Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 93 of 170
Found at i:29137900 original size:38 final size:35
Alignment explanation
Indices: 29137849--29137927 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 35
29137839 TTTTTCTTTA
29137849 AATTGAATCATGATAGTAAAC-TAAACACAACATTAAAT
1 AATT-AATCATGATA-TAAACAT-AACACAACA-TAAAT
* *
29137887 AATTAATGCATGATATAAACATAACATAAGATAAAT
1 AATTAAT-CATGATATAAACATAACACAACATAAAT
29137923 AATTA
1 AATTA
29137928 TAAAGCAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
36 10 0.27
37 15 0.41
38 12 0.32
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (35 bp):
AATTAATCATGATATAAACATAACACAACATAAAT
Found at i:29138118 original size:60 final size:61
Alignment explanation
Indices: 29138010--29138208 Score: 184
Period size: 60 Copynumber: 3.3 Consensus size: 61
29138000 CTTTTTGGGG
* * *
29138010 CTTGAACTTGACAATGGTTCTCACATGGAGGGTAAACTTTTCTCTTTTATCTAAGTTTA-TT
1 CTTGAACTTGACAATTGTTCTCACATGAAGGGTAAACTTTTATCTTTTATCTAAG-TTAGTT
*
29138071 CTTGAACTTG-CAATTGTTCTCACATTAAGGGTTAAA-TTATTAT-TTTTATCTAAGTTAGTT
1 CTTGAACTTGACAATTGTTCTCACATGAAGGG-TAAACTT-TTATCTTTTATCTAAGTTAGTT
* * * *
29138131 CCTGAACTTGACAATTGTT-TC-CAT-AAGGGCTTGAACCTTTT-T-TTTTGTCCAAGTTA-TT
1 CTTGAACTTGACAATTGTTCTCACATGAAGGG--T-AAACTTTTATCTTTTATCTAAGTTAGTT
*
29138189 CTTTGAACTAGACAATTGTT
1 C-TTGAACTTGACAATTGTT
29138209 TCCACTTTGA
Statistics
Matches: 120, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
58 8 0.07
59 37 0.31
60 48 0.40
61 27 0.22
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.44
Consensus pattern (61 bp):
CTTGAACTTGACAATTGTTCTCACATGAAGGGTAAACTTTTATCTTTTATCTAAGTTAGTT
Found at i:29144111 original size:14 final size:15
Alignment explanation
Indices: 29144092--29144122 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
29144082 GGGACTTTTA
29144092 TTTTTTTATTTG-GT
1 TTTTTTTATTTGTGT
29144106 TTTTTTTATTTGTGT
1 TTTTTTTATTTGTGT
29144121 TT
1 TT
29144123 ATCATTTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.06, C:0.00, G:0.13, T:0.81
Consensus pattern (15 bp):
TTTTTTTATTTGTGT
Found at i:29144833 original size:44 final size:44
Alignment explanation
Indices: 29144600--29144871 Score: 152
Period size: 44 Copynumber: 6.3 Consensus size: 44
29144590 AACTGCTGAC
* * *
29144600 CAGGGAGAT-AGAATTACTGGCTTCAATGTACTCCACTGTAATCT
1 CAGGGAGATAAG-ATTACTGGCTTCAATCTGCTCTACTGTAATCT
* *
29144644 CAGGGAGATAAGATTTCTTCGG-TT-TAT-T-C-C-ACTGTAATCT
1 CAGGGAGATAAGATTAC-T-GGCTTCAATCTGCTCTACTGTAATCT
* * * * * * *
29144684 CAAGGAGATAAGA--CCT-GATGCGATCTACTCTACTGTAATTT
1 CAGGGAGATAAGATTACTGGCTTCAATCTGCTCTACTGTAATCT
* * *** * * * * * *
29144725 CAGAGAGATAAGA-TCCTTTATTTTAATCCGGTCCACTATAATAT
1 CAGGGAGATAAGATTAC-TGGCTTCAATCTGCTCTACTGTAATCT
* * *
29144769 CAGGGAAATAGGATTACTGGCTTCAATCTGCTCTGCTGTAATCT
1 CAGGGAGATAAGATTACTGGCTTCAATCTGCTCTACTGTAATCT
* * *
29144813 CAGGGAGATAAGATTTCTGGCTTCAATCTGCTCTACTTTAACCT
1 CAGGGAGATAAGATTACTGGCTTCAATCTGCTCTACTGTAATCT
**
29144857 CACAGAGATAAGATT
1 CAGGGAGATAAGATT
29144872 CTTCGGTCTA
Statistics
Matches: 173, Mismatches: 42, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
35 1 0.01
36 1 0.01
37 3 0.02
38 2 0.01
39 1 0.01
40 23 0.13
41 21 0.12
42 3 0.02
43 2 0.01
44 107 0.62
45 7 0.04
46 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (44 bp):
CAGGGAGATAAGATTACTGGCTTCAATCTGCTCTACTGTAATCT
Found at i:29144974 original size:212 final size:213
Alignment explanation
Indices: 29144600--29144994 Score: 600
Period size: 212 Copynumber: 1.9 Consensus size: 213
29144590 AACTGCTGAC
* * **
29144600 CAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAATCTCAGGGAGATAAGATTTCTTCG
1 CAGGGAGATAGAATTACTGGCTTCAATCTACTCCACTGTAACCTCACAGAGATAAGATTTCTTCG
* *
29144665 GTTTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGTAATTTCAGAG
66 GTCTATTCCACTATAATCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGTAATTTCAGAG
* * *
29144730 AGATAAGATCCTTTATTTTAATCCGGTCCACTATAA-TATCAGGGAAATAGGATTACTGGCTTCA
131 AGATAAGATCCTTTACTTTAATCCGCTCCACTACAACT-TCAGGGAAATAGGATTACTGGCTTCA
29144794 ATCTGCTCTGCTGTAATCT
195 ATCTGCTCTGCTGTAATCT
* * * *
29144813 CAGGGAGATA-AGATTTCTGGCTTCAATCTGCTCTACTTTAACCTCACAGAGATAAGA-TTCTTC
1 CAGGGAGATAGA-ATTACTGGCTTCAATCTACTCCACTGTAACCTCACAGAGATAAGATTTCTTC
*
29144876 GGTCTATTCCACTATAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAATTTCAGA
65 GGTCTATTCCACTATAATCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGTAATTTCAGA
*
29144941 GAGATAAGAT-CTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGAT
130 GAGATAAGATCCT-TTACTTTAATCCGCTCCACTACAACTTCAGGGAAATAGGAT
29144995 CTGTAATTTC
Statistics
Matches: 164, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
211 2 0.01
212 114 0.70
213 48 0.29
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (213 bp):
CAGGGAGATAGAATTACTGGCTTCAATCTACTCCACTGTAACCTCACAGAGATAAGATTTCTTCG
GTCTATTCCACTATAATCTCAAGGAGATAAGACCTGATGCGATCTACTCTACTGTAATTTCAGAG
AGATAAGATCCTTTACTTTAATCCGCTCCACTACAACTTCAGGGAAATAGGATTACTGGCTTCAA
TCTGCTCTGCTGTAATCT
Found at i:29145171 original size:128 final size:128
Alignment explanation
Indices: 29144982--29145672 Score: 1055
Period size: 128 Copynumber: 5.4 Consensus size: 128
29144972 CTACAACTTC
* * * * *
29144982 AGGGAGATAGGATCTGTAATTTCCCAACCTATTCCACTACTGACCAGGAATATAGGACTTGTGGC
1 AGGGAGACAAGATCTGTAATTT-CCAACCTATTCCACTGCTGATCAGGGATATAGGACTTGTGGC
*
29145047 TTCAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTATTTGATCTGCTCCGCTACTGCTT
65 TTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTATTTGATCTGCTCCGCTACTGCTT
* * *
29145111 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGACATAGTACTTGTGGCT
1 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGATCAGGGATATAGGACTTGTGGCT
* * * *
29145176 TAAATCTGCTTCGTTACACTTGAAGATAAGATTTGTCGTCTTTGATCTGCTCCCCTACTGCTT
66 TAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTATTTGATCTGCTCCGCTACTGCTT
* * * * *
29145239 AGGGAGACAAGATATGTAATTTCCAACCTATCCCATTGCTAATCAGGGACATAGGACTTGTGGCT
1 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGATCAGGGATATAGGACTTGTGGCT
* * * *
29145304 TAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTTGATCTGCTCTGCTATTGCTT
66 TAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTATTTGATCTGCTCCGCTACTGCTT
29145367 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGATCAGGGATATAGGACTTGTGGCT
1 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGATCAGGGATATAGGACTTGTGGCT
** *
29145432 TAAATCTGCTTCCTTACTTTTGAAGATAAGATTTGCCGCT-TTCGATCTGCTCCGCTACTGCTT
66 TAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCG-TATTTGATCTGCTCCGCTACTGCTT
*
29145495 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGTTGATCAGGGATATAGGACTTGTGGCT
1 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGATCAGGGATATAGGACTTGTGGCT
* *
29145560 TAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCC--ACTTTCGATCTACTCCGCTACTGCTT
66 TAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTA-TTT-GATCTGCTCCGCTACTGCTT
*
29145623 AGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGGTCAGGGA
1 AGGGAGACAAGATCTGTAATTT-CCAACCTATTCCACTGCTGATCAGGGA
29145673 GCTAGGTTTT
Statistics
Matches: 517, Mismatches: 40, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
127 2 0.00
128 469 0.91
129 46 0.09
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (128 bp):
AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGATCAGGGATATAGGACTTGTGGCT
TAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTATTTGATCTGCTCCGCTACTGCTT
Found at i:29146974 original size:7 final size:7
Alignment explanation
Indices: 29146955--29146999 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
29146945 TTAGCCTCTC
29146955 CATTTTT
1 CATTTTT
29146962 -ACTTTTT
1 CA-TTTTT
29146969 CATTTTTT
1 CA-TTTTT
29146977 CATTTTT
1 CATTTTT
29146984 CA-TTTT
1 CATTTTT
29146990 CATTTTT
1 CATTTTT
29146997 CAT
1 CAT
29147000 CTCTTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
6 7 0.21
7 19 0.56
8 8 0.24
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:29146982 original size:15 final size:15
Alignment explanation
Indices: 29146955--29146999 Score: 60
Period size: 13 Copynumber: 3.2 Consensus size: 15
29146945 TTAGCCTCTC
*
29146955 CATTTTTAC-TTTTT
1 CATTTTTTCATTTTT
29146969 CATTTTTTCATTTTT
1 CATTTTTTCATTTTT
29146984 CA--TTTTCATTTTT
1 CATTTTTTCATTTTT
29146997 CAT
1 CAT
29147000 CTCTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 13 0.46
14 8 0.29
15 7 0.25
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (15 bp):
CATTTTTTCATTTTT
Found at i:29147894 original size:6 final size:6
Alignment explanation
Indices: 29147816--29147898 Score: 62
Period size: 6 Copynumber: 13.2 Consensus size: 6
29147806 GCCTCTCCTA
* *
29147816 TTCTTT TTCCTTTT TTCTTT CTCTCTTT TTCATT TTCATTT TGAC-TT
1 TTCTTT TT-C-TTT TTCTTT -T-TCTTT TTCTTT TTC-TTT T-TCTTT
**
29147863 TGATTT TTCTTT TTCTTT TTCTTT TTCTTT TT-TTT T
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT T
29147899 GCTTGAATCT
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
5 4 0.06
6 41 0.65
7 7 0.11
8 11 0.17
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (6 bp):
TTCTTT
Found at i:29149273 original size:14 final size:15
Alignment explanation
Indices: 29149240--29149276 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
29149230 GATAACAAAC
29149240 AAAAAAGAGAAACAG
1 AAAAAAGAGAAACAG
*
29149255 -AAAAAGA-AAATAG
1 AAAAAAGAGAAACAG
29149268 AAAAAAGAG
1 AAAAAAGAG
29149277 CAGAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.03
Consensus pattern (15 bp):
AAAAAAGAGAAACAG
Found at i:29149837 original size:22 final size:23
Alignment explanation
Indices: 29149773--29149850 Score: 80
Period size: 22 Copynumber: 3.7 Consensus size: 23
29149763 CTTAACATTG
* **
29149773 TTTTAAATTTATCATTAGTTTTA
1 TTTTAAATTTATCATAAGTACTA
29149796 TTTT-AA--TATCAT-A-TACTA
1 TTTTAAATTTATCATAAGTACTA
29149814 TTTTAAA-TTATCATAAGTACTA
1 TTTTAAATTTATCATAAGTACTA
29149836 -TTTAAATTTATCATA
1 TTTTAAATTTATCATA
29149851 TATCATAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
18 7 0.15
19 3 0.06
20 12 0.25
21 7 0.15
22 15 0.31
23 4 0.08
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (23 bp):
TTTTAAATTTATCATAAGTACTA
Found at i:29149838 original size:40 final size:42
Alignment explanation
Indices: 29149773--29149852 Score: 101
Period size: 40 Copynumber: 1.9 Consensus size: 42
29149763 CTTAACATTG
* ** *
29149773 TTTTAAATTTATCATTAGTTTTATTTTAA-TATCATATACTA
1 TTTTAAATTTATCATAAGTACTATTTAAATTATCATATACTA
29149814 TTTTAAA-TTATCATAAGTACTATTTAAATTTATCATATA
1 TTTTAAATTTATCATAAGTACTATTTAAA-TTATCATATA
29149853 TCATAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 17 0.52
41 7 0.21
42 9 0.27
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (42 bp):
TTTTAAATTTATCATAAGTACTATTTAAATTATCATATACTA
Found at i:29150088 original size:13 final size:14
Alignment explanation
Indices: 29150064--29150104 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
29150054 ATTTTCATAC
29150064 ATTATTATTATATAT
1 ATTATTA-TATATAT
*
29150079 ATT-TTATATATAA
1 ATTATTATATATAT
29150092 ATTATTAT-TATAT
1 ATTATTATATATAT
29150105 GATAGTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 13 0.57
14 7 0.30
15 3 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATTATATATAT
Found at i:29150118 original size:28 final size:28
Alignment explanation
Indices: 29150043--29150118 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
29150033 TCTAAAGAAA
* *
29150043 TATATGATAGTATTTTCATACATTATTAT
1 TATATGATAGTAATTT-ATAAATTATTAT
* * *
29150072 TATAT-ATATTTTATATATAAATTATTAT
1 TATATGATA-GTAATTTATAAATTATTAT
29150100 TATATGATAGTAATTTATA
1 TATATGATAGTAATTTATA
29150119 TTTTTATTCT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
