Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
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 139 of 171
Found at i:42856218 original size:23 final size:24
Alignment explanation
Indices: 42856167--42856218 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
42856157 AATTGGTATG
*
42856167 TTATTTTTAAATTAAAATATTAAA
1 TTATTTTTAAATTAAAATATCAAA
* * *
42856191 ATATTTTTAATTTAAATTA-CAAA
1 TTATTTTTAAATTAAAATATCAAA
42856214 TTATT
1 TTATT
42856219 ATAAGAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTATTTTTAAATTAAAATATCAAA
Found at i:42856664 original size:28 final size:25
Alignment explanation
Indices: 42856623--42856674 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
42856613 TATCTATCTG
42856623 AATTTTTTTAATTATAATTAATTTAA
1 AATTTTTTTAATTA-AATTAATTTAA
*
42856649 AATTTTTAATTAATTAAATTTATTTA
1 AATTTTT--TTAATTAAATTAATTTA
42856675 TTTAAAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 9 0.39
28 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AATTTTTTTAATTAAATTAATTTAA
Found at i:42858492 original size:9 final size:8
Alignment explanation
Indices: 42858480--42858513 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 8
42858470 TTAAAAATAT
42858480 TTTTTATAA
1 TTTTT-TAA
42858489 TTTTTTAA
1 TTTTTTAA
42858497 TATTTTTAA
1 T-TTTTTAA
42858506 TTTTTTAA
1 TTTTTTAA
42858514 AATTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 11 0.46
9 13 0.54
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTTAA
Found at i:42862979 original size:21 final size:21
Alignment explanation
Indices: 42862953--42863003 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
42862943 CAACCAAAGT
*
42862953 AACTACCGATACTTTGGTACC
1 AACTACCGACACTTTGGTACC
*
42862974 AACTACCGACACTTTGGTATC
1 AACTACCGACACTTTGGTACC
42862995 AACTACCGA
1 AACTACCGA
42863004 AACAAGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.25
Consensus pattern (21 bp):
AACTACCGACACTTTGGTACC
Found at i:42864649 original size:39 final size:38
Alignment explanation
Indices: 42864606--42864795 Score: 164
Period size: 39 Copynumber: 4.8 Consensus size: 38
42864596 TCATTACTGC
* * **
42864606 TTCAGTATAGCATTGCGATGTTTACAGTGTCACCACCAA
1 TTCAGTATATCATTG-AATGTTTACAGTGTCACTGCCAA
** * *
42864645 TTCAGTATGGCATTGTAGTGTTTACAGTGTCACTGCCAG
1 TTCAGTATATCATTG-AATGTTTACAGTGTCACTGCCAA
* ** * *
42864684 TGCAACATATCATTGTAGTGTTTACAATGTCACTGCCAA
1 TTCAGTATATCATTG-AATGTTTACAGTGTCACTGCCAA
* * *
42864723 TTCAATATATATCATTGCAATGTTTACAGTGTCACTGCTAG
1 TTC-A-GTATATCATTG-AATGTTTACAGTGTCACTGCCAA
*
42864764 TTCAGTATATCATTATAATGTTTACAGTGTCA
1 TTCAGTATATCATT-GAATGTTTACAGTGTCA
42864796 TTACCAGTTT
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
39 91 0.73
40 2 0.02
41 32 0.26
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.36
Consensus pattern (38 bp):
TTCAGTATATCATTGAATGTTTACAGTGTCACTGCCAA
Found at i:42864774 original size:80 final size:78
Alignment explanation
Indices: 42864585--42864795 Score: 210
Period size: 80 Copynumber: 2.7 Consensus size: 78
42864575 AGTCTAGAAG
* * * *
42864585 TGTTTACAGTGTCATTACT-GCTTCAGTATAGCATTG-CGATGTTTACAGTGTCACCACCAATTC
1 TGTTTACAGTGTCACTGCTAG-TTCAGTATATCATTGTAG-TGTTTACAGTGTCACCACCAATTC
* * * *
42864648 AGTATGGCATTGTAG
64 AATATAGCATTGCAA
* * ** * **
42864663 TGTTTACAGTGTCACTGCCAGTGCAACATATCATTGTAGTGTTTACAATGTCACTGCCAATTCAA
1 TGTTTACAGTGTCACTGCTAGTTCAGTATATCATTGTAGTGTTTACAGTGTCACCACCAATTC-A
*
42864728 TATATATCATTGCAA
65 -ATATAGCATTGCAA
* *
42864743 TGTTTACAGTGTCACTGCTAGTTCAGTATATCATTATAATGTTTACAGTGTCA
1 TGTTTACAGTGTCACTGCTAGTTCAGTATATCATTGTAGTGTTTACAGTGTCA
42864796 TTACCAGTTT
Statistics
Matches: 106, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
78 48 0.45
79 3 0.03
80 55 0.52
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (78 bp):
TGTTTACAGTGTCACTGCTAGTTCAGTATATCATTGTAGTGTTTACAGTGTCACCACCAATTCAA
TATAGCATTGCAA
Found at i:42866010 original size:24 final size:24
Alignment explanation
Indices: 42865982--42866034 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
42865972 CAGACGACAT
42865982 TTAGCCAACACGAGCCCAGAATGA
1 TTAGCCAACACGAGCCCAGAATGA
* ** *
42866006 TTAGCTATTACGAGCCTAGAATGA
1 TTAGCCAACACGAGCCCAGAATGA
42866030 TTAGC
1 TTAGC
42866035 TCTTACGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (24 bp):
TTAGCCAACACGAGCCCAGAATGA
Found at i:42866035 original size:24 final size:24
Alignment explanation
Indices: 42865991--42866073 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
42865981 TTTAGCCAAC
*
42865991 ACGAGCCCAGAATGATTAGCTATT
1 ACGAGCCCAGAATGATTAGCTCTT
*
42866015 ACGAGCCTAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
* * *
42866039 ACGAACCCAAAATAATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
42866063 ACGAGCCCAGA
1 ACGAGCCCAGA
42866074 TAGAGTGTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (24 bp):
ACGAGCCCAGAATGATTAGCTCTT
Found at i:42868118 original size:15 final size:13
Alignment explanation
Indices: 42868088--42868112 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42868078 TCTGACACAC
42868088 GCCCGTGTGTCTA
1 GCCCGTGTGTCTA
42868101 GCCCGTGTGTCT
1 GCCCGTGTGTCT
42868113 CAAGCCAGTA
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:0.04, C:0.32, G:0.32, T:0.32
Consensus pattern (13 bp):
GCCCGTGTGTCTA
Found at i:42869855 original size:15 final size:17
Alignment explanation
Indices: 42869827--42869858 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
42869817 TAACCTACAA
42869827 AAATATAATAAAATATT
1 AAATATAATAAAATATT
42869844 AAATA-AAT-AAATATT
1 AAATATAATAAAATATT
42869859 TATAAAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAATAAAATATT
Found at i:42870277 original size:31 final size:31
Alignment explanation
Indices: 42870242--42870319 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
42870232 ACTTAAATTT
42870242 TTTTTTTCAATTTGGTA-CTCAAACTTGACAC
1 TTTTTTTCAATTTGGTACCT-AAACTTGACAC
* *
42870273 -TTTTTCCTAATTTGATACCTAAACTTGACAC
1 TTTTTTTC-AATTTGGTACCTAAACTTGACAC
*
42870304 TTTTTTT-AAGTTGGTA
1 TTTTTTTCAATTTGGTA
42870320 GTTGAACTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
30 13 0.33
31 19 0.49
32 7 0.18
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (31 bp):
TTTTTTTCAATTTGGTACCTAAACTTGACAC
Found at i:42870636 original size:57 final size:56
Alignment explanation
Indices: 42870558--42870694 Score: 159
Period size: 57 Copynumber: 2.4 Consensus size: 56
42870548 TGAATCTTTA
* * * ** *
42870558 AAAAAAACTT-AGGTACCAAATTAGGAAATGTTAAGTTCAGGTTCCAAATTGGATCC
1 AAAAAAAGTTCAGGTACCAAATTAAGAAATGTCAAGTTCAAATACCAAATTGGAT-C
** * *
42870614 AAAAAAAGTTCAGGTGTCAAATTAAGAAGTGTCAAGTTCAAATACCAAATTGGGTC
1 AAAAAAAGTTCAGGTACCAAATTAAGAAATGTCAAGTTCAAATACCAAATTGGATC
*
42870670 AAAAAAAGTTTAGGTACCAAATTAA
1 AAAAAAAGTTCAGGTACCAAATTAA
42870695 AAAAAAGTTT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
56 32 0.48
57 35 0.52
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.26
Consensus pattern (56 bp):
AAAAAAAGTTCAGGTACCAAATTAAGAAATGTCAAGTTCAAATACCAAATTGGATC
Found at i:42873474 original size:12 final size:12
Alignment explanation
Indices: 42873423--42873466 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
42873413 ATAAAAAAAT
*
42873423 TAAATTTAAT-T
1 TAAATTTAATAA
42873434 TAAATTTAATAA
1 TAAATTTAATAA
42873446 TAAATTTAATAA
1 TAAATTTAATAA
42873458 TAAATTTAA
1 TAAATTTAA
42873467 AAACAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAATTTAATAA
Found at i:42873474 original size:24 final size:23
Alignment explanation
Indices: 42873424--42873474 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
42873414 TAAAAAAATT
* * *
42873424 AAATTTAATTTAAATTTAATAAT
1 AAATTTAATATAAATTTAAAAAC
42873447 AAATTTAATAATAAATTTAAAAAC
1 AAATTTAAT-ATAAATTTAAAAAC
42873471 AAAT
1 AAAT
42873475 AACAAGTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATTTAATATAAATTTAAAAAC
Found at i:42873998 original size:28 final size:28
Alignment explanation
Indices: 42873966--42874029 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
42873956 AGCCACTTAT
*
42873966 AAATATTTATAACATATATTTTATGGGA
1 AAATATTTATAACATATATTTTATGGAA
*
42873994 AAATACTTATAACATATATTTTATGGAA
1 AAATATTTATAACATATATTTTATGGAA
42874022 AAATATTT
1 AAATATTT
42874030 GGTACCTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (28 bp):
AAATATTTATAACATATATTTTATGGAA
Found at i:42874893 original size:29 final size:28
Alignment explanation
Indices: 42874858--42874919 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
42874848 AAAATATGTC
*
42874858 AAGTTCAGATACCAAATTGGGTCCAAAAA
1 AAGTTCAGATACCAAACTGGGT-CAAAAA
* *
42874887 AAGTTCAGGTATCAAACTGGGTCAAAAA
1 AAGTTCAGATACCAAACTGGGTCAAAAA
42874915 AAGTT
1 AAGTT
42874920 TAAGTATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.23
Consensus pattern (28 bp):
AAGTTCAGATACCAAACTGGGTCAAAAA
Found at i:42874926 original size:28 final size:29
Alignment explanation
Indices: 42874870--42874930 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
42874860 GTTCAGATAC
* *
42874870 CAAATTGGGTCCAAAAAAAGTTCAGGTAT
1 CAAACTGGGTCCAAAAAAAGTTCAAGTAT
*
42874899 CAAACTGGGT-CAAAAAAAGTTTAAGTAT
1 CAAACTGGGTCCAAAAAAAGTTCAAGTAT
42874927 CAAA
1 CAAA
42874931 TTAGGAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (29 bp):
CAAACTGGGTCCAAAAAAAGTTCAAGTAT
Found at i:42875253 original size:59 final size:58
Alignment explanation
Indices: 42875130--42875299 Score: 164
Period size: 59 Copynumber: 2.9 Consensus size: 58
42875120 GAATCTAAAA
* * * ** *
42875130 AAAAAAAAGCTTAGGTACCAAATTAAGAAAATATGTCAAGCTC-AATATCAAATTGGGT
1 AAAAAAAAGATTAAGTATCAAATTAAGAAAA-ATGTCAAATTCAAATATCAAATTGAGT
** * * *
42875188 CCAAAAAAGTTTAAGTATTAAATTAGGAAAAAGTGTCAAATTCAAATATCAAATTGAGT
1 AAAAAAAAGATTAAGTATCAAATTAAGAAAAA-TGTCAAATTCAAATATCAAATTGAGT
* * *
42875247 AAAAAAAAAATT-AGCTATCAAATTAAGAAAAAATGTCAAATTTAAATACCAAA
1 AAAAAAAAGATTAAG-TATCAAATTAAG-AAAAATGTCAAATTCAAATATCAAA
42875300 AAATTATATG
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
57 1 0.01
58 34 0.38
59 50 0.56
60 5 0.06
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (58 bp):
AAAAAAAAGATTAAGTATCAAATTAAGAAAAATGTCAAATTCAAATATCAAATTGAGT
Found at i:42878896 original size:29 final size:28
Alignment explanation
Indices: 42878862--42879015 Score: 125
Period size: 30 Copynumber: 5.3 Consensus size: 28
42878852 GTAAAATGAT
42878862 AATTTTGGTGAAATCGGGGTGAAAAATGG
1 AATTTTGGTGAAATCGGGGT-AAAAATGG
* ** * *
42878891 AATTTTGGAGAGTTTGGGGGT-AAAACGG
1 AATTTTGGTGA-AATCGGGGTAAAAATGG
42878919 TAATTTTTGGTGAAATCGGGGTTAAAAATGG
1 -AA-TTTTGGTGAAATCGGGG-TAAAAATGG
* *
42878950 AATTTTGG-AAAACTTAGGGGT-AAAATGG
1 AATTTTGGTGAAA--TCGGGGTAAAAATGG
* *
42878978 AAATTTTTGGTGAAATCGAGGTTAAAATGG
1 -AA-TTTTGGTGAAATCGGGGTAAAAATGG
42879008 AATTTTGG
1 AATTTTGG
42879016 AAAGTTTTGG
Statistics
Matches: 99, Mismatches: 15, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
28 22 0.22
29 33 0.33
30 35 0.35
31 9 0.09
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.32
Consensus pattern (28 bp):
AATTTTGGTGAAATCGGGGTAAAAATGG
Found at i:42878939 original size:59 final size:58
Alignment explanation
Indices: 42878850--42879041 Score: 269
Period size: 59 Copynumber: 3.3 Consensus size: 58
42878840 GGATACCCGA
* * *
42878850 GGGTAAAATGATAA-TTTTGGTGAAATCGGGGTGAAAAATGGAATTTTGGAGAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGT-AAAAATGGAATTTTGGAAAGTTTAG
* **
42878908 GGGTAAAACGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAACTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGG-TAAAAATGGAATTTTGGAAAGTTTAG
* * * *
42878967 GGGTAAAATGGAAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTGGAAAGTTTTG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTAAAAATGGAATTTTGGAAAGTTTAG
42879025 GGGTAAAATGGTAATTT
1 GGGTAAAATGGTAATTT
42879042 GATGAAAACA
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
58 50 0.42
59 67 0.57
60 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.32
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTAAAAATGGAATTTTGGAAAGTTTAG
Found at i:42879040 original size:29 final size:26
