Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 141 of 208
Found at i:43190358 original size:174 final size:174
Alignment explanation
Indices: 43190097--43190500 Score: 583
Period size: 174 Copynumber: 2.3 Consensus size: 174
43190087 AAGAAGATTG
* * ** ** * *
43190097 GATTCGCTGCCTTTAGCTTTAATCTGCTCTGCTATAACACCAGGGAAACAAGATTCTCTACCTTT
1 GATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAAACAAGATTCTCTACCTTT
* * * * *
43190162 AGCTTTAATCTGTTCCACTGTAAGGCCAAGCAGATAGGATTCGCTGCCTTCATCTTTAATCCATT
66 AGCTTTAATCTGTTCCACTGTAACGCCAAGCAGATAGGATTCGCTACCTTCAGCTTTAATACACT
* *
43190227 CCACTTCAACTTTAATTTATTCCAGTGCAACGCTAGGGAAATAT
131 CCACTTCAACTTTAATCTATTCCAGTGCAACGCTAGGGAAATAA
43190271 GATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAAACAAGATTCTCTACCTTT
1 GATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAAACAAGATTCTCTACCTTT
* * *
43190336 AGCTTTAATCTGTTCTACTGTAACGCCAAGGAGATAGGATTCGCTACCTTCAGCTTTAATACGCT
66 AGCTTTAATCTGTTCCACTGTAACGCCAAGCAGATAGGATTCGCTACCTTCAGCTTTAATACACT
* *
43190401 CCACTTCATCTTTAATCTATTCTAGTGCAACGCTAGGGAAATAA
131 CCACTTCAACTTTAATCTATTCCAGTGCAACGCTAGGGAAATAA
* * * * *
43190445 GATTCGCTATCTTTAGCTTTAATCTGTTCCACGGCAATGCCAAAGAAAAAAGATTC
1 GATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAAACAAGATTC
43190501 GCTGCCTACA
Statistics
Matches: 205, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
174 205 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (174 bp):
GATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAAACAAGATTCTCTACCTTT
AGCTTTAATCTGTTCCACTGTAACGCCAAGCAGATAGGATTCGCTACCTTCAGCTTTAATACACT
CCACTTCAACTTTAATCTATTCCAGTGCAACGCTAGGGAAATAA
Found at i:43191947 original size:88 final size:89
Alignment explanation
Indices: 43191810--43192006 Score: 369
Period size: 88 Copynumber: 2.2 Consensus size: 89
43191800 CAAGGTGCCC
43191810 TTTGCGAGTTTTCACCTTGGCCTCTTCTTTTTCTTTTTCTTCTTTCTTATTATTATTTTTTATAT
1 TTTGCGAGTTTTCACCTTGGCCTCTTCTTTTTCTTTTTCTTCTTTCTTATTATTATTTTTTATAT
43191875 TA-TTTTTATGACTCAAAGCACCA
66 TATTTTTTATGACTCAAAGCACCA
43191898 TTTGCGAGTTTTCACCTTGGCCTCTTCTTTTTCTTTTTCTTCTTTCTTATTATTATTTTTTATAT
1 TTTGCGAGTTTTCACCTTGGCCTCTTCTTTTTCTTTTTCTTCTTTCTTATTATTATTTTTTATAT
*
43191963 TATTTTTTATGACTCAAAGCACCC
66 TATTTTTTATGACTCAAAGCACCA
*
43191987 TTTGCGGGTTTTCACCTTGG
1 TTTGCGAGTTTTCACCTTGG
43192007 TCTTTTTTTT
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
88 67 0.63
89 39 0.37
ACGTcount: A:0.15, C:0.20, G:0.10, T:0.55
Consensus pattern (89 bp):
TTTGCGAGTTTTCACCTTGGCCTCTTCTTTTTCTTTTTCTTCTTTCTTATTATTATTTTTTATAT
TATTTTTTATGACTCAAAGCACCA
Found at i:43191965 original size:12 final size:12
Alignment explanation
Indices: 43191948--43191972 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43191938 TCTTTCTTAT
43191948 TATTATTTTTTA
1 TATTATTTTTTA
43191960 TATTATTTTTTA
1 TATTATTTTTTA
43191972 T
1 T
43191973 GACTCAAAGC
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:43192034 original size:46 final size:44
Alignment explanation
Indices: 43191965--43192094 Score: 154
Period size: 46 Copynumber: 2.9 Consensus size: 44
43191955 TTTTATATTA
* * *
43191965 TTTTTTATG-ACTCAAAGCACCCTTTGCGGGTTTTCACCTTGGTC
1 TTTTTTA-GAACTCAAAGCGCCCTTTACGGGTTTTCACCTTAGTC
* * *
43192009 TTTTTTTTAGAACTTAAGGCGCCCTTTACCGGTTTTCACCTTAGTC
1 --TTTTTTAGAACTCAAAGCGCCCTTTACGGGTTTTCACCTTAGTC
* *
43192055 TTTTTTAGAACTCAAAGCGCCCTTTACGAGTTTTCGCCTT
1 TTTTTTAGAACTCAAAGCGCCCTTTACGGGTTTTCACCTT
43192095 TGTCCCTTCT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
44 35 0.49
45 1 0.01
46 36 0.50
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.42
Consensus pattern (44 bp):
TTTTTTAGAACTCAAAGCGCCCTTTACGGGTTTTCACCTTAGTC
Found at i:43193009 original size:11 final size:11
Alignment explanation
Indices: 43192995--43193037 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
43192985 GGCCTCTCCT
*
43192995 TTTTCTTTTCC
1 TTTTCTTTTTC
43193006 TTTTCTTTTTC
1 TTTTCTTTTTC
*
43193017 TTCTCTTTTTC
1 TTTTCTTTTTC
43193028 TTTTCTTTTT
1 TTTTCTTTTT
43193038 TCATCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:43193015 original size:17 final size:17
Alignment explanation
Indices: 43192993--43193036 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
43192983 TTGGCCTCTC
43192993 CTTTTTCTTTTCCTTTT
1 CTTTTTCTTTTCCTTTT
* *
43193010 CTTTTTCTTCTCTTTTT
1 CTTTTTCTTTTCCTTTT
43193027 C-TTTTCTTTT
1 CTTTTTCTTTT
43193037 TTCATCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
CTTTTTCTTTTCCTTTT
Found at i:43193037 original size:6 final size:6
Alignment explanation
Indices: 43192993--43193037 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
43192983 TTGGCCTCTC
* *
43192993 CTTTTT C-TTTT CCTTTT CTTTTT C-TTCT CTTTTT C-TTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
43193038 TCATCATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
5 14 0.42
6 19 0.58
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:43193053 original size:22 final size:21
Alignment explanation
Indices: 43193000--43193057 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
43192990 CTCCTTTTTC
*
43193000 TTTTCCTTTTCTTTTTCTTCTCT
1 TTTT-CTTTTC-TTTTCTTCTCA
43193023 TTTTCTTTTCTTTT-TTCATCA
1 TTTTCTTTTCTTTTCTTC-TCA
43193044 TTTTCATTTT-TTTT
1 TTTTC-TTTTCTTTT
43193058 AAATATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.09
21 15 0.47
22 10 0.31
23 4 0.12
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTCTTTTCTTCTCA
Found at i:43198036 original size:26 final size:26
Alignment explanation
Indices: 43197979--43198037 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
43197969 AGCTTTTATA
*
43197979 AACCCAATTAACCTAGCCCAAAATCT
1 AACCCAATTAACCTAGCCCAAAACCT
43198005 AACCCAATTAACCTAGCCC-AAACCT
1 AACCCAATTAACCTAGCCCAAAACCT
43198030 AAGCCCAA
1 AA-CCCAA
43198038 CACCCTACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 7 0.23
26 24 0.77
ACGTcount: A:0.42, C:0.37, G:0.05, T:0.15
Consensus pattern (26 bp):
AACCCAATTAACCTAGCCCAAAACCT
Found at i:43198044 original size:25 final size:25
Alignment explanation
Indices: 43197979--43198050 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
43197969 AGCTTTTATA
* *
43197979 AACCCAATTAACCTAGCCCAAAATCT
1 AACCCAATCAACCTAGCCC-AAACCT
*
43198005 AACCCAATTAACCTAGCCCAAACCT
1 AACCCAATCAACCTAGCCCAAACCT
* *
43198030 AAGCCCAA-CACCCTACCCCAA
1 AA-CCCAATCAACCTAGCCCAA
43198051 CCGGCCTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
25 17 0.41
26 24 0.59
ACGTcount: A:0.40, C:0.42, G:0.04, T:0.14
Consensus pattern (25 bp):
AACCCAATCAACCTAGCCCAAACCT
Found at i:43199378 original size:4 final size:4
Alignment explanation
Indices: 43199371--43199441 Score: 142
Period size: 4 Copynumber: 17.8 Consensus size: 4
43199361 TCATATATAT
43199371 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
43199419 ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATA
43199442 ATCCATTGTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:43205027 original size:8 final size:8
Alignment explanation
Indices: 43205006--43205056 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
43204996 TTTGAGTCCA
43205006 AAAAAATG
1 AAAAAATG
*
43205014 TGAAAAATG
1 -AAAAAATG
43205023 AAAAAATG
1 AAAAAATG
43205031 AAAAAATG
1 AAAAAATG
43205039 --AAAATG
1 AAAAAATG
43205045 -AAAAATG
1 AAAAAATG
43205052 AAAAA
1 AAAAA
43205057 GTAAAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
6 6 0.16
7 6 0.16
8 19 0.50
9 7 0.18
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (8 bp):
AAAAAATG
Found at i:43205042 original size:14 final size:13
Alignment explanation
Indices: 43205014--43205055 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 13
43205004 CAAAAAAATG
43205014 TGAAAAATGAAAAAA
1 TGAAAAATG--AAAA
43205029 TGAAAAAATGAAAA
1 TG-AAAAATGAAAA
43205043 TGAAAAATGAAAA
1 TGAAAAATGAAAA
43205056 AGTAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.42
14 6 0.23
15 2 0.08
16 7 0.27
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
TGAAAAATGAAAA
Found at i:43205062 original size:14 final size:13
Alignment explanation
Indices: 43205015--43205064 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
43205005 AAAAAAATGT
43205015 GAAAAATGAAAAAA
1 GAAAAATG-AAAAA
*
43205029 TGAAAAAATGAAAAT
1 -G-AAAAATGAAAAA
43205044 GAAAAATGAAAAA
1 GAAAAATGAAAAA
43205057 GTAAAAAT
1 G-AAAAAT
43205065 AGAGAGGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 12 0.39
14 7 0.23
15 5 0.16
16 7 0.23
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
GAAAAATGAAAAA
Found at i:43206437 original size:50 final size:50
Alignment explanation
Indices: 43206379--43206538 Score: 164
Period size: 50 Copynumber: 3.2 Consensus size: 50
43206369 GCAGTGGAAC
* * *
43206379 AGATTAAAGCCATATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCAGACATTGAAGTTAAAA
* * * * * * ** *
43206429 AGATTAAAGCTACAACAGCGAATCTTAC-TCCCTAGGCGA-TGCAA-TGGAAT
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCC-AGAC-ATTG-AAGTTAAAA
43206479 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCAGACATTGAAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCAGACATTGAAGTTAAAA
43206529 AGATTAAAGC
1 AGATTAAAGC
43206539 TACAACAGCG
Statistics
Matches: 83, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
49 7 0.08
50 70 0.84
51 6 0.07
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (50 bp):
AGATTAAAGCCACATCGGTGAATCTTGCTTCCCAGACATTGAAGTTAAAA
Found at i:43206643 original size:36 final size:36
Alignment explanation
Indices: 43206603--43206675 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
43206593 TCTTGCTTCC
43206603 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAG
1 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAG
43206639 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAG
1 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAG
43206675 C
1 C
43206676 GAATCTTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (36 bp):
CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAG
Found at i:43206730 original size:50 final size:50
Alignment explanation
Indices: 43206674--43206782 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 50
43206664 AGCTACAACA
* * *
43206674 GCGAATCTTACTCCCTAGGC-GATGCAGTGGAACAGATTAAAGCCACATTG
1 GCGAATCTTACTCCCTAAGCAG-TGCAGTGGAACAGATAAAAGCCACAATG
* * * *
43206724 GTGAATCTTGCTTCTTAAGCAGTGCAGTGGAACAGATAAAAGCCACAATG
1 GCGAATCTTACTCCCTAAGCAGTGCAGTGGAACAGATAAAAGCCACAATG
43206774 GCGAATCTT
1 GCGAATCTT
43206783 GCTTCCCCGA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
50 49 0.98
51 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (50 bp):
GCGAATCTTACTCCCTAAGCAGTGCAGTGGAACAGATAAAAGCCACAATG
Found at i:43206900 original size:95 final size:93
Alignment explanation
Indices: 43206368--43206920 Score: 513
Period size: 100 Copynumber: 5.9 Consensus size: 93
43206358 TCCCAGGCGA
* * * *
43206368 TGCAGTGGAACAGATTAAAGCCA-TATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAAAGA
1 TGCAGTGGAACAGATAAAAGCCACAAT-GGCGAATCTTGCTTCCCCGACATTGAAGTTAAAAAGA
43206432 TTAAAGCTACAACAGCGAATCTTACTCCCTAGGC-G
65 TTAAAGCTACAACAGCGAATCTTA------A-GCAG
* * * * *
43206467 ATGCAATGGAATAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCCAGACATTGAAGTTAAAAAG
1 -TGCAGTGGAACAGATAAAAGCCACAAT-GGCGAATCTTGCTTCCCCGACATTGAAGTTAAAAAG
43206531 ATTAAAGCTACAACAGCGAATCTTAAGCAG
64 ATTAAAGCTACAACAGCGAATCTTAAGCAG
* *
43206561 TGCAGTGGAACAGATTAAAGCCACAATGGC-AATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
1 TGCAGTGGAACAGATAAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGAAGTTAAAAAGAT
* *
43206625 TAAAGCTACAACAGC----C--GA-CAT
66 TAAAGCTACAACAGCGAATCTTAAGCAG
** * * * ** * * * * ** *
43206646 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC-TCCCTAGGCGA-TGCAGTGGAACAG
1 TGCAGTGGAACAGATAAAAGCCACAATGGCGAATCTTGCTTCCC-CGAC-ATTGAAGTTAAAAAG
* *** *
43206709 ATTAAAGCCACATTGGTGAATCTTGCTTCTTAAGCAG
64 ATTAAAGCTACAACAGCGAA-------TCTTAAGCAG
43206746 TGCAGTGGAACAGATAAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGAAGTTAAAAAGAT
1 TGCAGTGGAACAGATAAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGAAGTTAAAAAGAT
43206811 TAAAAGCTACAAACAGCGAATCTTAAGCAG
66 T-AAAGCTAC-AACAGCGAATCTTAAGCAG
*
43206841 TGCAGTGGAACAGATTAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGCAA-TTAAAAAGA
1 TGCAGTGGAACAGATAAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTG-AAGTTAAAAAGA
43206905 TTAAAGCTACAACAGC
65 TTAAAGCTACAACAGC
43206921 CGACATTGCA
Statistics
Matches: 378, Mismatches: 50, Indels: 57
0.78 0.10 0.12
Matches are distributed among these distances:
85 30 0.08
86 32 0.08
87 1 0.00
88 1 0.00
92 47 0.12
93 32 0.08
94 12 0.03
95 72 0.19
96 2 0.01
97 1 0.00
99 2 0.01
100 130 0.34
101 11 0.03
102 5 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (93 bp):
TGCAGTGGAACAGATAAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGAAGTTAAAAAGAT
TAAAGCTACAACAGCGAATCTTAAGCAG
Found at i:43206936 original size:36 final size:36
Alignment explanation
Indices: 43206884--43206956 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
43206874 TCTTGCTTCC
43206884 CCGACATTGCAATTAAAAAGATTAAAGCTACAACAG
1 CCGACATTGCAATTAAAAAGATTAAAGCTACAACAG
*
43206920 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAG
1 CCGACATTGCAATTAAAAAGATTAAAGCTACAACAG
43206956 C
1 C
43206957 GAATCTTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (36 bp):
CCGACATTGCAATTAAAAAGATTAAAGCTACAACAG
Found at i:43206944 original size:281 final size:278
Alignment explanation
Indices: 43206468--43207018 Score: 978
Period size: 281 Copynumber: 2.0 Consensus size: 278
43206458 CCCTAGGCGA
* * *
43206468 TGCAATGGAATAGATTAAAGCCACATCGGTGAATCTTGCTTCCCAGACATTGAAGTTAAAAAGAT
1 TGCAATGGAACAGATAAAAGCCACATCGGCGAATCTTGCTTCCCAGACATTGAAGTTAAAAAGAT
43206533 TAAAGCTACAACAGCGAATCTTAAGCAGTGCAGTGGAACAGATTAAAGCCACAATGGCAATCTTG
66 TAAAGCTACAACAGCGAATCTTAAGCAGTGCAGTGGAACAGATTAAAGCCACAATGGCAATCTTG
*
43206598 CTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCCGACATTGCAGTTAAAAAGATTA
131 CTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACAACAGCCGACATTGCAGTTAAAAAGATTA
*
43206663 AAGCTACAACAGCGAATCTTACTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATTGGTGA
196 AAGCTACAACAGCGAATCTTACTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGA
*
43206728 ATCTTGCTTCTTAAGCAG
261 ATCTTACTTCTTAAGCAG
* *
43206746 TGCAGTGGAACAGATAAAAGCCACAAT-GGCGAATCTTGCTTCCCCGACATTGAAGTTAAAAAGA
1 TGCAATGGAACAGATAAAAGCCAC-ATCGGCGAATCTTGCTTCCCAGACATTGAAGTTAAAAAGA
43206810 TTAAAAGCTACAAACAGCGAATCTTAAGCAGTGCAGTGGAACAGATTAAAGCCACAATGGCGAAT
65 TT-AAAGCTAC-AACAGCGAATCTTAAGCAGTGCAGTGGAACAGATTAAAGCCACAATGGC-AAT
43206875 CTTGCTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACAACAGCCGACATTGCAGTTAAAAAG
127 CTTGCTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACAACAGCCGACATTGCAGTTAAAAAG
*
43206940 ATTAAAGCTACAACAGCGAATCTTACTCCCTAGGCGGTGCAGTGGAACAGATTAAAGCCACATCG
192 ATTAAAGCTACAACAGCGAATCTTACTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATCG
43207005 GTGAATCTTACTTC
257 GTGAATCTTACTTC
43207019 CCCGACATTG
Statistics
Matches: 260, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
278 58 0.22
279 10 0.04
280 49 0.19
281 143 0.55
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (278 bp):
TGCAATGGAACAGATAAAAGCCACATCGGCGAATCTTGCTTCCCAGACATTGAAGTTAAAAAGAT
TAAAGCTACAACAGCGAATCTTAAGCAGTGCAGTGGAACAGATTAAAGCCACAATGGCAATCTTG
CTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACAACAGCCGACATTGCAGTTAAAAAGATTA
AAGCTACAACAGCGAATCTTACTCCCTAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGA
ATCTTACTTCTTAAGCAG
Found at i:43207028 original size:136 final size:129
Alignment explanation
Indices: 43206513--43207056 Score: 610
Period size: 136 Copynumber: 4.0 Consensus size: 129
43206503 TTGCTTCCCA
43206513 GACATTGAAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTAAGCAGTGCAGTGGAACAGATTA
1 GACATTGAAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTAAGCAGTGCAGTGGAACAGATTA
*
43206578 AAGCCACAATGG-CAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCC
66 AAGCCACAATGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCC
*
43206641 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCTAGGC-GATGCAGTGGA
1 GACATTGAAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTA------A-GCAG-TGCAGTGGA
* *** * ** * * *
43206705 ACAGATTAAAGCCACATTGGTGAATCTTGCTT-CTTAAGCAGTGCAGTGGAACAGATAAAAGCCA
58 ACAGATTAAAGCCACAATGGTGAATCTTGCTTCCCCGA-CATTGCAGTTAAAAAGATTAAAGCTA
43206769 CAATGGCGAATCTTGCTTCCCC
122 CAA---C--A----G-----CC
43206791 GACATTGAAGTTAAAAAGATTAAAAGCTACAAACAGCGAATCTTAAGCAGTGCAGTGGAACAGAT
1 GACATTGAAGTTAAAAAGATT-AAAGCTAC-AACAGCGAATCTTAAGCAGTGCAGTGGAACAGAT
* *
43206856 TAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACAACAGC
64 TAAAGCCACAATGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
43206921 C
129 C
* *
43206922 GACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCTAGGCGGTGCAGTGGAA
1 GACATTGAAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTA------A-GCAGTGCAGTGGAA
*
43206987 CAGATTAAAGCCAC-ATCGGTGAATCTTACTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTAC
59 CAGATTAAAGCCACAAT-GGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTAC
43207051 AACAGC
123 AACAGC
43207057 GAATCTTACT
Statistics
Matches: 350, Mismatches: 30, Indels: 64
0.79 0.07 0.14
Matches are distributed among these distances:
128 42 0.12
129 14 0.04
130 8 0.02
131 22 0.06
134 2 0.01
135 35 0.10
136 111 0.32
139 1 0.00
140 1 0.00
141 1 0.00
142 1 0.00
145 64 0.18
146 4 0.01
150 22 0.06
151 8 0.02
152 14 0.04
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (129 bp):
GACATTGAAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTAAGCAGTGCAGTGGAACAGATTA
AAGCCACAATGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCC
Found at i:43207093 original size:100 final size:100
Alignment explanation
Indices: 43206920--43207446 Score: 761
Period size: 100 Copynumber: 5.3 Consensus size: 100
43206910 GCTACAACAG
* *
43206920 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCTAGGCGGTGCAGTGG
1 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
* *
43206985 AACAGATTAAAGCCACATCGGTGAATCTTACTTCC
66 AACAGATTAAAGCCACATCGGCGAATCTTGCTTCC
43207020 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
1 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
*
43207085 AATAGATTAAAGCCACAAT-GGCGAATCTTGCTTCC
66 AACAGATTAAAGCCAC-ATCGGCGAATCTTGCTTCC
*
43207120 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTACTCCCCAAGCGGTGCAGTGG
1 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
* *
43207185 AATAGATTAAAGCCACAAT-GGCGAACCTTGCTTCC
66 AACAGATTAAAGCCAC-ATCGGCGAATCTTGCTTCC
* * *
43207220 CCGACATTGCAGTTAAAAAGATTAAAGCTAGAACAGCGAATCTTACTTCTCAAGCGGTGCAGTGG
1 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
* * *
43207285 AACAGATTAACGCCACAACGGTGAATCTTGCTTCC
66 AACAGATTAAAGCCACATCGGCGAATCTTGCTTCC
* * * * * * *
43207320 TCGATATTGCAGTTAGAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGTAATGG
1 CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
* * * *
43207385 AACAGATTGAAGCTACAACAGCGAATCTTGCTTCC
66 AACAGATTAAAGCCACATCGGCGAATCTTGCTTCC
* ** *
43207420 TCGACATCACAGTTAAACAGATTAAAG
1 CCGACATTGCAGTTAAAAAGATTAAAG
43207447 TTACGAGTTA
Statistics
Matches: 391, Mismatches: 34, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
99 1 0.00
100 388 0.99
