Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014515.1 Kokia drynarioides strain JFW-HI SEQ_129554, 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: 207493
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 161 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:9313 original size:2 final size:2
Alignment explanation
Indices: 9306--9344 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
9296 TTTTCAATCT
* * *
9306 TC TC TC TC TC TC TC TT TC TT TC TC TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9345 TTTTTGTCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (2 bp):
TC
Found at i:9331 original size:14 final size:14
Alignment explanation
Indices: 9306--9344 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
9296 TTTTCAATCT
*
9306 TCTCTCTCTCTCTC
1 TCTCTTTCTCTCTC
*
9320 TTTCTTTCTCTCTC
1 TCTCTTTCTCTCTC
9334 TCTCTTTCTCT
1 TCTCTTTCTCT
9345 TTTTTGTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
TCTCTTTCTCTCTC
Found at i:10292 original size:13 final size:13
Alignment explanation
Indices: 10274--10303 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
10264 ATAGCCATGG
10274 CTTGGAACTACGA
1 CTTGGAACTACGA
*
10287 CTTGGAACTGCGA
1 CTTGGAACTACGA
10300 CTTG
1 CTTG
10304 TGACATTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (13 bp):
CTTGGAACTACGA
Found at i:24644 original size:27 final size:27
Alignment explanation
Indices: 24614--24678 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
24604 AATACCATTT
* *
24614 CTTCATAGTTTACCATAAATGTCGTTC
1 CTTCAGAGTTTACCATAAATATCGTTC
**
24641 CTTCAGAGTCCACCATAAATATCGTTC
1 CTTCAGAGTTTACCATAAATATCGTTC
24668 CTTCAGAGTTT
1 CTTCAGAGTTT
24679 GCCACAGTGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (27 bp):
CTTCAGAGTTTACCATAAATATCGTTC
Found at i:25285 original size:3 final size:3
Alignment explanation
Indices: 25277--25303 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
25267 CATGCAATAG
25277 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
25304 ACCATACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:29380 original size:11 final size:11
Alignment explanation
Indices: 29364--29394 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
29354 TTCTGACTTT
29364 GAAAAATTATA
1 GAAAAATTATA
29375 GAAAAA-TATA
1 GAAAAATTATA
29385 GAAAAATTAT
1 GAAAAATTAT
29395 TAGAGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:29896 original size:25 final size:24
Alignment explanation
Indices: 29868--29999 Score: 96
Period size: 23 Copynumber: 5.5 Consensus size: 24
29858 AGCACGTCTC
29868 GTGCTCTCTGTTATTAGCATTGTGT
1 GTGCTCTCTGTTATTAGCATT-TGT
*
29893 GTGCTCTC--TAATTAGCACTTTGT
1 GTGCTCTCTGTTATTAGCA-TTTGT
*
29916 GTGCTCTCTG--ATTAGTACTTTGT
1 GTGCTCTCTGTTATTAGCA-TTTGT
* * *
29939 GTACTCTCT-AT-TTAGCACTGTGT
1 GTGCTCTCTGTTATTAGCA-TTTGT
* * * *
29962 GTGCTCTCTGTTGTCCAGCACTTAT
1 GTGCTCTCTGTTAT-TAGCATTTGT
29987 GTGCTCTCTGTTA
1 GTGCTCTCTGTTA
30000 GTACTTTGAT
Statistics
Matches: 87, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
23 57 0.66
24 3 0.03
25 23 0.26
26 4 0.05
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (24 bp):
GTGCTCTCTGTTATTAGCATTTGT
Found at i:29899 original size:23 final size:23
Alignment explanation
Indices: 29868--29970 Score: 111
Period size: 23 Copynumber: 4.4 Consensus size: 23
29858 AGCACGTCTC
29868 GTGCTCTCTGTTATTAGCA-TTGTGT
1 GTGCTCTC--TTATTAGCACTT-TGT
*
29893 GTGCTCTCTAATTAGCACTTTGT
1 GTGCTCTCTTATTAGCACTTTGT
* *
29916 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTTATTAGCACTTTGT
* *
29939 GTACTCTC-TATTTAGCACTGTGT
1 GTGCTCTCTTA-TTAGCACTTTGT
29962 GTGCTCTCT
1 GTGCTCTCT
29971 GTTGTCCAGC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
22 1 0.01
23 56 0.84
24 2 0.03
25 8 0.12
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (23 bp):
GTGCTCTCTTATTAGCACTTTGT
Found at i:29947 original size:46 final size:48
Alignment explanation
Indices: 29868--29973 Score: 146
Period size: 46 Copynumber: 2.2 Consensus size: 48
29858 AGCACGTCTC
* * *
29868 GTGCTCTCTGTTATTAGCATTGTGTGTGCTCTCTAATTAGCACTTTGT
1 GTGCTCTCTGTTAGTAGCATTGTGTGTACTCTCTAATTAGCACTGTGT
*
29916 GTGCTCTCTGATTAGTA-C-TT-TGTGTACTCTCTATTTAGCACTGTGT
1 GTGCTCTCTG-TTAGTAGCATTGTGTGTACTCTCTAATTAGCACTGTGT
29962 GTGCTCTCTGTT
1 GTGCTCTCTGTT
29974 GTCCAGCACT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
45 2 0.04
46 33 0.62
47 2 0.04
48 11 0.21
49 5 0.09
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (48 bp):
GTGCTCTCTGTTAGTAGCATTGTGTGTACTCTCTAATTAGCACTGTGT
Found at i:31700 original size:18 final size:18
Alignment explanation
Indices: 31670--31734 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 18
31660 CATTACTTAC
31670 TTTTTTATACATTTTATAA
1 TTTTTTAT-CATTTTATAA
31689 TTTTTTATCATTTTAATAAA
1 TTTTTTATCATTTT-AT-AA
*
31709 TTTTATAATTCA-TTTATAA
1 TTTT-TTA-TCATTTTATAA
31728 TTCTTTT
1 TT-TTTT
31735 CTTGTTATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 6 0.15
19 15 0.38
20 10 0.26
21 5 0.13
22 3 0.08
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTTATCATTTTATAA
Found at i:34500 original size:2 final size:2
Alignment explanation
Indices: 34464--34488 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34454 TCAATATGAT
34464 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
34489 TAAAAGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35396 original size:14 final size:14
Alignment explanation
Indices: 35377--35405 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35367 AAAGTTCCTT
35377 AGCCACTAAGAAGC
1 AGCCACTAAGAAGC
35391 AGCCACTAAGAAGC
1 AGCCACTAAGAAGC
35405 A
1 A
35406 TACATCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.28, G:0.21, T:0.07
Consensus pattern (14 bp):
AGCCACTAAGAAGC
Found at i:40957 original size:43 final size:43
Alignment explanation
Indices: 40861--41119 Score: 254
Period size: 43 Copynumber: 6.0 Consensus size: 43
40851 ATCTGTTAAT
* * * * *
40861 TTTAGCGGCATTTGTGGAAAAAACGCCGCTAAAGAACACTATT-
1 TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGACCA-TGTTC
* * * *
40904 TATAGCGGCGTTTGTGGAGTACGTGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
* * * *
40947 TTTAGTGGCGTTTGT-GAGAAAAGCACCGTTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGGAG-AAAGCGCCGCTAAAGACCATGTTC
* *
40990 TTTAGCGGCGTTTGTGGTGTAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
** * *
41033 TTTAGCGGTTTTTGTGAGGGGAAGCGCCGCTAAA-ACCATGTTC
1 TTTAGCGGCGTTTGTG-GAGAAAGCGCCGCTAAAGACCATGTTC
* * * * *
41076 TTTAGCAGCATTTGTTGAAAAAGTGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
41119 T
1 T
41120 ATAGAAAAAA
Statistics
Matches: 176, Mismatches: 35, Indels: 10
0.80 0.16 0.05
Matches are distributed among these distances:
42 19 0.11
43 140 0.80
44 17 0.10
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGACCATGTTC
Found at i:41881 original size:17 final size:19
Alignment explanation
Indices: 41861--41895 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
41851 CTAAAATAGT
41861 AACAAAA-TTA-ACAATAA
1 AACAAAACTTACACAATAA
41878 AACAAAACTTACACAATA
1 AACAAAACTTACACAATA
41896 TTCAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (19 bp):
AACAAAACTTACACAATAA
Found at i:41959 original size:22 final size:22
Alignment explanation
Indices: 41903--41952 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
41893 ATATTCAAAC
* *
41903 AATAACAACAAAATAGTAACAA
1 AATAATAATAAAATAGTAACAA
* * *
41925 TATAATAATAAAATGGTAGCAA
1 AATAATAATAAAATAGTAACAA
41947 AATAAT
1 AATAAT
41953 GAAAAAACAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.22
Consensus pattern (22 bp):
AATAATAATAAAATAGTAACAA
Found at i:42001 original size:21 final size:22
Alignment explanation
Indices: 41960--42001 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
41950 AATGAAAAAA
*
41960 CAATAAGAAAATAACAGCAAAC
1 CAATAAGAAAATAACAACAAAC
*
41982 CAATAA-AAAATAGCAACAAA
1 CAATAAGAAAATAACAACAAA
42002 AAAAAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.10
Consensus pattern (22 bp):
CAATAAGAAAATAACAACAAAC
Found at i:45086 original size:298 final size:296
Alignment explanation
Indices: 44522--45082 Score: 649
Period size: 298 Copynumber: 1.9 Consensus size: 296
44512 TAATATAAAT
* *
44522 GGTAAATTAAAGGTTTTATTAATGCACTTGACGTGGGTTCAAATATTATCATATGTATATTTTTA
1 GGTAAATTAAAGGTTTTATTAATGCACTTAACGTGGGTTCAAATATTATCATATGCATATTTTTA
* * * *
44587 TTGATTTTTTTTAAAGTGAAAAGACTAAAGTACTCTCTAATAATATTACTTATTTTAATTACGGA
66 TTGAGTTTTTTTAAAGCGAAAAGACTAAAATACTCTCAAATAATATTACTTATTTTAATTACGGA
** * * * *
44652 TGGATACTCCTGTAACTTTCTAACCGAGTTGGTGACCTGAATGAGGGTGACATCGATTCAGTCAA
131 AAGATACTCCTATAACTTCCTAACCGAGTTGGTGACCTGAATGAGGGTCACATCGACTCAGTCAA
* * * * *
44717 GAGCTTAGATAATATTATAAATATACAACAGAAGAAGGTAATAAAATGTGCATAATAAAATTAAA
196 GAGCTTAAATAATAGTAT-AAGATACAACAGAAGAAGGTAATAAAATCTGCATAACAAAATTAAA
44782 ATATATAAAGTATTAAAAGGAAAAACTTTAACAGAAA
260 ATATATAAAGTATTAAAAGGAAAAACTTTAACAGAAA
* * *
44819 GGTAAATTAAATGTTTTATTAATGCACTTAAAATGTGGGTTCAAAT-TTCA-CTTTATGCATATT
1 GGTAAATTAAAGGTTTTATTAATGCACTT--AACGTGGGTTCAAATATT-ATC-ATATGCATATT
* *
44882 TTTATTG-GTTTTTTTAAAGCGAAAAGATTAAAATA-TCTTCAAATAATATTATTTATTTTAATT
62 TTTATTGAGTTTTTTTAAAGCGAAAAGACTAAAATACTC-TCAAATAATATTACTTATTTTAATT
* * * * *
44945 AC-GAAAGA-ACATTCTCATGACTTCCTGACCGAGTTGGTGA-CTCGATTGAGGGTCACATTGAC
126 ACGGAAAGATAC-TCCT-ATAACTTCCTAACCGAGTTGGTGACCT-GAATGAGGGTCACATCGAC
* * * * * *
45007 TCAG-CTAAGAGCTTAAATAATAGTAT-AGATA-GA-TGATGAATGTACTAAAATCTGCATGACA
188 TCAGTC-AAGAGCTTAAATAATAGTATAAGATACAACAGAAGAAGGTAATAAAATCTGCATAACA
*
45068 AAATTAAAATGTATA
252 AAATTAAAATATATA
45083 TATATATAAC
Statistics
Matches: 221, Mismatches: 34, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
294 35 0.16
295 1 0.00
296 6 0.03
297 40 0.18
298 109 0.49
299 30 0.14
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (296 bp):
GGTAAATTAAAGGTTTTATTAATGCACTTAACGTGGGTTCAAATATTATCATATGCATATTTTTA
TTGAGTTTTTTTAAAGCGAAAAGACTAAAATACTCTCAAATAATATTACTTATTTTAATTACGGA
AAGATACTCCTATAACTTCCTAACCGAGTTGGTGACCTGAATGAGGGTCACATCGACTCAGTCAA
GAGCTTAAATAATAGTATAAGATACAACAGAAGAAGGTAATAAAATCTGCATAACAAAATTAAAA
TATATAAAGTATTAAAAGGAAAAACTTTAACAGAAA
Found at i:46509 original size:21 final size:20
Alignment explanation
Indices: 46469--46509 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