Alignment explanation
Indices: 42878850--42879041 Score: 93
Period size: 30 Copynumber: 6.6 Consensus size: 26
42878840 GGATACCCGA
*
42878850 GGGTAAAATGATAATTTTGGTGAAA-TCG
1 GGGTAAAATG-GAATTTT-G-GAAATTCG
* *
42878878 GGGTGAAAAATGGAATTTTGGAGAGTTTGG
1 GGGT--AAAATGGAATTTTGGA-A-ATTCG
*
42878908 GGGTAAAACGGTAATTTTTGGTGAAA-TCG
1 GGGTAAAATGG-AA-TTTT-G-GAAATTCG
*
42878937 GGGTTAAAAATGGAATTTTGGAAAACTTAG
1 GGG-T-AAAATGGAATTTTGG-AAA-TTCG
42878967 GGGTAAAATGGAAATTTTTGGTGAAA-TCG
1 GGGTAAAATGG-AA-TTTT-G-GAAATTCG
* *
42878996 AGGTTAAAATGGAATTTTGGAAAGTTTTG
1 -GGGTAAAATGGAATTTTGGAAA--TTCG
42879025 GGGTAAAATGGTAATTT
1 GGGTAAAATGG-AATTT
42879042 GATGAAAACA
Statistics
Matches: 129, Mismatches: 12, Indels: 45
0.69 0.06 0.24
Matches are distributed among these distances:
26 4 0.03
27 4 0.03
28 37 0.29
29 31 0.24
30 38 0.29
31 12 0.09
32 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.32
Consensus pattern (26 bp):
GGGTAAAATGGAATTTTGGAAATTCG
Found at i:42879446 original size:24 final size:24
Alignment explanation
Indices: 42879415--42879460 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
42879405 CTTTTTCTTT
42879415 TAAATCCTTTTTTAT-TTTAAAAC
1 TAAATCCTTTTTTATCTTTAAAAC
*
42879438 TAAACTCCTTTTTTTTCTTTAAA
1 TAAA-TCCTTTTTTATCTTTAAA
42879461 GACCAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.54
Consensus pattern (24 bp):
TAAATCCTTTTTTATCTTTAAAAC
Found at i:42879468 original size:26 final size:24
Alignment explanation
Indices: 42879419--42879468 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
42879409 TTCTTTTAAA
*
42879419 TCCTTTTTTATTTTAAAACTAAAC
1 TCCTTTTTTATTTTAAAACCAAAC
*
42879443 TCCTTTTTTTTCTTTAAAGACCAAAC
1 TCCTTTTTTAT-TTTAAA-ACCAAAC
42879469 CCAGATCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 6 0.27
26 6 0.27
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (24 bp):
TCCTTTTTTATTTTAAAACCAAAC
Found at i:42879745 original size:3 final size:3
Alignment explanation
Indices: 42879739--42879822 Score: 51
Period size: 3 Copynumber: 26.7 Consensus size: 3
42879729 TATTGGTTGA
* * * * *
42879739 TAT TAT TAAT TAT TAA TAT TAAT TAT AAT TAT AAA TATT TAT TAC TAT
1 TAT TAT T-AT TAT TAT TAT T-AT TAT TAT TAT TAT TA-T TAT TAT TAT
* * * *
42879787 TAT TAAT TAT TAT GAT TAT TAA TAA TAT TTT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
42879823 ATGATATTTA
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
3 50 0.82
4 11 0.18
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:42879767 original size:6 final size:7
Alignment explanation
Indices: 42879740--42879809 Score: 67
Period size: 7 Copynumber: 10.3 Consensus size: 7
42879730 ATTGGTTGAT
42879740 ATTATTA
1 ATTATTA
42879747 ATTATTA
1 ATTATTA
42879754 A-TATTA
1 ATTATTA
42879760 ATTA-TA
1 ATTATTA
42879766 ATTA-TA
1 ATTATTA
* *
42879772 AATATTT
1 ATTATTA
*
42879779 ATTACT-
1 ATTATTA
42879785 ATTATTA
1 ATTATTA
42879792 ATTATTA
1 ATTATTA
42879799 TGATTATTA
1 --ATTATTA
42879808 AT
1 AT
42879810 AATATTTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
6 22 0.42
7 24 0.45
9 7 0.13
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (7 bp):
ATTATTA
Found at i:42879769 original size:19 final size:19
Alignment explanation
Indices: 42879739--42879815 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
42879729 TATTGGTTGA
*
42879739 TATTATTAATTATTAATAT
1 TATTACTAATTATTAATAT
*
42879758 TAATTA-TAATTATAAATATT
1 T-ATTACTAATTATTAATA-T
42879778 TATTACT-ATTATT-A-AT
1 TATTACTAATTATTAATAT
* *
42879794 TATTA-TGATTATTAATAA
1 TATTACTAATTATTAATAT
42879812 TATT
1 TATT
42879816 TTTATTAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
15 1 0.02
16 12 0.24
17 2 0.04
18 6 0.12
19 21 0.43
20 7 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (19 bp):
TATTACTAATTATTAATAT
Found at i:42879822 original size:15 final size:15
Alignment explanation
Indices: 42879802--42879831 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42879792 ATTATTATGA
42879802 TTATTAATAATATTT
1 TTATTAATAATATTT
*
42879817 TTATTAATGATATTT
1 TTATTAATAATATTT
42879832 ATGAAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTATTAATAATATTT
Found at i:42880530 original size:6 final size:6
Alignment explanation
Indices: 42880521--42880596 Score: 61
Period size: 6 Copynumber: 12.8 Consensus size: 6
42880511 TTAATATTAT
*
42880521 TTTAAA TTTAAA TTTAAA -ATAAA TTTAAATA TTTAAA TTTAAGA --TAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA-A TTTAAA TTTAA-A TTTAAA
* * *
42880569 TTTAAA TTCAAA -ATAAA TTTAAA ATTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
42880597 TTTGAACTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 10 0.18
6 36 0.64
7 5 0.09
8 4 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:42880541 original size:25 final size:25
Alignment explanation
Indices: 42880526--42880575 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
42880516 ATTATTTTAA
42880526 ATTTAAATTTAAAATAAATTTAAAT
1 ATTTAAATTTAAAATAAATTTAAAT
*
42880551 ATTTAAATTTAAGATAAATTTAAAT
1 ATTTAAATTTAAAATAAATTTAAAT
42880576 TCAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTTAAATTTAAAATAAATTTAAAT
Found at i:42880543 original size:17 final size:17
Alignment explanation
Indices: 42880521--42880596 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
42880511 TTAATATTAT
*
42880521 TTTAAATTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
*
42880539 -ATAAATTT-AAAT--A
1 TTTAAATTTAAAATAAA
*
42880552 TTTAAATTTAAGATAAA
1 TTTAAATTTAAAATAAA
*
42880569 TTTAAATTCAAAATAAA
1 TTTAAATTTAAAATAAA
*
42880586 TTTAAAATTAA
1 TTTAAATTTAA
42880597 TTTGAACTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
13 1 0.02
14 7 0.15
15 4 0.09
16 2 0.04
17 32 0.70
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:42880568 original size:11 final size:11
Alignment explanation
Indices: 42880529--42880574 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
42880519 ATTTTAAATT
42880529 TAAATTTAAAA
1 TAAATTTAAAA
42880540 TAAATTTAAATA
1 TAAATTTAAA-A
*
42880552 TTTAAATTTAAGA
1 --TAAATTTAAAA
42880565 TAAATTTAAA
1 TAAATTTAAA
42880575 TTCAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 19 0.63
12 1 0.03
13 1 0.03
14 9 0.30
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:42880599 original size:11 final size:11
Alignment explanation
Indices: 42880504--42880599 Score: 54
Period size: 11 Copynumber: 8.7 Consensus size: 11
42880494 TTTTTTATTT
*
42880504 ATTAATTTTAAT
1 ATTAA-TTTAAA
*
42880516 ATTATTTTAAA
1 ATTAATTTAAA
*
42880527 TTTAAATTTAAA
1 ATT-AATTTAAA
*
42880539 ATAAATTT-AA
1 ATTAATTTAAA
42880549 A-T-ATTTAAA
1 ATTAATTTAAA
* **
42880558 TTTAAGATAAA
1 ATTAATTTAAA
* *
42880569 TTTAAATTCAAA
1 ATT-AATTTAAA
*
42880581 ATAAATTTAAA
1 ATTAATTTAAA
42880592 ATTAATTT
1 ATTAATTT
42880600 GAACTTAAAA
Statistics
Matches: 62, Mismatches: 17, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
8 4 0.06
9 2 0.03
10 4 0.06
11 34 0.55
12 18 0.29
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (11 bp):
ATTAATTTAAA
Found at i:42880609 original size:28 final size:28
Alignment explanation
Indices: 42880529--42880599 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 28
42880519 ATTTTAAATT
**
42880529 TAAATTTAAAATAAATTTAAA-T--ATT
1 TAAATTTAAAATAAATTTAAATTCAAAA
*
42880554 TAAATTTAAGATAAATTTAAATTCAAAA
1 TAAATTTAAAATAAATTTAAATTCAAAA
*
42880582 TAAATTTAAAATTAATTT
1 TAAATTTAAAATAAATTT
42880600 GAACTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
25 20 0.53
26 1 0.03
28 17 0.45
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
TAAATTTAAAATAAATTTAAATTCAAAA
Found at i:42880986 original size:76 final size:76
Alignment explanation
Indices: 42880890--42881270 Score: 665
Period size: 76 Copynumber: 5.0 Consensus size: 76
42880880 TGCTCTTCAG
* * * *
42880890 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
42880955 ACTTCAATTTC
66 ACTTCAATTTC
*
42880966 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
42881031 ACTTCAATTTC
66 ACTTCAATTTC
* * *
42881042 GGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGA-CGTTGCTCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATC-TTGCTCT
42881106 TACTTCAATTTC
65 TACTTCAATTTC
42881118 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
42881183 ACTTCAATTTC
66 ACTTCAATTTC
*
42881194 AGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
42881259 ACTTCAATTTC
66 ACTTCAATTTC
42881270 A
1 A
42881271 AGCGGATAGG
Statistics
Matches: 292, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
75 1 0.00
76 290 0.99
77 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
ACTTCAATTTC
Found at i:42881264 original size:190 final size:190
Alignment explanation
Indices: 42881068--42881840 Score: 868
Period size: 190 Copynumber: 4.1 Consensus size: 190
42881058 TATCCAACTC
*
42881068 TACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTG
1 TACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTG
*
42881133 TTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAG
66 TTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTCCTCTTACTTCAATTTCAGAG
*
42881198 ATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCT
131 ATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCT
42881258 TACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTG
1 TACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTG
* *
42881323 TTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTCCTCTTACTTCAATTTCAGAG
66 TTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTCCTCTTACTTCAATTTCAGAG
* * *
42881388 ATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCT
131 ATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCT
* * *
42881448 TACTTCAATTTC-AG-AGAT---AAA-GACGTGTTATCCACTCTACTTCAATTTCAAGAGGAT-A
1 TACTTCAATTTCAAGCGGATAGGAAATGAC--G-T-TGCTCT-TACTTCAATTTC-AGA-GATAA
* ** *** * * ** *
42881506 GGAAATG--ATCTTGCTCTTACTTCAATTT-TAGA-GATAAAGACGTG-T-TATCCACTCTACTT
59 AGACGTGTTATCCAACTC-TACTTCAATTTCAAGAGGAT-AGGAAATGATCT-TCCTCT-TACTT
* ** * * * **
42881565 CAATTTCAAGAGGAT-AGGAAATGACGT-TGC-TCT-TACTTCAATTTC-AGAGAGATAAAGACT
120 CAATTTC-AGA-GATAAAGACGTGA--TATCCAACTCTACTTCAATTTCAAGAG-GAT-AGGAAA
* * *
42881625 TGAT-ATCCAACT
179 TGATCTTGC-TCT
*
42881637 CTACTTCAATTTCAAGAGGATAGGAAATGATC-TTGCTCTTACTTCAATTTCAGAGATAAAGACG
1 -TACTTCAATTTCAAGCGGATAGGAAATGA-CGTTGCTCTTACTTCAATTTCAGAGATAAAGACG
* *
42881701 TGTTATCCAACTCTCCTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAG
64 TGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTCCTCTTACTTCAATTTCAG
* *
42881766 AGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGA-CATTGCTCT
129 AGATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATC-TTGCTCT
42881828 TACTTCAATTTCA
1 TACTTCAATTTCA
42881841 GAGATAAAGA
Statistics
Matches: 476, Mismatches: 67, Indels: 80
0.76 0.11 0.13
Matches are distributed among these distances:
184 3 0.01
185 3 0.01
186 2 0.00
187 13 0.03
188 48 0.10
189 47 0.10
190 245 0.51
191 46 0.10
192 50 0.11
193 12 0.03
194 1 0.00
195 3 0.01
196 2 0.00
197 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (190 bp):
TACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTG
TTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTCCTCTTACTTCAATTTCAGAG
ATAAAGACGTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCT
Found at i:42881300 original size:76 final size:74
Alignment explanation
Indices: 42881220--42881977 Score: 759
Period size: 76 Copynumber: 10.0 Consensus size: 74
42881210 TATCCAACTC
* **
42881220 TACTTCAATTTCAAGAGGAT-AGGAAATGATCTTGCTCTTACTTCAATTTCAAGCGGATAGGAAA
1 TACTTCAATTTC-AGA-GATAAAGACGTGATCTTGCTCTTACTTCAATTTCAAGCGGATAGGAAA
42881284 TGACGTTGCTCT
64 TGAC-TTGCTCT
***
42881296 TACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTC-TACTTCAATTTCAAGCGGATAGGAAA
1 TACTTCAATTTCAGAGATAAAGACGTG--ATCTTGCTCTTACTTCAATTTCAAGCGGATAGGAAA
* *
42881360 AGATCTTCCTCT
64 TGA-CTTGCTCT
***
42881372 TACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTC-TACTTCAATTTCAAGCGGATAGGAAA
1 TACTTCAATTTCAGAGATAAAGACGTG--ATCTTGCTCTTACTTCAATTTCAAGCGGATAGGAAA
