA
*
42309834 GAAAATTGGAAGGAT
1 GAAAATTAGAAGGAT
*
42309849 GAAAATTTGAAGGAAT
1 GAAAATTAGAAGG-AT
* *
42309865 AGAAAACTAGAAAGAT
1 -GAAAATTAGAAGGAT
42309881 GAAAA
1 GAAAA
42309886 ACATAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 17 0.55
16 4 0.13
17 10 0.32
ACGTcount: A:0.56, C:0.02, G:0.25, T:0.17
Consensus pattern (15 bp):
GAAAATTAGAAGGAT
Found at i:42312205 original size:36 final size:35
Alignment explanation
Indices: 42312165--42312234 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 35
42312155 ATAGAAGTAA
*
42312165 ATTTGATAAATTGAGTAATTTATATAT-AGGATAATT
1 ATTTGATAAATT-AGGAATTT-TATATCAGGATAATT
42312201 ATTTGATAAATTAGGAATTTTATATGCAGGATAA
1 ATTTGATAAATTAGGAATTTTATAT-CAGGATAA
42312235 ATTGAGTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 5 0.16
35 7 0.23
36 19 0.61
ACGTcount: A:0.41, C:0.01, G:0.16, T:0.41
Consensus pattern (35 bp):
ATTTGATAAATTAGGAATTTTATATCAGGATAATT
Found at i:42315620 original size:148 final size:148
Alignment explanation
Indices: 42315352--42315623 Score: 388
Period size: 148 Copynumber: 1.8 Consensus size: 148
42315342 TGATAATACA
** *
42315352 CATAATAAAACTCGAATTTAGGCCCCAAAATTTAATTGTTGAGGAAAGCTATAGTTTTGATCTGA
1 CATAATAAAACTCGAATTTAGGCCCCAAAATTTAATTACTAAGGAAAGCTATAGTTTTGATCTGA
*
42315417 ACAACGTAACCTTCCACTCCTCTGACATTTTATCTTGTTTTCAAAGGATGAGTCACATTAGAGAC
66 ACAACGTAACCTTCCACTCCTCTGACATTTTATCTTGTTTTCAAAGGAAGAGTCACATTAGAGAC
42315482 TCGGATATGATAATTGTG
131 TCGGATATGATAATTGTG
* * * * * *
42315500 CATAATAAAACTCGAATTTGGGTCTCAAATTTTAATTACTAAGGAAAGCTATAGTTTTTATTTGA
1 CATAATAAAACTCGAATTTAGGCCCCAAAATTTAATTACTAAGGAAAGCTATAGTTTTGATCTGA
* *
42315565 ACAATGTAACCTTCCA-T-GTCTGTAACATTTTATCTTGTTTTC-AAGTGAAGAGTCACATT
66 ACAACGTAACCTTCCACTCCTCTG--ACATTTTATCTTGTTTTCAAAG-GAAGAGTCACATT
42315624 GGATACTCAC
Statistics
Matches: 109, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
146 4 0.04
147 4 0.04
148 101 0.93
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (148 bp):
CATAATAAAACTCGAATTTAGGCCCCAAAATTTAATTACTAAGGAAAGCTATAGTTTTGATCTGA
ACAACGTAACCTTCCACTCCTCTGACATTTTATCTTGTTTTCAAAGGAAGAGTCACATTAGAGAC
TCGGATATGATAATTGTG
Found at i:42316042 original size:19 final size:19
Alignment explanation
Indices: 42316020--42316064 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
42316010 TTATATTAGG
42316020 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
42316039 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
42316058 ATTTAAT
1 ATTTAAT
42316065 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:42316891 original size:22 final size:22
Alignment explanation
Indices: 42316865--42316907 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42316855 TCGACTTTCT
42316865 TATTTTCTATTT-CTTTTAATTA
1 TATTTTCT-TTTACTTTTAATTA
*
42316887 TATTTTCTTTTATTTTTAATT
1 TATTTTCTTTTACTTTTAATT
42316908 CCGTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTTTCTTTTACTTTTAATTA
Found at i:42318778 original size:28 final size:28
Alignment explanation
Indices: 42318735--42318799 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
42318725 CCAAAATGTA
42318735 AGCCTTTGTGGCTGAATCTATTAAAGTG
1 AGCCTTTGTGGCTGAATCTATTAAAGTG
* * *
42318763 AGCCTTTGTGGTTGAATTTTTTAAAGTG
1 AGCCTTTGTGGCTGAATCTATTAAAGTG
*
42318791 AGCTTTTGT
1 AGCCTTTGT
42318800 AACTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.43
Consensus pattern (28 bp):
AGCCTTTGTGGCTGAATCTATTAAAGTG
Found at i:42320973 original size:16 final size:16
Alignment explanation
Indices: 42320952--42320996 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
42320942 AATGGGATGA
42320952 AAATAAATTTTTAATT
1 AAATAAATTTTTAATT
42320968 AAATAAA--TTTAATT
1 AAATAAATTTTTAATT
*
42320982 AATTAAAATTTTTAA
1 AAAT-AAATTTTTAA
42320997 ACCTAAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 7 0.28
17 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATAAATTTTTAATT
Found at i:42325588 original size:22 final size:21
Alignment explanation
Indices: 42325563--42325628 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
42325553 ATACCAATAT
42325563 AATAGCAAAATGG-AATCAAAAC
1 AATAGCAAAATGGTAA-C-AAAC
*
42325585 AATATCAAAATGGTAACAAAC
1 AATAGCAAAATGGTAACAAAC
* * *
42325606 AATAGCGAAATAGCAACAAAC
1 AATAGCAAAATGGTAACAAAC
42325627 AA
1 AA
42325629 CAGTAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
21 23 0.61
22 13 0.34
23 2 0.05
ACGTcount: A:0.59, C:0.15, G:0.12, T:0.14
Consensus pattern (21 bp):
AATAGCAAAATGGTAACAAAC
Found at i:42325928 original size:25 final size:28
Alignment explanation
Indices: 42325893--42325946 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
42325883 TTATAGGAAC
*
42325893 TTGATCAAA-TTAG-TTCTACTATTAAA
1 TTGATCAAATTTAGCTTATACTATTAAA
42325919 TTGAT-AAATTTAGTCTTATACTATTAAA
1 TTGATCAAATTTAG-CTTATACTATTAAA
42325947 AGGAATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.12
26 9 0.38
28 12 0.50
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.44
Consensus pattern (28 bp):
TTGATCAAATTTAGCTTATACTATTAAA
Found at i:42326029 original size:23 final size:21
Alignment explanation
Indices: 42325983--42326030 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
42325973 TAGAGTTAAC
*
42325983 ATTTATTGTATAAAAAATATT
1 ATTTATTGTATAAAAAATAAT
*
42326004 ATTTATTGTTTAACAAAATGAAT
1 ATTTATTGTATAA-AAAAT-AAT
42326027 ATTT
1 ATTT
42326031 TTAAAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.52
22 5 0.22