101 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (100 bp):
CCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
AACAGATTAAAGCCACATCGGCGAATCTTGCTTCC
Found at i:43207419 original size:50 final size:50
Alignment explanation
Indices: 43206935--43207419 Score: 400
Period size: 50 Copynumber: 9.7 Consensus size: 50
43206925 ATTGCAGTTA
43206935 AAAAGATTAAAGCTACAACAGCGAATCTTAC-TCCCTAGGCGGTGCAGTGG
1 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCC-AGGCGGTGCAGTGG
* * * * * * * ** **
43206985 AACAGATTAAAGCCACATCGGTGAATCTTACTTCCCCGACATTGCAGTTA
1 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGG
* *
43207035 AAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGGTGCAGTGG
1 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGG
* * ** * * * ** **
43207085 AATAGATTAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGCAGTTA
1 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGG
* * *
43207135 AAAAGATTAAAGCTACAACAGTGAATCTTACTCCCCAAGCGGTGCAGTGG
1 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGG
* * ** * * * * ** **
43207185 AATAGATTAAAGCCACAATGGCGAACCTTGCTTCCCCGACATTGCAGTTA
1 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGG
* * *
43207235 AAAAGATTAAAGCTAGAACAGCGAATCTTACTTCTCAAGCGGTGCAGTGG
1 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGG
* * * * * * **** *
43207285 AACAGATTAACGCCACAACGGTGAATCTTGCTTCCTC-GATATTGCAGT-T
1 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCC-CAGGCGGTGCAGTGG
* *
43207334 AGAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGTAATGG
1 A-AAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGG
* * *
43207385 AACAGATTGAAGCTACAACAGCGAATCTTGCTTCC
1 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCC
43207420 TCGACATCAC
Statistics
Matches: 319, Mismatches: 111, Indels: 10
0.73 0.25 0.02
Matches are distributed among these distances:
49 2 0.01
50 311 0.97
51 6 0.02
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (50 bp):
AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGG
Found at i:43207976 original size:13 final size:13
Alignment explanation
Indices: 43207958--43207982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43207948 AACATATTGT
43207958 ATTTTTATTTTAG
1 ATTTTTATTTTAG
43207971 ATTTTTATTTTA
1 ATTTTTATTTTA
43207983 TTTTCCTTTT
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:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
ATTTTTATTTTAG
Found at i:43208941 original size:4 final size:4
Alignment explanation
Indices: 43208942--43209040 Score: 189
Period size: 4 Copynumber: 24.8 Consensus size: 4
43208932 ATATATATAT
*
43208942 ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
43208990 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
43209038 ATA
1 ATA
43209041 ATCCATTGTT
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 93 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:43210479 original size:3 final size:3
Alignment explanation
Indices: 43210471--43210512 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
43210461 ATAAGTAAAT
* *
43210471 ATA ATA ATA ATA ATA GTA GTA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
43210513 CAAAGATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:43210555 original size:21 final size:23
Alignment explanation
Indices: 43210518--43210565 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
43210508 TAATACAAAG
43210518 ATAATGGTATAATATAA-T-AAT
1 ATAATGGTATAATATAAGTAAAT
*
43210539 ATAATGGTAATGA-ATAAGTAAAT
1 ATAATGGT-ATAATATAAGTAAAT
43210562 ATAA
1 ATAA
43210566 AAAGAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 12 0.52
22 4 0.17
23 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (23 bp):
ATAATGGTATAATATAAGTAAAT
Found at i:43216509 original size:22 final size:21
Alignment explanation
Indices: 43216484--43216536 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
43216474 GAAATTGGTT
43216484 ATATATATTGCACTTAT-ATATA
1 ATATATATTG--CTTATAATATA
43216506 ATATAT-TGTGCTTATAGATATA
1 ATATATAT-TGCTTATA-ATATA
43216528 ATATATATT
1 ATATATATT
43216537 ATTAGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
20 5 0.19
21 1 0.04
22 20 0.74
23 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (21 bp):
ATATATATTGCTTATAATATA
Found at i:43216511 original size:20 final size:21
Alignment explanation
Indices: 43216486--43216533 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
43216476 AATTGGTTAT
43216486 ATATATTGCACTTAT-ATATA
1 ATATATTGCACTTATAATATA
**
43216506 ATATATTGTGCTTATAGATATA
1 ATATATTGCACTTATA-ATATA
43216528 ATATAT
1 ATATAT
43216534 ATTATTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
22 11 0.46
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (21 bp):
ATATATTGCACTTATAATATA
Found at i:43219926 original size:22 final size:22
Alignment explanation
Indices: 43219901--43219951 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
43219891 CATCAAAATG
43219901 TATATACAAATATAATATTTAT
1 TATATACAAATATAATATTTAT
*
43219923 TATATACGAATATAATATTTAT
1 TATATACAAATATAATATTTAT
43219945 TATATAC
1 TATATAC
43219952 CTATGTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (22 bp):
TATATACAAATATAATATTTAT
Found at i:43226038 original size:132 final size:131
Alignment explanation
Indices: 43225902--43226165 Score: 449
Period size: 132 Copynumber: 2.0 Consensus size: 131
43225892 AATAACAGCC
*
43225902 ACAATAACTGCAACACTCTTTTCAACCACAACCTGAAATGGTTCGTCC-GACTCAACCTGCTTCA
1 ACAATAACTGCAACACCCTTTTCAACCACAACCTGAAATGGTTCG-CCTGACTCAACCTGCTTCA
* *
43225966 CCTGTGCGTACTACGACTCCCCATAAGGTTGATCCTATTCGAGAAATTCAAAAAAGAGGTGTCAA
65 CCT-TGCCTACTACGACTCCCCATAAGGTTGATCCTATTCGAGAAATTCAAAAAAGAGGCGTCAA
43226031 GGA
129 GGA
43226034 ACAATAACTGCAACACCCTTTTCAACCACAACCTGAAATGGTTCGCCTGACTCAACCTGCTTCAC
1 ACAATAACTGCAACACCCTTTTCAACCACAACCTGAAATGGTTCGCCTGACTCAACCTGCTTCAC
* * *
43226099 CTTGCCTACTATGACTCCTCATAAGGTTGATCCTATTTGAGAAATTCAAAAAAGAGGCGTCAAGG
66 CTTGCCTACTACGACTCCCCATAAGGTTGATCCTATTCGAGAAATTCAAAAAAGAGGCGTCAAGG
43226164 A
131 A
43226165 A
1 A
43226166 TTTATTGGTG
Statistics
Matches: 125, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
131 62 0.50
132 63 0.50
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (131 bp):
ACAATAACTGCAACACCCTTTTCAACCACAACCTGAAATGGTTCGCCTGACTCAACCTGCTTCAC
CTTGCCTACTACGACTCCCCATAAGGTTGATCCTATTCGAGAAATTCAAAAAAGAGGCGTCAAGG
A
Found at i:43230497 original size:41 final size:39
Alignment explanation
Indices: 43230452--43230582 Score: 131
Period size: 40 Copynumber: 3.3 Consensus size: 39
43230442 CGACTTCGAG
43230452 TCGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAAT
1 TCGATGAGACACTGGGTGTCAATTTA-TACTTCGGATT-AT
* * * * * *
43230493 TCGATGAGGCACTGGGTGCCAA-TT-TACGTCAGTTTAG
1 TCGATGAGACACTGGGTGTCAATTTATACTTCGGATTAT
* *
43230530 TCGATGAGACACTAGGTGTCAATTTATTACTTCGAATTAT
1 TCGATGAGACACTGGGTGTCAATTTA-TACTTCGGATTAT
* *
43230570 TTGATGAGGCACT
1 TCGATGAGACACT
43230583 AAGTGCCAAA
Statistics
Matches: 71, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 20 0.28
38 10 0.14
40 21 0.30
41 20 0.28
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAATTTATACTTCGGATTAT
Found at i:43230553 original size:37 final size:38
Alignment explanation
Indices: 43230450--43230555 Score: 115
Period size: 37 Copynumber: 2.7 Consensus size: 38
43230440 TTCGACTTCG
* *
43230450 AGTCGATGAGACACTGGGTGTCAATTTACTACTTCGGATTA
1 AGTCGATGAGACACTGGGTGTCAA-TT--TACGTCAGATTA
* * * *
43230491 ATTCGATGAGGCACTGGGTGCCAATTTACGTCAG-TTT
1 AGTCGATGAGACACTGGGTGTCAATTTACGTCAGATTA
*
43230528 AGTCGATGAGACACTAGGTGTCAATTTA
1 AGTCGATGAGACACTGGGTGTCAATTTA
43230556 TTACTTCGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
37 26 0.47
38 6 0.11
40 2 0.04
41 21 0.38
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (38 bp):
AGTCGATGAGACACTGGGTGTCAATTTACGTCAGATTA
Found at i:43230731 original size:14 final size:14
Alignment explanation
Indices: 43230712--43230757 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
43230702 AATGGAAGTG
43230712 AAATAGTGAATTGA
1 AAATAGTGAATTGA
43230726 AAATA--GAATGTG-
1 AAATAGTGAAT-TGA
43230738 AAATAGTGAATTGA
1 AAATAGTGAATTGA
43230752 AAATAG
1 AAATAG
43230758 AATGTGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 9 0.32
13 4 0.14
14 15 0.54
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (14 bp):
AAATAGTGAATTGA
Found at i:43230739 original size:26 final size:26
Alignment explanation
Indices: 43230701--43230768 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
43230691 ATGGTATGAG
*
43230701 AAATGGAA-GTGAAATAGTGAATTGA
1 AAATAGAATGTGAAATAGTGAATTGA
43230726 AAATAGAATGTGAAATAGTGAATTGA
1 AAATAGAATGTGAAATAGTGAATTGA
43230752 AAATAGAATGTGAAATA
1 AAATAGAATGTGAAATA
43230769 TGTTGCAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
25 7 0.17
26 34 0.83
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.25
Consensus pattern (26 bp):
AAATAGAATGTGAAATAGTGAATTGA
Found at i:43230741 original size:12 final size:12
Alignment explanation
Indices: 43230700--43230768 Score: 54
Period size: 12 Copynumber: 5.5 Consensus size: 12
43230690 CATGGTATGA
*
43230700 GAAATGGAA-GT
1 GAAATAGAATGT
43230711 GAAATAGTGAAT-T
1 GAAATA--GAATGT
43230724 GAAAATAGAATGT
1 G-AAATAGAATGT
43230737 GAAATAGTGAAT-T
1 GAAATA--GAATGT
43230750 GAAAATAGAATGT
1 G-AAATAGAATGT
43230763 GAAATA
1 GAAATA
43230769 TGTTGCAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 17
0.73 0.02 0.26
Matches are distributed among these distances:
11 5 0.10
12 18 0.38
13 11 0.23
14 14 0.29
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25
Consensus pattern (12 bp):
GAAATAGAATGT
Found at i:43233219 original size:39 final size:40
Alignment explanation
Indices: 43233109--43233264 Score: 115