*
42881436 AGATCTTGCTCT
64 TGA-CTTGCTCT
* * *
42881448 TACTTCAATTTCAGAGATAAAGACGTG-T-TATCCACTCTACTTCAATTTCAAGAGGATAGGAAA
1 TACTTCAATTTCAGAGATAAAGACGTGATCT-TGCTCT-TACTTCAATTTCAAGCGGATAGGAAA
42881511 TGATCTTGCTCT
64 TGA-CTTGCTCT
* * * *
42881523 TACTTCAATTTTAGAGATAAAGACGTG-T-TATCCACTCTACTTCAATTTCAAGAGGATAGGAAA
1 TACTTCAATTTCAGAGATAAAGACGTGATCT-TGCTCT-TACTTCAATTTCAAGCGGATAGGAAA
42881586 TGACGTTGCTCT
64 TGAC-TTGCTCT
* * * * *
42881598 TACTTCAATTTCAGAGAGATAAAGACTTGAT-ATCCAACTCTACTTCAATTTCAAGAGGATAGGA
1 TACTTCAATTTC--AGAGATAAAGACGTGATCTTGC-TCT-TACTTCAATTTCAAGCGGATAGGA
42881662 AATGATCTTGCTCT
62 AATGA-CTTGCTCT
*** * *
42881676 TACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTC-TCCTTCAATTTCAAGAGGATAGGAAA
1 TACTTCAATTTCAGAGATAAAGACGTG--ATCTTGCTCTTACTTCAATTTCAAGCGGATAGGAAA
42881740 TGATCTTGCTCT
64 TGA-CTTGCTCT
***
42881752 TACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTC-TACTTCAATTTCAAGCGGATAGGAAA
1 TACTTCAATTTCAGAGATAAAGACGTG--ATCTTGCTCTTACTTCAATTTCAAGCGGATAGGAAA
42881816 TGACATTGCTCT
64 TGAC-TTGCTCT
* * * * *
42881828 TACTTCAATTTCAGAGATAAAGACTTGAT-ATCCAACTCTACTTCAATTTCAATCGGATAGGAAA
1 TACTTCAATTTCAGAGATAAAGACGTGATCTTGC-TCT-TACTTCAATTTCAAGCGGATAGGAAA
42881892 TGACGTTGCTCT
64 TGAC-TTGCTCT
* * * *
42881904 TACTTCATTTTCAAAGATAAAGACGTG-T-TATCCACTCTACTTCAATTTCAAGCGGATAGGAAA
1 TACTTCAATTTCAGAGATAAAGACGTGATCT-TGCTCT-TACTTCAATTTCAAGCGGATAGGAAA
*
42881967 AGATCTTGCTC
64 TGA-CTTGCTC
42881978 CGGTTTGATC
Statistics
Matches: 620, Mismatches: 40, Indels: 45
0.88 0.06 0.06
Matches are distributed among these distances:
73 4 0.01
74 7 0.01
75 166 0.27
76 361 0.58
77 24 0.04
78 56 0.09
79 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (74 bp):
TACTTCAATTTCAGAGATAAAGACGTGATCTTGCTCTTACTTCAATTTCAAGCGGATAGGAAATG
ACTTGCTCT
Found at i:42881338 original size:152 final size:152
Alignment explanation
Indices: 42881182--42881966 Score: 845
Period size: 152 Copynumber: 5.2 Consensus size: 152
42881172 ATCTTGCTCT
* ** *
42881182 TACTTCAATTTC-AGAGATAAAGACTTGATATCCAACTC-TACTTCAATTTCAAGAGGAT-AGGA
1 TACTTCAATTTCAAGAGAT-AGGAAATGATATCCAACTCTTACTTCAATTTC-AGA-GATAAAGA
*
42881244 AATGATCTTGCTCTTACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCTTACTTCAATTTCA
63 CATGATCTTGCTCTTACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCTTACTTCAATTTCA
42881309 GAGATAAAGACGTGTTATCCAACTC
128 GAGATAAAGACGTGTTATCCAACTC
* * * * *
42881334 TACTTCAATTTCAAGCGGATAGGAAAAGATCTTC--CTCTTACTTCAATTTCAGAGATAAAGACG
1 TACTTCAATTTCAAG-AGATAGGAAATGATATCCAACTCTTACTTCAATTTCAGAGATAAAGACA
*** *
42881397 TGTTATCCAACTC-TACTTCAATTTCAAGCGGATAGGAAAAGATC-TTGCTCTTACTTCAATTTC
65 TG--ATCTTGCTCTTACTTCAATTTCAAGCGGATAGGAAATGA-CGTTGCTCTTACTTCAATTTC
42881460 AGAGATAAAGACGTGTTATCC-ACTC
127 AGAGATAAAGACGTGTTATCCAACTC
*** * *
42881485 TACTTCAATTTCAAGAGGATAGGAAATG--ATCTTGCTCTTACTTCAATTTTAGAGATAAAGACG
1 TACTTCAATTTCAAGA-GATAGGAAATGATATCCAACTCTTACTTCAATTTCAGAGATAAAGACA
* * *
42881548 TG-T-TATCCACTCTACTTCAATTTCAAGAGGATAGGAAATGACGTTGCTCTTACTTCAATTTCA
65 TGATCT-TGCTCT-TACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCTTACTTCAATTTC-
* *
42881611 GAGAGATAAAGACTTGATATCCAACTC
127 -AGAGATAAAGACGTGTTATCCAACTC
*** *
42881638 TACTTCAATTTCAAGAGGATAGGAAATG--ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACG
1 TACTTCAATTTCAAGA-GATAGGAAATGATATCCAACTCTTACTTCAATTTCAGAGATAAAGACA
*** * *
42881701 TGTTATCCAACTC-TCCTTCAATTTCAAGAGGATAGGAAATGATC-TTGCTCTTACTTCAATTTC
65 TG--ATCTTGCTCTTACTTCAATTTCAAGCGGATAGGAAATGA-CGTTGCTCTTACTTCAATTTC
42881764 AGAGATAAAGACGTGTTATCCAACTC
127 AGAGATAAAGACGTGTTATCCAACTC
* * ** *
42881790 TACTTCAATTTCAAGCGGATAGGAAATGACAT--TGCTCTTACTTCAATTTCAGAGATAAAGACT
1 TACTTCAATTTCAAG-AGATAGGAAATGATATCCAACTCTTACTTCAATTTCAGAGATAAAGACA
* * * * *
42881853 TGAT-ATCCAACTCTACTTCAATTTCAATCGGATAGGAAATGACGTTGCTCTTACTTCATTTTCA
65 TGATCTTGC-TCT-TACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCTTACTTCAATTTCA
*
42881917 AAGATAAAGACGTGTTATCC-ACTC
128 GAGATAAAGACGTGTTATCCAACTC
*
42881941 TACTTCAATTTCAAGCGGATAGGAAA
1 TACTTCAATTTCAAG-AGATAGGAAA
42881967 AGATCTTGCT
Statistics
Matches: 557, Mismatches: 47, Indels: 59
0.84 0.07 0.09
Matches are distributed among these distances:
148 3 0.01
149 3 0.01
150 52 0.09
151 101 0.18
152 257 0.46
153 85 0.15
154 52 0.09
155 1 0.00
156 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (152 bp):
TACTTCAATTTCAAGAGATAGGAAATGATATCCAACTCTTACTTCAATTTCAGAGATAAAGACAT
GATCTTGCTCTTACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCTTACTTCAATTTCAGAG
ATAAAGACGTGTTATCCAACTC
Found at i:42881908 original size:38 final size:36
Alignment explanation
Indices: 42881068--42881917 Score: 219
Period size: 38 Copynumber: 22.4 Consensus size: 36
42881058 TATCCAACTC
42881068 TACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCT
1 TACTTCAATTTCAA-CGGATAGGAAATGAC-TTGCTCT
* ** * * *
42881106 TACTTCAATTTC-A-GAGATAAAGACTTG-TTATCCAACT
1 TACTTCAATTTCAACG-GAT-AGGAAATGACT-TGC-TCT
*
42881143 CTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCT
1 -TACTTCAATTTCAA-CGGATAGGAAATGA-CTTGCTCT
* ** * *
42881182 TACTTCAATTTC-A-GAGATAAAGACTTGA-TATCCAACT
1 TACTTCAATTTCAACG-GAT-AGGAAATGACT-TGC-TCT
*
42881219 CTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCT
1 -TACTTCAATTTCAA-CGGATAGGAAATGA-CTTGCTCT
42881258 TACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCT
1 TACTTCAATTTCAA-CGGATAGGAAATGAC-TTGCTCT
* ** * * *
42881296 TACTTCAATTTC-A-GAGATAAAGACGTG-TTATCCAACT
1 TACTTCAATTTCAACG-GAT-AGGAAATGACT-TGC-TCT
* *
42881333 CTACTTCAATTTCAAGCGGATAGGAAAAGATCTTCCTCT
1 -TACTTCAATTTCAA-CGGATAGGAAATGA-CTTGCTCT
* ** * * *
42881372 TACTTCAATTTC-A-GAGATAAAGACGTG-TTATCCAACT
1 TACTTCAATTTCAACG-GAT-AGGAAATGACT-TGC-TCT
*
42881409 CTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCT
1 -TACTTCAATTTCAA-CGGATAGGAAATGA-CTTGCTCT
* ** * * *
42881448 TACTTCAATTTC-A-GAGATAAAGACGTG-TTATCCACT
1 TACTTCAATTTCAACG-GAT-AGGAAATGACT-TGCTCT
*
42881484 CTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCT
1 -TACTTCAATTTCAA-CGGATAGGAAATGA-CTTGCTCT
* * ** * * *
42881523 TACTTCAATTT-TA-GAGATAAAGACGTG-TTATCCACT
1 TACTTCAATTTCAACG-GAT-AGGAAATGACT-TGCTCT
*
42881559 CTACTTCAATTTCAAGAGGATAGGAAATGACGTTGCTCT
1 -TACTTCAATTTCAA-CGGATAGGAAATGAC-TTGCTCT
* ** * *
42881598 TACTTCAATTTCAGA-GAGATAAAGACTTGA-TATCCAACT
1 TACTTCAATTTCA-ACG-GAT-AGGAAATGACT-TGC-TCT
*
42881637 CTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCT
1 -TACTTCAATTTCAA-CGGATAGGAAATGA-CTTGCTCT
* ** * * *
42881676 TACTTCAATTTC-A-GAGATAAAGACGTG-TTATCCAACT
1 TACTTCAATTTCAACG-GAT-AGGAAATGACT-TGC-TCT
* *
42881713 CTCCTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCT
1 -TACTTCAATTTCAA-CGGATAGGAAATGA-CTTGCTCT
* ** * * *
42881752 TACTTCAATTTC-A-GAGATAAAGACGTG-TTATCCAACT
1 TACTTCAATTTCAACG-GAT-AGGAAATGACT-TGC-TCT
42881789 CTACTTCAATTTCAAGCGGATAGGAAATGACATTGCTCT
1 -TACTTCAATTTCAA-CGGATAGGAAATGAC-TTGCTCT
* ** * *
42881828 TACTTCAATTTC-A-GAGATAAAGACTTGA-TATCCAACT
1 TACTTCAATTTCAACG-GAT-AGGAAATGACT-TGC-TCT
42881865 CTACTTCAATTTCAATCGGATAGGAAATGACGTTGCTCT
1 -TACTTCAATTTCAA-CGGATAGGAAATGAC-TTGCTCT
*
42881904 TACTTCATTTTCAA
1 TACTTCAATTTCAA
42881918 AGATAAAGAC
Statistics
Matches: 591, Mismatches: 122, Indels: 198
0.65 0.13 0.22
Matches are distributed among these distances:
35 18 0.03
36 50 0.08
37 94 0.16
38 267 0.45
39 88 0.15
40 58 0.10
41 16 0.03
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (36 bp):
TACTTCAATTTCAACGGATAGGAAATGACTTGCTCT
Found at i:42893891 original size:29 final size:29
Alignment explanation
Indices: 42893859--42894087 Score: 157
Period size: 29 Copynumber: 7.8 Consensus size: 29
42893849 TTTTGGATAC
*
42893859 TCGGGGGCAAAATGGTAATTTTGGTGAAA
1 TCGGGGGAAAAATGGTAATTTTGGTGAAA
* * **
42893888 TCGGGGTTAAAAATGG-AATTTTGGAGAGT
1 TCGGGG-GAAAAATGGTAATTTTGGTGAAA
* *
42893917 TCGGGGGTAAAATAGTAATTTTGGTGAAA
1 TCGGGGGAAAAATGGTAATTTTGGTGAAA
*
42893946 TCGGGGTTAAAAATGG-AATTTT-G-GAAA
1 TCGGGG-GAAAAATGGTAATTTTGGTGAAA
* *
42893973 GTTAGGGGGTAAAATGGTAATTTTTGGTGAAA
1 --TCGGGGGAAAAATGGTAA-TTTTGGTGAAA
* * *
42894005 TCGGGGTTAAAAATGG-AATTTTAG-AAAA
1 TCGGGG-GAAAAATGGTAATTTTGGTGAAA
* * *
42894033 CTTGGGGGTAAAATGGTATTTTTTGGTGAAA
1 -TCGGGGGAAAAATGGTA-ATTTTGGTGAAA
* **
42894064 TTAGGGTTAAAAATGG-AATTTTGG
1 -TCGGGGGAAAAATGGTAATTTTGG
42894088 AAAGTTTGGG
Statistics
Matches: 152, Mismatches: 34, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
27 4 0.03
28 24 0.16
29 68 0.45
30 30 0.20
31 22 0.14
32 4 0.03
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.32
Consensus pattern (29 bp):
TCGGGGGAAAAATGGTAATTTTGGTGAAA
Found at i:42893921 original size:58 final size:58
Alignment explanation
Indices: 42893825--42894113 Score: 386
Period size: 58 Copynumber: 5.0 Consensus size: 58
42893815 GAAGAAACGA
* * * * * *
42893825 TGAAATCGGGGTTGAAAATAAGACTTTTGGATA-CTCGGGGGCAAAATGGTAATTTTGG
1 TGAAATCGGGGTTAAAAAT-GGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGG
* *
42893883 TGAAATCGGGGTTAAAAATGGAATTTTGGAGAGTTCGGGGGTAAAATAGTAATTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGG
*
42893941 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTAGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAA-TTTTGG
* * *
42894000 TGAAATCGGGGTTAAAAATGGAATTTTAGAAAACTT-GGGGGTAAAATGGTATTTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTT-GGAAAGTTCGGGGGTAAAATGGTA-ATTTTGG
** *
42894059 TGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGG-AATTTT
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTT
42894114 TGGAAGTTTC
Statistics
Matches: 208, Mismatches: 18, Indels: 11
0.88 0.08 0.05
Matches are distributed among these distances:
57 14 0.07
58 96 0.46
59 92 0.44
60 6 0.03
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.32
Consensus pattern (58 bp):
TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGG
Found at i:42894103 original size:29 final size:28
Alignment explanation
Indices: 42893897--42894122 Score: 142
Period size: 29 Copynumber: 7.8 Consensus size: 28
42893887 ATCGGGGTTA
* *
42893897 AAAATGGAATTTTGGAGAGTTCGGGGGT
1 AAAATGGAATTTTGGAAAGTTTGGGGGT
* * *
42893925 AAAATAGTAATTTTGGTGAAA--TCGGGGTT
1 AAAAT-GGAATTTT-G-GAAAGTTTGGGGGT
*
42893954 AAAAATGGAATTTTGGAAAGTTAGGGGGT
1 -AAAATGGAATTTTGGAAAGTTTGGGGGT
* *
42893983 AAAATGGTAATTTTTGGTGAAA--TCGGGGTT
1 AAAATGG-AA-TTTT-G-GAAAGTTTGGGGGT
* **
42894013 AAAAATGGAATTTTAGAAAACTTGGGGGT
1 -AAAATGGAATTTTGGAAAGTTTGGGGGT
* * *
42894042 AAAATGGTATTTTTTGGTGAAA--TTAGGGTT
1 AAAATGG-A-ATTTT-G-GAAAGTTTGGGGGT
42894072 AAAAATGGAATTTTGGAAAGTTTGGGGGT
1 -AAAATGGAATTTTGGAAAGTTTGGGGGT
42894101 AAAATGGAATTTTTGG-AAGTTT
1 AAAATGGAA-TTTTGGAAAGTTT
42894123 CGAGGTCAGA
Statistics
Matches: 159, Mismatches: 18, Indels: 42
0.73 0.08 0.19
Matches are distributed among these distances:
27 12 0.08
28 36 0.23
29 56 0.35
30 29 0.18
31 18 0.11
32 8 0.05
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTGGGGGT
Found at i:42894135 original size:29 final size:29
Alignment explanation
Indices: 42894073--42894128 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
42894063 ATTAGGGTTA
* *
42894073 AAAATGGAA-TTTTGGAAAGTTTGGGGGT
1 AAAATGGAATTTTTGGAAAGTTTCGAGGT
42894101 AAAATGGAATTTTTGG-AAGTTTCGAGGT
1 AAAATGGAATTTTTGGAAAGTTTCGAGGT
42894129 CAGAATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.32, C:0.02, G:0.32, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAAGTTTCGAGGT
Found at i:42894907 original size:24 final size:25
Alignment explanation
Indices: 42894880--42894926 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
42894870 TCTTTTTCTT
42894880 TAAAATCCTTTTTTAT-TTTAAAAC
1 TAAAATCCTTTTTTATCTTTAAAAC
* *
42894904 TAAACTCCTTTTTTTTCTTTAAA
1 TAAAATCCTTTTTTATCTTTAAA
42894927 GACCAAACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (25 bp):
TAAAATCCTTTTTTATCTTTAAAAC
Found at i:42894934 original size:26 final size:24
Alignment explanation
Indices: 42894885--42894934 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
42894875 TTCTTTAAAA