23 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (21 bp):
ATTTATTGTATAAAAAATAAT
Found at i:42327490 original size:23 final size:23
Alignment explanation
Indices: 42327436--42327526 Score: 119
Period size: 23 Copynumber: 3.9 Consensus size: 23
42327426 ATTAACATTA
* *
42327436 TTCGTGAACGTGTTCAATTATATG
1 TTCGTGAACATGTTCGATTA-ATG
* *
42327460 TTCATGAATATGTTCGATTAATG
1 TTCGTGAACATGTTCGATTAATG
*
42327483 TTCGTGAACATGTTCGATTAATT
1 TTCGTGAACATGTTCGATTAATG
*
42327506 TTCGTGAACATGTTTGATTAA
1 TTCGTGAACATGTTCGATTAA
42327527 GCTAAATGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 43 0.73
24 16 0.27
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (23 bp):
TTCGTGAACATGTTCGATTAATG
Found at i:42339177 original size:19 final size:20
Alignment explanation
Indices: 42339141--42339179 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
42339131 AAAAATATTA
* *
42339141 ACATTGTTAAATAGTAAATG
1 ACATTGTTAAACAATAAATG
42339161 ACATT-TTAAACAATAAATG
1 ACATTGTTAAACAATAAATG
42339180 TTAACTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (20 bp):
ACATTGTTAAACAATAAATG
Found at i:42343370 original size:24 final size:24
Alignment explanation
Indices: 42343342--42343388 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
42343332 AGAAATAATC
*
42343342 TTTTAGTTAAACTCTGTTTATTTA
1 TTTTAATTAAACTCTGTTTATTTA
42343366 TTTTAATTAAACTCTGTTTATTT
1 TTTTAATTAAACTCTGTTTATTT
42343389 GTTTCACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTTAATTAAACTCTGTTTATTTA
Found at i:42343401 original size:24 final size:24
Alignment explanation
Indices: 42343350--42343404 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
42343340 TCTTTTAGTT
* *
42343350 AAACTCTGTTTATTTATTTTAATT
1 AAACTCTGTTTATTTATTTCAATC
* *
42343374 AAACTCTGTTTATTTGTTTCACTC
1 AAACTCTGTTTATTTATTTCAATC
42343398 AAACTCT
1 AAACTCT
42343405 TGTTAGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.51
Consensus pattern (24 bp):
AAACTCTGTTTATTTATTTCAATC
Found at i:42344093 original size:6 final size:6
Alignment explanation
Indices: 42344075--42344150 Score: 72
Period size: 6 Copynumber: 13.0 Consensus size: 6
42344065 TTAAATTGAT
42344075 TTTAAA TTT--A TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
* *
42344122 TTTAGA TTT-AC TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
42344151 ATAAAATTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
4 6 0.10
5 5 0.09
6 40 0.69
7 2 0.03
8 5 0.09
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:42344106 original size:17 final size:16
Alignment explanation
Indices: 42344075--42344148 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
42344065 TTAAATTGAT
*
42344075 TTTAAATTTATTTAAA
1 TTTAAATTTACTTAAA
42344091 TTTAAATTTATCTTAAA
1 TTTAAATTTA-CTTAAA
*
42344108 TTTAAATTTAATT--A
1 TTTAAATTTACTTAAA
*
42344122 TTTAGATTTACTTTAAA
1 TTTAAATTTAC-TTAAA
42344139 TTTAAATTTA
1 TTTAAATTTA
42344149 AAATAAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 12 0.24
17 25 0.51
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (16 bp):
TTTAAATTTACTTAAA
Found at i:42344120 original size:11 final size:11
Alignment explanation
Indices: 42344065--42344150 Score: 57
Period size: 11 Copynumber: 7.5 Consensus size: 11
42344055 TAATTTGGAG
* *
42344065 TTAAATTGATT
1 TTAAATTTAAT
42344076 TTAAATTT-AT
1 TTAAATTTAAT
42344086 TTAAATTTAAAT
1 TTAAATTT-AAT
** *
42344098 TTATCTTAAAT
1 TTAAATTTAAT
42344109 TTAAATTTAATTAT
1 TTAAATTT-A--AT
* *
42344123 TTAGATTTACT
1 TTAAATTTAAT
42344134 TTAAATTTAAAT
1 TTAAATTT-AAT
42344146 TTAAA
1 TTAAA
42344151 ATAAAATTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
10 9 0.16
11 23 0.40
12 15 0.26
13 1 0.02
14 9 0.16
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:42344131 original size:31 final size:32
Alignment explanation
Indices: 42344075--42344149 Score: 100
Period size: 31 Copynumber: 2.3 Consensus size: 32
42344065 TTAAATTGAT
*
42344075 TTTAAATTTATTTAAATTTAAATTTA-TCTTAAA
1 TTTAAATTTAATT-AATTTAAATTTACT-TTAAA
*
42344108 TTTAAATTTAATT-ATTTAGATTTACTTTAAA
1 TTTAAATTTAATTAATTTAAATTTACTTTAAA
42344139 TTTAAATTTAA
1 TTTAAATTTAA
42344150 AATAAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 26 0.67
32 1 0.03
33 12 0.31
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (32 bp):
TTTAAATTTAATTAATTTAAATTTACTTTAAA
Found at i:42344155 original size:17 final size:16
Alignment explanation
Indices: 42344075--42344161 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 16
42344065 TTAAATTGAT
**
42344075 TTTAAATTTATTTAAA
1 TTTAAATTTAAATAAA
**
42344091 TTTAAATTTATCTTAAA
1 TTTAAATTTA-AATAAA
*
42344108 TTTAAATTT-AAT-TA
1 TTTAAATTTAAATAAA
* **
42344122 TTTAGATTTACTTTAAA
1 TTTAAATTTA-AATAAA
42344139 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
*
42344156 ATTAAA
1 TTTAAA
42344162 ATACTAAACA
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
14 9 0.17
15 1 0.02
16 11 0.20
17 32 0.59
18 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:42344870 original size:3 final size:3
Alignment explanation
Indices: 42344864--42344902 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
42344854 AATATGATAT
*
42344864 TAA TAA TAA TTAA TAA TAA TAA TGA TAA TAA -AA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42344903 AAAAGGGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42344882 original size:13 final size:14
Alignment explanation
