Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_66
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: 296488
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
File 1 of 2
Found at i:5873 original size:22 final size:22
Alignment explanation
Indices: 5843--5886 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5833 TTTGGTATTT
5843 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
5865 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
5887 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:11353 original size:13 final size:13
Alignment explanation
Indices: 11337--11381 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
11327 AAAAAAATAT
11337 AAAAAAATTCG-A
1 AAAAAAATTCGAA
*
11349 AAAAAAATTTGAAA
1 AAAAAAATTCG-AA
11363 AAAAAAATTC-AA
1 AAAAAAATTCGAA
11375 AAAAAAA
1 AAAAAAA
11382 GTTTGTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 19 0.66
14 10 0.34
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:11365 original size:14 final size:14
Alignment explanation
Indices: 11348--11386 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
11338 AAAAAATTCG
11348 AAAAAAAATTTGAA
1 AAAAAAAATTTGAA
*
11362 AAAAAAAA-TTCAA
1 AAAAAAAATTTGAA
*
11375 AAAAAAAGTTTG
1 AAAAAAAATTTG
11387 TATTCAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (14 bp):
AAAAAAAATTTGAA
Found at i:11381 original size:12 final size:12
Alignment explanation
Indices: 11337--11381 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
11327 AAAAAAATAT
11337 AAAAAAATTCGAA
1 AAAAAAATTC-AA
* *
11350 AAAAAATTTGAAA
1 AAAAAAATT-CAA
11363 AAAAAAATTCAA
1 AAAAAAATTCAA
11375 AAAAAAA
1 AAAAAAA
11382 GTTTGTATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:11488 original size:29 final size:30
Alignment explanation
Indices: 11424--11496 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
11414 TTAGTATTGA
* **
11424 AGAAAAAAAGAAGAAAAAAAATTCGGAATT
1 AGAAAAAAAGAAGAAAAAAAAATCAAAATT
*
11454 AAAAAAAAAGAAGAAAAAAAAATCAAAATT
1 AGAAAAAAAGAAGAAAAAAAAATCAAAATT
*
11484 -GAAAAAAAAAAGA
1 AGAAAAAAAGAAGA
11497 GTGATTGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 11 0.30
30 26 0.70
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10
Consensus pattern (30 bp):
AGAAAAAAAGAAGAAAAAAAAATCAAAATT
Found at i:12331 original size:21 final size:20
Alignment explanation
Indices: 12302--12347 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
12292 AATCTTGAAT
*
12302 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
12323 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
12343 GAAAA
1 GAAAA
12348 ACAAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAAAAAAA
Found at i:12363 original size:6 final size:6
Alignment explanation
Indices: 12354--12389 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
12344 AAAAACAAAT
* *
12354 TTGAGA TTGAGA TTGAGA TTGATA TTGATA TTGAGA
1 TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA
12390 AAAAAATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (6 bp):
TTGAGA
Found at i:16643 original size:23 final size:22
Alignment explanation
Indices: 16591--16643 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
16581 TCCACGTCTT
*
16591 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
16613 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
16636 TTTCTTTT
1 TTTCTTTT
16644 TCAATCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:19839 original size:33 final size:33
Alignment explanation
Indices: 19801--19863 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
19791 GATTACTCAC
19801 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
19834 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
19864 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:19886 original size:15 final size:15
Alignment explanation
Indices: 19866--19916 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
19856 TCTCTTTCAA
19866 TTTCTTTTTTCGCTT
1 TTTCTTTTTTCGCTT
**
19881 TTTC-TTTTT--CAA
1 TTTCTTTTTTCGCTT
19893 TTTCTTTTTTCGCTT
1 TTTCTTTTTTCGCTT
19908 TTTCTTTTT
1 TTTCTTTTT
19917 CAATTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 5 0.17
13 5 0.17
14 5 0.17
15 14 0.48
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (15 bp):
TTTCTTTTTTCGCTT
Found at i:19887 original size:6 final size:6
Alignment explanation
Indices: 19878--20047 Score: 85
Period size: 6 Copynumber: 27.8 Consensus size: 6
19868 TCTTTTTTCG
** **
19878 CTTTTT CTTTTT CAATTT CTTTTTT CGCTTTTT CTTTTT CAATTT -TTTTT
1 CTTTTT CTTTTT CTTTTT C-TTTTT --CTTTTT CTTTTT CTTTTT CTTTTT
* * ** * * * **
19928 CATTCT CAATTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA
1 CTTTTT CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT
** * ** *
19979 CTTTTT CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
20027 CTTTTT -GTTTT CTTTTT -TTTT
1 CTTTTT CTTTTT CTTTTT CTTTT
20048 GAATTTTTTT
Statistics
Matches: 118, Mismatches: 39, Indels: 15
0.69 0.23 0.09
Matches are distributed among these distances:
5 11 0.09
6 86 0.73
7 12 0.10
8 8 0.07
9 1 0.01
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:19890 original size:27 final size:28
Alignment explanation
Indices: 19860--19973 Score: 137
Period size: 27 Copynumber: 4.1 Consensus size: 28
19850 TCAAGCTCTC
*
19860 TTTCAATTTCTTTT-TTCGCTTTTTCTT
1 TTTCAATTTCTTTTCTTCGCATTTTCTT
*
19887 TTTCAATTTCTTTT-TTCGCTTTTTCTT
1 TTTCAATTTCTTTTCTTCGCATTTTCTT
* * *
19914 TTTCAATTTTTTTTCATTCTCAATTTCTT
1 TTTCAATTTCTTTTC-TTCGCATTTTCTT
19943 TTTCAATTTTCTTTTCTT--CATTTTCTT
1 TTTCAA-TTTCTTTTCTTCGCATTTTCTT
19970 TTTC
1 TTTC
19974 TCTCACTTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
27 52 0.67
29 18 0.23
30 8 0.10
ACGTcount: A:0.11, C:0.18, G:0.02, T:0.69
Consensus pattern (28 bp):
TTTCAATTTCTTTTCTTCGCATTTTCTT
Found at i:20036 original size:11 final size:11
Alignment explanation
Indices: 20011--20047 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
20001 TGCAATTTCT
20011 TTTTCTTTTTCG
1 TTTTCTTTTT-G
20023 TTTTCTTTTTG
1 TTTTCTTTTTG
20034 TTTTCTTTTT-
1 TTTTCTTTTTG
20044 TTTT
1 TTTT
20048 GAATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.16
11 11 0.44
12 10 0.40
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:21715 original size:20 final size:19
Alignment explanation
Indices: 21692--21756 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
21682 AAGCTCAAAC
21692 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
21712 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
21732 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
21752 GAGCT
1 GAGCT
21757 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:23623 original size:30 final size:30
Alignment explanation
Indices: 23589--23686 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
23579 AGCTCACTCC
23589 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
23619 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* *
23649 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCC-
1 TAGCTCATA-TTCAGCTCACGAGCTAAA-CCT
23679 TAGCTCAT
1 TAGCTCAT
23687 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 16, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
30 48 0.98
31 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:26424 original size:6 final size:6
Alignment explanation
Indices: 26413--26439 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
26403 ATATTTTATA
26413 TGTATG TGTATG TGTATG TGTATG TGT
1 TGTATG TGTATG TGTATG TGTATG TGT
26440 TTTTATTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (6 bp):
TGTATG
Found at i:28873 original size:22 final size:22
Alignment explanation
Indices: 28845--28888 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