*
42894885 TCCTTTTTTATTTTAAAACTAAAC
1 TCCTTTTTTATTTTAAAACCAAAC
*
42894909 TCCTTTTTTTTCTTTAAAGACCAAAC
1 TCCTTTTTTAT-TTTAAA-ACCAAAC
42894935 CCAGATCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 6 0.27
26 6 0.27
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (24 bp):
TCCTTTTTTATTTTAAAACCAAAC
Found at i:42895222 original size:13 final size:13
Alignment explanation
Indices: 42895204--42895262 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
42895194 ATTGGTTGAT
42895204 ATTATTAATTATTA
1 ATTATTAA-TATTA
42895218 A-TATTAAT-TATA
1 ATTATTAATAT-TA
* *
42895230 ATTATAAATATTT
1 ATTATTAATATTA
* *
42895243 ATTACTATTATTA
1 ATTATTAATATTA
42895256 ATTATTA
1 ATTATTA
42895263 TGACTATTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
11 1 0.03
12 4 0.11
13 28 0.80
14 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATTAATATTA
Found at i:42895231 original size:6 final size:7
Alignment explanation
Indices: 42895204--42895262 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 7
42895194 ATTGGTTGAT
42895204 ATTATTA
1 ATTATTA
42895211 ATTATTA
1 ATTATTA
42895218 A-TATTA
1 ATTATTA
42895224 ATTA-TA
1 ATTATTA
42895230 ATTA-TA
1 ATTATTA
* *
42895236 AATATTT
1 ATTATTA
*
42895243 ATTACT-
1 ATTATTA
42895249 ATTATTA
1 ATTATTA
42895256 ATTATTA
1 ATTATTA
42895263 TGACTATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 22 0.50
7 22 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (7 bp):
ATTATTA
Found at i:42895233 original size:19 final size:20
Alignment explanation
Indices: 42895204--42895279 Score: 70
Period size: 19 Copynumber: 4.0 Consensus size: 20
42895194 ATTGGTTGAT
*
42895204 ATTATTAATTATTAATATTA
1 ATTACTAATTATTAATATTA
* *
42895224 ATTA-TAATTATAAATATTT
1 ATTACTAATTATTAATATTA
42895243 ATTACT-ATTATTAATTATT-
1 ATTACTAATTATTAA-TATTA
* *
42895262 ATGACT-ATTAATAATATT
1 ATTACTAATTATTAATATT
42895280 TTTATTAATG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
18 4 0.08
19 36 0.73
20 9 0.18
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (20 bp):
ATTACTAATTATTAATATTA
Found at i:42895994 original size:6 final size:6
Alignment explanation
Indices: 42895985--42896060 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
42895975 TTAATATTAT
**
42895985 TTTAAA TTTAAA TTTAAA -ACAAA TTTAAATA TTTAAA TTTAAGA --TAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA-A TTTAAA TTTAA-A TTTAAA
* * *
42896033 TTTAAA TTCAAA -ATAAA TTTAAA ATTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
42896061 TTTGAACTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
4 1 0.02
5 9 0.17
6 35 0.65
7 5 0.09
8 4 0.07
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:42896024 original size:25 final size:25
Alignment explanation
Indices: 42895990--42896039 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
42895980 ATTATTTTAA
42895990 ATTTAAATTTAAAACAAATTTAAAT
1 ATTTAAATTTAAAACAAATTTAAAT
* *
42896015 ATTTAAATTTAAGATAAATTTAAAT
1 ATTTAAATTTAAAACAAATTTAAAT
42896040 TCAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTTAAATTTAAAACAAATTTAAAT
Found at i:42896037 original size:17 final size:17
Alignment explanation
Indices: 42896015--42896060 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
42896005 AAATTTAAAT
*
42896015 ATTTAAATTTAAGATAA
1 ATTTAAATTTAAAATAA
*
42896032 ATTTAAATTCAAAATAA
1 ATTTAAATTTAAAATAA
*
42896049 ATTTAAAATTAA
1 ATTTAAATTTAA
42896061 TTTGAACTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:42896073 original size:28 final size:28
Alignment explanation
Indices: 42895993--42896063 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 28
42895983 ATTTTAAATT
* **
42895993 TAAATTTAAAACAAATTTAAA-T--ATT
1 TAAATTTAAAATAAATTTAAATTCAAAA
*
42896018 TAAATTTAAGATAAATTTAAATTCAAAA
1 TAAATTTAAAATAAATTTAAATTCAAAA
*
42896046 TAAATTTAAAATTAATTT
1 TAAATTTAAAATAAATTT
42896064 GAACTTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
25 19 0.51
26 1 0.03
28 17 0.46
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (28 bp):
TAAATTTAAAATAAATTTAAATTCAAAA
Found at i:42904932 original size:24 final size:24
Alignment explanation
Indices: 42904904--42904973 Score: 95
Period size: 25 Copynumber: 2.9 Consensus size: 24
42904894 AACTTTTTAG
*
42904904 TTAAATTCTGTTTATTTGTTTCAA
1 TTAAATTCTATTTATTTGTTTCAA
* *
42904928 TTAAAACTCTATTTATTTGTTTTAA
1 TT-AAATTCTATTTATTTGTTTCAA
*
42904953 TTAAATTCTAATTATTTGTTT
1 TTAAATTCTATTTATTTGTTT
42904974 GAATCAAGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.47
25 21 0.52
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.59
Consensus pattern (24 bp):
TTAAATTCTATTTATTTGTTTCAA
Found at i:42904990 original size:24 final size:24
Alignment explanation
Indices: 42904915--42904990 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
42904905 TAAATTCTGT
* * *
42904915 TTATTTGTTTCAATTAAAACTCTAT
1 TTATTTGTTTGAA-TCAAACTCTAA
* * *
42904940 TTATTTGTTTTAATTAAATTCTAA
1 TTATTTGTTTGAATCAAACTCTAA
* *
42904964 TTATTTGTTTGAATCAAGCTCTTA
1 TTATTTGTTTGAATCAAACTCTAA
42904988 TTA
1 TTA
42904991 GTCTAGAGTA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 30 0.71
25 12 0.29
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (24 bp):
TTATTTGTTTGAATCAAACTCTAA
Found at i:42906265 original size:25 final size:25
Alignment explanation
Indices: 42906220--42906267 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
42906210 ATAAAATATA
* *
42906220 AATTTAATAGATATAAAATAAACTC
1 AATTAAATAGATAAAAAATAAACTC
42906245 AATTAAATA-ATAAAAAGATAAAC
1 AATTAAATAGATAAAAA-ATAAAC
42906268 AATTCCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
AATTAAATAGATAAAAAATAAACTC
Found at i:42907822 original size:82 final size:82
Alignment explanation
Indices: 42907717--42908035 Score: 314
Period size: 82 Copynumber: 3.9 Consensus size: 82
42907707 AAAAGGTAAA
* * *
42907717 TCATTAGCGGCGC-TTACACAAAGCGCCGCTAAAGGTCGGGTCTTTAGCGGTGCTTTACCCACAA
1 TCATTAGCGGCGCTTTACA-AAAGCGCCGCTAAAGGTCGGGTCTTTAGCGGCGCTTTAACTACAA
42907781 GCGCCGCTAAAGGTCGAG
65 GCGCCGCTAAAGGTCGAG
* *
42907799 TCATTAGCGGCGCTTTACAAAAGCGCCGCTAAAAGTCGGGT-TATTAGCGGCGC-TTAACTACAT
1 TCATTAGCGGCGCTTTACAAAAGCGCCGCTAAAGGTCGGGTCT-TTAGCGGCGCTTTAACTACAA
* *
42907862 GCGCCGCTAATGGTCGGG
65 GCGCCGCTAAAGGTCGAG
* ** * *
42907880 TCATTAGCGGCGCTTCACCGCAAGCGCCGCTAAAGGTCGTGTCATTAGCGGCGCTTATATA-TA-
1 TCATTAGCGGCGCTTTA-CAAAAGCGCCGCTAAAGGTCGGGTCTTTAGCGGCGCTT-TA-ACTAC
* *
42907943 AAGCGTCGGTAAAGGTC-AGG
63 AAGCGCCGCTAAAGGTCGA-G
* * * * * * *
42907963 TTATTAGCGGCGCTTTTCTAATAAGCCCCGCTAAAGGT-GTG-CATTAGCGGCGCTTT-TCTATA
1 TCATTAGCGGCGCTTTAC-AA-AAGCGCCGCTAAAGGTCGGGTCTTTAGCGGCGCTTTAACTACA
42908025 AGCGCCGCTAA
64 AGCGCCGCTAA
42908036 TTTATTTAAA
Statistics
Matches: 198, Mismatches: 27, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
80 2 0.01
81 51 0.26
82 88 0.44
83 37 0.19
84 19 0.10
85 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.24
Consensus pattern (82 bp):
TCATTAGCGGCGCTTTACAAAAGCGCCGCTAAAGGTCGGGTCTTTAGCGGCGCTTTAACTACAAG
CGCCGCTAAAGGTCGAG
Found at i:42907878 original size:41 final size:40
Alignment explanation
Indices: 42907717--42908035 Score: 284
Period size: 42 Copynumber: 7.8 Consensus size: 40
42907707 AAAAGGTAAA
42907717 TCATTAGCGGCGCTT-ACACAAAGCGCCGCTAAAGGTCGGG
1 TCATTAGCGGCGCTTAACAC-AAGCGCCGCTAAAGGTCGGG
* * * *
42907757 TCTTTAGCGGTGCTTTACCCACAAGCGCCGCTAAAGGTCGAG
1 TCATTAGCGGCGC-TTA-ACACAAGCGCCGCTAAAGGTCGGG
* * *
42907799 TCATTAGCGGCGCTTTACAAAAGCGCCGCTAAAAGTCGGG
1 TCATTAGCGGCGCTTAACACAAGCGCCGCTAAAGGTCGGG
* * *
42907839 TTATTAGCGGCGCTTAACTACATGCGCCGCTAATGGTCGGG
1 TCATTAGCGGCGCTTAAC-ACAAGCGCCGCTAAAGGTCGGG
* * *
42907880 TCATTAGCGGCGCTTCACCGCAAGCGCCGCTAAAGGTCGTG
1 TCATTAGCGGCGCTT-AACACAAGCGCCGCTAAAGGTCGGG
* * * * *
42907921 TCATTAGCGGCGCTTATATATAAAGCGTCGGTAAAGGTCAGG
1 TCATTAGCGGCGCTTA-ACA-CAAGCGCCGCTAAAGGTCGGG
* ** * * *
42907963 TTATTAGCGGCGCTTTTCTAATAAGCCCCGCTAAAGGT-GTG
1 TCATTAGCGGCGCTTAAC--ACAAGCGCCGCTAAAGGTCGGG
** *
42908004 -CATTAGCGGCGCTTTTCTATAAGCGCCGCTAA
1 TCATTAGCGGCGCTTAAC-ACAAGCGCCGCTAA
42908036 TTTATTTAAA
Statistics
Matches: 226, Mismatches: 44, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
39 13 0.06
40 64 0.28
41 70 0.31
42 75 0.33
43 4 0.02
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.24
Consensus pattern (40 bp):
TCATTAGCGGCGCTTAACACAAGCGCCGCTAAAGGTCGGG
Found at i:42907930 original size:164 final size:163
Alignment explanation
Indices: 42907717--42908036 Score: 380
Period size: 164 Copynumber: 2.0 Consensus size: 163
42907707 AAAAGGTAAA
* * *
42907717 TCATTAGCGGCGCTTACACAAAGCGCCGCTAAAGGTCGGGTCTTTAGCGGTGCTT-TACCCACAA
1 TCATTAGCGGCGCTTACACAAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTATACACA-AA
* *
42907781 GCGCCGCTAAAGGTC-GAGTCATTAGCGGCGCTTTAC-AA-AAGCGCCGCTAAAAGTCGGGTTAT
65 GCGCCGCTAAAGGTCAG-GTCATTAGCGGCGCTTTACTAATAAGCCCCGCTAAAAGT-GGG-CAT
*
42907843 TAGCGGCGCTTAACTACATGCGCCGCTAATGGTCGGG
127 TAGCGGCGCTTAACTACAAGCGCCGCTAATGGTCGGG
* * * *
42907880 TCATTAGCGGCGCTT-CACCGCAAGCGCCGCTAAAGGTCGTGTCATTAGCGGCGCTTATATATAA
1 TCATTAGCGGCGCTTACA-C-AAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTATACACAA
* * * * * *
42907944 AGCGTCGGTAAAGGTCAGGTTATTAGCGGCGCTTTTCTAATAAGCCCCGCTAAAGGTGTGCATTA
64 AGCGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTACTAATAAGCCCCGCTAAAAGTGGGCATTA
** *
42908009 GCGGCGCTTTTCTATAAGCGCCGCTAAT
129 GCGGCGCTTAACTACAAGCGCCGCTAAT
42908037 TTATTTAAAT
Statistics
Matches: 132, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
162 2 0.02
163 16 0.12
164 92 0.70
165 8 0.06
166 14 0.11
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.24
Consensus pattern (163 bp):
TCATTAGCGGCGCTTACACAAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTATACACAAAG
CGCCGCTAAAGGTCAGGTCATTAGCGGCGCTTTACTAATAAGCCCCGCTAAAAGTGGGCATTAGC
GGCGCTTAACTACAAGCGCCGCTAATGGTCGGG
Found at i:42908210 original size:44 final size:44
Alignment explanation
Indices: 42908160--42908306 Score: 183
Period size: 44 Copynumber: 3.3 Consensus size: 44
42908150 CCTCCAAATC
* * *
42908160 GCAGAACCCTCTGT-TGTTTCCCTCACTCCGTTGCCTCTTCACCT
1 GCAGAACCCGCT-TCTGTTCCCCTCACTCCGTTCCCTCTTCACCT
*
42908204 GCAGAACCCGCTTCTGTTCCCCTCACCCCGTTCCCTCTTCACCCT
1 GCAGAACCCGCTTCTGTTCCCCTCACTCCGTTCCCTCTTCA-CCT
* *
42908249 -CAAAACCCGCTTCTCTTCCCCTCACTCCGTTCCCTCTTCACC-
1 GCAGAACCCGCTTCTGTTCCCCTCACTCCGTTCCCTCTTCACCT
*
42908291 CCTAGAACCCGCTTCT
1 GC-AGAACCCGCTTCT
42908307 TGAGCCGATC
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
43 4 0.04
44 84 0.92
45 3 0.03
ACGTcount: A:0.13, C:0.48, G:0.10, T:0.29
Consensus pattern (44 bp):
GCAGAACCCGCTTCTGTTCCCCTCACTCCGTTCCCTCTTCACCT
Found at i:42908287 original size:21 final size:20
Alignment explanation
Indices: 42908220--42908287 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 20
42908210 CCCGCTTCTG
42908220 TTCCCCTCACCCCGTTCCCTC
1 TTCCCCTCA-CCCGTTCCCTC
42908241 TTCACCCTCAAAACCCGCTT--CTC
1 TTC-CCCTC---ACCCG-TTCCCTC
42908264 TTCCCCTCACTCCGTTCCCTC
1 TTCCCCTCAC-CCGTTCCCTC
42908285 TTC
1 TTC
42908288 ACCCCTAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
19 4 0.10
20 3 0.08
21 9 0.23
22 10 0.26
23 6 0.15
24 4 0.10
25 3 0.08
ACGTcount: A:0.10, C:0.54, G:0.04, T:0.31
Consensus pattern (20 bp):
TTCCCCTCACCCGTTCCCTC
Found at i:42909032 original size:21 final size:21
Alignment explanation
Indices: 42909008--42909077 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
42908998 AGATGATGTG
42909008 GACGTGCCTTATATGGTGGGA
1 GACGTGCCTTATATGGTGGGA
* * * *
42909029 GACGATGCTTTAGAAGATGATGTG-
1 GACG-TGCCTT---ATATGGTGGGA
*
42909053 GACGTGCCTTGTATGGTGGGA
1 GACGTGCCTTATATGGTGGGA
42909074 GACG
1 GACG
42909078 ATGCTTTCTC
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
20 6 0.17
21 8 0.23
22 5 0.14
23 5 0.14
24 4 0.11
25 7 0.20
ACGTcount: A:0.21, C:0.13, G:0.39, T:0.27
Consensus pattern (21 bp):
GACGTGCCTTATATGGTGGGA
Found at i:42909044 original size:45 final size:45
Alignment explanation
Indices: 42908994--42909084 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
42908984 GGAGAGGGAG