Indices: 42344864--42344901 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
42344854 AATATGATAT
42344864 TAATAATAAT-TAA
1 TAATAATAATATAA
42344877 TAATAATAATGATAA
1 TAATAATAAT-ATAA
42344892 TAA-AATAATA
1 TAATAATAATA
42344902 AAAAAGGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.48
14 6 0.26
15 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:42345203 original size:23 final size:25
Alignment explanation
Indices: 42345170--42345232 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
42345160 TTTTTTTTAA
42345170 AAAATGAGAAAAAACAAAA-GGAAAG
1 AAAA-GAGAAAAAACAAAAGGGAAAG
*
42345195 AAAA-AGAAAACAA-AAAAGGGGAAG
1 AAAAGAGAAAA-AACAAAAGGGAAAG
*
42345219 AAAAGAGAAGAAAC
1 AAAAGAGAAAAAAC
42345233 CATACCTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
23 10 0.31
24 13 0.41
25 9 0.28
ACGTcount: A:0.71, C:0.05, G:0.22, T:0.02
Consensus pattern (25 bp):
AAAAGAGAAAAAACAAAAGGGAAAG
Found at i:42346019 original size:30 final size:30
Alignment explanation
Indices: 42345985--42346169 Score: 180
Period size: 30 Copynumber: 6.2 Consensus size: 30
42345975 GTAAGTCCAT
*
42345985 AAACTTTTCAAAAATTATATTTTAACCCTA
1 AAACTTTTCAAAAATTACATTTTAACCCTA
* *
42346015 AAAC-TTTCTAAAAATTACATTTTGACCCCA
1 AAACTTTTC-AAAAATTACATTTTAACCCTA
*
42346045 AAACTTTTCCAAAATTACATTTTAACCCTA
1 AAACTTTTCAAAAATTACATTTTAACCCTA
* * * * *
42346075 ATACTTTTCCAAAATCATATTTTGACCCTA
1 AAACTTTTCAAAAATTACATTTTAACCCTA
* * * * *
42346105 AAA-TTTCCAAAAAAATGCATTTTTACCCTG
1 AAACTTTTC-AAAAATTACATTTTAACCCTA
*
42346135 AAAC-TTTCAAAAATTACCATTTT-ACCCTC
1 AAACTTTTCAAAAATTA-CATTTTAACCCTA
42346164 AAACTT
1 AAACTT
42346170 CCCTAAATCC
Statistics
Matches: 126, Mismatches: 23, Indels: 12
0.78 0.14 0.07
Matches are distributed among these distances:
29 23 0.18
30 99 0.79
31 4 0.03
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.36
Consensus pattern (30 bp):
AAACTTTTCAAAAATTACATTTTAACCCTA
Found at i:42346140 original size:90 final size:89
Alignment explanation
Indices: 42345987--42346162 Score: 221
Period size: 90 Copynumber: 2.0 Consensus size: 89
42345977 AAGTCCATAA
* * *
42345987 ACTTTTCAAAAATTATATTTTAACCCTAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTT
1 ACTTTTCAAAAATCATATTTTAACCCTAAAACTTTCAAAAAAATACATTTTGACCCCAAAAC-TT
*
42346052 TCCAAAATTA-CATTTTAACCCTAAT
65 TCAAAAATTACCATTTT-ACCCTAAT
* * * * **
42346077 ACTTTTCCAAAATCATATTTTGACCCTAAAA-TTTCCAAAAAAATGCATTTTTACCCTGAAACTT
1 ACTTTTCAAAAATCATATTTTAACCCTAAAACTTT-CAAAAAAATACATTTTGACCCCAAAACTT
42346141 TCAAAAATTACCATTTTACCCT
65 TCAAAAATTACCATTTTACCCT
42346163 CAAACTTCCC
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
89 19 0.26
90 55 0.74
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (89 bp):
ACTTTTCAAAAATCATATTTTAACCCTAAAACTTTCAAAAAAATACATTTTGACCCCAAAACTTT
CAAAAATTACCATTTTACCCTAAT
Found at i:42346177 original size:29 final size:28
Alignment explanation
Indices: 42346093--42346185 Score: 69
Period size: 29 Copynumber: 3.2 Consensus size: 28
42346083 CCAAAATCAT
* * * *
42346093 ATTTTGACCCTAAAATTTCCAAAAAAATGC
1 ATTTT-ACCCTCAAACTTCCAAAAATA-CC
* *
42346123 ATTTTTACCCTGAAACTTTCAAAAATTACC
1 A-TTTTACCCTCAAACTTCCAAAAA-TACC
** *
42346153 ATTTTACCCTCAAACTTCCCTAAATCCC
1 ATTTTACCCTCAAACTTCCAAAAATACC
42346181 ATTTT
1 ATTTT
42346186 TAACCCTATT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
28 8 0.16
29 19 0.37
30 19 0.37
31 5 0.10
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (28 bp):
ATTTTACCCTCAAACTTCCAAAAATACC
Found at i:42348414 original size:18 final size:18
Alignment explanation
Indices: 42348388--42348428 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
42348378 AAAATTTAAA
42348388 AATTAAATTAAAATTTTT
1 AATTAAATTAAAATTTTT
* * *
42348406 AATTTAATTTAATTTTTT
1 AATTAAATTAAAATTTTT
42348424 AATTA
1 AATTA
42348429 GATGGATTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTAAATTAAAATTTTT
Found at i:42350967 original size:16 final size:16
Alignment explanation
Indices: 42350939--42350985 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
42350929 TTGCAATGCC
*
42350939 ATATATATATATATAT
1 ATATATATGTATATAT
*
42350955 ATATGTATGTATATAT
1 ATATATATGTATATAT
* *
42350971 GTGTATATGTATATA
1 ATATATATGTATATA
42350986 ACTTCTCTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (16 bp):
ATATATATGTATATAT
Found at i:42373627 original size:30 final size:30
Alignment explanation
Indices: 42373571--42373627 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
42373561 AAATAATATA
42373571 AAATATAATTAATTACGAAAATGGTATGAG
1 AAATATAATTAATTACGAAAATGGTATGAG
42373601 AAATA-AATTAATTACGAAAATAGGTAT
1 AAATATAATTAATTACGAAAAT-GGTAT
42373628 TTGCTATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.30
Consensus pattern (30 bp):
AAATATAATTAATTACGAAAATGGTATGAG
Found at i:42374696 original size:31 final size:31
Alignment explanation
Indices: 42374661--42374721 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
42374651 TATTTAAATG
* *
42374661 TATACAATTAAATTAAAATCGAATTTTTATT
1 TATACAATTAAATTAAAATCAAAGTTTTATT
*
42374692 TATACATTTAAATTAAAATCAAAGTTTTAT
1 TATACAATTAAATTAAAATCAAAGTTTTAT
42374722 CTGTATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (31 bp):
TATACAATTAAATTAAAATCAAAGTTTTATT
Found at i:42387136 original size:12 final size:12
Alignment explanation
Indices: 42387119--42387160 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
42387109 AATAGCTAAA
42387119 ATAAATAAATTT
1 ATAAATAAATTT