28835 TTTTGAACCA
28845 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
28867 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
28889 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:29212 original size:12 final size:12
Alignment explanation
Indices: 29197--29233 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
29187 AAAGGAGTTC
29197 GAAAAAAAAATT
1 GAAAAAAAAATT
*
29209 GAAAAAAAATTT
1 GAAAAAAAAATT
*
29221 AAAAAAAAAATT
1 GAAAAAAAAATT
29233 G
1 G
29234 CATACGGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (12 bp):
GAAAAAAAAATT
Found at i:29215 original size:11 final size:11
Alignment explanation
Indices: 29199--29228 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29189 AGGAGTTCGA
29199 AAAAAAAATTG
1 AAAAAAAATTG
*
29210 AAAAAAAATTT
1 AAAAAAAATTG
29221 AAAAAAAA
1 AAAAAAAA
29229 AATTGCATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:30036 original size:15 final size:15
Alignment explanation
Indices: 30003--30036 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29993 GTTCAACGAA
* *
30003 GAGGCCAACGCAATT
1 GAGGCCAACGAAATC
30018 GAGGCCAACGAAATC
1 GAGGCCAACGAAATC
30033 GAGG
1 GAGG
30037 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.32, T:0.09
Consensus pattern (15 bp):
GAGGCCAACGAAATC
Found at i:33753 original size:22 final size:22
Alignment explanation
Indices: 33725--33768 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33715 TTTTGAACCA
33725 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
33747 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
33769 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:34145 original size:30 final size:30
Alignment explanation
Indices: 34111--34207 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
34101 AGCTCACTCC
34111 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
34141 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * *
34171 CAGGTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
34201 TAGCTCA
1 TAGCTCA
34208 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:36365 original size:42 final size:42
Alignment explanation
Indices: 36306--36411 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
36296 CATTTAAGCC
36306 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
36348 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
36390 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
36412 TATTTAATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 53 0.84
43 10 0.16
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:36413 original size:14 final size:14
Alignment explanation
Indices: 36394--36438 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
36384 AACTCATCTT
*
36394 AGTTTAATTAAATG
1 AGTTTAATTTAATG
36408 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
36421 AATTTAATTTAATG
1 AGTTTAATTTAATG
36435 AGTT
1 AGTT
36439 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:37464 original size:15 final size:15
Alignment explanation
Indices: 37418--37465 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
37408 AAACCTACAA
*
37418 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
37433 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
37447 AAACTTCATATCCAT
1 AAACTTCATATCCAT
37462 AAAC
1 AAAC
37466 CCACCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:39895 original size:21 final size:21
Alignment explanation
Indices: 39831--39904 Score: 50
Period size: 21 Copynumber: 3.6 Consensus size: 21
39821 AAAAAAATCA
39831 GAAAAAGAAAACAAAAGAG-AG
1 GAAAAAGAAAA-AAAAGAGAAG
**
39852 TG-AAAAG-AAAATCAGTA-AA-
1 -GAAAAAGAAAAAAAAG-AGAAG
39871 GAAAAAGAAAAAAAAGAGAAG
1 GAAAAAGAAAAAAAAGAGAAG
**
39892 GAAATTGAAAAAA
1 GAAAAAGAAAAAA
39905 TGAGTGTCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
18 1 0.03
19 9 0.22
20 13 0.32
21 16 0.40
22 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (21 bp):
GAAAAAGAAAAAAAAGAGAAG
Found at i:42942 original size:20 final size:20
Alignment explanation
Indices: 42919--42972 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
42909 AGTTTTTCCC
*
42919 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
42939 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
42959 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
42973 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:42954 original size:30 final size:30
Alignment explanation
Indices: 42919--42992 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
42909 AGTTTTTCCC
42919 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
42949 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
42979 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
42993 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:42982 original size:20 final size:20
Alignment explanation
Indices: 42919--42983 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
42909 AGTTTTTCCC
* * * *
42919 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
42939 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
42958 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
42979 AGCTC
1 AGCTC
42984 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:44652 original size:10 final size:10
Alignment explanation
Indices: 44637--44673 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
44627 AGAAGTGAGC
44637 AAAAAAGAAA
1 AAAAAAGAAA
*
44647 AAAAAAGTAA
1 AAAAAAGAAA
44657 AAAAAAGAACA
1 AAAAAAGAA-A
44668 AAAAAA
1 AAAAAA
44674 AAGTGAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:45693 original size:12 final size:12
Alignment explanation
Indices: 45681--45798 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
45671 GAAAGAGATT
*
45681 GAAAAAGAAATT
1 GAAAAAGAAATA
45693 G--AAAGAAA-A
1 GAAAAAGAAATA
*
45702 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
45713 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
45726 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
45738 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
45750 GAAAAAGTGAGA
1 GAAAAAGAAATA
45762 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
45773 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
45789 GAAAAAGAAA
1 GAAAAAGAAA
45799 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:45724 original size:18 final size:18
Alignment explanation
Indices: 45698--45801 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
45688 AAATTGAAAG
*
45698 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
45716 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
45734 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
45752 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
45770 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
45791 AAAAGAAAAAG
1 AAAAGAAAAAG
45802 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:45726 original size:6 final size:6
Alignment explanation
Indices: 45694--45801 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
45684 AAAGAAATTG
* * ** *
45694 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
45741 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
45792 AAAGAA AAAG
1 AAAGAA AAAG
45802 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:45783 original size:14 final size:13
Alignment explanation
Indices: 45762--45799 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
45752 AAAAGTGAGA
45762 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
45774 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
45789 GAAAAAGAAAA
1 GAAAAAGAAAA
45800 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:45813 original size:21 final size:21
Alignment explanation
Indices: 45763--45813 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