46459 GAAAATTTAT
*
46469 ATTTTTAAAAACATTATAAA
1 ATTTTTAAAAAAATTATAAA
*
46489 ATTTTTAAAATAAATTCTAAA
1 ATTTTTAAAA-AAATTATAAA
46510 GAATATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTTTAAAAAAATTATAAA
Found at i:48971 original size:21 final size:21
Alignment explanation
Indices: 48938--48981 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
48928 AACCCAAAAC
* * * *
48938 CTTGAACCCTGAATCTTGAAT
1 CTTGAAACATGAACCTTAAAT
48959 CTTGAAACATGAACCTTAAAT
1 CTTGAAACATGAACCTTAAAT
48980 CT
1 CT
48982 CTAATCATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (21 bp):
CTTGAAACATGAACCTTAAAT
Found at i:53558 original size:3 final size:3
Alignment explanation
Indices: 53550--53580 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
53540 ACTCTTTCTG
*
53550 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
53581 TATTTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:54251 original size:8 final size:8
Alignment explanation
Indices: 54237--54266 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
54227 GCTTTAACTC
54237 CTTTTTTT
1 CTTTTTTT
54245 -TTTTTTT
1 CTTTTTTT
54252 CTTTTTTT
1 CTTTTTTT
54260 CTTTTTT
1 CTTTTTT
54267 GGGTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
CTTTTTTT
Found at i:54257 original size:15 final size:16
Alignment explanation
Indices: 54237--54266 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54227 GCTTTAACTC
54237 CTTTTTTT-TTTTTTT
1 CTTTTTTTCTTTTTTT
54252 CTTTTTTTCTTTTTT
1 CTTTTTTTCTTTTTT
54267 GGGTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
CTTTTTTTCTTTTTTT
Found at i:58063 original size:81 final size:79
Alignment explanation
Indices: 57962--58122 Score: 277
Period size: 81 Copynumber: 2.0 Consensus size: 79
57952 GCATGGAGAG
*
57962 AAAGAGGAAAAAATTAAGGAAAGATGATCAAAGTAAAGGAAAACTTTGAATTGAAAAGAAAAAAA
1 AAAGAGGAAAAAATGAAGGAAAGATGATCAAAGTAAAGGAAAACTTTGAATTGAAAAG--AAAAA
58027 GGTTAAGTTAAAGTGA
64 GGTTAAGTTAAAGTGA
*
58043 AAAGAGGAAACAATGAAGGAAAGATGATCAAAGTAAAGGAAAACTTTGAATTGAAAAGAAAAAGG
1 AAAGAGGAAAAAATGAAGGAAAGATGATCAAAGTAAAGGAAAACTTTGAATTGAAAAGAAAAAGG
*
58108 TTAAGTTCAAGTGA
66 TTAAGTTAAAGTGA
58122 A
1 A
58123 GAGGATAGGT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
79 21 0.27
81 56 0.73
ACGTcount: A:0.55, C:0.04, G:0.23, T:0.18
Consensus pattern (79 bp):
AAAGAGGAAAAAATGAAGGAAAGATGATCAAAGTAAAGGAAAACTTTGAATTGAAAAGAAAAAGG
TTAAGTTAAAGTGA
Found at i:65871 original size:29 final size:30
Alignment explanation
Indices: 65839--65897 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
65829 TATAGTTTAA
*
65839 TGTGCAATTGTATGCATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* *
65868 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
65898 GATCAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.47
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:66153 original size:29 final size:27
Alignment explanation
Indices: 66087--66153 Score: 62
Period size: 31 Copynumber: 2.3 Consensus size: 27
66077 GAGTTTTACG
*
66087 TGTATAATTGCACCAAATTAAAGTTCA
1 TGTATAATTGCACCAAATCAAAGTTCA
* * *
66114 TGTATACAATTGCACATTAAATCAAGGTTTA
1 TGTAT--AATTGCAC--CAAATCAAAGTTCA
66145 TGTATAATT
1 TGTATAATT
66154 TTGAGATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 5 0.16
29 12 0.38
31 15 0.47
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAGTTCA
Found at i:66397 original size:21 final size:20
Alignment explanation
Indices: 66373--66412 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
66363 CAAAACAGTG
66373 ACAAAAAGTGAAAAAACAACA
1 ACAAAAA-TGAAAAAACAACA
*
66394 ACAAAATATGGAAAAACAA
1 ACAAAA-ATGAAAAAACAA
66413 TAGCAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.70, C:0.12, G:0.10, T:0.07
Consensus pattern (20 bp):
ACAAAAATGAAAAAACAACA
Found at i:66860 original size:14 final size:15
Alignment explanation
Indices: 66841--66869 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
66831 AAATTTGAGA
66841 TTTAA-TTTTTATAT
1 TTTAATTTTTTATAT
66855 TTTAATTTTTTATAT
1 TTTAATTTTTTATAT
66870 AATTTAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTAATTTTTTATAT
Found at i:67860 original size:33 final size:32
Alignment explanation
Indices: 67812--67873 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
67802 AACAAAAAAA
67812 TTTAAATTTTTTTAAAGAA-AATTAATAAATTT
1 TTTAAATTTTTTTAAA-AATAATTAATAAATTT
67844 TTTAAATTTTTTTTAAAAATAATTAATAAA
1 TTTAAA-TTTTTTTAAAAATAATTAATAAA
67874 AATTACATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (32 bp):
TTTAAATTTTTTTAAAAATAATTAATAAATTT
Found at i:78925 original size:4 final size:4
Alignment explanation
Indices: 78916--78956 Score: 66
Period size: 4 Copynumber: 10.2 Consensus size: 4
78906 ATTATATGTA
78916 TATG TATG TATG TATG TATG TATG TATG -ATTG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TA-TG TATG TATG T
78957 TAAACCTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 1 0.03
4 33 0.94
5 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:84321 original size:6 final size:6
Alignment explanation
Indices: 84310--84353 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
84300 AAATTAAAAA
*
84310 AAATTT AAATTT AAATTT AAATTT AAATTT -ATTTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA
84354 ATGTTCAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:84355 original size:18 final size:18
Alignment explanation
Indices: 84310--84353 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
84300 AAATTAAAAA
84310 AAATTTAAATTTAAATTT
1 AAATTTAAATTTAAATTT
*
84328 AAATTTAAATTT-ATTTT
1 AAATTTAAATTTAAATTT
84345 AAATTTAAA
1 AAATTTAAA
84354 ATGTTCAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTTAAATTTAAATTT
Found at i:84886 original size:4 final size:4
Alignment explanation
Indices: 84877--84906 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
84867 AAACGTTTTT
84877 AATA AATA AATA TAATA AATA AATA AATA A
1 AATA AATA AATA -AATA AATA AATA AATA A
84907 TAATAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:84894 original size:13 final size:13
Alignment explanation
Indices: 84876--84906 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
84866 GAAACGTTTT
84876 TAATAAATAAATA
1 TAATAAATAAATA
84889 TAATAAATAAATA
1 TAATAAATAAATA
84902 -AATAA
1 TAATAA
84907 TAATAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
TAATAAATAAATA
Found at i:84899 original size:17 final size:18
Alignment explanation
Indices: 84877--84913 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
84867 AAACGTTTTT
84877 AATAAATAAAT-ATAATA
1 AATAAATAAATAATAATA
84894 AATAAATAAATAATAATA
1 AATAAATAAATAATAATA
84912 AA
1 AA
84914 AAGAAGAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAAATAAATAATAATA
Found at i:85870 original size:29 final size:29
Alignment explanation
Indices: 85781--86053 Score: 249
Period size: 28 Copynumber: 9.4 Consensus size: 29
85771 CTCAAGAGGT
*
85781 CCCTAAACTTTCCAAAAATCACATTTTAA
1 CCCTAAACTTTCCCAAAATCACATTTTAA
*
85810 CCCTTAAACTTTCCCAAAATCACA-TTTGA
1 CCC-TAAACTTTCCCAAAATCACATTTTAA
*
85839 CCCTAAACTTTCCCAAAATTACATTTTAA
1 CCCTAAACTTTCCCAAAATCACATTTTAA
* *
85868 CCCTAAAC-TTCCCAAAACCACATTATAA
1 CCCTAAACTTTCCCAAAATCACATTTTAA
*
85896 CCCCAAA-TGTTCCCAAAATCACATTTTTAA
1 CCCTAAACT-TTCCCAAAATCACA-TTTTAA
* *
85926 CTTCC-AAACTTTTCCAAAATCACATTTTGAC
1 C--CCTAAACTTTCCCAAAATCACATTTT-AA
85957 CCCTAAACCTTT-CCAAAATCACATTTTAA
1 CCCTAAA-CTTTCCCAAAATCACATTTTAA
* * ** * *
85986 TACC-AAATTTTTTC-AAATTACATTTTGA
1 -CCCTAAACTTTCCCAAAATCACATTTTAA
* *
86014 CCCTTAAAC-TTCCCAAAATTCA-TTTTTAC
1 CCC-TAAACTTTCCCAAAA-TCACATTTTAA
86043 CCCTAAACTTT
1 CCCTAAACTTT
86054 ACTAAAATTA
Statistics
Matches: 200, Mismatches: 26, Indels: 36
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.01
28 65 0.32
29 57 0.28
30 51 0.25
31 22 0.11
32 3 0.01
ACGTcount: A:0.36, C:0.29, G:0.01, T:0.33
Consensus pattern (29 bp):
CCCTAAACTTTCCCAAAATCACATTTTAA
Found at i:86060 original size:29 final size:28
Alignment explanation
Indices: 86000--86075 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
85990 AAATTTTTTC
* * *
86000 AAATTACATTTTGACCCTTAAACTTCCCA
1 AAATT-CATTTTTACCCCTAAACTTACCA
*
86029 AAATTCATTTTTACCCCTAAACTTTACTA
1 AAATTCATTTTTACCCCTAAAC-TTACCA
86058 AAATT-ATATTTTGACCCC
1 AAATTCAT-TTTT-ACCCC
86076 AAATTCTCTG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 17 0.43
29 18 0.45
30 5 0.12
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (28 bp):
AAATTCATTTTTACCCCTAAACTTACCA
Found at i:86062 original size:58 final size:58
Alignment explanation
Indices: 85781--86074 Score: 242
Period size: 58 Copynumber: 5.1 Consensus size: 58
85771 CTCAAGAGGT
* * *
85781 CCCTAAACTTTCCAAAAATCACATTTTAACCCTTAAACTTTCCCAAAATCACA-TTTGA
1 CCCTAAAC-TTCCCAAAATCACATTTTTACCCCTAAACTTTCCCAAAATCACATTTTGA
* * * * *
85839 CCCTAAACTTTCCCAAAATTACA-TTTTAACCCTAAAC-TTCCCAAAACCACATTATAA
1 CCCTAAAC-TTCCCAAAATCACATTTTTACCCCTAAACTTTCCCAAAATCACATTTTGA
* * * *
85896 CCCCAAATGTTCCCAAAATCACATTTTTAACTTCC-AAACTTTTCCAAAATCACATTTTGA
1 CCCTAAA-CTTCCCAAAATCACATTTTT-AC-CCCTAAACTTTCCCAAAATCACATTTTGA
* * ** * ** *
85956 CCCCTAAACCTTTCCAAAATCACATTTTAATACC-AAATTTTTTC-AAATTACATTTTGA
1 -CCCTAAA-CTTCCCAAAATCACATTTTTACCCCTAAACTTTCCCAAAATCACATTTTGA
* * * * *
86014 CCCTTAAACTTCCCAAAAT-TCATTTTTACCCCTAAACTTTACTAAAATTATATTTTGA
1 CCC-TAAACTTCCCAAAATCACATTTTTACCCCTAAACTTTCCCAAAATCACATTTTGA
86072 CCC
1 CCC
86075 CAAATTCTCT
Statistics
Matches: 189, Mismatches: 37, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
56 22 0.12
57 52 0.28
58 58 0.31
59 15 0.08
60 19 0.10
61 23 0.12
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (58 bp):
CCCTAAACTTCCCAAAATCACATTTTTACCCCTAAACTTTCCCAAAATCACATTTTGA
Found at i:91572 original size:49 final size:49
Alignment explanation
Indices: 91498--91686 Score: 202
Period size: 49 Copynumber: 3.9 Consensus size: 49
91488 ACCAAGGAAA
* * *
91498 CATGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACAAACCCGGTAC
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTAC
* ** * * *
91547 CATGAAGATTTGAAGGGAAAAGTTGAGGTTGCAATGGCGAACCTGGTAC
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTAC
* * * **
91596 CA-GAAGATATGATA-GGAAAGGTTGAGGTCACAACGGTGAACCCGGTAC
1 CATGAAGATTTGA-AGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTAC
* * *
91644 CGTGAAGATTTGAAGGGAAAGGTTGAGGCTGCAATGACGAACC
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGACGAACC
91687 TAGTACCTTA
Statistics
Matches: 113, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
48 39 0.35
49 74 0.65
ACGTcount: A:0.33, C:0.16, G:0.33, T:0.18
Consensus pattern (49 bp):
CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTAC
Found at i:91669 original size:97 final size:98
Alignment explanation
Indices: 91501--91706 Score: 281
Period size: 97 Copynumber: 2.1 Consensus size: 98
91491 AAGGAAACAT
* * *
91501 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCATGAAGATTTGAAGGGAA
1 GAAGATATGATAGGAAAGGTTGAGGCCACAACGACAAACCCGGTACCATGAAGATTTGAAGGGAA
* * *
91566 AAGTTGAGGTTGCAATGGCGAACCTGGTACC-A
66 AAGTTGAGGCTGCAATGACGAACCTAGTACCTA
* *** *
91598 GAAGATATGATAGGAAAGGTTGAGGTCACAACGGTGAACCCGGTACCGTGAAGATTTGAAGGGAA
1 GAAGATATGATAGGAAAGGTTGAGGCCACAACGACAAACCCGGTACCATGAAGATTTGAAGGGAA
*
91663 AGGTTGAGGCTGCAATGACGAACCTAGTACCTTA
66 AAGTTGAGGCTGCAATGACGAACCTAGTACC-TA
91697 GAA-ATATGAT
1 GAAGATATGAT
91707 GAAAAATTGA
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
97 84 0.88
98 7 0.07
99 4 0.04
ACGTcount: A:0.34, C:0.15, G:0.32, T:0.19
Consensus pattern (98 bp):
GAAGATATGATAGGAAAGGTTGAGGCCACAACGACAAACCCGGTACCATGAAGATTTGAAGGGAA
AAGTTGAGGCTGCAATGACGAACCTAGTACCTA
Found at i:92133 original size:42 final size:41
Alignment explanation
Indices: 91944--92175 Score: 243
Period size: 41 Copynumber: 5.6 Consensus size: 41
91934 AGTGAAGCTA
91944 CAATCTTTTACCCCTAATTAAGATGGGA-AAATTGAAGATTC
1 CAATCTTTTACCCCTAATTAAGA-GGGACAAATTGAAGATTC
* * ** *
91985 TAATATTTTACCCCTAATTAAGAGGGGTAAATTAAAGATTC
1 CAATCTTTTACCCCTAATTAAGAGGGACAAATTGAAGATTC
** * * *
92026 CAATCTTTTACCCCTAAACAAGAGGGGCAAATTAAAGAATC
1 CAATCTTTTACCCCTAATTAAGAGGGACAAATTGAAGATTC
* * * * *
92067 TAGA-ATTTTACCCTTAATAAAGAGGGACAGATTGAAGATTC
1 CA-ATCTTTTACCCCTAATTAAGAGGGACAAATTGAAGATTC
* * *
92108 CAGTCTCTTACCCCCTAATTAAGAGGGACAGATTGAAGATTC
1 CAATCTTTTA-CCCCTAATTAAGAGGGACAAATTGAAGATTC
* *
92150 CAATCTTTTACCCATAATCAAGAGGG
1 CAATCTTTTACCCCTAATTAAGAGGG
92176 GCATATTACA
Statistics
Matches: 158, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.02
41 117 0.74
42 38 0.24
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.28
Consensus pattern (41 bp):
CAATCTTTTACCCCTAATTAAGAGGGACAAATTGAAGATTC
Found at i:92172 original size:124 final size:123
Alignment explanation
Indices: 91949--92183 Score: 319
Period size: 124 Copynumber: 1.9 Consensus size: 123
91939 AGCTACAATC
* * * **
91949 TTTTACCCCTAATTAAGATGGGAAAATTGAAGATTCTAATATTTTACCCCTAATTAAGAGGGGTA
1 TTTTACCCCTAATAAAGATGGGAAAATTGAAGATTCCAATATCTTACCCCTAATTAAGAGGGACA
*
92014 AATTAAAGATTCCAATCTTTTACCCCTAAACAAGAGGGGCAAATTAAAGAATCTAGAA
66 AATTAAAGATTCCAATCTTTTACCCATAAACAAGAGGGGCAAATTAAAGAATCTAGAA
* * * *
92072 TTTTACCCTTAATAAAGA-GGGACAGATTGAAGATTCCAGTCTCTTACCCCCTAATTAAGAGGGA
1 TTTTACCCCTAATAAAGATGGGA-AAATTGAAGATTCCAATATCTTA-CCCCTAATTAAGAGGGA
* * * *
92136 CAGATTGAAGATTCCAATCTTTTACCCATAATCAAGAGGGGCATATTA
64 CAAATTAAAGATTCCAATCTTTTACCCATAAACAAGAGGGGCAAATTA
92184 CAGCCATCCA
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
122 4 0.04
123 34 0.35
124 58 0.60
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (123 bp):
TTTTACCCCTAATAAAGATGGGAAAATTGAAGATTCCAATATCTTACCCCTAATTAAGAGGGACA
AATTAAAGATTCCAATCTTTTACCCATAAACAAGAGGGGCAAATTAAAGAATCTAGAA
Found at i:92242 original size:39 final size:39
Alignment explanation
Indices: 92173--92298 Score: 144
Period size: 39 Copynumber: 3.2 Consensus size: 39
92163 ATAATCAAGA
* * * *
92173 GGGGCATATTACAGCCATCCAATCTCTTACCCCGATCAT
1 GGGGCAGATTGCAACCACCCAATCTCTTACCCCGATCAT
* * * *
92212 GGGGCAGATTGTAACCGCCCGATCTTTTACCCCGATCAT
1 GGGGCAGATTGCAACCACCCAATCTCTTACCCCGATCAT
* * * *
92251 GGGGCAAATTGCAACTATCCAATCTCTTACCCTGATCAT
1 GGGGCAGATTGCAACCACCCAATCTCTTACCCCGATCAT
92290 GGGGCAGAT
1 GGGGCAGAT
92299 CACAGTCATT
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (39 bp):
GGGGCAGATTGCAACCACCCAATCTCTTACCCCGATCAT
Found at i:94227 original size:30 final size:30
Alignment explanation
Indices: 94162--94488 Score: 291
Period size: 30 Copynumber: 11.1 Consensus size: 30
94152 AGGAGGTTCT
* * *
94162 TAAACCTTTCAAAAATCATATTTTGACCCC
1 TAAACTTTTCCAAAATCACATTTTGACCCC
* * *
94192 T-AACTTTTCCAAAATCAAATTTTAACCTC
1 TAAACTTTTCCAAAATCACATTTTGACCCC
* *
94221 TAAACTTTTCTAAAATTACATTTTGACCCC
1 TAAACTTTTCCAAAATCACATTTTGACCCC
*
94251 TAAACTTTCCCAAAATCACATTTTGACCCC
1 TAAACTTTTCCAAAATCACATTTTGACCCC
*
94281 TAAAC-TTTCCTAAAATCACATTTTGA-TCC
1 TAAACTTTTCC-AAAATCACATTTTGACCCC
* *
94310 TAAAC-TTCCCAAAACCACATTTTGACCCC
1 TAAACTTTTCCAAAATCACATTTTGACCCC
* *
94339 -GAA-TTTTCTCAAAATCACATTTTTAACTCCC
1 TAAACTTTTC-CAAAATCACA-TTTTGAC-CCC
* *
94370 -AAACTTTTCCAAAATCACATTTT-AACTC
1 TAAACTTTTCCAAAATCACATTTTGACCCC
* * *
94398 -AAACCTTTCCAAAATAACATTTTGA-CTC
1 TAAACTTTTCCAAAATCACATTTTGACCCC
* * * *
94426 TCAAACTTTCCCATAAT-TCATTTTTACCCC
1 T-AAACTTTTCCAAAATCACATTTTGACCCC
* **
94456 TAAACTTTTCCAAAATTATGTTTTGA-CCC
1 TAAACTTTTCCAAAATCACATTTTGACCCC
94485 TAAA
1 TAAA
94489 TTCTCTAAAA
Statistics
Matches: 245, Mismatches: 39, Indels: 27
0.79 0.13 0.09
Matches are distributed among these distances:
28 45 0.18
29 79 0.32
30 101 0.41
31 15 0.06
32 5 0.02
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (30 bp):
TAAACTTTTCCAAAATCACATTTTGACCCC
Found at i:94410 original size:88 final size:88
Alignment explanation
Indices: 94173--94471 Score: 333
Period size: 88 Copynumber: 3.4 Consensus size: 88
94163 AAACCTTTCA
* * * * *
94173 AAAATCATATTTTGACCCCT-AACTTTTCCAAAATCAAATTTTAACCTCTAAACTTTTCTAAAAT
1 AAAATCACATTTTTACCCCTAAACTTTTCCAAAATCACATTTTAA-CTCTAAACCTTTCCAAAAT
*
94237 TACATTTTGACCCCTAAACTTTCCC
65 AACATTTTGACCCC-AAACTTTCCC
* * *
94262 AAAATCACATTTTGACCCCTAAAC-TTTCCTAAAATCACATTTTGA-TCCTAAA-CTTCCCAAAA
1 AAAATCACATTTTTACCCCTAAACTTTTCC-AAAATCACATTTTAACT-CTAAACCTTTCCAAAA
** * * *
94324 CCACATTTTGACCCCGAATTTTCTC
64 TAACATTTTGACCCCAAACTTTCCC
94349 AAAATCACATTTTTAACTCCC-AAACTTTTCCAAAATCACATTTTAACTC-AAACCTTTCCAAAA
1 AAAATCACATTTTT-AC-CCCTAAACTTTTCCAAAATCACATTTTAACTCTAAACCTTTCCAAAA
*
94412 TAACATTTTGACTCTCAAACTTTCCC
64 TAACATTTTGAC-CCCAAACTTTCCC
* *
94438 ATAAT-TCATTTTTACCCCTAAACTTTTCCAAAAT
1 AAAATCACATTTTTACCCCTAAACTTTTCCAAAAT
94472 TATGTTTTGA
Statistics
Matches: 178, Mismatches: 22, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
86 3 0.02
87 40 0.22
88 68 0.38
89 51 0.29
90 16 0.09
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.35
Consensus pattern (88 bp):
AAAATCACATTTTTACCCCTAAACTTTTCCAAAATCACATTTTAACTCTAAACCTTTCCAAAATA
ACATTTTGACCCCAAACTTTCCC
Found at i:94727 original size:18 final size:19
Alignment explanation
Indices: 94704--94745 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
94694 AATTTTTCTA
*
94704 TTAATTT-CACATTCATAT
1 TTAATTTACACACTCATAT
*
94722 TTAATTTACACACTCATTT
1 TTAATTTACACACTCATAT
94741 TTAAT
1 TTAAT
94746 CAAATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATTTACACACTCATAT
Found at i:107563 original size:49 final size:50
Alignment explanation
Indices: 107478--107820 Score: 183
Period size: 50 Copynumber: 7.0 Consensus size: 50
107468 AAAAGGAAGA
* ** *
107478 TTGAGGCCGCAACGACGAA-TCTAATACCCTAG-AGATATGAAGGGAAAGG
1 TTGAGGCCGCAACGACAAACTC-GGTACCTTAGAAGATATGAAGGGAAAGG
*
107527 TTGAGGCCGCAACGACTAACTCGGTA-CTGT-GAAGATATGAAGGGAAAGG
1 TTGAGGCCGCAACGACAAACTCGGTACCT-TAGAAGATATGAAGGGAAAGG
* * * * * *
107576 TTGAGGCCGTAACGGCAAACTTGGTACCTTAGAAGATGTGATGGGAAAGA
1 TTGAGGCCGCAACGACAAACTCGGTACCTTAGAAGATATGAAGGGAAAGG
** * * * *
107626 TTGAGGCCG----G-TGAACCCGGTACCAT-GAAGATATGAAGGAAAAAG
1 TTGAGGCCGCAACGACAAACTCGGTACCTTAGAAGATATGAAGGGAAAGG
* ** * * * * * *
107670 TTAAGGCCATAATGGCGAACCCGGTACCTTAGAAGATGTGATGGG-AAGG
1 TTGAGGCCGCAACGACAAACTCGGTACCTTAGAAGATATGAAGGGAAAGG
* * * * * * * *
107719 ATTGAGGTCGCAACGGCGAACCCGATACTTTAGAAGATGTG-ATGGAAAGG
1 -TTGAGGCCGCAACGACAAACTCGGTACCTTAGAAGATATGAAGGGAAAGG
* *** * *
107769 ATTGAGGCCGTAACGGTGAA-TCCGATACCAT-GAAGATATGAAGGGAAAGG
1 -TTGAGGCCGCAACGACAAACT-CGGTACCTTAGAAGATATGAAGGGAAAGG
107819 TT
1 TT
107821 TAGGATGCAA
Statistics
Matches: 233, Mismatches: 46, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
44 21 0.09
45 10 0.04
46 1 0.00
48 3 0.01
49 89 0.38
50 109 0.47
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (50 bp):
TTGAGGCCGCAACGACAAACTCGGTACCTTAGAAGATATGAAGGGAAAGG
Found at i:107632 original size:50 final size:50
Alignment explanation
Indices: 107474--107873 Score: 257
Period size: 49 Copynumber: 8.2 Consensus size: 50
107464 TTTTAAAAGG
* * * *** * *
107474 AAGATTGAGGCCGCAACGACGAATCTAATACCCTAG-AGATATGAAGGGA
1 AAGATTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATATGATGGGA
* * * * * *
107523 AAGGTTGAGGCCGCAACGACTAACTCGGTA-CTGT-GAAGATATGAAGGGA
1 AAGATTGAGGCCGTAACGGCGAACCCGGTACCT-TAGAAGATATGATGGGA
* * ** *
107572 AAGGTTGAGGCCGTAACGGCAAACTTGGTACCTTAGAAGATGTGATGGGA
1 AAGATTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATATGATGGGA
* * *
107622 AAGATTGAGG-C----CGGTGAACCCGGTACCAT-GAAGATATGA-AGGA
1 AAGATTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATATGATGGGA
* * * * *
107665 AAAAGTTAAGGCCATAATGGCGAACCCGGTACCTTAGAAGATGTGATGGGA
1 AAGA-TTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATATGATGGGA
* * * * * *
107716 AGGATTGAGGTCGCAACGGCGAACCCGATACTTTAGAAGATGTGAT-GGA
1 AAGATTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATATGATGGGA
* * * * *
107765 AAGGATTGAGGCCGTAACGGTGAATCCGATACCAT-GAAGATATGAAGGGA
1 AA-GATTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATATGATGGGA
* * ** * * * * *
107815 AAGGTTTAGGATGCAATGGCGAACCCGGTACCTTAAGAAAACATGATGGAA
1 AAGATTGAGGCCGTAACGGCGAACCCGGTACCTT-AGAAGATATGATGGGA
107866 AAGATTGA
1 AAGATTGA
107874 AGTCGCAATG
Statistics
Matches: 272, Mismatches: 63, Indels: 30
0.75 0.17 0.08
Matches are distributed among these distances:
43 6 0.02
44 14 0.05
45 14 0.05
48 2 0.01
49 115 0.42
50 99 0.36
51 22 0.08
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (50 bp):
AAGATTGAGGCCGTAACGGCGAACCCGGTACCTTAGAAGATATGATGGGA
Found at i:107847 original size:149 final size:144
Alignment explanation
Indices: 107510--107888 Score: 374
Period size: 149 Copynumber: 2.6 Consensus size: 144