Period size: 39 Copynumber: 3.9 Consensus size: 40
43233099 CTTACGCAAC
* * * * *
43233109 ATACTAAAATTTCTAAAGGTATACCAAAATATCTGA-A-GAA
1 ATACCAAAATCTCTAATGG-ATACCAAAATTTCTAACACG-A
* * * *
43233149 ATATCAAAATTTCTAAAGGGGTACCAAAATTTCTAACACG-
1 ATACCAAAATCTCT-AATGGATACCAAAATTTCTAACACGA
* *
43233189 TTACCAAAATCTCTAATGGATACCAAAATTTCCT-A-ATGA
1 ATACCAAAATCTCTAATGGATACCAAAATTT-CTAACACGA
* * *
43233228 ATGCCAAAATCTCTAATGGATACCTACATTTCTAACA
1 ATACCAAAATCTCTAATGGATACCAAAATTTCTAACA
43233265 TATACCTACA
Statistics
Matches: 93, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
38 4 0.04
39 44 0.47
40 39 0.42
41 5 0.05
42 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (40 bp):
ATACCAAAATCTCTAATGGATACCAAAATTTCTAACACGA
Found at i:43233226 original size:20 final size:19
Alignment explanation
Indices: 43233190--43233251 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
43233180 TCTAACACGT
43233190 TACCAAAATCTCTAATGGA
1 TACCAAAATCTCTAATGGA
* *
43233209 TACCAAAATTTCCTAATGAA
1 TACCAAAATCT-CTAATGGA
*
43233229 TGCCAAAATCTCTAATGGA
1 TACCAAAATCTCTAATGGA
43233248 TACC
1 TACC
43233252 TACATTTCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (19 bp):
TACCAAAATCTCTAATGGA
Found at i:43233261 original size:19 final size:19
Alignment explanation
Indices: 43233109--43233262 Score: 103
Period size: 20 Copynumber: 7.8 Consensus size: 19
43233099 CTTACGCAAC
* *
43233109 ATACTAAAATTTCTAAAGG
1 ATACCAAAATTTCTAATGG
* *
43233128 TATACCAAAATATCTGAA-GAA
1 -ATACCAAAATTTCT-AATG-G
* *
43233149 ATATCAAAATTTCTAAAGGG
1 ATACCAAAATTTCT-AATGG
* **
43233169 GTACCAAAATTTCTAACACG
1 ATACCAAAATTTCTAA-TGG
* *
43233189 TTACCAAAATCTCTAATGG
1 ATACCAAAATTTCTAATGG
*
43233208 ATACCAAAATTTCCTAATGA
1 ATACCAAAATTT-CTAATGG
* *
43233228 ATGCCAAAATCTCTAATGG
1 ATACCAAAATTTCTAATGG
* *
43233247 ATACCTACATTTCTAA
1 ATACCAAAATTTCTAA
43233263 CATATACCTA
Statistics
Matches: 104, Mismatches: 25, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
19 31 0.30
20 70 0.67
21 3 0.03
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (19 bp):
ATACCAAAATTTCTAATGG
Found at i:43234425 original size:20 final size:20
Alignment explanation
Indices: 43234402--43234446 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
43234392 TGCATTATAG
*
43234402 ATTTTAGTA-TTAGTTAAAA
1 ATTTTAGTATTTAATTAAAA
*
43234421 AATTTAGTATTTAATTAAAA
1 ATTTTAGTATTTAATTAAAA
43234441 ATTTTA
1 ATTTTA
43234447 AAAATTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
ATTTTAGTATTTAATTAAAA
Found at i:43236989 original size:13 final size:13
Alignment explanation
Indices: 43236971--43236996 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43236961 AACTTAGCCG
43236971 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
43236984 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
43236997 AGTTTAGCTG
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:0.00, C:0.31, G:0.08, T:0.62
Consensus pattern (13 bp):
TTCCTTCTGTTTC
Found at i:43240494 original size:92 final size:90
Alignment explanation
Indices: 43240337--43240545 Score: 271
Period size: 92 Copynumber: 2.3 Consensus size: 90
43240327 TTGATTTTAG
* *
43240337 TAAATTCATATAAAAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAAAA-A-TTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
43240402 ATTTAAT-ATTAATTATTTTAAATTGTA
64 ATGTAATAATT-ATTATTTTAAATTATA
*
43240429 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAA-AAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
43240493 TATGTAATAATTATTATTTTAAATTATA
63 TATGTAATAATTATTATTTTAAATTATA
*
43240521 CAAATTCATA-AAATATAATTTATTA
1 TAAATTCATATAAA-A-AATTTATTA
43240546 GTTATAATTA
Statistics
Matches: 105, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
90 2 0.02
91 31 0.30
92 66 0.63
93 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAAATTCATATAAAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATAT
GTAATAATTATTATTTTAAATTATA
Found at i:43240508 original size:24 final size:25
Alignment explanation
Indices: 43240473--43240520 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
43240463 TTATGAAATT
43240473 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
43240497 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
43240521 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:43240674 original size:66 final size:64
Alignment explanation
Indices: 43240599--43240809 Score: 194
Period size: 66 Copynumber: 3.4 Consensus size: 64
43240589 AAATATATTT
43240599 AATATTAATTATTTCAAATTTTCATTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
43240664 G
64 G
* * * * **
43240665 AATATTAATTATTAAGAATTTTA-TTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTTTATTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
43240719 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCGTATA
1 AATATTAATTAT-TTAAATTT-TA-TTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
43240783 AG
63 AG
*
43240785 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
43240810 AAATTATATA
Statistics
Matches: 112, Mismatches: 16, Indels: 35
0.69 0.10 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.12
55 5 0.04
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 3 0.03
64 4 0.04
65 8 0.07
66 32 0.29
67 5 0.04
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (64 bp):
AATATTAATTATTTAAATTTTATTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:43240706 original size:120 final size:120
Alignment explanation
Indices: 43240568--43240853 Score: 479
Period size: 120 Copynumber: 2.4 Consensus size: 120
43240558 TTAAATTATT
* * * *
43240568 TTAAATCATATATCTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-TTTACAG
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-ATTTTACAG
43240630 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
63 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
43240688 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
*
43240753 CATATATTATGATTTGAGTAAATTCGTATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
43240808 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
43240854 TAAATATGAT
Statistics
Matches: 158, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
119 6 0.04
120 150 0.95
121 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
Found at i:43240721 original size:15 final size:15
Alignment explanation
Indices: 43240686--43240737 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
43240676 TTAAGAATTT
*
43240686 TATTAAATTAT-ATA
1 TATTTAATTATAATA
43240700 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
43240714 TATTTAATAATAAT-
1 TATTTAATTATAATA
43240728 TATGTTAATT
1 TAT-TTAATT
43240738 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:43240836 original size:16 final size:16
Alignment explanation
Indices: 43240815--43240856 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
43240805 TTATTAAATT
*
43240815 ATATATTTTAATTATA
1 ATATATTTTAATAATA
43240831 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
43240846 AT-TATGTTTAA
1 ATATAT-TTTAA
43240857 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:43240841 original size:15 final size:15
Alignment explanation
Indices: 43240806--43240847 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
43240796 TTAAGAATTT
*
43240806 TATTAAATTAT-ATA
1 TATTTAATTATAATA
43240820 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
43240834 TATTTAATAATAAT
1 TATTTAATTATAAT
43240848 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:43240985 original size:17 final size:16
Alignment explanation
Indices: 43240959--43240993 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
43240949 ATTATAAGAA
*
43240959 TTTTATTAAATTATAT
1 TTTTATTAAAATATAT
43240975 TTTTAATTAAAATATAT
1 TTTT-ATTAAAATATAT
43240992 TT
1 TT
43240994 AATAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTATTAAAATATAT
Found at i:43240991 original size:155 final size:157
Alignment explanation
Indices: 43240790--43241104 Score: 553
Period size: 155 Copynumber: 2.0 Consensus size: 157
43240780 ATAAGAATAT
*
43240790 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
** * *
43240855 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAAAATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
43240920 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
43240947 TAATTA-TAAGAATTTTATTAAATTATAT-TTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
43241010 AAATATGATTAAAAAATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAAAATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
43241075 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
43241102 TAA
1 TAA
43241105 GGGTATTCTA
Statistics
Matches: 151, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
155 123 0.81
156 22 0.15
157 6 0.04
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAAAATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:43241264 original size:16 final size:16
Alignment explanation
Indices: 43241228--43241277 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
43241218 GATTTCCTAT
*
43241228 TACACCTCTAATCC-A
1 TACACCTCAAATCCAA
*
43241243 -ACACCTCCAATCCAA
1 TACACCTCAAATCCAA
*
43241258 TACACCTCAAATCTAA
1 TACACCTCAAATCCAA
43241274 TACA
1 TACA
43241278 GCGAACCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.40
15 1 0.03
16 17 0.57
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (16 bp):
TACACCTCAAATCCAA
Found at i:43241898 original size:21 final size:21
Alignment explanation
Indices: 43241865--43241921 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
43241855 ATTTTTTTAA
* *
43241865 ATTAAACCCTGAACCTTGAAC
1 ATTAAATCTTGAACCTTGAAC
* * *
43241886 ATTAAATCTTGAACATTTACC