42387131 ATAAATTAAATTT
1 ATAAA-TAAATTT
*
42387144 GATAAA-AAATAT
1 -ATAAATAAATTT
42387156 ATAAA
1 ATAAA
42387161 AATCTAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 5 0.19
12 10 0.37
13 7 0.26
14 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (12 bp):
ATAAATAAATTT
Found at i:42395168 original size:129 final size:130
Alignment explanation
Indices: 42395021--42395280 Score: 459
Period size: 129 Copynumber: 2.0 Consensus size: 130
42395011 ACTTGAAAAG
* * *
42395021 CATAATTAAGGTTTGCAAAGAAAACTAAACCTAAAAACTTTCTCAAACTCATAAAGACCCTCAAT
1 CATAATTAAGGTTAGCAAAGAAAACTAAACCTAAAAACTTTATCAAACTCATAAAGACCCTAAAT
*
42395086 CTTGAAATGAGCTAAACTTGAAATACCCAAATAAGT-AATCCAAAATAACCTAAACTTGAGATGA
66 CTTGAAATGAGCTAAACTTGAAACACCCAAATAAGTAAATCCAAAATAACCTAAACTTGAGATGA
42395150 CATAATTAAGGTTAGCAAAGAAAACTAAACCTAAAAACTTTATCAAACTCATAAAGACCCTAAAT
1 CATAATTAAGGTTAGCAAAGAAAACTAAACCTAAAAACTTTATCAAACTCATAAAGACCCTAAAT
* *
42395215 CTTGAAATGAGCTAAACTTGAAACGCCCGAATAAGTAAATCCAAAATAACCTAAACTTGAGATGA
66 CTTGAAATGAGCTAAACTTGAAACACCCAAATAAGTAAATCCAAAATAACCTAAACTTGAGATGA
42395280 C
1 C
42395281 CCAAATGACT
Statistics
Matches: 124, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
129 95 0.77
130 29 0.23
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (130 bp):
CATAATTAAGGTTAGCAAAGAAAACTAAACCTAAAAACTTTATCAAACTCATAAAGACCCTAAAT
CTTGAAATGAGCTAAACTTGAAACACCCAAATAAGTAAATCCAAAATAACCTAAACTTGAGATGA
Found at i:42395627 original size:18 final size:18
Alignment explanation
Indices: 42395587--42395630 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
42395577 AAATTGTCAT
*
42395587 AAAAAATAATTTAATTAA
1 AAAAAATAAGTTAATTAA
42395605 AAAAAATAAGGTTAA-TAA
1 AAAAAATAA-GTTAATTAA
*
42395623 TAAAAATA
1 AAAAAATA
42395631 CTAGGGAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAAAATAAGTTAATTAA
Found at i:42403533 original size:36 final size:36
Alignment explanation
Indices: 42403482--42403551 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
42403472 CGACTACAGA
* *
42403482 AAATTGTCAAGTGCATTCTTGTGA-TCATCTATCAAG
1 AAATTGCCAAATGCATTCTTGTGATTC-TCTATCAAG
*
42403518 AAATTGCCAAATGCATTTTTGTGATTCTCTATCA
1 AAATTGCCAAATGCATTCTTGTGATTCTCTATCA
42403552 CAGTGTAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 28 0.93
37 2 0.07
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (36 bp):
AAATTGCCAAATGCATTCTTGTGATTCTCTATCAAG
Found at i:42405537 original size:15 final size:17
Alignment explanation
Indices: 42405502--42405539 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
42405492 AAAACAAAAA
42405502 TAATTTAGTCATTTGTT
1 TAATTTAGTCATTTGTT
*
42405519 TAATTT-GTC-TTTTTT
1 TAATTTAGTCATTTGTT
42405534 TAATTT
1 TAATTT
42405540 TTAAACTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 3 0.15
17 6 0.30
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.66
Consensus pattern (17 bp):
TAATTTAGTCATTTGTT
Found at i:42406288 original size:12 final size:13
Alignment explanation
Indices: 42406262--42406286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42406252 ATTATTAAAT
42406262 TTATTAAAAAAAA
1 TTATTAAAAAAAA
42406275 TTATTAAAAAAA
1 TTATTAAAAAAA
42406287 TTTAAATGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTATTAAAAAAAA
Found at i:42413855 original size:28 final size:28
Alignment explanation
Indices: 42413824--42413883 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
42413814 AAAACGGGAC
* *
42413824 TTTTGGATACCCAGGGGTAAAATGGTAA
1 TTTTGGACACCCAGGGGCAAAATGGTAA
* * *
42413852 TTTTGGACGCGCGGGGGCAAAATGGTAA
1 TTTTGGACACCCAGGGGCAAAATGGTAA
42413880 TTTT
1 TTTT
42413884 TTTGTGAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.32, T:0.30
Consensus pattern (28 bp):
TTTTGGACACCCAGGGGCAAAATGGTAA
Found at i:42413958 original size:29 final size:30
Alignment explanation
Indices: 42413929--42414080 Score: 142
Period size: 30 Copynumber: 5.2 Consensus size: 30
42413919 AGTTTGAGGG
42413929 TAAAATGGTAATTTTTGATGAAATCGGGGT
1 TAAAATGGTAATTTTTGATGAAATCGGGGT
42413959 TAATAATGG-AA-TTTTG--GAAAGTTCAGGGG-
1 TAA-AATGGTAATTTTTGATGAAA--TC-GGGGT
*
42413988 TAAAATGGTAATTTTTGATTAAATCGGGGT
1 TAAAATGGTAATTTTTGATGAAATCGGGGT
*
42414018 TAAAATGG-AA-TTTTG--GAAAGTTCGGGGG
1 TAAAATGGTAATTTTTGATGAAA--TCGGGGT
* * *
42414046 TAAAATAGTAATTTTCGATGAAACCGGGGT
1 TAAAATGGTAATTTTTGATGAAATCGGGGT
42414076 TAAAA
1 TAAAA
42414081 CAGAATTTTA
Statistics
Matches: 100, Mismatches: 7, Indels: 30
0.73 0.05 0.22
Matches are distributed among these distances:
26 3 0.03
27 4 0.04
28 23 0.23
29 20 0.20
30 38 0.38
31 5 0.05
32 7 0.07
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.33
Consensus pattern (30 bp):
TAAAATGGTAATTTTTGATGAAATCGGGGT
Found at i:42414057 original size:58 final size:58
Alignment explanation
Indices: 42413837--42414118 Score: 311
Period size: 58 Copynumber: 4.8 Consensus size: 58
42413827 TGGATACCCA
* ** *
42413837 GGGG-TAAAATGGTAATTTTGG-ACGCGCGGGGGCAAAATGGTAATTTTTTTG-TGAAACC
1 GGGGTTAAAATGG-AATTTTGGAAAGTTCGGGGGTAAAATGGTAA--TTTTTGATGAAACC
* * * *
42413895 GGGGTTAAAAATGGAATCTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGATGAAATC
1 GGGGTT-AAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAACC
* * *
42413954 GGGGTTAATAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGATTAAATC
1 GGGGTTAA-AATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAACC
* *
42414013 GGGGTTAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATAGTAATTTTCGATGAAACC
1 GGGGTTAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAACC
** * ***
42414071 GGGGTTAAAACAGAATTTTAGAAAGGTT-AAAGGTAAAATGGTAATTTT
1 GGGGTTAAAATGGAATTTTGGAAA-GTTCGGGGGTAAAATGGTAATTTT
42414119 CGGACAGTCC
Statistics
Matches: 193, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
58 94 0.49
59 76 0.39
60 23 0.12
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (58 bp):
GGGGTTAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGATGAAACC
Found at i:42414853 original size:13 final size:13
Alignment explanation
Indices: 42414835--42414860 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42414825 GCCTGTTTTG
42414835 GACATTGTAAATA
1 GACATTGTAAATA
42414848 GACATTGTAAATA
1 GACATTGTAAATA
42414861 ATTTTTATTT
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
GACATTGTAAATA
Found at i:42414923 original size:6 final size:6
Alignment explanation
Indices: 42414914--42414982 Score: 61
Period size: 6 Copynumber: 11.7 Consensus size: 6
42414904 AAATTAAAAC
** * *
42414914 TAAATT TAAATT TAAAAA TGAATT TAAATT TAAATT TAAA-G TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
42414961 TAATTT TAGAA-A TAAATT TAAA
1 TAAATT TA-AATT TAAATT TAAA
42414983 AATCATTTCA
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
5 6 0.12
6 41 0.85
7 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:42414926 original size:24 final size:23
Alignment explanation
Indices: 42414899--42414958 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
42414889 TTTTAAAATT
*
42414899 ATTTCAAATTAAAACTAAATTTAA
1 ATTT-AAAATAAAACTAAATTTAA
* **
42414923 ATTTAAAAATGAATTTAAATTTAA
1 ATTT-AAAATAAAACTAAATTTAA
*
42414947 ATTTAAAGTAAA
1 ATTTAAAATAAA
42414959 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (23 bp):
ATTTAAAATAAAACTAAATTTAA
Found at i:42414944 original size:18 final size:17
Alignment explanation
Indices: 42414880--42414947 Score: 66
Period size: 18 Copynumber: 3.9 Consensus size: 17
42414870 TTGGGCTTTT
* *
42414880 TAATTTTAATTTTAAAA
1 TAATTTAAATTTAAAAA
* *
42414897 TTATTTCAAA-TTAAAAC
1 TAATTT-AAATTTAAAAA
42414914 TAAATTTAAATTTAAAAA
1 T-AATTTAAATTTAAAAA
42414932 TGAATTTAAATTTAAA
1 T-AATTTAAATTTAAA
42414948 TTTAAAGTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
17 14 0.34
18 27 0.66
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TAATTTAAATTTAAAAA
Found at i:42414949 original size:41 final size:42
Alignment explanation
Indices: 42414899--42414982 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 42
42414889 TTTTAAAATT
*
42414899 ATTTCAAATTAAAACTAAATTTAAATTTAAAAATGAATTTAA
1 ATTTCAAATTAAAACTAAATTTAAATTTAAAAATAAATTTAA
* * * *
42414941 ATTT-AAATTTAAAGTAAATTTAATTTTAGAAATAAATTTAA
1 ATTTCAAATTAAAACTAAATTTAAATTTAAAAATAAATTTAA
42414982 A
1 A
42414983 AATCATTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 33 0.89
42 4 0.11
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (42 bp):
ATTTCAAATTAAAACTAAATTTAAATTTAAAAATAAATTTAA
Found at i:42414960 original size:17 final size:18
Alignment explanation
Indices: 42414938--42414982 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
42414928 AAAATGAATT
*
42414938 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
*
42414955 TAAATTTAATTTTAGAAA
1 TAAATTTAAATTTAGAAA
42414973 TAAATTTAAA
1 TAAATTTAAA
42414983 AATCATTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:42416697 original size:129 final size:129
Alignment explanation
Indices: 42416552--42416810 Score: 473
Period size: 129 Copynumber: 2.0 Consensus size: 129
42416542 ACTTGAAAAG
* *
42416552 CATAATTAAGGTTAGCAAAGAAAACTAAACCTAAAAACTTTCTCAAACTCATAAAGACCCTCAAT
1 CATAATTAAGGTTAGCAAAGAAAACTAAACCTAAAAACTTTATCAAACTCATAAAGACCCTAAAT
* *
42416617 TTTGAAATGAGCTAAACTTGAAATGCCCAAATAAGTAATCCAAAATAACCTAAACTTGAGATGA
66 CTTGAAATGAGCTAAACTTGAAACGCCCAAATAAGTAATCCAAAATAACCTAAACTTGAGATGA
42416681 CATAATTAAGGTTAGCAAAGAAAACTAAACCTAAAAACTTTATCAAACTCATAAAGACCCTAAAT
1 CATAATTAAGGTTAGCAAAGAAAACTAAACCTAAAAACTTTATCAAACTCATAAAGACCCTAAAT
*
42416746 CTTGAAATGAGCTAAACTTGAAACGCCCAAATAAGTAATTCAAAATAACCTAAACTTGAGATGA
66 CTTGAAATGAGCTAAACTTGAAACGCCCAAATAAGTAATCCAAAATAACCTAAACTTGAGATGA
42416810 C
1 C
42416811 CCAAATGACT
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 125 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.24
Consensus pattern (129 bp):
CATAATTAAGGTTAGCAAAGAAAACTAAACCTAAAAACTTTATCAAACTCATAAAGACCCTAAAT
CTTGAAATGAGCTAAACTTGAAACGCCCAAATAAGTAATCCAAAATAACCTAAACTTGAGATGA
Found at i:42417157 original size:18 final size:18
Alignment explanation
Indices: 42417117--42417160 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
42417107 AAATTATCAT
*
42417117 AAAAAATAATTTAATTAA
1 AAAAAATAAGTTAATTAA
42417135 AAAAAATAAGGTTAA-TAA
1 AAAAAATAA-GTTAATTAA
*
42417153 TAAAAATA
1 AAAAAATA
42417161 CTAGGGAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAAAATAAGTTAATTAA
Found at i:42421641 original size:24 final size:25
Alignment explanation
Indices: 42421613--42421662 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
42421603 CTGTTAAATT
*
42421613 AATTT-AAATTGGCAGCTGTTTTTC
1 AATTTAAAATTGGCAGCTGTATTTC
42421637 AATTTAAAATTGGCAGCTGTATTTC
1 AATTTAAAATTGGCAGCTGTATTTC
42421662 A
1 A
42421663 TTATCCTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (25 bp):
AATTTAAAATTGGCAGCTGTATTTC
Found at i:42421818 original size:40 final size:40
Alignment explanation