107500 AATACCCTAG
* ** * * * * *
107510 AGATATGAAGGGAAAGGTTGAGGCCGCAACGACTAACTCGGTA-CTGT-GAAGATATGAAGGGAA
1 AGATATGAAGGGAAAGGTTAAGGATGCAATGGCGAACCCGGTACCT-TAGAAGATATGATGGG-A
* * * ** *
107573 AGG-TTGAGGCCGTAACGGCAAACTTGGTACCTTAGAAGATGTGATGGGAAAGATTGAGGCCGGT
64 AGGATTGAGGTCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAAAGATTGAGGCCGGT
*
107637 GAACCCGGTACCATGA
129 GAACCCGATACCATGA
* * *
107653 AGATATGAAGGAAAAAGTTAAGGCCAT--AATGGCGAACCCGGTACCTTAGAAGATGTGATGGGA
1 AGATATGAAGGGAAAGGTTAAGG--ATGCAATGGCGAACCCGGTACCTTAGAAGATATGATGGGA
*
107716 AGGATTGAGGTCGCAACGGCGAACCCGATACTTTAGAAGATGTGAT-GGAAAGGATTGAGGCCGT
64 AGGATTGAGGTCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAAA-GATTGAGG-C--
*
107780 AACGGTGAATCCGATACCATGA
125 --CGGTGAACCCGATACCATGA
* * * *
107802 AGATATGAAGGGAAAGGTTTAGGATGCAATGGCGAACCCGGTACCTTAAGAAAACATGATGGAAA
1 AGATATGAAGGGAAAGGTTAAGGATGCAATGGCGAACCCGGTACCTT-AGAAGATATGATGGGAA
* * *
107867 AGATTGAAGTCGCAATGGCGAA
65 GGATTGAGGTCGCAACGGCGAA
107889 TCTTATACCC
Statistics
Matches: 192, Mismatches: 30, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
143 42 0.22
144 57 0.30
145 1 0.01
147 2 0.01
149 58 0.30
150 32 0.17
ACGTcount: A:0.35, C:0.15, G:0.32, T:0.19
Consensus pattern (144 bp):
AGATATGAAGGGAAAGGTTAAGGATGCAATGGCGAACCCGGTACCTTAGAAGATATGATGGGAAG
GATTGAGGTCGCAACGGCGAACCCGATACCTTAGAAGATGTGATGGGAAAGATTGAGGCCGGTGA
ACCCGATACCATGA
Found at i:107992 original size:49 final size:48
Alignment explanation
Indices: 107866--108004 Score: 170
Period size: 49 Copynumber: 2.8 Consensus size: 48
107856 CATGATGGAA
*
107866 AAGATTGAAGTCGCAATGGCGAATCTTATACCCTAAAGTTGAAGAGGAG
1 AAGATTGAAGTCGCAATGGCGAATCTTATACCC-AAAGTTGAAAAGGAG
* *
107915 AAGATTAAAATCGCAATGGCGAATCTTATACCGCAAAGTTGAAAAGGAG
1 AAGATTGAAGTCGCAATGGCGAATCTTATACC-CAAAGTTGAAAAGGAG
* * * * * *
107964 CAGATTGAAGTCGTAATGACAAACCTTATACCTCGAAGTTG
1 AAGATTGAAGTCGCAATGGCGAATCTTATACC-CAAAGTTG
108005 CAATAAAGTG
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 76 0.99
50 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (48 bp):
AAGATTGAAGTCGCAATGGCGAATCTTATACCCAAAGTTGAAAAGGAG
Found at i:108523 original size:17 final size:17
Alignment explanation
Indices: 108503--108560 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
108493 CAATTTTTAT
*
108503 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
*
108520 TTTAAAATTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
108538 TTTTATTTTATTTTAAA
1 TTTAAATTTATTTTAAA
108555 TTTAAA
1 TTTAAA
108561 ATTTGAAAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
17 20 0.61
18 13 0.39
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:108527 original size:18 final size:18
Alignment explanation
Indices: 108501--108564 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
108491 CCCAATTTTT
*
108501 ATTTTAAATTTATTTTAA
1 ATTTAAAATTTATTTTAA
*
108519 GTTTAAAA-TTATTTTTAA
1 ATTTAAAATTTA-TTTTAA
* *
108537 ATTT-TATTTTATTTTAA
1 ATTTAAAATTTATTTTAA
108554 ATTTAAAATTT
1 ATTTAAAATTT
108565 GAAAGATTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
17 14 0.39
18 22 0.61
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTAAAATTTATTTTAA
Found at i:109207 original size:9 final size:9
Alignment explanation
Indices: 109193--109217 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
109183 ATGTATAATG
109193 TATTATCAT
1 TATTATCAT
109202 TATTATCAT
1 TATTATCAT
109211 TATTATC
1 TATTATC
109218 TTGAACGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (9 bp):
TATTATCAT
Found at i:110501 original size:30 final size:30
Alignment explanation
Indices: 110465--110620 Score: 117
Period size: 30 Copynumber: 5.3 Consensus size: 30
110455 CTCTCGGGTG
*
110465 TCCAAAAATTGCATTTTTCACCCTGAACTT
1 TCCAAAAATTGCATTTTTCACCCTAAACTT
* * * *
110495 TCCAAAAA-TGCATTTTAC-CCCCAGA-TG
1 TCCAAAAATTGCATTTTTCACCCTAAACTT
* * *
110522 TCCAAAAATTGTATTTTTGA-CATCAAACTT
1 TCCAAAAATTGCATTTTTCACCCT-AAACTT
* * * *
110552 TCCAAAAATTACCATTTTAC-CCCCAAA-TG
1 TCCAAAAATT-GCATTTTTCACCCTAAACTT
* * *
110581 TCCAAAAAATACATTTTTGACCCTAAACTT
1 TCCAAAAATTGCATTTTTCACCCTAAACTT
110611 TCCAAAAATT
1 TCCAAAAATT
110621 ACCATTTTAC
Statistics
Matches: 92, Mismatches: 26, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
27 9 0.10
28 18 0.20
29 27 0.29
30 32 0.35
31 6 0.07
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.33
Consensus pattern (30 bp):
TCCAAAAATTGCATTTTTCACCCTAAACTT
Found at i:110525 original size:27 final size:29
Alignment explanation
Indices: 110463--110530 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
110453 TACTCTCGGG
* *
110463 TGTCCAAAAATTGCATTTTTCACCCTGAAC
1 TGTCCAAAAA-TGCATTTTACACCCAGAAC
* *
110493 TTTCCAAAAATGCATTTTACCCCCAG-A-
1 TGTCCAAAAATGCATTTTACACCCAGAAC
110520 TGTCCAAAAAT
1 TGTCCAAAAAT
110531 TGTATTTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 10 0.30
28 1 0.03
29 13 0.39
30 9 0.27
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (29 bp):
TGTCCAAAAATGCATTTTACACCCAGAAC
Found at i:110585 original size:29 final size:29
Alignment explanation
Indices: 110552--110843 Score: 207
Period size: 29 Copynumber: 10.1 Consensus size: 29
110542 CATCAAACTT
* **
110552 TCCAAAAATTACCATTTTACCCCCAAATG
1 TCCAAAAATTACCATTTTACCCCCGAACA
* ** *
110581 TCCAAAAAATA-CATTTTTGA-CCCTAAACTT
1 TCCAAAAATTACCA-TTTT-ACCCCCGAAC-A
110611 TCCAAAAATTACCATTTTACCCCCGAACA
1 TCCAAAAATTACCATTTTACCCCCGAACA
* * *
110640 TCCAAAAATTACAATATTACCCTCGAACA
1 TCCAAAAATTACCATTTTACCCCCGAACA
* ** *
110669 TCCGAAAATTACCATTTTACTTCTGAACA
1 TCCAAAAATTACCATTTTACCCCCGAACA
* *
110698 TCTAAAAATTATCATTTTACCCCCGAACA
1 TCCAAAAATTACCATTTTACCCCCGAACA
** * * **
110727 TCTTAAAATTACCAATTTT-CCCTCTAGTA
1 TCCAAAAATTACC-ATTTTACCCCCGAACA
** *
110756 TCCAAAAATTACCATTTT-GTCCCGAAGTA
1 TCCAAAAATTACCATTTTACCCCCGAA-CA
* * * * *
110785 TTC-AAAATTACCATTTTATCCTCGAGCG
1 TCCAAAAATTACCATTTTACCCCCGAACA
* * *
110813 TCCAAAAATTATCGTTTTACCCCCAAACA
1 TCCAAAAATTACCATTTTACCCCCGAACA
110842 TC
1 TC
110844 TGAATATTAT
Statistics
Matches: 202, Mismatches: 52, Indels: 18
0.74 0.19 0.07
Matches are distributed among these distances:
28 26 0.13
29 148 0.73
30 26 0.13
31 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.31
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCGAACA
Found at i:110597 original size:59 final size:59
Alignment explanation
Indices: 110406--110688 Score: 285
Period size: 59 Copynumber: 4.9 Consensus size: 59
110396 GTCCCTGAAC
* * ***
110406 TGTCCAAAAA-T-CATATTTTGACCCTAAACTTTCC-AAAATTACCATTTTACTCTCGGG
1 TGTCCAAAAATTACAT-TTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCCCCAAA
* * * * *
110463 TGTCCAAAAATTGCATTTTTCACCCTGAACTTTCCAAAAA-T-GCATTTTACCCCCAGA
1 TGTCCAAAAATTACATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCCCCAAA
** *
110520 TGTCCAAAAATTGTATTTTTGA-CATCAAACTTTCCAAAAATTACCATTTTACCCCCAAA
1 TGTCCAAAAATTACATTTTTGACCCT-AAACTTTCCAAAAATTACCATTTTACCCCCAAA
* *
110579 TGTCCAAAAAATACATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCCCCGAA
1 TGTCCAAAAATTACATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCCCCAAA
** * * * * *
110638 CATCCAAAAATTACAATATT-ACCCTCGAAC-ATCCGAAAATTACCATTTTAC
1 TGTCCAAAAATTACATTTTTGACCCT-AAACTTTCCAAAAATTACCATTTTAC
110689 TTCTGAACAT
Statistics
Matches: 192, Mismatches: 26, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
56 2 0.01
57 54 0.28
58 44 0.23
59 90 0.47
60 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (59 bp):
TGTCCAAAAATTACATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCCCCAAA
Found at i:110714 original size:87 final size:87
Alignment explanation
Indices: 110614--110773 Score: 232
Period size: 87 Copynumber: 1.8 Consensus size: 87
110604 TAAACTTTCC
*
110614 AAAAATTACCATTTTACCCCCGAACATCCAAAAATTA-CAATATTACCCTCGAACATCCGAAAAT
1 AAAAATTACCATTTTACCCCCGAACATCCAAAAATTACCAAT-TTACCCTCGAACATCCAAAAAT
110678 TACCATTTTACTTCTGAACATCT
65 TACCATTTTACTTCTGAACATCT
* ** * * **
110701 AAAAATTATCATTTTACCCCCGAACATCTTAAAATTACCAATTTTCCCTCTAGTATCCAAAAATT
1 AAAAATTACCATTTTACCCCCGAACATCCAAAAATTACCAATTTACCCTCGAACATCCAAAAATT
110766 ACCATTTT
66 ACCATTTT
110774 GTCCCGAAGT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
87 60 0.94
88 4 0.06
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (87 bp):
AAAAATTACCATTTTACCCCCGAACATCCAAAAATTACCAATTTACCCTCGAACATCCAAAAATT
ACCATTTTACTTCTGAACATCT
Found at i:112353 original size:6 final size:6
Alignment explanation
Indices: 112342--112401 Score: 56
Period size: 6 Copynumber: 10.2 Consensus size: 6
112332 TATACATATA
*
112342 TATTTT TGTTTT TA-TTT TATTTT ATATTATT TATTTT TATGTTT TA---T
1 TATTTT TATTTT TATTTT TATTTT -TATT-TT TATTTT TAT-TTT TATTTT
112389 TATTTT TATTTT T
1 TATTTT TATTTT T
112402 CTTTATTTCG
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
3 3 0.07
5 5 0.11
6 22 0.49
7 13 0.29
8 2 0.04
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:112381 original size:20 final size:19
Alignment explanation
Indices: 112352--112393 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
112342 TATTTTTGTT
112352 TTTATTTTAT-TTTATATTA
1 TTTATTTTATGTTT-TATTA
112371 TTTATTTTTATGTTTTATTA
1 TTTA-TTTTATGTTTTATTA
112391 TTT
1 TTT
112394 TTATTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 14 0.67
21 3 0.14
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTATTTTATGTTTTATTA
Found at i:112386 original size:27 final size:24
Alignment explanation
Indices: 112340--112409 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 24
112330 CATATACATA
*
112340 TATATTTTTGTTTTTATTTTATTT
1 TATATTTTTATTTTTATTTTATTT
* *
112364 TATATTATTTATTTTTATGTT-TTA
1 TATATT-TTTATTTTTATTTTATTT
*
112388 T-TATTTTTATTTTT-CTTTATTT
1 TATATTTTTATTTTTATTTTATTT
112410 CGAAACTACA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.05
22 11 0.29
23 4 0.11
24 9 0.24
25 12 0.32
ACGTcount: A:0.19, C:0.01, G:0.03, T:0.77
Consensus pattern (24 bp):
TATATTTTTATTTTTATTTTATTT
Found at i:112389 original size:13 final size:13
Alignment explanation
Indices: 112340--112389 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
112330 CATATACATA
*
112340 TATATTTTTGTTT
1 TATATTTTTATTT
112353 T-TA-TTTTATTT
1 TATATTTTTATTT
112364 TATATTATTTATTT
1 TATATT-TTTATTT
112378 T-TATGTTTTATT
1 TATAT-TTTTATT
