Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 21 of 320
Found at i:5969608 original size:43 final size:43
Alignment explanation
Indices: 5969555--5969652 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
5969545 TTCATATTCT
*
5969555 AGAAATATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAG
1 AGAACTATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAG
* * *
5969598 GGAACTATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAG
1 AGAACTATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAG
5969641 AGAACTATTTTC
1 AGAACTATTTTC
5969653 CCAATTAGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
43 48 0.98
44 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (43 bp):
AGAACTATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAG
Found at i:5974486 original size:17 final size:15
Alignment explanation
Indices: 5974456--5974489 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
5974446 AATCGAGCAA
5974456 AAAGAAAAGAAGAAG
1 AAAGAAAAGAAGAAG
5974471 AAAGAAAACGGAAGAAG
1 AAAGAAAA--GAAGAAG
5974488 AA
1 AA
5974490 GCAATGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAGAAG
Found at i:5977953 original size:29 final size:28
Alignment explanation
Indices: 5977918--5977973 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
5977908 AGTTATACCA
5977918 ATTTGGCTTCGGGCCATGCATATCAGTTG
1 ATTTGGCTTCGGGCCATG-ATATCAGTTG
*
5977947 ATTTGGCTTTGGGCCATGATATCAGTT
1 ATTTGGCTTCGGGCCATGATATCAGTT
5977974 CTTCGGAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (28 bp):
ATTTGGCTTCGGGCCATGATATCAGTTG
Found at i:5989846 original size:40 final size:36
Alignment explanation
Indices: 5989743--5989877 Score: 123
Period size: 35 Copynumber: 3.7 Consensus size: 36
5989733 TTTTCCTCAT
* *
5989743 TGAAATACCATACCTACATTTTACAACTCGGTATG-
1 TGAAATACCATACCTACATTTCACAACTCAGTATGA
* * ***
5989778 GGAAATGCCATACCTACATTTTTTAACTCAGTATGAA
1 TGAAATACCATACCTACATTTCACAACTCAGTATG-A
*
5989815 TTTGATAATACCATACCTACATTTCACAACTCAGTGTGGA
1 --TGA-AATACCATACCTACATTTCACAACTCAGTAT-GA
*
5989855 TG--ATAACATACCTACATTTCACA
1 TGAAATACCATACCTACATTTCACA
5989878 CTTTTCCATG
Statistics
Matches: 82, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
35 50 0.61
38 2 0.02
39 2 0.02
40 27 0.33
41 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (36 bp):
TGAAATACCATACCTACATTTCACAACTCAGTATGA
Found at i:6003616 original size:21 final size:22
Alignment explanation
Indices: 6003579--6003625 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
6003569 TAATTTTCAG
* *
6003579 TTTT-TTTCATGTTCAAGTTTT
1 TTTTATTTCATGTACAAGATTT
6003600 TTTTATTTCAT-TACAAGATTT
1 TTTTATTTCATGTACAAGATTT
*
6003621 CTTTA
1 TTTTA
6003626 CTCCCCATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.21, C:0.11, G:0.06, T:0.62
Consensus pattern (22 bp):
TTTTATTTCATGTACAAGATTT
Found at i:6004236 original size:34 final size:34
Alignment explanation
Indices: 6004193--6004259 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
6004183 GCATGCTTAG
6004193 CATGAGGATGATCAAAAAGCACCGAGAAACCTAT
1 CATGAGGATGATCAAAAAGCACCGAGAAACCTAT
* *
6004227 CATGAGGATGATCGAAAAGCGCCGAGAAACCTA
1 CATGAGGATGATCAAAAAGCACCGAGAAACCTA
6004260 CCCTACTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (34 bp):
CATGAGGATGATCAAAAAGCACCGAGAAACCTAT
Found at i:6006461 original size:19 final size:19
Alignment explanation
Indices: 6006433--6006471 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
6006423 AAAGCGAAAG
6006433 AAACGAGAAAA-GGGCCAA
1 AAACGAGAAAATGGGCCAA
6006451 AAACGGAGAAAATGGGCCAA
1 AAAC-GAGAAAATGGGCCAA
6006471 A
1 A
6006472 GTACGAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 7 0.37
20 8 0.42
ACGTcount: A:0.54, C:0.15, G:0.28, T:0.03
Consensus pattern (19 bp):
AAACGAGAAAATGGGCCAA
Found at i:6012784 original size:16 final size:16
Alignment explanation
Indices: 6012765--6012800 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6012755 TTTCTTTCTT
* *
6012765 TTTTCTTCTTCTTTGA
1 TTTTCTTCTCCTTCGA
6012781 TTTTCTTCTCCTTCGA
1 TTTTCTTCTCCTTCGA
6012797 TTTT
1 TTTT
6012801 TCGTTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.22, G:0.06, T:0.67
Consensus pattern (16 bp):
TTTTCTTCTCCTTCGA
Found at i:6013942 original size:38 final size:39
Alignment explanation
Indices: 6013851--6013944 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 39
6013841 CGGTACCTTT
* * * * *
6013851 TGGTGTGCAGGGTTAGATGGGTTGATTATATCCCCATACT
1 TGGTGTGTAGGGTTGGGTGGGTCGATTATATCCCCA-ACA
*
6013891 TGGTGTGTAGGGTTGGGTGGGTCGATTCTATCCCC-ACA
1 TGGTGTGTAGGGTTGGGTGGGTCGATTATATCCCCAACA
*
6013929 TGGTGTGTTGGGTTGG
1 TGGTGTGTAGGGTTGG
6013945 TCAAAGATGG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 17 0.36
40 30 0.64
ACGTcount: A:0.14, C:0.14, G:0.37, T:0.35
Consensus pattern (39 bp):
TGGTGTGTAGGGTTGGGTGGGTCGATTATATCCCCAACA
Found at i:6015515 original size:52 final size:52
Alignment explanation
Indices: 6015437--6015537 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
6015427 ATCAAATTTG
6015437 GAATTGGATCGGGGAAAAGATAAAAGTATTCAACTAATCGACTTGATTCTTT
1 GAATTGGATCGGGGAAAAGATAAAAGTATTCAACTAATCGACTTGATTCTTT
*
6015489 GAATTGGATCGGGGAAAAGATAAAAGTATTCGACTAATCGACTTGATTC
1 GAATTGGATCGGGGAAAAGATAAAAGTATTCAACTAATCGACTTGATTC
6015538 ATTGTTTCCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.29
Consensus pattern (52 bp):
GAATTGGATCGGGGAAAAGATAAAAGTATTCAACTAATCGACTTGATTCTTT
Found at i:6018128 original size:49 final size:48
Alignment explanation
Indices: 6018073--6018189 Score: 135
Period size: 49 Copynumber: 2.4 Consensus size: 48
6018063 TGGATGACCC
* * * *
6018073 AACAATGATGACTTTTACTGTTTGCATATTCTACCATCCCGAGTGGCCT
1 AACAATGATG-CTTTGAATATTTGCATATTCTACCATCCCGAGCGGCCT
* **
6018122 AACAATGATCGCTTTGAATATTTGCATATTCTATCATCTTGAGCGGCCT
1 AACAATGAT-GCTTTGAATATTTGCATATTCTACCATCCCGAGCGGCCT
*
6018171 AACAATGATGGTTTTGAAT
1 AACAATGAT-GCTTTGAAT
6018190 TATTATATCG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 57 0.98
50 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (48 bp):
AACAATGATGCTTTGAATATTTGCATATTCTACCATCCCGAGCGGCCT
Found at i:6023970 original size:18 final size:18
Alignment explanation
Indices: 6023947--6023981 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6023937 TTTATTGCTT
6023947 TTCAAAAGCACTTCTGGC
1 TTCAAAAGCACTTCTGGC
6023965 TTCAAAAGCACTTCTGG
1 TTCAAAAGCACTTCTGG
6023982 AAGAAAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (18 bp):
TTCAAAAGCACTTCTGGC
Found at i:6024281 original size:20 final size:21
Alignment explanation
Indices: 6024235--6024287 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
6024225 TACTAATTAC
6024235 AAATATTTAATAATTATATTT
1 AAATATTTAATAATTATATTT
6024256 AAATATTTAA-AA-TATAGTTT
1 AAATATTTAATAATTATA-TTT
*
6024276 ATATATTCTAAT
1 AAATATT-TAAT
6024288 TAAATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.14
20 11 0.39
21 13 0.46
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATATTTAATAATTATATTT
Found at i:6024548 original size:13 final size:13
Alignment explanation
Indices: 6024532--6024571 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
6024522 TTTAAACCAA
*
6024532 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
*
6024545 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
6024558 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
6024571 A
1 A
6024572 ATGAAGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:6025153 original size:21 final size:22
Alignment explanation
Indices: 6025115--6025155 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
6025105 CTCAATTAAA
6025115 ATTTATATGAAATCTAATTTAT
1 ATTTATATGAAATCTAATTTAT
* *
6025137 ATTTAT-TTAAATTTAATTT
1 ATTTATATGAAATCTAATTT
6025156 TCTATGTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTATATGAAATCTAATTTAT
Found at i:6031935 original size:13 final size:13
Alignment explanation
Indices: 6031917--6031946 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6031907 AATACTTTCA
*
6031917 AAAAAAATTTAAT
1 AAAAAAATTAAAT
6031930 AAAAAAATTAAAT
1 AAAAAAATTAAAT
6031943 AAAA
1 AAAA
6031947 TATTGTCAAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAAATTAAAT
Found at i:6036584 original size:19 final size:20
Alignment explanation
Indices: 6036556--6036605 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
6036546 ATACATAGGT
*
6036556 TTAA-CTTTAATAAAT-TTA
1 TTAATCTTTAATAAATCTAA
*
6036574 TTAATCTTTAATTAATCTAA
1 TTAATCTTTAATAAATCTAA
*
6036594 TCAATCTTTAAT
1 TTAATCTTTAAT
6036606 TCACTTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 4 0.15
19 10 0.37
20 13 0.48
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATCTTTAATAAATCTAA
Found at i:6039637 original size:22 final size:22
Alignment explanation
Indices: 6039612--6039656 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
6039602 ATAATATCTA
*
6039612 TTAATTCATAATTTAA-TTAATT
1 TTAATT-ATAATCTAATTTAATT
*
6039634 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATCTAATTTAATT
6039656 T
1 T
6039657 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTATAATCTAATTTAATT
Found at i:6039642 original size:16 final size:16
Alignment explanation
Indices: 6039623--6039656 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