Indices: 42421773--42421849 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
42421763 CACATTCAAA
* *
42421773 TTCAAATTGATAATAGAAGATAATTTCCTTAAAAGTATTT
1 TTCAAATTAATAATAGAAAATAATTTCCTTAAAAGTATTT
* **
42421813 TTCAAATTAATAATAGAAAATATTTTTTTTAAAAGTA
1 TTCAAATTAATAATAGAAAATAATTTCCTTAAAAGTA
42421850 CTTTAAGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (40 bp):
TTCAAATTAATAATAGAAAATAATTTCCTTAAAAGTATTT
Found at i:42433864 original size:3 final size:3
Alignment explanation
Indices: 42433856--42433880 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42433846 CTAATGAAAT
42433856 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
42433881 AGTCATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:42435147 original size:27 final size:28
Alignment explanation
Indices: 42435079--42435145 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
42435069 CTGTTTACAA
42435079 AAAAAGCCCAAATTAAAGGCCCGATTAC
1 AAAAAGCCCAAATTAAAGGCCCGATTAC
42435107 AAAAAGCCCAAATTAAAGGCCCGATTAC
1 AAAAAGCCCAAATTAAAGGCCCGATTAC
42435135 AAAAAGCCCAA
1 AAAAAGCCCAA
42435146 TTGGGCTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.49, C:0.25, G:0.13, T:0.12
Consensus pattern (28 bp):
AAAAAGCCCAAATTAAAGGCCCGATTAC
Found at i:42436517 original size:5 final size:5
Alignment explanation
Indices: 42436507--42436533 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
42436497 TTGGATCTAT
42436507 CCGAC CCGAC CCGAC CCGAC CCGAC CC
1 CCGAC CCGAC CCGAC CCGAC CCGAC CC
42436534 ACCTAGGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.63, G:0.19, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:42437139 original size:30 final size:30
Alignment explanation
Indices: 42437080--42437296 Score: 222
Period size: 30 Copynumber: 7.3 Consensus size: 30
42437070 AATTGTCAAG
* *
42437080 AAATTATATTTTCACCCC-AAAACTTTCCA
1 AAATTATATTTTGACCCCAAAAATTTTCCA
*
42437109 AAATTATATTTTAACCCCAAAAATTTTCCA
1 AAATTATATTTTGACCCCAAAAATTTTCCA
* * * * * **
42437139 AAATTACATGTCGACACCAAAACTTTTTGA
1 AAATTATATTTTGACCCCAAAAATTTTCCA
*
42437169 AAATTATATTTTGACCCTAAAAATTTTCCA
1 AAATTATATTTTGACCCCAAAAATTTTCCA
* * *
42437199 AAATTATATTTCGACCCC-AAAACTTTCTAA
1 AAATTATATTTTGACCCCAAAAATTTTC-CA
* *
42437229 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTATATTTTGACCCCAAAAATTTTCCA
* * * * *
42437259 AAATTACATTTTGGCTCCAAAACTTTTCTA
1 AAATTATATTTTGACCCCAAAAATTTTCCA
42437289 AAATTATA
1 AAATTATA
42437297 CTTTAACCTC
Statistics
Matches: 154, Mismatches: 31, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
29 25 0.16
30 122 0.79
31 7 0.05
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (30 bp):
AAATTATATTTTGACCCCAAAAATTTTCCA
Found at i:42437314 original size:60 final size:60
Alignment explanation
Indices: 42437096--42437304 Score: 260
Period size: 60 Copynumber: 3.5 Consensus size: 60
42437086 TATTTTCACC
* *
42437096 CCAAAACTTTC-CAAAATTATATTTTAACCCCAAAAATTTTCCAAAATTACATGTCGACA
1 CCAAAACTTTCTAAAAATTATATTTTAACCCCAAAAATTTTCCAAAATTACATTTCGACA
* * * * * *
42437155 CCAAAACTTTTTGAAAATTATATTTTGACCCTAAAAATTTTCCAAAATTATATTTCGACC
1 CCAAAACTTTCTAAAAATTATATTTTAACCCCAAAAATTTTCCAAAATTACATTTCGACA
* * * * * *
42437215 CCAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGGCT
1 CCAAAACTTTCTAAAAATTATATTTTAACCCCAAAAATTTTCCAAAATTACATTTCGACA
*
42437275 CCAAAACTTTTCT-AAAATTATACTTTAACC
1 CCAAAAC-TTTCTAAAAATTATATTTTAACC
42437305 TCGAAACTTT
Statistics
Matches: 129, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
59 10 0.08
60 114 0.88
61 5 0.04
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (60 bp):
CCAAAACTTTCTAAAAATTATATTTTAACCCCAAAAATTTTCCAAAATTACATTTCGACA
Found at i:42437329 original size:90 final size:87
Alignment explanation
Indices: 42437080--42437339 Score: 272
Period size: 90 Copynumber: 2.9 Consensus size: 87
42437070 AATTGTCAAG
* * * *
42437080 AAATTATATTTTCACCCCAAAAC-TTTCCAAAATTATATTTTAACCCCAAAAATTTTCCAAAATT
1 AAATTACATTTTGA-CCCAAAACTTTTCCAAAATTATA-TTTAACCCC-AAAACTTTCAAAAATT
* * * **
42437144 ACATGTCGACACCAAAACTTTTTGA
63 ACATTTTGACCCCAAAACTTTTCCA
* * *
42437169 AAATTATATTTTGACCCTAAAAATTTTCCAAAATTATATTTCGACCCCAAAACTTTCTAAAAATT
1 AAATTACATTTTGACCC-AAAACTTTTCCAAAATTATATTT-AACCCCAAAACTTTC-AAAAATT
42437234 ACATTTTGACCCCAAAACTTTTCCA
63 ACATTTTGACCCCAAAACTTTTCCA
* * * *
42437259 AAATTACATTTTGGCTCCAAAACTTTTCTAAAATTATACTTTAACCTCGAAACTTTCAAAAATTA
1 AAATTACATTTTGAC-CCAAAACTTTTCCAAAATTATA-TTTAACCCCAAAACTTTCAAAAATTA
42437324 CCATTTT-ATCCCCAAA
64 -CATTTTGA-CCCCAAA
42437340 CTTCCCTAAA
Statistics
Matches: 146, Mismatches: 17, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
88 3 0.02
89 37 0.25
90 101 0.69
91 5 0.03
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.35
Consensus pattern (87 bp):
AAATTACATTTTGACCCAAAACTTTTCCAAAATTATATTTAACCCCAAAACTTTCAAAAATTACA
TTTTGACCCCAAAACTTTTCCA
Found at i:42437330 original size:60 final size:59
Alignment explanation
Indices: 42437096--42437329 Score: 238
Period size: 60 Copynumber: 3.9 Consensus size: 59
42437086 TATTTTCACC
* * *
42437096 CCAAAACTTTC-CAAAATTATATTTTAACCCCAAAAATTTTCCAAAATTACATGTCGACA
1 CCAAAACTTTCTAAAAATTATATTTTAACCCC-AAAACTTTCCAAAATTACATTTCGACA
* * * * * * *
42437155 CCAAAACTTTTTGAAAATTATATTTTGACCCTAAAAATTTTCCAAAATTATATTTCGACC
1 CCAAAACTTTCTAAAAATTATATTTTAACCC-CAAAACTTTCCAAAATTACATTTCGACA
* * * * *
42437215 CCAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGGCT
1 CCAAAACTTTCTAAAAATTATATTTTAACCCCAAAAC-TTTCCAAAATTACATTTCGACA