1 ATTAAATCTTGAACCTTGAAC
*
43241907 CTTAAATCTTGAACC
1 ATTAAATCTTGAACC
43241922 CTAAATATTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.32
Consensus pattern (21 bp):
ATTAAATCTTGAACCTTGAAC
Found at i:43242088 original size:20 final size:20
Alignment explanation
Indices: 43242063--43242101 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43242053 TTTAATTCAA
* *
43242063 GATTTAGGGTTTAGGGTTTG
1 GATTTAGAGTTTAAGGTTTG
43242083 GATTTAGAGTTTAAGGTTT
1 GATTTAGAGTTTAAGGTTT
43242102 CAAGTTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (20 bp):
GATTTAGAGTTTAAGGTTTG
Found at i:43248771 original size:14 final size:14
Alignment explanation
Indices: 43248752--43248779 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43248742 CATATTGACT
43248752 CCTAATCTAAATCA
1 CCTAATCTAAATCA
43248766 CCTAATCTAAATCA
1 CCTAATCTAAATCA
43248780 TTATTCAAGA
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:0.29, G:0.00, T:0.29
Consensus pattern (14 bp):
CCTAATCTAAATCA
Found at i:43252830 original size:24 final size:24
Alignment explanation
Indices: 43252803--43252854 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
43252793 AATCAAAGTC
* *
43252803 AAATATATTATGTTAATAAATGCT
1 AAATATATTATATTAATAAATACT
*
43252827 AAATATATTATATTCATAAATACT
1 AAATATATTATATTAATAAATACT
43252851 AAAT
1 AAAT
43252855 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATATTAATAAATACT
Found at i:43257244 original size:24 final size:24
Alignment explanation
Indices: 43257202--43257253 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
43257192 AATCAAAGTC
** *
43257202 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
43257226 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
43257250 AAAT
1 AAAT
43257254 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:43259534 original size:66 final size:67
Alignment explanation
Indices: 43259408--43259542 Score: 166
Period size: 66 Copynumber: 2.0 Consensus size: 67
43259398 TTACCGTAAA
* * ** *
43259408 ATAAAAAATAGAAATCTTCATTTTTTTTAAAAAAAATTGATAAAATTATGTTGATTTGTTTTTCA
1 ATAAAAAATAGAAATATTCATTTTTTTT-AAAAAAAGTGATAAAATTATGTCCATGTGTTTTTCA
43259473 TTC
65 TTC
** *
43259476 ATAAAAAATAGAAATTATTC-TTTTTTTT-TTAAAAGTGATAGAATTATGTCCATGTGTTTTTCA
1 ATAAAAAATAGAAA-TATTCATTTTTTTTAAAAAAAGTGATAAAATTATGTCCATGTGTTTTTCA
43259539 TTC
65 TTC
43259542 A
1 A
43259543 ATACGTTGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
66 32 0.55
68 22 0.38
69 4 0.07
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (67 bp):
ATAAAAAATAGAAATATTCATTTTTTTTAAAAAAAGTGATAAAATTATGTCCATGTGTTTTTCAT
TC
Found at i:43260484 original size:2 final size:2
Alignment explanation
Indices: 43260477--43260502 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43260467 CCTCTTGCTA
43260477 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
43260503 TTGTTTTTTT
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:43261396 original size:2 final size:2
Alignment explanation
Indices: 43261389--43261415 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43261379 TTTCTTTCTT
43261389 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
43261416 TAAATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43282693 original size:20 final size:21
Alignment explanation
Indices: 43282653--43282693 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43282643 CCAAAAAAAA
* *
43282653 TATAAAAAAGTTATCATTTAT
1 TATAAAAAAATTATCAATTAT
43282674 TATAAAAAAATTAT-AATTAT
1 TATAAAAAAATTATCAATTAT
43282694 GTGAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TATAAAAAAATTATCAATTAT
Found at i:43289870 original size:51 final size:50
Alignment explanation
Indices: 43289713--43289907 Score: 219
Period size: 51 Copynumber: 3.8 Consensus size: 50
43289703 ATGATCAATG
* *
43289713 CTATCCGGTGCACATAGTAGCCTACACTTAGTACTACACATGTGACCAATA
1 CTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAA-A
* * * * *
43289764 CCATCCGGTACACGTAGTAGCCTGCACATAGTACTACACAAGTAACCAAA
1 CTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAA
*
43289814 GCTATCCGGTACATATAGTAGCCTGCACTTAGTACTACACATGTGACCATAA
1 -CTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCA-AA
*** * * * * *
43289866 CTATCTTATACTCATAGTAGCATACGCATAGTACTACACATG
1 CTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATG
43289908 AGTTCTCATG
Statistics
Matches: 120, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
50 1 0.01
51 117 0.98
52 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (50 bp):
CTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAA
Found at i:43289884 original size:102 final size:102
Alignment explanation
Indices: 43289712--43289905 Score: 264
Period size: 102 Copynumber: 1.9 Consensus size: 102
43289702 TATGATCAAT
* *
43289712 GCTATCCGGTGCACATAGTAGCCTACACTTAGTACTACACATGTGACCAATACCATCCGGTACAC
1 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATACCATCCGATACAC
* * *
43289777 GTAGTAGCCTGCACATAGTACTACACAAGTAACCAAA
66 ATAGTAGCATACACATAGTACTACACAAGTAACCAAA
* * * ** *
43289814 GCTATCCGGTACATATAGTAGCCTGCACTTAGTACTACACATGTGACC-ATAACTATCTTATACT
1 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAAT-ACCATCCGATACA
*
43289878 CATAGTAGCATACGCATAGTACTACACA
65 CATAGTAGCATACACATAGTACTACACA
43289906 TGAGTTCTCA
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 2 0.03
102 77 0.97
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (102 bp):
GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATACCATCCGATACAC
ATAGTAGCATACACATAGTACTACACAAGTAACCAAA
Found at i:43308783 original size:56 final size:56
Alignment explanation
Indices: 43308697--43308811 Score: 203
Period size: 56 Copynumber: 2.1 Consensus size: 56
43308687 ATGCTTATGT
43308697 TATTTTTTGTGTTAAGTGTGTCAGTTATGCATGTCAAGACCACATTAAGGATTTGA
1 TATTTTTTGTGTTAAGTGTGTCAGTTATGCATGTCAAGACCACATTAAGGATTTGA
* * *
43308753 TATTTTTTGTTTTGAGTGTGTCAGTTATGCATGTCAAGACCACATTAATGATTTGA
1 TATTTTTTGTGTTAAGTGTGTCAGTTATGCATGTCAAGACCACATTAAGGATTTGA
43308809 TAT
1 TAT
43308812 ATTGAGATGA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.43
Consensus pattern (56 bp):
TATTTTTTGTGTTAAGTGTGTCAGTTATGCATGTCAAGACCACATTAAGGATTTGA
Found at i:43310519 original size:28 final size:28
Alignment explanation
Indices: 43310466--43310543 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
43310456 ACACACACAG
* * *
43310466 GGTTAGCACATAT-GGTTCGCACCTAGT
1 GGTTCGCACATATGGGTTTGCACCTAGA
**
43310493 GGTTCTTACATATGGGTTTGCACCTAGA
1 GGTTCGCACATATGGGTTTGCACCTAGA
43310521 GGTTCGCACATATAGGGTTTGCA
1 GGTTCGCACATAT-GGGTTTGCA
43310544 TATACATATA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 10 0.24
28 23 0.55
29 9 0.21
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (28 bp):
GGTTCGCACATATGGGTTTGCACCTAGA
Found at i:43310774 original size:14 final size:14
Alignment explanation
Indices: 43310757--43310819 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
43310747 CACATACAGA
43310757 GGTTCACTTATAGG
1 GGTTCACTTATAGG
* *
43310771 GGTTC-GTATACAGG
1 GGTTCACT-TATAGG
* * * *
43310785 CGCTCGCCTATAGG
1 GGTTCACTTATAGG
43310799 GGTTCACTTATAGG
1 GGTTCACTTATAGG
43310813 GGTTCAC
1 GGTTCAC
43310820 ATACATGGGC
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
13 1 0.03
14 35 0.97
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (14 bp):
GGTTCACTTATAGG
Found at i:43315068 original size:9 final size:9
Alignment explanation
Indices: 43315056--43315080 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
43315046 TTTTCATTTA
43315056 TTATTATTG
1 TTATTATTG
43315065 TTATTATTG
1 TTATTATTG
43315074 TTATTAT
1 TTATTAT
43315081 AACATATGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTATTG
Found at i:43320235 original size:22 final size:23
Alignment explanation
Indices: 43320210--43320259 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
43320200 ATCTCATGCA
*
43320210 TATTTTATGTATA-TCTTTTCCT
1 TATTTTATGTATATTATTTTCCT
43320232 TA-TTTATGTATATTATTTTCCT
1 TATTTTATGTATATTATTTTCCT
43320254 TGATTT
1 T-ATTT
43320260 ATGGGCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.42
22 11 0.46
23 1 0.04
24 2 0.08
ACGTcount: A:0.20, C:0.10, G:0.06, T:0.64
Consensus pattern (23 bp):
TATTTTATGTATATTATTTTCCT
Found at i:43320239 original size:21 final size:23
Alignment explanation
Indices: 43320213--43320262 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 23
43320203 TCATGCATAT
*
43320213 TTTATGTATA-TCTTTTCCTT-A
1 TTTATGTATATTATTTTCCTTGA
43320234 TTTATGTATATTATTTTCCTTGA
1 TTTATGTATATTATTTTCCTTGA
43320257 TTTATG
1 TTTATG
43320263 GGCTAATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 10 0.38
22 9 0.35
23 7 0.27
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.62
Consensus pattern (23 bp):
TTTATGTATATTATTTTCCTTGA
Found at i:43325597 original size:3 final size:3
Alignment explanation
Indices: 43325589--43325643 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
43325579 GCAGAAGAGG
43325589 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
43325637 AGA AGA A
1 AGA AGA A
43325644 AGAAAGAAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:43325889 original size:53 final size:53
Alignment explanation
Indices: 43325831--43325938 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 53
43325821 TTTTTTATAA
* *
43325831 TTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTATTGTG
1 TTATTTTAAAATTAATATATTAGTAATTTAGGATTATGTTATAAATTATTGTG
* *
43325884 TTATTTTAAAATTAATATATTAGTAATTTAGGATTATGTTATAAGTTGTTGTG
1 TTATTTTAAAATTAATATATTAGTAATTTAGGATTATGTTATAAATTATTGTG
43325937 TT
1 TT
43325939 TAGTTTAGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (53 bp):
TTATTTTAAAATTAATATATTAGTAATTTAGGATTATGTTATAAATTATTGTG