45753 AAAGTGAGAG
*
45763 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
45784 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
45805 AAAAAGAAA
1 AAAAAGAAA
45814 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:45853 original size:33 final size:33
Alignment explanation
Indices: 45816--45878 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
45806 AAAAGAAATT
45816 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
45849 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
45879 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:47680 original size:20 final size:20
Alignment explanation
Indices: 47657--47710 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
47647 AGTTTTTCCC
*
47657 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
47677 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
47697 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
47711 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:47701 original size:30 final size:30
Alignment explanation
Indices: 47657--47730 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
47647 AGTTTTTCCC
47657 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
47687 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
47717 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
47731 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:47720 original size:20 final size:20
Alignment explanation
Indices: 47657--47721 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
47647 AGTTTTTCCC
* * * *
47657 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
47677 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
47696 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
47717 AGCTC
1 AGCTC
47722 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:48402 original size:20 final size:20
Alignment explanation
Indices: 48356--48402 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
48346 AGCTCGTTTC
*
48356 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
48376 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
48396 CAGCTCA
1 CAGCTCA
48403 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:49932 original size:23 final size:24
Alignment explanation
Indices: 49906--49952 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
49896 AAAAATTGAT
*
49906 TGAAAAAAAATTCAA-AAAAAAAG
1 TGAAAAAAAAATCAACAAAAAAAG
49929 TGAAAAAAAAATCAAGCAAAAAAA
1 TGAAAAAAAAATCAA-CAAAAAAA
49953 AAGAAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
25 7 0.33
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.11
Consensus pattern (24 bp):
TGAAAAAAAAATCAACAAAAAAAG
Found at i:51018 original size:12 final size:12
Alignment explanation
Indices: 51006--51123 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
50996 GAAAGAGATT
*
51006 GAAAAAGAAATT
1 GAAAAAGAAATA
51018 G--AAAGAAA-A
1 GAAAAAGAAATA
*
51027 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
51038 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
51051 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
51063 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
51075 GAAAAAGTGAGA
1 GAAAAAGAAATA
51087 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
51098 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
51114 GAAAAAGAAA
1 GAAAAAGAAA
51124 GAAAAGAGAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:51049 original size:18 final size:18
Alignment explanation
Indices: 51023--51123 Score: 76
Period size: 18 Copynumber: 5.4 Consensus size: 18
51013 AAATTGAAAG
*
51023 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
51041 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
51059 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
51077 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
51095 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
51116 AAAAGAAA
1 AAAAGAAA
51124 GAAAAGAGAA
Statistics
Matches: 63, Mismatches: 17, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
18 47 0.75
19 2 0.03
20 8 0.13
21 6 0.10
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:51051 original size:6 final size:6
Alignment explanation
Indices: 51019--51123 Score: 68
Period size: 6 Copynumber: 17.2 Consensus size: 6
51009 AAAGAAATTG
* * ** *
51019 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
51066 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
51117 AAAGAA A
1 AAAGAA A
51124 GAAAAGAGAA
Statistics
Matches: 72, Mismatches: 24, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 58 0.81
7 7 0.10
8 4 0.06
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:52839 original size:20 final size:20
Alignment explanation
Indices: 52793--52839 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
52783 AGCTCGTTTC
*
52793 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
52813 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
52833 CAGCTCA
1 CAGCTCA
52840 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:54323 original size:14 final size:14
Alignment explanation
Indices: 54292--54324 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
54282 CAAAAGAGAC
*
54292 TGAAAAGAAAATGA
1 TGAAAAGAAAAAGA
54306 -GAAAAGAAAAAGA
1 TGAAAAGAAAAAGA
54319 TGAAAA
1 TGAAAA
54325 ACAAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (14 bp):
TGAAAAGAAAAAGA
Found at i:58568 original size:818 final size:818
Alignment explanation
Indices: 56993--58629 Score: 2941
Period size: 818 Copynumber: 2.0 Consensus size: 818
56983 CCTTCAAAAA
* *
56993 TGATACGATCACGGCTTCCCATAAGTCAAGTCCAAGTCAAGATCCGATGGTGCTACCTCAAGGGC
1 TGATACGATCACGGCTTCCCATAAGCCAAGTCCAAGCCAAGATCCGATGGTGCTACCTCAAGGGC
*
57058 CAATCACAAGGGCTCGTGCAAAACAATTTAAAGAAGCCGTTATAGCTTTAGTTCAGCATGTGTGG
66 CAATCACAAGGGCTCGTGCAAAACAATTTAAAGAAGCCGCTATAGCTTTAGTTCAGCATGTGTGG
*
57123 GATGATGTCAATGCTAGACCTATCGAACCAGTTAGTGGCCATTTTGGAAATCCATGCTGAACTTT
131 GATGATGTCAATGCTAGACCTATCGAACCAGTTAGTGGCCATTTTGGAAATCCATGCCGAACTTT
* *
57188 TCTACAAGTTCGGTTCAGCTCACCGAGCTCACCTTCAGTTCAAGTTAGCTCCCATGTAGCTCCAC
196 TCTACAAGTTCAGTTCAGCTCACCAAGCTCACCTTCAGTTCAAGTTAGCTCCCATGTAGCTCCAC
* * *
57253 ACCAGCTTATTAGCTCGGGACCAGCTCATTATCAGCTCACGAATTTAAGCCCAGCTCAAGTTTAG
261 ACCAGCTCATTAGCTCAGGACCAGCTCATTATCAGCTCACGAATTTAAGCCCAGCTCAAGTTTAA
*
57318 CTCATGAATTAACCATCAGCTCGTGGAGTTCACTTTGAATTCATTTGACTACTATTGAATTTTTA
326 CTCATGAATTAACCATCAGCTCATGGAGTTCACTTTGAATTCATTTGACTACTATTGAATTTTTA
57383 ATTAATAAGTTCAATAATTAGTTAATTAATATCCTACATATTAAATTTAGTTCACATTAGTTATA
391 ATTAATAAGTTCAATAATTAGTTAATTAATATCCTACATATTAAATTTAGTTCACATTAGTTATA
57448 TTAAGTATGTCTTAAAAGTGTTAATTGATGATAATTAAATTTGTCATAACCGAATTTAATGTTGA
456 TTAAGTATGTCTTAAAAGTGTTAATTGATGATAATTAAATTTGTCATAACCGAATTTAATGTTGA
* *
57513 TATTTCTGTTCACATTAGTTTAAATTAATTCTGTTCACATTTCTTGTAGAAACGCAATGGACATA
521 TATTTCTGTTCACATCAGTTTAAATTAATTATGTTCACATTTCTTGTAGAAACGCAATGGACATA
* * *
57578 TGGAGATTAAAAGCAAGCATGAATTTTGAAGGTGCATGGACGGTTGGGGGACTTGAATCTCTTGG
586 TAGAGATTAAAAGCAAGCATGAATTTTGAAGGTACATGGACGGTTGGGGGACTTGAATCTCTTAG
57643 GTGCATGTTCGGCCAAGTGCATGTATGACCATATTCAATGTCTTTAAGGTTCATGAATGTTTCCA
651 GTGCATGTTCGGCCAAGTGCATGTATGACCATATTCAATGTCTTTAAGGTTCATGAATGTTTCCA
*
57708 TTCATGTATGGTGTGCTATCTCTTCATTCTCCAAGGTGACCATTCGGCCAAAGGACACTCACACA
716 TTCATGTATGGTGTGCTATCTCTTCATTCTCCAAGGTGACCATTCAGCCAAAGGACACTCACACA
*
57773 TGCATGAAGATAGCTTGGCCAATTAGCTTCCCTATGAC
781 TGCATGAAGATAGCTTGGCCAATTAGCTTCCCCATGAC
*
57811 TGATACGATCACGGCTTCCCATAAGCCAAGTCCAAGCCGAGATCCGATGGTGCTACCTCAAGGGC
1 TGATACGATCACGGCTTCCCATAAGCCAAGTCCAAGCCAAGATCCGATGGTGCTACCTCAAGGGC
* * *
57876 CGATCACAAGGGCTCGTGCAAAATAATTTAAAGAAGCTGCTATAGCTTTAGTTCAGCATGTGTGG
