Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015057.1 Kokia drynarioides strain JFW-HI SEQ_130101, whole genome shotgun sequence
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: 320182
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 202 characters in sequence are not A, C, G, or T
Found at i:2281 original size:26 final size:27
Alignment explanation
Indices: 2231--2285 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
2221 GACCGACACG
2231 TTGACCGTTCACCATTGATCATTGACT
1 TTGACCGTTCACCATTGATCATTGACT
*
2258 TTGACCGTTGACC-TTGA-CAATTGACT
1 TTGACCGTTCACCATTGATC-ATTGACT
2284 TT
1 TT
2286 TTTACAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 1 0.04
26 13 0.50
27 12 0.46
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (27 bp):
TTGACCGTTCACCATTGATCATTGACT
Found at i:6782 original size:29 final size:30
Alignment explanation
Indices: 6730--6803 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
6720 TTTAAATTTA
* *
6730 ATTTAAGGATTAAGTTGTAATTTT-G-GAGG
1 ATTTAAGGACTAAATTGTAATTTTAGTGA-G
6759 ATTTAAGGACTAAATTG-AATTTTTAGTGAG
1 ATTTAAGGACTAAATTGTAA-TTTTAGTGAG
*
6789 TTTTAAGGACTAAAT
1 ATTTAAGGACTAAAT
6804 CAAACTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.05
29 19 0.49
30 16 0.41
31 2 0.05
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.41
Consensus pattern (30 bp):
ATTTAAGGACTAAATTGTAATTTTAGTGAG
Found at i:8209 original size:14 final size:14
Alignment explanation
Indices: 8190--8216 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8180 TACGGTGAAA
8190 GATTGGATGGGGAC
1 GATTGGATGGGGAC
8204 GATTGGATGGGGA
1 GATTGGATGGGGA
8217 GGGGTTCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.52, T:0.22
Consensus pattern (14 bp):
GATTGGATGGGGAC
Found at i:8982 original size:36 final size:36
Alignment explanation
Indices: 8942--9028 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
8932 TTAACACAAT
* *
8942 ATATTCACTGTCACATGGCATGAATATCATACCCAC
1 ATATTCACTGTCACATGACATGAATAACATACCCAC
* *
8978 ATATTTACTGTCTCATGACATGAATAACATACCCAC
1 ATATTCACTGTCACATGACATGAATAACATACCCAC
*
9014 ATATTCACTTTCACA
1 ATATTCACTGTCACA
9029 ACAGTCATCA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.31
Consensus pattern (36 bp):
ATATTCACTGTCACATGACATGAATAACATACCCAC
Found at i:13480 original size:24 final size:25
Alignment explanation
Indices: 13448--13506 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
13438 TGTCATATGC
13448 TTAACCATGTACAAAAAATCAT-AA
1 TTAACCATGTACAAAAAATCATCAA
* * *
13472 TTAATCATG-GCATAAAATCATCAA
1 TTAACCATGTACAAAAAATCATCAA
* *
13496 TTTAGCATGTA
1 TTAACCATGTA
13507 ACATTTCATA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (25 bp):
TTAACCATGTACAAAAAATCATCAA
Found at i:18584 original size:45 final size:46
Alignment explanation
Indices: 18510--18608 Score: 141
Period size: 45 Copynumber: 2.2 Consensus size: 46
18500 AGATTATATC
* * *
18510 TTTTT-TTTATCTTAGATATATAGGTTTTTTTAAAATTTGAAT-TAT
1 TTTTTATTTATCTTAGATAAATAGGTTTTTTT-AAATTTAAATCAAT
18555 TTTTTATTTATCTTAGATAAATA-GTTTTTTTAAATTTAAATCAAT
1 TTTTTATTTATCTTAGATAAATAGGTTTTTTTAAATTTAAATCAAT
18600 TTTTTATTT
1 TTTTTATTT
18609 CAAAATCCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 9 0.18
45 24 0.49
46 16 0.33
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (46 bp):
TTTTTATTTATCTTAGATAAATAGGTTTTTTTAAATTTAAATCAAT
Found at i:31638 original size:21 final size:21
Alignment explanation
Indices: 31614--31666 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
31604 TCTAATGATA
31614 AATATTTTAATGTAAAATATT
1 AATATTTTAATGTAAAATATT
31635 AATATTTTAATGTAAAATATT
1 AATATTTTAATGTAAAATATT
31656 AATATTTTAAT
1 AATATTTTAAT
31667 AGTATAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
AATATTTTAATGTAAAATATT
Found at i:33597 original size:47 final size:47
Alignment explanation
Indices: 33527--33619 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 47
33517 AGTGTCAAAT
* *
33527 CCAATATACGTCCAATAGGAGTATGGTCATATTCATAAGTTTTGCAC
1 CCAATATACATCCAATAGGAGTATGGTCATATTCAGAAGTTTTGCAC
* *
33574 CCAATATACATCCAATAGTAGTATGGTCATTTTCAGAAGTTTTGCA
1 CCAATATACATCCAATAGGAGTATGGTCATATTCAGAAGTTTTGCA
33620 AATATGCAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (47 bp):
CCAATATACATCCAATAGGAGTATGGTCATATTCAGAAGTTTTGCAC
Found at i:37923 original size:12 final size:12
Alignment explanation
Indices: 37889--37915 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
37879 GCATCCAAAC
37889 AATCAAAATAAT
1 AATCAAAATAAT
37901 AATCAAAATAAT
1 AATCAAAATAAT
37913 AAT
1 AAT
37916 AATAATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (12 bp):
AATCAAAATAAT
Found at i:38147 original size:21 final size:21
Alignment explanation
Indices: 38063--38194 Score: 85
Period size: 21 Copynumber: 6.3 Consensus size: 21
38053 AAATAGAAAA
* *
38063 AAAACAA-AAATAACAGCATC
1 AAAACAATAAAAAACAACATC
*
38083 AAAACACTAAAACAACAAC--C
1 AAAACAATAAAA-AACAACATC
* * *
38103 AAAATAAT-AATAATAA-ATAC
1 AAAACAATAAAAAACAACAT-C
38123 AAAACAATAAAAAACAACATC
1 AAAACAATAAAAAACAACATC
** * *
38144 AAAACAGCAAAAAAAAAGCAACC
1 AAAACAATAAAAAACAA-C-ATC
* *
38167 AAAACAATAAAAAAAAACACC
1 AAAACAATAAAAAACAACATC
38188 AAAACAA
1 AAAACAA
38195 CAATATAATT
Statistics
Matches: 87, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
18 4 0.05
19 2 0.02
20 21 0.24
21 34 0.39
22 9 0.10
23 17 0.20
ACGTcount: A:0.70, C:0.19, G:0.02, T:0.08
Consensus pattern (21 bp):
AAAACAATAAAAAACAACATC
Found at i:38166 original size:64 final size:61
Alignment explanation
Indices: 38063--38194 Score: 149
Period size: 64 Copynumber: 2.1 Consensus size: 61
38053 AAATAGAAAA
* * * * * * * *
38063 AAAACAAAAATAACAGCATCAAAACACTAAAACAACAACCAAAATAATAATAATAAATA-C
1 AAAACAAAAAAAACAACATCAAAACACAAAAAAAACAACCAAAACAATAAAAAAAAACACC
38123 AAAACAATAAAAAACAACATCAAAACAGCAAAAAAAAAGCAACCAAAACAATAAAAAAAAACACC
1 AAAACAA-AAAAAACAACATCAAAACA-C-AAAAAAAA-CAACCAAAACAATAAAAAAAAACACC
38188 AAAACAA
1 AAAACAA
38195 CAATATAATT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
60 7 0.12
61 17 0.29
62 1 0.02
63 6 0.10
64 20 0.34
65 8 0.14
ACGTcount: A:0.70, C:0.19, G:0.02, T:0.08
Consensus pattern (61 bp):
AAAACAAAAAAAACAACATCAAAACACAAAAAAAACAACCAAAACAATAAAAAAAAACACC
Found at i:38169 original size:23 final size:21
Alignment explanation
Indices: 38122--38197 Score: 89
Period size: 21 Copynumber: 3.5 Consensus size: 21
38112 ATAATAAATA
* * *
38122 CAAAACAATAAAAAACAACAT
1 CAAAACAACAAAAAAAAACAC
*
38143 CAAAACAGCAAAAAAAAAGCAAC
1 CAAAACAACAAAAAAAAA-C-AC
*
38166 CAAAACAATAAAAAAAAACAC
1 CAAAACAACAAAAAAAAACAC
38187 CAAAACAACAA
1 CAAAACAACAA
38198 TATAATTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 27 0.59
22 2 0.04
23 17 0.37
ACGTcount: A:0.72, C:0.21, G:0.03, T:0.04
Consensus pattern (21 bp):
CAAAACAACAAAAAAAAACAC
Found at i:38196 original size:24 final size:24
Alignment explanation
Indices: 38125--38199 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 24
38115 ATAAATACAA
* *
38125 AACAATAAAAAACAACATCAAAAC
1 AACAATAAAAAAAAACACCAAAAC
* *
38149 AGC-A-AAAAAAAAGCAACC--AA-
1 AACAATAAAAAAAAAC-ACCAAAAC
38169 AACAATAAAAAAAAACACCAAAAC
1 AACAATAAAAAAAAACACCAAAAC
38193 AACAATA
1 AACAATA
38200 TAATTTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
20 2 0.05
21 6 0.15
22 17 0.44
23 5 0.13
24 9 0.23
ACGTcount: A:0.72, C:0.20, G:0.03, T:0.05
Consensus pattern (24 bp):
AACAATAAAAAAAAACACCAAAAC
Found at i:48350 original size:21 final size:21
Alignment explanation
Indices: 48326--48367 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48316 TGATACTTGA
* *
48326 GTAAGTTCTACCAATAGAAGT
1 GTAACTTCTACCAATACAAGT
*
48347 GTAACTTCTACCGATACAAGT
1 GTAACTTCTACCAATACAAGT
48368 CATGATTCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (21 bp):
GTAACTTCTACCAATACAAGT
Found at i:49182 original size:52 final size:52
Alignment explanation
Indices: 49121--49257 Score: 229
Period size: 52 Copynumber: 2.6 Consensus size: 52
49111 TAGTAATCGA
*
49121 ACCTCATAATCCGTAAAGGATTCATATACTCATGATGACACATAATCATCAG
1 ACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACATAATCATCAG
* *
49173 ACCTTATAATCCGTAAAGGATTCATATACTCACGATGACACATAGTCATCAG
1 ACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACATAATCATCAG
* *
49225 ACCTCATACTCCATAAAGGATTCATATACTCAC
1 ACCTCATAATCCGTAAAGGATTCATATACTCAC
49258 ATAGTCATCG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 79 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (52 bp):
ACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACATAATCATCAG
Found at i:62391 original size:12 final size:12
Alignment explanation
Indices: 62374--62400 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
62364 GACTGATGCG
62374 GAAAAAGAAGAA
1 GAAAAAGAAGAA
62386 GAAAAAGAAGAA
1 GAAAAAGAAGAA
62398 GAA
1 GAA
62401 TGAGTGGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAAAAGAAGAA
Found at i:63682 original size:18 final size:18
Alignment explanation
Indices: 63659--63704 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
63649 AGAATGGCTA
63659 TTGCTTTGACAAAACTTT
1 TTGCTTTGACAAAACTTT
63677 TTGCTTTGACAAAACTTT
1 TTGCTTTGACAAAACTTT
*
63695 TTGCTATGAC
1 TTGCTTTGAC
63705 TTTGCTAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (18 bp):
TTGCTTTGACAAAACTTT
Found at i:63881 original size:20 final size:20
Alignment explanation
Indices: 63839--63881 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
63829 TGCATTTTTA
*
63839 GCATTTTTAACTCAGTGACT
1 GCATTTTTAACTCAATGACT
63859 GCATTTTCTAACTCAATGA-T
1 GCATTTT-TAACTCAATGACT
63879 GCA
1 GCA
63882 CGATTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (20 bp):
GCATTTTTAACTCAATGACT
Found at i:66452 original size:52 final size:52
Alignment explanation
Indices: 66370--66639 Score: 364
Period size: 52 Copynumber: 5.2 Consensus size: 52
66360 TCATGATGGA
* * * * *
66370 ACATAATCATCGAACCTCATAATCCATAAAGGATTCGTATACTCACGATGAC
1 ACATAGTCATCGGACTTCATAATCCGTAAAGGATTCATATACTCACGATGAC
* *