6039613 TAATTCATAA
6039623 TTTAAT-TAATTTTAAT
1 TTTAATCTAA-TTTAAT
6039639 TTTAATCTAATTTAAT
1 TTTAATCTAATTTAAT
6039655 TT
1 TT
6039657 GGGTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAATCTAATTTAAT
Found at i:6040074 original size:10 final size:10
Alignment explanation
Indices: 6040059--6040083 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6040049 CACTTTTCTC
6040059 TCTTCATTGT
1 TCTTCATTGT
6040069 TCTTCATTGT
1 TCTTCATTGT
6040079 TCTTC
1 TCTTC
6040084 CCTATTCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (10 bp):
TCTTCATTGT
Found at i:6041940 original size:2 final size:2
Alignment explanation
Indices: 6041933--6041958 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6041923 GGTATAAAAC
6041933 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6041959 TTAAAAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6050130 original size:23 final size:22
Alignment explanation
Indices: 6050087--6050144 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
6050077 AAAAGGTATC
* *
6050087 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
6050108 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
6050131 TGCATATCATATCT
1 TACAAATCATATCT
6050145 AAGATTGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:6050159 original size:18 final size:19
Alignment explanation
Indices: 6050123--6050177 Score: 85
Period size: 18 Copynumber: 2.9 Consensus size: 19
6050113 AATCATATCT
6050123 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
6050142 TCTAAGATTGTA-ATCATA
1 TCTAAGATTGCATATCATA
*
6050160 TTTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
6050178 TGAAGATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:6057883 original size:10 final size:10
Alignment explanation
Indices: 6057870--6057917 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
6057860 TTATTTTCAT
6057870 TTATCTTTAA
1 TTATCTTTAA
*
6057880 TTATCTTAAA
1 TTATCTTTAA
*
6057890 TTATCTTTAT
1 TTATCTTTAA
* * *
6057900 TTATATGTAT
1 TTATCTTTAA
6057910 TTATCTTT
1 TTATCTTT
6057918 TAGAATTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:6057913 original size:20 final size:20
Alignment explanation
Indices: 6057868--6057917 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
6057858 ATTTATTTTC
*
6057868 ATTTATCTTTAATTATCTTA
1 ATTTATCTTTAATTATATTA
* *
6057888 AATTATCTTTATTTATATGT-
1 ATTTATCTTTAATTATAT-TA
6057908 ATTTATCTTT
1 ATTTATCTTT
6057918 TAGAATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTATCTTTAATTATATTA
Found at i:6058682 original size:43 final size:39
Alignment explanation
Indices: 6058615--6058704 Score: 94
Period size: 43 Copynumber: 2.2 Consensus size: 39
6058605 CTCAACTTTT
*
6058615 TTTTATTTCTATTGTTTTTAATTTTCGAAATTCCA-ATCAAAAC
1 TTTTAATTCTATTGTTTTTAATTTT-----TTCCAGATCAAAAC
*
6058658 TTTTAATTCTATT-TTATTTTATTTTTTCCAGATCAAAAC
1 TTTTAATTCTATTGTT-TTTAATTTTTTCCAGATCAAAAC
6058697 TTTTAATT
1 TTTTAATT
6058705 TTTTTCCAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
38 5 0.12
39 16 0.37
42 2 0.05
43 20 0.47
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (39 bp):
TTTTAATTCTATTGTTTTTAATTTTTTCCAGATCAAAAC
Found at i:6059245 original size:49 final size:49
Alignment explanation
Indices: 6059173--6059271 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
6059163 TAACGCTAGG
6059173 GTTAACAAAAACCCAAATCTAGCATATCAACAAATGGCTCAAACAATTC
1 GTTAACAAAAACCCAAATCTAGCATATCAACAAATGGCTCAAACAATTC
*
6059222 GTTAACGAAAACCCAAATCTAGCATATCAACAAATGGCTCAAACAATTC
1 GTTAACAAAAACCCAAATCTAGCATATCAACAAATGGCTCAAACAATTC
6059271 G
1 G
6059272 GCAACTGGTC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.20
Consensus pattern (49 bp):
GTTAACAAAAACCCAAATCTAGCATATCAACAAATGGCTCAAACAATTC
Found at i:6080099 original size:15 final size:14
Alignment explanation
Indices: 6080037--6080104 Score: 64
Period size: 15 Copynumber: 4.6 Consensus size: 14
6080027 CCAATTTTTA
*
6080037 TTTATTTTTCTTAAT
1 TTTATTTTTATT-AT
* *
6080052 TTTAATTTTAATAT
1 TTTATTTTTATTAT
* *
6080066 TTTATTTTATTTTAC
1 TTTATTTT-TATTAT
6080081 TTTATTATTTATTAT
1 TTTATT-TTTATTAT
6080096 TTTATTTTT
1 TTTATTTTT
6080105 GGATGTTAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
14 12 0.29
15 28 0.67
16 2 0.05
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTTTATTAT
Found at i:6082751 original size:97 final size:95
Alignment explanation
Indices: 6082631--6082813 Score: 269
Period size: 97 Copynumber: 1.9 Consensus size: 95
6082621 TTTTTAAGAA
*
6082631 TATGTTGGGCTGAGTAACTGGGGTAAGGTGCTTGGCTGTCATCTCTCCTCGCGTCAAAAAGTTCG
1 TATGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTGTCATCTCT--TCGCGTCAAAAAGTTCG
* *
6082696 ATATGTTCTTAA-AGAAAAATAAAAATTAGGAG
64 ATATATTCCTAAGA-AAAAATAAAAATTAGGAG
** * *
6082728 TATGTTGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTTATCTCTTCGCGTCAAAAGGTTCGAT
1 TATGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTGTCATCTCTTCGCGTCAAAAAGTTCGAT
6082793 ATATTCCTAAGAAAAAATAAA
66 ATATTCCTAAGAAAAAATAAA
6082814 TAATAATAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
95 35 0.45
96 1 0.01
97 42 0.54
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (95 bp):
TATGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTGTCATCTCTTCGCGTCAAAAAGTTCGAT
ATATTCCTAAGAAAAAATAAAAATTAGGAG
Found at i:6082851 original size:14 final size:15
Alignment explanation
Indices: 6082807--6082851 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
6082797 TCCTAAGAAA
6082807 AAAT-AAATAATAAT
1 AAATAAAATAATAAT
*
6082821 -AATTAAATAATAAT
1 AAATAAAATAATAAT
6082835 AAATAAAATAA-AAT
1 AAATAAAATAATAAT
6082849 AAA
1 AAA
6082852 AAGATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 3 0.11
14 16 0.57
15 9 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAAAATAATAAT
Found at i:6082860 original size:13 final size:14
Alignment explanation
Indices: 6082807--6082861 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
6082797 TCCTAAGAAA
6082807 AAAT-AAATAATAAT
1 AAATAAAATAA-AAT
*
6082821 -AATTAAATAATAAT
1 AAATAAAATAA-AAT
6082835 AAATAAAATAAAAT
1 AAATAAAATAAAAT
*
6082849 AAA-AAGATAAAAT
1 AAATAAAATAAAAT
6082862 TTAGGGACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
13 12 0.32
14 16 0.43
15 9 0.24
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:6086016 original size:25 final size:25
Alignment explanation
Indices: 6085933--6086012 Score: 85
Period size: 24 Copynumber: 3.3 Consensus size: 25
6085923 TATATAACGA
6085933 GAAGCTCATAAGAGCCA-TAATCGG
1 GAAGCTCATAAGAGCCATTAATCGG
** * *
6085957 GAAGCTCATGGGAGCCAATAA-CCG
1 GAAGCTCATAAGAGCCATTAATCGG
*
6085981 GTAGCTCCA-AAGAGCCATTAATCGG
1 GAAGCT-CATAAGAGCCATTAATCGG
6086006 GAAGCTC
1 GAAGCTC
6086013 CAAATAGCCA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
24 32 0.73
25 12 0.27
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (25 bp):
GAAGCTCATAAGAGCCATTAATCGG
Found at i:6086029 original size:25 final size:25
Alignment explanation
Indices: 6085930--6086034 Score: 76
Period size: 24 Copynumber: 4.3 Consensus size: 25
6085920 GGCTATATAA
6085930 CGAGAAGCT-CATAAGAGCCA-TAAT
1 CGAGAAGCTCCA-AAGAGCCATTAAT
* ** * *
6085954 CGGGAAGCT-CATGGGAGCCAATAAC
1 CGAGAAGCTCCA-AAGAGCCATTAAT
*
6085979 CG-GTAGCTCCAAAGAGCCATTAAT
1 CGAGAAGCTCCAAAGAGCCATTAAT
* *
6086003 CGGGAAGCTCCAAATAGCCATGT-AT
1 CGAGAAGCTCCAAAGAGCCAT-TAAT
6086028 CGAGAAG
1 CGAGAAG
6086035 TTCAAGCGAG
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
24 33 0.51
25 31 0.48
26 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.16
Consensus pattern (25 bp):
CGAGAAGCTCCAAAGAGCCATTAAT
Found at i:6086106 original size:25 final size:27
Alignment explanation
Indices: 6086071--6086121 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
6086061 CTGAGATTTA
*
6086071 TTAATTAGG-AAGCTCACAAAAAGCCT
1 TTAATTAGGAAAACTCACAAAAAGCCT
*
6086097 TTAATT-GGAAAACTCACGAAAAGCC
1 TTAATTAGGAAAACTCACAAAAAGCC
6086122 ATATAACGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (27 bp):
TTAATTAGGAAAACTCACAAAAAGCCT
Found at i:6094471 original size:20 final size:19
Alignment explanation
Indices: 6094449--6094502 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
6094439 CTTTTACTAT
*
6094449 TTTTGGTTTTTTT-TTATTC
1 TTTTGGTTTTTTTATT-TTA
6094468 TTTT-GTTTGTTTTATTTTA
1 TTTTGGTTT-TTTTATTTTA
6094487 GTTTTGGTTTTTTTAT
1 -TTTTGGTTTTTTTAT
6094503 GGGCCCAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.13
19 10 0.33
20 12 0.40
21 4 0.13
ACGTcount: A:0.07, C:0.02, G:0.13, T:0.78
Consensus pattern (19 bp):
TTTTGGTTTTTTTATTTTA
Found at i:6096164 original size:26 final size:24
Alignment explanation
Indices: 6096102--6096163 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
6096092 TCACTATTCT
6096102 AAATATTAAAAAATTTATAATTATA
1 AAATA-TAAAAAATTTATAATTATA
* *
6096127 AAATATTAAAAATTTATAAAATTATG
1 AAATATAAAAAATTTAT--AATTATA
6096153 AAAT-TAAAAAA
1 AAATATAAAAAA
6096164 ACTTAACTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 11 0.34
25 11 0.34
26 10 0.31
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATATAAAAAATTTATAATTATA
Found at i:6096226 original size:21 final size:22
Alignment explanation