66 CAATCACAAGGGCTCGTGCAAAACAATTTAAAGAAGCCGCTATAGCTTTAGTTCAGCATGTGTGG
* *
57941 GATGATGTCAATGCTAGACTTATTGAACCAGTTAGTGGCCATTTTGGAAATCCATGCCGAACTTT
131 GATGATGTCAATGCTAGACCTATCGAACCAGTTAGTGGCCATTTTGGAAATCCATGCCGAACTTT
*
58006 TCTACAAGTTCATTTCAGCTCACCAAGCTCACCTTCAGTTCAAGTTAGCTCCCATGTAGCTCCAC
196 TCTACAAGTTCAGTTCAGCTCACCAAGCTCACCTTCAGTTCAAGTTAGCTCCCATGTAGCTCCAC
* * * * **
58071 ACCAGCTCATTAGCTTAGGACCAGCTCATTATCAGCTCGCGAGTTTAGGCCCAGCTCGGGTTTAA
261 ACCAGCTCATTAGCTCAGGACCAGCTCATTATCAGCTCACGAATTTAAGCCCAGCTCAAGTTTAA
*
58136 CTCATGAATTAACCATCAGCTCATGGAGTTCACTTTGAATTCATTTGACTACTATTGACTTTTTA
326 CTCATGAATTAACCATCAGCTCATGGAGTTCACTTTGAATTCATTTGACTACTATTGAATTTTTA
58201 ATTAATAAGTTCAATAATTAGTTAATTAATATCCTACATATTAAATTTAGTTCACATTAGTTATA
391 ATTAATAAGTTCAATAATTAGTTAATTAATATCCTACATATTAAATTTAGTTCACATTAGTTATA
*
58266 TTAAGTATGTCTTAAAAGTGTTTATTGATGATAATTAAATTTGTCATAACCGAATTTAATGTTGA
456 TTAAGTATGTCTTAAAAGTGTTAATTGATGATAATTAAATTTGTCATAACCGAATTTAATGTTGA
* * *
58331 TATTTGTGTTCACATCAGTTTGAATTAATTATGTTCACATTTCTTGTAGGAACGCAATGGACATA
521 TATTTCTGTTCACATCAGTTTAAATTAATTATGTTCACATTTCTTGTAGAAACGCAATGGACATA
*
58396 TAGAGATTAAAAGCAAGCATGAATTTTGAAGGTACATGGACGGTTGGGGGGCTTGAATCTCTTAG
586 TAGAGATTAAAAGCAAGCATGAATTTTGAAGGTACATGGACGGTTGGGGGACTTGAATCTCTTAG
58461 GTGCATGTTCGGCCAAGTGCATGTATGACCATATTCAATGTCTTTAAGGTTCATGAATGTTTCCA
651 GTGCATGTTCGGCCAAGTGCATGTATGACCATATTCAATGTCTTTAAGGTTCATGAATGTTTCCA
*
58526 TTCATGTATGGTGTGCTATCTCTTCATTCTCCAAGGTGACCATTCAGCCAAAGGGCACTCACACA
716 TTCATGTATGGTGTGCTATCTCTTCATTCTCCAAGGTGACCATTCAGCCAAAGGACACTCACACA
58591 TGCATGAAGATAGCTTGGCCAATTAGCTTCCCCATGAC
781 TGCATGAAGATAGCTTGGCCAATTAGCTTCCCCATGAC
58629 T
1 T
58630 CTCCTTAATT
Statistics
Matches: 782, Mismatches: 37, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
818 782 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (818 bp):
TGATACGATCACGGCTTCCCATAAGCCAAGTCCAAGCCAAGATCCGATGGTGCTACCTCAAGGGC
CAATCACAAGGGCTCGTGCAAAACAATTTAAAGAAGCCGCTATAGCTTTAGTTCAGCATGTGTGG
GATGATGTCAATGCTAGACCTATCGAACCAGTTAGTGGCCATTTTGGAAATCCATGCCGAACTTT
TCTACAAGTTCAGTTCAGCTCACCAAGCTCACCTTCAGTTCAAGTTAGCTCCCATGTAGCTCCAC
ACCAGCTCATTAGCTCAGGACCAGCTCATTATCAGCTCACGAATTTAAGCCCAGCTCAAGTTTAA
CTCATGAATTAACCATCAGCTCATGGAGTTCACTTTGAATTCATTTGACTACTATTGAATTTTTA
ATTAATAAGTTCAATAATTAGTTAATTAATATCCTACATATTAAATTTAGTTCACATTAGTTATA
TTAAGTATGTCTTAAAAGTGTTAATTGATGATAATTAAATTTGTCATAACCGAATTTAATGTTGA
TATTTCTGTTCACATCAGTTTAAATTAATTATGTTCACATTTCTTGTAGAAACGCAATGGACATA
TAGAGATTAAAAGCAAGCATGAATTTTGAAGGTACATGGACGGTTGGGGGACTTGAATCTCTTAG
GTGCATGTTCGGCCAAGTGCATGTATGACCATATTCAATGTCTTTAAGGTTCATGAATGTTTCCA
TTCATGTATGGTGTGCTATCTCTTCATTCTCCAAGGTGACCATTCAGCCAAAGGACACTCACACA
TGCATGAAGATAGCTTGGCCAATTAGCTTCCCCATGAC
Found at i:59416 original size:14 final size:14
Alignment explanation
Indices: 59397--59441 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
59387 AACTCATCTT
*
59397 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
59411 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
59424 AATTTAATTTAATG
1 AGTTTAATTTAATG
59438 AGTT
1 AGTT
59442 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:60456 original size:29 final size:29
Alignment explanation
Indices: 60423--60482 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
60413 ATAACCAAAC
*
60423 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
60452 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
60481 CT
1 CT
60483 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:60475 original size:15 final size:15
Alignment explanation
Indices: 60429--60476 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
60419 AAACCTACAA
*
60429 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
60444 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
60458 AAACTTCATATCCAT
1 AAACTTCATATCCAT
60473 AAAC
1 AAAC
60477 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:61069 original size:24 final size:23
Alignment explanation
Indices: 61015--61092 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
61005 GGATAATTAA
**
61015 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
61038 GCTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
61062 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
61083 GAAATAGTAT
1 GAAATGGTAT
61093 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.04, G:0.31, T:0.38
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:61077 original size:21 final size:21
Alignment explanation
Indices: 61051--61112 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
61041 TTGGTATTTG
61051 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
61072 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
61093 GGTATTTGGTACGAATTGGT
1 GG-AATTGGTACGAAATGGT
61113 TATGATTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 21 0.62
22 13 0.38
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:62632 original size:14 final size:14
Alignment explanation
Indices: 62610--62657 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
62600 ACCTAAACCG
* *
62610 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
62624 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
62638 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
62652 ACCATT
1 ACCATT
62658 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:62999 original size:21 final size:21
Alignment explanation
Indices: 62973--63035 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
62963 TTGGTATTTG
62973 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
62994 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
63015 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
63036 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:67168 original size:20 final size:20
Alignment explanation
Indices: 67122--67168 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
67112 AGCTCGTTTC
*
67122 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
67142 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
67162 CAGCTCA
1 CAGCTCA
67169 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:71205 original size:30 final size:30
Alignment explanation
Indices: 71110--71206 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
71100 AGCTCACTCC
* * *
71110 TAGCTC-ACTTTCAACTCATGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
71140 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
71170 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
71200 TAGCTCA
1 TAGCTCA
71207 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:74643 original size:19 final size:19
Alignment explanation
Indices: 74619--74658 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
74609 AGCTCCCATG
74619 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
74638 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
74657 TA
1 TA
74659 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:78116 original size:23 final size:22
Alignment explanation
Indices: 78064--78116 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
78054 TCCACGTCTT
*
78064 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
78086 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
78109 TTTCTTTT
1 TTTCTTTT
78117 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:84276 original size:13 final size:13
Alignment explanation
Indices: 84260--84285 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
84250 AAAAAGAAGG
84260 AAAAAAAATTGCA
1 AAAAAAAATTGCA
84273 AAAAAAAATTGCA
1 AAAAAAAATTGCA
84286 TACGGTCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTGCA
Found at i:84332 original size:1 final size:1
Alignment explanation
Indices: 84326--84355 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