28 26 0.70
29 11 0.30
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (28 bp):
TATATGATAGTAATTTATAAATTATTAT
Found at i:29154884 original size:19 final size:19
Alignment explanation
Indices: 29154862--29154901 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
29154852 AATCAAAATC
29154862 AAAATCAAAAACCAAAAAGA
1 AAAATCAAAAA-CAAAAAGA
*
29154882 AAAATCAAAGACAAAAAGA
1 AAAATCAAAAACAAAAAGA
29154901 A
1 A
29154902 GAAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.75, C:0.12, G:0.07, T:0.05
Consensus pattern (19 bp):
AAAATCAAAAACAAAAAGA
Found at i:29155300 original size:7 final size:7
Alignment explanation
Indices: 29155285--29155334 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
29155275 TGCAAAAAAA
29155285 AAAAGATG
1 AAAA-ATG
29155293 AAAAATG
1 AAAAATG
29155300 -AAAATG
1 AAAAATG
*
29155306 AAAAGTG
1 AAAAATG
29155313 AAAAAATG
1 -AAAAATG
29155321 AAAAA-G
1 AAAAATG
29155327 TAAAAATG
1 -AAAAATG
29155335 GAGAGGCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
6 7 0.19
7 18 0.50
8 11 0.31
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:29155303 original size:21 final size:21
Alignment explanation
Indices: 29155279--29155325 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
29155269 ATGAATTGCA
29155279 AAAAAAAAAAGATG-AAAAATG
1 AAAAAAAAAAG-TGAAAAAATG
**
29155300 AAAATGAAAAGTGAAAAAATG
1 AAAAAAAAAAGTGAAAAAATG
29155321 AAAAA
1 AAAAA
29155326 GTAAAAATGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (21 bp):
AAAAAAAAAAGTGAAAAAATG
Found at i:29155477 original size:42 final size:42
Alignment explanation
Indices: 29155418--29155510 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
29155408 GGCTCAAATA
* *
29155418 TTGATCAGAATGGGGCATGAAGTGATTAGAGCTA-CTTGTATC
1 TTGATCAAAATGGGGCATGAAGTGATTAGAAC-AGCTTGTATC
29155460 TTGATCAAAATGGGGCATGAAGTGATTAGAACAGCTTGTATC
1 TTGATCAAAATGGGGCATGAAGTGATTAGAACAGCTTGTATC
29155502 TTGATCAAA
1 TTGATCAAA
29155511 TCGAGGCGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (42 bp):
TTGATCAAAATGGGGCATGAAGTGATTAGAACAGCTTGTATC
Found at i:29156826 original size:44 final size:44
Alignment explanation
Indices: 29156778--29157251 Score: 224
Period size: 44 Copynumber: 10.8 Consensus size: 44
29156768 CCAGTAATTC
*
29156778 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
** * * ** * *
29156822 TATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGCGGATTT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* * * * * *
29156866 TACCTCCCTGTGGTTA-TAGTGGAGTA-CTTGAAGCCAGTA-A-TTC-
1 TATCTCCCTG-GG-CAGCAGTGGAGTAGATTGAAG--ATTACAGATCT
* * *
29156909 TATCTCCTTGGGCAGCAGTGGAATAGATTAAAGATTACAGATCT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
** * * ** *
29156953 TATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGCAGATTT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* * * * *
29156997 TAACTCCCTGTGGTTA-CAGTAGAGTACATTGAA-A--CCAGTAAT-T
1 TATCTCCCTG-GG-CAGCAGTGGAGTAGATTGAAGATTACAG--ATCT
* *
29157040 CTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATTACAGATCT
1 -TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
** * ** *** *
29157085 TATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGAGGGCAGATTT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* * * *
29157129 TACCTCCTTGTGGTTA-CAGTGGAGTACATTGAAG--T-CAGTAAT-T
1 TATCTCCCTG-GG-CAGCAGTGGAGTAGATTGAAGATTACAG--ATCT
* *
29157172 CTA-CTTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCT
1 -TATC-TCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* ** * * *
29157217 TATCTCCTTAAGCAGTAGTGGAGCAGATCGAAGAT
1 TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGAT
29157252 GGCGGATTTT
Statistics
Matches: 312, Mismatches: 87, Indels: 62
0.68 0.19 0.13
Matches are distributed among these distances:
41 4 0.01
42 19 0.06
43 51 0.16
44 184 0.59
45 44 0.14
46 10 0.03
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
Found at i:29157104 original size:132 final size:132
Alignment explanation
Indices: 29156714--29157419 Score: 1059
Period size: 132 Copynumber: 5.5 Consensus size: 132
29156704 ACAGTAAAGC
**
29156714 AGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
1 AGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
*
29156779 ATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
66 ATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
29156844 GT
131 GT
* *
29156846 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTAC-TTGAAGCCAGTAATTCT
1 AGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
*
29156910 ATCTCCTTGGGCAGCAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
66 ATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
29156975 GT
131 GT
* * *
29156977 AGATCGAAGATGGCAGATTTTAACTCCCTGTGGTTACAGTAGAGTACATTGAAACCAGTAATTCT
1 AGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
29157042 ATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
66 ATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
29157107 GT
131 GT
* * * *
29157109 AGATCAAAGAGGGCAGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGTCAGTAATTCT
1 AGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
* * *
29157174 A-CTTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGG
66 ATC-TCCCTGGGCAGCAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
*
29157238 AGC
130 AGT
*
29157241 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
1 AGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
* *
29157306 ACCTCCCT-------AGT----CAG--T--AGATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
66 ATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
29157356 GT
131 GT
* ** * *
29157358 AGATCGAAGGTGGCAGATTTTACCTCCCTCAGGTTACAGTGGAGTATATTGAAGCCACTAAT
1 AGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
29157420 CTTATCCCCC
Statistics
Matches: 536, Mismatches: 35, Indels: 21
0.91 0.06 0.04
Matches are distributed among these distances:
117 91 0.17
119 1 0.00
121 2 0.00
125 3 0.01
131 126 0.24
132 312 0.58
133 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (132 bp):
AGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
ATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGA
GT
Found at i:29157431 original size:117 final size:117
Alignment explanation
Indices: 29157204--29157419 Score: 360
Period size: 117 Copynumber: 1.8 Consensus size: 117
29157194 AATAGATTGA
* *
29157204 AGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCC
1 AGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCC
** *
29157269 TGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACCTCCCTAGTCAGT
66 TCAGGTTACAGTGGAGTACATTGAAGCCACTAATTCTACCTCCCTAGTCAGT
* *
29157321 AGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGGTGGCAGATTTTACCTCCC
1 AGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCC
*
29157386 TCAGGTTACAGTGGAGTATATTGAAGCCACTAAT
66 TCAGGTTACAGTGGAGTACATTGAAGCCACTAAT
29157420 CTTATCCCCC
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
117 91 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (117 bp):
AGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCC
TCAGGTTACAGTGGAGTACATTGAAGCCACTAATTCTACCTCCCTAGTCAGT
Found at i:29159260 original size:64 final size:64
Alignment explanation
Indices: 29159100--29159269 Score: 201
Period size: 61 Copynumber: 2.7 Consensus size: 64
29159090 ATTTAGTTTT
* ** * *
29159100 TTATTAATTTAAT-TTTAAATCTAATTAGTGCATATTTTTGACATGGTTTTTTTTAAGATCTAGT
1 TTATTAA-TTAATGTTTAAATCTAATTAGTGCATATTTTT-ATATAATTATGTTTAAGATCTAGT
29159164 A
64 A
*
29159165 TTA-T--TTAATGTTT-AATCTCATTAGTGCATATTTTTATATAATTAATGTTT-A-ATCTAGTA
1 TTATTAATTAATGTTTAAATCTAATTAGTGCATATTTTTATATAATT-ATGTTTAAGATCTAGTA
29159224 TTATCTAATTAATGTTTAAATCTAATTAGTGCATATTTTTATATAA
1 TTAT-TAATTAATGTTTAAATCTAATTAGTGCATATTTTTATATAA
29159270 GTTTAATATA
Statistics
Matches: 91, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
59 11 0.12
60 6 0.07
61 31 0.34
62 3 0.03
63 9 0.10
64 28 0.31
65 3 0.03
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (64 bp):
TTATTAATTAATGTTTAAATCTAATTAGTGCATATTTTTATATAATTATGTTTAAGATCTAGTA
Found at i:29159430 original size:29 final size:28
Alignment explanation
Indices: 29159360--29159434 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 28
29159350 TCTAAAGAAA
* * *
29159360 TATATGATAGTATTTTCATACATTATTAT
1 TATATGATAGTAATTT-ATATATAATTAT
*
29159389 TAAAT-ATA-T-ATTTATATATAAATTAT
1 TATATGATAGTAATTTATATAT-AATTAT
29159415 TATATGATAGTAATTTATAT
1 TATATGATAGTAATTTATAT
29159435 TTTTATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
25 5 0.14
26 12 0.32
27 4 0.11
28 4 0.11
29 12 0.32
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (28 bp):
TATATGATAGTAATTTATATATAATTAT
Found at i:29170281 original size:23 final size:22
Alignment explanation
Indices: 29170255--29170303 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 22
29170245 TTTTTCTTCT
29170255 TTTTAAATATTT-ATATCATTTTA
1 TTTTAAATATTTAATAT-A-TTTA
29170278 TTTT-AATATTTAATATATTTA
1 TTTTAAATATTTAATATATTTA
29170299 TTTTA
1 TTTTA
29170304 TTTTATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 8 0.33
22 8 0.33
23 8 0.33
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTAAATATTTAATATATTTA
Found at i:29171150 original size:45 final size:45
Alignment explanation
Indices: 29171072--29171726 Score: 1093
Period size: 45 Copynumber: 14.5 Consensus size: 45
29171062 TACGTATGAT
* *
29171072 CACTTATCAC-TTGTC-CCTGATCAGATAAATGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
*
29171115 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
*
29171161 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
29171207 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
*
29171252 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTA-
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
* * *
29171297 AATCTTATTACTTTGTCACTTGATCAGATAAGTGCAGCTAGGCTAC
1 CA-CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
29171343 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
*
29171388 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
29171434 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
*
29171479 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTA-
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
29171524 CATCTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
1 CA-CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
*
29171570 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
29171616 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
*
29171661 CACTTATCACTTTGTCACTTGAACAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
*
29171706 CACTTATCACTTTTTCACTTG
1 CACTTATCACTTTGTCACTTG
29171727 GCTACCACTT
Statistics
Matches: 581, Mismatches: 20, Indels: 20
0.94 0.03 0.03
Matches are distributed among these distances:
43 10 0.02
44 5 0.01
45 305 0.52
46 261 0.45
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (45 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
Found at i:29171196 original size:91 final size:91
Alignment explanation
Indices: 29171072--29171726 Score: 1117
Period size: 91 Copynumber: 7.2 Consensus size: 91
29171062 TACGTATGAT
* *
29171072 CACTTATCAC-TTGTC-CCTGATCAGATAAATGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
29171135 GATCAGATAAGTGTAGCTAAAGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
*
29171161 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACT
*
29171226 TGATCAGATAAGTGTAGCT-AGGCTAC
65 TGATCAGATAAGTGTAGCTAAAGCTAC
* * *
29171252 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTA-AATCTTATTACTTTGTCAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTACCA-CTTATCACTTTGTCAC
* *
29171316 TTGATCAGATAAGTGCAGCT-AGGCTAC