Indices: 6096188--6096246 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
6096178 TTATTAAATT
6096188 AAAT-TAAATTATAAAAACT-ATA
1 AAATATAAA-TAT-AAAACTAATA
6096210 AAATATAAATATAAAACTAATA
1 AAATATAAATATAAAACTAATA
*
6096232 ATATATAAA-ATAAAA
1 AAATATAAATATAAAA
6096247 AAAAGTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 12 0.35
22 18 0.53
23 4 0.12
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATATAAATATAAAACTAATA
Found at i:6097398 original size:56 final size:56
Alignment explanation
Indices: 6097336--6097447 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
6097326 AGTAAATATG
* * *
6097336 TCTGCAACTTGTTTATTGGTTCGTACTTTTTGCAGCTCAATATCTTGAGATAACAC
1 TCTGCAACTTGTTCATCGGTTCGTACTTTTTGCAACTCAATATCTTGAGATAACAC
6097392 TCTGCAACTTGTTCATCGGTTCGTACTTTTTGCAACTCAATATCTTGAGATAACAC
1 TCTGCAACTTGTTCATCGGTTCGTACTTTTTGCAACTCAATATCTTGAGATAACAC
6097448 ATTTTCTTGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (56 bp):
TCTGCAACTTGTTCATCGGTTCGTACTTTTTGCAACTCAATATCTTGAGATAACAC
Found at i:6104042 original size:10 final size:10
Alignment explanation
Indices: 6104027--6104054 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6104017 GCGTGATAGA
6104027 ATTAAAATAT
1 ATTAAAATAT
6104037 ATTAAAATAT
1 ATTAAAATAT
6104047 ATTAAAAT
1 ATTAAAAT
6104055 TAAACTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:6106074 original size:19 final size:18
Alignment explanation
Indices: 6106032--6106070 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6106022 TCCTTATAAT
**
6106032 AAATTTATTTATTTTTGG
1 AAATTTATTTATTTTTAA
*
6106050 AAATTTTTTTATTTTTAA
1 AAATTTATTTATTTTTAA
6106068 AAA
1 AAA
6106071 ATTTGTTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
AAATTTATTTATTTTTAA
Found at i:6116724 original size:14 final size:14
Alignment explanation
Indices: 6116705--6116732 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6116695 AGATATGTTC
6116705 GGTGATGGAAATAA
1 GGTGATGGAAATAA
6116719 GGTGATGGAAATAA
1 GGTGATGGAAATAA
6116733 AAGCTTGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (14 bp):
GGTGATGGAAATAA
Found at i:6117508 original size:30 final size:31
Alignment explanation
Indices: 6117453--6117539 Score: 140
Period size: 30 Copynumber: 2.8 Consensus size: 31
6117443 TGAAACATAG
6117453 GAGTGATCAAATTATAAATTTATTAATAATT
1 GAGTGATCAAATTATAAATTTATTAATAATT
* *
6117484 GAGTGATTAAATTATAAA-TTATTAATTATT
1 GAGTGATCAAATTATAAATTTATTAATAATT
*
6117514 GAGGGATCAAATTATAAATTTATTAA
1 GAGTGATCAAATTATAAATTTATTAA
6117540 CCCATCTAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 27 0.53
31 24 0.47
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (31 bp):
GAGTGATCAAATTATAAATTTATTAATAATT
Found at i:6120401 original size:34 final size:33
Alignment explanation
Indices: 6120353--6120416 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
6120343 TTTAAATTAC
*
6120353 AAAAATAATAAA-TTTAAAAGTATAAAAATAACA
1 AAAAATAATAAATTTTAAAAATA-AAAAATAACA
*
6120386 AAAAAGTACTAAATTTTAAAAATAAAAAATA
1 AAAAA-TAATAAATTTTAAAAATAAAAAATA
6120417 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 5 0.19
34 13 0.48
35 9 0.33
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (33 bp):
AAAAATAATAAATTTTAAAAATAAAAAATAACA
Found at i:6122777 original size:56 final size:56
Alignment explanation
Indices: 6122714--6122849 Score: 227
Period size: 56 Copynumber: 2.4 Consensus size: 56
6122704 ACCATGGCAT
6122714 CGATATATGTGTGCGAGTAAGACCACGTTTAATAAGTTGGCAACGATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATAAGTTGGCAACGATATGTGATTC
** * * *
6122770 CGATATATGTGTATGAGTAAGACCACGTTTAATACGTTGGCATCTATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATAAGTTGGCAACGATATGTGATTC
6122826 CGATATATGTGTGCGAGTAAGACC
1 CGATATATGTGTGCGAGTAAGACC
6122850 TTGTCTGGGA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 73 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (56 bp):
CGATATATGTGTGCGAGTAAGACCACGTTTAATAAGTTGGCAACGATATGTGATTC
Found at i:6123089 original size:16 final size:16
Alignment explanation
Indices: 6123065--6123095 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6123055 TGGTTATTTA
*
6123065 ATATTTGATGCAAATT
1 ATATATGATGCAAATT
6123081 ATATATGATGCAAAT
1 ATATATGATGCAAAT
6123096 GAAAATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (16 bp):
ATATATGATGCAAATT
Found at i:6126567 original size:11 final size:11
Alignment explanation
Indices: 6126551--6126579 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6126541 GTAATGTTAA
6126551 AATATATACAT
1 AATATATACAT
6126562 AATATATACAT
1 AATATATACAT
6126573 -ATATATA
1 AATATATA
6126580 AAAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATATACAT
Found at i:6126948 original size:22 final size:22
Alignment explanation
Indices: 6126859--6126975 Score: 76
Period size: 24 Copynumber: 5.0 Consensus size: 22
6126849 AGTGTTTAAG
* *
6126859 AATATATACATAAGATGATATGGA
1 AATATATACATAATAT-ATAT-AA
*
6126883 AATATGTACATGGAATAGTATATAA
1 AATATATACAT--AATA-TATATAA
*
6126908 AAAATATA-ACTAATA-ATATTGAA
1 AATATATACA-TAATATATA-T-AA
6126931 AATATATACATAATATATATAA
1 AATATATACATAATATATATAA
* *
6126953 AACATATACGATATATACATATA
1 AATATATAC-ATA-ATATATATA
6126976 CATTAGAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
21 3 0.04
22 11 0.15
23 22 0.29
24 23 0.31
25 8 0.11
26 7 0.09
27 1 0.01
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.32
Consensus pattern (22 bp):
AATATATACATAATATATATAA
Found at i:6128125 original size:5 final size:5
Alignment explanation
Indices: 6128115--6128152 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
6128105 TTATGAGTAG
*
6128115 GAAAA GAAAA GAAAA GAAAA AAAAA G-AAA G-AAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
6128153 TCTATTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:6129441 original size:75 final size:75
Alignment explanation
Indices: 6129263--6129481 Score: 277
Period size: 75 Copynumber: 3.0 Consensus size: 75
6129253 CTCTTTAAAA
* * *
6129263 CTCAGCGTGTCTTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA-ATTCTTGAAAAGCAGAAA
1 CTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAA
6129327 TTGAAAATAC
66 TTGAAAATAC
* * * * *
6129337 CTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGATGAA-CAGAA
1 CTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGA-AAAGCAGAA
6129401 ATT-AAAATTAC
65 ATTGAAAA-TAC
* * *
6129412 CTCAGTGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTCTTTAAAA-CATAAA
1 CTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAA
*
6129475 TTAAAAA
66 TTGAAAA
6129482 ACAAAAATTG
Statistics
Matches: 126, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
73 9 0.07
74 56 0.44
75 59 0.47
76 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (75 bp):
CTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAA
TTGAAAATAC
Found at i:6129597 original size:73 final size:72
Alignment explanation
Indices: 6129475--6129634 Score: 223
Period size: 73 Copynumber: 2.2 Consensus size: 72
6129465 AAAACATAAA
* * *
6129475 TTAAAAAACAAAAATTGAACATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCT-AGCAATATG
1 TTAAAAAACAGAAATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCA-CAATATG
6129539 AGTCGATTT
65 AGTCGA-TT
* * *
6129548 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
1 TTAAAAAACAGAAATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGA
*
6129613 GTTGATT
66 GTCGATT
*
6129620 TTAAAAAATAGAAAT
1 TTAAAAAACAGAAAT
6129635 AAAAATATCA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
72 15 0.19
73 61 0.79
74 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (72 bp):
TTAAAAAACAGAAATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGA
GTCGATT
Found at i:6129618 original size:160 final size:161
Alignment explanation
Indices: 6129324--6129620 Score: 454
Period size: 160 Copynumber: 1.8 Consensus size: 161
6129314 TGAAAAGCAG
* * *
6129324 AAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTCGA-TTTTT
** ** * *
6129389 TGATGAACAGAAATTAAAATTACCTCAGTGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAG
65 TGAAAAACAGAAATTAAAATTACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAG
6129454 TTGATTTCTTTAAAACATAAATTAAAAAACAA
130 TTGATTTCTTTAAAACATAAATTAAAAAACAA
* *
6129486 AAATTGAACATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTCGA-TTTTT
1 AAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTCGATTTTTT
*
6129550 GAAAAACAGAAATTGAAAA-TACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGAG
66 GAAAAACAGAAATT-AAAATTACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAG
6129614 TTGATTT
130 TTGATTT
6129621 TAAAAAATAG
Statistics
Matches: 122, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
160 64 0.52
161 4 0.03
162 54 0.44
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (161 bp):
AAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTCGATTTTTT
GAAAAACAGAAATTAAAATTACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGT
TGATTTCTTTAAAACATAAATTAAAAAACAA
Found at i:6151143 original size:49 final size:47
Alignment explanation
Indices: 6150850--6151164 Score: 163
Period size: 47 Copynumber: 6.7 Consensus size: 47
6150840 TTTCTTGTGT
* *