84316 AAATATCCGT
84326 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
84356 GAGTTTGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:86585 original size:24 final size:25
Alignment explanation
Indices: 86558--86611 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
86548 ATGAGTGATA
*
86558 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
86582 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
86606 AAAAAA
1 AAAAAA
86612 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:95278 original size:30 final size:30
Alignment explanation
Indices: 95176--95280 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 30
95166 ATCGGGTTTA
* *
95176 AGCT-AAAATGAGCTAAGCTTTAGCCCTTG
1 AGCTGAAAATGAGCTAAGGTTTAGCTCTTG
* * * * * *
95205 AGCT-AAAGTTGAGCTGAGGTTAAACTCCTA
1 AGCTGAAA-ATGAGCTAAGGTTTAGCTCTTG
**
95235 AGCTGAAGTTGAGCTAAGGTTTAGCTCTTG
1 AGCTGAAAATGAGCTAAGGTTTAGCTCTTG
*
95265 AGTTGAAAATGAGCTA
1 AGCTGAAAATGAGCTA
95281 GGAGTAAGCT
Statistics
Matches: 57, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
29 7 0.12
30 48 0.84
31 2 0.04
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (30 bp):
AGCTGAAAATGAGCTAAGGTTTAGCTCTTG
Found at i:96485 original size:11 final size:11
Alignment explanation
Indices: 96436--96487 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
96426 ATTAAATTGA
96436 ACTTATTAAAC
1 ACTTATTAAAC
*
96447 ACAT-TTAAAC
1 ACTTATTAAAC
96457 ACTTATTGAACATGC
1 ACTTATT-AA-A--C
96472 ACTTATTAAAC
1 ACTTATTAAAC
96483 ACTTA
1 ACTTA
96488 ACTTAGATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
10 9 0.26
11 11 0.32
12 2 0.06
13 2 0.06
14 2 0.06
15 8 0.24
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (11 bp):
ACTTATTAAAC
Found at i:108931 original size:11 final size:11
Alignment explanation
Indices: 108903--108949 Score: 58
Period size: 11 Copynumber: 4.0 Consensus size: 11
108893 AGACCGTATG
108903 CAATTTTTTTT
1 CAATTTTTTTT
108914 CAAAATTTTTTTT
1 C--AATTTTTTTT
108927 CAATTTTTTTT
1 CAATTTTTTTT
*
108938 TAGATTTTTTTT
1 CA-ATTTTTTTT
108950 TGATTTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 12 0.38
12 9 0.28
13 11 0.34
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:108934 original size:12 final size:12
Alignment explanation
Indices: 108906--108950 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
108896 CCGTATGCAA
*
108906 TTTTTTTTCAAAA
1 TTTTTTTTC-AAT
108919 TTTTTTTTCAAT
1 TTTTTTTTCAAT
108931 TTTTTTTT-AGAT
1 TTTTTTTTCA-AT
108943 TTTTTTTT
1 TTTTTTTT
108951 GATTTCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 1 0.03
12 20 0.67
13 9 0.30
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:108936 original size:80 final size:80
Alignment explanation
Indices: 108771--108938 Score: 275
Period size: 80 Copynumber: 2.1 Consensus size: 80
108761 TGTCTCCAGA
* *
108771 CTTTTTTTTTACGGATCTTTCACGTTCTTTTTGTCCGCACCTAGACCGTATGCAATTTTTTTTCG
1 CTTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCACCTAGACCGTATGCAATTTTTTTTCA
* * *
108836 ATTTTTTTTTGATTT
66 AATTTTTTTTCAATT
108851 CTTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCACCTAGACCGTATGCAATTTTTTTTCA
1 CTTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCACCTAGACCGTATGCAATTTTTTTTC-
108916 AAATTTTTTTTCAATT
65 AAATTTTTTTTCAATT
108932 -TTTTTTT
1 CTTTTTTT
108939 AGATTTTTTT
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 70 0.85
81 12 0.15
ACGTcount: A:0.15, C:0.19, G:0.11, T:0.55
Consensus pattern (80 bp):
CTTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCACCTAGACCGTATGCAATTTTTTTTCA
AATTTTTTTTCAATT
Found at i:108960 original size:12 final size:12
Alignment explanation
Indices: 108918--108962 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
108908 TTTTTTCAAA
*
108918 ATTTTTTTTCA-
1 ATTTTTTTTTAG
108929 ATTTTTTTTTAG
1 ATTTTTTTTTAG
108941 ATTTTTTTTT-G
1 ATTTTTTTTTAG
108952 ATTTCTTTTTT
1 ATTT-TTTTTT
108963 TTTTTACAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 15 0.48
12 16 0.52
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.78
Consensus pattern (12 bp):
ATTTTTTTTTAG
Found at i:108980 original size:107 final size:107
Alignment explanation
Indices: 108826--109045 Score: 354
Period size: 107 Copynumber: 2.1 Consensus size: 107
108816 CCGTATGCAA
* * *
108826 TTTTTTTTCGATTTTTTTTTGATTTCTTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCAC
1 TTTTTTTTAGATTTTTTTTTGATTTCTTTTTTTTTACAGATCTTTCACGTTCTTTTCGTCCACAC
108891 CTAGACCGTATGCAA-T-TTTTTTTCAAAATTTTTTTTCAAT
66 CTAGACCGTATGCAATTCTTTTTTTCAAAATTTTTTTTCAAT
108931 TTTTTTTTAGATTTTTTTTTGATTTCTTTTTTTTTTTACAGATCTTTCACGTTCTTTTCGTCCAC
1 TTTTTTTTAGATTTTTTTTTGATTTC--TTTTTTTTTACAGATCTTTCACGTTCTTTTCGTCCAC
* **
108996 ACCTAGACCGTATGCAATTCTTTTTTTCAAATTTTTTTTTTGAT
64 ACCTAGACCGTATGCAATTCTTTTTTTCAAAATTTTTTTTCAAT
109040 TTTTTT
1 TTTTTT
109046 ATTTCTTTTT
Statistics
Matches: 105, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
105 25 0.24
107 52 0.50
108 1 0.01
109 27 0.26
ACGTcount: A:0.16, C:0.16, G:0.09, T:0.60
Consensus pattern (107 bp):
TTTTTTTTAGATTTTTTTTTGATTTCTTTTTTTTTACAGATCTTTCACGTTCTTTTCGTCCACAC
CTAGACCGTATGCAATTCTTTTTTTCAAAATTTTTTTTCAAT
Found at i:113206 original size:16 final size:16
Alignment explanation
Indices: 113185--113216 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
113175 TAATGTGTTT
113185 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
113201 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
113217 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:113398 original size:45 final size:45
Alignment explanation
Indices: 113330--113683 Score: 591
Period size: 45 Copynumber: 7.9 Consensus size: 45
113320 AAGAGGTGGA
** * * *
113330 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
113375 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
*
113420 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
113465 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
*
113510 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
113555 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* *
113600 CAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* * * *
113645 CAACATCATGCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCA
113684 CCATGGCCGA
Statistics
Matches: 293, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 293 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
Found at i:123359 original size:14 final size:14
Alignment explanation
Indices: 123317--123361 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
123307 TTAAAGAAGC
123317 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
123331 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
123344 AACTCATTTAATTA
1 AACTCATTAAATTA
123358 AACT
1 AACT
123362 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:124896 original size:22 final size:22
Alignment explanation
Indices: 124845--124910 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
124835 GGTATTTGGG
* *
124845 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
124866 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
124888 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
124911 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:127380 original size:18 final size:18
Alignment explanation
Indices: 127359--127408 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
127349 AAACTCTTTT
127359 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
127377 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
127395 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
127409 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:127414 original size:24 final size:24
Alignment explanation