Found at i:43326290 original size:50 final size:50
Alignment explanation
Indices: 43326236--43326393 Score: 135
Period size: 50 Copynumber: 3.1 Consensus size: 50
43326226 AATAATTTTA
*
43326236 TAGTTATTTTGTTAGTAATTTATGATTAGGTTATACAAATTGTTAGTGTT
1 TAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAAAATTGTTAGTGTT
** * * * * * *
43326286 TAGTTATGTGTT-TTATGATTTTTTAGTAATGTA--TTTTAAAAAAT-ATAATTTT
1 TAGTTAT-T-TTGTTA-G-TAATTTA-TGAT-TAGGTTATAAAAATTGTTAGTGTT
*
43326338 ATAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTT
1 -TAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAAAATTGTTAGTGTT
43326389 TAGTT
1 TAGTT
43326394 TAGTATTTTG
Statistics
Matches: 79, Mismatches: 18, Indels: 22
0.66 0.15 0.18
Matches are distributed among these distances:
48 2 0.03
49 3 0.04
50 25 0.32
51 12 0.15
52 12 0.15
53 20 0.25
54 3 0.04
55 2 0.03
ACGTcount: A:0.30, C:0.01, G:0.16, T:0.54
Consensus pattern (50 bp):
TAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAAAATTGTTAGTGTT
Found at i:43326354 original size:103 final size:104
Alignment explanation
Indices: 43326134--43326449 Score: 391
Period size: 103 Copynumber: 3.1 Consensus size: 104
43326124 TTATAGTTAT
*
43326134 TTATTTTGTTAATAATTTATGGGATTAGG-T-TACAAATTGTTAGTGTTTAG-TATAG-GATTTT
1 TTATTTTGTTAGTAATTTAT--GATTAGGTTATACAAATTGTTAGTGTTTAGTTATAGTG-TTTT
* * * *
43326195 TTGATTTTTTTGTGATGTAATGTTTTTTTAAA-ATAATTTTATAG
63 ATGA-TTTTTTGTAATGTAA--TTTTATAAAATATAATTTTATAG
43326239 TTATTTTGTTAGTAATTTATGATTAGGTTATACAAATTGTTAGTGTTTAGTTAT-GTGTTTTATG
1 TTATTTTGTTAGTAATTTATGATTAGGTTATACAAATTGTTAGTGTTTAGTTATAGTGTTTTATG
*
43326303 ATTTTTTAGTAATGT-ATTTTAAAAAATATAATTTTATAG
66 ATTTTTT-GTAATGTAATTTTATAAAATATAATTTTATAG
* * *
43326342 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTT-TAGTATTTTGTG
1 TTATTTTGTTAGTAATTTATGATTAGGTTATACAAATTGTTAGTGTTTAGTTATAGTGTTTTATG
* * *
43326406 ATTTTTT-TAATGTAATTTTATATAATGTAATTTTAT-T
66 ATTTTTTGTAATGTAATTTTATAAAATATAATTTTATAG
43326443 TTATTTT
1 TTATTTT
43326450 TCTTTATTTG
Statistics
Matches: 190, Mismatches: 13, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
101 13 0.07
102 27 0.14
103 85 0.45
104 8 0.04
105 53 0.28
106 4 0.02
ACGTcount: A:0.28, C:0.01, G:0.15, T:0.56
Consensus pattern (104 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTATACAAATTGTTAGTGTTTAGTTATAGTGTTTTATG
ATTTTTTGTAATGTAATTTTATAAAATATAATTTTATAG
Found at i:43326433 original size:15 final size:15
Alignment explanation
Indices: 43326413--43326441 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43326403 GTGATTTTTT
43326413 TAATGTAATTTTATA
1 TAATGTAATTTTATA
43326428 TAATGTAATTTTAT
1 TAATGTAATTTTAT
43326442 TTTATTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
TAATGTAATTTTATA
Found at i:43328449 original size:13 final size:13
Alignment explanation
Indices: 43328427--43328460 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
43328417 GTATTCAATT
43328427 CAATCCAATTACC
1 CAATCCAATTACC
*
43328440 CAATCTAATTACC
1 CAATCCAATTACC
*
43328453 CAACCCAA
1 CAATCCAA
43328461 CCCAATCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (13 bp):
CAATCCAATTACC
Found at i:43328689 original size:9 final size:9
Alignment explanation
Indices: 43328568--43328688 Score: 147
Period size: 9 Copynumber: 13.4 Consensus size: 9
43328558 TGTATGATTC
*
43328568 AATTAGGTT
1 AATTCGGTT
43328577 AATTCAGG-T
1 AATTC-GGTT
*
43328586 AATTCGGGT
1 AATTCGGTT
43328595 AATTCGGTT
1 AATTCGGTT
43328604 AATTCGGTT
1 AATTCGGTT
43328613 AATTCGGTT
1 AATTCGGTT
*
43328622 AATTCGGGT
1 AATTCGGTT
43328631 AATTCGAG-T
1 AATTCG-GTT
*
43328640 AATTTGGTT
1 AATTCGGTT
*
43328649 AATTCGGGT
1 AATTCGGTT
43328658 AATTCGGTT
1 AATTCGGTT
*
43328667 AATTTGGTT
1 AATTCGGTT
*
43328676 AATTTGGTT
1 AATTCGGTT
43328685 AATT
1 AATT
43328689 TTTAACCAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
8 3 0.03
9 94 0.94
10 3 0.03
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:43329176 original size:33 final size:33
Alignment explanation
Indices: 43329139--43329202 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
43329129 CGTTCCTTCT
*
43329139 GGCCCGTATCAACCACCGTACTCCACTCCTCTA
1 GGCCCGCATCAACCACCGTACTCCACTCCTCTA
* ***
43329172 GGCCCGCATCCATTGCCGTACTCCACTCCTC
1 GGCCCGCATCAACCACCGTACTCCACTCCTC
43329203 CCGGCTCAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.17, C:0.47, G:0.14, T:0.22
Consensus pattern (33 bp):
GGCCCGCATCAACCACCGTACTCCACTCCTCTA
Found at i:43329555 original size:79 final size:80
Alignment explanation
Indices: 43329399--43329577 Score: 281
Period size: 79 Copynumber: 2.2 Consensus size: 80
43329389 AATAACTTCA
* * *
43329399 TATTTATGTAATGAATTTTTTTCCATTTTATTTATCAATTTTATGTTTTTTTTTTTTTGCAATTT
1 TATTTATGTAATGACTTTTTTTCCATTTTATTTATCAATTTTATGTGTTTGTTTTTTTGCAATTT
* *
43329464 AAATAGTCAACTTTG
66 AAATAATAAACTTTG
*
43329479 TATTTATGTAATGACTTTTTTTGTCATTTTATTTATCAATTTTATG-GTTTGTTTTTTT-CAATT
1 TATTTATGTAATGACTTTTTTT-CCATTTTATTTATCAATTTTATGTGTTTGTTTTTTTGCAATT
43329542 TAAATAATAAACTTTG
65 TAAATAATAAACTTTG
43329558 TATTTATGTAATGACTTTTT
1 TATTTATGTAATGACTTTTT
43329578 CGCTATTTCA
Statistics
Matches: 92, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
79 39 0.42
80 31 0.34
81 22 0.24
ACGTcount: A:0.26, C:0.07, G:0.08, T:0.59
Consensus pattern (80 bp):
TATTTATGTAATGACTTTTTTTCCATTTTATTTATCAATTTTATGTGTTTGTTTTTTTGCAATTT
AAATAATAAACTTTG
Found at i:43345676 original size:2 final size:2
Alignment explanation
Indices: 43345669--43345706 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
43345659 CTTGAAATTA
43345669 AT AT AT AT AT AT 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 AT AT AT AT AT AT
43345707 TGTTTTATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43346231 original size:2 final size:2
Alignment explanation
Indices: 43346210--43346266 Score: 89
Period size: 2 Copynumber: 28.0 Consensus size: 2
43346200 TACTTACTAC
43346210 TA TA CTA TA TA GTA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43346253 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
43346267 AGTGTGTGCC
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.02
2 47 0.90
3 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:43348129 original size:2 final size:2
Alignment explanation
Indices: 43348122--43348150 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43348112 ATCCTTGTAT
43348122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43348151 GTTTCAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43348565 original size:29 final size:29
Alignment explanation
Indices: 43348512--43348568 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
43348502 TTTTATGCTA
*
43348512 ATTTTTTTAATTTCAAGTTATTTTATTAT
1 ATTTTTTTAATTTCAAATTATTTTATTAT
*
43348541 ATTTTTTTAATTATTAAATTA-TTTATTA
1 ATTTTTTTAATT-TCAAATTATTTTATTA
43348569 ACGTGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
ATTTTTTTAATTTCAAATTATTTTATTAT
Found at i:43349075 original size:5 final size:5
Alignment explanation
Indices: 43349065--43349098 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
43349055 GTTGATAGAG
43349065 AAAAT AAAAT AAACA- AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAA
43349099 ACAAATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 25 0.93
6 1 0.04
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:43350883 original size:21 final size:20
Alignment explanation
Indices: 43350857--43350896 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
43350847 AGATCCCTAT
43350857 AAAATAATTACAAAAATATTC
1 AAAATAATTA-AAAAATATTC
* *
43350878 AAAATATTTATAAAATATT
1 AAAATAATTAAAAAATATT
43350897 TTTCCCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATAATTAAAAAATATTC
Found at i:43352699 original size:72 final size:73
Alignment explanation
Indices: 43352549--43352701 Score: 184
Period size: 72 Copynumber: 2.1 Consensus size: 73
43352539 CAAACTTTAC
* * * *
43352549 TTGATGCT-TCTCACACAAGCTTCAGAGAATTCATAACACGTGTCGAATCTCAAGCCATCGGTAA
1 TTGATGCTATCTCACACAAGCTTCAGAAAATCCACAACACGTGTCGAATCTCAAGCCATCGATAA
**
43352613 AGGATAAT
66 ACAATAAT
* * * *
43352621 TCGATGCTAT-TCACACAAGCTTTAGAAAATCCACAACACGTGTTGGATCTCAAGCCATCGATAA
1 TTGATGCTATCTCACACAAGCTTCAGAAAATCCACAACACGTGTCGAATCTCAAGCCATCGATAA
* *
43352685 TCAATGAT
66 ACAATAAT
43352693 TTGATGCTA
1 TTGATGCTA
43352702 CTTACTGATA
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
72 66 0.99
73 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (73 bp):
TTGATGCTATCTCACACAAGCTTCAGAAAATCCACAACACGTGTCGAATCTCAAGCCATCGATAA
ACAATAAT
Found at i:43359287 original size:5 final size:5
Alignment explanation
Indices: 43359273--43359301 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
43359263 ATAATAGTTT
43359273 ATTT- ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
43359302 TACTAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTA
Found at i:43359297 original size:15 final size:14
Alignment explanation
Indices: 43359270--43359302 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
43359260 ACTATAATAG
43359270 TTTATTT-ATTTAA
1 TTTATTTAATTTAA
43359283 TTTAATTTAATTTAA
1 TTT-ATTTAATTTAA
43359298 TTTAT
1 TTTAT
43359303 ACTAGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 6 0.33
15 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTAATTTAA
Found at i:43376718 original size:16 final size:16
Alignment explanation
Indices: 43376697--43376729 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43376687 TATAATTTTT
43376697 AAAAA-TAAAACATATA
1 AAAAATTAAAA-ATATA
43376713 AAAAATTAAAAATATA
1 AAAAATTAAAAATATA
43376729 A
1 A
43376730 TTTTGTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATTAAAAATATA
Found at i:43376811 original size:15 final size:16