6150850 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATTAT-AAG-T-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCTC--TATGAGGATA
* * * * * *
6150896 GTCAGTTTAATACCATGTCTAGGACATGACATC-AGC-GTA-GA-GATGA
1 GCCAGTGTAAGA-CATGTCTGGGACATG-CATCGACCTCTATGAGGAT-A
* * * * * *
6150942 GTGCCAGTGTAAGACGTGTCTGAGACATGCATCGGCCTCGACGATGATA
1 --GCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCTATGAGGATA
* * *
6150991 GCCAGTGTAAGACATGTCTGGGACTTGCATCG---GCTAAGAGTTG-T-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCTATGAG--GATA
* * * * * * *
6151035 GCTAGTGTAAGACATGTCCGGAACATGCATCAGCACGTATAT-ACGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-G-ACCTCTATGAGGATA
* *
6151083 GCTAGTATAAGACCATGTCTGGGACATGGCATCGACCTCTATGAGGATA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTCTATGAGGATA
6151132 GCCAGTGTAAGACCATGTCT-GGACATGGCATCG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCG
6151165 GCAACTTATC
Statistics
Matches: 204, Mismatches: 41, Indels: 46
0.70 0.14 0.16
Matches are distributed among these distances:
43 1 0.00
44 35 0.17
45 2 0.01
46 15 0.07
47 58 0.28
48 45 0.22
49 40 0.20
50 8 0.04
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (47 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCTATGAGGATA
Found at i:6153065 original size:29 final size:28
Alignment explanation
Indices: 6153029--6153109 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 28
6153019 CACACCCGGA
6153029 ATAATATAAATCCTCCATAACACACCAGT
1 ATAATAT-AATCCTCCATAACACACCAGT
* *
6153058 ATAATAT-AGCCTCTCA-AACACACTAGT
1 ATAATATAATCCTC-CATAACACACCAGT
*
6153085 A-AAT-TATATCCTCCCTAACACACCA
1 ATAATATA-ATCCTCCATAACACACCA
6153110 ATAAGGCATT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
25 1 0.02
26 4 0.09
27 29 0.67
28 2 0.05
29 7 0.16
ACGTcount: A:0.42, C:0.30, G:0.04, T:0.25
Consensus pattern (28 bp):
ATAATATAATCCTCCATAACACACCAGT
Found at i:6153638 original size:17 final size:18
Alignment explanation
Indices: 6153608--6153641 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6153598 AATTTTTATT
*
6153608 CAATTTATTCCCTAATTC
1 CAATTTAATCCCTAATTC
6153626 CAATTTAAT-CCTAATT
1 CAATTTAATCCCTAATT
6153642 AACTCTTTTA
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:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (18 bp):
CAATTTAATCCCTAATTC
Found at i:6154077 original size:17 final size:17
Alignment explanation
Indices: 6154055--6154087 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6154045 GTTTTCGTTT
6154055 TGTTC-TCTGTTCTTTTC
1 TGTTCTTCT-TTCTTTTC
6154072 TGTTCTTCTTTCTTTT
1 TGTTCTTCTTTCTTTT
6154088 ATTTTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.00, C:0.21, G:0.09, T:0.70
Consensus pattern (17 bp):
TGTTCTTCTTTCTTTTC
Found at i:6158675 original size:57 final size:57
Alignment explanation
Indices: 6158605--6158717 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
6158595 AAGGGGATCC
*
6158605 ATAGATCGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAATGTCTCAATTATTCT
1 ATAGATCGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAAGGTCTCAATTATTCT
*
6158662 ATAGATTGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAAGGTCTCAATTATTC
1 ATAGATCGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAAGGTCTCAATTATTC
6158718 AATCTAGGGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (57 bp):
ATAGATCGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAAGGTCTCAATTATTCT
Found at i:6160520 original size:13 final size:13
Alignment explanation
Indices: 6160481--6160544 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
6160471 AGTTCTTCAT
6160481 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
6160494 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
6160507 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
6160520 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
*
6160533 TGCTTTGGAAAA
1 TGCTTTTGAAAA
6160545 ATTTAAGTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
12 3 0.07
13 36 0.86
14 3 0.07
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:6174976 original size:11 final size:10
Alignment explanation
Indices: 6174950--6174983 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
6174940 GGAGAGCACC
*
6174950 AAGAGTCAAA
1 AAGAGCCAAA
6174960 AAGAGCCAAA
1 AAGAGCCAAA
6174970 AACGAGCCAAA
1 AA-GAGCCAAA
6174981 AAG
1 AAG
6174984 GGACAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.59, C:0.18, G:0.21, T:0.03
Consensus pattern (10 bp):
AAGAGCCAAA
Found at i:6175415 original size:18 final size:17
Alignment explanation
Indices: 6175392--6175426 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6175382 CCCTTCAAGG
6175392 GTTTTGGATTTTCTTTAT
1 GTTTTGGATTTT-TTTAT
*
6175410 GTTTTGTATTTTTTTAT
1 GTTTTGGATTTTTTTAT
6175427 TCTTCTGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.11, C:0.03, G:0.14, T:0.71
Consensus pattern (17 bp):
GTTTTGGATTTTTTTAT
Found at i:6179068 original size:162 final size:166
Alignment explanation
Indices: 6178702--6179185 Score: 518
Period size: 162 Copynumber: 2.9 Consensus size: 166
6178692 GTTACACTTG
* * * *
6178702 TATTGCGGTTAATTACCCCTAAAATTAGTTATATGACACATCTTAATCTCCGTAC-ATTACTTCA
1 TATTGCGGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTACTTCA
* * * *
6178766 TGGTCATTTCTTTAGCCCACCATGCTTTTTTGCACTACACCCTGTACTAGAACCTGACTTACATG
66 TGGTCATTTGTTTAGCCCACCATGCCTTTTTGCACGACACCCTGTACTAGAACCAGACTTACATG
* *
6178831 TCAACAATTAGGACTAGTACAGGAATAATGGGCATGTCTT
131 TCAACAATTAGAACTAATACAGG----ATGGGCATGTCTT
** * * * ** *
6178871 TATTATGGTTGATCACCCCTGAAGTTAGTTGTATGACACATCTCAGTCTTTGTACAACTACTTCA
1 TATTGCGGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTACTTCA
* * ** * *
6178936 TGGTCATTTGTTTAGCCCA-CATTCCTTTTTGCGCGACATTCTGTACTGGAATCAGACTTACATG
66 TGGTCATTTGTTTAGCCCACCATGCCTTTTTGCACGACACCCTGTACTAGAACCAGACTTACATG
* *
6179000 TCGATAATTAGAAC-AATACA-G-TGGGCATGTCTT
131 TCAACAATTAGAACTAATACAGGATGGGCATGTCTT
* *
6179033 TATTGCAGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTGCTTCA
1 TATTGCGGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTACTTCA
** * ** *
6179098 TGGTCATTTGTTTAGCCTGCAATG-CTTTTCTATACGACA-CCTCGTAC-AGAA-CTGAACTTAC
66 TGGTCATTTGTTTAGCCCACCATGCCTTTT-TGCACGACACCCT-GTACTAGAACCAG-ACTTAC
* *
6179159 ATGTCGACAATTAGGACTAATACAGGA
128 ATGTCAACAATTAGAACTAATACAGGA
6179186 ATAGTACGAA
Statistics
Matches: 259, Mismatches: 48, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
161 2 0.01
162 115 0.44
163 18 0.07
164 1 0.00
167 1 0.00
168 5 0.02
169 91 0.35
170 26 0.10
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (166 bp):
TATTGCGGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTACTTCA
TGGTCATTTGTTTAGCCCACCATGCCTTTTTGCACGACACCCTGTACTAGAACCAGACTTACATG
TCAACAATTAGAACTAATACAGGATGGGCATGTCTT
Found at i:6183119 original size:75 final size:75
Alignment explanation
Indices: 6182996--6183145 Score: 264
Period size: 75 Copynumber: 2.0 Consensus size: 75
6182986 CTCTGAGAAG
**
6182996 CGCTTATTTATAGTCTAAGCTCGACTTACCTTTTTATTGAATGGTTATGGTGGTTCGAGGAGATT
1 CGCTTATTTATAGTCTAAGCTCGACTTACCTTTCCATTGAATGGTTATGGTGGTTCGAGGAGATT
*
6183061 ATCCTCCTCA
66 ATACTCCTCA
*
6183071 CGCTTATTTATAGTCTAAGCTTGACTTACCTTTCCATTGAATGGTTATGGTGGTTCGAGGAGATT
1 CGCTTATTTATAGTCTAAGCTCGACTTACCTTTCCATTGAATGGTTATGGTGGTTCGAGGAGATT
6183136 ATACTCCTCA
66 ATACTCCTCA
6183146 TTCCTGCTGT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (75 bp):
CGCTTATTTATAGTCTAAGCTCGACTTACCTTTCCATTGAATGGTTATGGTGGTTCGAGGAGATT
ATACTCCTCA
Found at i:6193628 original size:40 final size:41
Alignment explanation
Indices: 6193568--6193661 Score: 154
Period size: 40 Copynumber: 2.3 Consensus size: 41
6193558 GGCTATTTGG
*
6193568 AAAAATACATACTGGTTCCACTTGACACAGTGGCGACAGCCA
1 AAAAATATATA-TGGTTCCACTTGACACAGTGGCGACAGCCA
*
6193610 AAAAATATATAT-GTTCCACTTGACATAGTGGCGACAGCCA
1 AAAAATATATATGGTTCCACTTGACACAGTGGCGACAGCCA
6193650 AAAAATATATAT
1 AAAAATATATAT
6193662 TTTTAAAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 39 0.78
41 1 0.02
42 10 0.20
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.23
Consensus pattern (41 bp):
AAAAATATATATGGTTCCACTTGACACAGTGGCGACAGCCA
Found at i:6195810 original size:31 final size:31
Alignment explanation
Indices: 6195772--6195889 Score: 209
Period size: 31 Copynumber: 3.8 Consensus size: 31
6195762 ACAAATGACA
6195772 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
6195803 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
6195834 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
6195865 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
6195890 AAGTGACAAG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 82 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:6196064 original size:42 final size:42
Alignment explanation
Indices: 6195989--6196115 Score: 168
Period size: 42 Copynumber: 3.0 Consensus size: 42
6195979 GCATCAGTGA
*
6195989 GATATGTGATT-CGTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATGTGATTACGTGTAAGACCATAGCTAGGCTATGGCATC
6196030 GATATGTGATTACGTGTAAGACCATAGCTAGGCTATGGCATC
1 GATATGTGATTACGTGTAAGACCATAGCTAGGCTATGGCATC
* ** * * *
6196072 AATATGTGAAGATGTGTAAGACCATAG-TTGAACTATGGCATC