66422 ACATAGTCATCAGACTTTATAATCCGTAAAGGATTCATATACTCACGATGAC
1 ACATAGTCATCGGACTTCATAATCCGTAAAGGATTCATATACTCACGATGAC
* * * * *
66474 ACATAATCATCGGGCCTCATAATCTGTAAAGGATTCATATAATCACGATGAC
1 ACATAGTCATCGGACTTCATAATCCGTAAAGGATTCATATACTCACGATGAC
* *
66526 ACATAGTCATCGGA-TCTCATAATCCGTGAAGGATTCATATACTCACGATGGC
1 ACATAGTCATCGGACT-TCATAATCCGTAAAGGATTCATATACTCACGATGAC
* * *
66578 ACATAGTCATTGGAC-TCATAATCCATAAAGGATTCATATACTCACGATGGC
1 ACATAGTCATCGGACTTCATAATCCGTAAAGGATTCATATACTCACGATGAC
66629 ACATAGTCATC
1 ACATAGTCATC
66640 AAACCTTTTT
Statistics
Matches: 191, Mismatches: 25, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
51 44 0.23
52 147 0.77
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.27
Consensus pattern (52 bp):
ACATAGTCATCGGACTTCATAATCCGTAAAGGATTCATATACTCACGATGAC
Found at i:74806 original size:36 final size:36
Alignment explanation
Indices: 74754--74822 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
74744 AGCTTCGATC
*
74754 TGCTTACGTCTCGGTTAGAGCGTAAGGCTATGTGAT
1 TGCTTACGTCTCGGTTAAAGCGTAAGGCTATGTGAT
* *
74790 TGCTTATGTCTTGGTTAAAGCGTAAGGCTATGT
1 TGCTTACGTCTCGGTTAAAGCGTAAGGCTATGT
74823 ATAGCTCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.20, C:0.14, G:0.29, T:0.36
Consensus pattern (36 bp):
TGCTTACGTCTCGGTTAAAGCGTAAGGCTATGTGAT
Found at i:74876 original size:56 final size:56
Alignment explanation
Indices: 74790--74934 Score: 227
Period size: 56 Copynumber: 2.6 Consensus size: 56
74780 GCTATGTGAT
* *
74790 TGCTTATGTCTTGGTTAAAGCGTAAGGCTATGTATAGCTCAAGTAGAGCTCTAGAA
1 TGCTTACGTCTTGGTTAGAGCGTAAGGCTATGTATAGCTCAAGTAGAGCTCTAGAA
* ** * *
74846 TGCTTACGTCTCGGTTAGAGCGTAAGGCTATGTATAGCTCGGGTAGAGCTTTGGAA
1 TGCTTACGTCTTGGTTAGAGCGTAAGGCTATGTATAGCTCAAGTAGAGCTCTAGAA
74902 TGCTTACGTCTTGGTTAGAGCGTAAGGCTATGT
1 TGCTTACGTCTTGGTTAGAGCGTAAGGCTATGT
74935 GATTGTTTAC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 81 1.00
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.32
Consensus pattern (56 bp):
TGCTTACGTCTTGGTTAGAGCGTAAGGCTATGTATAGCTCAAGTAGAGCTCTAGAA
Found at i:75804 original size:17 final size:18
Alignment explanation
Indices: 75782--75818 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
75772 GGCCTATAAC
*
75782 AATATAAAC-ATCAATTA
1 AATATAAACAAGCAATTA
75799 AATATAAACAAGCAATTA
1 AATATAAACAAGCAATTA
75817 AA
1 AA
75819 CACAATCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.62, C:0.11, G:0.03, T:0.24
Consensus pattern (18 bp):
AATATAAACAAGCAATTA
Found at i:78346 original size:42 final size:42
Alignment explanation
Indices: 78283--78410 Score: 195
Period size: 42 Copynumber: 3.0 Consensus size: 42
78273 AACGCATATA
*
78283 TATATAAGCTGACGAGCGTAAACGTGTGCAAGCTGATAAGCG
1 TATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGATAAGCG
* *
78325 TATATAAGCTGACGAGTGTAAACGTGAGCAAGCT-AGTGAGCG
1 TATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGA-TAAGCG
* *
78367 TATATAAGCTGACGAGTGTAAACATGTGCAAGCTGGTAAGCG
1 TATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGATAAGCG
78409 TA
1 TA
78411 AACGCATATA
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 76 0.99
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.23
Consensus pattern (42 bp):
TATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGATAAGCG
Found at i:78399 original size:24 final size:24
Alignment explanation
Indices: 78372--78541 Score: 90
Period size: 24 Copynumber: 6.8 Consensus size: 24
78362 GAGCGTATAT
*
78372 AAGCTGACGAGTGTAAACATGTGC
1 AAGCTGACGAGCGTAAACATGTGC
*** * **
78396 AAGCTGGTAAGCGTAAACGCATATAT
1 AAGCTGACGAGCGTAAA--CATGTGC
* *
78422 ATACGCTGACGAGTGTAAACGTGTGC
1 A-A-GCTGACGAGCGTAAACATGTGC
* * *
78448 AAGCT-AGCGAGTGTAAACGCATATAC
1 AAGCTGA-CGAGCGTAAA--CATGTGC
*
78474 ATAAGCTGACGAGCGTAAACGTGTGC
1 --AAGCTGACGAGCGTAAACATGTGC
** *
78500 AAGCTGGTGAGCGTAAACTTGTGC
1 AAGCTGACGAGCGTAAACATGTGC
* *
78524 AAGCTGGCGAGCATAAAC
1 AAGCTGACGAGCGTAAAC
78542 GCATATATAT
Statistics
Matches: 109, Mismatches: 27, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
23 1 0.01
24 63 0.58
25 1 0.01
26 17 0.16
27 1 0.01
28 25 0.23
29 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (24 bp):
AAGCTGACGAGCGTAAACATGTGC
Found at i:78423 original size:52 final size:52
Alignment explanation
Indices: 78367--78517 Score: 230
Period size: 52 Copynumber: 2.9 Consensus size: 52
78357 CTAGTGAGCG
* *
78367 TATATAAGCTGACGAGTGTAAACATGTGCAAGCTGGTAAGCGTAAACGCATA
1 TATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGGTGAGCGTAAACGCATA
* * * *
78419 TATATACGCTGACGAGTGTAAACGTGTGCAAGCTAGCGAGTGTAAACGCATA
1 TATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGGTGAGCGTAAACGCATA
* *
78471 TACATAAGCTGACGAGCGTAAACGTGTGCAAGCTGGTGAGCGTAAAC
1 TATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGGTGAGCGTAAAC
78518 TTGTGCAAGC
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 87 1.00
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (52 bp):
TATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGGTGAGCGTAAACGCATA
Found at i:78440 original size:28 final size:27
Alignment explanation
Indices: 78408--78494 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 27
78398 GCTGGTAAGC
*
78408 GTAAACGCATATATATACGCTGACGAGT
1 GTAAACGCATATACATA-GCTGACGAGT
* *
78436 GTAAACG--TGTGCA-AGCT-AGCGAGT
1 GTAAACGCATATACATAGCTGA-CGAGT
*
78460 GTAAACGCATATACATAAGCTGACGAGC
1 GTAAACGCATATACAT-AGCTGACGAGT
78488 GTAAACG
1 GTAAACG
78495 TGTGCAAGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
23 1 0.02
24 15 0.32
25 1 0.02
26 7 0.15
28 22 0.47
29 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (27 bp):
GTAAACGCATATACATAGCTGACGAGT
Found at i:78572 original size:80 final size:76
Alignment explanation
Indices: 78426--78595 Score: 232
Period size: 80 Copynumber: 2.2 Consensus size: 76
78416 ATATATATAC
* * **
78426 GCTGACGAGTGTAAACGTGTGCAAGCTAGCGAGTGTAAACGCATATACATAAGCTGACGAGCGTA
1 GCTGATGAGCGTAAACGTGTGCAAGCTAGCGAGCATAAACGCATATACATAAGCTGACGAGCGTA
78491 AACGTGTGCAA
66 AACGTGTGCAA
* * * *
78502 GCTGGTGAGCGTAAACTTGTGCAAGCTGGCGAGCATAAACGCATATATATTTATAAGCTGACGAG
1 GCTGATGAGCGTAAACGTGTGCAAGCTAGCGAGCATAAACGC--ATATA--CATAAGCTGACGAG
78567 CGTAAACGTGTGCAA
62 CGTAAACGTGTGCAA
78582 GCTGATGAGCGTAA
1 GCTGATGAGCGTAA
78596 GTGCGTATAT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
76 35 0.43
78 5 0.06
80 41 0.51
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.22
Consensus pattern (76 bp):
GCTGATGAGCGTAAACGTGTGCAAGCTAGCGAGCATAAACGCATATACATAAGCTGACGAGCGTA
AACGTGTGCAA
Found at i:78629 original size:54 final size:52
Alignment explanation
Indices: 78508--78701 Score: 219
Period size: 54 Copynumber: 3.6 Consensus size: 52
78498 GCAAGCTGGT
* * *
78508 GAGCGTAAACTTGTGCAAGCTGGCGAGCATAAACGCATATATATTTATAAGCTGAC
1 GAGCGTAAACGTGTGCAAGCTGACGAGCGTAAACG--TATATA--TATAAGCTGAC
* *
78564 GAGCGTAAACGTGTGCAAGCTGATGAGCGTAAGTGCGTATATATATAAGCTGAC
1 GAGCGTAAACGTGTGCAAGCTGACGAGCGTAA--ACGTATATATATAAGCTGAC
* * * * *
78618 GAGTGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATTTATAT-AGCTGAA
1 GAGCGTAAACGTGTGCAAGCTGACGAGCGTAAACGTATATATATAAGCTGAC
* *
78669 GAGCGTAAACGTGTGAAAGCTGACAAGCGTAAA
1 GAGCGTAAACGTGTGCAAGCTGACGAGCGTAAA
78702 GCACAATTAG
Statistics
Matches: 120, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
51 35 0.29
52 9 0.08
54 40 0.33
56 34 0.28
58 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.23
Consensus pattern (52 bp):
GAGCGTAAACGTGTGCAAGCTGACGAGCGTAAACGTATATATATAAGCTGAC
Found at i:78697 original size:24 final size:24
Alignment explanation
Indices: 78610--78701 Score: 71
Period size: 24 Copynumber: 3.7 Consensus size: 24
78600 GTATATATAT
* * *
78610 AAGCTGACGAGTGTAAACGTGTGC
1 AAGCTGACAAGCGTAAACGTGTGA
* * *
78634 AAGCTGGCGAGCGTAAACGCAT-TTA
1 AAGCTGACAAGCGTAAACG--TGTGA
78659 TATAGCTGA-AGAGCGTAAACGTGTGA
1 -A-AGCTGACA-AGCGTAAACGTGTGA
78685 AAGCTGACAAGCGTAAA
1 AAGCTGACAAGCGTAAA
78702 GCACAATTAG
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
24 31 0.57
25 4 0.07
26 4 0.07
27 15 0.28
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (24 bp):
AAGCTGACAAGCGTAAACGTGTGA
Found at i:82852 original size:19 final size:20
Alignment explanation
Indices: 82828--82865 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
82818 AAATAAAGAA
82828 AACTAAAAA-AAAAACAAAT
1 AACTAAAAAGAAAAACAAAT
82847 AACTAAAAAGAAAAACAAA
1 AACTAAAAAGAAAAACAAA
82866 CACTAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.79, C:0.11, G:0.03, T:0.08
Consensus pattern (20 bp):
AACTAAAAAGAAAAACAAAT
Found at i:99582 original size:5 final size:5
Alignment explanation
Indices: 99572--99603 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
99562 CAATATAAAC
99572 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA AT
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA AT
99604 ATTAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:107435 original size:60 final size:60
Alignment explanation
Indices: 107338--107462 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
107328 GTTGATTTTA
* *
107338 ATGGAAAGAACGTCCAATTGGGCAAGTTTTGTGGAAAGAGCGTCCAGCTTGGCAAGCTTT
1 ATGGAAAGAACGTCCAACTGGGCAAGCTTTGTGGAAAGAGCGTCCAGCTTGGCAAGCTTT
* * * * * * *
107398 ATGGAAAGAGCGTCCAGCTGGGCAAGCTTTGTTGAAAGCGCGTCTAGTTTGGCGAGCTTT
1 ATGGAAAGAACGTCCAACTGGGCAAGCTTTGTGGAAAGAGCGTCCAGCTTGGCAAGCTTT
*
107458 TTGGA
1 ATGGA
107463 CAGGTGTCAG
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (60 bp):
ATGGAAAGAACGTCCAACTGGGCAAGCTTTGTGGAAAGAGCGTCCAGCTTGGCAAGCTTT
Found at i:107456 original size:30 final size:30
Alignment explanation
Indices: 107339--107462 Score: 133
Period size: 30 Copynumber: 4.1 Consensus size: 30
107329 TTGATTTTAA
* * *
107339 TGGAAAGAACGTCCA-ATTGGGCAAGTTTTG
1 TGGAAAGAGCGTCCAGCTT-GGCAAGCTTTG
*
107369 TGGAAAGAGCGTCCAGCTTGGCAAGCTTTA
1 TGGAAAGAGCGTCCAGCTTGGCAAGCTTTG
*
107399 TGGAAAGAGCGTCCAGCTGGGCAAGCTTTG
1 TGGAAAGAGCGTCCAGCTTGGCAAGCTTTG
* * * * * *
107429 TTGAAAGCGCGTCTAGTTTGGCGAGCTTTT