42908994 TAGAAGATGATGTGGACGTGCCTTATATGGTGGGAGACGATGCTT
1 TAGAAGATGATGTGGACGTGCCTTATATGGTGGGAGACGATGCTT
*
42909039 TAGAAGATGATGTGGACGTGCCTTGTATGGTGGGAGACGATGCTT
1 TAGAAGATGATGTGGACGTGCCTTATATGGTGGGAGACGATGCTT
42909084 T
1 T
42909085 CTCTTTATCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (45 bp):
TAGAAGATGATGTGGACGTGCCTTATATGGTGGGAGACGATGCTT
Found at i:42914573 original size:5 final size:5
Alignment explanation
Indices: 42914551--42914620 Score: 58
Period size: 5 Copynumber: 14.4 Consensus size: 5
42914541 TTTAAGAATG
* * *
42914551 AAAGTA AAAGA CAAGA AATGA AAAG- AAAGA AAAG- AAAGA AAGAGA AATGA
1 AAAG-A AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA-AGA AAAGA
*
42914601 AAAG- AAAGA ACA-A AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AA
42914621 GAGAGAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
4 15 0.29
5 27 0.53
6 9 0.18
ACGTcount: A:0.73, C:0.03, G:0.20, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:42914577 original size:29 final size:29
Alignment explanation
Indices: 42914564--42914624 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
42914554 GTAAAAGACA
42914564 AGAAATGAAAAGAAAGAAAAGAAAGAAAG
1 AGAAATGAAAAGAAAGAAAAGAAAGAAAG
42914593 AGAAATGAAAAGAAAGAACAA-AAAGAAAG
1 AGAAATGAAAAGAAAGAA-AAGAAAGAAAG
42914622 AGA
1 AGA
42914625 GAAAAAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 29 0.94
30 2 0.06
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.03
Consensus pattern (29 bp):
AGAAATGAAAAGAAAGAAAAGAAAGAAAG
Found at i:42914578 original size:10 final size:9
Alignment explanation
Indices: 42914557--42914634 Score: 79
Period size: 10 Copynumber: 8.3 Consensus size: 9
42914547 AATGAAAGTA
*
42914557 AAAGACAAG
1 AAAGAAAAG
42914566 AAATGAAAAG
1 AAA-GAAAAG
42914576 AAAGAAAAG
1 AAAGAAAAG
42914585 AAAGAAAGAG
1 AAAGAAA-AG
42914595 AAATGAAAAG
1 AAA-GAAAAG
42914605 AAAGAACAA-
1 AAAGAA-AAG
42914614 AAAG-AAAG
1 AAAGAAAAG
*
42914622 AGAGAAAAAG
1 AAAG-AAAAG
42914632 AAA
1 AAA
42914635 CTTTTAGAAC
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
7 2 0.03
8 4 0.07
9 23 0.39
10 26 0.44
11 4 0.07
ACGTcount: A:0.73, C:0.03, G:0.22, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:42926316 original size:22 final size:23
Alignment explanation
Indices: 42926291--42926364 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 23
42926281 TATTTTGATT
42926291 TTTTA-AAATTTATAATAATATA
1 TTTTATAAATTTATAATAATATA
*
42926313 TTTTATAATTTTATAATACAT-TA
1 TTTTATAAATTTATAATA-ATATA
*
42926336 TTTTTAATAAATTTAT-ATATTATA
1 -TTTT-ATAAATTTATAATAATATA
42926360 TTTTA
1 TTTTA
42926365 ATCAATATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
22 6 0.14
23 18 0.41
24 11 0.25
25 9 0.20
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTATAAATTTATAATAATATA
Found at i:42926316 original size:23 final size:24
Alignment explanation
Indices: 42926290--42926363 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
42926280 TTATTTTGAT
42926290 TTTTTA-AAATTTATAATAATATA
1 TTTTTATAAATTTATAATAATATA
*
42926313 -TTTTATAATTTTATAATACAT-TA
1 TTTTTATAAATTTATAATA-ATATA
*
42926336 TTTTTAATAAATTTAT-ATATTATA
1 TTTTT-ATAAATTTATAATAATATA
42926360 TTTT
1 TTTT
42926364 AATCAATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
22 5 0.12
23 14 0.33
24 15 0.35
25 9 0.21
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTTATAAATTTATAATAATATA
Found at i:42926377 original size:24 final size:23
Alignment explanation
Indices: 42926324--42926379 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
42926314 TTTATAATTT
*
42926324 TATAATACATTATTTTTAATAAA
1 TATAATATATTATTTTTAATAAA
* *
42926347 T-TTATATATTATATTTTAATCAA
1 TATAATATATTAT-TTTTAATAAA
42926370 TATAATATAT
1 TATAATATAT
42926380 ATAGTACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 9 0.33
23 11 0.41
24 7 0.26
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
TATAATATATTATTTTTAATAAA
Found at i:42927089 original size:17 final size:17
Alignment explanation
Indices: 42927069--42927111 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
42927059 TAGTGCTCTT
42927069 TAAAAGTACTTTTG-AC
1 TAAAAGTACTTTTGAAC
*
42927085 ATAAAAAGTAGTTTTGAAC
1 -T-AAAAGTACTTTTGAAC
42927104 TAAAAGTA
1 TAAAAGTA
42927112 ATGTTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 13 0.57
19 2 0.09
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.33
Consensus pattern (17 bp):
TAAAAGTACTTTTGAAC
Found at i:42929297 original size:37 final size:37
Alignment explanation
Indices: 42929253--42929327 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
42929243 GGATATCAAA
42929253 ACTCCTTTCTTTTCTATGTCTTTCTTTGCTGAAAACG
1 ACTCCTTTCTTTTCTATGTCTTTCTTTGCTGAAAACG
42929290 ACTCCTTTCTTTTCTATGTCTTTCTTTGCTGAAAACG
1 ACTCCTTTCTTTTCTATGTCTTTCTTTGCTGAAAACG
42929327 A
1 A
42929328 GACTGTTGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.17, C:0.24, G:0.11, T:0.48
Consensus pattern (37 bp):
ACTCCTTTCTTTTCTATGTCTTTCTTTGCTGAAAACG
Found at i:42929647 original size:50 final size:50
Alignment explanation
Indices: 42929489--42929650 Score: 168
Period size: 50 Copynumber: 3.2 Consensus size: 50
42929479 CACACGAGCA
** *
42929489 GACACACGGGAGTGTGTCCAGGCCGTGTAACTCATTGTTTGTGTAATAAG
1 GACACACGGGCTTGTGTCCAGGCCGTGTAACTCATTGTTTGTGTATTAAG
* * * * ** *
42929539 GCCACACGAG-TGTCTGTTCAGGCCGTGTAACTCCCTGTTT-TGAATATT-TG
1 GACACACGGGCT-TGTGTCCAGGCCGTGTAACTCATTGTTTGTG--TATTAAG
*
42929589 GACACACGGGCTTGTGTCCAGGTCGTGTAACTCATTGTTTGTGTATTAAG
1 GACACACGGGCTTGTGTCCAGGCCGTGTAACTCATTGTTTGTGTATTAAG
*
42929639 GTCACACGGGCT
1 GACACACGGGCT
42929651 GACACATGAG
Statistics
Matches: 88, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
49 6 0.07
50 76 0.86
51 6 0.07
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (50 bp):
GACACACGGGCTTGTGTCCAGGCCGTGTAACTCATTGTTTGTGTATTAAG
Found at i:42942117 original size:16 final size:16
Alignment explanation
Indices: 42942084--42942117 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42942074 TAATAAATTG
* *
42942084 AATAAATAAATAACCA
1 AATAAATAAAGAAACA
42942100 AATAAATAAAGAAACA
1 AATAAATAAAGAAACA
42942116 AA
1 AA
42942118 CAAACAAACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.15
Consensus pattern (16 bp):
AATAAATAAAGAAACA
Found at i:42942509 original size:30 final size:30
Alignment explanation
Indices: 42942255--42942499 Score: 311
Period size: 30 Copynumber: 8.2 Consensus size: 30
42942245 TAAAACCAGA
* * *
42942255 TCAAATTTGAATTTTTGGAAGGTTTAAGGG
1 TCAAATTTGAATTTTTGAAAAGTTTGAGGG
* **
42942285 TCAAATTAGAATTTTTGAAAAGTTCAAGGG
1 TCAAATTTGAATTTTTGAAAAGTTTGAGGG
42942315 TCAAATTTGAATTTTT-AGAAA-TTCT-AGGGG
1 TCAAATTTGAATTTTTGA-AAAGTT-TGA-GGG
* *
42942345 TTAAATTGGAATTTTTGAAAAGTTT-AGGG
1 TCAAATTTGAATTTTTGAAAAGTTTGAGGG
* *
42942374 GCTAAATTTAAATTTTTGAAAAGTTTGAGGG
1 TC-AAATTTGAATTTTTGAAAAGTTTGAGGG
42942405 TCAAATTTGAATTTTTGAAAAGTTTGAGGG
1 TCAAATTTGAATTTTTGAAAAGTTTGAGGG
*
42942435 TCAAATTTGAATTTTTGAAAAGTTTGAGAG
1 TCAAATTTGAATTTTTGAAAAGTTTGAGGG
42942465 TCAAATTTGAATTTTTGAAAAGTTATG-GGG
1 TCAAATTTGAATTTTTGAAAAGTT-TGAGGG
42942495 TCAAA
1 TCAAA
42942500 ACATAATTTT
Statistics
Matches: 191, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.04
30 174 0.91
31 10 0.05
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (30 bp):
TCAAATTTGAATTTTTGAAAAGTTTGAGGG
Found at i:42943649 original size:20 final size:20
Alignment explanation
Indices: 42943624--42943663 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42943614 TTATAAATAG
42943624 ATAAATAAATAAAATTAAAA
1 ATAAATAAATAAAATTAAAA
42943644 ATAAATAAATAAAATTAAAA
1 ATAAATAAATAAAATTAAAA
42943664 TAGAATTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (20 bp):
ATAAATAAATAAAATTAAAA
Found at i:42943725 original size:12 final size:12
Alignment explanation
Indices: 42943708--42943737 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
42943698 GTTTTGGGTA
42943708 TTTTATTTTATT
1 TTTTATTTTATT
42943720 TTTTATTTTATT
1 TTTTATTTTATT
42943732 TATTTA
1 T-TTTA
42943738 CTTATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:42943742 original size:17 final size:16
Alignment explanation
Indices: 42943706--42943748 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
42943696 TTGTTTTGGG
*
42943706 TATTTTATTTTATTTTT
1 TATTTTA-TTTATTTCT
42943723 TATTTTATTTATTTACT
1 TATTTTATTTATTT-CT
42943740 TATATTTAT
1 TAT-TTTAT
42943749 AAAATGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTATTTATTTCT
Found at i:42944680 original size:118 final size:118
Alignment explanation
Indices: 42944532--42944744 Score: 290
Period size: 118 Copynumber: 1.8 Consensus size: 118
42944522 CCTCTAGTTA
42944532 GGGTAAAAGATTGGATTGCTTCAATCTGCCC-CATGATCGA-GGTAAAAAATTAAATGGTCTTCA
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCTC-TGAT-GAGGGTAAAAAATTAAATGGTCTTCA
42944595 ATCTGCACTCTGATTAGGGTAAAAGATTGGATTACTTCAATCTTCCTTAAGGTCG
64 ATCTGCACTCTGATTAGGGTAAAAGATTGGATTACTTCAATCTTCCTTAAGGTCG
* * * **
42944650 GGGT-AAAGATTGG-TTGGCCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTCTTCA
1 GGGTAAAAGATTGGATT-G-CTTCAATCTGCCCTCTGATGAGGGTAAAAAATTAAATGGTCTTCA
* * *
42944713 ATTTGCCCTTTGATTAGGGTAAAAGATTGGAT
64 ATCTGCACTCTGATTAGGGTAAAAGATTGGAT
42944745 GGCTGTAACT
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
116 2 0.02
117 11 0.13
118 69 0.83
119 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (118 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCTCTGATGAGGGTAAAAAATTAAATGGTCTTCAAT
CTGCACTCTGATTAGGGTAAAAGATTGGATTACTTCAATCTTCCTTAAGGTCG
Found at i:42944704 original size:78 final size:79
Alignment explanation
Indices: 42944511--42944704 Score: 246
Period size: 79 Copynumber: 2.5 Consensus size: 79
42944501 ATTTGATAGT
* * *
42944511 CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGATCGAGGTA
1 CTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATTACTTCAATCTGCCCCAAGATCGAGGTA
*
42944576 AAAAATTAAATGGT
66 AAAAATTAAATGGC
* * * ** * *
42944590 CTTCAATCTGCACTCTGATTAGGGTAAAAGATTGGATTACTTCAATCTTCCTTAAGGTCGGGGT-
1 CTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATTACTTCAATCTGCCCCAAGATCGAGGTA
* ***
42944654 AAAGATTGGTTGGC
66 AAAAATTAAATGGC
42944668 CTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGAT
1 CTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGAT
42944705 GGTCTTCAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
78 44 0.45
79 54 0.55
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (79 bp):
CTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATTACTTCAATCTGCCCCAAGATCGAGGTA
AAAAATTAAATGGC
Found at i:42944737 original size:40 final size:40
Alignment explanation
Indices: 42944491--42944746 Score: 238
Period size: 40 Copynumber: 6.5 Consensus size: 40
42944481 TACAGCTTTA
* * *
42944491 AGGGTAAAATATTTGATAGTCTTCAATCTGCCCTCT-AGTT
1 AGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGA-TT
*
42944531 AGGGTAAAAGATTGGATTG-CTTCAATCTGCCC-CATGA-T
1 AGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TGATT
* * ** *
42944569 CGAGGTAAAAAATTAAATGGTCTTCAATCTGCACTCTGATT
1 AG-GGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGATT
* * ** * *
42944610 AGGGTAAAAGATTGGAT--TACTTCAATCTTCCTTAAGGTC
1 AGGGTAAAAGATTGGATGGT-CTTCAATCTGCCCTCTGATT
* * * *
42944649 GGGGT-AAAGATTGGTTGGCCTTCAATCTGCCCTCTGGTT
1 AGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGATT
* *
42944688 AGGGTAAAAGATTGGATGGTCTTCAATTTGCCCTTTGATT
1 AGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGATT
42944728 AGGGTAAAAGATTGGATGG
1 AGGGTAAAAGATTGGATGG
42944747 CTGTAACTTC
Statistics
Matches: 172, Mismatches: 34, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
38 14 0.08
39 63 0.37
40 92 0.53
41 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (40 bp):
AGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGATT
Found at i:42954568 original size:66 final size:66
Alignment explanation
Indices: 42954464--42954596 Score: 194
Period size: 66 Copynumber: 2.0 Consensus size: 66
42954454 TTATATATGG
* *
42954464 TTTTCGGTTCTAAAGTAATGGTACCCAAACCAGCAGATTTCACAATCCTCACCCATTATAGACTC