64 TTGATCAGATAAGTGTAGCTAAAGCTAC
29171343 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
29171408 GATCAGATAAGTGTAGCTAAAGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
29171434 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
29171499 GATCAGATAAGTGTAGCTAAAGCTA-
66 GATCAGATAAGTGTAGCTAAAGCTAC
29171524 CATCTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACT
1 CA-CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACT
29171589 TGATCAGATAAGTGTAGCTAAAGCTAC
65 TGATCAGATAAGTGTAGCTAAAGCTAC
29171616 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
* *
29171681 GAACAGATAAGTGTAGCT-AGGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
*
29171706 CACTTATCACTTTTTCACTTG
1 CACTTATCACTTTGTCACTTG
29171727 GCTACCACTT
Statistics
Matches: 543, Mismatches: 15, Indels: 15
0.95 0.03 0.03
Matches are distributed among these distances:
89 10 0.02
90 73 0.13
91 414 0.76
92 46 0.08
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (91 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
GATCAGATAAGTGTAGCTAAAGCTAC
Found at i:29171485 original size:227 final size:228
Alignment explanation
Indices: 29171074--29171850 Score: 1278
Period size: 227 Copynumber: 3.5 Consensus size: 228
29171064 CGTATGATCA
* *
29171074 CTTATCAC-TTGTC-CCTGATCAGATAAATGTAGCTAGGCTACCACTTATCACTTTGTCACTTGA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGA
29171137 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
66 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
29171202 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGT
131 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGT
*
29171267 CACTTGATCAGATAAGTGTAGCTAAAGCTAAAT
196 CACTTGATCAGATAAGTGTAGCTAAAGCTACAT
* *
29171300 CTTATTACTTTGTCACTTGATCAGATAAGTGCAGCTAGGCTACCACTTATCACTTTGTCACTTGA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGA
*
29171365 TCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
66 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
29171429 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGT
131 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGT
29171494 CACTTGATCAGATAAGTGTAGCTAAAGCTACAT
196 CACTTGATCAGATAAGTGTAGCTAAAGCTACAT
29171527 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGA
*
29171592 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AG
66 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
*
29171656 GCTACCACTTATCACTTTGTCACTTGAACAGATAAGTGTAGCTAGGCTACCACTTATCAC--T-T
131 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGT
*
29171718 ---TT--TCA-CT---TG--GCT--A-C--CA-
196 CACTTGATCAGATAAGTGTAGCTAAAGCTACAT
* *
29171734 CTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTG
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACTTG
29171799 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
65 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
29171851 AGTACTCAAA
Statistics
Matches: 533, Mismatches: 14, Indels: 26
0.93 0.02 0.05
Matches are distributed among these distances:
207 35 0.07
208 81 0.15
210 1 0.00
211 1 0.00
213 3 0.01
215 2 0.00
218 1 0.00
219 3 0.01
221 2 0.00
224 1 0.00
225 1 0.00
226 7 0.01
227 288 0.54
228 107 0.20
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (228 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGA
TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGT
CACTTGATCAGATAAGTGTAGCTAAAGCTACAT
Found at i:29171736 original size:26 final size:26
Alignment explanation
Indices: 29171700--29171752 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
29171690 AGTGTAGCTA
29171700 GGCTACCACTTATCACTTTTTCACTT
1 GGCTACCACTTATCACTTTTTCACTT
29171726 GGCTACCACTTATCACTTTTTCACTT
1 GGCTACCACTTATCACTTTTTCACTT
29171752 G
1 G
29171753 ATCAGATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.30, G:0.09, T:0.42
Consensus pattern (26 bp):
GGCTACCACTTATCACTTTTTCACTT
Found at i:29171739 original size:71 final size:72
Alignment explanation
Indices: 29171655--29171798 Score: 245
Period size: 71 Copynumber: 2.0 Consensus size: 72
29171645 AGTGTAGCTA
*
29171655 GGCTACCACTTATCACTTTGTCACTTGAACAGATAAGTGTAGCT-AGGCTACCACTTATCACTTT
1 GGCTACCACTTATCACTTTGTCACTTGAACAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
*
29171719 TTCACTT
66 GTCACTT
* *
29171726 GGCTACCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1 GGCTACCACTTATCACTTTGTCACTTGAACAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
29171791 GTCACTT
66 GTCACTT
29171798 G
1 G
29171799 ATCAGATAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
71 42 0.62
72 26 0.38
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (72 bp):
GGCTACCACTTATCACTTTGTCACTTGAACAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
GTCACTT
Found at i:29171796 original size:46 final size:46
Alignment explanation
Indices: 29171727--29171850 Score: 239
Period size: 46 Copynumber: 2.7 Consensus size: 46
29171717 TTTTCACTTG
*
29171727 GCTACCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAA
1 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
29171773 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
1 GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
29171819 GCTACCACTTATCACTTTGTCACTTGATCAGA
1 GCTACCACTTATCACTTTGTCACTTGATCAGA
29171851 AGTACTCAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (46 bp):
GCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAA
Found at i:29175642 original size:55 final size:55
Alignment explanation
Indices: 29175550--29175659 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 55
29175540 AAATTATAGA
* * * *
29175550 TTGCAAATTAATTATTCATGAGCACTATTCAAGTTAAAAGTGATGATTTATCATC
1 TTGCAAATTAATTATTCATAAGCAATAATCAAATTAAAAGTGATGATTTATCATC
29175605 TTGCAAATTAATTATTCATAAGCAATAATCAAATTAAAAGTGATGATTTATCATC
1 TTGCAAATTAATTATTCATAAGCAATAATCAAATTAAAAGTGATGATTTATCATC
29175660 CAATGAATAC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (55 bp):
TTGCAAATTAATTATTCATAAGCAATAATCAAATTAAAAGTGATGATTTATCATC
Found at i:29180479 original size:55 final size:55
Alignment explanation
Indices: 29180419--29180528 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
29180409 AAATTACAGA
* *
29180419 TTGCAAATTAATTATTAATGAGCACTATTCAAATTAAAAGTGATGATTTATCATC
1 TTGCAAATTAATTATTAATAAGCACTAATCAAATTAAAAGTGATGATTTATCATC
*
29180474 TTGCAAATTAATTATTCATAAGCACTAATCAAATTAAAAGTGATGATTTATCATC
1 TTGCAAATTAATTATTAATAAGCACTAATCAAATTAAAAGTGATGATTTATCATC
29180529 CAACGAATAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (55 bp):
TTGCAAATTAATTATTAATAAGCACTAATCAAATTAAAAGTGATGATTTATCATC
Found at i:29185337 original size:16 final size:17
Alignment explanation
Indices: 29185307--29185339 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29185297 TTTCAAATAT
*
29185307 AATTTCCCCACAACCAA
1 AATTTCCCCAAAACCAA
29185324 AATTT-CCCAAAACCAA
1 AATTTCCCCAAAACCAA
29185340 CCAATTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.18
Consensus pattern (17 bp):
AATTTCCCCAAAACCAA
Found at i:29185469 original size:38 final size:39
Alignment explanation
Indices: 29185424--29185497 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
29185414 AAATTTTAAA
* * *
29185424 TCAACATATGCGTTT-ACCCCAACGGCTAAAAGAAATTT
1 TCAACATATCCATTTCACCCCAACAGCTAAAAGAAATTT
* *
29185462 TCAACATATCCATTTCATCCCAACAGTTAAAAGAAA
1 TCAACATATCCATTTCACCCCAACAGCTAAAAGAAA
29185498 ATTCCAAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 13 0.43
39 17 0.57
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (39 bp):
TCAACATATCCATTTCACCCCAACAGCTAAAAGAAATTT
Found at i:29189306 original size:32 final size:32
Alignment explanation
Indices: 29189257--29189335 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
29189247 TCCTAATTGG
* * * *
29189257 TTTAGTTGTTT-GTTTATTTTATTTTTATTTGT
1 TTTAGTTATTTAG-TTATTTTATATTTATCTCT
29189289 TTTAGTTATTTAGTTATTTTATATTTATCTCT
1 TTTAGTTATTTAGTTATTTTATATTTATCTCT
29189321 TTTA-TTATTTA-TTAT
1 TTTAGTTATTTAGTTAT
29189336 AATATAGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 4 0.10
31 7 0.17
32 30 0.71
33 1 0.02
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.71
Consensus pattern (32 bp):
TTTAGTTATTTAGTTATTTTATATTTATCTCT
Found at i:29195690 original size:25 final size:25
Alignment explanation
Indices: 29195662--29195714 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
29195652 ACATTTTTCC
** *
29195662 AAATATTCAAAAATTTATAATTATA
1 AAATATTCAAAAAAATAAAATTATA
*
29195687 AAATATTTAAAAAAATAAAATTATA
1 AAATATTCAAAAAAATAAAATTATA
29195712 AAA
1 AAA
29195715 ATAAAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
AAATATTCAAAAAAATAAAATTATA
Found at i:29197127 original size:18 final size:18
Alignment explanation
Indices: 29197104--29197146 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29197094 ACCCAATCTA
**
29197104 AACCCAACTATTCAACCC
1 AACCCAACTACCCAACCC
*
29197122 AACCCAATTACCCAACCC
1 AACCCAACTACCCAACCC
29197140 AACCCAA
1 AACCCAA
29197147 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.47, G:0.00, T:0.12
Consensus pattern (18 bp):
AACCCAACTACCCAACCC
Found at i:29197258 original size:9 final size:9
Alignment explanation
Indices: 29197244--29197301 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
29197234 GTAGTGATTC
29197244 AATTCGGTT
1 AATTCGGTT
29197253 AATTCGAG-T
1 AATTCG-GTT
29197262 AATTCGGTT
1 AATTCGGTT
29197271 AATTCAGG-T
1 AATTC-GGTT
*
29197280 AATTAGGTT
1 AATTCGGTT
29197289 AATTCGGTT
1 AATTCGGTT
29197298 AATT
1 AATT
29197302 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 3 0.07
9 37 0.86
10 3 0.07
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:29197378 original size:25 final size:25
Alignment explanation
Indices: 29197350--29197398 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
29197340 TCGGTTAACC
29197350 AACCGAATTAACCAAAAAAATTTCA
1 AACCGAATTAACCAAAAAAATTTCA
*
29197375 AACCGAATTAACCGAAAAAATTTC
1 AACCGAATTAACCAAAAAAATTTC
29197399 GGTTTGGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.53, C:0.20, G:0.06, T:0.20
Consensus pattern (25 bp):
AACCGAATTAACCAAAAAAATTTCA
Found at i:29208537 original size:17 final size:18
Alignment explanation
Indices: 29208517--29208552 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
29208507 CACACTCATT
29208517 TTCTCAATGTTTTT-TTC
1 TTCTCAATGTTTTTCTTC
*
29208534 TTCTCCATGTTTTTCTTC
1 TTCTCAATGTTTTTCTTC
29208552 T
1 T
29208553 ATTGCTTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.08, C:0.22, G:0.06, T:0.64
Consensus pattern (18 bp):
TTCTCAATGTTTTTCTTC
Found at i:29216413 original size:5 final size:5
Alignment explanation
Indices: 29216403--29216427 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29216393 TTGTATACGA
29216403 ATCAT ATCAT ATCAT ATCAT ATCAT
1 ATCAT ATCAT ATCAT ATCAT ATCAT
29216428 GTCCTACCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATCAT
Found at i:29219182 original size:34 final size:35
Alignment explanation
Indices: 29219138--29219204 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
29219128 CAGTAAAATA
*
29219138 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
29219172 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
29219205 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:29220396 original size:16 final size:16
Alignment explanation
Indices: 29220377--29220410 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29220367 TTTTTTTAAA
29220377 TTTCCTTTATTTCATT
1 TTTCCTTTATTTCATT
*
29220393 TTTCCTTTGTTTCATT
1 TTTCCTTTATTTCATT
29220409 TT
1 TT
29220411 CTATGTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTCCTTTATTTCATT
Found at i:29221613 original size:56 final size:56
Alignment explanation
Indices: 29221552--29221665 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