Indices: 127334--127411 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
127324 CTTGTTCACA
*
127334 TTCTTTCTCTCTCTCAAACTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
* * * *
127358 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTCTCTCTCTCAATCTCTTT
* *
127382 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
127406 TTCTTT
1 TTCTTT
127412 TTCTTTCATT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (24 bp):
TTCTTTCTCTCTCTCAATCTCTTT
Found at i:128416 original size:14 final size:14
Alignment explanation
Indices: 128374--128418 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
128364 TTAAAGAAGC
128374 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
128388 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
128401 AACTCATTTAATTA
1 AACTCATTAAATTA
128415 AACT
1 AACT
128419 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:133514 original size:22 final size:22
Alignment explanation
Indices: 133486--133529 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
133476 TTTTGAACCA
133486 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
133508 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
133530 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:134349 original size:23 final size:22
Alignment explanation
Indices: 134297--134349 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
134287 TCCACGTCTT
*
134297 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
134319 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
134342 TTTCTTTT
1 TTTCTTTT
134350 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:137961 original size:12 final size:12
Alignment explanation
Indices: 137944--137991 Score: 71
Period size: 13 Copynumber: 4.0 Consensus size: 12
137934 AGACCGTATG
137944 CAATTTTTTTTT
1 CAATTTTTTTTT
137956 CAATTTTTTTTTT
1 CAA-TTTTTTTTT
137969 CAA-TTTTTTTT
1 CAATTTTTTTTT
*
137980 CGATTTTTTTTT
1 CAATTTTTTTTT
137992 GAATCTACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
11 10 0.30
12 11 0.33
13 12 0.36
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:137964 original size:11 final size:11
Alignment explanation
Indices: 137948--137990 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
137938 CGTATGCAAT
137948 TTTTTTTTCAA
1 TTTTTTTTCAA
137959 TTTTTTTTTTCAA
1 --TTTTTTTTCAA
*
137972 TTTTTTTTCGA
1 TTTTTTTTCAA
137983 TTTTTTTT
1 TTTTTTTT
137991 TGAATCTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 18 0.62
13 11 0.38
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:143203 original size:42 final size:42
Alignment explanation
Indices: 143144--143249 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
143134 CATTTAAGCC
143144 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
143186 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
143228 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
143250 TATTTAATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 53 0.84
43 10 0.16
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:143251 original size:14 final size:14
Alignment explanation
Indices: 143232--143276 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
143222 AACTCATCTT
*
143232 AGTTTAATTAAATG
1 AGTTTAATTTAATG
143246 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
143259 AATTTAATTTAATG
1 AGTTTAATTTAATG
143273 AGTT
1 AGTT
143277 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:162169 original size:16 final size:15
Alignment explanation
Indices: 162143--162172 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
162133 TTTCAATCCA
162143 TCATCCCAATCAAAG
1 TCATCCCAATCAAAG
162158 TCATCACCAATCAAA
1 TCATC-CCAATCAAA
162173 AATTGATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
TCATCCCAATCAAAG
Found at i:166500 original size:14 final size:14
Alignment explanation
Indices: 166483--166522 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
166473 CGAACGGCAT
*
166483 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
166497 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
166511 GATATGAACAAA
1 GGTAGGAACAAA
166523 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:170292 original size:21 final size:22
Alignment explanation
Indices: 170266--170309 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
170256 AAACGAGCTC
170266 GTTGAGCTAAGTTGAG-TTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
* *
170287 GTTGAGCTGATTTGAGCTTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
170309 G
1 G
170310 GAGTATGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.25, C:0.07, G:0.34, T:0.34
Consensus pattern (22 bp):
GTTGAGCTAAGTTGAGCTTGAA
Found at i:174427 original size:14 final size:15
Alignment explanation
Indices: 174410--174445 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
174400 AAAAAAAAAT
174410 AAAAAAAAA-TTGAA
1 AAAAAAAAATTTGAA
174424 AAAAAAAAATTTGAA
1 AAAAAAAAATTTGAA
174439 AAAAAAA
1 AAAAAAA
174446 TTGCATACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (15 bp):
AAAAAAAAATTTGAA
Found at i:174446 original size:13 final size:12
Alignment explanation
Indices: 174390--174448 Score: 68
Period size: 12 Copynumber: 4.8 Consensus size: 12
174380 TTGTAGATTC
*
174390 AAAAAAATCGAA
1 AAAAAAATTGAA
174402 AAAAAAA-T-AA
1 AAAAAAATTGAA
174412 AAAAAAATTGAAAA
1 AAAAAAATTG--AA
174426 AAAAAAATTTGAA
1 AAAAAAA-TTGAA
174439 AAAAAAATTG
1 AAAAAAATTG
174449 CATACGGTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.22
11 1 0.02
12 10 0.24
13 9 0.22
14 9 0.22
15 3 0.07
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:180457 original size:23 final size:22
Alignment explanation
Indices: 180405--180457 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
180395 TTCACGTCTT
*
180405 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
180427 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
180450 TTTCTTTT
1 TTTCTTTT
180458 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:191886 original size:21 final size:22
Alignment explanation
Indices: 191860--191902 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
191850 AACGAGCTCA
191860 TTGAGCTAAGTTGAG-TTGAAG
1 TTGAGCTAAGTTGAGCTTGAAG
* *
191881 TTGAGCTGATTTGAGCTTGAAG
1 TTGAGCTAAGTTGAGCTTGAAG
191903 GAGTATGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.35
Consensus pattern (22 bp):
TTGAGCTAAGTTGAGCTTGAAG
Found at i:193143 original size:12 final size:12
Alignment explanation
Indices: 193126--193176 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
193116 TATACAAGTT
193126 AAAAAAATTCGA
1 AAAAAAATTCGA
193138 AAAAAAATTCGA
1 AAAAAAATTCGA
193150 AAAAAAA-T--A
1 AAAAAAATTCGA
*
193159 AAAAAAATTTGA
1 AAAAAAATTCGA
193171 AAAAAA
1 AAAAAA
193177 GTGATTTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.22
10 1 0.03
11 1 0.03
12 26 0.72
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.16
Consensus pattern (12 bp):
AAAAAAATTCGA
Found at i:193161 original size:21 final size:21
Alignment explanation
Indices: 193137--193176 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
193127 AAAAAATTCG
193137 AAAAAAAATTCGAAAAAAAAT
1 AAAAAAAATTCGAAAAAAAAT
*
193158 AAAAAAAATTTGAAAAAAA
1 AAAAAAAATTCGAAAAAAA
193177 GTGATTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (21 bp):
AAAAAAAATTCGAAAAAAAAT
Found at i:196653 original size:245 final size:244
Alignment explanation
Indices: 196202--196690 Score: 897
Period size: 245 Copynumber: 2.0 Consensus size: 244
196192 AAAGTGTTCC
196202 TGATAAAGAGGCGCACGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGATC
1 TGATAAAGAGGCGCACGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGATC
* * *
196267 CTAGACGAACAGATCTGAAATCAAAAACAAAGATTAAGATTAAACCGAATCAGATTTGAATTTAA