1 TTTTCGGTTCTAAAGTAATGGTACCCAAACCAACAGATTCCACAATCCTCACCCATTATAGACTC
42954529 A
66 A
* ** * * *
42954530 TTTTCGGTTCTAAAGTAATGGTACCCAAACCAATAGATTCCTGAGTCCTTACCCATTATAGGCTC
1 TTTTCGGTTCTAAAGTAATGGTACCCAAACCAACAGATTCCACAATCCTCACCCATTATAGACTC
42954595 A
66 A
42954596 T
1 T
42954597 ACAAACGAGT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (66 bp):
TTTTCGGTTCTAAAGTAATGGTACCCAAACCAACAGATTCCACAATCCTCACCCATTATAGACTC
A
Found at i:42957031 original size:17 final size:18
Alignment explanation
Indices: 42957000--42957046 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
42956990 ATTTGATTTG
* *
42957000 TATTTGTTTAGTTTT-AT
1 TATTTATTTATTTTTCAT
42957017 TATTTATTTATTTTTCAT
1 TATTTATTTATTTTTCAT
*
42957035 T-TGTATTTATTT
1 TATTTATTTATTT
42957047 ATATAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 23 0.88
18 3 0.12
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.72
Consensus pattern (18 bp):
TATTTATTTATTTTTCAT
Found at i:42957072 original size:18 final size:18
Alignment explanation
Indices: 42957049--42957094 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
42957039 ATTTATTTAT
42957049 ATAAATAAATACAAACGA
1 ATAAATAAATACAAACGA
42957067 ATAAATAAATACAAACGA
1 ATAAATAAATACAAACGA
42957085 A-AAATAAATA
1 ATAAATAAATA
42957095 AATTAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.70, C:0.09, G:0.04, T:0.17
Consensus pattern (18 bp):
ATAAATAAATACAAACGA
Found at i:42960252 original size:21 final size:21
Alignment explanation
Indices: 42960222--42960276 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
42960212 TTCTATAAAA
* *
42960222 TATTATAATTTATTTATTTTT
1 TATTAAAATTTATTTAATTTT
*
42960243 TATTAAAATTTA-ATAATTTT
1 TATTAAAATTTATTTAATTTT
*
42960263 T-CTAAAATTTATTT
1 TATTAAAATTTATTT
42960277 TTTATAACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 9 0.32
20 8 0.29
21 11 0.39
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTAAAATTTATTTAATTTT
Found at i:42960506 original size:91 final size:93
Alignment explanation
Indices: 42960304--42960528 Score: 279
Period size: 91 Copynumber: 2.5 Consensus size: 93
42960294 ATTTTTAAAG
* * * *
42960304 AGCAATGGCTTAATTGC--TTTTTTGAA-AAATTTTGAGGG-TCTTTTTTATGCATTTTGAAAGT
1 AGCAGTGGCTTAATTGCTTTTTTTTTAAGAAAGTTTGAGGGCTTTTTTTTATGCATTTTGAAAGT
* *
42960365 TCAAGTACCTAATTGAGTGGAGAAAAAA
66 TCAAGTACCTAATTGAATGCAGAAAAAA
*
42960393 AGCAGTGGCTTAATTGCTTTTTTTTTAAG-AAGTTTGAGGGCTTTTTTTTTTGCATTTTGAAAGT
1 AGCAGTGGCTTAATTGCTTTTTTTTTAAGAAAGTTTGAGGGCTTTTTTTTATGCATTTTGAAAGT
*
42960457 TCAAGT-GCTCAATTGAATGCA-AAAAAA
66 TCAAGTACCT-AATTGAATGCAGAAAAAA
* *
42960484 AG-AG-GGACTTAATTGCTTTTTTTTTGAGAAAGTTTGAGAGCTTTT
1 AGCAGTGG-CTTAATTGCTTTTTTTTTAAGAAAGTTTGAGGGCTTTT
42960529 ACACCCTTAA
Statistics
Matches: 119, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
89 18 0.15
90 22 0.18
91 43 0.36
92 36 0.30
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (93 bp):
AGCAGTGGCTTAATTGCTTTTTTTTTAAGAAAGTTTGAGGGCTTTTTTTTATGCATTTTGAAAGT
TCAAGTACCTAATTGAATGCAGAAAAAA
Found at i:42961859 original size:22 final size:22
Alignment explanation
Indices: 42961822--42961878 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
42961812 TGTAATTTAA
*
42961822 AAAAGTTTAAAA-ATATCTTTTAT
1 AAAA-TTTAAAATATAT-TATTAT
*
42961845 AAAATTCTAAAATATATTATTCT
1 AAAATT-TAAAATATATTATTAT
42961868 AAAATTTAAAA
1 AAAATTTAAAA
42961879 AAAGTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 7 0.23
23 19 0.63
24 4 0.13
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAATTTAAAATATATTATTAT
Found at i:42961948 original size:18 final size:18
Alignment explanation
Indices: 42961916--42961969 Score: 81
Period size: 19 Copynumber: 2.9 Consensus size: 18
42961906 ACTTGAAATT
42961916 TATTTTTTAATTTTTATAA
1 TATTTTTTAATTTTTAT-A
42961935 TATTTTTTAATTTTTATA
1 TATTTTTTAATTTTTATA
*
42961953 TATTATTTTGATTTTTA
1 TATT-TTTTAATTTTTA
42961970 AAAATCTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 5 0.15
19 28 0.85
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TATTTTTTAATTTTTATA
Found at i:42962274 original size:6 final size:6
Alignment explanation
Indices: 42962265--42962346 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
42962255 TTATTTTTGT
** * * *
42962265 TTTAAA TTTAAA GCTAAA TTT-AA TTTGAG TTTAAA TTTAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
42962312 TTT-AA TTTGAG TTTAAA TTT-AT TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
42962347 ATTATTATAA
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
5 14 0.24
6 40 0.69
7 4 0.07
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:42962299 original size:17 final size:17
Alignment explanation
Indices: 42962279--42962332 Score: 73
Period size: 17 Copynumber: 3.5 Consensus size: 17
42962269 AATTTAAAGC
42962279 TAAATTTAATTTGAGTT
1 TAAATTTAATTTGAGTT
42962296 TAAATTTAA----AG-T
1 TAAATTTAATTTGAGTT
42962308 TAAATTTAATTTGAGTT
1 TAAATTTAATTTGAGTT
42962325 TAAATTTA
1 TAAATTTA
42962333 TTTTCAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 10 0.31
13 2 0.06
16 2 0.06
17 18 0.56
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (17 bp):
TAAATTTAATTTGAGTT
Found at i:42962345 original size:29 final size:29
Alignment explanation
Indices: 42962265--42962332 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
42962255 TTATTTTTGT
*
42962265 TTTAAATTTAAAGCTAAATTTAATTTGAG
1 TTTAAATTTAAAGTTAAATTTAATTTGAG
42962294 TTTAAATTTAAAGTTAAATTTAATTTGAG
1 TTTAAATTTAAAGTTAAATTTAATTTGAG
42962323 TTTAAATTTA
1 TTTAAATTTA
42962333 TTTTCAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (29 bp):
TTTAAATTTAAAGTTAAATTTAATTTGAG
Found at i:42962360 original size:17 final size:18
Alignment explanation
Indices: 42962323--42962362 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
42962313 TTAATTTGAG
* *
42962323 TTTAAATTTATTTTCAAA
1 TTTAAAATTATTATCAAA
42962341 TTTAAAATTATTAT-AAA
1 TTTAAAATTATTATCAAA
42962358 TTTAA
1 TTTAA
42962363 TTAAAATGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAAATTATTATCAAA
Found at i:42962385 original size:14 final size:15
Alignment explanation
Indices: 42962361--42962397 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
42962351 TTATAAATTT
42962361 AATTA-AAATGTC-A
1 AATTACAAATGTCTA
42962374 AATTACAAATGTCTA
1 AATTACAAATGTCTA
42962389 AATTACAAA
1 AATTACAAA
42962398 GGTCCAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 7 0.32
15 10 0.45
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (15 bp):
AATTACAAATGTCTA
Found at i:42964310 original size:56 final size:57
Alignment explanation
Indices: 42964241--42964451 Score: 230
Period size: 59 Copynumber: 3.7 Consensus size: 57
42964231 TTAAACTGGC
* * * * * *
42964241 CAAAAATTGTATTTTGACCCCCAAACTTCTCCAAAATTGCATTTT-TCCT-TAACTTT
1 CAAAAATTCTATTTTGACCCCAAAACTTC-CAAAAATTACATTTTGCCCTCAAACTTT
42964297 CAAAAATTCTATTTTGACCCCAAAACTTCCAAAAATTACATTTTGCCCTCAAACTTT
1 CAAAAATTCTATTTTGACCCCAAAACTTCCAAAAATTACATTTTGCCCTCAAACTTT
* * * * * *
42964354 CAAAATTTTTCATTTTTGACCCTAAAACTTCCAAAAATTACATTTTGCCCCCGAACTTC
1 CAAAAATTCT-A-TTTTGACCCCAAAACTTCCAAAAATTACATTTTGCCCTCAAACTTT
* * *
42964413 CAAAAATTCCATTTTTAACCCCAAAACTTTC-AAAATTAC
1 CAAAAATTCTA-TTTTGACCCCAAAACTTCCAAAAATTAC
42964452 CATTCTACCC
Statistics
Matches: 133, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
55 13 0.10
56 30 0.23
57 22 0.17
58 19 0.14
59 49 0.37
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (57 bp):
CAAAAATTCTATTTTGACCCCAAAACTTCCAAAAATTACATTTTGCCCTCAAACTTT
Found at i:42964330 original size:29 final size:28
Alignment explanation
Indices: 42964240--42964447 Score: 140
Period size: 30 Copynumber: 7.2 Consensus size: 28
42964230 CTTAAACTGG
* *
42964240 CCAAAAATTGTATTTTGACCCCCAAACTT
1 CCAAAAATT-CATTTTGACCCCAAAACTT
* * **
42964269 CTCCAAAATTGCATTTT---TCCTTAACTT
1 C-CAAAAATT-CATTTTGACCCCAAAACTT
*
42964296 TCAAAAATTCTATTTTGACCCCAAAACTT
1 CCAAAAATTC-ATTTTGACCCCAAAACTT
42964325 CCAAAAATTACATTTTG-CCCTC-AAACTT
1 CCAAAAATT-CATTTTGACCC-CAAAACTT
* * *
42964353 TCAAAATTTTTCATTTTTGACCCTAAAACTT
1 CCAAAA--ATTCA-TTTTGACCCCAAAACTT
**
42964384 CCAAAAATTACATTTTG-CCCCCGAACTT
1 CCAAAAATT-CATTTTGACCCCAAAACTT
*
42964412 CCAAAAATTCCATTTTTAACCCCAAAACTT
1 CCAAAAATT-CA-TTTTGACCCCAAAACTT
*
42964442 TCAAAA
1 CCAAAA
42964448 TTACCATTCT
Statistics
Matches: 140, Mismatches: 24, Indels: 29
0.73 0.12 0.15
Matches are distributed among these distances:
25 1 0.01
26 12 0.09
27 7 0.05
28 33 0.24
29 36 0.26
30 37 0.26
31 14 0.10
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (28 bp):
CCAAAAATTCATTTTGACCCCAAAACTT
Found at i:42964351 original size:28 final size:29
Alignment explanation
Indices: 42964240--42964427 Score: 147
Period size: 28 Copynumber: 6.6 Consensus size: 29
42964230 CTTAAACTGG
** *
42964240 CCAAAAATTGTATTTTGACCCCCAAACTT
1 CCAAAAATTACATTTTGACCCTCAAACTT
* * * *
42964269 CTCCAAAATTGCATTTT--TCCT-TAACTT
1 C-CAAAAATTACATTTTGACCCTCAAACTT
*
42964296 TCAAAAATT-CTATTTTGACCC-CAAAACTT
1 CCAAAAATTAC-ATTTTGACCCTC-AAACTT
42964325 CCAAAAATTACATTTTG-CCCTCAAACTT
1 CCAAAAATTACATTTTGACCCTCAAACTT
* * * *
42964353 TCAAAATTTTTCATTTTTGACCCTAAAACTT
1 CCAAAA-ATTACA-TTTTGACCCTCAAACTT
* *
42964384 CCAAAAATTACATTTTG-CCCCCGAACTT
1 CCAAAAATTACATTTTGACCCTCAAACTT
*
42964412 CCAAAAATTCCATTTT
1 CCAAAAATTACATTTT
42964428 TAACCCCAAA
Statistics
Matches: 127, Mismatches: 21, Indels: 23
0.74 0.12 0.13
Matches are distributed among these distances:
25 1 0.01
26 12 0.09
27 5 0.04
28 41 0.32
29 30 0.24
30 23 0.18
31 15 0.12
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
CCAAAAATTACATTTTGACCCTCAAACTT
Found at i:42964448 original size:29 final size:28
Alignment explanation
Indices: 42964291--42964461 Score: 130
Period size: 29 Copynumber: 5.9 Consensus size: 28
42964281 ATTTTTCCTT
* *
42964291 AACTTTCAAAAATTCTATTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTT-ACCCCAA
* *
42964320 AACTTCCAAAAATTACATTTTGCCCTC-A
1 AACTTCCAAAAATTCCATTTTACCC-CAA
* * * *
42964348 AACTTTCAAAATTTTTCATTTTTGACCCTAA
1 AACTTCCAAAA-ATTCCA-TTTT-ACCCCAA
* * **
42964379 AACTTCCAAAAATTACATTTTGCCCCCG
1 AACTTCCAAAAATTCCATTTTACCCCAA
42964407 AACTTCCAAAAATTCCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCA-TTTT-ACCCCAA
* *
42964437 AACTTTC-AAAATTACCATTCTACCC
1 AACTTCCAAAAATT-CCATTTTACCC
42964462 TCGGATGTCG
Statistics
Matches: 112, Mismatches: 22, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
28 37 0.33
29 40 0.36
30 21 0.19
31 14 0.12
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTACCCCAA
Found at i:42964514 original size:30 final size:28
Alignment explanation
Indices: 42964480--42964577 Score: 76
Period size: 28 Copynumber: 3.4 Consensus size: 28
42964470 CGAAAAACTT
42964480 CATTTTTGATCCCAATTTTTCTAAAATTAC
1 CATTTTT-A-CCCAATTTTTCTAAAATTAC
*** *
42964510 CA-TTTTACCCAATGACGTCTAAAATT-T
1 CATTTTTACCCAAT-TTTTCTAAAATTAC
*
42964537 CATTTTTAGCCCCAAATTTTCCTAAAATTAC
1 CATTTTTA--CCC-AATTTTTCTAAAATTAC
42964568 CA-TTTTACCC
1 CATTTTTACCC
42964578 TTAAGAGTCC
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
27 8 0.15
28 18 0.34
29 4 0.08
30 18 0.34
31 5 0.09
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (28 bp):
CATTTTTACCCAATTTTTCTAAAATTAC
Found at i:42964592 original size:58 final size:57
Alignment explanation
Indices: 42964413--42964593 Score: 172
Period size: 58 Copynumber: 3.1 Consensus size: 57
42964403 CCCGAACTTC
* * * * ** *
42964413 CAAAAATTCCATTTTTAACCCCAAAACTTTC-AAAATTACCATTCTACCCTCGGATGT
1 CAAAAATTTCATTTTTAGCCCC-AAATTTTCTAAAATTACCATTTTACCCTAAGACGT
* * *
42964470 CGAAAAACTTCATTTTT-GATCCCAATTTTTCTAAAATTACCATTTTACCC-AATGACGT
1 C-AAAAATTTCATTTTTAG-CCCCAAATTTTCTAAAATTACCATTTTACCCTAA-GACGT
*
42964528 CTAAAATTTCATTTTTAGCCCCAAATTTTCCTAAAATTACCATTTTACCCTTAAGA-GT
1 CAAAAATTTCATTTTTAGCCCCAAATTTT-CTAAAATTACCATTTTACCC-TAAGACGT
*
42964586 CCAAAATT
1 CAAAAATT
42964594 ACCATTTTGC
Statistics
Matches: 101, Mismatches: 15, Indels: 15
0.77 0.11 0.11
Matches are distributed among these distances:
57 29 0.29
58 68 0.67
59 2 0.02