29221542 TTGATAATTT
29221552 AAATAAAATATATCATACTCAATTAATTTACCCATAGTTCAAACTCATGAAAAACC
1 AAATAAAATATATCATACTCAATTAATTTACCCATAGTTCAAACTCATGAAAAACC
29221608 AAATAAAATATATCATACTCAATTAATTTACCCATAGTTCAAACTCATGAAAAACC
1 AAATAAAATATATCATACTCAATTAATTTACCCATAGTTCAAACTCATGAAAAACC
29221664 AA
1 AA
29221666 CCGTAAAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.49, C:0.19, G:0.04, T:0.28
Consensus pattern (56 bp):
AAATAAAATATATCATACTCAATTAATTTACCCATAGTTCAAACTCATGAAAAACC
Found at i:29224588 original size:11 final size:11
Alignment explanation
Indices: 29224569--29224616 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
29224559 TTATATCAAC
29224569 AAATGATTTTA
1 AAATGATTTTA
*
29224580 AAATTATTTTTA
1 AAATGA-TTTTA
29224592 AAA--ATTATTA
1 AAATGATT-TTA
29224602 AAATGATTTTA
1 AAATGATTTTA
29224613 AAAT
1 AAAT
29224617 CATCATCATC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
9 2 0.06
10 7 0.22
11 12 0.38
12 11 0.34
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (11 bp):
AAATGATTTTA
Found at i:29224810 original size:20 final size:20
Alignment explanation
Indices: 29224782--29224821 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29224772 CTGTATTAAA
*
29224782 GAAATCTGTTCTTAAAATTC
1 GAAACCTGTTCTTAAAATTC
29224802 GAAACCTGTTCTTAAAATTC
1 GAAACCTGTTCTTAAAATTC
29224822 TTACACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (20 bp):
GAAACCTGTTCTTAAAATTC
Found at i:29226038 original size:22 final size:22
Alignment explanation
Indices: 29226013--29226104 Score: 105
Period size: 22 Copynumber: 4.2 Consensus size: 22
29226003 AAATTCAATA
* *
29226013 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
29226035 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTC
*
29226057 TCAATTCCCTTCAAAATTTC-C
1 TCAATTCCCTTCAAAAATTCTC
* *
29226078 ATCAATTTCCTTCCAAAATTCTC
1 -TCAATTCCCTTCAAAAATTCTC
29226101 TCAA
1 TCAA
29226105 ACTCTCAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
21 1 0.02
22 60 0.97
23 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.41
Consensus pattern (22 bp):
TCAATTCCCTTCAAAAATTCTC
Found at i:29226070 original size:44 final size:44
Alignment explanation
Indices: 29226013--29226104 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
29226003 AAATTCAATA
* * *
29226013 TCAATTTCTTTCAAAAATTCTC-TCAA-TTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTC-CATCAATTTCCTTCCAAAA-TTCTC
*
29226057 TCAATTCCCTTCAAAATTTCCATCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCCATCAATTTCCTTCCAAAATTCTC
29226101 TCAA
1 TCAA
29226105 ACTCTCAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 30 0.71
45 11 0.26
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.41
Consensus pattern (44 bp):
TCAATTCCCTTCAAAAATTCCATCAATTTCCTTCCAAAATTCTC
Found at i:29226153 original size:22 final size:22
Alignment explanation
Indices: 29226103--29226157 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
29226093 AAATTCTCTC
*
29226103 AAACTCTCAAATTCCTTCCAAA
1 AAACTCTCAAATTCCTTCAAAA
** *
29226125 ATCCTCTCAATTTCCTTCAAAA
1 AAACTCTCAAATTCCTTCAAAA
29226147 AAACTCT-AAAT
1 AAACTCTCAAAT
29226158 CCATATTAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (22 bp):
AAACTCTCAAATTCCTTCAAAA
Found at i:29226244 original size:29 final size:29
Alignment explanation
Indices: 29226189--29226244 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
29226179 ATTAAATTTC
29226189 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTT
*
29226218 ATTTTTTTAA-ATAATTTTAAAATTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTT
29226245 AATATTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTT
Found at i:29226252 original size:29 final size:29
Alignment explanation
Indices: 29226189--29226252 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
29226179 ATTAAATTTC
*
29226189 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTA
*
29226218 ATTTTTTTAA-ATAATTTTAAAATTTTTA
1 ATTTTTTTAAGAAAATTTTAAAATTTTTA
*
29226246 ATATTTT
1 ATTTTTT
29226253 CAACAATGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTA
Found at i:29228552 original size:23 final size:24
Alignment explanation
Indices: 29228516--29228605 Score: 76
Period size: 23 Copynumber: 3.8 Consensus size: 24
29228506 ACATTATTTG
* *
29228516 ATTAAAATCTCTAACCCTACTT-A
1 ATTAAAAACCCTAACCCTACTTAA
* ** *
29228539 CTTAAAAACCCTAA-TTTAATTAA
1 ATTAAAAACCCTAACCCTACTTAA
29228562 ATTAAAAACCCTAAACCCTACTTAA
1 ATTAAAAACCCT-AACCCTACTTAA
* * *
29228587 TTTTATAACCCTAACCCTA
1 ATTAAAAACCCTAACCCTA
29228606 ACCTAATTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
22 4 0.08
23 23 0.45
24 9 0.18
25 15 0.29
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (24 bp):
ATTAAAAACCCTAACCCTACTTAA
Found at i:29228634 original size:28 final size:28
Alignment explanation
Indices: 29228599--29228850 Score: 362
Period size: 28 Copynumber: 9.4 Consensus size: 28
29228589 TTATAACCCT
**
29228599 AACCCTAACCTAATTTAATTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
*
29228627 AACCCTAACCTAACCTAATTTAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
*
29228655 AAACCTAACCTAACCTAATTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
29228683 AACCCTAACCTAACCTAATTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
*
29228711 AACCCTAACCTAACCTACTTAAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
*
29228739 AACCCTAACCTAACCTAATTTAATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
29228767 AACCCTAACCTAA--T--TT-AATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
* *
29228790 AACCCTAACCTAACCTAATTTAATTCAA
1 AACCCTAACCTAACCTAATTAAATTAAA
29228818 AACCCTAACCTAA--T--TT-AATTAAA
1 AACCCTAACCTAACCTAATTAAATTAAA
29228841 AACCCTAACC
1 AACCCTAACC
29228851 CTATTTAATT
Statistics
Matches: 208, Mismatches: 11, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
23 36 0.17
24 4 0.02
25 1 0.00
26 2 0.01
27 2 0.01
28 163 0.78
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (28 bp):
AACCCTAACCTAACCTAATTAAATTAAA
Found at i:29228797 original size:18 final size:20
Alignment explanation
Indices: 29228751--29228793 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
29228741 CCCTAACCTA
29228751 ACCTAATTTAATTAAAAACCC
1 ACCTAATTTAATTAAAAA-CC
29228772 TAACCTAATTTAATTAAAAACC
1 --ACCTAATTTAATTAAAAACC
29228794 CTAACCTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
ACCTAATTTAATTAAAAACC
Found at i:29228847 original size:18 final size:18
Alignment explanation
Indices: 29228826--29228878 Score: 52
Period size: 23 Copynumber: 2.7 Consensus size: 18
29228816 AAAACCCTAA
29228826 CCTAATTTAATTAAAAAC
1 CCTAATTTAATTAAAAAC
29228844 CCTAACCCTATTTAATTAAAAAC
1 CCT-A----ATTTAATTAAAAAC
*
29228867 CCTAATTAAATT
1 CCTAATTTAATT
29228879 GTAGTTTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
18 10 0.34
19 1 0.03
22 1 0.03
23 17 0.59
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (18 bp):
CCTAATTTAATTAAAAAC
Found at i:29232161 original size:85 final size:85
Alignment explanation
Indices: 29232018--29232218 Score: 348
Period size: 85 Copynumber: 2.4 Consensus size: 85
29232008 CTTGCTACTA
* * *
29232018 TAGCGAAATCGTGTCTACGAGGGCGCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAATT
1 TAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTACTCAGAAACGTCAAAAAAAAATT
* *
29232083 ATTTCCTACATGACCAACTG
66 ATTTCCTAAACGACCAACTG
*
29232103 TAGCGAAATCGCGTCCACAAGGGCGCGATTTGACACTATTTACTCAGAAACGTCAAAAAAAAATT
1 TAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTACTCAGAAACGTCAAAAAAAAATT
29232168 ATTTCCTAAACGACCAACTG
66 ATTTCCTAAACGACCAACTG
29232188 TAGCGAAATCGCGTCCACGAGGGCGCGATTT
1 TAGCGAAATCGCGTCCACGAGGGCGCGATTT
29232219 CATAATTTCT
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 109 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (85 bp):
TAGCGAAATCGCGTCCACGAGGGCGCGATTTGACACTATTTACTCAGAAACGTCAAAAAAAAATT
ATTTCCTAAACGACCAACTG
Found at i:29232351 original size:125 final size:125
Alignment explanation
Indices: 29232127--29232408 Score: 318
Period size: 125 Copynumber: 2.3 Consensus size: 125
29232117 CCACAAGGGC
29232127 GCGATTTGACACTATTTACTCAGAAACGTCAAAAAAAAATTATTTCCTAAACGACCAACTGTAGC
1 GCGATTTGACACTATTTACTCAGAAACGTCAAAAAAAAATTATTTCCTAAACGACCAACTGTAGC
* * *
29232192 GAAATCGCGTCCACGAGGGCGCGATTTCATAATTTCTTCTCATATAACATCCTGGTATCA
66 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCATATAACATCCTGGTATCA
* * * * * * *
29232252 GCGATTTTATACTATTTCCTCAGAAATTGTCAAAAAATAATTATTT-CTCACATGACC-ACTGTA
1 GCGATTTGACACTATTTACTCAGAAA-CGTCAAAAAAAAATTATTTCCT-AAACGACCAACTGTA
* * * * * * * * **
29232315 GCGAAATTGCGTCCACGAGTCCACTATTTCACAATTTCTTCTTAAATAGCATTCTAGTAGAA
64 GCGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCATATAACATCCTGGTATCA
**
29232377 GCGATTTCCCACTATTTAAC-CAGAAACGTCAA
1 GCGATTTGACACTATTT-ACTCAGAAACGTCAA
29232409 CTCGAAAAAA
Statistics
Matches: 129, Mismatches: 25, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
124 5 0.04
125 100 0.78
126 24 0.19
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (125 bp):
GCGATTTGACACTATTTACTCAGAAACGTCAAAAAAAAATTATTTCCTAAACGACCAACTGTAGC
GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCATATAACATCCTGGTATCA
Found at i:29236590 original size:5 final size:5
Alignment explanation
Indices: 29236580--29236604 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29236570 ACTCTTTTTT
29236580 TCCTC TCCTC TCCTC TCCTC TCCTC
1 TCCTC TCCTC TCCTC TCCTC TCCTC
29236605 CTTTGCCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
TCCTC
Found at i:29238917 original size:551 final size:551
Alignment explanation
Indices: 29237868--29238963 Score: 1843
Period size: 551 Copynumber: 2.0 Consensus size: 551
29237858 TTTCTGGTGG
* *
29237868 CTTGTCCACAATATTATGTATCTGGCAGTAAATCCATAATTTCTGGTGGTTGGACCACATTTTGG
1 CTTGTCCACAATATTATGTATCTGGCAGTAAATCCACAATTTCTAGTGGTTGGACCACATTTTGG
*
29237933 TGTGTTATTGGTTGGATGAGTTATGAGGAACTCTGTATGGCGTGTAGCGGAGTTGGGTAGGATTT
66 TGTGTTATTGGTTGGATGAGTTATGAGGAACTCTATATGGCGTGTAGCGGAGTTGGGTAGGATTT
29237998 AAGTTCTAATATCTGTATTGTATTCTAAAAATGTTGTATTAAATACGTCATTACACAATCTGCCA
131 AAGTTCTAATATCTGTATTGTATTCTAAAAATGTTGTATTAAATACGTCATTACACAATCTGCCA
29238063 TATTTGATTTATAATTGAGTAATTTATATATGTTATGGACTGATTAATATGATGTTATAATGAAT
196 TATTTGATTTATAATTGAGTAATTTATATATGTTATGGACTGATTAATATGATGTTATAATGAAT
* * ** * *
29238128 TGTTTTTGTGAAATAATTGTTATTTAAGACCTACATTGAGCCTTTTTAATCTTACCTCCTTAAAC
261 TATTTTTGTGAAATAATTGTTACTTAAGACCTACATTGAGAATTTTTAAGCTTACCCCCTTAAAC
* * **
29238193 TTTGATTTTAGATAATAGGGACTAGGATGGGCTTGGCTACGAAGGTACTCTTGGTTATTTTTTGA
326 TTTGATTTCAGATAATAGAGACTAGGATGGGCTTGGCTACGAAGGTACTCTTGGTTATTTTCCGA
*
29238258 AAAACCTTGCAAGTAGTGGTATTGGAAATTTTAGTTTTTGTTCATGCTTTATGGACTTTAATTTT
391 AAAACCTTGCAAGTAGTGGTATTGGAAATTTTAGTTTGTGTTCATGCTTTATGGACTTTAATTTT
*** * *
29238323 GGGACTTTGGTTTGGATTTTTGATTTGCGAAATTTGTATAATGTTTTGGGGTTTTTCTTTTCTGC
456 GGGACTTTGGTTCAAATTTTTGATTTGCGAAATTTGGATAATGTTTTGGAGTTTTTCTTTTCTGC
29238388 ATGATTTGTTAGGTTAAATTATAATGTTTTT
521 ATGATTTGTTAGGTTAAATTATAATGTTTTT
* *
29238419 CTTGTCCACAATATTATGTATCTGGCAGTAAATCTACAATTTTTAGTGGTTGGACCACATTTTGG
1 CTTGTCCACAATATTATGTATCTGGCAGTAAATCCACAATTTCTAGTGGTTGGACCACATTTTGG
*
29238484 TGTGTTATTGGTTGGATGAGTTAT-AGGGAACTCTATGTGGCGTGTAGCGGAGTTGGGTAGGATT
66 TGTGTTATTGGTTGGATGAGTTATGA-GGAACTCTATATGGCGTGTAGCGGAGTTGGGTAGGATT
* *
29238548 TAAGTTCTAATATCTGTATTGTATTCTAAAAATGTTGTATTAATTACGTCATTACACGATCTGCC
130 TAAGTTCTAATATCTGTATTGTATTCTAAAAATGTTGTATTAAATACGTCATTACACAATCTGCC
* *
29238613 ATATTTGATTTATAATTGAGTAATTTATATATGTTATGGGCTGATTAATATGATGTTATAATGAG
195 ATATTTGATTTATAATTGAGTAATTTATATATGTTATGGACTGATTAATATGATGTTATAATGAA
* * *
29238678 TTATTTTTGTTAAATTATTGTTACTTAAGACCTACATTGGGAATTTTTAAGCTTACCCCCTTAAA