112390 ATTTTTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
11 8 0.25
12 4 0.12
13 11 0.34
14 9 0.28
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (13 bp):
TATATTTTTATTT
Found at i:112396 original size:22 final size:19
Alignment explanation
Indices: 112350--112401 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 19
112340 TATATTTTTG
112350 TTTTTA-TTTTATTTTATA
1 TTTTTATTTTTATTTTATA
112368 TTATTTATTTTTATGTTTTATTA
1 TT-TTTATTTTTA--TTTTA-TA
112391 TTTTTATTTTT
1 TTTTTATTTTT
112402 CTTTATTTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.07
19 4 0.14
20 5 0.17
22 14 0.48
23 4 0.14
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTATTTTTATTTTATA
Found at i:112407 original size:16 final size:16
Alignment explanation
Indices: 112371--112409 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
112361 TTTTATATTA
112371 TTTATTTTTATGTTTT
1 TTTATTTTTATGTTTT
*
112387 ATTATTTTTAT-TTTT
1 TTTATTTTTATGTTTT
112402 CTTTATTT
1 -TTTATTT
112410 CGAAACTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTATTTTTATGTTTT
Found at i:115326 original size:17 final size:17
Alignment explanation
Indices: 115306--115344 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
115296 TTGTTTAGAA
115306 TATTTTTT-TCCCAAAAG
1 TATTTTTTGTCCC-AAAG
115323 TATTTTTTGTCCCAAAG
1 TATTTTTTGTCCCAAAG
115340 TATTT
1 TATTT
115345 CTTAGAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (17 bp):
TATTTTTTGTCCCAAAG
Found at i:122605 original size:32 final size:32
Alignment explanation
Indices: 122552--122632 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
122542 AAGCTTAGTC
* ** *
122552 AAAATTGTTTATTTTATTAATTTTGTTTTTACT
1 AAAATTG-TTATTTTACTAATTTCATTTTGACT
*
122585 AAAATTGTTATTTTCCTAATTTCATTTTGACT
1 AAAATTGTTATTTTACTAATTTCATTTTGACT
*
122617 AAAATTATTTATTTTA
1 AAAATT-GTTATTTTA
122633 AGTAAATAGG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 26 0.65
33 14 0.35
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.58
Consensus pattern (32 bp):
AAAATTGTTATTTTACTAATTTCATTTTGACT
Found at i:123555 original size:11 final size:11
Alignment explanation
Indices: 123539--123569 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
123529 TTACACTTTA
123539 TTTATTTTATT
1 TTTATTTTATT
123550 TTTATTTTATT
1 TTTATTTTATT
*
123561 TTTAGTTTA
1 TTTATTTTA
123570 ACATTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:131508 original size:26 final size:25
Alignment explanation
Indices: 131456--131520 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 25
131446 GATAATCACT
131456 TTAAATTAAATTAATAAAATAATTA
1 TTAAATTAAATTAATAAAATAATTA
*
131481 TTAAATTAAATTTAATATAA-AATCTA
1 TTAAATTAAA-TTAATAAAATAAT-TA
*
131507 TTAAAATAATATTA
1 TTAAATTAA-ATTA
131521 TTTTTGGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 13 0.37
26 21 0.60
27 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
TTAAATTAAATTAATAAAATAATTA
Found at i:135364 original size:3 final size:3
Alignment explanation
Indices: 135356--135381 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
135346 AAAGCTGCTA
135356 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
135382 CTGCATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:138817 original size:22 final size:20
Alignment explanation
Indices: 138779--138818 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
138769 AGATTTAATA
138779 TTTTAATGTTAAATAAATTT
1 TTTTAATGTTAAATAAATTT
*
138799 TTTTAAATGATTAATTAAAT
1 TTTT-AATG-TTAAATAAAT
138819 AAAAAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTAATGTTAAATAAATTT
Found at i:139792 original size:21 final size:21
Alignment explanation
Indices: 139766--139805 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
139756 TAGATTTGAT
* *
139766 TGAAAATATACAAAAAAAAAA
1 TGAAAACACACAAAAAAAAAA
139787 TGAAAACACACAAAAAAAA
1 TGAAAACACACAAAAAAAA
139806 TCAAGGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.10, G:0.05, T:0.10
Consensus pattern (21 bp):
TGAAAACACACAAAAAAAAAA
Found at i:141162 original size:11 final size:11
Alignment explanation
Indices: 141148--141172 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
141138 TCCAAACAAC
141148 AAATAATAGCA
1 AAATAATAGCA
141159 AAATAATAGCA
1 AAATAATAGCA
141170 AAA
1 AAA
141173 CAACAACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (11 bp):
AAATAATAGCA
Found at i:144770 original size:17 final size:17
Alignment explanation
Indices: 144748--144781 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
144738 GAAAAAATTT
*
144748 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
144765 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
144782 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:145179 original size:16 final size:18
Alignment explanation
Indices: 145154--145193 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
145144 TTTGATTTAT
*
145154 TATTTTGAAATAA-TA-A
1 TATTTAGAAATAAGTATA
145170 TATTTAGAAATAAGTATA
1 TATTTAGAAATAAGTATA
145188 TATTTA
1 TATTTA
145194 AATAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
17 2 0.10
18 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (18 bp):
TATTTAGAAATAAGTATA
Found at i:147269 original size:6 final size:6
Alignment explanation
Indices: 147255--147287 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
147245 ACTTTCAACC
*
147255 GCCTGA GCCTAA GCCTGA GCCTGA GCCTGA GCC
1 GCCTGA GCCTGA GCCTGA GCCTGA GCCTGA GCC
147288 GCAGCACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.36, G:0.30, T:0.15
Consensus pattern (6 bp):
GCCTGA
Found at i:151240 original size:14 final size:14
Alignment explanation
Indices: 151203--151246 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
151193 ATTAATTTTG
151203 TTTTTTGTATTATAT
1 TTTTTTGTATTAT-T
** *
151218 TTTGGTGTATAATT
1 TTTTTTGTATTATT
151232 TTTTTTGTATTATT
1 TTTTTTGTATTATT
151246 T
1 T
151247 ATGTCAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.70
Consensus pattern (14 bp):
TTTTTTGTATTATT
Found at i:151335 original size:27 final size:28
Alignment explanation
Indices: 151305--151371 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 28
151295 TGCAGGCTGC
151305 CAGGTAGGCACCACTAG-TGCCGCCTAT
1 CAGGTAGGCACCACTAGCTGCCGCCTAT
* * *
151332 CAGGTAGGCACC-TTTGCTGCCGCCTGT
1 CAGGTAGGCACCACTAGCTGCCGCCTAT
*
151359 CAGATAGGCACCA
1 CAGGTAGGCACCA
151372 TCCCTTGTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.21, C:0.33, G:0.27, T:0.19
Consensus pattern (28 bp):
CAGGTAGGCACCACTAGCTGCCGCCTAT
Found at i:156337 original size:50 final size:51
Alignment explanation
Indices: 156262--156379 Score: 166
Period size: 50 Copynumber: 2.3 Consensus size: 51
156252 AGCCTTTCCG
* * * *
156262 AAAACCTAAATTCTATTTTTTATTTATTTATAAATAAA-AATGAATAAAAT
1 AAAACCCAAATTTTATTTATTATTTATTTATAAATAAATAATAAATAAAAT
*
156312 AAAACCCAAATTTTATTTATTATTTATTTATAAATAAATAATAAATTAAAT
1 AAAACCCAAATTTTATTTATTATTTATTTATAAATAAATAATAAATAAAAT
* *
156363 AAAGCCCAAAATTTATT
1 AAAACCCAAATTTTATT
156380 AAACTCAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
50 35 0.58
51 25 0.42
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.41
Consensus pattern (51 bp):
AAAACCCAAATTTTATTTATTATTTATTTATAAATAAATAATAAATAAAAT
Found at i:156379 original size:51 final size:50
Alignment explanation
Indices: 156269--156379 Score: 159
Period size: 51 Copynumber: 2.2 Consensus size: 50
156259 CCGAAAACCT
* *
156269 AAATTCTATTTTTTATTTATTTATAAATAAAAATGAATAAAATAAAACCCA
1 AAATT-TATTTATTATTTATTTATAAATAAAAATAAATAAAATAAAACCCA
* * *
156320 AATTTTATTTATTATTTATTTATAAATAAATAATAAATTAAATAAAGCCCA
1 AAATTTATTTATTATTTATTTATAAATAAA-AATAAATAAAATAAAACCCA
156371 AAATTTATT
1 AAATTTATT
156380 AAACTCAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 24 0.45
51 29 0.55
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (50 bp):
AAATTTATTTATTATTTATTTATAAATAAAAATAAATAAAATAAAACCCA
Found at i:156543 original size:3 final size:3
Alignment explanation
Indices: 156535--156559 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
156525 ATGCTACCGT
156535 CGC CGC CGC CGC CGC CGC CGC CGC C
1 CGC CGC CGC CGC CGC CGC CGC CGC C
156560 AGAGCCATGT
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:0.68, G:0.32, T:0.00
Consensus pattern (3 bp):
CGC
Found at i:160115 original size:31 final size:31
Alignment explanation
Indices: 160070--160130 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
160060 CTCGCTCTAC
* *
160070 TTAGTGTCTGTTTTCACAAAATAAACCCCAT
1 TTAGTGTATATTTTCACAAAATAAACCCCAT
*
160101 TTAGTGTATATTTTCACAAAATAATCCCCA
1 TTAGTGTATATTTTCACAAAATAAACCCCA
160131 CTGTTTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.36
Consensus pattern (31 bp):
TTAGTGTATATTTTCACAAAATAAACCCCAT
Found at i:160169 original size:25 final size:23
Alignment explanation
Indices: 160140--160201 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
160130 ACTGTTTTCA
*
160140 TTTTTGTTTAATTTGATTTTTTTAT
1 TTTTTGTTT-ATTTGA-TTTATTAT
*
160165 TTTTTGTATTATTTTATTTATTAT
1 TTTTTGT-TTATTTGATTTATTAT
160189 TTATTTG-TTATTT
1 TT-TTTGTTTATTT
160202 TTTATTCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 6 0.18
24 9 0.27
25 16 0.48
26 2 0.06
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (23 bp):
TTTTTGTTTATTTGATTTATTAT
Found at i:160204 original size:25 final size:24
Alignment explanation
Indices: 160161--160207 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
160151 TTTGATTTTT
160161 TTATTTTTTGTATTATTTTATTTA
1 TTATTTTTTGTATTATTTTATTTA
160185 TTATTTATTTGTTATT-TTTTATT
1 TTATTT-TTTG-TATTATTTTATT
160208 CATTCATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (24 bp):
TTATTTTTTGTATTATTTTATTTA
Found at i:160207 original size:21 final size:22
Alignment explanation
Indices: 160156--160204 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
160146 TTTAATTTGA
160156 TTTTT-TTATTTTTTGTATTATT
1 TTTTTATTATTTTTTG-ATTATT
160178 TTATTTATTATTTATTTG-TTATT
1 TT-TTTATTATTT-TTTGATTATT
160201 TTTT
1 TTTT
160205 ATTCATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
22 4 0.17
23 10 0.42
24 6 0.25
25 4 0.17
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (22 bp):
TTTTTATTATTTTTTGATTATT
Found at i:161608 original size:52 final size:52
Alignment explanation
Indices: 161551--161892 Score: 358