1 TGGAAAGAGCGTCCAGCTTGGCAAGCTTTG
107459 TGGA
1 TGGA
107463 CAGGTGTCAG
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
30 77 0.97
31 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (30 bp):
TGGAAAGAGCGTCCAGCTTGGCAAGCTTTG
Found at i:107543 original size:23 final size:24
Alignment explanation
Indices: 107513--107572 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
107503 TTTCTCTCTC
*
107513 TAGGGTTACGGTTTTTTATTTT-T
1 TAGGGTTAAGGTTTTTTATTTTAT
107536 TAGGGTTAAGG-TTTTTATTTTAT
1 TAGGGTTAAGGTTTTTTATTTTAT
* *
107559 TAGGATTAGGGTTT
1 TAGGGTTAAGGTTT
107573 AAGGGTTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.31
23 20 0.62
24 2 0.06
ACGTcount: A:0.18, C:0.02, G:0.25, T:0.55
Consensus pattern (24 bp):
TAGGGTTAAGGTTTTTTATTTTAT
Found at i:111858 original size:3 final size:3
Alignment explanation
Indices: 111850--111879 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
111840 ACTACAATTA
111850 TTG TTG TTG TTG TTG TTG TTG TTG TT- TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
111880 AAATCGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (3 bp):
TTG
Found at i:116434 original size:171 final size:171
Alignment explanation
Indices: 116143--116482 Score: 592
Period size: 171 Copynumber: 2.0 Consensus size: 171
116133 TTTGTCATTA
* *
116143 ATATATATATGAAATTAAAAGAAGAAGAAAAACATATTTTCCTTCTTTTTCATCTTCTTCACGCG
1 ATATATATATGAAATTAAAAGAAGAAGAAAAACATATTTCCCTTCTTTTTCATCTTCTTCACACG
* *
116208 GCCAAGAGGAAGGAATTTAGGGTTTTTCATTCAATCTTGAAGCTTTAAATTGAGTAAGTAAATGA
66 ACCAAGAGGAAGGAATTTAGGGTTTTTCATTCAAACTTGAAGCTTTAAATTGAGTAAGTAAATGA
116273 TGCTCGTTTTTAGTAATTTTTATGTTTTTGAGTCCATATAT
131 TGCTCGTTTTTAGTAATTTTTATGTTTTTGAGTCCATATAT
*
116314 ATATATATATGAAATTAAAAGAGGAA-AGAAAACATATTTCCCTTCTTTTTCATCTTCTTCACAC
1 ATATATATATGAAATTAAAAGAAGAAGA-AAAACATATTTCCCTTCTTTTTCATCTTCTTCACAC
* *
116378 GACCAAGAGGAAGGAATTTAGGGTTTTTCATTCAAACTTTAAGCTTTAATTTGAGTAAGTAAATG
65 GACCAAGAGGAAGGAATTTAGGGTTTTTCATTCAAACTTGAAGCTTTAAATTGAGTAAGTAAATG
*
116443 ATGCTCGTTTTTAGTAATTTTTATGTTTTTGAGTTCATAT
130 ATGCTCGTTTTTAGTAATTTTTATGTTTTTGAGTCCATAT
116483 TAGCTTAATC
Statistics
Matches: 160, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
170 1 0.01
171 159 0.99
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (171 bp):
ATATATATATGAAATTAAAAGAAGAAGAAAAACATATTTCCCTTCTTTTTCATCTTCTTCACACG
ACCAAGAGGAAGGAATTTAGGGTTTTTCATTCAAACTTGAAGCTTTAAATTGAGTAAGTAAATGA
TGCTCGTTTTTAGTAATTTTTATGTTTTTGAGTCCATATAT
Found at i:134117 original size:23 final size:22
Alignment explanation
Indices: 134091--134147 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
134081 AAACCCACCA
* *
134091 AAAAGAAATGGAGAAGAGCAAAG
1 AAAAGAAATGAAGAA-AGAAAAG
* *
134114 AAAAGTAGTGAAGAAAGAAAAG
1 AAAAGAAATGAAGAAAGAAAAG
*
134136 AAAAAAAATGAA
1 AAAAGAAATGAA
134148 AAATGGTTGT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.67, C:0.02, G:0.25, T:0.07
Consensus pattern (22 bp):
AAAAGAAATGAAGAAAGAAAAG
Found at i:134532 original size:29 final size:29
Alignment explanation
Indices: 134460--134539 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
134450 TAGATTTAAG
* * *
134460 TTTT-CATTTAAAATTTAGATATCAATAA
1 TTTTACATTTAGATTTTAGATTTCAATAA
* *
134488 TTTTACTTTTAGATTTTAGATTTCCATAA
1 TTTTACATTTAGATTTTAGATTTCAATAA
* *
134517 TTTTTAGATTTA-ATTTTAAATTT
1 -TTTTACATTTAGATTTTAGATTT
134540 AGCTTTGGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 4 0.10
29 29 0.69
30 9 0.21
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (29 bp):
TTTTACATTTAGATTTTAGATTTCAATAA
Found at i:136558 original size:24 final size:24
Alignment explanation
Indices: 136525--136571 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
136515 GTTAAGAGTA
*
136525 AAAATTGTTAGTGCAAATATAATAT
1 AAAATTGTTAGAGCAAAT-TAATAT
136550 AAAA-TGTTAGAGCAAATTAATA
1 AAAATTGTTAGAGCAAATTAATA
136572 AAAGATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (24 bp):
AAAATTGTTAGAGCAAATTAATAT
Found at i:140935 original size:15 final size:15
Alignment explanation
Indices: 140915--140945 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
140905 GTCACCGCAC
*
140915 CATGTGAAAATGCTT
1 CATGTGAAAATACTT
140930 CATGTGAAAATACTT
1 CATGTGAAAATACTT
140945 C
1 C
140946 GACAACTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (15 bp):
CATGTGAAAATACTT
Found at i:157973 original size:25 final size:23
Alignment explanation
Indices: 157876--157998 Score: 160
Period size: 23 Copynumber: 5.3 Consensus size: 23
157866 ACAAATGAAT
*
157876 GGAGAGCACAAAC-GTGCTAAAC
1 GGAGAGCACACACAGTGCTAAAC
* *
157898 GGAGAGCACCCAAAGTGCTAAAC
1 GGAGAGCACACACAGTGCTAAAC
157921 GGAGAGCACACACAGTGCTAAAC
1 GGAGAGCACACACAGTGCTAAAC
157944 GGAGAGCACACACAGTGCTAATAAC
1 GGAGAGCACACACAGTGCT-A-AAC
* *
157969 AGAGAGCACGAGACA-TGCTAAAC
1 GGAGAGCAC-ACACAGTGCTAAAC
157992 GGAGAGC
1 GGAGAGC
157999 GTTGAGGTTC
Statistics
Matches: 89, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
22 10 0.11
23 58 0.65
24 2 0.02
25 15 0.17
26 4 0.04
ACGTcount: A:0.40, C:0.24, G:0.28, T:0.09
Consensus pattern (23 bp):
GGAGAGCACACACAGTGCTAAAC
Found at i:159951 original size:121 final size:121
Alignment explanation
Indices: 159788--160030 Score: 486
Period size: 121 Copynumber: 2.0 Consensus size: 121
159778 CTCTCTTTCC
159788 CATGTTGCTTCTTTTGAATTATGATGCATTCATAAAACTTTTACCAAAGGAACTCTTTTATTTCT
1 CATGTTGCTTCTTTTGAATTATGATGCATTCATAAAACTTTTACCAAAGGAACTCTTTTATTTCT
159853 CAACTCCTTTACTTCTCGAGCTAGAATCTTTATCGATTCTTCCTCATAAGTCAGAT
66 CAACTCCTTTACTTCTCGAGCTAGAATCTTTATCGATTCTTCCTCATAAGTCAGAT
159909 CATGTTGCTTCTTTTGAATTATGATGCATTCATAAAACTTTTACCAAAGGAACTCTTTTATTTCT
1 CATGTTGCTTCTTTTGAATTATGATGCATTCATAAAACTTTTACCAAAGGAACTCTTTTATTTCT
159974 CAACTCCTTTACTTCTCGAGCTAGAATCTTTATCGATTCTTCCTCATAAGTCAGAT
66 CAACTCCTTTACTTCTCGAGCTAGAATCTTTATCGATTCTTCCTCATAAGTCAGAT
160030 C
1 C
160031 CGGTTGTATT
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (121 bp):
CATGTTGCTTCTTTTGAATTATGATGCATTCATAAAACTTTTACCAAAGGAACTCTTTTATTTCT
CAACTCCTTTACTTCTCGAGCTAGAATCTTTATCGATTCTTCCTCATAAGTCAGAT
Found at i:165530 original size:121 final size:121
Alignment explanation
Indices: 165316--165556 Score: 322
Period size: 121 Copynumber: 2.0 Consensus size: 121
165306 GATTTCGGGC
165316 ATTACAGGTTATATGGGGACCGGTCTTAGATGTCCTACCGATGGCTGAGATCCAACATTCATTGC
1 ATTACAGGTTATATGGGGACCGGTCTTAGATGTCCTACCGATGGCTGAGATCCAACATTCATTGC
* * * * *
165381 GGATTCTCTACTGCTCGTGTGAGCAACATCGTGTAGCATAACATCTCGACCCACAG
66 GGATTCTCCACAGCTCGTGTAAGCAACATCATGTAGCACAACATCTCGACCCACAG
* * * ** *
165437 ATTACAGGTTATATGGGTG-CTGGTCTTAGATGTCCTACCGATGGTTGTGATCTGACATTCGTTG
1 ATTACAGGTTATATGGG-GACCGGTCTTAGATGTCCTACCGATGGCTGAGATCCAACATTCATTG
* * * * *
165501 TGGATTCTCCACAGCTTGTTTAAGCAACATCATGTAGCGCAACCTCTCGACCCACA
65 CGGATTCTCCACAGCTCGTGTAAGCAACATCATGTAGCACAACATCTCGACCCACA
165557 ACTCATGTGA
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
121 102 0.99
122 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (121 bp):
ATTACAGGTTATATGGGGACCGGTCTTAGATGTCCTACCGATGGCTGAGATCCAACATTCATTGC
GGATTCTCCACAGCTCGTGTAAGCAACATCATGTAGCACAACATCTCGACCCACAG
Found at i:167670 original size:202 final size:202
Alignment explanation
Indices: 167319--167721 Score: 680
Period size: 202 Copynumber: 2.0 Consensus size: 202
167309 AGACTTAAAT
* * * * *
167319 ATGCGCACTAACCACAACTTTCGATGTTGGTAATGCAACATATTCAAGAACAAGTGGATTAAATT
1 ATGCACACTAACCACAACTTCCGATGTTGGCAATGCAACATAATCAAGAACAAGTGAATTAAATT
* * *
167384 CCTCCAATCTCCAAGTAACTTTCGGTGTCTTGCTTGTTAGTTTAAATTGTCATTGCACCTTCCAG
66 CCTCCAATCCCCAAGCAACTTCCGGTGTCTTGCTTGTTAGTTTAAATTGTCATTGCACCTTCCAG
*
167449 TGATAGTGACTGCAATAACACTTCCATGGTCAAAACATTCAAACCCAAATATTAAACAATAAAAG
131 TGACAGTGACTGCAATAACACTTCCATGGTCAAAACATTCAAACCCAAATATTAAACAATAAAAG
167514 AAAGCTC
196 AAAGCTC
167521 ATGCACACTAACCACAACTTCCGATGTTGGCAATGCAACATAATCAAGAACAAGTGAATTAAATT
1 ATGCACACTAACCACAACTTCCGATGTTGGCAATGCAACATAATCAAGAACAAGTGAATTAAATT
* * *
167586 CCTTCAATCCCCAAGCAACTTCCGGTGTCTTGCTTGTTAGTTTAAATTGTCGTTGCACGTTCCAG
66 CCTCCAATCCCCAAGCAACTTCCGGTGTCTTGCTTGTTAGTTTAAATTGTCATTGCACCTTCCAG
*
167651 TGACAGTGACTGCAATAACACTTCCGTGGTCAAAACATTCAAACCCAAATATTAAACAATAAAAG
131 TGACAGTGACTGCAATAACACTTCCATGGTCAAAACATTCAAACCCAAATATTAAACAATAAAAG
*
167716 CAAGCT
196 AAAGCT
167722 TAGATAAAAT
Statistics
Matches: 187, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
202 187 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (202 bp):
ATGCACACTAACCACAACTTCCGATGTTGGCAATGCAACATAATCAAGAACAAGTGAATTAAATT
CCTCCAATCCCCAAGCAACTTCCGGTGTCTTGCTTGTTAGTTTAAATTGTCATTGCACCTTCCAG
TGACAGTGACTGCAATAACACTTCCATGGTCAAAACATTCAAACCCAAATATTAAACAATAAAAG
AAAGCTC
Found at i:169300 original size:17 final size:17
Alignment explanation
Indices: 169233--169303 Score: 106
Period size: 17 Copynumber: 4.2 Consensus size: 17
169223 TACAATTACA
* * *
169233 AATGGAAATGCAACGAA
1 AATGCAAATGCAATGAC
169250 AATGCAAATGCAATGAC
1 AATGCAAATGCAATGAC
169267 AATGCAAATGCAATGAC
1 AATGCAAATGCAATGAC
*
169284 AATGTAAATGCAATGAC
1 AATGCAAATGCAATGAC
169301 AAT
1 AAT
169304 TAAAATGTAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.18
Consensus pattern (17 bp):
AATGCAAATGCAATGAC
Found at i:169303 original size:23 final size:23
Alignment explanation
Indices: 169267--169312 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
169257 ATGCAATGAC
*
169267 AATGCAAATGCAATGACAATGTA
1 AATGCAAATGCAATGAAAATGTA
*
169290 AATGC-AATGACAATTAAAATGTA
1 AATGCAAATG-CAATGAAAATGTA
169313 GTGACAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (23 bp):
AATGCAAATGCAATGAAAATGTA
Found at i:169310 original size:34 final size:34
Alignment explanation
Indices: 169233--169321 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
169223 TACAATTACA
* * *
169233 AATGGAAATGCAACGAAAATGCAAATGCAATGAC
1 AATGAAAATGCAATGACAATGCAAATGCAATGAC
* *
169267 AATGCAAATGCAATGACAATGTAAATGCAATGAC
1 AATGAAAATGCAATGACAATGCAAATGCAATGAC
* * *
169301 AATTAAAATGTAGTGACAATG
1 AATGAAAATGCAATGACAATG