260 TTATTTTTGTGAAATAATTGTTACTTAAGACCTACATTGAGAATTTTTAAGCTTACCCCCTTAAA
* *
29238743 CTTTGATTTCAGATAATCGAGACTAGGATGGGCTTGGCTACGAAGGTACTCTTGGTTGTTTTCCG
325 CTTTGATTTCAGATAATAGAGACTAGGATGGGCTTGGCTACGAAGGTACTCTTGGTTATTTTCCG
* * *
29238808 GAAAACCTTGCAAGTAGTGGTATTGGACATTTTAGTTTGTGTTCATGCTTTATGGACTTTATTTT
390 AAAAACCTTGCAAGTAGTGGTATTGGAAATTTTAGTTTGTGTTCATGCTTTATGGACTTTAATTT
* *
29238873 TGGGACTTTGGTTCAAATTTTTGATTTGTGAACTTTGGATAATGTTTTGGAGTTTTTCTTTTCTG
455 TGGGACTTTGGTTCAAATTTTTGATTTGCGAAATTTGGATAATGTTTTGGAGTTTTTCTTTTCTG
*
29238938 CATGATTTGTTATGTTAAATTATAAT
520 CATGATTTGTTAGGTTAAATTATAAT
29238964 TTAAATAATT
Statistics
Matches: 507, Mismatches: 37, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
550 1 0.00
551 506 1.00
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (551 bp):
CTTGTCCACAATATTATGTATCTGGCAGTAAATCCACAATTTCTAGTGGTTGGACCACATTTTGG
TGTGTTATTGGTTGGATGAGTTATGAGGAACTCTATATGGCGTGTAGCGGAGTTGGGTAGGATTT
AAGTTCTAATATCTGTATTGTATTCTAAAAATGTTGTATTAAATACGTCATTACACAATCTGCCA
TATTTGATTTATAATTGAGTAATTTATATATGTTATGGACTGATTAATATGATGTTATAATGAAT
TATTTTTGTGAAATAATTGTTACTTAAGACCTACATTGAGAATTTTTAAGCTTACCCCCTTAAAC
TTTGATTTCAGATAATAGAGACTAGGATGGGCTTGGCTACGAAGGTACTCTTGGTTATTTTCCGA
AAAACCTTGCAAGTAGTGGTATTGGAAATTTTAGTTTGTGTTCATGCTTTATGGACTTTAATTTT
GGGACTTTGGTTCAAATTTTTGATTTGCGAAATTTGGATAATGTTTTGGAGTTTTTCTTTTCTGC
ATGATTTGTTAGGTTAAATTATAATGTTTTT
Found at i:29246798 original size:51 final size:51
Alignment explanation
Indices: 29246739--29247178 Score: 444
Period size: 51 Copynumber: 8.7 Consensus size: 51
29246729 TATCGATGAA
* * *
29246739 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
** * * * * * *
29246790 CAAATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATGTTGGT
* * * *
29246841 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
* * * * *
29246892 CACATGTGTAGTATTAAGTGAAGGCTACTATGTGTACCGA-AAA-GCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATG--TTGGT
* * * * *
29246943 CACGTGTGTAATATTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
* * * * *
29246994 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAA-GCTTTGGC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATG--TTGGT
* ** *
29247045 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
* ** *
29247095 CACGTGTGTAGTACTATGTAAAGGCTACTACGTGAACC-ATAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
29247145 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
29247179 TATCGAATGA
Statistics
Matches: 319, Mismatches: 59, Indels: 23
0.80 0.15 0.06
Matches are distributed among these distances:
49 2 0.01
50 90 0.28
51 222 0.70
52 4 0.01
53 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
Found at i:29246915 original size:102 final size:102
Alignment explanation
Indices: 29246739--29247184 Score: 646
Period size: 102 Copynumber: 4.4 Consensus size: 102
29246729 TATCGATGAA
* *
29246739 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCAAATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
* *
29246804 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
*
29246841 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAT
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
29246906 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* * *
29246943 CACGTGTGTAATATTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
*
29247008 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGC
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* * * *** *
29247045 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
* * * * * *
29247109 TATGTAAAGGCTACTACGTGAACC-ATAAAAC-TTGAT
66 TAAGTGAAGGCTACTATGTGTACCGA-AAAGCTTTGGT
* *
29247145 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGA
29247185 ATGATAAAAG
Statistics
Matches: 312, Mismatches: 30, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
100 40 0.13
101 44 0.14
102 228 0.73
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGATCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
Found at i:29254137 original size:16 final size:16
Alignment explanation
Indices: 29254104--29254149 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
29254094 TTATCACCCA
*
29254104 TTTCATCTT--CTTCC
1 TTTCATCTTCACTTCT
29254118 TTTCATCTTCACTTCT
1 TTTCATCTTCACTTCT
29254134 TTTCATCTTCACTTCT
1 TTTCATCTTCACTTCT
29254150 CTCTCTAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 9 0.31
16 20 0.69
ACGTcount: A:0.11, C:0.33, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTCATCTTCACTTCT
Found at i:29254342 original size:13 final size:13
Alignment explanation
Indices: 29254308--29254347 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
29254298 AAGAGAGGAG
29254308 AAAA-GAAGAAAA
1 AAAATGAAGAAAA
29254320 AACAAT--AGAAAA
1 AA-AATGAAGAAAA
29254332 AAAATGAAGAAAA
1 AAAATGAAGAAAA
29254345 AAA
1 AAA
29254348 GGAGAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 3 0.12
12 10 0.42
13 11 0.46
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.05
Consensus pattern (13 bp):
AAAATGAAGAAAA
Found at i:29254357 original size:25 final size:24
Alignment explanation
Indices: 29254308--29254359 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
29254298 AAGAGAGGAG
*
29254308 AAAAGAAGAAAAAACAATAGAAAA
1 AAAAGAAGAAAAAACAAGAGAAAA
* *
29254332 AAAATGAAGAAAAAA-AGGAGAGAA
1 AAAA-GAAGAAAAAACAAGAGAAAA
29254356 AAAA
1 AAAA
29254360 CATTAGTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (24 bp):
AAAAGAAGAAAAAACAAGAGAAAA
Found at i:29266059 original size:16 final size:15
Alignment explanation
Indices: 29266027--29266067 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
29266017 ATAAATAATA
*
29266027 AAAAGAATAAA-CAG
1 AAAAGAAAAAACCAG
29266041 AAAACGAAAAAACCAG
1 AAAA-GAAAAAACCAG
29266057 AAAAGAAAAAA
1 AAAAGAAAAAA
29266068 GAGCAAACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 13 0.54
16 7 0.29
ACGTcount: A:0.76, C:0.10, G:0.12, T:0.02
Consensus pattern (15 bp):
AAAAGAAAAAACCAG
Found at i:29266906 original size:22 final size:23
Alignment explanation
Indices: 29266872--29266915 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
29266862 ACCCTACCCC
29266872 TAAAATATTAAAAACCATAACCT
1 TAAAATATTAAAAACCATAACCT
*
29266895 TAAAA-ATTAAAAACCTTAACC
1 TAAAATATTAAAAACCATAACC
29266916 CTATAAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.25
Consensus pattern (23 bp):
TAAAATATTAAAAACCATAACCT
Found at i:29273502 original size:19 final size:19
Alignment explanation
Indices: 29273461--29273502 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
29273451 GAATAAAACT
*
29273461 TAAAATTAAATTTAGTTAA
1 TAAAATTAAACTTAGTTAA
*
29273480 TAAAATTAGACTTA-TTAA
1 TAAAATTAAACTTAGTTAA
29273498 CTAAA
1 -TAAA
29273503 TTTTTTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (19 bp):
TAAAATTAAACTTAGTTAA
Found at i:29275618 original size:22 final size:23
Alignment explanation
Indices: 29275572--29275636 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 23
29275562 ATAAAATTGT
*
29275572 TAAATA-TTAAAATAATATAATA
1 TAAATATTTAAAATAATATAAAA
29275594 TAAATATTTAAAA-AAT-TAAAAA
1 TAAATATTTAAAATAATAT-AAAA
*
29275616 TAAATGAGTTTAAATTAATAT
1 TAAAT-A-TTTAAAATAATAT
29275637 GATAGGATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
21 1 0.03
22 17 0.49
23 7 0.20
24 6 0.17
25 3 0.09
26 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (23 bp):
TAAATATTTAAAATAATATAAAA
Found at i:29279715 original size:22 final size:22
Alignment explanation
Indices: 29279687--29279731 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29279677 TCTGTGCCTC
29279687 AGTTGTTCATGCTTCCAATTAA
1 AGTTGTTCATGCTTCCAATTAA
29279709 AGTTGTTCATGCTTCCAATTAA
1 AGTTGTTCATGCTTCCAATTAA
29279731 A
1 A
29279732 ATCATTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (22 bp):
AGTTGTTCATGCTTCCAATTAA
Found at i:29279739 original size:22 final size:22
Alignment explanation
Indices: 29279692--29279742 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
29279682 GCCTCAGTTG
* **
29279692 TTCATGCTTCCAATTAAAGTTG
1 TTCATGCTTCCAATTAAAATCA
29279714 TTCATGCTTCCAATTAAAATCA
1 TTCATGCTTCCAATTAAAATCA
29279736 TTCATGC
1 TTCATGC
29279743 ATTAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (22 bp):
TTCATGCTTCCAATTAAAATCA
Found at i:29285619 original size:6 final size:6
Alignment explanation
Indices: 29285608--29285634 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29285598 AAGTGGCTTT
29285608 TTATAA TTATAA TTATAA TTATAA TTA
1 TTATAA TTATAA TTATAA TTATAA TTA
29285635 CTATGTTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Found at i:29285747 original size:17 final size:18
Alignment explanation
Indices: 29285725--29285758 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
29285715 TGTCCGCGAC
29285725 AAACGCGA-CGCGACCGA
1 AAACGCGACCGCGACCGA
29285742 AAACGCGACCGCGACCG
1 AAACGCGACCGCGACCG
29285759 CAATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.38, G:0.29, T:0.00
Consensus pattern (18 bp):
AAACGCGACCGCGACCGA
Found at i:29286448 original size:50 final size:50
Alignment explanation
Indices: 29286386--29286486 Score: 132
Period size: 50 Copynumber: 2.0 Consensus size: 50
29286376 CGGACCATAC
*
29286386 TGCACAAATAAAATCCATATAGAATTACTCT-TCTTCTATTTGACATTGAT
1 TGCACAAATAAAATCCATATAGAACTACTCTCT-TTCTATTTGACATTGAT
* * * **
29286436 TGCACAAGTAAAATTCGTATAGAACTGGTCTCTTTCTATTTGACATTGAT
1 TGCACAAATAAAATCCATATAGAACTACTCTCTTTCTATTTGACATTGAT
29286486 T
1 T
29286487 AGAATAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
50 43 0.98
51 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (50 bp):
TGCACAAATAAAATCCATATAGAACTACTCTCTTTCTATTTGACATTGAT
Found at i:29287447 original size:13 final size:13
Alignment explanation
Indices: 29287426--29287455 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29287416 AAATATATAA
*
29287426 ATTTGTAAAATTT
1 ATTTATAAAATTT
29287439 ATTTATAAAATTT
1 ATTTATAAAATTT
29287452 ATTT
1 ATTT
29287456 TTGTTCAAAA
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:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
ATTTATAAAATTT
Found at i:29288614 original size:30 final size:29
Alignment explanation
Indices: 29288559--29288627 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
29288549 TGCTCGGACT
* *
29288559 AAATTT-TCAAAAAAAGATC-ATTTTTTTA
1 AAATTTAT-AAAAAAAGACCAATTTTTTGA
29288587 AAATATTATAAAAAATAGACCAATTTTTTGA
1 AAAT-TTATAAAAAA-AGACCAATTTTTTGA
29288618 AAATTTATAA
1 AAATTTATAA
29288628 GAATTAGCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 4 0.11
29 8 0.23
30 11 0.31
31 12 0.34
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (29 bp):
AAATTTATAAAAAAAGACCAATTTTTTGA
Found at i:29289690 original size:3 final size:3
Alignment explanation
Indices: 29289682--29289745 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
29289672 GGGTTTTAAA
* * * *
29289682 AAT AAT AAT ACT AAT AAT AAT GAG AAT AAT -AT GAAT GAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
29289726 AAT AAT AAAT AAT GAAT AAT
1 AAT AAT -AAT AAT -AAT AAT
29289746 CTAAGGTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
2 4 0.08
3 36 0.75
4 8 0.17
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:29289801 original size:19 final size:20
Alignment explanation
Indices: 29289770--29289807 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
29289760 CATATAAAAG
29289770 AATGTGAATAAATA-AATAT
1 AATGTGAATAAATAGAATAT
29289789 AATGTG-ATAAAATAGAATA
1 AATGTGAAT-AAATAGAATA
29289808 GATGTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.12
19 11 0.65
20 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (20 bp):
AATGTGAATAAATAGAATAT
Found at i:29290976 original size:17 final size:19
Alignment explanation
Indices: 29290956--29290993 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