Period size: 52 Copynumber: 6.6 Consensus size: 52
161541 TAAACGAAAG
* * * * *
161551 GGTCTGATGACTAAGTGTCATTGTGAGTAAACGAATCCCTTATGAATTAAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAA
* *
161603 GGTCTGATGACTAAGTGTCATCGTGAGTAAACGAATCCTTTACGAATT-AAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAA
* * * * *
161654 GGAATCCAATGACTAAGTGTTATTGTGAGTAAATGAATCCTTTACGGATTAAAG
1 GG--TCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAA
*
161708 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTAC-AGATTAAAG
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGA-ATTAAAA
** * *
161760 GGTTTGATGACTAAGTGTCATCGTGACTAAATGAATCCATGATA-G-ATT-AAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCC-T-TTACGAATTAAAA
* * * *
161811 GGTCCGATGACTCAA-TGTCATCGTGAGTATATGAATTCCTATACGGAA-CAAGA
1 GGTCCGATGACT-AAGTGTCATCGTGAGTAAATGAA-TCCTTTAC-GAATTAAAA
161864 GGTCCGATGACTATA-TGTCATCGTGAGTA
1 GGTCCGATGACTA-AGTGTCATCGTGAGTA
161893 TTAAATGAAA
Statistics
Matches: 251, Mismatches: 25, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
50 3 0.01
51 36 0.14
52 135 0.54
53 71 0.28
54 6 0.02
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (52 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAA
Found at i:161682 original size:105 final size:104
Alignment explanation
Indices: 161557--161839 Score: 358
Period size: 105 Copynumber: 2.7 Consensus size: 104
161547 AAAGGGTCTG
* * *
161557 ATGACTAAGTGTCATTGTGAGTAAACGAATCCCTTATGAATTAAAAGGTCTGATGACTAAGTGTC
1 ATGACTAAGTGTCATTGTGAGTAAATGAATCCATTATGAATTAAAAGGTCCGATGACTAAGTGTC
161622 ATCGTGAGTAAACGAATCCTTTAC-GAATTAAAGGAATCCA
66 ATCGTGAGTAAACGAATCCTTTACAG-ATTAAAGG-ATCCA
* * * * *
161662 ATGACTAAGTGTTATTGTGAGTAAATGAATCCTTTACGGATTAAAGGGTCCGATGACTAAGTGTC
1 ATGACTAAGTGTCATTGTGAGTAAATGAATCCATTATGAATTAAAAGGTCCGATGACTAAGTGTC
* * ***
161727 ATCGTGAGTAAATGAATCCTTTACAGATTAAAGGGTTTG
66 ATCGTGAGTAAACGAATCCTTTACAGATTAAAGGATCCA
* * *
161766 ATGACTAAGTGTCATCGTGACTAAATGAATCCATGAT-AGATT-AAAGGTCCGATGACTCAA-TG
1 ATGACTAAGTGTCATTGTGAGTAAATGAATCCATTATGA-ATTAAAAGGTCCGATGACT-AAGTG
161828 TCATCGTGAGTA
64 TCATCGTGAGTA
161840 TATGAATTCC
Statistics
Matches: 155, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
103 28 0.18
104 37 0.24
105 89 0.57
106 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (104 bp):
ATGACTAAGTGTCATTGTGAGTAAATGAATCCATTATGAATTAAAAGGTCCGATGACTAAGTGTC
ATCGTGAGTAAACGAATCCTTTACAGATTAAAGGATCCA
Found at i:164026 original size:19 final size:19
Alignment explanation
Indices: 164002--164071 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
163992 AATTTAGAAC
164002 AAAATTATAAAAATCGTAA
1 AAAATTATAAAAATCGTAA
* * *
164021 AAAATTATGATATATTGTAA
1 AAAATTAT-AAAAATCGTAA
** *
164041 AATTTTATAAAAATCCTAA
1 AAAATTATAAAAATCGTAA
164060 AAAATTATAAAA
1 AAAATTATAAAA
164072 TGCATAAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 25 0.64
20 14 0.36
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAATTATAAAAATCGTAA
Found at i:164394 original size:20 final size:19
Alignment explanation
Indices: 164343--164394 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
164333 TTTCTATATA
164343 TTTTATAT-TTTTTAAGAT
1 TTTTATATATTTTTAAGAT
* *
164361 TTTTATAAAATTTTACA-AT
1 TTTTATATATTTTTA-AGAT
164380 TTATTATATATTTTT
1 TT-TTATATATTTTT
164395 TTATTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 7 0.26
19 9 0.33
20 11 0.41
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTATATATTTTTAAGAT
Found at i:164436 original size:11 final size:10
Alignment explanation
Indices: 164414--164478 Score: 57
Period size: 10 Copynumber: 6.8 Consensus size: 10
164404 TTAAAAATTC
164414 TAATTTTTAA
1 TAATTTTTAA
164424 TAATTTTT-A
1 TAATTTTTAA
164433 -AATATTTT-A
1 TAAT-TTTTAA
*
164442 T-ATTTTTAT
1 TAATTTTTAA
**
164451 TAAAATTTAA
1 TAATTTTTAA
*
164461 TAATTTTTAT
1 TAATTTTTAA
164471 TAATTTTT
1 TAATTTTT
164479 TTATCATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
8 7 0.16
9 9 0.20
10 28 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:164453 original size:20 final size:21
Alignment explanation
Indices: 164430--164489 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
164420 TTAATAATTT
164430 TTAAATATTTTAT-ATTTTTA
1 TTAAATATTTTATAATTTTTA
*
164450 TTAAA-ATTTAATAATTTTTA
1 TTAAATATTTTATAATTTTTA
* * *
164470 TTAATTTTTTTATCATTTTT
1 TTAAATATTTTATAATTTTT
164490 TGCCACATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 6 0.18
20 16 0.48
21 11 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TTAAATATTTTATAATTTTTA
Found at i:164458 original size:19 final size:21
Alignment explanation
Indices: 164419--164473 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
164409 AATTCTAATT
164419 TTTAATAA--TTT-TTAAATA
1 TTTAATAATTTTTATTAAATA
*
164437 TTTTAT-ATTTTTATTAAA-A
1 TTTAATAATTTTTATTAAATA
164456 TTTAATAATTTTTATTAA
1 TTTAATAATTTTTATTAA
164474 TTTTTTTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 1 0.03
18 5 0.16
19 9 0.29
20 16 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAATAATTTTTATTAAATA
Found at i:164459 original size:27 final size:26
Alignment explanation
Indices: 164402--164465 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
164392 TTTTTATTTT
*
164402 ATTTAAAAATTCTAATTTTTAATAAT
1 ATTTAAAAATTCTAATTTTTAATAAA
* * * *
164428 TTTTAAATATTTTATATTTTTATTAAA
1 ATTTAAAAATTCTA-ATTTTTAATAAA
*
164455 ATTTAATAATT
1 ATTTAAAAATT
164466 TTTATTAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTAAAAATTCTAATTTTTAATAAA
Found at i:164693 original size:88 final size:86
Alignment explanation
Indices: 164552--164794 Score: 264
Period size: 88 Copynumber: 2.8 Consensus size: 86
164542 TTAAAAGTGA
* *
164552 TTCAAGTACCCAA--T-TGAGTAAAAAAATAAGAGCTTAATTTCTTTTTTGAAAAAGTTTGAAGA
1 TTCAAGTACCCAATGTGTGAGAAAAAAAATAA-AGCTTAATTGCTTTTTTGAAAAAGTTTGAAGA
164614 TCATTTTGAAACATTATGAAAG
65 TCATTTTGAAACATTATGAAAG
164636 TTCAAGTACCCAATTGTGTGAGAAAAAAAATAAATGCTTAATTGCTTTTTTGAAAAAGTTTGAAG
1 TTCAAGTACCCAA-TGTGTGAGAAAAAAAATAAA-GCTTAATTGCTTTTTTGAAAAAGTTTGAAG
* * **
164701 ATCTTTTTTATGCATTATGAAAG
64 ATCATTTTGAAACATTATGAAAG
* * * * * * *
164724 TTCATGTACCAAAATGAGT--GCAAAAGAATAGAGGTTTAATTGCTTTTTTTGAAAAAGTTT-AA
1 TTCAAGTACC-CAATGTGTGAGAAAAAAAATA-AAGCTTAATTGC-TTTTTTGAAAAAGTTTGAA
*
164786 GAGCATTTT
63 GATCATTTT
164795 ACACCCTTAA
Statistics
Matches: 136, Mismatches: 15, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
84 13 0.10
86 27 0.20
87 19 0.14
88 75 0.55
89 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (86 bp):
TTCAAGTACCCAATGTGTGAGAAAAAAAATAAAGCTTAATTGCTTTTTTGAAAAAGTTTGAAGAT
CATTTTGAAACATTATGAAAG
Found at i:177071 original size:49 final size:49
Alignment explanation
Indices: 176889--177365 Score: 304
Period size: 49 Copynumber: 9.7 Consensus size: 49
176879 GAAACATGAT
* * * * ** *
176889 GGGAAAGATTGAAGCCACAACGGCGAATCTAATACCATGAAGATATGGA
1 GGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACGAAGATATGGA
* * * * * * *
176938 GGGAAAGGTTTAAGTCTCAACAGCGAACCTTTTACCTCAGAA-ACATGAA
1 GGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCAC-GAAGATATGGA
* * * ** * *
176987 AGGAAAGATTGT-AGCCACAACGATGAATCTAGTACCACGAAGATATGGA
1 GGGAAAGATT-TAAGTCGCAACGGCGAACCTTGTACCACGAAGATATGGA
* * * * *
177036 GGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAA-ACATGCTA
1 GGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCAC-GAAGATATG-GA
* * * * * *
177086 -GGAAAGATTGAAGCCGCAATGGC-AATTCTGGTACCACGAAGATCTGGA
1 GGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGTACCACGAAGATATGGA
* * * * * **
177134 GGGAAAGCTTTAAATCGCGACGGCGAACCTTGTACCTCAGAA-ACATGCT
1 GGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCAC-GAAGATATGGA
* * * *
177183 GGGAAAGATTGAAGCCGCAACGGCGAATCTGGTACCACGAAGATATGGA
1 GGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACGAAGATATGGA
* * * * * * * *
177232 GGTAAAGGTTTAAGTCGCAACGGTGAACCTTGCACCTC-AAAAGCATGAA
1 GGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACGAAGA-TATGGA
* * * *
177281 GGGAAAGATTGAAGCCGTAACGGCGAA-TTTAGTACCACGAAGATATGGA
1 GGGAAAGATTTAAGTCGCAACGGCGAACCTT-GTACCACGAAGATATGGA
* **
177330 GGGAAAGGTTTAAGTCGCAACGGTAAACCTTGTACC
1 GGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC
177366 TCAAAAACAT
Statistics
Matches: 311, Mismatches: 101, Indels: 32
0.70 0.23 0.07
Matches are distributed among these distances:
48 18 0.06
49 275 0.88
50 18 0.06
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (49 bp):
GGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCACGAAGATATGGA
Found at i:177383 original size:49 final size:48
Alignment explanation
Indices: 176865--177416 Score: 261
Period size: 49 Copynumber: 11.3 Consensus size: 48
176855 ATTTTGAAAC
* * * *
176865 AACCTTGTACCTCAGAAACATGATGGGAAAGATTGAAGCCACAACGGCG
1 AACCTTGTACCTCAAAAACATGA-GGGAAAGATTTAAGTCGCAACGGCG
* ** * * * * * *
176914 AATCTAATACCAT-GAAGATATGGAGGGAAAGGTTTAAGTCTCAACAGCG
1 AACCTTGTACC-TCAAAAACAT-GAGGGAAAGATTTAAGTCGCAACGGCG
* * * * * **
176963 AACCTTTTACCTCAGAAACATGAAAGGAAAGATTGT-AGCCACAACGATG
1 AACCTTGTACCTCAAAAACATG-AGGGAAAGATT-TAAGTCGCAACGGCG
* * * * * * * *
177012 AATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAATGGCG
1 AACCTTGTACCTCAAAAACAT-GAGGGAAAGATTTAAGTCGCAACGGCG
* * * *
177061 AACCTTGTACCTCAGAAACATGCTA-GGAAAGATTGAAGCCGCAATGGC-
1 AACCTTGTACCTCAAAAACATG--AGGGAAAGATTTAAGTCGCAACGGCG
* * * * * * * *
177109 AATTCTGGTACCACGAAGATC-TGGAGGGAAAGCTTTAAATCGCGACGGCG
1 AA-CCTTGTACCTC-AAAAACAT-GAGGGAAAGATTTAAGTCGCAACGGCG
* * * *
177159 AACCTTGTACCTCAGAAACATGCTGGGAAAGATTGAAGCCGCAACGGCG
1 AACCTTGTACCTCAAAAACATG-AGGGAAAGATTTAAGTCGCAACGGCG
* * * * * * * * *
177208 AATCTGGTACCACGAAGATATGGAGGTAAAGGTTTAAGTCGCAACGGTG
1 AACCTTGTACCTCAAAAACAT-GAGGGAAAGATTTAAGTCGCAACGGCG
* * * * *
177257 AACCTTGCACCTCAAAAGCATGAAGGGAAAGATTGAAGCCGTAACGGCG
1 AACCTTGTACCTCAAAAACATG-AGGGAAAGATTTAAGTCGCAACGGCG
* * * * * * **
177306 AA-TTTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGTA
1 AACCTT-GTACCTCAAAAACAT-GAGGGAAAGATTTAAGTCGCAACGGCG
* * * *
177355 AACCTTGTACCTCAAAAACATGATGGGAAAGATTGAAGCCGTAACAGCG
1 AACCTTGTACCTCAAAAACATGA-GGGAAAGATTTAAGTCGCAACGGCG
* *
177404 AATCTTCTACCTC
1 AACCTTGTACCTC
177417 GAAGTTACAT
Statistics
Matches: 352, Mismatches: 129, Indels: 44
0.67 0.25 0.08
Matches are distributed among these distances:
48 16 0.05
49 320 0.91
50 16 0.05
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (48 bp):
AACCTTGTACCTCAAAAACATGAGGGAAAGATTTAAGTCGCAACGGCG
Found at i:177394 original size:294 final size:294
Alignment explanation
Indices: 176865--177395 Score: 830
Period size: 294 Copynumber: 1.8 Consensus size: 294
176855 ATTTTGAAAC
*
176865 AACCTTGTACCTCAGAAACATGATGGGAAAGATTGAAGCCACAACGGCGAATCTAATACCATGAA
1 AACCTTGTACCTCAGAAACATGATGGGAAAGATTGAAGCCACAACGGCGAATCTAATACCACGAA
* **
176930 GATATGGAGGGAAAGGTTTAAGTCTCAACAGCGAACCTTTTACCTCAGAAACATGAAAGGAAAGA
66 GATATGGAGGGAAAGGTTTAAGTCGCAACAGCGAACCTTGCACCTCAGAAACATGAAAGGAAAGA
* * *
176995 TTGTAGCCACAACGATGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAATGGC
131 TTGAAGCCACAACGACGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGC
* * *
177060 GAACCTTGTACCTCAGAAACATGCTAGGAAAGATTGAAGCCGCAATGGCAATTCTGGTACCACGA
196 AAACCTTGTACCTCAAAAACATGATAGGAAAGATTGAAGCCGCAATGGCAATTCTGGTACCACGA
177125 AGATCTGGAGGGAAAGCTTTAAATCGCGACGGCG
261 AGATCTGGAGGGAAAGCTTTAAATCGCGACGGCG
* * **
177159 AACCTTGTACCTCAGAAACATGCTGGGAAAGATTGAAGCCGCAACGGCGAATCTGGTACCACGAA
1 AACCTTGTACCTCAGAAACATGATGGGAAAGATTGAAGCCACAACGGCGAATCTAATACCACGAA
* * * *
177224 GATATGGAGGTAAAGGTTTAAGTCGCAACGGTGAACCTTGCACCTCA-AAAGCATGAAGGGAAAG
66 GATATGGAGGGAAAGGTTTAAGTCGCAACAGCGAACCTTGCACCTCAGAAA-CATGAAAGGAAAG
** * *
177288 ATTGAAGCCGTAACGGCGAATTTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGG
130 ATTGAAGCCACAACGACGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGG
* *
177353 TAAACCTTGTACCTCAAAAACATGATGGGAAAGATTGAAGCCG
195 CAAACCTTGTACCTCAAAAACATGATAGGAAAGATTGAAGCCG
177396 TAACAGCGAA
Statistics
Matches: 212, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
293 3 0.01
294 209 0.99
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (294 bp):
AACCTTGTACCTCAGAAACATGATGGGAAAGATTGAAGCCACAACGGCGAATCTAATACCACGAA
GATATGGAGGGAAAGGTTTAAGTCGCAACAGCGAACCTTGCACCTCAGAAACATGAAAGGAAAGA
TTGAAGCCACAACGACGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGC
AAACCTTGTACCTCAAAAACATGATAGGAAAGATTGAAGCCGCAATGGCAATTCTGGTACCACGA
AGATCTGGAGGGAAAGCTTTAAATCGCGACGGCG
Found at i:177420 original size:98 final size:98
Alignment explanation
Indices: 176865--177408 Score: 750
Period size: 98 Copynumber: 5.6 Consensus size: 98
176855 ATTTTGAAAC
* * *
176865 AACCTTGTACCTCAGAAACATGATGGGAAAGATTGAAGCCACAACGGCGAATCTAATACCATGAA
1 AACCTTGTACCTCAGAAACATGATGGGAAAGATTGAAGCCGCAACGGCGAATCTAGTACCACGAA
* *
176930 GATATGGAGGGAAAGGTTTAAGTCTCAACAGCG
66 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCG
* ** * * **
176963 AACCTTTTACCTCAGAAACATGAAAGGAAAGATTGTAGCCACAACGATGAATCTAGTACCACGAA
1 AACCTTGTACCTCAGAAACATGATGGGAAAGATTGAAGCCGCAACGGCGAATCTAGTACCACGAA
*
177028 GATATGGAGGGAAAGGTTTAAGTCGCAATGGCG
66 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCG
* * * *
177061 AACCTTGTACCTCAGAAACATGCTAGGAAAGATTGAAGCCGCAATGGC-AATTCTGGTACCACGA
1 AACCTTGTACCTCAGAAACATGATGGGAAAGATTGAAGCCGCAACGGCGAA-TCTAGTACCACGA
* * * *
177125 AGATCTGGAGGGAAAGCTTTAAATCGCGACGGCG
65 AGATATGGAGGGAAAGGTTTAAGTCGCAACGGCG
* *
177159 AACCTTGTACCTCAGAAACATGCTGGGAAAGATTGAAGCCGCAACGGCGAATCTGGTACCACGAA
1 AACCTTGTACCTCAGAAACATGATGGGAAAGATTGAAGCCGCAACGGCGAATCTAGTACCACGAA
* *
177224 GATATGGAGGTAAAGGTTTAAGTCGCAACGGTG
66 GATATGGAGGGAAAGGTTTAAGTCGCAACGGCG
* * * *
177257 AACCTTGCACCTCA-AAAGCATGAAGGGAAAGATTGAAGCCGTAACGGCGAATTTAGTACCACGA
1 AACCTTGTACCTCAGAAA-CATGATGGGAAAGATTGAAGCCGCAACGGCGAATCTAGTACCACGA
**
177321 AGATATGGAGGGAAAGGTTTAAGTCGCAACGGTA
65 AGATATGGAGGGAAAGGTTTAAGTCGCAACGGCG
* * *
177355 AACCTTGTACCTCAAAAACATGATGGGAAAGATTGAAGCCGTAACAGCGAATCT
1 AACCTTGTACCTCAGAAACATGATGGGAAAGATTGAAGCCGCAACGGCGAATCT
177409 TCTACCTCGA
Statistics
Matches: 397, Mismatches: 45, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
97 5 0.01
98 387 0.97
99 5 0.01
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (98 bp):
AACCTTGTACCTCAGAAACATGATGGGAAAGATTGAAGCCGCAACGGCGAATCTAGTACCACGAA
GATATGGAGGGAAAGGTTTAAGTCGCAACGGCG
Found at i:181907 original size:13 final size:14
Alignment explanation
Indices: 181888--181920 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
181878 AATTTGACCT
181888 ATTACAAA-CCCAA
1 ATTACAAAGCCCAA
*
181901 CTTACAAAGCCCAA
1 ATTACAAAGCCCAA
181915 ATTACA
1 ATTACA
181921 CTCAATACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.48, C:0.30, G:0.03, T:0.18
Consensus pattern (14 bp):
ATTACAAAGCCCAA
Found at i:182448 original size:19 final size:18
Alignment explanation
Indices: 182421--182470 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
182411 CATTAAATTT
*
182421 ATAATTAATAATAAATAA
1 ATAAATAATAATAAATAA
*
182439 CATAAATAATAA-AAATTA
1 -ATAAATAATAATAAATAA
182457 AT-AATAATAATAAA
1 ATAAATAATAATAAA
182471 GAAAAAACGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.29
17 5 0.18
18 5 0.18
19 10 0.36
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAAATAATAATAAATAA
Found at i:182462 original size:16 final size:17
Alignment explanation
Indices: 182414--182470 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
182404 ATAAGTACAT
*
182414 TAAATTTATAATTAATAA
1 TAAATTAATAA-TAATAA
*
182432 TAAATAACATAAATAATAA
1 TAAATTA-AT-AATAATAA
182451 -AAATTAATAATAATAA
1 TAAATTAATAATAATAA
182467 TAAA
1 TAAA
182471 GAAAAAACGT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 8 0.24
17 5 0.15
18 10 0.30
19 8 0.24
20 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATTAATAATAATAA
Found at i:183351 original size:30 final size:29
Alignment explanation
Indices: 183314--183387 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
183304 CTAAACTGTC
*
183314 CAAAAATTATATTTTGA-CCACCGAACTTT
1 CAAAAATTACATTTTGATCC-CCGAACTTT
* *
183343 CTAAAAATTACATTTTTATCCTCGAACTTT
1 C-AAAAATTACATTTTGATCCCCGAACTTT
183373 CAAAAATTACATTTT
1 CAAAAATTACATTTT
183388 TACCCCCTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 15 0.38
30 23 0.57
31 2 0.05
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (29 bp):
CAAAAATTACATTTTGATCCCCGAACTTT
Found at i:183415 original size:20 final size:21
Alignment explanation
Indices: 183375--183417 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
183365 CGAACTTTCA
*
183375 AAAATTACATTTTTACCCCCT
1 AAAATTACATTTTTACACCCT
*
183396 AAAATTCCATTTTT-CACCCT
1 AAAATTACATTTTTACACCCT
183416 AA
1 AA
183418 TTTCATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.35, C:0.28, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATTACATTTTTACACCCT
Found at i:183443 original size:29 final size:30
Alignment explanation
Indices: 183396--183490 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
183386 TTTACCCCCT
183396 AAAATTCCATTTTTCACCCT-AATTTCATCA
1 AAAATTCCATTTTTCACCCTCAATTTCA-CA
*
183426 AAAATTACCA-TTTT-ACCCTTGAACTTTC-C-
1 AAAATT-CCATTTTTCACCC-TCAA-TTTCACA
* *
183455 AAAATTCCATTTTTGA-CCTCGATTTCACCA
1 AAAATTCCATTTTTCACCCTCAATTTCA-CA
183485 AAAATT
1 AAAATT
183491 ACTATTTTAC
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
27 4 0.07
28 5 0.09
29 17 0.31
30 19 0.35
31 5 0.09
32 4 0.07
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTCCATTTTTCACCCTCAATTTCACA
Found at i:183524 original size:59 final size:59
Alignment explanation
Indices: 183417--183538 Score: 147
Period size: 59 Copynumber: 2.1 Consensus size: 59
183407 TTTCACCCTA
* ** * * *
183417 ATTTCATCAAAAATTACCATTTTACCCTTGAACTTTCCAAAATTCCATTTTTGACCTCG
1 ATTTCACCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCCCATTTTTAACCTCG
* * *
183476 ATTTCACCAAAAATTACTATTTTACCCCCGAA-ATTCCTATAATCCCATTTTTAACCTTG
1 ATTTCACCAAAAATTACCATTTTACCCCCGAACATTCC-AAAATCCCATTTTTAACCTCG
183535 ATTT
1 ATTT
183539 TTTTCTAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 4 0.08
59 49 0.92
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (59 bp):
ATTTCACCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCCCATTTTTAACCTCG
Found at i:183604 original size:28 final size:28
Alignment explanation
Indices: 183545--183604 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
183535 ATTTTTTTCT
* * *
183545 AAAATTACCATTTTGCCCTCGAGTGTCT
1 AAAATTACCATTTTGCCCCCGAGTATCA
183573 AAAATTACCATTTTGCCCCC-AGGTATCA
1 AAAATTACCATTTTGCCCCCGA-GTATCA
183601 AAAA
1 AAAA
183605 ATCTAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCCGAGTATCA
Found at i:195281 original size:194 final size:194
Alignment explanation
Indices: 194948--195978 Score: 1371
Period size: 194 Copynumber: 5.2 Consensus size: 194
194938 CACAAACAGT
* ** *
194948 GAGGCGGTCGTCTTCCTGATGAGATACAGAGAAGTATACCAACTAAAGGTTCAATATGAGCAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAC-------TCAATGCGAACAAAT
* * *
195013 CTTTGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGTAATAAAAAGGTTAGCTTC
59 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTC
195078 CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAA
124 CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAA
*
195143 ACAAGT
189 ACAAGC
195149 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
* *
195214 CCCCAGCTTCCTGATGAGATACTGAGAAGTAGGGCAAAGCAATAAAAAGGTTAGCTTCCTGATGA
66 CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGA
* *
195279 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCAGATTGAAACAAGT
131 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGC
* * * * *
195343 GAGGCGGTAATCTTCCTGATGAGACACAGAGAAGTATATCAACTCAATGCGAACAAATCATCAAA
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
* * * *
195408 CCCCAACTTCCTGATGAGATACAGAGAAGCAAGGCGAAGCAATAAAAATGTTAGCTTCCTGATGA
66 CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGA
* * * * ** *
195473 GACACTGAGAAGTAGACCAAATCCGTTTTCCTGATGAGGTACAGAGAATTGGATTGAAACAAAC
131 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGC
* *
195537 GGGGCGGTTATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
* *
195602 CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCAAAGCAATAAAAAGGTTAGCTTCTTGATGA
66 CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGA
* * * * * * *
195667 GACATTAAGAAGTGGATCAAATCCGTCTTCCTGATGAGGTACAGAGAAGTGGATTGAAACAAAC
131 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGC
* * * * **
195731 GGGGCGATTATCTTCCTGATGAGATATAGAGAAGTATACCAACTCAGGGCTCGAAGTGAGCAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATG--CG-A---A-CAAAT