169322 GGAATGTGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.20
Consensus pattern (34 bp):
AATGAAAATGCAATGACAATGCAAATGCAATGAC
Found at i:179075 original size:9 final size:9
Alignment explanation
Indices: 179061--179086 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
179051 TGGTTGGGAA
179061 TATTGTTGT
1 TATTGTTGT
179070 TATTGTTGT
1 TATTGTTGT
179079 TATTGTTG
1 TATTGTTG
179087 ATGTCGTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.23, T:0.65
Consensus pattern (9 bp):
TATTGTTGT
Found at i:179186 original size:18 final size:18
Alignment explanation
Indices: 179144--179187 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
179134 AGCTTGTGGC
*
179144 TGCATCTGGTTATATGAA
1 TGCATCTGATTATATGAA
* * *
179162 TGTATCTGATTTTATGAT
1 TGCATCTGATTATATGAA
179180 TGCATCTG
1 TGCATCTG
179188 GTCATGTGAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.45
Consensus pattern (18 bp):
TGCATCTGATTATATGAA
Found at i:183123 original size:55 final size:55
Alignment explanation
Indices: 183057--183167 Score: 150
Period size: 55 Copynumber: 2.0 Consensus size: 55
183047 TTATCCAGAC
* * * * **
183057 AGCTGTTAGATGTGACGATAATTTTGGGTGCAATTCTGGATATGCTCATGCAGCG
1 AGCTGTCAGATGCGACGACAATTCTGGGCACAATTCTGGATATGCTCATGCAGCG
* *
183112 AGCTGTCAGATGCGGCGACAATTCTGGGCACAATTTTGGATATGCTCATGCAGCG
1 AGCTGTCAGATGCGACGACAATTCTGGGCACAATTCTGGATATGCTCATGCAGCG
183167 A
1 A
183168 CATTAGTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (55 bp):
AGCTGTCAGATGCGACGACAATTCTGGGCACAATTCTGGATATGCTCATGCAGCG
Found at i:190184 original size:3 final size:3
Alignment explanation
Indices: 190178--190202 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
190168 CTTGTTATTA
190178 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
190203 GGATGTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:196047 original size:17 final size:17
Alignment explanation
Indices: 196025--196058 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
196015 CAACAAAATT
196025 CCAAAATA-TTATGAAAA
1 CCAAAATAGTT-TGAAAA
196042 CCAAAATAGTTTGAAAA
1 CCAAAATAGTTTGAAAA
196059 TCATAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.24
Consensus pattern (17 bp):
CCAAAATAGTTTGAAAA
Found at i:196708 original size:30 final size:30
Alignment explanation
Indices: 196606--196701 Score: 138
Period size: 30 Copynumber: 3.2 Consensus size: 30
196596 ATAATATCAA
**
196606 ACACACAACAAGCATGTAGCACAAACAGAG
1 ACACACAACAAGCATGTAGCACGGACAGAG
* * *
196636 ACACACAACAAACATGTAACATGGACAGAG
1 ACACACAACAAGCATGTAGCACGGACAGAG
*
196666 ACACACAACAAGCATGTAGCACGGACTGAG
1 ACACACAACAAGCATGTAGCACGGACAGAG
196696 ACACAC
1 ACACAC
196702 TTCAAGCGGC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.08
Consensus pattern (30 bp):
ACACACAACAAGCATGTAGCACGGACAGAG
Found at i:208826 original size:58 final size:57
Alignment explanation
Indices: 208748--209024 Score: 177
Period size: 58 Copynumber: 4.8 Consensus size: 57
208738 TCTCGAGAGC
* *
208748 AAAATGGTAATTTTGGGAAAATTTAGGGTTTAAAATGGAATTTTAGACATCCGAGGGT
1 AAAATGGTAATTTT-TGAAAATTTAGGGTTAAAAATGGAATTTTAGACATCCGAGGGT
* * * * * * **
208806 AAAACGGTAATTTTTAGAAAA-ATCGGGATAAAAAATGAAATTTTTTGACATTTGAGGGT
1 AAAATGGTAATTTTT-GAAAATTTAGGG-TTAAAAATGGAA-TTTTAGACATCCGAGGGT
* * * ** ** *
208865 AAAATGGTAATTTTTGAAAGTTTTGGGGTAAAAATGGAATATTTAGAGGTTTGGGGGT
1 AAAATGGTAATTTTTGAAAATTTAGGGTTAAAAATGGAAT-TTTAGACATCCGAGGGT
** * * * * **
208923 AAAAAT-GTAATTTTTGGAAGTTTTAAGGTTAAAAATTGAAATTTAAGAAATTTGAGGGT
1 -AAAATGGTAATTTTT-GAAAATTTAGGGTTAAAAA-TGGAATTTTAGACATCCGAGGGT
*
208982 AAAAAT-GTAA-TCTT-AAAAGTTTTAGGGTTAAAAATGGAATTTT
1 -AAAATGGTAATTTTTGAAAA--TTTAGGGTTAAAAATGGAATTTT
209025 TGGAAGTTCG
Statistics
Matches: 172, Mismatches: 37, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
56 2 0.01
57 12 0.07
58 78 0.45
59 75 0.44
60 5 0.03
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (57 bp):
AAAATGGTAATTTTTGAAAATTTAGGGTTAAAAATGGAATTTTAGACATCCGAGGGT
Found at i:208868 original size:29 final size:29
Alignment explanation
Indices: 208836--209053 Score: 126
Period size: 29 Copynumber: 7.5 Consensus size: 29
208826 AATCGGGATA
* *
208836 AAAAATGAAATTTTTTGACATTTGAGGGT
1 AAAAATGAAATTTTTAGAAATTTGAGGGT
*
208865 -AAAATGGTAATTTTT-GAAAGTTTTG-GGGT
1 AAAAAT-GAAATTTTTAGAAA--TTTGAGGGT
* * ** *
208894 AAAAATGGAATATTTAGAGGTTTGGGGGT
1 AAAAATGAAATTTTTAGAAATTTGAGGGT
* * * * *
208923 AAAAATGTAATTTTTGGAAGTTTTAAGGTT
1 AAAAATGAAATTTTTAGAA-ATTTGAGGGT
*
208953 AAAAATTGAAA-TTTAAGAAATTTGAGGGT
1 AAAAA-TGAAATTTTTAGAAATTTGAGGGT
* * *
208982 AAAAATGTAA-TCTTA-AAAGTTTTAGGGTT
1 AAAAATGAAATTTTTAGAAA-TTTGAGGG-T
* * * *
209011 AAAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAAATGAAATTTTTAGAAATTTGAGGGT
209040 AAAAAT-ATAATTTT
1 AAAAATGA-AATTTT
209054 CAAAAGTTTT
Statistics
Matches: 145, Mismatches: 31, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
27 3 0.02
28 26 0.18
29 73 0.50
30 37 0.26
31 6 0.04
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAAATGAAATTTTTAGAAATTTGAGGGT
Found at i:209038 original size:58 final size:59
Alignment explanation
Indices: 208836--209068 Score: 249
Period size: 58 Copynumber: 4.0 Consensus size: 59
208826 AATCGGGATA
* * * *
208836 AAAAATGAAATTTTTTGACA-TTTGAGGGT-AAAATGGTAATTTTTGAAAGTTTT-GGGGT
1 AAAAATGGAATTTTTAGA-AGTTTGAGGGTAAAAAT-GTAATTTTTAAAAGTTTTAGGGTT
* * * ** *
208894 AAAAATGGAATATTTAGAGGTTTGGGGGTAAAAATGTAATTTTTGGAAGTTTTAAGGTT
1 AAAAATGGAATTTTTAGAAGTTTGAGGGTAAAAATGTAATTTTTAAAAGTTTTAGGGTT
* * * * *
208953 AAAAATTGAAATTTAAGAAATTTGAGGGTAAAAATGTAA-TCTTAAAAGTTTTAGGGTT
1 AAAAATGGAATTTTTAGAAGTTTGAGGGTAAAAATGTAATTTTTAAAAGTTTTAGGGTT
* * * *
209011 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCAAAAGTTTTAGGGT
1 AAAAATGGAATTTTTAGAAGTTTGAGGGTAAAAATGTAATTTTTAAAAGTTTTAGGGT
209069 CGAAGGTGGA
Statistics
Matches: 143, Mismatches: 28, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
58 87 0.61
59 56 0.39
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (59 bp):
AAAAATGGAATTTTTAGAAGTTTGAGGGTAAAAATGTAATTTTTAAAAGTTTTAGGGTT
Found at i:209067 original size:29 final size:28
Alignment explanation
Indices: 208860--209068 Score: 134
Period size: 29 Copynumber: 7.2 Consensus size: 28
208850 TTGACATTTG
*
208860 AGGGT-AAAATGGTAATTTTTGAAAGTTTT
1 AGGGTAAAAAT-GTAA-TTTTAAAAGTTTT
* * * * *
208889 GGGGTAAAAATGGAATATTTAGAGGTTTG
1 AGGGTAAAAATGTAAT-TTTAAAAGTTTT
* **
208918 GGGGTAAAAATGTAATTTTTGGAAGTTTT
1 AGGGTAAAAATGTAA-TTTTAAAAGTTTT
* * * *
208947 AAGGTTAAAAAT-TGAAATTTAAGAAATTTG
1 -AGGGTAAAAATGT-AATTTTAA-AAGTTTT
*
208977 AGGGTAAAAATGTAATCTTAAAAGTTTT
1 AGGGTAAAAATGTAATTTTAAAAGTTTT
* ** **
209005 AGGGTTAAAAATGGAATTTTTGGAAGTTCG
1 AGGG-TAAAAATGTAA-TTTTAAAAGTTTT
*
209035 AGGGTAAAAATATAATTTTCAAAAGTTTT
1 AGGGTAAAAATGTAATTTT-AAAAGTTTT
209064 AGGGT
1 AGGGT
209069 CGAAGGTGGA
Statistics
Matches: 136, Mismatches: 34, Indels: 20
0.72 0.18 0.11
Matches are distributed among these distances:
28 14 0.10
29 87 0.64
30 35 0.26
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.36
Consensus pattern (28 bp):
AGGGTAAAAATGTAATTTTAAAAGTTTT
Found at i:209079 original size:59 final size:59
Alignment explanation
Indices: 208976--209092 Score: 164
Period size: 59 Copynumber: 2.0 Consensus size: 59
208966 TAAGAAATTT
* *
208976 GAGGGTAAAAATGTAATCTTAAAAGTTTTAGGGTTAAAAATGGAATTTTTGGA-AGTTC
1 GAGGGTAAAAATATAATCTTAAAAGTTTTAGGGTCAAAAATGGAATTTTTGGATAGTTC
* * **
209034 GAGGGTAAAAATATAATTTTCAAAAGTTTTAGGGTCGAAGGTGGAATTTTTGGATAGTT
1 GAGGGTAAAAATATAATCTT-AAAAGTTTTAGGGTCAAAAATGGAATTTTTGGATAGTT
209093 TAGGGACCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
58 18 0.35
59 29 0.57
60 4 0.08
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (59 bp):
GAGGGTAAAAATATAATCTTAAAAGTTTTAGGGTCAAAAATGGAATTTTTGGATAGTTC
Found at i:210098 original size:9 final size:9
Alignment explanation
Indices: 210086--210164 Score: 52
Period size: 9 Copynumber: 8.7 Consensus size: 9
210076 TAATATTTAA
210086 TATTAATAT
1 TATTAATAT
210095 TATTAATAT
1 TATTAATAT
* *
210104 TATTATTGT
1 TATTAATAT
*
210113 TAATTAATAC
1 T-ATTAATAT
* *
210123 CATTAGTAT
1 TATTAATAT
*
210132 TA-TACTTAT
1 TATTA-ATAT
*
210141 GATTAATAT
1 TATTAATAT
*
210150 TATTATTAT
1 TATTAATAT
*
210159 CATTAA
1 TATTAA
210165 GGCTATTTAT
Statistics
Matches: 51, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
8 2 0.04
9 42 0.82
10 7 0.14
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (9 bp):
TATTAATAT
Found at i:210100 original size:15 final size:15
Alignment explanation
Indices: 210082--210116 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
210072 TTTTTAATAT
210082 TTAATATTAATATTA
1 TTAATATTAATATTA
* *
210097 TTAATATTATTATTG
1 TTAATATTAATATTA
210112 TTAAT
1 TTAAT
210117 TAATACCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TTAATATTAATATTA
Found at i:210864 original size:6 final size:6
Alignment explanation
Indices: 210855--210950 Score: 85
Period size: 6 Copynumber: 16.7 Consensus size: 6
210845 TTTGGACATT
* *
210855 AATTTA AATTTA AATTTA AACTTA AATTTA TAA--TA AATTTA AATTTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * * * *
210902 AA-GTA AATTTA AACTTA AA-ATA AATTTA ATTTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
210947 AATT
1 AATT
210951 CTGTTAGGCC
Statistics
Matches: 71, Mismatches: 13, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
4 2 0.03
5 13 0.18
6 54 0.76
7 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:210891 original size:17 final size:17
Alignment explanation
Indices: 210855--210950 Score: 120
Period size: 17 Copynumber: 5.6 Consensus size: 17
210845 TTTGGACATT
*
210855 AATTTAAATTTAAATTTA
1 AATTTAAATTTAAA-ATA
* *
210873 AACTTAAATTTATAATA
1 AATTTAAATTTAAAATA
* *
210890 AATTTAAATTTTAAGTA
1 AATTTAAATTTAAAATA
*
210907 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
*
210924 AATTTAATTTTAAAATA
1 AATTTAAATTTAAAATA
210941 AATTTAAATT
1 AATTTAAATT
210951 CTGTTAGGCC
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
17 53 0.82