66 CTAGACAAACAGATCTGAAAACAAAAACAAAGATTAAGATTAAACCAAATCAGATTTGAATTTAA
196332 AATTCCCAAATTCAATTAAAAGAGCAGCAAGAAGAAAAGAAATAGAATCGATGAATCAAACGAAA
131 AATTCCCAAATTCAATTAAAAGAGCAGCAAGAAGAAAAGAAATAGAATCGATGAATCAAACGAAA
196397 TTGAGAAGAAAGAAAAGATGCGAATCTGCCAAGGAATTGATTCGGCCAA
196 TTGAGAAGAAAGAAAAGATGCGAATCTGCCAAGGAATTGATTCGGCCAA
* * *
196446 TGATATAGAGGCGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGGTC
1 TGATAAAGAGGCGCACGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGATC
* *
196511 CTAGACAAATAGATCTGAAAACAGAAACAAAGATTAAGATTAAACCCAAATCAGATTTGAATTTA
66 CTAGACAAACAGATCTGAAAACAAAAACAAAGATTAAGATTAAA-CCAAATCAGATTTGAATTTA
196576 AAATTCCCAAATTCAATTAAAAGAGCAGCAAGAAGAAAAGAAATAGAATCGATGAATCAAACGAA
130 AAATTCCCAAATTCAATTAAAAGAGCAGCAAGAAGAAAAGAAATAGAATCGATGAATCAAACGAA
196641 ATTGAGAAGAAAGAAAAGATGCGAATCTGCCAAGGAATTGATTCGGCCAA
195 ATTGAGAAGAAAGAAAAGATGCGAATCTGCCAAGGAATTGATTCGGCCAA
196691 GAATGCCCAA
Statistics
Matches: 236, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
244 102 0.43
245 134 0.57
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (244 bp):
TGATAAAGAGGCGCACGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGATC
CTAGACAAACAGATCTGAAAACAAAAACAAAGATTAAGATTAAACCAAATCAGATTTGAATTTAA
AATTCCCAAATTCAATTAAAAGAGCAGCAAGAAGAAAAGAAATAGAATCGATGAATCAAACGAAA
TTGAGAAGAAAGAAAAGATGCGAATCTGCCAAGGAATTGATTCGGCCAA
Found at i:211181 original size:30 final size:30
Alignment explanation
Indices: 211147--211243 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
211137 AGCTCACTCC
*
211147 TAGCTCACTTTCAACTCACGAGCTAAACCT
1 TAGCTCACTTTCAGCTCACGAGCTAAACCT
* * * * * *
211177 TAGCTTAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGC-TCACTTTCAGCTCACGAGCTAAACCT
* *
211207 TAGCTCAACTTT-AGCTCACGAACTAAAGCT
1 TAGCTC-ACTTTCAGCTCACGAGCTAAACCT
211237 TAGCTCA
1 TAGCTCA
211244 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
29 2 0.04
30 42 0.86
31 5 0.10
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (30 bp):
TAGCTCACTTTCAGCTCACGAGCTAAACCT
Found at i:213835 original size:16 final size:15
Alignment explanation
Indices: 213814--213881 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 15
213804 ACATTCTTGT
213814 AAAGAAAAAACAAAGA
1 AAAGAAAAAA-AAAGA
213830 AAAGAAAAGAAAAAGA
1 AAAGAAAA-AAAAAGA
*
213846 AAA-AGAAGAAAAAGA
1 AAAGA-AAAAAAAAGA
*
213861 AAACGAAATAAAAAGA
1 AAA-GAAAAAAAAAGA
213877 AAAGA
1 AAAGA
213882 GAGGCAAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
15 13 0.28
16 30 0.65
17 3 0.07
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.01
Consensus pattern (15 bp):
AAAGAAAAAAAAAGA
Found at i:213840 original size:21 final size:21
Alignment explanation
Indices: 213815--213879 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
213805 CATTCTTGTA
213815 AAGAAAAA-ACAAAGAAAAG-AA
1 AAGAAAAAGA-AAA-AAAAGAAA
*
213836 AAGAAAAAGAAAAAGAAGAAA
1 AAGAAAAAGAAAAAAAAGAAA
*
213857 AAGAAAACGAAATAAAAAGAAA
1 AAGAAAAAGAAA-AAAAAGAAA
213879 A
1 A
213880 GAGAGGCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
20 4 0.11
21 24 0.63
22 10 0.26
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (21 bp):
AAGAAAAAGAAAAAAAAGAAA
Found at i:213879 original size:6 final size:6
Alignment explanation
Indices: 213814--213868 Score: 50
Period size: 6 Copynumber: 10.2 Consensus size: 6
213804 ACATTCTTGT
*
213814 AAAGAA AAA-AC AAAG-A AAAG-A AAAGAA AAAGAA AAAG-- -AAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
*
213856 AAAGAA AACGAA A
1 AAAGAA AAAGAA A
213869 TAAAAAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
3 3 0.07
5 13 0.32
6 25 0.61
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:213971 original size:18 final size:18
Alignment explanation
Indices: 213944--213999 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
213934 AAAGCCTTTG
*
213944 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* * *
213963 AAATGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
213981 AAAAGAGAATGAAAA-GA
1 AAAAGAAAATGAAAATGA
213998 AA
1 AA
214000 TTTGAGAGAG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 4 0.14
18 21 0.72
19 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.20, T:0.11
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:213984 original size:30 final size:30
Alignment explanation
Indices: 213950--214031 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
213940 TTTGAAAAGC
**
213950 AAAAAGAAAATGAAAATGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAA-GAAATATGAGAGAG
* *
213980 AAAAAGAGAATGAAAAGAAATTTGAGAGAG
1 AAAAAGAAAATGAAAAGAAATATGAGAGAG
**
214010 AAAAAGAAGTTGAAAAAGAAAT
1 AAAAAGAAAATG-AAAAGAAAT
214032 TGAAAAAGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 4 0.09
30 30 0.70
31 9 0.21
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (30 bp):
AAAAAGAAAATGAAAAGAAATATGAGAGAG
Found at i:214026 original size:12 final size:12
Alignment explanation
Indices: 214009--214053 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
213999 ATTTGAGAGA
*
214009 GAAAAAGAAGTT
1 GAAAAAGAAATT
214021 GAAAAAGAAATT
1 GAAAAAGAAATT
*
214033 GAAAAAGAGATT
1 GAAAAAGAAATT
*
214045 -AAAGAGAAA
1 GAAAAAGAAA
214054 GAAATTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 7 0.24
12 22 0.76
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.13
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:216207 original size:30 final size:30
Alignment explanation
Indices: 216173--216269 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
216163 AGCTCACTCC
*
216173 TAGCTCACTTTCAACTCACGAGCTAAACCT
1 TAGCTCACTTTCAGCTCACGAGCTAAACCT
* * * * *
216203 TAGCTTAAC-TTCAGCTTC-GGAGTTTAGCCT
1 TAGC-TCACTTTCAGC-TCACGAGCTAAACCT
*
216233 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTC-ACTTTCAGCTCACGAGCTAAACCT
216263 TAGCTCA
1 TAGCTCA
216270 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 12, Indels: 11
0.68 0.16 0.15
Matches are distributed among these distances:
29 4 0.08
30 39 0.78
31 7 0.14
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCACTTTCAGCTCACGAGCTAAACCT
Found at i:216839 original size:14 final size:14
Alignment explanation
Indices: 216822--216861 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
216812 CGAATGGAAT
*
216822 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
*
216836 GGTAGGAACAAAAT
1 GGTAGGAACAAAAG
*
216850 GGTATGAACAAA
1 GGTAGGAACAAA
216862 TTGGACGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.07, G:0.33, T:0.12
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:226697 original size:17 final size:17
Alignment explanation
Indices: 226672--226726 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
226662 TCTCTTTTCA
*
226672 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
226689 TTCTTTTTTTTATCATTT
1 TTCTTTTTTTT-TGAATT
* *
226707 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
226724 TTC
1 TTC
226727 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:232771 original size:20 final size:20
Alignment explanation
Indices: 232748--232801 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
232738 AGTTTTTCCC
*
232748 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
232768 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
232788 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
232802 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:232783 original size:30 final size:30
Alignment explanation
Indices: 232748--232821 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
232738 AGTTTTTCCC
232748 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
232778 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
232808 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