Alignment explanation
Indices: 43376788--43376826 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
43376778 TATTGAATTA
43376788 TTTATAAAAAAT-AAAT
1 TTTA-AAAAAATAAAAT
*
43376804 TTTAAAAATATAAAAT
1 TTTAAAAAAATAAAAT
43376820 TTTAAAA
1 TTTAAAA
43376827 TGAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTAAAAAAATAAAAT
Found at i:43377338 original size:3 final size:3
Alignment explanation
Indices: 43377330--43377362 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
43377320 TTTTCCTTAT
43377330 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
43377363 AATTTCATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:43378024 original size:16 final size:16
Alignment explanation
Indices: 43378005--43378046 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
43377995 GTTTATAATT
43378005 TTTTGGATTTAGGGAG
1 TTTTGGATTTAGGGAG
* **
43378021 TTTTGGGTTTAGGGTT
1 TTTTGGATTTAGGGAG
43378037 TTTTGGATTT
1 TTTTGGATTT
43378047 CTTTGTTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.55
Consensus pattern (16 bp):
TTTTGGATTTAGGGAG
Found at i:43379698 original size:42 final size:43
Alignment explanation
Indices: 43379651--43379799 Score: 162
Period size: 43 Copynumber: 3.5 Consensus size: 43
43379641 CGAGATTACA
*
43379651 TGTAAGACCATATCTAGGATA-TGGCATCGATATGA-GACTTCG
1 TGTAAGACCATATCTGGGATATTGGCATCGATAT-ATGACTTCG
* * *
43379693 TGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTTCG
1 TGTAAGACCATATCTGGGATATTGGCATCGATATATGACTTCG
* * * *
43379736 TGTAAGACCATAGCTGGGCTATTGGCATCGATA-AAGA-TTACA
1 TGTAAGACCATATCTGGGATATTGGCATCGATATATGACTT-CG
* *
43379778 TGTAAGACTATATATGGGATAT
1 TGTAAGACCATATCTGGGATAT
43379800 GACATTGTTA
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.02
42 41 0.46
43 47 0.52
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (43 bp):
TGTAAGACCATATCTGGGATATTGGCATCGATATATGACTTCG
Found at i:43381671 original size:46 final size:46
Alignment explanation
Indices: 43381621--43381783 Score: 188
Period size: 46 Copynumber: 3.6 Consensus size: 46
43381611 GATATTGTTT
43381621 TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATGAAAAAAA
1 TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATGAAAAAAA
* ** * **
43381667 TGGATTTCTTTGTATTTTATTGTCT-GCCATGTGT--ATGAAAAAAA
1 TGGATTTGTTTGTATTAAATTGTTTGGTTAT-TGTACATGAAAAAAA
* * *
43381711 TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATTATAGAAA
1 TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATGAAAAAAA
* * *
43381757 TTGATTTATTTGTATTGAATTGTTTGG
1 TGGATTTGTTTGTATTAAATTGTTTGG
43381784 CTATCTCTAT
Statistics
Matches: 95, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
44 34 0.36
45 6 0.06
46 55 0.58
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.49
Consensus pattern (46 bp):
TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATGAAAAAAA
Found at i:43381813 original size:29 final size:28
Alignment explanation
Indices: 43381781--43382010 Score: 129
Period size: 29 Copynumber: 7.9 Consensus size: 28
43381771 TTGAATTGTT
*
43381781 TGGCTATCTCTATTAAATGGAAGCCTTTG
1 TGGCGATCTCTATTAAA-GGAAGCCTTTG
* * *
43381810 TGGCGAACTTTGTTAAAATGGAAGCCTTTG
1 TGGCGATCTCTATT-AAA-GGAAGCCTTTG
* *
43381840 TGGCGATCTCTATTATAAGAAAGCCTTTA
1 TGGCGATCTCTATTA-AAGGAAGCCTTTG
* * * *
43381869 TGGCGACCTCTGTTATAAGAAAACCTTTG
1 TGGCGATCTCTATTA-AAGGAAGCCTTTG
* ** *
43381898 TGTCGATCTCTATTATAAATATA-TCTTTG
1 TGGCGATCTCTATTA-AAGGA-AGCCTTTG
* * * *
43381927 TGGCTAACTCAATTGAAAGGATGCCTTTG
1 TGGCGATCTCTATT-AAAGGAAGCCTTTG
* * * * * **
43381956 TAGCTATCTCTATCAGAATGATGAATTTG
1 TGGCGATCTCTATTA-AAGGAAGCCTTTG
* *
43381985 TGGTGATCTCTATTAAAGGAATCCTT
1 TGGCGATCTCTATTAAAGGAAGCCTT
43382011 GGTGACAAAC
Statistics
Matches: 152, Mismatches: 43, Indels: 13
0.73 0.21 0.06
Matches are distributed among these distances:
28 7 0.05
29 115 0.76
30 30 0.20
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (28 bp):
TGGCGATCTCTATTAAAGGAAGCCTTTG
Found at i:43381883 original size:59 final size:59
Alignment explanation
Indices: 43381781--43381915 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 59
43381771 TTGAATTGTT
* * * * * *
43381781 TGGCTATCTCTATTA-AATGGAAGCCTTTGTGGCGAACTTTGTTAAAATGGAAGCCTTTG
1 TGGCGATCTCTATTATAATGAAAGCCTTTATGGCGAACTCTGTTAAAA-GAAAACCTTTG
* *
43381840 TGGCGATCTCTATTATAA-GAAAGCCTTTATGGCGACCTCTGTTATAAGAAAACCTTTG
1 TGGCGATCTCTATTATAATGAAAGCCTTTATGGCGAACTCTGTTAAAAGAAAACCTTTG
*
43381898 TGTCGATCTCTATTATAA
1 TGGCGATCTCTATTATAA
43381916 ATATATCTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
58 26 0.39
59 38 0.58
60 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (59 bp):
TGGCGATCTCTATTATAATGAAAGCCTTTATGGCGAACTCTGTTAAAAGAAAACCTTTG
Found at i:43384457 original size:20 final size:21
Alignment explanation
Indices: 43384434--43384483 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
43384424 ATTATTTAAG
43384434 ATTTTTTG-ATAAT-TTTCACA
1 ATTTTTTGAATAATGTTT-ACA
*
43384454 A-TTTCTGAATAATGTTTACA
1 ATTTTTTGAATAATGTTTACA
43384474 A-TTTTTGAAT
1 ATTTTTTGAAT
43384484 TTTTTTGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 5 0.19
20 18 0.69
21 3 0.12
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (21 bp):
ATTTTTTGAATAATGTTTACA
Found at i:43389474 original size:22 final size:22
Alignment explanation
Indices: 43389445--43389512 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
43389435 TGCACTAATG
43389445 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
43389467 TACAGAGAGCAC-ATATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
* *
43389489 AACAGAGAGCACTGACGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
43389511 AA
1 AA
43389513 TATCAGGGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.97
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:43390638 original size:13 final size:13
Alignment explanation
Indices: 43390615--43390715 Score: 75
Period size: 13 Copynumber: 7.7 Consensus size: 13
43390605 TCTGTTGTTT
43390615 TATATATATAATAA
1 TATA-ATATAATAA
*
43390629 TACAATATAATATTA
1 TATAATATAATA--A
*
43390644 TATAATATTAT-A
1 TATAATATAATAA
43390656 -ATAATATAATAA
1 TATAATATAATAA
43390668 TATAATATAATAA
1 TATAATATAATAA
* * *
43390681 CATACT-TATTAA
1 TATAATATAATAA
*
43390693 T-TAAGTAAATATAA
1 TATAA-TATA-ATAA
43390707 TATAATATA
1 TATAATATA
43390716 TATTTTAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 16
0.71 0.13 0.17
Matches are distributed among these distances:
11 11 0.16
12 8 0.12
13 25 0.37
14 10 0.15
15 13 0.19
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (13 bp):
TATAATATAATAA
Found at i:43390640 original size:5 final size:5
Alignment explanation
Indices: 43390625--43390715 Score: 68
Period size: 5 Copynumber: 18.6 Consensus size: 5
43390615 TATATATATA
* * *
43390625 ATAAT ACAAT ATAAT ATTAT ATAAT ATTAT AATAAT AT-A- ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT
*
43390674 ATAAT A-ACAT ACTTAT -TAAT -TAAGT A-AAT ATAAT ATAAT ATA
1 ATAAT ATA-AT A-TAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATA
43390716 TATTTTAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
3 2 0.03
4 11 0.16
5 50 0.72
6 6 0.09
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:43391020 original size:19 final size:19
Alignment explanation
Indices: 43390992--43391029 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
43390982 CATTTTTTTA
*
43390992 TTTAATCCATTTAAATCAAT
1 TTTAATCCATAT-AATCAAT
43391012 TTTAA-CCATATAATCAAT
1 TTTAATCCATATAATCAAT
43391030 AAAATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAATCCATATAATCAAT
Found at i:43407807 original size:12 final size:13
Alignment explanation
Indices: 43407784--43407815 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
43407774 AAAAATATTT
43407784 TAATAA-AATAAA
1 TAATAATAATAAA
43407796 TAA-AATAATAAA
1 TAATAATAATAAA
43407808 TAATAATA
1 TAATAATA
43407816 TTTTATTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 12 0.67
13 4 0.22
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:43408102 original size:8 final size:7
Alignment explanation
Indices: 43408084--43408140 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
43408074 TTTTTATTAA
43408084 ATAAAAT
1 ATAAAAT
*
43408091 A-AAATT
1 ATAAAAT
43408097 ATAAAAACT
1 AT-AAAA-T
43408106 ATAAAAT
1 ATAAAAT
43408113 AT-AAAT
1 ATAAAAT
43408119 ATAAAACT
1 ATAAAA-T
43408127 AATAAAAT
1 -ATAAAAT
43408135 ATAAAA
1 ATAAAA
43408141 AATTGTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
6 11 0.26
7 13 0.31
8 9 0.21
9 9 0.21
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (7 bp):
ATAAAAT
Found at i:43408109 original size:22 final size:22
Alignment explanation
Indices: 43408083--43408139 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
43408073 ATTTTTATTA
43408083 AATAAAATA-AAATTATAAAAACT
1 AATAAAATATAAA-TAT-AAAACT
43408106 -ATAAAATATAAATATAAAACT
1 AATAAAATATAAATATAAAACT
43408127 AATAAAATATAAA
1 AATAAAATATAAA
43408140 AAATTGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.19
22 23 0.72
23 3 0.09
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (22 bp):
AATAAAATATAAATATAAAACT
Found at i:43408116 original size:29 final size:29
Alignment explanation
Indices: 43408084--43408140 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
43408074 TTTTTATTAA
*
43408084 ATAAA-ATAAAA-TTATAAAAACTATAAAAT
1 ATAAATATAAAACTAAT-AAAA-TATAAAAT
43408113 ATAAATATAAAACTAATAAAATATAAAA
1 ATAAATATAAAACTAATAAAATATAAAA
43408141 AATTGTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 12 0.48
30 10 0.40
31 3 0.12
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (29 bp):
ATAAATATAAAACTAATAAAATATAAAAT
Found at i:43409027 original size:17 final size:16
Alignment explanation