1 GATATGTGATTACGTGTAAGACCATAGCTAG-GCTATGGCATC
6196114 GA
1 GA
6196116 GAAAACGAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
41 13 0.17
42 63 0.83
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (42 bp):
GATATGTGATTACGTGTAAGACCATAGCTAGGCTATGGCATC
Found at i:6197141 original size:6 final size:6
Alignment explanation
Indices: 6197130--6197156 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6197120 ACTTAGTAAC
6197130 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
6197157 GAGTAAACAC
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:6197507 original size:18 final size:18
Alignment explanation
Indices: 6197486--6197525 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
6197476 TAAAAATTCT
* *
6197486 GAAATTTATATTTTTTTA
1 GAAAATTATATATTTTTA
6197504 GAAAATTATATATTTTTA
1 GAAAATTATATATTTTTA
6197522 -AAAA
1 GAAAA
6197526 AAATTAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
GAAAATTATATATTTTTA
Found at i:6197528 original size:20 final size:20
Alignment explanation
Indices: 6197487--6197531 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
6197477 AAAAATTCTG
** *
6197487 AAATT-TATATTTTTTTAGA
1 AAATTATATATTTTTAAAAA
6197506 AAATTATATATTTTTAAAAA
1 AAATTATATATTTTTAAAAA
6197526 AAATTA
1 AAATTA
6197532 AAGTATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AAATTATATATTTTTAAAAA
Found at i:6197538 original size:21 final size:20
Alignment explanation
Indices: 6197505--6197564 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
6197495 ATTTTTTTAG
* *
6197505 AAAATTATATATTTTTAAAA
1 AAAATTAAATATTTATAAAA
*
6197525 AAAATTAAAGTATTTATAAAG
1 AAAATTAAA-TATTTATAAAA
* *
6197546 AAAGTTAAAAATTT-TAAAA
1 AAAATTAAATATTTATAAAA
6197565 TTTTCTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 4 0.12
20 12 0.36
21 17 0.52
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
AAAATTAAATATTTATAAAA
Found at i:6198986 original size:18 final size:16
Alignment explanation
Indices: 6198938--6198989 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
6198928 TTATATTCTT
* * *
6198938 TATAAATTTAAAATTC
1 TATAAAATTAAAAATA
*
6198954 TAAAAAATTAAAAATA
1 TATAAAATTAAAAATA
6198970 TATAAAATCTAATAAATA
1 TATAAAAT-TAA-AAATA
6198988 TA
1 TA
6198990 ATATTTGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 19 0.66
17 3 0.10
18 7 0.24
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
TATAAAATTAAAAATA
Found at i:6201050 original size:13 final size:14
Alignment explanation
Indices: 6201023--6201056 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
6201013 AACTATCGAA
6201023 GTTTAAAAGCATTT
1 GTTTAAAAGCATTT
6201037 GTTTAAAA-CATTT
1 GTTTAAAAGCATTT
6201050 GCTTTAA
1 G-TTTAA
6201057 CTTTGGGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (14 bp):
GTTTAAAAGCATTT
Found at i:6202776 original size:39 final size:39
Alignment explanation
Indices: 6202717--6202856 Score: 217
Period size: 39 Copynumber: 3.6 Consensus size: 39
6202707 ATCGTGATCT
** *
6202717 GAAGCCCGAAATCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
6202756 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
6202795 GAAGCCCGGAGGCTAACTGAAGCATATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
6202834 AAAGCCTGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
6202857 TCATTAGAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 93 1.00
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:6205998 original size:12 final size:12
Alignment explanation
Indices: 6205975--6206006 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
6205965 GAATGCATTA
6205975 AAAGTG-TTGAG
1 AAAGTGATTGAG
6205986 AAAGTGATTGAG
1 AAAGTGATTGAG
6205998 AAAGT-ATTG
1 AAAGTGATTG
6206007 TTAACAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (12 bp):
AAAGTGATTGAG
Found at i:6207515 original size:25 final size:25
Alignment explanation
Indices: 6207481--6207530 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
6207471 ATCAGGGACT
6207481 CAATTGAGTGAAATAAAACTCTAAA
1 CAATTGAGTGAAATAAAACTCTAAA
6207506 CAATTGAGTGAAATAAAACTCTAAA
1 CAATTGAGTGAAATAAAACTCTAAA
6207531 AATAGTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (25 bp):
CAATTGAGTGAAATAAAACTCTAAA
Found at i:6210346 original size:30 final size:29
Alignment explanation
Indices: 6210307--6210365 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
6210297 AACACTCTTC
*
6210307 TTCAGCAAATTGATGAACAAAAACTGAAAA
1 TTCAACAAATTGATGAACAAAAACT-AAAA
6210337 TTCAACAAATTGATGAACAAAAACTAAAA
1 TTCAACAAATTGATGAACAAAAACTAAAA
6210366 CTTGTTTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.56, C:0.14, G:0.10, T:0.20
Consensus pattern (29 bp):
TTCAACAAATTGATGAACAAAAACTAAAA
Found at i:6213707 original size:31 final size:31
Alignment explanation
Indices: 6213639--6213709 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
6213629 TAAATTTACA
* * *
6213639 TAAAAAAAATTAAAAATTATTGTTTCATATT
1 TAAAAAAATTTAAAAATTATTATATCATATT
*
6213670 TAAAAAAATTTAAAAATTATATATAT-ATTTT
1 TAAAAAAATTTAAAAATTAT-TATATCATATT
*
6213701 TTAAAAAAT
1 TAAAAAAAT
6213710 AATAACTCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (31 bp):
TAAAAAAATTTAAAAATTATTATATCATATT
Found at i:6214200 original size:5 final size:5
Alignment explanation
Indices: 6214190--6214216 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6214180 AAAATTTGTG
6214190 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
6214217 TCACAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:6218341 original size:14 final size:15
Alignment explanation
Indices: 6218322--6218378 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
6218312 AATCTTTAAG
6218322 GATATG-CAATCTTA
1 GATATGACAATCTTA
6218336 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
6218353 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
6218372 GATATGA
1 GATATGA
6218379 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:6218363 original size:36 final size:38
Alignment explanation
Indices: 6218322--6218400 Score: 126
Period size: 36 Copynumber: 2.1 Consensus size: 38
6218312 AATCTTTAAG
6218322 GATATGCAATCTTAGATATGATA-CAATCTT-AGATAT
1 GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
6218358 GATATGCAATCTTAGATATGATATGCAATCTTGAAGATAT
1 GATATGCAATCTTAGATATGATA-GCAATCTT-AAGATAT
6218398 GAT
1 GAT
6218401 CTTGTAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 23 0.59
38 7 0.18
40 9 0.23
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
Found at i:6218369 original size:19 final size:19
Alignment explanation
Indices: 6218322--6218400 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
6218312 AATCTTTAAG
6218322 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6218341 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6218358 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6218377 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
6218398 GAT
1 GAT
6218401 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:6221496 original size:12 final size:12
Alignment explanation
Indices: 6221479--6221503 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6221469 TAAAGTTATC
6221479 AAAAAGAGAAAG
1 AAAAAGAGAAAG
6221491 AAAAAGAGAAAG
1 AAAAAGAGAAAG
6221503 A
1 A
6221504 GAGAGAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAG
Found at i:6224097 original size:6 final size:6
Alignment explanation
Indices: 6224054--6224083 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
6224044 AAAAAAAGAA
6224054 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
6224084 GAGAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:6225229 original size:175 final size:175
Alignment explanation
Indices: 6224938--6225306 Score: 614
Period size: 175 Copynumber: 2.1 Consensus size: 175
6224928 CAAAGAAACA
6224938 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
* *
6225003 ACAGCGAAGCTGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATT
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
* * * * *
6225068 TCAGCA-TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
131 GCA-AATTGGCATCCCTGTATTTATAGGGAACAAATCGAAGATAGC
*
6225113 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
6225178 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
6225243 GCAAATTTGGCATCCCTGTATTTATAGGGAACAAATCGAAGATAGC
131 GCAAA-TTGGCATCCCTGTATTTATAGGGAACAAATCGAAGATAGC
* * *
6225289 AGATCTGACATTCCTGTG
1 AGATTTGGCATCCCTGTG
6225307 CTTACAGCAA
Statistics
Matches: 181, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
174 1 0.01
175 129 0.71
176 51 0.28
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (175 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GCAAATTGGCATCCCTGTATTTATAGGGAACAAATCGAAGATAGC
Found at i:6225231 original size:132 final size:132
Alignment explanation
Indices: 6224943--6225416 Score: 607
Period size: 132 Copynumber: 3.6 Consensus size: 132
6224933 AAACAAGATT
* * * *
6224943 TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACA-CTCCTGTGCTTACAG
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATC-CCTGTGCTTACAG
* ** ** * * * * * *
6225007 CGAAGCTGATCGAAGATTTCAG--CATGGCATCCCTGTGTTTATAGGGAA-CA-AGTTGAAGATT
65 GGAA-CAAATCGAAGATAGCAGATC-TGACATTCCTGTGCTTACAGCGAAGCAGA-TCGAAGATT