29290946 TTTGTTATAA
29290956 TTTTTTTTTGT-TTT-GGT
1 TTTTTTTTTGTCTTTAGGT
29290973 TTTTTTTTTGTCTTTAGGT
1 TTTTTTTTTGTCTTTAGGT
29290992 TT
1 TT
29290994 CTGTTTAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 3 0.16
19 5 0.26
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.79
Consensus pattern (19 bp):
TTTTTTTTTGTCTTTAGGT
Found at i:29291235 original size:44 final size:44
Alignment explanation
Indices: 29291198--29291839 Score: 496
Period size: 44 Copynumber: 14.5 Consensus size: 44
29291188 CTTCGACCCA
* * **
29291198 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCGATCCA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTG
* * * * * * *
29291242 TTCCACTGTAATTTCAAGGAGACAAGACTTATAGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTG
* * * * * *
29291286 CTCCACTACAACTTTAGGGAGACAATATTTGTAACTTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAAC-TTCAATCTG
* * * * * *
29291331 CTCCACTACAACTTTAGAGAGATAAAACTTGTAATTTCAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTG
* * * ** ** *
29291375 CTTCACTGTAACTTCAGGGAGATGAGGTTTGTGTCTTCAATATG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTG
* * * *
29291419 CTCCACTGCGACCTCAAGGAGATAAGA-TCTATAACTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACT-TGTAACTTCAATCTG
* * * * *
29291463 CTCCACTGTAACTTCAGGGAGATAAGATTTGTAATTTTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAA-CTTCAATCTG
*
29291508 CTCCACTGCAACTTCAGGGAGATAATACTTGTAACTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTG
* * * * **
29291552 CTCCGCTGCAACTTCAAGGAGATGAGATTTGTGTCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTG
* * * * *
29291596 CTCCACTACGACTTCAGAGAGATAAGA-TCTATAACTTAAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACT-TGTAACTTCAATCTG
* * * * * * * * * **
29291640 TTCTATTGTAATTTTAAGGAGATAAGATTTATGTCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTG
* * * ** * *
29291684 CTCCACTACAACTTTAGGAAGATAAGACTTACAACTTCAATATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTG
* * * * * * * *
29291728 CTCCGCTACAACTTCAAGAAGATGAGATTTGTAATTTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAA-CTTCAATCTG
*
29291773 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATATG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTG
* *
29291817 CTCCGCTGCAACTTCAAGGAGAT
1 CTCCACTGCAACTTCAGGGAGAT
29291840 GAGATTCGCC
Statistics
Matches: 459, Mismatches: 132, Indels: 14
0.76 0.22 0.02
Matches are distributed among these distances:
43 2 0.00
44 345 0.75
45 112 0.24
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTG
Found at i:29291440 original size:133 final size:133
Alignment explanation
Indices: 29291198--29291845 Score: 507
Period size: 133 Copynumber: 4.9 Consensus size: 133
29291188 CTTCGACCCA
* * * ** * * * * * *
29291198 CTCCACTGCAACTTCAGGGAGATAAGACTTGT-AGCTTCGATCCATTCCACTGTAATTTCAAGGA
1 CTCCACTACAACTTCAGAGAGATAAAACTTGTAATTTTCAATCTACTCCACTGCAACTTCAGGGA
* * * * * * * * *
29291262 GACAAGACTTATAGCTTCAATCTGCTCCACTACAACTTTAGGGAGACAATATTTGTAACTTTCAG
66 GATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAAC-TTCAA
29291327 TCTG
130 TCTG
* * *
29291331 CTCCACTACAACTTTAGAGAGATAAAACTTGTAA-TTTCAATCTACTTCACTGTAACTTCAGGGA
1 CTCCACTACAACTTCAGAGAGATAAAACTTGTAATTTTCAATCTACTCCACTGCAACTTCAGGGA
* ** ** * * * * *
29291395 GATGAGGTTTGTGTCTTCAATATGCTCCACTGCGACCTCAAGGAGATAAGATCTATAACTTCAAT
66 GATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAAT
29291460 CTG
131 CTG
** * * * * * *
29291463 CTCCACTGTAACTTCAGGGAGATAAGATTTGTAATTTTTAGTCTGCTCCACTGCAACTTCAGGGA
1 CTCCACTACAACTTCAGAGAGATAAAACTTGTAATTTTCAATCTACTCCACTGCAACTTCAGGGA
* * * **
29291528 GATAATACTTGTAACTTCAATCTGCTCCGCTGCAACTTCAAGGAGATGAGATTTGTGTCTTCAAT
66 GATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAAT
29291593 CTG
131 CTG
* * * * * ** * * * * * *
29291596 CTCCACTACGACTTCAGAGAGATAAGA-TCTATAA-CTTAAATCTGTTCTATTGTAATTTTAAGG
1 CTCCACTACAACTTCAGAGAGATAAAACT-TGTAATTTTCAATCTACTCCACTGCAACTTCAGGG
* * ** * * * **
29291659 AGATAAGATTTATGTCTTCAATCTGCTCCACTACAACTT-TAGGAAGATAAGACTTACAACTTCA
65 AGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAAGG-AGATAAGATTTGTAACTTCA
* *
29291723 ATATA
129 ATCTG
* * * * * *
29291728 CTCCGCTACAACTTCA-AGAAGATGAGATTTGTAATTTTCAGTCTGCTCCACTGCAACTTCAGGG
1 CTCCACTACAACTTCAGAG-AGATAAAACTTGTAATTTTCAATCTACTCCACTGCAACTTCAGGG
* * *
29291792 AGATAAGACTTGTAACTTCAATATGCTCCGCTGCAACTTCAAGGAGATGAGATT
65 AGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT
29291846 CGCCATAATG
Statistics
Matches: 397, Mismatches: 110, Indels: 16
0.76 0.21 0.03
Matches are distributed among these distances:
131 5 0.01
132 130 0.33
133 258 0.65
134 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (133 bp):
CTCCACTACAACTTCAGAGAGATAAAACTTGTAATTTTCAATCTACTCCACTGCAACTTCAGGGA
GATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAAT
CTG
Found at i:29291508 original size:177 final size:176
Alignment explanation
Indices: 29291254--29291845 Score: 643
Period size: 177 Copynumber: 3.3 Consensus size: 176
29291244 CCACTGTAAT
* * * * * * *
29291254 TTCAAGGAGACAAGACTTATAGCTTCAATCTGCTCCACTACAACTTTAGGGAGACAATATTTGTA
1 TTCAAGGAGATAAGACTTATAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTA
* * * * *
29291319 ACTTTCAGTCTGCTCCACTACAACTTTAGAGAGATAAAACTTGTAATTTCAATCTACTTCACTGT
66 ATTTTCAGTCTGCTCCACTACAACTTTAG-GAGATAAAACTTGTAACTTCAATCTACTCCGCTGC
* * *
29291384 AACTTCAGGGAGATGAGGTTTGTGTCTTCAATATGCTCCACTGCGAC
130 AACTTCAAGGAGATGAGATTTGTGTCTTCAATCTGCTCCACTGCGAC
* * *
29291431 CTCAAGGAGATAAGA-TCTATAACTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGT
1 TTCAAGGAGATAAGACT-TATAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGT
* * * * *
29291495 AATTTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAATACTTGTAACTTCAATCTGCTCCGCTG
65 AATTTTCAGTCTGCTCCACTACAACTTTA-GGAGATAAAACTTGTAACTTCAATCTACTCCGCTG
*
29291560 CAACTTCAAGGAGATGAGATTTGTGTCTTCAATCTGCTCCACTACGAC
129 CAACTTCAAGGAGATGAGATTTGTGTCTTCAATCTGCTCCACTGCGAC
* * * * * * * *
29291608 TTC-AGAGAGATAAGA-TCTATAACTTAAATCTGTTCTATTGTAATTTTAAGGAGATAAGATTTA
1 TTCAAG-GAGATAAGACT-TATAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTG
* * * * ** *
29291671 T-GTCTTCAATCTGCTCCACTACAACTTTAGGAAGATAAGACTTACAACTTCAATATACTCCGCT
64 TAATTTTCAGTCTGCTCCACTACAACTTTAGG-AGATAAAACTTGTAACTTCAATCTACTCCGCT
* * * * * *
29291735 ACAACTTCAAGAAGATGAGATTTGTAATTTTCAGTCTGCTCCACTGCAAC
128 GCAACTTCAAGGAGATGAGATTTGT-GTCTTCAATCTGCTCCACTGCGAC
* * * * *
29291785 TTCAGGGAGATAAGACTTGTAACTTCAATATGCTCCGCTGCAACTTCAAGGAGATGAGATT
1 TTCAAGGAGATAAGACTTATAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT
29291846 CGCCATAATG
Statistics
Matches: 347, Mismatches: 61, Indels: 14
0.82 0.14 0.03
Matches are distributed among these distances:
175 2 0.01
176 75 0.22
177 267 0.77
178 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (176 bp):
TTCAAGGAGATAAGACTTATAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTA
ATTTTCAGTCTGCTCCACTACAACTTTAGGAGATAAAACTTGTAACTTCAATCTACTCCGCTGCA
ACTTCAAGGAGATGAGATTTGTGTCTTCAATCTGCTCCACTGCGAC
Found at i:29291688 original size:265 final size:266
Alignment explanation
Indices: 29291197--29291845 Score: 727
Period size: 265 Copynumber: 2.4 Consensus size: 266
29291187 GCTTCGACCC
* ** *** * * *
29291197 ACTCCACTGCAACTTCAGGGAGATAAGACTTGT-AGCTTC-GATCCATTCCACTGTAATTTCAAG
1 ACTCCACTGCAACTTCAGGGAGATAAGATTTGTAATTTTCAG-TCTGCTCCACTGCAACTTCAGG
* * * * * * * ** *
29291260 GAGACAAGACTTATAGCTTCAATCTGCTCCACTACAACTTTAGGGAGACAATATTTGTAACTTTC
65 GAGATAAGACTTGTAACTTCAATCTGCTCCGCTGCAACTTCAAGGAGATGAGATTTGTAACTTTC
* * * * *
29291325 AGTCTGCTCCACTACAACTTTAGAGAGATAAAACTTGTAATTTCAATCTACTTCACTGTAACTTC
130 AATCTGCTCCACTACAACTTCAGAGAGATAAAACTTATAACTTAAATCTACTTCACTGTAACTTC
* * * * * * *
29291390 AGGGAGATGAGGTTTGTGTCTTCAATATGCTCCACTGCGACCTCAAGG-AGATAAGA-TCTATAA
195 AAGGAGATAAGATTTATGTCTTCAATATGCTCCACTAC-AACTCAAGGAAGATAAGACT-TACAA
*
29291453 CTTCAATCT
258 CTTCAATAT
* * *
29291462 GCTCCACTGTAACTTCAGGGAGATAAGATTTGTAATTTTTAGTCTGCTCCACTGCAACTTCAGGG
1 ACTCCACTGCAACTTCAGGGAGATAAGATTTGTAATTTTCAGTCTGCTCCACTGCAACTTCAGGG
* **
29291527 AGATAATACTTGTAACTTCAATCTGCTCCGCTGCAACTTCAAGGAGATGAGATTTGTGTC-TTCA
66 AGATAAGACTTGTAACTTCAATCTGCTCCGCTGCAACTTCAAGGAGATGAGATTTGTAACTTTCA
* * * * *
29291591 ATCTGCTCCACTACGACTTCAGAGAGATAAGA-TCTATAACTTAAATCT-GTTCTATTGTAATTT
131 ATCTGCTCCACTACAACTTCAGAGAGATAAAACT-TATAACTTAAATCTACTTC-ACTGTAACTT
* * **
29291654 TAAGGAGATAAGATTTATGTCTTCAATCTGCTCCACTACAACTTTAGGAAGATAAGACTTACAAC
194 CAAGGAGATAAGATTTATGTCTTCAATATGCTCCACTACAACTCAAGGAAGATAAGACTTACAAC
29291719 TTCAATAT
259 TTCAATAT
* * * * *
29291727 ACTCCGCTACAACTTCAAGAAGATGAGATTTGTAATTTTCAGTCTGCTCCACTGCAACTTCAGGG
1 ACTCCACTGCAACTTCAGGGAGATAAGATTTGTAATTTTCAGTCTGCTCCACTGCAACTTCAGGG
*
29291792 AGATAAGACTTGTAACTTCAATATGCTCCGCTGCAACTTCAAGGAGATGAGATT
66 AGATAAGACTTGTAACTTCAATCTGCTCCGCTGCAACTTCAAGGAGATGAGATT
29291846 CGCCATAATG
Statistics
Matches: 321, Mismatches: 57, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
264 10 0.03
265 242 0.75
266 68 0.21
267 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (266 bp):
ACTCCACTGCAACTTCAGGGAGATAAGATTTGTAATTTTCAGTCTGCTCCACTGCAACTTCAGGG
AGATAAGACTTGTAACTTCAATCTGCTCCGCTGCAACTTCAAGGAGATGAGATTTGTAACTTTCA
ATCTGCTCCACTACAACTTCAGAGAGATAAAACTTATAACTTAAATCTACTTCACTGTAACTTCA
AGGAGATAAGATTTATGTCTTCAATATGCTCCACTACAACTCAAGGAAGATAAGACTTACAACTT
CAATAT
Found at i:29292458 original size:44 final size:44
Alignment explanation
Indices: 29292408--29292496 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
29292398 ATTTGAGAAG
29292408 AATAAATTAATCAAAGAAAGCAGACATTGGTAAAATACAAAATT
1 AATAAATTAATCAAAGAAAGCAGACATTGGTAAAATACAAAATT
* *
29292452 AATAAATTAATCAACGAAAGCAGACATTGGTGAAATACAAAATT
1 AATAAATTAATCAAAGAAAGCAGACATTGGTAAAATACAAAATT
29292496 A
1 A
29292497 GTAAGAAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.22
Consensus pattern (44 bp):
AATAAATTAATCAAAGAAAGCAGACATTGGTAAAATACAAAATT
Found at i:29296551 original size:50 final size:50
Alignment explanation
Indices: 29296448--29296725 Score: 265
Period size: 50 Copynumber: 5.5 Consensus size: 50
29296438 AAGAGATCCA
* *
29296448 ATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCAC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCAC
* *
29296504 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCAC
* *
29296554 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTTC-C
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG-TCAC
** * * * ** *
29296604 CCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAATTCTC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCAC
* * * * * **
29296654 ATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAGAAACATCAC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTCAC
*
29296703 ATGTAAGACTATGTCTGGGACAT
1 ATGTAAGACCATGTCTGGGACAT
29296726 AGCTTTGGTT
Statistics
Matches: 191, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
49 30 0.16
50 124 0.65
51 2 0.01
53 3 0.02
55 1 0.01
56 31 0.16
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (50 bp):
ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCAC
Found at i:29301276 original size:3 final size:3
Alignment explanation
Indices: 29301268--29301328 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
29301258 GGGTTTTAAA
* * * * *
29301268 AAT AAT AAT ACT AAT AAT AAT GAG AAT AAT -AT GAAT GAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
29301313 AAT AAT AAT GAAT AAT
1 AAT AAT AAT -AAT AAT
29301329 CTAAGGTTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
2 2 0.04
3 38 0.84
4 5 0.11
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:29301384 original size:19 final size:20