* * * *
42437275 CCAAAACTTTTCT-AAAATTATACTTTAACCTCGAAACTTTCAAAAATTACCATTT
1 CCAAAAC-TTTCTAAAAATTATATTTTAACCCCAAAACTTTCCAAAATTA-CATTT
42437330 TATCCCCAAA
Statistics
Matches: 148, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
59 25 0.17
60 118 0.80
61 5 0.03
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (59 bp):
CCAAAACTTTCTAAAAATTATATTTTAACCCCAAAACTTTCCAAAATTACATTTCGACA
Found at i:42437339 original size:60 final size:60
Alignment explanation
Indices: 42437075--42437339 Score: 182
Period size: 60 Copynumber: 4.4 Consensus size: 60
42437065 CCTTAAATTG
* * * * *
42437075 TCAAGAAATTATATTTTCA-CCCCAAAACTTTC-CAAAATTATATTTTAACCCCAAAAATTT
1 TCAA-AAATTACATTTT-AGCCCCAAAACTTTCTAAAAATTACACTTTAACCCCAAAACTTT
* * * * * * * * * * *
42437135 TCCAAAATTACA-TGTCGACACCAAAACTTTTTGAAAATTATATTTTGACCCTAAAAATTT
1 TCAAAAATTACATTTTAG-CCCCAAAACTTTCTAAAAATTACACTTTAACCCCAAAACTTT
* * * * *
42437195 TCCAAAATTATA-TTTCGACCCCAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTT
1 TCAAAAATTACATTTTAG-CCCCAAAACTTTCTAAAAATTACACTTTAACCCCAAAACTTT
* * * * * *
42437255 TCCAAAATTACATTTTGGCTCCAAAACTTTTCT-AAAATTATACTTTAACCTCGAAAC-TT
1 TCAAAAATTACATTTTAGCCCCAAAAC-TTTCTAAAAATTACACTTTAACCCCAAAACTTT
*
42437314 TCAAAAATTACCATTTTATCCCCAAA
1 TCAAAAATTA-CATTTTAGCCCCAAA
42437340 CTTCCCTAAA
Statistics
Matches: 170, Mismatches: 29, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
58 2 0.01
59 29 0.17
60 130 0.76
61 9 0.05
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (60 bp):
TCAAAAATTACATTTTAGCCCCAAAACTTTCTAAAAATTACACTTTAACCCCAAAACTTT
Found at i:42437378 original size:59 final size:58
Alignment explanation
Indices: 42437315--42437511 Score: 195
Period size: 59 Copynumber: 3.4 Consensus size: 58
42437305 TCGAAACTTT
* *
42437315 CAAAAATTACCATTTTATCCCCAAACTTCCCTAAATCCCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTATCCCCAAACTTTCC-AAATTCCATTTTTAACCTCGATTTCAC
* *** * * * * * *
42437374 CAAAACTTACCGCCTT-GCCTCCGAACTTTCCAAAATTTCATTTTTGACCT-TATTTTTAC
1 CAAAAATTACCATTTTATCC-CCAAACTTTCC-AAATTCCATTTTTAACCTCGA-TTTCAC
* *
42437433 CAAAATTTACCATTTTATTCCCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCA-
1 CAAAAATTACCATTTTA-TCCCCAAACTTTCCAAATTCCATTTTTAACCTCGATTTCAC
42437491 CAAAAATTACCATTTTA-CCCC
1 CAAAAATTACCATTTTATCCCC
42437512 TAAAAACCCA
Statistics
Matches: 108, Mismatches: 25, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
56 4 0.04
58 19 0.18
59 72 0.67
60 11 0.10
61 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.36
Consensus pattern (58 bp):
CAAAAATTACCATTTTATCCCCAAACTTTCCAAATTCCATTTTTAACCTCGATTTCAC
Found at i:42449317 original size:37 final size:36
Alignment explanation
Indices: 42449275--42449390 Score: 98
Period size: 37 Copynumber: 3.3 Consensus size: 36
42449265 CCAATCTGCT
42449275 TGAAATTGAAGTAGAGTGGATAACACATCTGCATCTC
1 TGAAATTGAAGTAGAGTGGATAACACATCT-CATCTC
* * *** *
42449312 TGAAATTGAAGTA-AGAGCA-ATGTCATC-C--CTT
1 TGAAATTGAAGTAGAGTGGATAACACATCTCATCTC
** *
42449343 TGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTC
1 TGAAATTGAAGTAGAGTGGATAACACATC-TCATCTC
42449380 TGAAATTGAAG
1 TGAAATTGAAG
42449391 CAAGAGCAAT
Statistics
Matches: 58, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
31 15 0.26
32 4 0.07
33 4 0.07
35 5 0.09
36 4 0.07
37 26 0.45
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (36 bp):
TGAAATTGAAGTAGAGTGGATAACACATCTCATCTC
Found at i:42449603 original size:76 final size:76
Alignment explanation
Indices: 42449403--42450057 Score: 992
Period size: 76 Copynumber: 8.7 Consensus size: 76
42449393 AGAGCAATGT
* *
42449403 TATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCA
*
42449468 ACG-TC--GT-C
66 A-GATCATTTCC
* * * *
42449476 ---CC-CTTGAAATTGAAGTAGAG-TGGATAACATGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCA
42449536 AGATCATTTCC
66 AGATCATTTCC
* * *
42449547 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTCCGAAAATGAAGTAAGAGCA
1 TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCA
42449612 AGATCATTTCC
66 AGATCATTTCC
* *
42449623 TATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCA
42449688 AGATCATTTCC
66 AGATCATTTCC
* * *
42449699 TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTTTTTATCTCCGAAAATGAAGTAATAGCA
1 TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCA
42449764 AGATCATTTCC
66 AGATCATTTCC
* *
42449775 TATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCA
42449840 AGATCATTTCC
66 AGATCATTTCC
* * *
42449851 TATCCTCTTGAAATTGAAGTAAATTTGGATATCAGGTCTTTATCTCCGAAAATGAAGTAAGAGCA
1 TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCA
42449916 AGATCATTTCC
66 AGATCATTTCC
*
42449927 TATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCA
1 TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCA
42449992 ACG-TCATTTCC
66 A-GATCATTTCC
*
42450003 TATCCGT-TTGAAATTGAAGTAGAA-TTGGGTATCAAGTCTTTATCTCCGAAATTGA
1 TATCC-TCTTGAAATTGAAGTA-AAGTTGGATATCAAGTCTTTATCTCCGAAATTGA
42450058 GCAAGACAAA
Statistics
Matches: 535, Mismatches: 35, Indels: 21
0.91 0.06 0.04
Matches are distributed among these distances:
67 1 0.00
68 41 0.08
69 18 0.03
70 3 0.01
71 1 0.00
74 2 0.00
75 17 0.03
76 449 0.84
77 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (76 bp):
TATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCA
AGATCATTTCC
Found at i:42449706 original size:152 final size:152
Alignment explanation