6225068 TCAGCA
127 TCAGCA
* *
6225074 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGG
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGCTTACAGG
6225139 GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTCAG
66 GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTCAG
6225204 CA
131 CA
* ** *
6225206 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAAATTTGGCATCCCTGTATTTATAGG
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGCTTACAGG
* * *
6225271 GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGCAAAGCAGATCGAAGATTTTAA
66 GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTCAG
6225336 CA
131 CA
* * ** *
6225338 TGGCATCCATGTGTTTATAGGGAACAAGTTAAAGATAGCAGATTTGGCATCATTGTGCTTACAAG
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGCTTACAGG
*
6225403 AAACAAATCGAAGA
66 GAACAAATCGAAGA
6225417 CATAGCTGAT
Statistics
Matches: 306, Mismatches: 32, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
130 13 0.04
131 78 0.25
132 214 0.70
133 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (132 bp):
TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGCTTACAGG
GAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTCAG
CA
Found at i:6225388 original size:44 final size:44
Alignment explanation
Indices: 6224938--6225388 Score: 366
Period size: 44 Copynumber: 10.3 Consensus size: 44
6224928 CAAAGAAACA
*
6224938 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * * **
6224982 AGATCTGACA-CTCCTGTGCTTACAGCGAAGC-TGATCGAAGATTTC
1 AGATTTGGCATC-CCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
* **
6225027 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATTTC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
*
6225070 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
*
6225113 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * * **
6225157 AGATCTGACATTCCTGTGCTTACAGCGAAGC-AGATCGAAGATTTC
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
*
6225202 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * *
6225245 AAATTTGGCATCCCTGTATTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * ** ***
6225289 AGATCTGACATTCCTGTGCTTACAGCAAAGC-AGATCGAAGATTTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
** * **
6225334 A-ACATGGCATCCATGTGTTTATAGGGAACAAGTTAAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
6225377 AGATTTGGCATC
1 AGATTTGGCATC
6225389 ATTGTGCTTA
Statistics
Matches: 320, Mismatches: 69, Indels: 36
0.75 0.16 0.08
Matches are distributed among these distances:
42 2 0.01
43 73 0.23
44 208 0.65
45 35 0.11
46 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
Found at i:6225399 original size:88 final size:87
Alignment explanation
Indices: 6225250--6225416 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 87
6225240 ATAGCAAATT
* *
6225250 TGGCATCCCTGTATTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTAC-AG
1 TGGCATCCATGTATTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTGTGCTTACAAG
*
6225314 CAAAGCAGATCGAAGATTTTAACA
66 -AAA-CAAATCGAAGATTTTAACA
* * * * * *
6225338 TGGCATCCATGTGTTTATAGGGAACAAGTTAAAGATAGCAGATTTGGCA-TCATTGTGCTTACAA
1 TGGCATCCATGTATTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTC-CTGTGCTTACAA
6225402 GAAACAAATCGAAGA
65 GAAACAAATCGAAGA
6225417 CATAGCTGAT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
87 12 0.18
88 54 0.79
89 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (87 bp):
TGGCATCCATGTATTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTGTGCTTACAAG
AAACAAATCGAAGATTTTAACA
Found at i:6225628 original size:205 final size:205
Alignment explanation
Indices: 6225378--6226324 Score: 1529
Period size: 206 Copynumber: 4.6 Consensus size: 205
6225368 AAAGATAGCA
* *
6225378 GATTTGGCATCATTGTGCTTACAAGAAACAAATCGAAGACATAGCTGATTTGGCTTTCACGGTTT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGGTTT
* *
6225443 ACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGC
66 ACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGC
*** * *
6225508 GTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGGCTTCATATGTTTATACTAAAGCA
131 GTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCA
*
6225573 GATCCAAGGT
196 GATCCAAGAT
6225583 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGGTTT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGGTTT
*
6225648 ACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGC
66 ACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGC
* * ** *
6225713 GTCTCCATATTCGACGGAGAGCAGACACAAAGCAGATTTGGCCTTCATATGTTTATACTGAAGCA
131 GTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCA
*
6225778 GATCCAAGGT
196 GATCCAAGAT
* *
6225788 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACATGCT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCAC-GGTT
6225853 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
65 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
* *
6225918 GGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGA
130 CGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGC
6225983 AGATCCAAGAT
195 AGATCCAAGAT
* * *
6225994 GATTTGGCATTCTTGTGCTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACG-GTT
6226059 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
65 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
* * * *
6226124 CGTCTCCATATTCGATGGAGGGCAGACACATAGCAGATCTAACCTTCAGATGGTTAGACTGAAGC
130 CGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGC
6226189 AGATCCAAGAT
195 AGATCCAAGAT
* * * *
6226200 GGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGTTGATTTGG-TTT-ACGCGTG
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACG-GT-
* *
6226263 CTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAAAACAGATCGAAG
64 -TTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAG
6226325 ATAACAGATT
Statistics
Matches: 701, Mismatches: 37, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
204 4 0.01
205 261 0.37
206 436 0.62
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (205 bp):
GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGGTTT
ACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGC
GTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCA
GATCCAAGAT
Found at i:6226736 original size:19 final size:19
Alignment explanation
Indices: 6226712--6226809 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
6226702 AATCTTTAAG
6226712 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6226731 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6226750 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6226767 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6226786 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
6226807 GAT
1 GAT
6226810 CTTGTAATCT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:6226742 original size:36 final size:35
Alignment explanation
Indices: 6226702--6226809 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 35
6226692 ATGGAAATAT
6226702 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATGC
6226738 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATGC
*
6226774 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTT---TAAGATATGCAATCTT--AGATATGAT
6226810 CTTGTAATCT
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 28 0.46
37 1 0.02
38 7 0.11
40 10 0.16
41 6 0.10
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATGC
Found at i:6231248 original size:29 final size:28
Alignment explanation
Indices: 6231216--6231270 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
6231206 GAGTTTTGTT
6231216 TTTTAATAA-AATAATAAATTATTAATATG
1 TTTTAATAATAA-AATAAATTA-TAATATG
* *
6231245 TTTTTATAATAAAATAATTTATAATA
1 TTTTAATAATAAAATAAATTATAATA
6231271 CATCTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.22
29 16 0.70
30 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
TTTTAATAATAAAATAAATTATAATATG
Found at i:6234046 original size:5 final size:5
Alignment explanation
Indices: 6234031--6234059 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
6234021 ATATTCTAAT
6234031 TTTTA -TTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
6234060 GTGTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:6235416 original size:14 final size:14
Alignment explanation
Indices: 6235382--6235419 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
6235372 TTTTAATTTT
*
6235382 TGTTTAATTTTAAA
1 TGTTTATTTTTAAA
*
6235396 T-TTTATTTTTCAA
1 TGTTTATTTTTAAA
6235409 TGTTTATTTTT
1 TGTTTATTTTT
6235420 TTGTATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (14 bp):
TGTTTATTTTTAAA
Found at i:6237926 original size:41 final size:41
Alignment explanation
Indices: 6237880--6237961 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
6237870 GCTGTGTATG
* * *
6237880 ACACACGGTCGTATGACAACCCATGTCTCAGGCCGTGTGTA
1 ACACACAGTCGTATGACAACCCATGTCCCAGGCCATGTGTA
* * *
6237921 ACACACAGTTGTGTGACAACCCATTTCCCAGGCCATGTGTA
1 ACACACAGTCGTATGACAACCCATGTCCCAGGCCATGTGTA
6237962 CCTTAAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (41 bp):
ACACACAGTCGTATGACAACCCATGTCCCAGGCCATGTGTA
Found at i:6240798 original size:18 final size:20