18 12 0.18
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:212142 original size:205 final size:206
Alignment explanation
Indices: 211273--212289 Score: 1509
Period size: 206 Copynumber: 4.9 Consensus size: 206
211263 GTCTGGTTTC
* * ** ** **
211273 TTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTG
1 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTG
* * * *
211338 TGTTTCATCAGGAAGACGAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCATTTTAT
66 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
211403 TACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
131 TACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
*
211468 ATGGGTTT-AGT
196 GTGGGTTTGA-T
* *
211479 TTGGTCTTCTTCTCTGTGTCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTG
1 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTG
* * *
211544 TATCTCATCAGGAAGATGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGGTAACCATTTTAT
66 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * * *
211609 TACTTCGACCTGCTTCTTAGTATCTTATCAGGAAGCTAGGGTTCGAAGATTTGCTAACATCGAGC
131 TACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
211674 GTGGGTTTGAT
196 GTGGGTTTGAT
*
211685 TTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTG
1 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTG
*
211750 TATCTCATCAGGAAGACGAATTTAGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
66 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * * * *
211815 TACTTCGACTTGCTTCTCAATATCTCATTAGGATGTTGGGGTTCGAAGATTTGCTCACATCGAGC
131 TACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
*
211880 GTGGGTTTTAT
196 GTGGGTTTGAT
* * * *
211891 TTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACTGCGTCGTTTGTTTTAATCTGATTCTCTG
1 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTG
* *
211956 TATCTTATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGAAAGCTAACC-TTTTAT
66 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * * *
212020 TGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGTTTCAAAGATTTGCTCACATCGAGC
131 TACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
212085 GTGGGTTTGAT
196 GTGGGTTTGAT
* ** **
212096 TTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGATTGTATCGTTTGTTTCAATCTGCTTCTCTG
1 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTG
* * * *
212161 TAACTCATTAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACC-TTTTAT
66 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* * * * * *
212225 TGCTTCGCCCTGCTTCTCAGTATCTCATCAGGAAGTTGTGATTTGAAGATTTGCTCACATCGAGC
131 TACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
212290 CCTGAGTTGG
Statistics
Matches: 735, Mismatches: 75, Indels: 3
0.90 0.09 0.00
Matches are distributed among these distances:
205 246 0.33
206 488 0.66
207 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (206 bp):
TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTG
TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
TACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
GTGGGTTTGAT
Found at i:223757 original size:58 final size:58
Alignment explanation
Indices: 223690--223986 Score: 275
Period size: 59 Copynumber: 5.1 Consensus size: 58
223680 TAGGTTCTCG
* * * * *
223690 GGGGCAAAATGGTAATTTTGGGAAATTTTAGAGTTTAAAATGGAA-TTTTAGACATTT-
1 GGGGTAAAATGGTAATTTT-AGAAAGTTTCGAGTTTAAAATGGAATTTTTGGACATTTA
** **
223747 GAGGGTAAAATGGTAATTTTTAGAAA-AATCGAGATAAAAAATGGAATTTTTGGACATTTA
1 G-GGGTAAAATGGTAA-TTTTAGAAAGTTTCGAG-TTTAAAATGGAATTTTTGGACATTTA
* * *
223807 GGGGTAAAATGGTAATTTTTA-AAAGTTTTGAGGTTAAAATGGAATTTTTGGAAATTTA
1 GGGGTAAAATGGTAA-TTTTAGAAAGTTTCGAGTTTAAAATGGAATTTTTGGACATTTA
* * *
223865 GGGGTAAAATTGTAATTTTAAAAAGTTTCGAGGTTAAAAATGGAATTTTTGGA-AGTTT-
1 GGGGTAAAATGGTAATTTTAGAAAGTTTCGA-GTTTAAAATGGAATTTTTGGACA-TTTA
* * * *
223923 GAGGGTAAAAAT-ATAATTTTTGAAAGTTTCGAGGTCTAAAATGGAATTTTTGGATAGTTTA
1 G-GGGT-AAAATGGTAATTTTAGAAAGTTTCGA-GTTTAAAATGGAATTTTTGGACA-TTTA
223984 GGG
1 GGG
223987 ACTTTTAGGG
Statistics
Matches: 203, Mismatches: 24, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
57 10 0.05
58 77 0.38
59 102 0.50
60 13 0.06
61 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTAGAAAGTTTCGAGTTTAAAATGGAATTTTTGGACATTTA
Found at i:223870 original size:117 final size:115
Alignment explanation
Indices: 223690--223986 Score: 327
Period size: 117 Copynumber: 2.5 Consensus size: 115
223680 TAGGTTCTCG
* * * * *
223690 GGGGCAAAATGGTAATTTTGGGAAA-TTTTAGAGTTTAAAATGGAA-TTTTAGACATTT-GAGGG
1 GGGGTAAAATGGTAATTTT-TGAAAGTTTT-GAGGTTAAAATGGAATTTTTGGAAATTTAG-GGG
223752 TAAAATGGTAATTTTTAGAAAA-ATCGAGATAAAAAATGGAATTTTTGGACA-TTT
63 TAAAATGGTAA-TTTTA-AAAAGATCGAGATAAAAAATGGAATTTTTGGA-AGTTT
*
223806 AGGGGTAAAATGGTAATTTTTAAAAGTTTTGAGGTTAAAATGGAATTTTTGGAAATTTAGGGGTA
1 -GGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTTAAAATGGAATTTTTGGAAATTTAGGGGTA
* * * *
223871 AAATTGTAATTTTAAAAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTT
65 AAATGGTAATTTTAAAAAG-ATCGAGATAAAAAATGGAATTTTTGGAAGTTT
* * *
223923 GAGGGTAAAAAT-ATAATTTTTGAAAGTTTCGAGGTCTAAAATGGAATTTTTGGATAGTTTAGGG
1 G-GGGT-AAAATGGTAATTTTTGAAAGTTTTGAGGT-TAAAATGGAATTTTTGGA-AATTTAGGG
223987 ACTTTTAGGG
Statistics
Matches: 156, Mismatches: 14, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
115 4 0.03
116 24 0.15
117 96 0.62
118 24 0.15
119 8 0.05
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (115 bp):
GGGGTAAAATGGTAATTTTTGAAAGTTTTGAGGTTAAAATGGAATTTTTGGAAATTTAGGGGTAA
AATGGTAATTTTAAAAAGATCGAGATAAAAAATGGAATTTTTGGAAGTTT
Found at i:223912 original size:30 final size:30
Alignment explanation
Indices: 223695--223974 Score: 163
Period size: 30 Copynumber: 9.5 Consensus size: 30
223685 TCTCGGGGGC
* * * *
223695 AAAATGGTAATTTTGGGAAATTTTAGA-GTTT
1 AAAATGG-AATTTT-TGAAAGTTTCGAGGTTA
* * *
223726 AAAATGGAATTTTAGACA-TTT-GAGGGT-
1 AAAATGGAATTTTTGAAAGTTTCGAGGTTA
** * *
223753 AAAATGGTAATTTTTAGAAA-AATCGAGATAA
1 AAAATGG-AATTTTT-GAAAGTTTCGAGGTTA
* * *
223784 AAAATGGAATTTTTGGACA-TTTAG-GGGT-
1 AAAATGGAATTTTT-GAAAGTTTCGAGGTTA
* *
223812 AAAATGGTAATTTTTAAAAGTTTTGAGGTT-
1 AAAATGG-AATTTTTGAAAGTTTCGAGGTTA
* *
223842 AAAATGGAATTTTTGGAAA-TTTAG-GGGTA
1 AAAATGGAATTTTT-GAAAGTTTCGAGGTTA
* * **
223871 AAATTGTAATTTTAAAAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGAAAGTTTCGAGGTTA
* *
223901 AAAATGGAATTTTTGGAAGTTT-GAGGGTA
1 AAAATGGAATTTTTGAAAGTTTCGAGGTTA
**
223930 AAAATATAATTTTTGAAAGTTTCGAGGTCT-
1 AAAATGGAATTTTTGAAAGTTTCGAGGT-TA
223960 AAAATGGAATTTTTG
1 AAAATGGAATTTTTG
223975 GATAGTTTAG
Statistics
Matches: 192, Mismatches: 43, Indels: 29
0.73 0.16 0.11
Matches are distributed among these distances:
27 9 0.05
28 26 0.14
29 70 0.36
30 72 0.38
31 15 0.08
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
AAAATGGAATTTTTGAAAGTTTCGAGGTTA
Found at i:223940 original size:29 final size:29
Alignment explanation
Indices: 223783--223986 Score: 152
Period size: 29 Copynumber: 7.0 Consensus size: 29
223773 AATCGAGATA
223783 AAAAATGGAATTTTTGGACA-TTT-AGGGGT
1 AAAAATGGAATTTTTGGA-AGTTTGA-GGGT
**
223812 -AAAATGGTAATTTTTAAAAGTTTTGA-GGT
1 AAAAATGG-AATTTTTGGAAG-TTTGAGGGT
* *
223841 TAAAATGGAATTTTTGGAAATTT-AGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGA-GGGT
* * *** *
223870 AAAATTGTAATTTTAAAAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTT-GAGGGT
223900 AAAAATGGAATTTTTGGAAGTTTGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTGAGGGT
** *
223929 AAAAATATAATTTTTGAAAGTTTCGA-GGT
1 AAAAATGGAATTTTTGGAAGTTT-GAGGGT
*
223958 CTAAAATGGAATTTTTGGATAGTTT-AGGG
1 -AAAAATGGAATTTTTGGA-AGTTTGAGGG
223987 ACTTTTAGGG
Statistics
Matches: 136, Mismatches: 26, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
27 1 0.01
28 11 0.08
29 68 0.50
30 49 0.36
31 7 0.05
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGAGGGT
Found at i:224988 original size:9 final size:9
Alignment explanation
Indices: 224976--225054 Score: 52
Period size: 9 Copynumber: 8.7 Consensus size: 9
224966 TAATATTTAA
224976 TATTAATAT
1 TATTAATAT
224985 TATTAATAT
1 TATTAATAT
* *
224994 CATTATTAT
1 TATTAATAT
* *
225003 TAATTAACAC
1 T-ATTAATAT
* *
225013 CATTAGTAT
1 TATTAATAT
*
225022 TA-TACTTAT
1 TATTA-ATAT
225031 TATTAATAT
1 TATTAATAT
*
225040 TATTATTAT
1 TATTAATAT
*
225049 CATTAA
1 TATTAA
225055 GGCTATTTAT
Statistics
Matches: 51, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
8 2 0.04
9 42 0.82
10 7 0.14
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.51
Consensus pattern (9 bp):
TATTAATAT
Found at i:224990 original size:15 final size:15
Alignment explanation
Indices: 224972--225006 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
224962 TTTTTAATAT
*
224972 TTAATATTAATATTA
1 TTAATATCAATATTA
*
224987 TTAATATCATTATTA
1 TTAATATCAATATTA
225002 TTAAT
1 TTAAT
225007 TAACACCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAATATCAATATTA
Found at i:225752 original size:6 final size:6
Alignment explanation
Indices: 225743--225781 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
225733 TTTGGACATT
* *
225743 AATTTA AATTTA AATTTA AACTTA AA-ATA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATT
225782 CTGTTGGGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:230067 original size:20 final size:20
Alignment explanation
Indices: 230042--230085 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
230032 CGAAAAATGA
230042 TTTTT-GAAAAATAAATTATT
1 TTTTTGGAAAAATAAA-TATT
* *
230062 TTTTTGGAAAAGTTAATATT
1 TTTTTGGAAAAATAAATATT
230082 TTTT
1 TTTT
230086 GGTATTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTTGGAAAAATAAATATT
Found at i:232599 original size:7 final size:7
Alignment explanation
Indices: 232587--232632 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
232577 GAGAATGAGA
232587 AAGGGGG
1 AAGGGGG
232594 AAGGGGG
1 AAGGGGG
232601 AAGGGGG
1 AAGGGGG
*
232608 AAGGTGG
1 AAGGGGG
*
232615 AAGGTGG
1 AAGGGGG
*
232622 AAGGTGG
1 AAGGGGG
232629 AAGG
1 AAGG