232822 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:232811 original size:20 final size:20
Alignment explanation
Indices: 232748--232812 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
232738 AGTTTTTCCC
* * * *
232748 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
232768 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
232787 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
232808 AGCTC
1 AGCTC
232813 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:235059 original size:16 final size:14
Alignment explanation
Indices: 235025--235074 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
235015 CAAAAAAATC
235025 AAAAAAAAATTTGA
1 AAAAAAAAATTTGA
235039 AAAAAAAAATTTGA
1 AAAAAAAAATTTGA
* *
235053 TTGAAAAAAAA-TTCA
1 --AAAAAAAAATTTGA
235068 AAAAAAA
1 AAAAAAA
235075 GTGAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 6 0.19
14 14 0.45
15 3 0.10
16 8 0.26
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (14 bp):
AAAAAAAAATTTGA
Found at i:236052 original size:17 final size:18
Alignment explanation
Indices: 236020--236053 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
236010 AGAAAAGAAA
236020 ATTGAAAAAGAAATTGAG
1 ATTGAAAAAGAAATTGAG
*
236038 ATTGAGAAA-AAATTGA
1 ATTGAAAAAGAAATTGA
236054 AAAAGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (18 bp):
ATTGAAAAAGAAATTGAG
Found at i:240550 original size:10 final size:11
Alignment explanation
Indices: 240528--240553 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
240518 AAAAGAGAAG
240528 AAATTCAAAAA
1 AAATTCAAAAA
240539 AAATTCAAAAA
1 AAATTCAAAAA
240550 AAAT
1 AAAT
240554 AGAAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:241634 original size:6 final size:6
Alignment explanation
Indices: 241622--241729 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
241612 AAAGAAATTG
* * ** *
241622 AAAGAA AACG-A AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
241669 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
241720 AAAGAA AAAG
1 AAAGAA AAAG
241730 CGAAAAAAGA
Statistics
Matches: 74, Mismatches: 22, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
5 5 0.07
6 57 0.77
7 8 0.11
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:241638 original size:11 final size:11
Alignment explanation
Indices: 241622--241657 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
241612 AAAGAAATTG
241622 AAAGAAAACGA
1 AAAGAAAACGA
241633 AAAGAAAACGAA
1 AAAGAAAACG-A
*
241645 AAAGAAAAAGA
1 AAAGAAAACGA
241656 AA
1 AA
241658 TTGCAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.78, C:0.06, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAGAAAACGA
Found at i:241709 original size:14 final size:13
Alignment explanation
Indices: 241690--241727 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
241680 AAAAGTGAGA
241690 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
241702 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
241717 GAAAAAGAAAA
1 GAAAAAGAAAA
241728 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:241724 original size:13 final size:12
Alignment explanation
Indices: 241608--241727 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
241598 AGAAAGAGAT
*
241608 TGAAAAAGAAAT
1 TGAAAAAGAAAA
241620 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
241630 CG-AAAAGAAAA
1 TGAAAAAGAAAA
*
241641 CGAAAAAGAAAA
1 TGAAAAAGAAAA
* **
241653 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
241666 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* * *
241676 TCAAAAAAGTGAGA
1 T-GAAAAAG-AAAA
241690 -GAAAAAGAAAA
1 TGAAAAAGAAAA
241701 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
241715 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
241728 AGCGAAAAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
10 11 0.13
11 12 0.14
12 34 0.40
13 14 0.16
14 12 0.14
15 2 0.02
ACGTcount: A:0.70, C:0.03, G:0.18, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:241741 original size:21 final size:21
Alignment explanation
Indices: 241691--241741 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
241681 AAAGTGAGAG
*
241691 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
241712 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
241733 AAAAAGAAA
1 AAAAAGAAA
241742 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:246274 original size:13 final size:13
Alignment explanation
Indices: 246256--246280 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
246246 GTATTGATCA
246256 TGTGTTCACACCT
1 TGTGTTCACACCT
246269 TGTGTTCACACC
1 TGTGTTCACACC
246281 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:247344 original size:11 final size:12
Alignment explanation
Indices: 247328--247361 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
247318 ATTGGAGTAA
247328 CAAAAAAAAA-T
1 CAAAAAAAAATT
247339 CAAAAAAAAATT
1 CAAAAAAAAATT
247351 CGAAAAAAAAA
1 C-AAAAAAAAA
247362 ATTTGATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 2 0.10
13 9 0.43
ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (12 bp):
CAAAAAAAAATT
Found at i:247346 original size:12 final size:13
Alignment explanation
Indices: 247329--247363 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
247319 TTGGAGTAAC
247329 AAAAAAAAATC-A
1 AAAAAAAAATCGA
*
247341 AAAAAAAATTCGA
1 AAAAAAAAATCGA
247354 AAAAAAAAAT
1 AAAAAAAAAT
247364 TTGATTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAAAAAAATCGA
Found at i:247357 original size:14 final size:13
Alignment explanation
Indices: 247329--247392 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 13
247319 TTGGAGTAAC
247329 AAAAAAAAA-TC-
1 AAAAAAAAATTCA
247340 AAAAAAAAATTCGA
1 AAAAAAAAATTC-A
*
247354 AAAAAAAAATTTGA
1 AAAAAAAAA-TTCA
247368 TTGAAAAAAAAATTCA
1 ---AAAAAAAAATTCA
247384 AAAAAAAAA
1 AAAAAAAAA
247393 AGAGGTGACC
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
11 9 0.20
12 2 0.05
13 9 0.20
14 10 0.23
15 2 0.05
16 3 0.07
17 9 0.20
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:247393 original size:14 final size:14
Alignment explanation
Indices: 247329--247393 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 14
247319 TTGGAGTAAC
247329 AAAAAAAAA-TC--
1 AAAAAAAAATTCAA
247340 AAAAAAAAATTCGAA
1 AAAAAAAAATTC-AA
* * *
247355 AAAAAAAATTTGATTG
1 AAAAAAAAATTCA--A
247371 AAAAAAAAATTCAA
1 AAAAAAAAATTCAA
247385 AAAAAAAAA
1 AAAAAAAAA
247394 GAGGTGACCA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
11 9 0.21
12 2 0.05
14 10 0.24
15 10 0.24
16 11 0.26
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAAAAAAATTCAA
Found at i:248325 original size:18 final size:18
Alignment explanation
Indices: 248304--248338 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
248294 AGAAAAGAAA
248304 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
248322 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
248339 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:250568 original size:13 final size:13
Alignment explanation
Indices: 250550--250574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
250540 GTATTGATCA
250550 TGTGTTCACACCT
1 TGTGTTCACACCT
250563 TGTGTTCACACC
1 TGTGTTCACACC
250575 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:252975 original size:21 final size:21
Alignment explanation
Indices: 252926--252992 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
252916 CCTCTTTGAA
* * *
252926 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
252949 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
252970 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
252991 CC
1 CC
252993 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Done.