Alignment explanation
Indices: 6240775--6240811 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
6240765 TTTATACATA
6240775 TGAA-TTTTAAAT-ATTTTT
1 TGAATTTTTAAATAATTTTT
6240793 TGAATTTTTAAATAATTTT
1 TGAATTTTTAAATAATTTT
6240812 CTATAGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TGAATTTTTAAATAATTTTT
Found at i:6241859 original size:20 final size:20
Alignment explanation
Indices: 6241836--6241885 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
6241826 AAATCCAAAT
6241836 TAAAATACTAAAATTCAAGA
1 TAAAATACTAAAATTCAAGA
* *
6241856 TAAAAT-CTTGAAATTCAGGA
1 TAAAATAC-TAAAATTCAAGA
6241876 TAAGAATACT
1 TAA-AATACT
6241886 GATGTGGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 19 0.76
21 4 0.16
22 1 0.04
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (20 bp):
TAAAATACTAAAATTCAAGA
Found at i:6243831 original size:28 final size:28
Alignment explanation
Indices: 6243798--6243853 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
6243788 AAAGCACAAA
6243798 AGCTTAATAAAGTCAAATTAACAAAAAC
1 AGCTTAATAAAGTCAAATTAACAAAAAC
6243826 AGCTTAATAAAGTCAAATTAACAAAAAC
1 AGCTTAATAAAGTCAAATTAACAAAAAC
6243854 TATAAAGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (28 bp):
AGCTTAATAAAGTCAAATTAACAAAAAC
Found at i:6250307 original size:27 final size:26
Alignment explanation
Indices: 6250245--6250386 Score: 113
Period size: 27 Copynumber: 5.3 Consensus size: 26
6250235 AGCATGGCTG
* * *
6250245 CCAGAACAGACAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
6250271 CCAGATACAGATAATCATGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
6250299 CCAGAACAGATATATGTGGTAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * **
6250326 CCAGATCAGATATTTGTGGCAGAGAAA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * * * *
6250353 CTAGATCAGGTATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
6250380 CCAGAAC
1 CCAGAAC
6250387 GCTTCCTCCA
Statistics
Matches: 95, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
26 5 0.05
27 74 0.78
28 16 0.17
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:6252041 original size:26 final size:26
Alignment explanation
Indices: 6252003--6252112 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
6251993 CATGAAATTC
*
6252003 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
6252029 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
6252055 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
* *
6252081 TTATCATTGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
6252107 TTATCA
1 TTATCA
6252113 ATTTGTACCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:6256790 original size:18 final size:17
Alignment explanation
Indices: 6256732--6256792 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 17
6256722 ACATTTTACT
*
6256732 TTATATATTATT-TATT
1 TTATATATTATTATATA
6256748 TTACTATA-T-TTATATA
1 TTA-TATATTATTATATA
6256764 TGTA-A-ATTATTATATA
1 T-TATATATTATTATATA
6256780 TTATTATATTATT
1 TTA-TATATTATT
6256793 TTTTATTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
14 1 0.03
15 6 0.17
16 16 0.44
17 7 0.19
18 6 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TTATATATTATTATATA
Found at i:6260538 original size:40 final size:40
Alignment explanation
Indices: 6260494--6260586 Score: 177
Period size: 40 Copynumber: 2.3 Consensus size: 40
6260484 TCTTTCAATA
6260494 AAATCAGCATATAAACAATTTAAAGCTCTAATTCCATGCC
1 AAATCAGCATATAAACAATTTAAAGCTCTAATTCCATGCC
6260534 AAATCAGCATATAAACAATTTAAAGCTCTAATTCCATGCC
1 AAATCAGCATATAAACAATTTAAAGCTCTAATTCCATGCC
*
6260574 AAATCATCATATA
1 AAATCAGCATATA
6260587 CTTCCAGCAC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (40 bp):
AAATCAGCATATAAACAATTTAAAGCTCTAATTCCATGCC
Found at i:6262815 original size:19 final size:20
Alignment explanation
Indices: 6262791--6262828 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6262781 GAAACTACAT
6262791 TATTTT-CTAAACCAGAAGC
1 TATTTTACTAAACCAGAAGC
*
6262810 TATTTTACTAAACTAGAAG
1 TATTTTACTAAACCAGAAG
6262829 AGAATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (20 bp):
TATTTTACTAAACCAGAAGC
Found at i:6265881 original size:17 final size:17
Alignment explanation
Indices: 6265822--6265881 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
6265812 TAATAAATTT
6265822 AAAATATAATATATAATAA
1 AAAATATAAT-TAT-ATAA
6265841 AAAATAT-ATT-TAT-A
1 AAAATATAATTATATAA
*
6265855 AGAATAATAATTATATAA
1 AAAAT-ATAATTATATAA
6265873 AAAATATAA
1 AAAATATAA
6265882 AATATAATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
17 8 0.23
18 7 0.20
19 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATATAATTATATAA
Found at i:6266400 original size:18 final size:18
Alignment explanation
Indices: 6266364--6266535 Score: 260
Period size: 18 Copynumber: 9.6 Consensus size: 18
6266354 AATCATATCT
*
6266364 TCTAAGATTGTATATCATA
1 TCTAAGATTGCA-ATCATA
6266383 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
6266401 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
6266418 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
6266436 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
*
6266454 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
6266471 TCTAAGATTGCAATCATA
1 TCTAAGATTGCAATCATA
* *
6266489 TCTAACATTG-TATCATA
1 TCTAAGATTGCAATCATA
6266506 TCTAAGATTGCATATCATA
1 TCTAAGATTGCA-ATCATA
6266525 TCTAAGATTGC
1 TCTAAGATTGC
6266536 TTATCATTGA
Statistics
Matches: 140, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
17 47 0.34
18 65 0.46
19 28 0.20
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:6266422 original size:35 final size:36
Alignment explanation
Indices: 6266364--6266535 Score: 251
Period size: 35 Copynumber: 4.8 Consensus size: 36
6266354 AATCATATCT
*
6266364 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG-CTATCATATCTAAGATTGCAATCATA
6266401 TCTAAGATTG-TATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATATCTAAGATTGCAATCATA
* *
6266436 TCTAAGATTGCAATCATATCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATATCTAAGATTGCAATCATA
* * *
6266471 TCTAAGATTGCAATCATATCTAACATTG-TATCATA
1 TCTAAGATTGCTATCATATCTAAGATTGCAATCATA
6266506 TCTAAGATTGCATATCATATCTAAGATTGC
1 TCTAAGATTGC-TATCATATCTAAGATTGC
6266536 TTATCATTGA
Statistics
Matches: 127, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
35 86 0.68
36 31 0.24
37 10 0.08
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (36 bp):
TCTAAGATTGCTATCATATCTAAGATTGCAATCATA
Found at i:6266443 original size:53 final size:53
Alignment explanation
Indices: 6266364--6266535 Score: 283
Period size: 53 Copynumber: 3.2 Consensus size: 53
6266354 AATCATATCT
*
6266364 TCTAAGATTGTATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCA-ATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
6266418 TCTAAGATTGCAATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
1 TCTAAGATTGCAATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
* *
6266471 TCTAAGATTGCAATCATATCTAACATTG-TATCATATCTAAGATTGCATATCATA
1 TCTAAGATTGCAATCATATCTAAGATTGCAATCATATCTAAGATTG--TATCATA
6266525 TCTAAGATTGC
1 TCTAAGATTGC
6266536 TTATCATTGA
Statistics
Matches: 113, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
52 16 0.14
53 68 0.60
54 29 0.26
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (53 bp):
TCTAAGATTGCAATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATA
Found at i:6266550 original size:88 final size:89
Alignment explanation
Indices: 6266367--6266535 Score: 295
Period size: 88 Copynumber: 1.9 Consensus size: 89
6266357 CATATCTTCT
*
6266367 AAGATTGTATATCATATCTAAGATTGCAATCATATCTAAGATTGTATCATATCTAAGATTGCAAT
1 AAGATTG-ATATCATATCTAAGATTGCAATCATATCTAACATTGTATCATATCTAAGATTGCAAT
*
6266432 CATATCTAAGATTGCAATCATATCT
65 CATATCTAAGATTGCAATCATATCG
6266457 AAGATTG-TATCATATCTAAGATTGCAATCATATCTAACATTGTATCATATCTAAGATTGCATAT
1 AAGATTGATATCATATCTAAGATTGCAATCATATCTAACATTGTATCATATCTAAGATTGCA-AT
6266521 CATATCTAAGATTGC
65 CATATCTAAGATTGC
6266536 TTATCATTGA
Statistics
Matches: 77, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
88 53 0.69
89 17 0.22
90 7 0.09
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (89 bp):
AAGATTGATATCATATCTAAGATTGCAATCATATCTAACATTGTATCATATCTAAGATTGCAATC
ATATCTAAGATTGCAATCATATCG
Found at i:6267422 original size:83 final size:83
Alignment explanation
Indices: 6267311--6267922 Score: 1073
Period size: 83 Copynumber: 7.4 Consensus size: 83
6267301 GTGAAAGCCA
* *
6267311 AATCAGCTATGT-CTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGAGTCTGTTT
1 AATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGAGTCTGTTT
*
6267375 GAGAACATCTGAGAGTCA
66 GAGAACATCTGAGAGTCT
* * * *
6267393 AATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATGCCAAATCATCTTGAGTCTGTTT
1 AATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGAGTCTGTTT
*
6267458 GAGAACATCTGAGAGTCA
66 GAGAACATCTGAGAGTCT
6267476 AATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGAGTCTGTTT
1 AATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGAGTCTGTTT
6267541 GAGAACATCTGAGAGTCT
66 GAGAACATCTGAGAGTCT
*
6267559 AATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTCAGTCTGTTT
1 AATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGAGTCTGTTT
6267624 GAGAACATCTGAGAGTCT
66 GAGAACATCTGAGAGTCT
*
6267642 AATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGACGCCAAACCATCTTGAGTCTGTTT
1 AATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGAGTCTGTTT
*
6267707 GAGAACATCCGAGAGTCT
66 GAGAACATCTGAGAGTCT
* *
6267725 AATCTGCTATGTCGTCGATTTGTTCATTGTAAGCACAAGGATGCCAAACCATCTTGAGTCTGTTT
1 AATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGAGTCTGTTT
6267790 GAGAACATCTGAGAGTCT
66 GAGAACATCTGAGAGTCT
* *
6267808 AATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGACGCCAAACCATCTTGAGTCAGTTT
1 AATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGAGTCTGTTT
*
6267873 GAGAACATCCGAGAGTCT
66 GAGAACATCTGAGAGTCT
6267891 AATCTGCTATGTCCTCGATTTGTTCCTTGTAA
1 AATCTGCTATGTCCTCGATTTGTTCCTTGTAA
6267923 TCTTGAGTCT
Statistics
Matches: 507, Mismatches: 22, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
82 11 0.02
83 496 0.98
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (83 bp):
AATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGAGTCTGTTT
GAGAACATCTGAGAGTCT
Found at i:6267959 original size:64 final size:64
Alignment explanation
Indices: 6267858--6267986 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
6267848 ACGCCAAACC
6267858 ATCTTGAGTCAGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTA
1 ATCTTGAGTCAGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTA
*
6267922 ATCTTGAGTCTGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTA
1 ATCTTGAGTCAGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTA
6267986 A
1 A
6267987 ATACAAGGAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (64 bp):
ATCTTGAGTCAGTTTGAGAACATCCGAGAGTCTAATCTGCTATGTCCTCGATTTGTTCCTTGTA
Found at i:6268091 original size:44 final size:44
Alignment explanation
Indices: 6268043--6268222 Score: 213
Period size: 44 Copynumber: 4.1 Consensus size: 44
6268033 TGAAGGTTAG
*
6268043 ATCTGTTATCTTCAATCTGTTCCCTATAAACACAGGGATGCCAA
1 ATCTGCTATCTTCAATCTGTTCCCTATAAACACAGGGATGCCAA
*
6268087 ATCTGCTATCTTCAA-CTCGTTCCCTATGAACACAGGGATGCC--
1 ATCTGCTATCTTCAATCT-GTTCCCTATAAACACAGGGATGCCAA
** * * * * * *
6268129 ATGCTGAAATCTTCAATCTGCTTCGCTGTAAGCACAGGAATGTCAG
1 AT-CTGCTATCTTCAATCTG-TTCCCTATAAACACAGGGATGCCAA
*
6268175 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAA
1 ATCTGCTATCTTCAATCTGTTCCCTATAAACACAGGGATGCCAA
6268219 ATCT
1 ATCT
6268223 TGTTTCTTTT
Statistics
Matches: 111, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
42 2 0.02
43 14 0.13
44 79 0.71
45 14 0.13
46 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (44 bp):
ATCTGCTATCTTCAATCTGTTCCCTATAAACACAGGGATGCCAA
Found at i:6268184 original size:88 final size:87
Alignment explanation
Indices: 6268050--6268217 Score: 239
Period size: 88 Copynumber: 1.9 Consensus size: 87
6268040 TAGATCTGTT
*
6268050 ATCTTCAATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAA-CTCGTTCCCTAT
1 ATCTTCAATCTGTTCCCTATAAACACAGGAATGCCAAATCTGCTATCTTCAATCT-GTTCCCTAT
*
6268114 GAACACAGGGATGCCATGCTGAA
65 AAACACAGGGATGCCATGCTGAA
* * * * * *
6268137 ATCTTCAATCTGCTTCGCTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATCTGTTCCCTAT
1 ATCTTCAATCTG-TTCCCTATAAACACAGGAATGCCAAATCTGCTATCTTCAATCTGTTCCCTAT
6268202 AAACACAGGGATGCCA
65 AAACACAGGGATGCCA
6268218 AATCTTGTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
87 12 0.17
88 57 0.80
89 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (87 bp):
ATCTTCAATCTGTTCCCTATAAACACAGGAATGCCAAATCTGCTATCTTCAATCTGTTCCCTATA
AACACAGGGATGCCATGCTGAA
Found at i:6269141 original size:6 final size:6
Alignment explanation
Indices: 6269130--6269225 Score: 80
Period size: 6 Copynumber: 16.8 Consensus size: 6
6269120 GGCCTCTCTA
* * *
6269130 TTTTTC TTTTTC TTTTT- TTTTCC TTTCT- TTTTTC TTTTTTA TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC
* *
6269177 -CTTTC TTTTTTA TTTTTC -TTTTC -TTTTC TTTTTC -TTTTC TTTTT-
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
6269221 TTTTT
1 TTTTT
6269226 GAAATAGAAG
Statistics
Matches: 73, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
5 32 0.44
6 33 0.45
7 8 0.11
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:6269145 original size:5 final size:5
Alignment explanation
Indices: 6269131--6269223 Score: 70
Period size: 5 Copynumber: 18.8 Consensus size: 5
6269121 GCCTCTCTAT
* * *
6269131 TTTTC TTTTTC TTTTT TTTTC CTTTC TTTT- TTCTT- TTTTAT TTTTC
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTT-C TTTTC
* *
6269177 CTTTC TTTT- TTAT- TTTTC TTTTC TTTTC TTTTTC TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTT
6269224 TTGAAATAGA
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
4 14 0.19
5 45 0.62
6 14 0.19
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:6269150 original size:11 final size:11
Alignment explanation
Indices: 6269130--6269225 Score: 86
Period size: 11 Copynumber: 8.4 Consensus size: 11
6269120 GGCCTCTCTA
6269130 TTTTTCTTTTTC
1 TTTTT-TTTTTC
*
6269142 TTTTTTTTTCC
1 TTTTTTTTTTC
*
6269153 TTTCTTTTTTC
1 TTTTTTTTTTC
6269164 TTTTTTATTTTTCC
1 -TTTTT-TTTTT-C
* *
6269178 TTTCTTTTTTA
1 TTTTTTTTTTC
*
6269189 TTTTTCTTTTC
1 TTTTTTTTTTC
*
6269200 TTTTCTTTTTC
1 TTTTTTTTTTC
6269211 TTTTCTTTTTT-
1 TTTT-TTTTTTC
6269222 TTTT
1 TTTT
6269226 GAAATAGAAG
Statistics
Matches: 68, Mismatches: 12, Indels: 9
0.76 0.13 0.10
Matches are distributed among these distances:
11 39 0.57
12 19 0.28
13 9 0.13
14 1 0.01
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:6275471 original size:35 final size:35
Alignment explanation
Indices: 6275413--6275554 Score: 241
Period size: 35 Copynumber: 4.0 Consensus size: 35
6275403 AATCATATCT
6275413 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
6275450 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
6275485 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
6275520 TCT-AGCATTGTATCATATCTAAGATTGCATATCAT
1 TCTAAG-ATTGTATCATATCTAAGATTGCA-ATCAT
6275555 TGAAGATTAA
Statistics
Matches: 103, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
34 2 0.02
35 86 0.83
36 5 0.05
37 10 0.10
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:6279945 original size:3 final size:3
Alignment explanation
Indices: 6279887--6279929 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
6279877 TGTTTTAAAA
6279887 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6279930 TTGAACCGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6280004 original size:17 final size:16
Alignment explanation
Indices: 6279982--6280020 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
6279972 TATTAAACGG
6279982 TTTTATATATATATGTA
1 TTTTATATATAT-TGTA
* *
6279999 TTTTATATGTATTTTA
1 TTTTATATATATTGTA
6280015 TTTTAT
1 TTTTAT
6280021 TTTAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (16 bp):
TTTTATATATATTGTA
Found at i:6280007 original size:11 final size:11
Alignment explanation
Indices: 6279991--6280024 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6279981 GTTTTATATA
6279991 TATATGTATTT
1 TATATGTATTT
6280002 TATATGTATTT
1 TATATGTATTT
*
6280013 TAT-TTTATTT
1 TATATGTATTT
6280023 TA
1 TA
6280025 AATATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (11 bp):
TATATGTATTT
Found at i:6280089 original size:26 final size:26
Alignment explanation
Indices: 6280060--6280109 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
6280050 TATCTGTTAA
*
6280060 TTTAAATTGTTTTATAAATTATTTAT
1 TTTAAATTATTTTATAAATTATTTAT
* *
6280086 TTTAAGTTATTTTATACATTATTT
1 TTTAAATTATTTTATAAATTATTT
6280110 TATTGCTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTAAATTATTTTATAAATTATTTAT
Found at i:6283750 original size:10 final size:10
Alignment explanation
Indices: 6283735--6283773 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
6283725 TATACAAGTT
6283735 AAAAAAATCG
1 AAAAAAATCG
*
6283745 AAAAAAATTCA
1 AAAAAAA-TCG
6283756 AAAAAAATCG
1 AAAAAAATCG
6283766 AAAAAAAT
1 AAAAAAAT
6283774 GTGATTTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (10 bp):
AAAAAAATCG
Found at i:6283751 original size:11 final size:11
Alignment explanation
Indices: 6283735--6283772 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
6283725 TATACAAGTT
6283735 AAAAAAATCGA
1 AAAAAAATCGA
*
6283746 AAAAAATTC-A
1 AAAAAAATCGA
6283756 AAAAAAATCGA
1 AAAAAAATCGA
6283767 AAAAAA
1 AAAAAA
6283773 TGTGATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.76, C:0.08, G:0.05, T:0.11
Consensus pattern (11 bp):
AAAAAAATCGA
Found at i:6289862 original size:28 final size:29
Alignment explanation
Indices: 6289797--6289895 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
6289787 CATGAGATTG
* *
6289797 GCACTAAGTGTGCG-GGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGGTTC-GATTATATA
6289826 GCACTAAGTGTGCGAGGTT-GATTATATA
1 GCACTAAGTGTGCGAGGTTCGATTATATA
*
6289854 GCACTAAGTGTGCGA-GTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGGTTCGATTATAT-A
6289882 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
6289896 GGCTTATTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
27 4 0.06
28 42 0.66
29 14 0.22
30 4 0.06
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGGTTCGATTATATA
Done.