232633 AAAAAGAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.30, C:0.00, G:0.63, T:0.07
Consensus pattern (7 bp):
AAGGGGG
Found at i:232606 original size:14 final size:14
Alignment explanation
Indices: 232587--232632 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
232577 GAGAATGAGA
*
232587 AAGGGGGAAGGGGG
1 AAGGGGGAAGGTGG
232601 AAGGGGGAAGGTGG
1 AAGGGGGAAGGTGG
*
232615 AAGGTGGAAGGTGG
1 AAGGGGGAAGGTGG
232629 AAGG
1 AAGG
232633 AAAAAGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.63, T:0.07
Consensus pattern (14 bp):
AAGGGGGAAGGTGG
Found at i:236503 original size:155 final size:155
Alignment explanation
Indices: 236221--236528 Score: 580
Period size: 155 Copynumber: 2.0 Consensus size: 155
236211 ACAATAGAGT
*
236221 TCAATGAAATCTTACCAATAACAATCATCCGTTTAATCAAGACTCAAGTACCCACAATCACCCCA
1 TCAATGAAATCTTACCAATAACAATCATCCGTTTAATCAAGACTCAAGTACCCACAATCACCCAA
236286 CCTCTCGGTGTGAACAACGTTGTGCACTCAAGAACAAGTGACTAGAATCCCTTCTAATCTCAAGC
66 CCTCTCGGTGTGAACAACGTTGTGCACTCAAGAACAAGTGACTAGAATCCCTTCTAATCTCAAGC
236351 AACTCTCATTGTCTTGCTTGTTAGC
131 AACTCTCATTGTCTTGCTTGTTAGC
*
236376 TCAATGAAGTCTTACCAATAACAATCATCCGTTTAATCAAGACTCAAGTACCCACAATCACCCAA
1 TCAATGAAATCTTACCAATAACAATCATCCGTTTAATCAAGACTCAAGTACCCACAATCACCCAA
* *
236441 CCTCTCGGTGTGAACAATGTTGTGCACTCAAGAACAAGTGACTAGAATCTCTTCTAATCTCAAGC
66 CCTCTCGGTGTGAACAACGTTGTGCACTCAAGAACAAGTGACTAGAATCCCTTCTAATCTCAAGC
236506 AACTCTCATTGTCTTGCTTGTTA
131 AACTCTCATTGTCTTGCTTGTTA
236529 ACCTAACTTG
Statistics
Matches: 149, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 149 1.00
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (155 bp):
TCAATGAAATCTTACCAATAACAATCATCCGTTTAATCAAGACTCAAGTACCCACAATCACCCAA
CCTCTCGGTGTGAACAACGTTGTGCACTCAAGAACAAGTGACTAGAATCCCTTCTAATCTCAAGC
AACTCTCATTGTCTTGCTTGTTAGC
Found at i:237009 original size:20 final size:21
Alignment explanation
Indices: 236969--237022 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
236959 GTGGATTGGT
*
236969 ATGATTTATATTAAGTATAAAT
1 ATGATTTA-ATTAAGTATAAAA
236991 A-GATTTAATTAAG-ATTAAAA
1 ATGATTTAATTAAGTA-TAAAA
237011 ATGA-TTAATTAA
1 ATGATTTAATTAA
237023 AGCTTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
20 19 0.66
21 8 0.28
22 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (21 bp):
ATGATTTAATTAAGTATAAAA
Found at i:247328 original size:16 final size:16
Alignment explanation
Indices: 247307--247337 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
247297 ATAACAAACA
247307 TTTTTTTCTTCTTTTC
1 TTTTTTTCTTCTTTTC
*
247323 TTTTTTTTTTCTTTT
1 TTTTTTTCTTCTTTT
247338 TGTCATTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTCTTCTTTTC
Found at i:254286 original size:15 final size:14
Alignment explanation
Indices: 254262--254293 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
254252 CTATTGATGG
254262 TTGTTATAACTCCC
1 TTGTTATAACTCCC
254276 TTGTCTATAACTCCC
1 TTGT-TATAACTCCC
254291 TTG
1 TTG
254294 ATTTGTGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (14 bp):
TTGTTATAACTCCC
Found at i:256747 original size:11 final size:12
Alignment explanation
Indices: 256731--256807 Score: 51
Period size: 11 Copynumber: 6.8 Consensus size: 12
256721 CTTAATCACT
256731 TTAATATTAA-A
1 TTAATATTAAGA
256742 TTAATA-TAAGA
1 TTAATATTAAGA
256753 TT--TATTAAGA
1 TTAATATTAAGA
*
256763 TAAATATT-AGA
1 TTAATATTAAGA
*
256774 TTAA-ATTTAATA
1 TTAATA-TTAAGA
256786 TTAAATTATTAA-A
1 TT-AA-TATTAAGA
*
256799 ATAATATTA
1 TTAATATTA
256808 TTTTTGGAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
9 2 0.04
10 10 0.19
11 22 0.42
12 10 0.19
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (12 bp):
TTAATATTAAGA
Found at i:256774 original size:21 final size:20
Alignment explanation
Indices: 256735--256775 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
256725 ATCACTTTAA
*
256735 TATTAAATTAATATAAGATT
1 TATTAAATAAATATAAGATT
*
256755 TATTAAGATAAATATTAGATT
1 TATTAA-ATAAATATAAGATT
256776 AAATTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
TATTAAATAAATATAAGATT
Found at i:256777 original size:37 final size:36
Alignment explanation
Indices: 256736--256807 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
256726 TCACTTTAAT
*
256736 ATTAAA-TTAATA-TAAGATTTATTAAGATAAATATTAG
1 ATTAAATTTAATATTAA-A-TTATTAAAAT-AATATTAG
256773 ATTAAATTTAATATTAAATTATTAAAATAATATTA
1 ATTAAATTTAATATTAAATTATTAAAATAATATTA
256808 TTTTTGGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 7 0.22
37 15 0.47
38 7 0.22
39 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (36 bp):
ATTAAATTTAATATTAAATTATTAAAATAATATTAG
Found at i:259135 original size:122 final size:123
Alignment explanation
Indices: 258902--259395 Score: 672
Period size: 123 Copynumber: 4.0 Consensus size: 123
258892 ATTCTGCTAT
* * * * * * **
258902 ATTTCATTTTATTTAATATCTCATATTAAAATGGAATTATTCTTTTATAGAAATATATTTAAGGT
1 ATTTCTTTTTATTTAATATCTCATATTAAAACGGAAATATTCCTTTAAAAAAATATATGAAAGGT
*
258967 TTATTAAAACCATTATATCTC-TTCCAAAAGAATATTAACTTCCATGTTTTTAATATTCA
66 TTATTAAAA-CATTATATC-CATTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCA
* * * * * *
259026 ATTTCTTTTTAATTAATATCTCATATTAAAACGAAAATATTTCTTT-CAAAAATATAAGGAAGGT
1 ATTTCTTTTTATTTAATATCTCATATTAAAACGGAAATATTCCTTTAAAAAAATATATGAAAGGT
* *
259090 TAATTAAAACATTATATCCATTCCAAAAGGATATTAACTTTCATGTTTTTAATATTCA
66 TTATTAAAACATTATATCCATTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCA
259148 ATTTCTTTTTATTTAATATCT-ACTATTAAAACGGAAATATTCCTTTAAAAAAATATATGAAAGG
1 ATTTCTTTTTATTTAATATCTCA-TATTAAAACGGAAATATTCCTTTAAAAAAATATATGAAAGG
* * * * *
259212 TTTGTTAAAACATTATATCCTTTCCAAAATGATATTAACTTCAATGTTTTTAGTATTCA
65 TTTATTAAAACATTATATCCATTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCA
* *
259271 ATTTCCTTTTATTTAATATCTCATATTAAAACGGAAATATTCCTTTAGAAAAATATATGAAAGGT
1 ATTTCTTTTTATTTAATATCTCATATTAAAACGGAAATATTCCTTTAAAAAAATATATGAAAGGT
* * * *
259336 TTATTAAAATATTATAT-TATTTCCAAAAAGATATTAACTTCCATTTTTTTAATATTCA
66 TTATTAAAACATTATATCCA-TTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCA
259394 AT
1 AT
259396 GAAATCATTA
Statistics
Matches: 327, Mismatches: 38, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
121 2 0.01
122 86 0.26
123 199 0.61
124 40 0.12
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (123 bp):
ATTTCTTTTTATTTAATATCTCATATTAAAACGGAAATATTCCTTTAAAAAAATATATGAAAGGT
TTATTAAAACATTATATCCATTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCA
Found at i:259152 original size:21 final size:22
Alignment explanation
Indices: 259120--259166 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
259110 TTCCAAAAGG
259120 ATATTAACTTTCATGTT-TTTA
1 ATATTAACTTTCATGTTATTTA
* *
259141 ATATTCAA-TTTCTTTTTATTTA
1 ATATT-AACTTTCATGTTATTTA
259163 ATAT
1 ATAT
259167 CTACTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.60
Consensus pattern (22 bp):
ATATTAACTTTCATGTTATTTA
Found at i:274214 original size:50 final size:50
Alignment explanation
Indices: 274058--274214 Score: 165
Period size: 50 Copynumber: 3.1 Consensus size: 50
274048 CCTATACCCT
* * *
274058 TAAAGCTGCAGAGGAACGGATTGAAGTCGCAATGGCAAATCTCATACAT-C
1 TAAAGCTGTAGAGGGACAGATTGAAGTCGCAATGGCAAATCTCATAC-TCC
* * * * * *
274108 AAAAGCTGTAGAGGGACAGATTGAAATTGCAATGGCGAATCTCATTCGCC
1 TAAAGCTGTAGAGGGACAGATTGAAGTCGCAATGGCAAATCTCATACTCC
* * *
274158 TAAAGCTGTAGAGGGGCAGATTGAAGTCGCAA-GTACAAATCTTATACTCC
1 TAAAGCTGTAGAGGGACAGATTGAAGTCGCAATG-GCAAATCTCATACTCC
*
274208 TGAAGCT
1 TAAAGCT
274215 AAAAAGGAGC
Statistics
Matches: 86, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
49 1 0.01
50 85 0.99
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (50 bp):
TAAAGCTGTAGAGGGACAGATTGAAGTCGCAATGGCAAATCTCATACTCC
Found at i:274343 original size:40 final size:40
Alignment explanation
Indices: 274299--274466 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
274289 CTTAGCTAGA
* ** *
274299 GGGCAGATTGAAGATCATCTGATCTCTTACCCCGACCATG
1 GGGCAGATTGAAGACCATCAAATCTCTTACCCCAACCATG
* ** * * * **
274339 GGGCAGATTGAAG-CAATTTAATCTTTTACCCTAACTAAA
1 GGGCAGATTGAAGACCATCAAATCTCTTACCCCAACCATG
* * *
274378 GGGCAAATTGAAGACCATCAAATCTTTTACCCTAACCA-G
1 GGGCAGATTGAAGACCATCAAATCTCTTACCCCAACCATG
* *
274417 AGGGCAGATTGAAGACCATCAGATCTCTTACCCCGACCATG
1 -GGGCAGATTGAAGACCATCAAATCTCTTACCCCAACCATG
*
274458 GGGTAGATT
1 GGGCAGATT
274467 AAAAACAATC
Statistics
Matches: 103, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
39 28 0.27
40 74 0.72
41 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (40 bp):
GGGCAGATTGAAGACCATCAAATCTCTTACCCCAACCATG
Found at i:274382 original size:39 final size:40
Alignment explanation
Indices: 274279--274449 Score: 139
Period size: 40 Copynumber: 4.3 Consensus size: 40
274269 AAAGTAATAC
* * * * *
274279 AATCTTTTACCTTAGCTAGAGGGCAGATTGAAGATC-ATCT
1 AATCTTTTACCCTAACCAAAGGGCAGATTGAAGA-CAATCA
* * ** ** **
274319 GATCTCTTACCCCGACCATGGGGCAGATTGAAG-CAATTT
1 AATCTTTTACCCTAACCAAAGGGCAGATTGAAGACAATCA
* * *
274358 AATCTTTTACCCTAACTAAAGGGCAAATTGAAGACCATCA
1 AATCTTTTACCCTAACCAAAGGGCAGATTGAAGACAATCA
* *
274398 AATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCA
1 AATCTTTTACCCTAACCAAAGGGCAGATTGAAGACAATCA
* *
274438 GATCTCTTACCC
1 AATCTTTTACCC
274450 CGACCATGGG
Statistics
Matches: 103, Mismatches: 26, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
38 1 0.01
39 28 0.27
40 74 0.72
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (40 bp):
AATCTTTTACCCTAACCAAAGGGCAGATTGAAGACAATCA
Found at i:274408 original size:79 final size:79
Alignment explanation
Indices: 274240--274430 Score: 213
Period size: 79 Copynumber: 2.4 Consensus size: 79
274230 TATGACCCTG
* * * * * * * * *
274240 AATCTTTTACCTCGACCATGGAGCAAATTAAAGTAATACAATCTTTTACCTTAGCTAGAGGGCAG
1 AATCTTTTACCCCGACCATGGGGCAGATTGAAGCAATACAATCTTTTACCCTAACTAAAGGGCAA
* *
274305 ATTGAAGATCATCT
66 ATTGAAGACCATCA
* * **
274319 GATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATTTAATCTTTTACCCTAACTAAAGGGCAA
1 AATCTTTTACCCCGACCATGGGGCAGATTGAAGCAATACAATCTTTTACCCTAACTAAAGGGCAA