Indices: 43409005--43409041 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
43408995 ATAGAAAGTC
*
43409005 AAATATATGGGTATCA
1 AAATATATGGATATCA
43409021 GAAATATATGGATATCA
1 -AAATATATGGATATCA
43409038 AAAT
1 AAAT
43409042 CTGGGATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (16 bp):
AAATATATGGATATCA
Found at i:43409194 original size:2 final size:2
Alignment explanation
Indices: 43409187--43409215 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43409177 GGCATTATTT
43409187 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
43409216 GTAAATTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:43412181 original size:17 final size:17
Alignment explanation
Indices: 43412159--43412191 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43412149 ATAGAAATTT
*
43412159 AAAGATATGGGTATCAG
1 AAAGATATGAGTATCAG
43412176 AAAGATATGAGTATCA
1 AAAGATATGAGTATCA
43412192 AAATTTGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.24
Consensus pattern (17 bp):
AAAGATATGAGTATCAG
Found at i:43413844 original size:29 final size:28
Alignment explanation
Indices: 43413815--43413920 Score: 106
Period size: 28 Copynumber: 3.8 Consensus size: 28
43413805 AGCAAATGGA
*
43413815 AAAAACTATAAAATATGAAAAATAAGGG
1 AAAAACTATAAAATTTGAAAAATAAGGG
* ** *
43413843 AAAAA-TGTAAAATCTAAAAAAATAAAGG
1 AAAAACTATAAAAT-TTGAAAAATAAGGG
* *
43413871 TAAAACTATAAAATTTGAAAAATATGGG
1 AAAAACTATAAAATTTGAAAAATAAGGG
* * *
43413899 CAAAATTGTAAAATTTGAAAAA
1 AAAAACTATAAAATTTGAAAAA
43413921 CAGGGGATAC
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
27 7 0.11
28 48 0.77
29 7 0.11
ACGTcount: A:0.61, C:0.04, G:0.12, T:0.23
Consensus pattern (28 bp):
AAAAACTATAAAATTTGAAAAATAAGGG
Found at i:43414979 original size:21 final size:21
Alignment explanation
Indices: 43414938--43414979 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
43414928 ATTAATATAA
* *
43414938 TAATACTTGATTATATTATTT
1 TAATACTTAATTATATCATTT
43414959 TAATACTTCAATTATA-CATTT
1 TAATACTT-AATTATATCATTT
43414980 ATGACCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (21 bp):
TAATACTTAATTATATCATTT
Found at i:43417873 original size:14 final size:15
Alignment explanation
Indices: 43417854--43417882 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43417844 TCTATATAAA
43417854 TATTTTA-GATTTAT
1 TATTTTATGATTTAT
43417868 TATTTTATGATTTAT
1 TATTTTATGATTTAT
43417883 CATCCAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
TATTTTATGATTTAT
Found at i:43419200 original size:6 final size:6
Alignment explanation
Indices: 43419189--43419222 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
43419179 TAATATTATG
43419189 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
43419223 GTTTACACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:43420005 original size:28 final size:30
Alignment explanation
Indices: 43419942--43420006 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
43419932 AAATATATTT
*
43419942 ATTTTTTTATTTTAATATATTTTTAAAATAC
1 ATTTTTTTATTTT-ATATATTTTTAAAATAA
*
43419973 TTTTTTTTATTTT-T-TATTTTTAAAATAA
1 ATTTTTTTATTTTATATATTTTTAAAATAA
43420001 ATTTTT
1 ATTTTT
43420007 GGTGTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 18 0.58
29 1 0.03
31 12 0.39
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (30 bp):
ATTTTTTTATTTTATATATTTTTAAAATAA
Found at i:43424769 original size:35 final size:35
Alignment explanation
Indices: 43424730--43424830 Score: 121
Period size: 35 Copynumber: 2.9 Consensus size: 35
43424720 GGGAAAAATT
* *
43424730 GTGGAAACAATTATTAGGTCATTCGGGGCGACACC
1 GTGGAAACGATTATTAGGTCCTTCGGGGCGACACC
* * * *
43424765 GTGGAAATGATTATTAGGTCCTTCGGAGTGACATC
1 GTGGAAACGATTATTAGGTCCTTCGGGGCGACACC
* * *
43424800 TTAGAAACGATTATTAGGTCCTTCAGGGCGA
1 GTGGAAACGATTATTAGGTCCTTCGGGGCGA
43424831 AACCTTGAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (35 bp):
GTGGAAACGATTATTAGGTCCTTCGGGGCGACACC
Found at i:43427602 original size:6 final size:6
Alignment explanation
Indices: 43427591--43427631 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
43427581 TAGTTCATGT
* *
43427591 TTTCCA TTTCCA TTGCCA TTTCCA TTTCCAA TTTCAA TTTC
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCC-A TTTCCA TTTC
43427632 AATTCACAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.20, C:0.29, G:0.02, T:0.49
Consensus pattern (6 bp):
TTTCCA
Found at i:43427855 original size:21 final size:21
Alignment explanation
Indices: 43427831--43427883 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
43427821 CGACACATAA
* *
43427831 GTGCTTGAAATGATACACGAG
1 GTGCCTGAAATGACACACGAG
* * *
43427852 GTGCCTGATACGACCCACGAG
1 GTGCCTGAAATGACACACGAG
43427873 GTGCCTGAAAT
1 GTGCCTGAAAT
43427884 ACGACACATA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (21 bp):
GTGCCTGAAATGACACACGAG
Found at i:43427899 original size:23 final size:23
Alignment explanation
Indices: 43427873--43427922 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
43427863 GACCCACGAG
43427873 GTGCCTGAAATACGACACATAAA
1 GTGCCTGAAATACGACACATAAA
* *
43427896 GTGCCTGATATACGACACATATA
1 GTGCCTGAAATACGACACATAAA
43427919 GTGC
1 GTGC
43427923 TTCATCGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (23 bp):
GTGCCTGAAATACGACACATAAA
Found at i:43429136 original size:27 final size:26
Alignment explanation
Indices: 43429078--43429136 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
43429068 TCTGCTGTTC
*
43429078 GTTTT-GTTTCTTTTACTTCTTTTTT
1 GTTTTAGTTTCTTTTACTTCTTTATT
* *
43429103 TTCTTTAGTTTCTTTTATTTACTTTATT
1 GT-TTTAGTTTCTTTTACTT-CTTTATT
43429131 GTTTTA
1 GTTTTA
43429137 ATTACTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
25 1 0.04
26 3 0.11
27 16 0.59
28 7 0.26
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.73
Consensus pattern (26 bp):
GTTTTAGTTTCTTTTACTTCTTTATT
Found at i:43430407 original size:280 final size:271
Alignment explanation
Indices: 43429913--43430455 Score: 750
Period size: 280 Copynumber: 2.0 Consensus size: 271
43429903 CTTACGGCAC
* *
43429913 CCCGAGCCGGTTCGATTGTTACCAGTTCTGTCTGGGTCAATGACGACACGACAAGTCTGATCTAG
1 CCCGAGCCGGTTCGATTATTACCAGTTCTGTCTGGGTCAATGACGACACAACAAGTCTGATCTAG
* * *
43429978 CCACCGGTTGGACTGTCGATTCGGTTTCACATAGTTTGACCAGTTTTTGGGCCTTGGTCTCGATT
66 CCACCGGTTGGACCGTCGATCCAGTTTCACATAGTTTGACCAGTTTTTGGGCCTTGGTCTCGATT
* *
43430043 TTGGGCTCCCGTACCCAATTTACGATTTCAAGTCCAATTTTCAAGTTTAATTACCCATTGGGCCA
131 TTGGGCTCCCGTACCCAATTTACGATCTCAAGTCCAATTTTCAAGTTCAATTACCCATTGGGCCA
* ** *
43430108 ATTGTCTGACTTAAAAATTAACTTTCAAATTTATCATATTAATTTTAATTGATTTGATTAATTTA
196 ATCGTCTGACTTAAAAATTAACTTTCAAAAATATCATATTAATTTTAATTGATTTAATTAATTTA
43430173 ATTTTACTTAA
261 ATTTTACTTAA
* * *
43430184 CCCGAGCCGGTTCGGTTATTATC-GATTCTGTCTGGGTCAATGACGACACAACCAGTCTGATCTA
1 CCCGAGCCGGTTCGATTATTACCAG-TTCTGTCTGGGTCAATGACGACACAACAAGTCTGATCTA
* **
43430248 GCCACCGGTTGGACCGTC-AGTCCAGTTTCACATACTGGGCCTAGTTCGATCAGTTTTTGGGTTT
65 GCCACCGGTTGGACCGTCGA-TCCAGTTTCACATA----G--T--TT-GACCAGTTTTTGGGCCT
* * *
43430312 TGGTCTCGATTTTGGGCTCCCGTACCTAATTTACGATCTC-AGATTCAATTTTTAAGTTCAATTA
120 TGGTCTCGATTTTGGGCTCCCGTACCCAATTTACGATCTCAAG-TCCAATTTTCAAGTTCAATTA
* *
43430376 CCCATTGGGCCAATCGTCTTACTTGAAAATTAACTTTCAAAAATATCATATTAATTTTAATTGAT
184 CCCATTGGGCCAATCGTCTGACTTAAAAATTAACTTTCAAAAATATCATATTAATTTTAATTGAT
*
43430441 TTAATTGATTTAATT
249 TTAATTAATTTAATT
43430456 AATTTAATTA
Statistics
Matches: 237, Mismatches: 23, Indels: 15
0.86 0.08 0.05
Matches are distributed among these distances:
270 2 0.01
271 86 0.36
275 1 0.00
277 1 0.00
279 4 0.02
280 143 0.60
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (271 bp):
CCCGAGCCGGTTCGATTATTACCAGTTCTGTCTGGGTCAATGACGACACAACAAGTCTGATCTAG
CCACCGGTTGGACCGTCGATCCAGTTTCACATAGTTTGACCAGTTTTTGGGCCTTGGTCTCGATT
TTGGGCTCCCGTACCCAATTTACGATCTCAAGTCCAATTTTCAAGTTCAATTACCCATTGGGCCA
ATCGTCTGACTTAAAAATTAACTTTCAAAAATATCATATTAATTTTAATTGATTTAATTAATTTA
ATTTTACTTAA
Found at i:43430445 original size:9 final size:9
Alignment explanation
Indices: 43430425--43430473 Score: 71
Period size: 9 Copynumber: 5.3 Consensus size: 9
43430415 AAAATATCAT
43430425 ATTAATTTTA
1 ATTAA-TTTA
*
43430435 ATTGATTTA
1 ATTAATTTA
*
43430444 ATTGATTTA
1 ATTAATTTA
43430453 ATTAATTTA
1 ATTAATTTA
43430462 ATTAATTTA
1 ATTAATTTA
43430471 ATT
1 ATT
43430474 TTACTTGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
9 33 0.89
10 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (9 bp):
ATTAATTTA
Found at i:43435922 original size:21 final size:21
Alignment explanation
Indices: 43435897--43435940 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
43435887 TGTTATATGG
* *
43435897 CCTAGCCACACGATCGTGTAA
1 CCTAGCCACACAACCGTGTAA
43435918 CCTAGCCACACAACCGTGTAA
1 CCTAGCCACACAACCGTGTAA
43435939 CC
1 CC
43435941 CCTTCATACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.39, G:0.16, T:0.16
Consensus pattern (21 bp):
CCTAGCCACACAACCGTGTAA
Found at i:43436446 original size:4 final size:4
Alignment explanation
Indices: 43436437--43436574 Score: 91
Period size: 4 Copynumber: 34.2 Consensus size: 4
43436427 TGTCTTAACT
* * *
43436437 TGCA TGCA TGCA TGCA T--A TTCA TGCA TGCA TGTA TGATA TGCA TGCA
1 TGCA TGCA TGCA TGCA TGCA TGCA TGCA TGCA TGCA TG-CA TGCA TGCA
* * * * * * *
43436484 TACA TGCA TGCA TGTA TGATA TGCA TGCA TGCA TGTA TGATA TGAA TACA
1 TGCA TGCA TGCA TGCA TG-CA TGCA TGCA TGCA TGCA TG-CA TGCA TGCA
* * * * * *
43436534 TGCA TGTA TGCA TGTA TGTA TGTA TGCA TGTA GGCA TGCA T
1 TGCA TGCA TGCA TGCA TGCA TGCA TGCA TGCA TGCA TGCA T
43436575 ATATGCTTGT
Statistics
Matches: 109, Mismatches: 20, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
2 2 0.02
4 95 0.87
5 12 0.11
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (4 bp):
TGCA
Done.