Alignment explanation
Indices: 29301353--29301390 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
29301343 CATATAAAAG
29301353 AATGTGAATAAATA-AATAT
1 AATGTGAATAAATAGAATAT
29301372 AATGTG-ATAAAATAGAATA
1 AATGTGAAT-AAATAGAATA
29301391 GATGTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.12
19 11 0.65
20 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (20 bp):
AATGTGAATAAATAGAATAT
Found at i:29302642 original size:18 final size:17
Alignment explanation
Indices: 29302606--29302649 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
29302596 GTTATAATTT
29302606 TTTTATTTTTGTTTTGG
1 TTTTATTTTTGTTTTGG
29302623 TTTT-TTTTTGTATTTGGG
1 TTTTATTTTTGT-TTT-GG
29302641 TTTCTATTT
1 TTT-TATTT
29302650 GGGCCCGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.30
17 7 0.30
18 5 0.22
19 1 0.04
20 3 0.13
ACGTcount: A:0.07, C:0.02, G:0.16, T:0.75
Consensus pattern (17 bp):
TTTTATTTTTGTTTTGG
Found at i:29306329 original size:27 final size:27
Alignment explanation
Indices: 29306281--29306336 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
29306271 AATAAATTAA
* *
29306281 AAATAAATTTTAAAAAATATGTATACTT
1 AAATAAATATTAAAAAAGATGTA-ACTT
*
29306309 AAAT-AATATTAAAATAGATGTAACTT
1 AAATAAATATTAAAAAAGATGTAACTT
29306335 AA
1 AA
29306337 CAAACAGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.24
27 15 0.60
28 4 0.16
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (27 bp):
AAATAAATATTAAAAAAGATGTAACTT
Found at i:29306378 original size:12 final size:12
Alignment explanation
Indices: 29306351--29306383 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29306341 CAGATGTCTC
29306351 TAAAAT-AATAA
1 TAAAATAAATAA
*
29306362 CAAAATAAATAA
1 TAAAATAAATAA
29306374 TAAAATAAAT
1 TAAAATAAAT
29306384 TTTATATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAAATAAATAA
Found at i:29308085 original size:20 final size:20
Alignment explanation
Indices: 29308056--29308109 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
29308046 CATATATCAT
* *
29308056 AATTTTATTTGATTCCAATC
1 AATTTGATTTAATTCCAATC
**
29308076 AATTTGATTTAATTTTAATC
1 AATTTGATTTAATTCCAATC
*
29308096 AAATTGATTTAATT
1 AATTTGATTTAATT
29308110 GCTCATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.52
Consensus pattern (20 bp):
AATTTGATTTAATTCCAATC
Found at i:29308861 original size:86 final size:84
Alignment explanation
Indices: 29308714--29308875 Score: 216
Period size: 86 Copynumber: 1.9 Consensus size: 84
29308704 AATAAAAATA
* * *
29308714 AAAATTGAATAAAATCTGTTTCGGGGTTTATTCCCGTCGTTCAACAAATTTTATTCCATCTTTGA
1 AAAATTAAATAAAATCTGTTTCGGGATTTATTACCGTCGTTCAACAAATTTTATTCCATC-TTGA
*
29308779 TTTATTTTCCAAACGAATATT
65 TTT-GTTTCCAAACGAATATT
* ** * * *
29308800 AAAATTAAATAAATTCTGTTTCGGGATTTATTACTTTCGTTTAACAGATTTTATTCGATCTTGAT
1 AAAATTAAATAAAATCTGTTTCGGGATTTATTACCGTCGTTCAACAAATTTTATTCCATCTTGAT
29308865 TTGTTTCCAAA
66 TTGTTTCCAAA
29308876 TGAAAACTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
84 8 0.12
85 7 0.11
86 51 0.77
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (84 bp):
AAAATTAAATAAAATCTGTTTCGGGATTTATTACCGTCGTTCAACAAATTTTATTCCATCTTGAT
TTGTTTCCAAACGAATATT
Found at i:29310713 original size:30 final size:30
Alignment explanation
Indices: 29310677--29310736 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
29310667 ATATTTAAGA
*
29310677 AGCCACATGGGCTAGACACACGACCATGTG
1 AGCCACACGGGCTAGACACACGACCATGTG
* * * *
29310707 AGCCACACGGTCTGGACACATGGCCATGTG
1 AGCCACACGGGCTAGACACACGACCATGTG
29310737 CTAGACCGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (30 bp):
AGCCACACGGGCTAGACACACGACCATGTG
Found at i:29318057 original size:5 final size:5
Alignment explanation
Indices: 29318047--29318076 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
29318037 AACTGAAACT
29318047 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
29318077 GAACGGCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:29326434 original size:20 final size:20
Alignment explanation
Indices: 29326411--29326462 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
29326401 TTTATTCCAG
29326411 TCAATTTGATTTGATTTTAA
1 TCAATTTGATTTGATTTTAA
29326431 TCAAATTT-ATTTGATTTTAA
1 TC-AATTTGATTTGATTTTAA
*
29326451 TCAAATTGATTT
1 TCAATTTGATTT
29326463 AATTGCTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 4 0.14
20 20 0.69
21 5 0.17
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.54
Consensus pattern (20 bp):
TCAATTTGATTTGATTTTAA
Found at i:29326950 original size:22 final size:23
Alignment explanation
Indices: 29326909--29326955 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
29326899 TTCAATTTAT
29326909 TTTATTTTATACTTAAATATTTG
1 TTTATTTTATACTTAAATATTTG
* *
29326932 TTTA-TTTATATTTATATATTTG
1 TTTATTTTATACTTAAATATTTG
29326954 TT
1 TT
29326956 AGCTAACGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (23 bp):
TTTATTTTATACTTAAATATTTG
Found at i:29338506 original size:11 final size:11
Alignment explanation
Indices: 29338490--29338523 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
29338480 TTCTATTAGT
29338490 TTTTTAATTAA
1 TTTTTAATTAA
29338501 TTTTTAATTAA
1 TTTTTAATTAA
29338512 TTATTTATATTA
1 TT-TTTA-ATTA
29338524 CAGTAAGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 13 0.62
12 4 0.19
13 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTTTAATTAA
Found at i:29360093 original size:3 final size:3
Alignment explanation
Indices: 29360085--29360130 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
29360075 GAAGAAATAG
29360085 AGA AGA AGA AGA AGA AGA AGA A-A AGA AGA AGA AG- AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
29360131 TGAGAAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:29360098 original size:20 final size:20
Alignment explanation
Indices: 29360046--29360130 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 20
29360036 ACTGGGTAGT
*
29360046 AGAAGAGGAAG-AGAA-AAA
1 AGAAGAAGAAGAAGAAGAAA
* *
29360064 A-AAGAATAAG-CGAAGAAA
1 AGAAGAAGAAGAAGAAGAAA
29360082 TAG-AGAAGAAGAAGAAGAAGA
1 -AGAAGAAGAAGAAGAAGAA-A
*
29360103 AGAA-AAGAAGAAGAAGAGA
1 AGAAGAAGAAGAAGAAGAAA
29360122 AGAAGAAGA
1 AGAAGAAGA
29360131 TGAGAAAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
17 10 0.19
18 4 0.07
19 13 0.24
20 25 0.46
21 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.31, T:0.02
Consensus pattern (20 bp):
AGAAGAAGAAGAAGAAGAAA
Found at i:29360124 original size:14 final size:14
Alignment explanation
Indices: 29360085--29360136 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
29360075 GAAGAAATAG
29360085 AGAAGAAGAAGAAGA
1 AGAAG-AGAAGAAGA
*
29360100 AGAAGAAAAGAAGA
1 AGAAGAGAAGAAGA
29360114 AGAAGAGAAGAAGA
1 AGAAGAGAAGAAGA
*
29360128 AGATGAGAA
1 AGAAGAGAA
29360137 AATAGAAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 29 0.85
15 5 0.15
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (14 bp):
AGAAGAGAAGAAGA
Found at i:29360136 original size:11 final size:11
Alignment explanation
Indices: 29360065--29360130 Score: 80
Period size: 11 Copynumber: 5.9 Consensus size: 11
29360055 AGAGAAAAAA
* *
29360065 AAGAATAAGCG
1 AAGAAGAAGAG
29360076 AAGAA-ATAGAG
1 AAGAAGA-AGAG
29360087 AAGAAGAAGAAG
1 AAGAAGAAG-AG
*
29360099 AAGAAGAAAAG
1 AAGAAGAAGAG
29360110 AAGAAGAAGAG
1 AAGAAGAAGAG
29360121 AAGAAGAAGA
1 AAGAAGAAGA
29360131 TGAGAAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
10 1 0.02
11 37 0.76
12 11 0.22
ACGTcount: A:0.65, C:0.02, G:0.30, T:0.03
Consensus pattern (11 bp):
AAGAAGAAGAG
Found at i:29361751 original size:29 final size:28
Alignment explanation
Indices: 29361718--29361789 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 28
29361708 AGCTTACACT
29361718 TTGGTCACTCAATTTTAAAAAGTTACAAG
1 TTGGTCACTCAATTTT-AAAAGTTACAAG
* *
29361747 TTGGTCACTAAACTACTTAAAAGTTACAAG
1 TTGGTCACTCAA-T-TTTAAAAGTTACAAG
*
29361777 TTGTTCA-TCAATT
1 TTGGTCACTCAATT
29361790 GTAATGGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
28 1 0.03
29 14 0.39
30 19 0.53
31 2 0.06
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (28 bp):
TTGGTCACTCAATTTTAAAAGTTACAAG
Found at i:29364407 original size:36 final size:36
Alignment explanation
Indices: 29364360--29364434 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
29364350 TATTTGCAAC
29364360 AATTTATAATTTCAATTTATAAAAAAACTAACATCA
1 AATTTATAATTTCAATTTATAAAAAAACTAACATCA
29364396 AATTTATAATTTCAATTTATAAAAAAACTAACATCA
1 AATTTATAATTTCAATTTATAAAAAAACTAACATCA
29364432 AAT
1 AAT
29364435 ACAATTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (36 bp):
AATTTATAATTTCAATTTATAAAAAAACTAACATCA
Found at i:29366860 original size:41 final size:41
Alignment explanation
Indices: 29366815--29366952 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
29366805 TAATTCACCG
** * *
29366815 GCACAAAGCTTGCTAGGCTTAAGGCTTGATAATATACACTA
1 GCACAAAGCTTGCTAGGCACAAAGCCTGATAATATACACTA
* * *
29366856 GCACAAAGCCTGCTAGGCACAAAGCCTAATAATATACAC-C
1 GCACAAAGCTTGCTAGGCACAAAGCCTGATAATATACACTA
* * *
29366896 GACACAAAGCTTGCTAGACACAAAACCTGATAATATACACTG
1 G-CACAAAGCTTGCTAGGCACAAAGCCTGATAATATACACTA
*
29366938 GCACAAAGCTAGCTA
1 GCACAAAGCTTGCTA
29366953 ATATCTCATT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.01
41 80 0.98
42 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (41 bp):
GCACAAAGCTTGCTAGGCACAAAGCCTGATAATATACACTA
Found at i:29372858 original size:46 final size:44
Alignment explanation
Indices: 29372762--29373123 Score: 344
Period size: 46 Copynumber: 8.6 Consensus size: 44
29372752 TACGTATGAT
* *
29372762 CACTTATCAC-TTGTC-CCTGATTAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTA-GCTAC
29372805 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-A-GCTAC
* *
29372851 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGACTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AG-CTAC
*
29372897 CACTTATCACTTTATCACTTGATCAGATAA--GTA--TA---A-
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
29372933 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
29372969 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT--AGCTAC
* *
29373015 CACTTATCACTTTGTCTCTTAATCAGATAA--GT-G-TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
29373051 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT--AGCTAC
* * *
29373097 CATTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
29373124 AGTACTCAAA
Statistics
Matches: 279, Mismatches: 15, Indels: 47
0.82 0.04 0.14
Matches are distributed among these distances:
36 91 0.33
37 1 0.00
38 5 0.02
39 1 0.00
40 4 0.01
41 1 0.00
42 6 0.02
43 11 0.04
44 10 0.04
45 20 0.07
46 129 0.46
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (44 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
Found at i:29372935 original size:36 final size:36
Alignment explanation
Indices: 29372894--29373082 Score: 225
Period size: 36 Copynumber: 5.0 Consensus size: 36
29372884 TAGCTAAGAC
*
29372894 TAACACTTATCACTTTATCACTTGATCAGATAAGTA
1 TAACACTTATCACTTTTTCACTTGATCAGATAAGTA
29372930 TAACACTTATCACTTTTTCACTTGATCAGATAAGTA
1 TAACACTTATCACTTTTTCACTTGATCAGATAAGTA
*
29372966 TAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTA
1 TAACACTTATCACTTTTTCACTTGATCAGATAA--GTA
* * * *
29373004 GCTAAAGCTACCACTTATCACTTTGTCTCTTAATCAGATAAGTG
1 --T--A---A-CACTTATCACTTTTTCACTTGATCAGATAAGTA
*
29373048 TAGCACTTATCACTTTTTCACTTGATCAGATAAGT
1 TAACACTTATCACTTTTTCACTTGATCAGATAAGT
29373083 GTAGCTAAAG
Statistics
Matches: 132, Mismatches: 11, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
36 96 0.73
38 3 0.02
40 2 0.02
42 2 0.02
44 2 0.02
46 27 0.20
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
TAACACTTATCACTTTTTCACTTGATCAGATAAGTA
Found at i:29373019 original size:82 final size:82
Alignment explanation