Indices: 42449254--42450053 Score: 1095
Period size: 152 Copynumber: 5.4 Consensus size: 152
42449244 TCAGACCAAA
* * * ** *
42449254 CAAGATCATTTCCAAT-CTGCTTGAAATTGAAGTAGAG-TGGATAACACA-TCTGCATCTCTGAA
1 CAAGATCATTTCCTATCCT-CTTGAAATTGAAGTAAAGTTGGATATCA-AGTCTTTATCTCCGAA
* * *
42449316 ATTGAAGTAAGAGCAATG-TCA--T-C---CCT-TTGAAATTGAAGTAGAG-TGGATAACATGTC
64 AATGAAGTAAGAGCAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTC
*
42449372 TTTATCTCTGAAATTGAAGCAAGAG
128 TTTATCTCTGAAATTGAAGTAAGAG
* * * *
42449397 C---A--ATGT--TATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAAA
* * *
42449455 TGAAGTAAGAGCAACG-TC--GT-C---CC-CTTGAAATTGAAGTAGAG-TGGATAACATGTCTT
66 TGAAGTAAGAGCAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTT
42449511 TATCTCTGAAATTGAAGTAAGAG
130 TATCTCTGAAATTGAAGTAAGAG
* *
42449534 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTCCGAAAA
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAAA
42449599 TGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTT
66 TGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTT
42449664 ATCTCTGAAATTGAAGTAAGAG
131 ATCTCTGAAATTGAAGTAAGAG
*
42449686 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTTTTTATCTCCGAAAA
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAAA
*
42449751 TGAAGTAATAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTT
66 TGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTT
42449816 ATCTCTGAAATTGAAGTAAGAG
131 ATCTCTGAAATTGAAGTAAGAG
* *
42449838 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAATTTGGATATCAGGTCTTTATCTCCGAAAA
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAAA
42449903 TGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTT
66 TGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTT
*
42449968 ATCTCCGAAATTGAAGTAAGAG
131 ATCTCTGAAATTGAAGTAAGAG
*
42449990 CAACG-TCATTTCCTATCCGT-TTGAAATTGAAGTAGAA-TTGGGTATCAAGTCTTTATCTCCGA
1 CAA-GATCATTTCCTATCC-TCTTGAAATTGAAGTA-AAGTTGGATATCAAGTCTTTATCTCCGA
42450052 AA
63 AA
42450054 TTGAGCAAGA
Statistics
Matches: 608, Mismatches: 25, Indels: 39
0.90 0.04 0.06
Matches are distributed among these distances:
136 21 0.03
137 100 0.16
138 3 0.00
140 2 0.00
142 3 0.00
143 2 0.00
144 63 0.10
146 1 0.00
147 1 0.00
150 2 0.00
151 18 0.03
152 388 0.64
153 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (152 bp):
CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTCTTTATCTCCGAAAA
TGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTT
ATCTCTGAAATTGAAGTAAGAG
Found at i:42449819 original size:228 final size:228
Alignment explanation
Indices: 42449254--42450057 Score: 1074
Period size: 228 Copynumber: 3.6 Consensus size: 228
42449244 TCAGACCAAA
* * ** *
42449254 CAAGATCATTTCCAAT-CTGCTTGAAATTGAAGTAGAG-TGGATAACACA-TCTGCATCTCTGAA
1 CAAGATCATTTCCTATCCT-CTTGAAATTGAAGTAGAGTTGGATATCA-AGTCTTTATCTCCGAA
* *
42449316 ATTGAAGTAAGAGCAATG-TCA--T-C---CCT-TTGAAATTGAAGTAGAG-TGGATAACATGTC
64 ATTGAAGTAAGAGCAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTC
* * *
42449372 TTTATCTCTGAAATTGAAGCAAGAGC---A--ATGT--TATCCTCTTGAAATTGAAGTAGAGTTG
128 TTTATCTCCGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTG
42449430 GATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAG
193 GATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAG
* * * *
42449466 CAACG-TC--GT-C---CC-CTTGAAATTGAAGTAGAG-TGGATAACATGTCTTTATCTCTGAAA
1 CAA-GATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAAA
* * *
42449522 TTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTT
65 TTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTT
*
42449587 TATCTCCGAAAATGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGA
130 TATCTCCGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGA
42449652 TATCAAGTCTTTATCTCTGAAATTGAAGTAAGAG
195 TATCAAGTCTTTATCTCTGAAATTGAAGTAAGAG
* * *
42449686 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATATCAAGTTTTTATCTCCGAAAA
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAAAT
*
42449751 TGAAGTAATAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTT
66 TGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTT
* * *
42449816 ATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAATTTGGAT
131 ATCTCCGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGAT
* * *
42449881 ATCAGGTCTTTATCTCCGAAAATGAAGTAAGAG
196 ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAG
42449914 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAAAT
1 CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAAAT
* *
42449979 TGAAGTAAGAGCAACG-TCATTTCCTATCCGT-TTGAAATTGAAGTAGAATTGGGTATCAAGTCT
66 TGAAGTAAGAGCAA-GATCATTTCCTATCC-TCTTGAAATTGAAGTAGAGTTGGATATCAAGTCT
42450042 TTATCTCCGAAATTGA
129 TTATCTCCGAAATTGA
42450058 GCAAGACAAA
Statistics
Matches: 525, Mismatches: 37, Indels: 44
0.87 0.06 0.07
Matches are distributed among these distances:
204 1 0.00
205 58 0.11
207 2 0.00
208 1 0.00
209 1 0.00
210 1 0.00
211 3 0.01
212 21 0.04
213 34 0.06
216 1 0.00
218 3 0.01
219 1 0.00
220 68 0.13
222 1 0.00
223 1 0.00
226 2 0.00
227 17 0.03
228 307 0.58
229 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (228 bp):
CAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAAAT
TGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTT
ATCTCCGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGAT
ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAG
Done.