* * * * * *
195796 CTTCGAATCTCAGCTTCTTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATGGTTAGCTTC
59 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTC
* * * *
195861 CTGATGAAATACTAAGAAGTAGACCAAATTCGTCTTCCTGATGAGGTACAGAGATGCGGATTGAA
124 CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAA
195926 ACAAGC
189 ACAAGC
** * * * *
195932 GATACGGTCATCTTCTTGATAAGATACTA-AGAAGTAGACCAAATCAA
1 GAGGCGGTCATCTTCCTGATGAGATAC-AGAGAAGTATACCAACTCAA
195979 CGACACCAAA
Statistics
Matches: 742, Mismatches: 80, Indels: 16
0.89 0.10 0.02
Matches are distributed among these distances:
194 537 0.72
196 2 0.00
197 1 0.00
200 1 0.00
201 200 0.27
202 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (194 bp):
GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGA
GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAGC
Found at i:196343 original size:28 final size:28
Alignment explanation
Indices: 196311--196403 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 28
196301 TTAAGTTGGG
196311 TTTAAATTGATTTAAAATTATTTTTAAA
1 TTTAAATTGATTTAAAATTATTTTTAAA
* *
196339 TTTAAATTTGGTTTAAATTTAAATTTAATTAAAA
1 TTTAAA-TTGATTTAAAATT--ATTT--TT-AAA
* * *
196373 TTTAAATTGACTTAAAACTTAATATTAAA
1 TTTAAATTGATTTAAAA-TTATTTTTAAA
196402 TT
1 TT
196404 AAAAGTCCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
28 6 0.12
29 16 0.31
30 2 0.04
31 4 0.08
32 2 0.04
33 10 0.20
34 11 0.22
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (28 bp):
TTTAAATTGATTTAAAATTATTTTTAAA
Found at i:196344 original size:6 final size:6
Alignment explanation
Indices: 196333--196380 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
196323 TAAAATTATT
** *
196333 TTTAAA TTTAAA TTT-GG TTTAAA TTTAAA TTT-AA TTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
196379 TT
1 TT
196381 GACTTAAAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 27 0.79
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:196353 original size:17 final size:17
Alignment explanation
Indices: 196333--196380 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
196323 TAAAATTATT
**
196333 TTTAAATTTAAATTTGG
1 TTTAAATTTAAATTTAA
196350 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
*
196367 TTAAAATTTAAATT
1 TTTAAATTTAAATT
196381 GACTTAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:196387 original size:17 final size:17
Alignment explanation
Indices: 196353--196407 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
196343 AATTTGGTTT
*
196353 AAATTTAAATTTAATTA
1 AAATTTAAATTGAATTA
*
196370 AAATTTAAATTGACTTA
1 AAATTTAAATTGAATTA
* *
196387 AAACTTAATATTAAATTA
1 AAATTTAA-ATTGAATTA
196405 AAA
1 AAA
196408 GTCCAAGACA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 22 0.69
18 10 0.31
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATTTAAATTGAATTA
Found at i:197224 original size:3 final size:3
Alignment explanation
Indices: 197206--197257 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
197196 ACATTGTTCG
*
197206 TAA TAAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
197252 TAA TAA
1 TAA TAA
197258 CATTTATTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:198363 original size:29 final size:29
Alignment explanation
Indices: 198316--198578 Score: 250
Period size: 30 Copynumber: 8.9 Consensus size: 29
198306 CCTTAGAGGT
*
198316 CCCTAAACTGTC-CAAAAAATATATTTTAA
1 CCCTAAACT-TCTCAAAAATTATATTTTAA
*
198345 CCCTTAAACTTCTCTAAAATTATATTTTAA
1 CCC-TAAACTTCTCAAAAATTATATTTTAA
** *
198375 CCCCGAACTTTTCAAAAATTATATTTTAA
1 CCCTAAACTTCTCAAAAATTATATTTTAA
* *
198404 CACCTAAACTTCTCCAAAATTATATTTTTGA
1 C-CCTAAACTTCTCAAAAATTATA-TTTTAA
*
198435 -CCTCAAACTT-TCCAAAAATTACATTTTAA
1 CCCT-AAACTTCT-CAAAAATTATATTTTAA
* * *
198464 CCCTAAACTTCTCCAAAACTATATTTTGA
1 CCCTAAACTTCTCAAAAATTATATTTTAA
* *
198493 CCC-AAACTT-TCCAAAAATTACATTTTGAC
1 CCCTAAACTTCT-CAAAAATTATATTTT-AA
*
198522 CCCTAAACTTCCTC-AAAATTATATTTTTGA
1 CCCTAAACTT-CTCAAAAATTATA-TTTTAA
* *
198552 CCCTAAACTTTTCAAAAATTACATTTT
1 CCCTAAACTTCTCAAAAATTATATTTT
198579 TACAATTGAA
Statistics
Matches: 191, Mismatches: 28, Indels: 30
0.77 0.11 0.12
Matches are distributed among these distances:
27 1 0.01
28 18 0.09
29 68 0.36
30 93 0.49
31 10 0.05
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTCTCAAAAATTATATTTTAA
Found at i:198423 original size:59 final size:59
Alignment explanation
Indices: 198320--198754 Score: 361
Period size: 59 Copynumber: 7.4 Consensus size: 59
198310 AGAGGTCCCT
* * * * *
198320 AAACTGTCCAAAAAATATATTTTAACCCTTAAACTTCTCTAAAATTATA-TTTTAACCCC
1 AAACTTTCCAAAAATTACATTTTAACCC-TAAACTTCTCCAAAATTATATTTTTGACCCC
* * * *
198379 GAACTTTTCAAAAATTATATTTTAACACCTAAACTTCTCCAAAATTATATTTTTGACCTC
1 AAACTTTCCAAAAATTACATTTTAAC-CCTAAACTTCTCCAAAATTATATTTTTGACCCC
*
198439 AAACTTTCCAAAAATTACATTTTAACCCTAAACTTCTCCAAAACTATA-TTTTGA-CCC
1 AAACTTTCCAAAAATTACATTTTAACCCTAAACTTCTCCAAAATTATATTTTTGACCCC
* *
198496 AAACTTTCCAAAAATTACATTTTGACCCCTAAACTTC-CTCAAAATTATATTTTTGACCCT
1 AAACTTTCCAAAAATTACATTTT-AACCCTAAACTTCTC-CAAAATTATATTTTTGACCCC
* * ** * * ** * *
198556 AAACTTTTCAAAAATTACATTTTTACAATTGAACTT-TCTAAAAAAAAAAATTTTGACCCGC
1 AAACTTTCCAAAAATTACATTTTAAC-CCTAAACTTCTC-CAAAATTATATTTTTGACCC-C
** * ** *
198617 --TTTTTCCAAAAATTACATTTTTACCCTAAACTT-TCCAAAATTCCATTTTTGACCTC
1 AAACTTTCCAAAAATTACATTTTAACCCTAAACTTCTCCAAAATTATATTTTTGACCCC
* * * * * * * * *
198673 -GATTTTCTAAAAATTACCAATTTACCCCTGAACTTCT-AAAAATTCTATTTTTGATCCC
1 AAACTTTCCAAAAATTA-CATTTTAACCCTAAACTTCTCCAAAATTATATTTTTGACCCC
**
198731 -ATTTTTCCAAAAATTACCATTTTA
1 AAACTTTCCAAAAATTA-CATTTTA
198755 CCATTGGATT
Statistics
Matches: 310, Mismatches: 54, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
56 1 0.00
57 52 0.17
58 86 0.28
59 91 0.29
60 80 0.26
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (59 bp):
AAACTTTCCAAAAATTACATTTTAACCCTAAACTTCTCCAAAATTATATTTTTGACCCC
Found at i:198686 original size:29 final size:29
Alignment explanation
Indices: 198606--198753 Score: 78
Period size: 29 Copynumber: 5.1 Consensus size: 29
198596 AAAAAAAAAA
* *
198606 TTTTGACCCGCTTTTTCCAAAAATTA-CAT
1 TTTTGACCCG-ATTTTCTAAAAATTACCAT
* * *
198635 TTTT-ACCCTAAACTTTC-CAAAATT-CCAT
1 TTTTGACCC--GATTTTCTAAAAATTACCAT
198663 TTTTGACCTCGATTTTCTAAAAATTACCA-
1 TTTTGACC-CGATTTTCTAAAAATTACCAT
* ** *
198692 ATTT-ACCCCTGAACTTCTAAAAATT-CTAT
1 TTTTGA-CCC-GATTTTCTAAAAATTACCAT
*
198721 TTTTGATCCC-ATTTTTCCAAAAATTACCAT
1 TTTTGA-CCCGA-TTTTCTAAAAATTACCAT
198751 TTT
1 TTT
198754 ACCATTGGAT
Statistics
Matches: 89, Mismatches: 17, Indels: 25
0.68 0.13 0.19
Matches are distributed among these distances:
28 27 0.30
29 48 0.54
30 14 0.16
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTTGACCCGATTTTCTAAAAATTACCAT
Found at i:198769 original size:58 final size:58
Alignment explanation
Indices: 198618--198757 Score: 146
Period size: 58 Copynumber: 2.4 Consensus size: 58
198608 TTGACCCGCT
* * *
198618 TTTTCCAAAAATTA-CATTTTTACC-CTAAACTT-TCCAAAATTCCATTTTTGACCTCGA
1 TTTTCCAAAAATTACCA-ATTTACCACTGAACTTCT-AAAAATTCCATTTTTGACCTCGA
* * *
198675 TTTTCTAAAAATTACCAATTTACCCCTGAACTTCTAAAAATTCTATTTTTGATCC-C-A
1 TTTTCCAAAAATTACCAATTTACCACTGAACTTCTAAAAATTCCATTTTTGA-CCTCGA
*
198732 TTTTTCCAAAAATTACCATTTTACCA
1 -TTTTCCAAAAATTACCAATTTACCA
198758 TTGGATTTCT
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
57 20 0.29
58 47 0.67
59 3 0.04
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.41
Consensus pattern (58 bp):
TTTTCCAAAAATTACCAATTTACCACTGAACTTCTAAAAATTCCATTTTTGACCTCGA
Found at i:198823 original size:28 final size:29
Alignment explanation
Indices: 198791--198852 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
198781 ACGAACTTTA
198791 CAAAATTACCATTTT-ACCCTCGAG-AGTC
1 CAAAATTACCATTTTGACCCTCGAGTA-TC
*
198819 CAAAATTACCATTTTGCCCCTCGAGTATC
1 CAAAATTACCATTTTGACCCTCGAGTATC
198848 CAAAA
1 CAAAA
198853 ATCACATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 15 0.48
29 15 0.48
30 1 0.03
ACGTcount: A:0.34, C:0.29, G:0.10, T:0.27
Consensus pattern (29 bp):
CAAAATTACCATTTTGACCCTCGAGTATC
Found at i:198860 original size:29 final size:29
Alignment explanation
Indices: 198791--198862 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
198781 ACGAACTTTA
* *
198791 CAAAATTACCATTTT-ACCCTCGAGAGTC
1 CAAAATCACCATTTTGCCCCTCGAGAGTC
*
198819 CAAAATTACCATTTTGCCCCTCGAGTA-TC
1 CAAAATCACCATTTTGCCCCTCGAG-AGTC
198848 CAAAAATCA-CATTTT
1 C-AAAATCACCATTTT
198863 CAAACCCCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 15 0.38
29 17 0.44
30 7 0.18
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (29 bp):
CAAAATCACCATTTTGCCCCTCGAGAGTC
Found at i:201408 original size:14 final size:14
Alignment explanation
Indices: 201391--201424 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
201381 ATAATTTTGT
201391 TATTATATTATTAC
1 TATTATATTATTAC
* *
201405 TATTTTATTATTAT
1 TATTATATTATTAC
201419 TATTAT
1 TATTAT
201425 TTAAATATTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATATTATTAC
Found at i:201433 original size:17 final size:17
Alignment explanation
Indices: 201395--201433 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
201385 TTTTGTTATT
*
201395 ATATTATTACTATTTTA
1 ATATTATTACTATTTAA
* *
201412 TTATTATTATTATTTAA
1 ATATTATTACTATTTAA
201429 ATATT
1 ATATT
201434 GTATAACTCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTATTACTATTTAA
Found at i:202436 original size:24 final size:24
Alignment explanation
Indices: 202412--202457 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
202402 ACCCCTCAAC
*
202412 CCTAAACC-TAATAAAGTATAAAA
1 CCTAAACCTTAATAAAATATAAAA
*
202435 CCTAACCCTTAATAAAATATAAA
1 CCTAAACCTTAATAAAATATAAA
202458 CTATAACCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.54, C:0.20, G:0.02, T:0.24
Consensus pattern (24 bp):
CCTAAACCTTAATAAAATATAAAA
Found at i:202464 original size:24 final size:24
Alignment explanation
Indices: 202420--202467 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
202410 ACCCTAAACC
* *
202420 TAATAAAGTATAAAACCTAACCCT
1 TAATAAAATATAAAACATAACCCT
202444 TAATAAAATAT-AAACTATAACCCT
1 TAATAAAATATAAAAC-ATAACCCT
202468 AAAAAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27
Consensus pattern (24 bp):
TAATAAAATATAAAACATAACCCT
Done.