274384 ATTGAAGACCATCA
66 ATTGAAGACCATCA
**
274398 AATCTTTTACCCTAACCA-GAGGGCAGATTGAAG
1 AATCTTTTACCCCGACCATG-GGGCAGATTGAAG
274431 ACCATCAGAT
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 1 0.01
79 91 0.99
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (79 bp):
AATCTTTTACCCCGACCATGGGGCAGATTGAAGCAATACAATCTTTTACCCTAACTAAAGGGCAA
ATTGAAGACCATCA
Found at i:274831 original size:149 final size:151
Alignment explanation
Indices: 274641--274952 Score: 432
Period size: 149 Copynumber: 2.1 Consensus size: 151
274631 AATTTTTATC
* * * *
274641 TCTCTTAAGTTGCAGTAGAGCAGGATGAAGCTACAAGAACAAATCCTATACCCCTGAATTTGC-A
1 TCTCTGAAGTTGCAGTAAAGCAGGATGAAGCTACAAAAACAAATCCTATACCCCTGAAGTT-CTA
* * * * *
274705 GTGGGTCAAATT-AAATCATGAAAACAAATCTTTA-CTTCTTGAAGTTGCAGTGAAGCAAGATGA
65 GTGGGTCAAATTAAAATCATGAAAACAAATATTTATCTCCCTGAAGTTACAGTGAAGCAAAATGA
* *
274768 AGTTACGACATCGAATCCTATA
130 AGCTACGACATCAAATCCTATA
* * *
274790 TCTCTGAATTTGCAGTAAAGTAGGATGAAGCTACAAAAACAAATCCTATACCCCTGAGGTTCTAG
1 TCTCTGAAGTTGCAGTAAAGCAGGATGAAGCTACAAAAACAAATCCTATACCCCTGAAGTTCTAG
**
274855 TGGGTCGGATTAAAATCATGAAAACAAATATTTATCTCCCTGAAGTTACAGTGAAGCAAAATGAA
66 TGGGTCAAATTAAAATCATGAAAACAAATATTTATCTCCCTGAAGTTACAGTGAAGCAAAATGAA
*
274920 GCTACGACATCAAATCTTATA
131 GCTACGACATCAAATCCTATA
*
274941 TCCCTGAAGTTG
1 TCTCTGAAGTTG
274953 TAGTGGATTG
Statistics
Matches: 141, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
148 1 0.01
149 65 0.46
150 21 0.15
151 54 0.38
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (151 bp):
TCTCTGAAGTTGCAGTAAAGCAGGATGAAGCTACAAAAACAAATCCTATACCCCTGAAGTTCTAG
TGGGTCAAATTAAAATCATGAAAACAAATATTTATCTCCCTGAAGTTACAGTGAAGCAAAATGAA
GCTACGACATCAAATCCTATA
Found at i:275395 original size:13 final size:14
Alignment explanation
Indices: 275379--275408 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
275369 AGCCCAAAAG
275379 AAAAAA-AAACCTA
1 AAAAAACAAACCTA
275392 AAAAAACAAACCTA
1 AAAAAACAAACCTA
275406 AAA
1 AAA
275409 TCTAAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.77, C:0.17, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAAACAAACCTA
Found at i:280355 original size:28 final size:28
Alignment explanation
Indices: 280307--280361 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
280297 TTATTTTAAG
280307 TTTGAATTTAGTATAAATTTAAATTTAT
1 TTTGAATTTAGTATAAATTTAAATTTAT
* *
280335 TTTGAATTTAAGT-TCATTTTAAATTTA
1 TTTGAATTT-AGTATAAATTTAAATTTA
280362 AATTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (28 bp):
TTTGAATTTAGTATAAATTTAAATTTAT
Found at i:280360 original size:7 final size:6
Alignment explanation
Indices: 280320--280374 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
280310 GAATTTAGTA
* * * * *
280320 TAAATT TAAATT T-ATTT TGAATT T-AAGT TCATTT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
280366 TAAATT TAA
1 TAAATT TAA
280375 TTAAAAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
5 8 0.20
6 32 0.80
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (6 bp):
TAAATT
Found at i:280376 original size:17 final size:17
Alignment explanation
Indices: 280294--280367 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 17
280284 ACCCATTTTT
* *
280294 AATTTATTTTAAGTTTG
1 AATTTATTTTAAATTTA
* *
280311 AATTTAGTATAAATTTA
1 AATTTATTTTAAATTTA
*
280328 AATTTATTTTGAATTTA
1 AATTTATTTTAAATTTA
* *
280345 AGTTCATTTTAAATTTA
1 AATTTATTTTAAATTTA
280362 AATTTA
1 AATTTA
280368 AATTTAATTA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:282298 original size:88 final size:87
Alignment explanation
Indices: 282169--282447 Score: 273
Period size: 88 Copynumber: 3.2 Consensus size: 87
282159 CCAAACATTC
* * *
282169 CAAAAATTACATTTTAGCCCCTAAACTTTCTAAAAATTACATTTTGA-CTC-TAAGTTTTCAAAA
1 CAAAAATTACATTTT-GACCCTGAACTTTC-AAAAATTACATTTTGACCTCTTAA-CTTTCAAAA
*
282232 ATTACAATTTAACCCTCGAACTTCT
63 ATTACAATTTAACCCTCGAACATCT
* *
282257 CAAAAATTACATTTTGACTCCTGAACTTCTCAAAACTTACATTTTGACCTCTTAACTTTCCAAAA
1 CAAAAATTACATTTTGAC-CCTGAACTT-TCAAAAATTACATTTTGACCTCTTAACTTTCAAAAA
* * * *
282322 TTATATTTTTATCCTCGAACATCT
64 TTACAATTTAACCCTCGAACATCT
* * * *
282346 C-AAAATTACATTTTTGACCCCGAACTTTCCAAAAATTACCATTTT-ACCCCTTTGACATTCAAA
1 CAAAAATTACA-TTTTGACCCTGAACTTT-CAAAAATTA-CATTTTGACCTC-TTAACTTTCAAA
* * *
282409 AATTACCATTTTACCCT-GAATATC-
62 AATTACAATTTAACCCTCGAACATCT
*
282433 CAAAAAATACATTTT
1 CAAAAATTACATTTT
282448 TTACCTCAAA
Statistics
Matches: 160, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
87 8 0.05
88 81 0.51
89 68 0.43
90 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (87 bp):
CAAAAATTACATTTTGACCCTGAACTTTCAAAAATTACATTTTGACCTCTTAACTTTCAAAAATT
ACAATTTAACCCTCGAACATCT
Found at i:282391 original size:59 final size:57
Alignment explanation
Indices: 282171--282543 Score: 216
Period size: 58 Copynumber: 6.4 Consensus size: 57
282161 AAACATTCCA
* * * ** *
282171 AAAATTA-CATTTTAGCCCCTAAACTTTCTAAAAATTACATTTTGA--CTCTAAGTTTTC
1 AAAATTACCATTTTA-CCCC-GAACTTTCCAAAAATTACATTTT-ATCCTCGAACATCTC
* * *
282228 AAAAATTACAATTTAACCCTCGAAC-TTCTCAAAAATTACATTTTGACTCCT-GAACTTCTC
1 -AAAATTACCATTTTACCC-CGAACTTTC-CAAAAATTACATTTT-A-TCCTCGAACATCTC
** *
282288 AAAACTTA-CATTTTGACCTCTTAACTTTCC-AAAATTATATTTTTATCCTCGAACATCTC
1 AAAA-TTACCATTTT-ACC-CCGAACTTTCCAAAAATTACA-TTTTATCCTCGAACATCTC
* *
282347 AAAATTA-CATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCCCTTTG-ACAT-TC
1 AAAATTACCA-TTTT-ACCCCGAACTTTCCAAAAATTA-CATTTTA-TCC-TCGAACATCTC
* * * * * *
282406 AAAAATTACCATTTTACCCTGAA-TATCCAAAAAATACATTTTTTACCTCAAAC-TTTC
1 -AAAATTACCATTTTACCCCGAACTTTCCAAAAATTACATTTTAT-CCTCGAACATCTC
* * * *
282463 TAAAATTACCATTTTACCCCCGAAC-ATCCAAAAATTACCATTTCATCCCCGAGCATC-C
1 -AAAATTACCATTTTA-CCCCGAACTTTCCAAAAATTA-CATTTTATCCTCGAACATCTC
282521 AAAATTACCATTTATTACCCCGA
1 AAAATTACCA-TT-TTACCCCGA
282544 GTTTTTTAAA
Statistics
Matches: 253, Mismatches: 34, Indels: 56
0.74 0.10 0.16
Matches are distributed among these distances:
56 2 0.01
57 40 0.16
58 89 0.35
59 74 0.29
60 38 0.15
61 10 0.04
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCGAACTTTCCAAAAATTACATTTTATCCTCGAACATCTC
Found at i:282394 original size:29 final size:28
Alignment explanation
Indices: 282157--282514 Score: 171
Period size: 30 Copynumber: 12.2 Consensus size: 28
282147 ATGTTTTGAT
* *
282157 CCCCAAACATTCCAAAAATTACATTTTA
1 CCCCGAACTTTCCAAAAATTACATTTTA
* *
282185 GCCCCTAAACTTTCTAAAAATTACATTTTGA
1 -CCCC-GAACTTTCCAAAAATTACATTTT-A
* * * * *
282216 -CTCTAAGTTTTCAAAAATTACAATTTAA
1 CCCCGAACTTTCCAAAAATTAC-ATTTTA
282244 CCCTCGAAC-TTCTCAAAAATTACATTTTGA
1 CCC-CGAACTTTC-CAAAAATTACATTTT-A
* *
282274 CTCCTGAAC-TTCTCAAAACTTACATTTTGA
1 C-CCCGAACTTTC-CAAAAATTACATTTT-A
** *
282304 CCTCTTAACTTTCC-AAAATTATATTTTTA
1 CC-CCGAACTTTCCAAAAATTACA-TTTTA
* *
282333 TCCTCGAAC-ATCTC-AAAATTACATTTTTGA
1 -CCCCGAACTTTC-CAAAAATTACA-TTTT-A
282363 CCCCGAACTTTCCAAAAATTACCATTTTA
1 CCCCGAACTTTCCAAAAATTA-CATTTTA
*
282392 CCCCTTTG-ACATT-CAAAAATTACCATTTTA
1 CCCC---GAACTTTCCAAAAATTA-CATTTTA
* * *
282422 CCCTGAA-TATCCAAAAAATACATTTTTTA
1 CCCCGAACTTTCCAAAAATTACA--TTTTA
* * *
282451 CCTCAAACTTT-CTAAAATTACCATTTTA
1 CCCCGAACTTTCCAAAAATTA-CATTTTA
* *
282479 CCCCCGAAC-ATCCAAAAATTACCATTTCA
1 -CCCCGAACTTTCCAAAAATTA-CATTTTA
282508 TCCCCGA
1 -CCCCGA
282515 GCATCCAAAA
Statistics
Matches: 259, Mismatches: 42, Indels: 56
0.73 0.12 0.16
Matches are distributed among these distances:
27 4 0.02
28 32 0.12
29 99 0.38
30 111 0.43
31 12 0.05
32 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (28 bp):
CCCCGAACTTTCCAAAAATTACATTTTA
Found at i:282436 original size:58 final size:58
Alignment explanation
Indices: 282334--282505 Score: 161
Period size: 57 Copynumber: 2.9 Consensus size: 58
282324 ATATTTTTAT
* * *
282334 CCTCGAACATCTC-AAAATTA-CATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACC
1 CCTCAAACAT-TCAAAAATTACCA-TTTT-ACCCCGAA-TATCCAAAAATTACCATTTTACA
*** * * **
282394 CCTTTGACATTCAAAAATTACCATTTTACCCTGAATATCCAAAAAATA-CATTTTTTA
1 CCTCAAACATTCAAAAATTACCATTTTACCCCGAATATCCAAAAATTACCATTTTACA
* * *
282451 CCTCAAACTTTCTAAAATTACCATTTTACCCCCGAACATCCAAAAATTACCATTT
1 CCTCAAACATTCAAAAATTACCATTTTA-CCCCGAATATCCAAAAATTACCATTT
282506 CATCCCCGAG
Statistics
Matches: 91, Mismatches: 17, Indels: 9
0.78 0.15 0.08
Matches are distributed among these distances:
57 29 0.32
58 28 0.31
59 14 0.15
60 18 0.20
61 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (58 bp):
CCTCAAACATTCAAAAATTACCATTTTACCCCGAATATCCAAAAATTACCATTTTACA
Found at i:282495 original size:28 final size:27
Alignment explanation
Indices: 282315--282640 Score: 158
Period size: 29 Copynumber: 11.3 Consensus size: 27
282305 CTCTTAACTT
* *
282315 TCCAAAATTA-TATTTTTATCCTCGAACA
1 TCCAAAATTACCA-TTTTA-CCCCGAACA
*
282343 TCTCAAAATTA-CATTTTTGACCCCGAACTT
1 TC-CAAAATTACCA-TTTT-ACCCCGAAC-A
282373 TCCAAAAATTACCATTTTACCCCTTTG-ACA
1 TCC-AAAATTACCATTTTACCCC---GAACA
* * *
282403 TTCAAAAATTACCATTTTACCCTGAATA
1 -TCCAAAATTACCATTTTACCCCGAACA
* * * *
282431 TCCAAAAAATA-CATTTTTTACCTCAAACTT
1 TCC-AAAATTACCA--TTTTACCCCGAAC-A
*
282461 TCTAAAATTACCATTTTACCCCCGAACA
1 TCCAAAATTACCATTTTA-CCCCGAACA
* *
282489 TCCAAAAATTACCATTTCATCCCCGAGCA
1 TCC-AAAATTACCATTTTA-CCCCGAACA
***
282518 TCCAAAATTACCATTTATTACCCCGAGTTT
1 TCCAAAATTACCA-TT-TTACCCCGA-ACA
** * * *
282548 TTTAAAATTACTATTTTACCCCTAGGCA
1 TCCAAAATTACCATTTTACCCCGA-ACA
* * *
282576 TCCACAAATT-GCATCTTTACCCCTAAAA
1 TCCA-AAATTACCAT-TTTACCCCGAACA
* *
282604 TCTAAAATTACCATTTTACCCCGAGCA
1 TCCAAAATTACCATTTTACCCCGAACA
282631 TCCACAAATT
1 TCCA-AAATT
282641 GCATCTTTAC
Statistics
Matches: 228, Mismatches: 46, Indels: 48
0.71 0.14 0.15
Matches are distributed among these distances:
27 23 0.10
28 52 0.23
29 98 0.43
30 48 0.21
31 6 0.03
32 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (27 bp):
TCCAAAATTACCATTTTACCCCGAACA
Found at i:282521 original size:87 final size:85
Alignment explanation
Indices: 282337--282627 Score: 257
Period size: 87 Copynumber: 3.4 Consensus size: 85