60 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (57 bp):
CAAAAATTTCATTTTTAGCCCCAAATTTTCTAAAATTACCATTTTACCCTAAGACGT
Found at i:42966521 original size:39 final size:40
Alignment explanation
Indices: 42966412--42966521 Score: 168
Period size: 40 Copynumber: 2.8 Consensus size: 40
42966402 TTTGGACAGA
*
42966412 AAACACCGCAAAAGGTAAAGCAATAGTGGCGTTTTTCTAT
1 AAACACCGCAAAAGGTAAAGCAATAGTGGCGTTTTTCCAT
* *
42966452 AAACACCACAAAAGGTAAAGCAATAATGGCGTTTTTCCAT
1 AAACACCGCAAAAGGTAAAGCAATAGTGGCGTTTTTCCAT
* *
42966492 -AACATCGCAAAAGGTAAAGTAATAGTGGCG
1 AAACACCGCAAAAGGTAAAGCAATAGTGGCG
42966522 CTTATAAGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 26 0.41
40 37 0.59
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (40 bp):
AAACACCGCAAAAGGTAAAGCAATAGTGGCGTTTTTCCAT
Found at i:42966677 original size:42 final size:42
Alignment explanation
Indices: 42966560--42966693 Score: 162
Period size: 42 Copynumber: 3.2 Consensus size: 42
42966550 GAGCATTAAT
* *
42966560 GGCGTTTATAGGAAAGCACCACTAAAGATCATGTTCTTTAGC
1 GGCGTTTATAGGAAAGCACCGCTAAAGACCATGTTCTTTAGC
* *
42966602 GGCTTTTGT-GGAAAAAGCACCGCTAAAGACCATGTTCTTTAGC
1 GGCGTTTATAGG--AAAGCACCGCTAAAGACCATGTTCTTTAGC
* * * * *
42966645 GGCGTTTATAGGAAAGCGCCGTTAAAAACCATGTTCTATAGT
1 GGCGTTTATAGGAAAGCACCGCTAAAGACCATGTTCTTTAGC
42966687 GGCGTTT
1 GGCGTTT
42966694 TTCCTCATAA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
41 2 0.03
42 39 0.50
43 35 0.45
44 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (42 bp):
GGCGTTTATAGGAAAGCACCGCTAAAGACCATGTTCTTTAGC
Found at i:42969308 original size:58 final size:55
Alignment explanation
Indices: 42969236--42969430 Score: 169
Period size: 58 Copynumber: 3.4 Consensus size: 55
42969226 TAGGTTTTTA
42969236 GGGGTAAAATGGTAATTTTTGTGAAATCGAGGCTAAAAATGGAATTTGGAAAGTTT
1 GGGGTAAAATGGTAATTTTTGTGAAATCGAGG-TAAAAATGGAATTTGGAAAGTTT
* * * * *
42969292 GGGGAATAAAATGGTAAATTTTG-GCAAAACAAGGTCAAAAATGAAATTTTGGAAAGTTC
1 GGGG--TAAAATGGTAATTTTTGTG-AAATCGAGGT-AAAAATGGAA-TTTGGAAAGTTT
** * * * *
42969351 GGAGGCGAAATGGTAAGTTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTT
1 GG-GGTAAAATGGTAA-TTTTTGTGAAATCGAGG-TAAAAATGGAATTT-GGAAAGTTT
42969410 GAGGGTCAAAAT-GTAATTTTT
1 G-GGGT-AAAATGGTAATTTTT
42969431 AGAAAGTTTT
Statistics
Matches: 108, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
56 4 0.04
57 2 0.02
58 48 0.44
59 45 0.42
60 9 0.08
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.30
Consensus pattern (55 bp):
GGGGTAAAATGGTAATTTTTGTGAAATCGAGGTAAAAATGGAATTTGGAAAGTTT
Found at i:42969446 original size:30 final size:30
Alignment explanation
Indices: 42969407--42969790 Score: 400
Period size: 30 Copynumber: 12.8 Consensus size: 30
42969397 TTTAGGGAAG
*
42969407 TTTGAGGGTCAAAATGTAATTTTTAGAAAGT
1 TTTG-GGGTCAAAATATAATTTTTAGAAAGT
* *
42969438 TTTGGGGTCAAAATATAATTTTGAAAAAGT
1 TTTGGGGTCAAAATATAATTTTTAGAAAGT
* * *
42969468 TTTAGGGTCAAAATGTAATATTTAGAAAGT
1 TTTGGGGTCAAAATATAATTTTTAGAAAGT
* *
42969498 TTTAGGGTTAAAATATAATTTTTAGAAAGT
1 TTTGGGGTCAAAATATAATTTTTAGAAAGT
* *
42969528 TTTGGGGTCGAAATATAA-TTTTGGAAAAGT
1 TTTGGGGTCAAAATATAATTTTTAG-AAAGT
*
42969558 TTTGGGGTCAAAATATAA-TTTTGGAAAAGT
1 TTTGGGGTCAAAATATAATTTTTAG-AAAGT
* * * *
42969588 TTAGGGGTCAAAATGTAATTTTCAAAAAGT
1 TTTGGGGTCAAAATATAATTTTTAGAAAGT
* *
42969618 TTTGGGGTTAAAATATTATTTTT-GAAAAGT
1 TTTGGGGTCAAAATATAATTTTTAG-AAAGT
* * * *
42969648 TTTGGGGTCGAGATGTAA-TTTTGGAAAAGT
1 TTTGGGGTCAAAATATAATTTTTAG-AAAGT
** * *
42969678 TTTAAGGTTAAAATATAA-TTTTGGAAAAGT
1 TTTGGGGTCAAAATATAATTTTTAG-AAAGT
* *
42969708 TTAGGGGTCAAAATGTAATTTTTAGAAAGT
1 TTTGGGGTCAAAATATAATTTTTAGAAAGT
42969738 TTTGGGGTCAAAATATAATTTTTAGAAAGT
1 TTTGGGGTCAAAATATAATTTTTAGAAAGT
* ** *
42969768 TTTAGGGTTGAAATGTAATTTTT
1 TTTGGGGTCAAAATATAATTTTT
42969791 GGACAATTTA
Statistics
Matches: 298, Mismatches: 50, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
29 9 0.03
30 277 0.93
31 12 0.04
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (30 bp):
TTTGGGGTCAAAATATAATTTTTAGAAAGT
Found at i:42969528 original size:120 final size:119
Alignment explanation
Indices: 42969407--42969789 Score: 556
Period size: 120 Copynumber: 3.2 Consensus size: 119
42969397 TTTAGGGAAG
* * *
42969407 TTTGAGGGTCAAAATGTAATTTT-TAGAAAGTTTTGGGGTCAAAATATAATTTTGAAAAAGTTTT
1 TTTG-GGGTCGAAATGTAATTTTGGA-AAAGTTTTGGGGTCAAAATATAATTTTGGAAAAG-TTT
*
42969471 A-GGGTCAAAATGTAATATTTAGAAAGTTTTAGGGTTAAAATATAATTTTTAGAAAGT
63 AGGGGTCAAAATGTAAT-TTTAGAAAGTTTTGGGGTTAAAATATAATTTTTAGAAAGT
*
42969528 TTTGGGGTCGAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTAGG
1 TTTGGGGTCGAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTAGG
* *
42969593 GGTCAAAATGTAATTTTCAAAAAGTTTTGGGGTTAAAATATTATTTTT-GAAAAGT
66 GGTCAAAATGTAATTTT-AGAAAGTTTTGGGGTTAAAATATAATTTTTAG-AAAGT
* ** *
42969648 TTTGGGGTCGAGATGTAATTTTGGAAAAGTTTTAAGGTTAAAATATAATTTTGGAAAAGTTTAGG
1 TTTGGGGTCGAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTAGG
*
42969713 GGTCAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTTAGAAAGT
66 GGTCAAAATGTAA-TTTTAGAAAGTTTTGGGGTTAAAATATAATTTTTAGAAAGT
* *
42969768 TTTAGGGTTGAAATGTAATTTT
1 TTTGGGGTCGAAATGTAATTTT
42969790 TGGACAATTT
Statistics
Matches: 238, Mismatches: 18, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
119 8 0.03
120 220 0.92
121 10 0.04
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (119 bp):
TTTGGGGTCGAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTAGG
GGTCAAAATGTAATTTTAGAAAGTTTTGGGGTTAAAATATAATTTTTAGAAAGT
Found at i:42969803 original size:90 final size:91
Alignment explanation
Indices: 42969404--42969790 Score: 466
Period size: 90 Copynumber: 4.3 Consensus size: 91
42969394 GGATTTAGGG
* * *
42969404 AAGTTTGAGGGTCAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGA-AAAAGT
1 AAGTTTTAGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTTAGAAAAGT
* *
42969468 TTTAGGGTCAAAATGTAATATTTAG-A
66 TTTGGGGTCAAAATATAAT-TTTAGAA
* * *
42969494 AAGTTTTAGGGTTAAAATATAATTTTTAGAAAGTTTTGGGGTCGAAATATAA-TTTTGGAAAAGT
1 AAGTTTTAGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTTAGAAAAGT
*
42969558 TTTGGGGTCAAAATATAATTTTGGAA
66 TTTGGGGTCAAAATATAATTTTAGAA
* * * * *
42969584 AAG-TTTAGGGGTCAAAATGTAATTTTCAAAAAGTTTTGGGGTTAAAATATTATTTTT-GAAAAG
1 AAGTTTTA-GGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTTAGAAAAG
* * * *
42969647 TTTTGGGGTCGAGATGTAATTTTGGAA
65 TTTTGGGGTCAAAATATAATTTTAGAA
* * * * *
42969674 AAGTTTTAAGGTTAAAATATAA-TTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTTAG-AAAG
1 AAGTTTTAGGGTTAAAATGTAATTTTTAG-AAAGTTTTGGGGTCAAAATATAATTTTTAGAAAAG
42969737 TTTTGGGGTCAAAATATAATTTTTAG-A
65 TTTTGGGGTCAAAATATAA-TTTTAGAA
*
42969764 AAGTTTTAGGGTTGAAATGTAATTTTT
1 AAGTTTTAGGGTTAAAATGTAATTTTT
42969791 GGACAATTTA
Statistics
Matches: 252, Mismatches: 36, Indels: 17
0.83 0.12 0.06
Matches are distributed among these distances:
89 14 0.06
90 220 0.87
91 18 0.07
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (91 bp):
AAGTTTTAGGGTTAAAATGTAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTTAGAAAAGT
TTTGGGGTCAAAATATAATTTTAGAA
Found at i:42971798 original size:6 final size:6
Alignment explanation
Indices: 42971784--42971863 Score: 85
Period size: 6 Copynumber: 13.3 Consensus size: 6
42971774 AATGTTTAGT
* * *
42971784 ATTTTA ATTTAA ATTTAA ATTTAA ATTTAA A-GTAA ATTTAA ATAAATAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
42971833 ATTTAA ATTTAA GA--TAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA AT
42971864 AAAATCAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
4 1 0.02
5 7 0.11
6 49 0.78
7 1 0.02
8 5 0.08
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:42971837 original size:31 final size:32
Alignment explanation
Indices: 42971799--42971866 Score: 104
Period size: 31 Copynumber: 2.1 Consensus size: 32
42971789 AATTTAAATT
42971799 TAAATTTAAATTTAA-AGTAAATTTAAA-TAAA
1 TAAATTTAAATTTAAGA-TAAATTTAAATTAAA
42971830 TAAATTTAAATTTAAGATAAATTTAAATTTAAA
1 TAAATTTAAATTTAAGATAAATTTAAA-TTAAA
42971863 TAAA
1 TAAA
42971867 ATCAATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 25 0.74
32 1 0.03
33 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (32 bp):
TAAATTTAAATTTAAGATAAATTTAAATTAAA
Found at i:42971839 original size:37 final size:38
Alignment explanation
Indices: 42971793--42971876 Score: 111
Period size: 37 Copynumber: 2.2 Consensus size: 38
42971783 TATTTTAATT
42971793 TAAATTTAAATTTAA-ATTTAAA-GTAAATTTAAAT-AAA
1 TAAATTTAAATTTAAGA--TAAATGTAAATTTAAATAAAA
*
42971830 TAAATTTAAATTTAAGATAAATTTAAATTTAAATAAAA
1 TAAATTTAAATTTAAGATAAATGTAAATTTAAATAAAA
*
42971868 TCAATTTAA
1 TAAATTTAA
42971877 CTCCAAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 4 0.10
37 26 0.62
38 12 0.29
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (38 bp):
TAAATTTAAATTTAAGATAAATGTAAATTTAAATAAAA
Found at i:42971868 original size:17 final size:16
Alignment explanation
Indices: 42971784--42971866 Score: 107
Period size: 17 Copynumber: 5.1 Consensus size: 16
42971774 AATGTTTAGT
*
42971784 ATTTTAATTTAAATTTAA
1 ATTTAAATTTAAA--TAA
42971802 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAA-TAA
42971819 ATTTAAA--TAAATAA
1 ATTTAAATTTAAATAA
42971833 ATTTAAATTTAAGATAA
1 ATTTAAATTTAA-ATAA
42971850 ATTTAAATTTAAATAA
1 ATTTAAATTTAAATAA
42971866 A
1 A
42971867 ATCAATTTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
14 10 0.17
15 4 0.07
16 8 0.13
17 26 0.43
18 12 0.20
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:42972336 original size:37 final size:37
Alignment explanation
Indices: 42972287--42972617 Score: 211
Period size: 37 Copynumber: 9.4 Consensus size: 37
42972277 ATCTTGCTCT
42972287 TACTTCAATTTCAGAGATAAAGACATGTTATCCACTC
1 TACTTCAATTTCAGAGATAAAGACATGTTATCCACTC
*** * * *
42972324 TACTTCAATTTCA-AGGGGATGACA--TT-GCTA-T-
1 TACTTCAATTTCAGAGATAAAGACATGTTATCCACTC
* *
42972355 TACTTCAATTTCAGAGATAAAGACGTGTTATCCAATC
1 TACTTCAATTTCAGAGATAAAGACATGTTATCCACTC
** * * *
42972392 TACTTCAATTTCA-AGAGGATGAC--G-T-TGCTCT-
1 TACTTCAATTTCAGAGATAAAGACATGTTATCCACTC
*
42972423 TACTTTAATTTCAGAGATAAAGACATGTTATCCAACTC
1 TACTTCAATTTCAGAGATAAAGACATGTTATCC-ACTC
* *
42972461 TACTTCAATTTCAAGCAGAT---GAC--G-T-TGCTCT-
1 TACTTCAATTTC-AG-AGATAAAGACATGTTATCCACTC
* *
42972492 TACTTCAATTTCAGAGATAAAGACGTATTATCCACTC
1 TACTTCAATTTCAGAGATAAAGACATGTTATCCACTC
** * * * *
42972529 TACTTCAATTTCAAGAGGAT-TGGAAATGATCTTTGCTC-C
1 TACTTCAATTTC-AGA-GATAAAGACATG-T-TATCCACTC
* *
42972568 TACTTCAATTTCAGAGATGAAGACTTGTTATCCACTC
1 TACTTCAATTTCAGAGATAAAGACATGTTATCCACTC
42972605 TACTTCAATTTCA
1 TACTTCAATTTCA
42972618 AGCGGATTGG
Statistics
Matches: 219, Mismatches: 46, Indels: 58
0.68 0.14 0.18
Matches are distributed among these distances:
29 4 0.02
30 2 0.01
31 37 0.17
32 22 0.10
33 5 0.02
34 7 0.03
35 5 0.02
36 25 0.11
37 61 0.28
38 24 0.11
39 19 0.09
40 8 0.04
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (37 bp):
TACTTCAATTTCAGAGATAAAGACATGTTATCCACTC
Found at i:42972394 original size:68 final size:68
Alignment explanation
Indices: 42972280--42972624 Score: 474
Period size: 68 Copynumber: 4.9 Consensus size: 68
42972270 GGAAATGATC
*
42972280 TTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGCGGATG
*
42972345 ACA
66 ACG
* * * *
42972348 TTGCTATTACTTCAATTTCAGAGATAAAGACGTGTTATCCAATCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGCGGATG
42972413 ACG
66 ACG
* *
42972416 TTGCTCTTACTTTAATTTCAGAGATAAAGACATGTTATCCAACTCTACTTCAATTTCAAGCAGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAGCGGAT
42972481 GACG
65 GACG
* * *
42972485 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTC-A-A-G--C
*
42972550 GGAAATGATCT
61 GG--ATGA-CG
* * *
42972561 TTGCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGCGGAT
42972625 TGGAAATGAT
Statistics
Matches: 246, Mismatches: 22, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
68 116 0.47
69 65 0.26
70 1 0.00
71 3 0.01
73 2 0.01
74 1 0.00
75 5 0.02
76 53 0.22
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (68 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCCACTCTACTTCAATTTCAAGCGGATG