Indices: 29372805--29373123 Score: 379
Period size: 82 Copynumber: 3.9 Consensus size: 82
29372795 GCTAGGCTAC
* * *
29372805 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
29372870 TGATCAGATAAGTGTAGCTAAG
66 TGATCAGATAA--GTA--T-AG
* *
29372892 ACTAACACTTATCACTTTATCACTTGATCAGATAA--GTA--T--A---A-CACTTATCACTTTT
1 -----CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTA
29372947 TCACTTGATCAGATAAGTATAG
61 TCACTTGATCAGATAAGTATAG
* *
29372969 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
* *
29373034 TAATCAGATAAGTGTAG
66 TGATCAGATAAGTATAG
* *
29373051 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCATTTATCACTTTATCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
29373116 TGATCAGA
66 TGATCAGA
29373124 AGTACTCAAA
Statistics
Matches: 206, Mismatches: 11, Indels: 30
0.83 0.04 0.12
Matches are distributed among these distances:
72 29 0.14
74 3 0.01
76 1 0.00
77 2 0.01
78 2 0.01
80 3 0.01
81 1 0.00
82 131 0.64
83 1 0.00
88 1 0.00
90 3 0.01
92 29 0.14
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
TGATCAGATAAGTATAG
Found at i:29373059 original size:118 final size:118
Alignment explanation
Indices: 29372851--29373087 Score: 386
Period size: 118 Copynumber: 2.0 Consensus size: 118
29372841 CTAAGGCTAC
29372851 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGACTAACACTTATCACTTTATCACT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGACTAACACTTATCACTTTATCACT
*
29372916 TGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATAAGTATAG
66 TAATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATAAGTATAG
* * * *
29372969 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAA-AGCTACCACTTATCACTTTGTCTC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGA-CTAACACTTATCACTTTATCAC
* * *
29373033 TTAATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
65 TTAATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATAAGTATAG
29373087 C
1 C
29373088 TAAAGCTACC
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
117 1 0.01
118 109 0.99
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (118 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGACTAACACTTATCACTTTATCACT
TAATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:29384096 original size:104 final size:103
Alignment explanation
Indices: 29383916--29384282 Score: 598
Period size: 104 Copynumber: 3.6 Consensus size: 103
29383906 TAACCGTTAT
* * *
29383916 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACATAGCACCACC-ATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
29383981 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* *
29384020 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATCA-CGCACATAGCACCACC-ATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
29384084 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
64 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
29384124 TGGTGGATCACGCACATAGCACCACCCATAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACATAGCACCA-CCATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
29384189 AATCAGCACATAGCAA-CCCCTTT-ACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
**
29384226 TGGTGGATCACGCACATAGCACCACCAT-AATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCACGCACATAGCACCACCATGAATCGGGGAATCAGCACTTAGCAACCCCT
29384283 TTATATACAA
Statistics
Matches: 251, Mismatches: 9, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
100 27 0.11
101 4 0.02
102 38 0.15
103 7 0.03
104 172 0.69
105 3 0.01
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.19
Consensus pattern (103 bp):
TGGTGGATCACGCACATAGCACCACCATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:29384190 original size:27 final size:27
Alignment explanation
Indices: 29384158--29384209 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
29384148 CCCATAAATC
*
29384158 GGGGAATCAGCACTTAGCAACCCCTCG
1 GGGGAATCAGCACATAGCAACCCCTCG
29384185 GGGGAATCAGCACATAGCAACCCCT
1 GGGGAATCAGCACATAGCAACCCCT
29384210 TTACATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.25, T:0.13
Consensus pattern (27 bp):
GGGGAATCAGCACATAGCAACCCCTCG
Found at i:29384638 original size:29 final size:29
Alignment explanation
Indices: 29384605--29384668 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
29384595 TAATCCACCA
29384605 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
29384634 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
29384664 CCCAA
1 CCCAA
29384669 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:29384642 original size:30 final size:30
Alignment explanation
Indices: 29384612--29384668 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29384602 CCACCCAACT
29384612 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
29384641 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
29384669 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:29391756 original size:26 final size:26
Alignment explanation
Indices: 29391726--29391776 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
29391716 ACCAATGAAC
*
29391726 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
29391752 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
29391777 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:29391757 original size:103 final size:104
Alignment explanation
Indices: 29391488--29391854 Score: 627
Period size: 103 Copynumber: 3.6 Consensus size: 104
29391478 TAACCGTTAT
* **
29391488 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
29391553 AATCAGCACATAGCAACCCCCTTT--CATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
29391590 TGGTGGATATCGCACTTAGCACCACCAATGAA-CGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
29391654 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
29391693 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
29391757 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* **
29391796 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
29391855 TTATATACAA
Statistics
Matches: 254, Mismatches: 7, Indels: 7
0.95 0.03 0.03
Matches are distributed among these distances:
101 56 0.22
102 29 0.11
103 141 0.56
104 28 0.11
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:29392214 original size:29 final size:29
Alignment explanation
Indices: 29392181--29392244 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
29392171 TAATCCACCA
29392181 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
29392210 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
29392240 CCCAA
1 CCCAA
29392245 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:29392218 original size:30 final size:30
Alignment explanation
Indices: 29392188--29392244 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29392178 CCACCCAACT
29392188 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
29392217 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
29392245 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:29394622 original size:45 final size:45
Alignment explanation
Indices: 29394558--29394710 Score: 168
Period size: 45 Copynumber: 3.4 Consensus size: 45
29394548 GATCGGAGGG
* * *
29394558 TGCCATGGTCTCTTTCAACCACT-GTCTTATTTATTCTCGTCTTGA
1 TGCCATAGTGTCTTTCAACCA-TGGTCTTATTTATTCTCGTCGTGA
* * * *
29394603 TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTCCCATCGTGT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTA-TTCTCGTCGTGA
* *
29394649 TGCCATAGTGTCTTTCAACTATGGTCTTATTTCTT-T-GATTCGTGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCG--TCGTGA
29394694 TGCCATAGTGTCTTTCA
1 TGCCATAGTGTCTTTCA
29394711 GGTATAGTCT
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
44 1 0.01
45 52 0.57
46 38 0.42
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.44
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCGTCGTGA
Found at i:29394667 original size:46 final size:45
Alignment explanation
Indices: 29394558--29394813 Score: 164
Period size: 45 Copynumber: 5.7 Consensus size: 45
29394548 GATCGGAGGG
* * * * *
29394558 TGCCATGGTCTCTTTCAACCACT-GTCTTATTTA-TTCTCGTCTTGA
1 TGCCATAGTGTCTTTCAACCA-TGGTCTTATTCATTTC-CATCGTGA
*
29394603 TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTCCCATCGTGT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTT-CCATCGTGA
* *
29394649 TGCCATAGTGTCTTTCAACTATGGTCTTATTTC-TTT-GATTCGTGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTA-TTCATTTCCA-TCGTGA
*** * * ***
29394694 TGCCATAGTGTCTTTCAGGTATAGTCTTACTCGA-TAGAATCGTGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTC-ATTTCCATCGTGA
* * * * * * * *
29394739 TGCCATAATATCTTTCAGCTATGGTCTTACTCATTTCTAAT-ATGG
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTC-CATCGTGA
* * *
29394784 TGTCATAGTGTCTTTCAACTATGGTATTAT
1 TGCCATAGTGTCTTTCAACCATGGTCTTAT
29394814 CTATTCCCGG
Statistics
Matches: 172, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
44 5 0.03
45 121 0.70
46 42 0.24
47 4 0.02
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.43
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTCCATCGTGA
Found at i:29394721 original size:45 final size:44
Alignment explanation
Indices: 29394600--29394813 Score: 182
Period size: 45 Copynumber: 4.8 Consensus size: 44
29394590 ATTCTCGTCT
* *
29394600 TGATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTCCCATCG
1 TGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTT--GATCG
*
29394646 TGTTGCCATAGTGTCTTTCAACTATGGTCTTATTTC-TTTGATTCG
1 TGATGCCATAGTGTCTTTCAACTATGGTCTTA-TTCATTTGA-TCG
** * * *
29394691 TGATGCCATAGTGTCTTTCAGGTATAGTCTTACTCGA-TAGAATCG
1 TGATGCCATAGTGTCTTTCAACTATGGTCTTATTC-ATTTG-ATCG
* * * * * *
29394736 TGATGCCATAATATCTTTCAGCTATGGTCTTACTCATTTCTAAT-A
1 TGATGCCATAGTGTCTTTCAACTATGGTCTTATTCA-TT-TGATCG
* * *
29394781 TGGTGTCATAGTGTCTTTCAACTATGGTATTAT
1 TGATGCCATAGTGTCTTTCAACTATGGTCTTAT
29394814 CTATTCCCGG
Statistics
Matches: 137, Mismatches: 23, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
44 4 0.03
45 93 0.68
46 37 0.27
47 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (44 bp):
TGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTGATCG
Found at i:29394843 original size:45 final size:45
Alignment explanation
Indices: 29394739--29394863 Score: 126
Period size: 45 Copynumber: 2.8 Consensus size: 45
29394729 AGAATCGTGA
* * * * *
29394739 TGCCATAATATCTTTCAGCTATGGTCTTACTCATTTCTAATATGG
1 TGCCATAATATCTTTCAACTATGGTATTACTCATTCCCAATATAG
* * * **
29394784 TGTCATAGTGTCTTTCAACTATGGTATTA-TCTATTCCCGGTATAG
1 TGCCATAATATCTTTCAACTATGGTATTACTC-ATTCCCAATATAG
* *
29394829 TGCCATAATATCTTTCAACTATGGTCTTAATCATT
1 TGCCATAATATCTTTCAACTATGGTATTACTCATT
29394864 TCCTTCAAGC
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
44 2 0.03
45 60 0.94
46 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (45 bp):
TGCCATAATATCTTTCAACTATGGTATTACTCATTCCCAATATAG
Found at i:29397458 original size:90 final size:90
Alignment explanation
Indices: 29397312--29397489 Score: 212
Period size: 90 Copynumber: 2.0 Consensus size: 90
29397302 TTTGTATCTT
* * * * * * ** * *
29397312 TTTGAAAATGCGTGACTAAATTGTAAATTTACACATCTCACATCTAACGTTTGTTACCAAGTTAA
1 TTTGAAAATGAGTGACCAAATTATAAATTTACACATCACACACCTAACATCCGTTACAAAGCTAA
*
29397377 AAGGCCAGTGACCAGCTTGTAACCG
66 AAGGCCAGTGACCAACTTGTAACCG
* * *
29397402 TTTGAAATTGAGTGACCAAATTATAAATTTACCCATCACACACCTGACATCCGTTACAAAGCTAA
1 TTTGAAAATGAGTGACCAAATTATAAATTTACACATCACACACCTAACATCCGTTACAAAGCTAA
* *
29397467 TAGGCCTGTGACCAACTTGTAAC
66 AAGGCCAGTGACCAACTTGTAAC
29397490 TTTTGAATTT
Statistics
Matches: 72, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
90 72 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (90 bp):
TTTGAAAATGAGTGACCAAATTATAAATTTACACATCACACACCTAACATCCGTTACAAAGCTAA
AAGGCCAGTGACCAACTTGTAACCG
Done.