282327 TTTTTATCCT
* * *
282337 CGAACATCTCAAAATTACATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCCCTTTGAC
1 CGAACATC-CAAAATTACATTTTTTACCCCGAACTTT-CTAAAATTACCATTTTACCCC-TCGAC
* *
282402 ATTCAAAAATTACCATTTTACCC
63 ATCCAAAAATTACCATTTCACCC
* * * * *
282425 TGAATATCCAAAAAATACATTTTTTACCTCAAACTTTCTAAAATTACCATTTTACCCC-CGAACA
1 CGAACATCC-AAAATTACATTTTTTACCCCGAACTTTCTAAAATTACCATTTTACCCCTCG-ACA
282489 TCCAAAAATTACCATTTCATCCC
64 TCCAAAAATTACCATTTCA-CCC
* * ** * * * *
282512 CGAGCATCCAAAATTACCATTTATTACCCCGAGTTTTTTAAAATTACTATTTTACCCCTAGGCAT
1 CGAACATCCAAAATTA-CATTTTTTACCCCGAACTTTCTAAAATTACCATTTTACCCCTCGACAT
* * *
282577 CCACAAATT-GCATCTTTACCC
65 CCAAAAATTACCAT-TTCACCC
* * *
282598 CTAAAATCTAAAATTACCA--TTTTACCCCGA
1 CGAACATCCAAAATTA-CATTTTTTACCCCGA
282628 GCATCCACAA
Statistics
Matches: 166, Mismatches: 31, Indels: 16
0.78 0.15 0.08
Matches are distributed among these distances:
84 10 0.06
85 1 0.01
86 47 0.28
87 78 0.47
88 30 0.18
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (85 bp):
CGAACATCCAAAATTACATTTTTTACCCCGAACTTTCTAAAATTACCATTTTACCCCTCGACATC
CAAAAATTACCATTTCACCC
Found at i:282649 original size:28 final size:28
Alignment explanation
Indices: 282562--282651 Score: 103
Period size: 27 Copynumber: 3.2 Consensus size: 28
282552 AAATTACTAT
282562 TTTACCCCTAGGCATCCACAAATTGCATC
1 TTTACCCCTA-GCATCCACAAATTGCATC
** * *
282591 TTTACCCCTAAAATCTA-AAATTACCAT-
1 TTTACCCCTAGCATCCACAAATT-GCATC
*
282618 TTTACCCCGAGCATCCACAAATTGCATC
1 TTTACCCCTAGCATCCACAAATTGCATC
282646 TTTACC
1 TTTACC
282652 ATTTGCCCTC
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
27 21 0.43
28 18 0.37
29 10 0.20
ACGTcount: A:0.31, C:0.32, G:0.07, T:0.30
Consensus pattern (28 bp):
TTTACCCCTAGCATCCACAAATTGCATC
Found at i:282701 original size:29 final size:28
Alignment explanation
Indices: 282667--282735 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
282657 CCCTCGGGTG
* * *
282667 TCCAAAAATTATCGTTTTACTCTCGGACG
1 TCCAAAAATTACCGTTTTACCCTCGG-CA
* *
282696 TTCAAAAACTACCGTTTTACCCTCGGCA
1 TCCAAAAATTACCGTTTTACCCTCGGCA
282724 TCCAAAAATTAC
1 TCCAAAAATTAC
282736 ATTTTATGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.30
Consensus pattern (28 bp):
TCCAAAAATTACCGTTTTACCCTCGGCA
Found at i:286876 original size:16 final size:16
Alignment explanation
Indices: 286840--286879 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
286830 AAATACACTT
286840 TTAAATAATAAAAATTA
1 TTAAA-AATAAAAATTA
*
286857 -TAAAAATATAAATTA
1 TTAAAAATAAAAATTA
286872 TTAAAAAT
1 TTAAAAAT
286880 TAGAATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAAAATAAAAATTA
Found at i:287814 original size:29 final size:30
Alignment explanation
Indices: 287771--287858 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 30
287761 TTCCAAAATT
* *
287771 ACTCTCGAACCTTTTAAAAATTATATTTTG
1 ACTCCCGAATCTTTTAAAAATTATATTTTG
*
287801 ACTCCCGAATTTTTTAAAAATTATATTTTG
1 ACTCCCGAATCTTTTAAAAATTATATTTTG
* * * *
287831 ACTCCTGAA-CTTCTCAAAATTACATTTT
1 ACTCCCGAATCTTTTAAAAATTATATTTT
287859 TATTCTTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
29 15 0.30
30 35 0.70
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (30 bp):
ACTCCCGAATCTTTTAAAAATTATATTTTG
Found at i:287899 original size:28 final size:27
Alignment explanation
Indices: 287817--287921 Score: 88
Period size: 29 Copynumber: 3.7 Consensus size: 27
287807 GAATTTTTTA
*
287817 AAAATTATATTTTGACTCCTGAACTTCTC
1 AAAATTACATTTTGACT-C-GAACTTCTC
* **
287846 AAAATTACATTTTTATTCTTAAACTTCTC
1 AAAATTACATTTTGA--CTCGAACTTCTC
287875 AAAATTACATTTTGACCTCGAACTT-TCC
1 AAAATTACATTTTGA-CTCGAACTTCT-C
287903 AAAAATTACCATTTT-ACTC
1 -AAAATTA-CATTTTGACTC
287922 AGGATATCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
27 1 0.02
28 11 0.17
29 43 0.68
30 6 0.10
31 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (27 bp):
AAAATTACATTTTGACTCGAACTTCTC
Found at i:287907 original size:29 final size:30
Alignment explanation
Indices: 287875--288120 Score: 112
Period size: 29 Copynumber: 8.5 Consensus size: 30
287865 TAAACTTCTC
*
287875 AAAATTA-CATTTTGACCTCGAACTTTCCA
1 AAAATTACCATTTTGACCTCGAACTATCCA
*
287904 AAAATTACCATTTT-A-CTCAGGA-TATCCA
1 AAAATTACCATTTTGACCTC-GAACTATCCA
* * * * *
287932 AAAATTA-TATTTTTTATCTCGAACTTTCTA
1 AAAATTACCA-TTTTGACCTCGAACTATCCA
* *
287962 AATATTATCATTTT-ACCCCCTCGAAC-ATCCA
1 AAAATTACCATTTTGA---CCTCGAACTATCCA
* * *
287993 AAAATTACCA-TTTCATCCCCGAGC-ATCC-
1 AAAATTACCATTTTGA-CCTCGAACTATCCA
* *
288021 AAAATTACCATTTTTGACC-CGAGCTTTCC-
1 AAAATTACCA-TTTTGACCTCGAACTATCCA
* *
288050 AAAATTACCATTTTG-CCCCGAGC-ATCCA
1 AAAATTACCATTTTGACCTCGAACTATCCA
* * * *
288078 CAAATT-GCATCTTT-ACCCCCGAAC-ATCCG
1 AAAATTACCAT-TTTGA-CCTCGAACTATCCA
288107 AAAATTACCATTTT
1 AAAATTACCATTTT
288121 ACCCCTGGGC
Statistics
Matches: 172, Mismatches: 25, Indels: 40
0.73 0.11 0.17
Matches are distributed among these distances:
27 9 0.05
28 52 0.30
29 58 0.34
30 33 0.19
31 13 0.08
32 7 0.04
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (30 bp):
AAAATTACCATTTTGACCTCGAACTATCCA
Found at i:288099 original size:57 final size:55
Alignment explanation
Indices: 287973--288152 Score: 177
Period size: 57 Copynumber: 3.1 Consensus size: 55
287963 ATATTATCAT
* * *
287973 TTTACCCCCTCGAACATCCAAAAATTACCATTTCATCCCCGAGCATCCAAAATTACCATT
1 TTTA-CCCC-CGAACATCCGAAAATTACCATTT--TCCCCGAGCATCCAAAATT-GCATC
* *
288033 TTTGA--CCCGAGCTTTCC-AAAATTACCATTTTGCCCCGAGCATCCACAAATTGCATC
1 TTT-ACCCCCGAAC-ATCCGAAAATTACCATTTT-CCCCGAGCATCCA-AAATTGCATC
*
288089 TTTACCCCCGAACATCCGAAAATTACCATTTTACCCCTGGGCATCCATAAATTGCATC
1 TTTACCCCCGAACATCCGAAAATTACCATTTT-CCCC-GAGCATCCA-AAATTGCATC
288147 TTTACC
1 TTTACC
288153 ATTTTGCCCC
Statistics
Matches: 103, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
55 2 0.02
56 22 0.21
57 46 0.45
58 29 0.28
60 3 0.03
61 1 0.01
ACGTcount: A:0.29, C:0.33, G:0.09, T:0.28
Consensus pattern (55 bp):
TTTACCCCCGAACATCCGAAAATTACCATTTTCCCCGAGCATCCAAAATTGCATC
Found at i:288121 original size:29 final size:28
Alignment explanation
Indices: 287965--288141 Score: 151
Period size: 29 Copynumber: 6.1 Consensus size: 28
287955 CTTTCTAAAT
* *
287965 ATTATCATTTTACCCCCTCGAACATCCAAAA
1 ATTACCATTTTA-CCCC-CGAGCATCC-AAA
* *
287996 ATTACCATTTCATCCCCGAGCATCCAAA
1 ATTACCATTTTACCCCCGAGCATCCAAA
*** *
288024 ATTACCATTTTTGACCCGAGCTTTCCAAA
1 ATTACCATTTTACCCCCGAGC-ATCCAAA
*
288053 ATTACCATTTT-GCCCCGAGCATCCACAA
1 ATTACCATTTTACCCCCGAGCATCCA-AA
* *
288081 ATT-GCATCTTTACCCCCGAACATCCGAAA
1 ATTACCAT-TTTACCCCCGAGCATCC-AAA
* *
288110 ATTACCATTTTACCCCTGGGCATCCATAA
1 ATTACCATTTTACCCCCGAGCATCCA-AA
288139 ATT
1 ATT
288142 GCATCTTTAC
Statistics
Matches: 121, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
27 7 0.06
28 37 0.31
29 60 0.50
30 7 0.06
31 10 0.08
ACGTcount: A:0.31, C:0.32, G:0.08, T:0.29
Consensus pattern (28 bp):
ATTACCATTTTACCCCCGAGCATCCAAA
Found at i:288231 original size:28 final size:29
Alignment explanation
Indices: 288173--288235 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
288163 CGGGTGTCCC
* * * *
288173 AAAATTATCGTTTTACCCTCGGACGTTCA
1 AAAATTAACGTTTTACCCTCCGACATCCA
*
288202 AAAATTAACGTTTTGCCC-CCGACATCCA
1 AAAATTAACGTTTTACCCTCCGACATCCA
288230 AAAATT
1 AAAATT
288236 CCATTTTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.30
Consensus pattern (29 bp):
AAAATTAACGTTTTACCCTCCGACATCCA
Found at i:297821 original size:103 final size:103
Alignment explanation
Indices: 297642--297848 Score: 387
Period size: 103 Copynumber: 2.0 Consensus size: 103
297632 TCTAGGGAGA
297642 TTCGTTCTGTCACTATTAGTCCAACATCCATCATGCTGTGCTATCCATTGGCATCTATCTCTCTC
1 TTCGTTCTGTCACTATTAGTCCAACATCCATCATGCTGTGCTATCCATTGGCATCTATCTCTCTC
* *
297707 TAAACTTTCCCTTCTGACCAGCATTAATTACAGATGCT
66 TAAACTTTCCCTTCTAACCAGCATTAATTACAAATGCT
*
297745 TTCGTTCTGTCACTATTAGTCTAACATCCATCATGCTGTGCTATCCATTGGCATCTATCTCTCTC
1 TTCGTTCTGTCACTATTAGTCCAACATCCATCATGCTGTGCTATCCATTGGCATCTATCTCTCTC
297810 TAAACTTTCCCTTCTAACCAGCATTAATTACAAATGCT
66 TAAACTTTCCCTTCTAACCAGCATTAATTACAAATGCT
297848 T
1 T
297849 CCTTTCGTCG
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.38
Consensus pattern (103 bp):
TTCGTTCTGTCACTATTAGTCCAACATCCATCATGCTGTGCTATCCATTGGCATCTATCTCTCTC
TAAACTTTCCCTTCTAACCAGCATTAATTACAAATGCT
Found at i:299279 original size:18 final size:18
Alignment explanation
Indices: 299253--299300 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
299243 CATAAACATA
*
299253 AAATAAAATAAGCAAAGG
1 AAATGAAATAAGCAAAGG
*
299271 GAATGAAATAAGCAAAGG
1 AAATGAAATAAGCAAAGG
*
299289 AAATGAGATAAG
1 AAATGAAATAAG
299301 GATTCGATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.60, C:0.04, G:0.23, T:0.12
Consensus pattern (18 bp):
AAATGAAATAAGCAAAGG
Found at i:299876 original size:24 final size:25
Alignment explanation
Indices: 299828--299876 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
299818 TTTCGAAAAT
* * *
299828 GAAATGAAAATAACTAAAGCTTAAA
1 GAAATGAAAAAAACTAAAACCTAAA
299853 GAAAT-AAAAAAACTAAAACCTAAA
1 GAAATGAAAAAAACTAAAACCTAAA
299877 TTACAAGAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.65, C:0.10, G:0.08, T:0.16
Consensus pattern (25 bp):
GAAATGAAAAAAACTAAAACCTAAA
Found at i:319168 original size:21 final size:22
Alignment explanation
Indices: 319142--319184 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
319132 AGGAGCAAGA
319142 GAAGAAGAGAAAGAAGA-AAAG
1 GAAGAAGAGAAAGAAGACAAAG
*
319163 GAAGAAGAGAAGGAAGACAAAG
1 GAAGAAGAGAAAGAAGACAAAG
319185 AAAGCATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (22 bp):
GAAGAAGAGAAAGAAGACAAAG
Found at i:319175 original size:12 final size:12
Alignment explanation
Indices: 319141--319179 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
319131 AAGGAGCAAG
* *
319141 AGAAGAAGAGAA
1 AGAAGAAAAGGA
319153 AGAAGAAAAGGA
1 AGAAGAAAAGGA
*
319165 AGAAGAGAAGGA
1 AGAAGAAAAGGA
319177 AGA
1 AGA
319180 CAAAGAAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAGGA
Done.