ACG
Found at i:42972499 original size:137 final size:142
Alignment explanation
Indices: 42972247--42972620 Score: 555
Period size: 137 Copynumber: 2.6 Consensus size: 142
42972237 GATATCCAGC
42972247 TCTACTTCAATTTCAAGAGGATAGGAAATGATC-TTGCTCTTACTTCAATTTCAGAGATAAAGAC
1 TCTACTTCAATTTCAAGAGGAT-GG-AATGATCGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
**
42972311 ATGTTATCCACTCTACTTCAATTTCAAGGGGATGACATTGCTATTACTTCAATTTCAGAGATAAA
64 ATGTTATCCACTCTACTTCAATTTCAAGCAGATGACATTGCTATTACTTCAATTTCAGAGATAAA
*
42972376 GACGTGTTATCCAA
129 GACGTATTATCCAA
*
42972390 TCTACTTCAATTTC-A-A-GA-GG-ATGA-CGTTGCTCTTACTTTAATTTCAGAGATAAAGACAT
1 TCTACTTCAATTTCAAGAGGATGGAATGATCGTTGCTCTTACTTCAATTTCAGAGATAAAGACAT
* *
42972449 GTTATCCAACTCTACTTCAATTTCAAGCAGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAG
66 GTTATCC-ACTCTACTTCAATTTCAAGCAGATGACATTGCTATTACTTCAATTTCAGAGATAAAG
*
42972514 ACGTATTATCCAC
130 ACGTATTATCCAA
* * *
42972527 TCTACTTCAATTTCAAGAGGATTGGAAATGATCTTTGCTCCTACTTCAATTTCAGAGATGAAGAC
1 TCTACTTCAATTTCAAGAGGA-TGG-AATGATCGTTGCTCTTACTTCAATTTCAGAGATAAAGAC
*
42972592 TTGTTATCCACTCTACTTCAATTTCAAGC
64 ATGTTATCCACTCTACTTCAATTTCAAGC
42972621 GGATTGGAAA
Statistics
Matches: 209, Mismatches: 12, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
135 1 0.00
136 43 0.21
137 78 0.37
138 3 0.01
139 1 0.00
140 4 0.02
141 1 0.00
142 3 0.01
143 14 0.07
144 24 0.11
145 37 0.18
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.34
Consensus pattern (142 bp):
TCTACTTCAATTTCAAGAGGATGGAATGATCGTTGCTCTTACTTCAATTTCAGAGATAAAGACAT
GTTATCCACTCTACTTCAATTTCAAGCAGATGACATTGCTATTACTTCAATTTCAGAGATAAAGA
CGTATTATCCAA
Found at i:42972571 original size:39 final size:40
Alignment explanation
Indices: 42972522--42972637 Score: 120
Period size: 37 Copynumber: 3.0 Consensus size: 40
42972512 AGACGTATTA
42972522 TCCACTCTACTTCAATTTCAAGAGGATTGGAAATGATCTT
1 TCCACTCTACTTCAATTTCAAGAGGATTGGAAATGATCTT
* * *
42972562 TGCTC-CTACTTCAATTTC-AGA-GA-T-GAAGACTTG-T-TA
1 TCCACTCTACTTCAATTTCAAGAGGATTGGAA-A--TGATCTT
*
42972598 TCCACTCTACTTCAATTTCAAGCGGATTGGAAATGATCTT
1 TCCACTCTACTTCAATTTCAAGAGGATTGGAAATGATCTT
42972638 GTTTGGTCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
35 3 0.05
36 6 0.10
37 16 0.27
38 9 0.15
39 16 0.27
40 6 0.10
41 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (40 bp):
TCCACTCTACTTCAATTTCAAGAGGATTGGAAATGATCTT
Found at i:42972611 original size:76 final size:76
Alignment explanation
Indices: 42972485--42972637 Score: 261
Period size: 76 Copynumber: 2.0 Consensus size: 76
42972475 GCAGATGACG
*
42972485 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATT
1 TTGCTCCTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATT
42972550 GGAAATGATCT
66 GGAAATGATCT
* * * *
42972561 TTGCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
1 TTGCTCCTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATT
42972626 GGAAATGATCT
66 GGAAATGATCT
42972637 T
1 T
42972638 GTTTGGTCTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (76 bp):
TTGCTCCTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATTTCAAGAGGATT
GGAAATGATCT
Found at i:42983417 original size:30 final size:30
Alignment explanation
Indices: 42983378--42983761 Score: 380
Period size: 30 Copynumber: 12.8 Consensus size: 30
42983368 TTTAGGGAAG
42983378 TTTGAGGGTCAAAATGTAATTTTTAAAAAGT
1 TTTG-GGGTCAAAATGTAATTTTTAAAAAGT
*
42983409 TTTGGGGTCAAAATATAA-TTTTAGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTTA-AAAAGT
* *
42983439 TTTGGGGTTAAAATGTAATTTTTAGAAAGT
1 TTTGGGGTCAAAATGTAATTTTTAAAAAGT
* * *
42983469 TTCGAGGTCAAAATAT-ATTTTTCAAAAAGT
1 TTTGGGGTCAAAATGTAATTTTT-AAAAAGT
* **
42983499 TTTGGGGAT-GAAATGTAATTTTGGAAAAGT
1 TTTGGGG-TCAAAATGTAATTTTTAAAAAGT
* * **
42983529 TTTAGGGTCAAAATATAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTTAAAAAGT
* * * *
42983559 TTAGGGATCAAAATGTAATTTTCAAAAAAT
1 TTTGGGGTCAAAATGTAATTTTTAAAAAGT
* *
42983589 TTT-GGGTCAAAATATAATTTTCAAAAAGT
1 TTTGGGGTCAAAATGTAATTTTTAAAAAGT
* **
42983618 TTTGGGGTCAAGATGTAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTTAAAAAGT
* * * **
42983648 TTTAGGGTTAAAATATAATTTTGGAAAAGT
1 TTTGGGGTCAAAATGTAATTTTTAAAAAGT
* *
42983678 TTAGGGGTCAAAATGTAATTTTCAAAAAGT
1 TTTGGGGTCAAAATGTAATTTTTAAAAAGT
* * * * *
42983708 TTTGAGGTTAAAATATAATTTTCAGAAAGT
1 TTTGGGGTCAAAATGTAATTTTTAAAAAGT
* *
42983738 TTTGGGATCGAAATGTAATTTTTA
1 TTTGGGGTCAAAATGTAATTTTTA
42983762 GATAATTTAA
Statistics
Matches: 292, Mismatches: 54, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
29 38 0.13
30 239 0.82
31 15 0.05
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (30 bp):
TTTGGGGTCAAAATGTAATTTTTAAAAAGT
Found at i:42985803 original size:33 final size:33
Alignment explanation
Indices: 42985766--42985832 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
42985756 AATGTTTAGT
*
42985766 ATTTAAATTTAA-ATTTAAATTT-AATTTAATTAA
1 ATTTAAATTTAAGA--TAAATTTAAATTTAAATAA
42985799 ATTTAAATTTAAGATAAATTTAAATTTAAATAA
1 ATTTAAATTTAAGATAAATTTAAATTTAAATAA
42985832 A
1 A
42985833 ATCAATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 7 0.23
33 23 0.74
34 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (33 bp):
ATTTAAATTTAAGATAAATTTAAATTTAAATAA
Found at i:42985804 original size:6 final size:6
Alignment explanation
Indices: 42985766--42985829 Score: 84
Period size: 6 Copynumber: 11.3 Consensus size: 6
42985756 AATGTTTAGT
42985766 ATTTAA ATTTAA ATTTAA ATTT-A ATTT-A A-TTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
42985811 GA--TAA ATTTAA ATTTAA AT
1 -ATTTAA ATTTAA ATTTAA AT
42985830 AAAATCAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
4 3 0.06
5 12 0.23
6 37 0.70
7 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:42985818 original size:27 final size:27
Alignment explanation
Indices: 42985768--42985821 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
42985758 TGTTTAGTAT
*
42985768 TTAAATTTAAATTTAAATTTAATTTAA
1 TTAAATTTAAATTTAAATTAAATTTAA
42985795 TTAAATTTAAATTTAAGA-TAAATTTAA
1 TTAAATTTAAATTTAA-ATTAAATTTAA
42985822 ATTTAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TTAAATTTAAATTTAAATTAAATTTAA
Found at i:42985841 original size:21 final size:22
Alignment explanation
Indices: 42985769--42985842 Score: 80
Period size: 21 Copynumber: 3.4 Consensus size: 22
42985759 GTTTAGTATT
* *
42985769 TAAATTTAAATTTAAATTTAAT
1 TAAATTTAAATTTAAATTAAAA
* *
42985791 TTAA-TTAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAA-TTAAAA
42985813 TAAATTTAAATTTAAA-TAAAA
1 TAAATTTAAATTTAAATTAAAA
*
42985834 TCAATTTAA
1 TAAATTTAA
42985843 CTCCAAATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
21 23 0.53
22 9 0.21
23 11 0.26
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (22 bp):
TAAATTTAAATTTAAATTAAAA
Found at i:42989815 original size:41 final size:41
Alignment explanation
Indices: 42989737--42990093 Score: 225
Period size: 41 Copynumber: 8.7 Consensus size: 41
42989727 GCGGCACTTT
* *
42989737 TAGCGGCGTTTA-GACAGAAAACGCCG-TAAAAGAT-AAAGCAA
1 TAGCGGCGTTTATG--AGAAAGCGCCGCT-AAAGGTCAAAGCAA
* *
42989778 TAGCGGCGTTTATGAGAAACCGCCGCTAAAGGTTAAAGCAA
1 TAGCGGCGTTTATGAGAAAGCGCCGCTAAAGGTCAAAGCAA
* * * * *
42989819 TAGCGACGCTTCTTAGAAAGCGCCGCTAAAGGTTAGAA-CAA
1 TAGCGGCGTTTATGAGAAAGCGCCGCTAAAGGTCA-AAGCAA
* * *
42989860 TAGCGGCGTTTAAG-GAAAAGCACCGCAAAAGGTCAGAA-CAA
1 TAGCGGCGTTTATGAG-AAAGCGCCGCTAAAGGTCA-AAGCAA
** * * * *
42989901 TAGCGATGCTTCTTAAAAAGCGCCGCTAAAGGTCAAAGCAA
1 TAGCGGCGTTTATGAGAAAGCGCCGCTAAAGGTCAAAGCAA
* * *
42989942 TAGCGGCGCTTCT-TG-GAAAGCGTCGCTAAAGGTCAGATCAA
1 TAGCGGCG-TT-TATGAGAAAGCGCCGCTAAAGGTCAAAGCAA
* * *
42989983 TAGCGGCGCTTCT-TGA-AAAGCGCTGTTAAAGGTCAGAGCAA
1 TAGCGGCG-TT-TATGAGAAAGCGCCGCTAAAGGTCAAAGCAA
* * * * * *
42990024 TAGCAGCGCTTT-TGA-AAAGCGTCGCAAAAGATCAGAGCAT
1 TAGCGGCG-TTTATGAGAAAGCGCCGCTAAAGGTCAAAGCAA
* * * *
42990064 TAGCGGCGCTTGTAAGAAAGTGCCGCTAAA
1 TAGCGGCGTTTATGAGAAAGCGCCGCTAAA
42990094 AGTGGATTTT
Statistics
Matches: 255, Mismatches: 49, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.01
40 50 0.20
41 197 0.77
42 5 0.02
43 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (41 bp):
TAGCGGCGTTTATGAGAAAGCGCCGCTAAAGGTCAAAGCAA
Found at i:42989961 original size:123 final size:122
Alignment explanation
Indices: 42989798--42990093 Score: 342
Period size: 123 Copynumber: 2.4 Consensus size: 122
42989788 TATGAGAAAC
* * *
42989798 CGCCGCTAAAGGTTAAAGCAATAGCGACGCTTCTTAGAAAGCGCCGCTAAAGGTTAGAACAATAG
1 CGCCGCTAAAGGTCAAAGCAATAGCGGCGCTTCTTAGAAAGCGCCGCTAAAGGTCAGAACAATAG
* *
42989863 CGGCGTTTAAGGAAAAGCACCGCAAAAGGTCAGAACAATAGC-GATGCTTCTTAAAAAG
66 CGGCGCTTAAGGAAAAGCACCGCAAAAGGTCAGAACAATAGCAG-CGCTT-TTAAAAAG
* * *
42989921 CGCCGCTAAAGGTCAAAGCAATAGCGGCGCTTCTTGGAAAGCGTCGCTAAAGGTCAGATCAATAG
1 CGCCGCTAAAGGTCAAAGCAATAGCGGCGCTTCTTAGAAAGCGCCGCTAAAGGTCAGAACAATAG
*** * * ** * *
42989986 CGGCGCTTCTTGAAAAGCGCTGTTAAAGGTCAGAGCAATAGCAGCGCTTTTGAAAAG
66 CGGCGCTTAAGGAAAAGCACCGCAAAAGGTCAGAACAATAGCAGCGCTTTTAAAAAG
* * * * * * * *
42990043 CGTCGCAAAAGATCAGAGCATTAGCGGCGCTTGTAAGAAAGTGCCGCTAAA
1 CGCCGCTAAAGGTCAAAGCAATAGCGGCGCTTCTTAGAAAGCGCCGCTAAA
42990094 AGTGGATTTT
Statistics
Matches: 145, Mismatches: 27, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
122 48 0.33
123 96 0.66
124 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (122 bp):
CGCCGCTAAAGGTCAAAGCAATAGCGGCGCTTCTTAGAAAGCGCCGCTAAAGGTCAGAACAATAG
CGGCGCTTAAGGAAAAGCACCGCAAAAGGTCAGAACAATAGCAGCGCTTTTAAAAAG
Found at i:42990059 original size:40 final size:41
Alignment explanation
Indices: 42989773--42990074 Score: 306
Period size: 41 Copynumber: 7.4 Consensus size: 41
42989763 TAAAAGATAA
* * *
42989773 AGCAATAGCGGCG-TT-TATGAGAAACCGCCGCTAAAGGTTAA
1 AGCAATAGCGGCGCTTCT-TGA-AAAGCGCCGCTAAAGGTCAG
* *
42989814 AGCAATAGCGACGCTTCTT-AGAAAGCGCCGCTAAAGGTTAG
1 AGCAATAGCGGCGCTTCTTGA-AAAGCGCCGCTAAAGGTCAG
* * *** * *
42989855 AACAATAGCGGCGTTTAAGGAAAAGCACCGCAAAAGGTCAG
1 AGCAATAGCGGCGCTTCTTGAAAAGCGCCGCTAAAGGTCAG
* ** * *
42989896 AACAATAGCGATGCTTCTTAAAAAGCGCCGCTAAAGGTCAA
1 AGCAATAGCGGCGCTTCTTGAAAAGCGCCGCTAAAGGTCAG
* *
42989937 AGCAATAGCGGCGCTTCTTGGAAAGCGTCGCTAAAGGTCAG
1 AGCAATAGCGGCGCTTCTTGAAAAGCGCCGCTAAAGGTCAG
* * *
42989978 ATCAATAGCGGCGCTTCTTGAAAAGCGCTGTTAAAGGTCAG
1 AGCAATAGCGGCGCTTCTTGAAAAGCGCCGCTAAAGGTCAG
* * * *
42990019 AGCAATAGCAGCGCTT-TTGAAAAGCGTCGCAAAAGATCAG
1 AGCAATAGCGGCGCTTCTTGAAAAGCGCCGCTAAAGGTCAG
*
42990059 AGCATTAGCGGCGCTT
1 AGCAATAGCGGCGCTT
42990075 GTAAGAAAGT
Statistics
Matches: 215, Mismatches: 43, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
40 33 0.15
41 177 0.82
42 4 0.02
43 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (41 bp):
AGCAATAGCGGCGCTTCTTGAAAAGCGCCGCTAAAGGTCAG
Found at i:42994225 original size:43 final size:43
Alignment explanation
Indices: 42994163--42994476 Score: 377
Period size: 43 Copynumber: 7.3 Consensus size: 43
42994153 CGTTTATTAG
* * *
42994163 AAAAAGCGCCGCTATAGAACATGGTTTTTAGCGGTGCTTTTCAC
1 AAAAA-CGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCAC
*
42994207 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCTC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCAC
* *
42994249 AAAAACGCAGCTAAAGAACATGGTCTTTAGCGGTGCTTTTTCGAC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTTC-AC
*
42994294 --AAACGCCGCTAAAGAACATGGTCTTCAGCGGCGCTTTTCAC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCAC
* * * * * * *
42994335 ACAAATGCCACTAAAGAACATTG-CTTTTAACGGCGCTTTACCC
1 AAAAACGCCGCTAAAGAACATGGTC-TTTAGCGGCGCTTTTCAC
* * *
42994378 ACAAACGCCGCTAAAGAACATGCTCTTTAGCGGCGC-TTTCTC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCAC
**
42994420 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTTC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCAC
*
42994463 ACAAACGCCGCTAA
1 AAAAACGCCGCTAA
42994477 CATTAATAAA
Statistics
Matches: 234, Mismatches: 28, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
41 2 0.01
42 83 0.35
43 138 0.59
44 10 0.04
45 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCAC
Done.