Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012160.1 Kokia drynarioides strain JFW-HI SEQ_127161, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58496
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Warning! 286 characters in sequence are not A, C, G, or T
Found at i:5882 original size:5 final size:6
Alignment explanation
Indices: 5867--5891 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5857 TCACCCAAAG
5867 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
5892 TTATCCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:8828 original size:21 final size:20
Alignment explanation
Indices: 8788--8843 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 20
8778 TATCTTTATT
*
8788 TTATTTTTATAATTTTAATA
1 TTATTTTTATAATTTAAATA
8808 TTATCTTTTAT-ATTATAAATA
1 TTAT-TTTTATAATT-TAAATA
8829 TT-TTTAATTATAATT
1 TTATTT--TTATAATT
8844 CATTAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 2 0.07
20 8 0.27
21 17 0.57
22 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTTTATAATTTAAATA
Found at i:8877 original size:24 final size:23
Alignment explanation
Indices: 8823--8878 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
8813 TTTTATATTA
** *
8823 TAAATATTTTTAATTATAATTCAT
1 TAAA-ATTTTTAAAAATAATTAAT
8847 TAAAATTTTTAAAAATAATTAACT
1 TAAAATTTTTAAAAATAATTAA-T
*
8871 TATAATTT
1 TAAAATTT
8879 AATTTTAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAAATTTTTAAAAATAATTAAT
Found at i:17283 original size:2 final size:2
Alignment explanation
Indices: 17276--17305 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17266 TATTTTAAAA
17276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17306 TTTTTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17897 original size:13 final size:12
Alignment explanation
Indices: 17865--17940 Score: 52
Period size: 13 Copynumber: 6.1 Consensus size: 12
17855 ACAATTGATA
17865 AATAA-TAAAAT
1 AATAATTAAAAT
17876 AA-AATTTAAAAGT
1 AATAA-TTAAAA-T
17889 AATAATTAAAAT
1 AATAATTAAAAT
17901 AAT-ATGTAATAAT
1 AATAAT-TAA-AAT
17914 AA-AATTTTAAAAT
1 AATAA--TTAAAAT
*
17927 AATATTATAAAAT
1 AATAAT-TAAAAT
17940 A
1 A
17941 CTTATTATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 20
0.72 0.01 0.27
Matches are distributed among these distances:
10 2 0.04
11 4 0.08
12 13 0.25
13 27 0.51
14 6 0.11
15 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (12 bp):
AATAATTAAAAT
Found at i:17929 original size:19 final size:19
Alignment explanation
Indices: 17868--17930 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
17858 ATTGATAAAT
17868 AATAA-AATAAAA-TTTAA
1 AATAATAATAAAATTTTAA
**
17885 AAGTAATAATTAAAATAAT-A
1 AA-TAATAA-TAAAATTTTAA
**
17905 TGTAATAATAAAATTTTAA
1 AATAATAATAAAATTTTAA
17924 AATAATA
1 AATAATA
17931 TTATAAAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
17 2 0.06
18 10 0.30
19 14 0.42
20 6 0.18
21 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AATAATAATAAAATTTTAA
Found at i:17940 original size:26 final size:25
Alignment explanation
Indices: 17865--17940 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 25
17855 ACAATTGATA
*
17865 AATAA-TAAAATAAAATT-TAAAAGT
1 AATAATTAAAATAATATTATAAAA-T
17889 AATAATTAAAATAATATGTAATAATAA-
1 AATAATTAAAATAATAT-T-ATAA-AAT
*
17916 AAT-TTTAAAATAATATTATAAAAT
1 AATAATTAAAATAATATTATAAAAT
17940 A
1 A
17941 CTTATTATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
23 2 0.05
24 10 0.23
25 11 0.25
26 13 0.30
27 3 0.07
28 3 0.07
29 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (25 bp):
AATAATTAAAATAATATTATAAAAT
Found at i:18842 original size:22 final size:22
Alignment explanation
Indices: 18765--18831 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 22
18755 TAATTTGATT
*
18765 TTTTAT-A-AAATTTA-TAATT
1 TTTTATGATAAATTTAGTAATA
18784 TTTTATGATAAATTTAGTAATA
1 TTTTATGATAAATTTAGTAATA
18806 TTTTATGATAAATTTAGTAATA
1 TTTTATGATAAATTTAGTAATA
18828 TTTT
1 TTTT
18832 TCGTTTAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
19 6 0.14
20 1 0.02
21 7 0.16
22 30 0.68
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTTATGATAAATTTAGTAATA
Found at i:21210 original size:6 final size:6
Alignment explanation
Indices: 21199--21282 Score: 56
Period size: 6 Copynumber: 14.7 Consensus size: 6
21189 CTGAGCCTAA
* * *
21199 TAAATT TAAATT T-ATTT TAAAAT TAAGTT T--ATT CTAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
*
21245 T--ATT TGAAATT TAAGTT T--ATT ATAAATT TAAATT TAAA
1 TAAATT T-AAATT TAAATT TAAATT -TAAATT TAAATT TAAA
21283 ATCTATTTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
4 8 0.13
5 6 0.10
6 36 0.60
7 10 0.17
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:21224 original size:17 final size:17
Alignment explanation
Indices: 21199--21280 Score: 110
Period size: 17 Copynumber: 4.8 Consensus size: 17
21189 CTGAGCCTAA
21199 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* * *
21216 TAAAATTAAGTTTATTC
1 TAAATTTAAATTTATTT
21233 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* * *
21250 GAAATTTAAGTTTATTA
1 TAAATTTAAATTTATTT
21267 TAAATTTAAATTTA
1 TAAATTTAAATTTA
21281 AAATCTATTT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:21242 original size:34 final size:34
Alignment explanation
Indices: 21198--21280 Score: 139
Period size: 34 Copynumber: 2.4 Consensus size: 34
21188 TCTGAGCCTA
*
21198 ATAAATTTAAATTTATTTTAAAATTAAGTTTATT
1 ATAAATTTAAATTTATTTGAAAATTAAGTTTATT
* *
21232 CTAAATTTAAATTTATTTGAAATTTAAGTTTATT
1 ATAAATTTAAATTTATTTGAAAATTAAGTTTATT
21266 ATAAATTTAAATTTA
1 ATAAATTTAAATTTA
21281 AAATCTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (34 bp):
ATAAATTTAAATTTATTTGAAAATTAAGTTTATT
Found at i:22043 original size:15 final size:15
Alignment explanation
Indices: 22023--22066 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
22013 GACATTAATA
*
22023 TTAATAATAATATTT
1 TTAATAATAATACTT
22038 TTAATAATAATAACTT
1 TTAATAATAAT-ACTT
22054 TTAATAATTAATA
1 TTAATAA-TAATA
22067 ATAAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 11 0.42
16 11 0.42
17 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAATAATAATACTT
Found at i:23034 original size:29 final size:28
Alignment explanation
Indices: 23002--23159 Score: 165
Period size: 30 Copynumber: 5.4 Consensus size: 28
22992 AAACTGTTTG
* *
23002 AAAATTACATTTGTACCCTTGAACTTCCA
1 AAAATTCCATTTTTACCC-TGAACTTCCA
**
23031 AAAATTCCATTTTTAACCACAAAACTTCCA
1 AAAATTCCATTTTT-ACC-CTGAACTTCCA
23061 AAAATTCCATTTTTTACCCTGAAACTTCCA
1 AAAATTCCA-TTTTTACCCTG-AACTTCCA
23091 AAAATTCCATTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTACCCT-GAACTTCCA
* *
23120 AAAATTCAATTTTTGA-TCTCGAAACTTCCA
1 AAAATTCCATTTTT-ACCCT-G-AACTTCCA
*
23150 AAAACTCCAT
1 AAAATTCCAT
23160 CCTCGACCCC
Statistics
Matches: 112, Mismatches: 10, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
29 48 0.43
30 58 0.52
31 6 0.05
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCTGAACTTCCA
Found at i:23059 original size:30 final size:30
Alignment explanation
Indices: 23023--23159 Score: 179
Period size: 30 Copynumber: 4.6 Consensus size: 30
23013 TGTACCCTTG
* *
23023 AACTTCCAAAAATTCCATTTTTAACCACAA
1 AACTTCCAAAAATTCCATTTTTAACCTCGA
*
23053 AACTTCCAAAAATTCCATTTTTTACC-CTGA
1 AACTTCCAAAAATTCCATTTTTAACCTC-GA
*
23083 AACTTCCAAAAATTCCATTTTTACCCTCG-
1 AACTTCCAAAAATTCCATTTTTAACCTCGA
* * *
23112 AACTTCCAAAAATTCAATTTTTGATCTCGA
1 AACTTCCAAAAATTCCATTTTTAACCTCGA
*
23142 AACTTCCAAAAACTCCAT
1 AACTTCCAAAAATTCCAT
23160 CCTCGACCCC
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
29 26 0.28
30 67 0.71
31 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTAACCTCGA
Found at i:23119 original size:59 final size:60
Alignment explanation
Indices: 23002--23159 Score: 189
Period size: 59 Copynumber: 2.7 Consensus size: 60
22992 AAACTGTTTG
* *
23002 AAAATTACA-TTTGTACCCTTG-AACTTCCAAAAATTCCATTTTTAACCACAAAACTTCCA
1 AAAATTCCATTTTTTACCC-TGAAACTTCCAAAAATTCCATTTTTAACCACAAAACTTCCA
* * *
23061 AAAATTCCATTTTTTACCCTGAAACTTCCAAAAATTCCATTTTTACCCTC-GAACTTCCA
1 AAAATTCCATTTTTTACCCTGAAACTTCCAAAAATTCCATTTTTAACCACAAAACTTCCA
* * * *
23120 AAAATTCAATTTTTGA-TCTCGAAACTTCCAAAAACTCCAT
1 AAAATTCCATTTTTTACCCT-GAAACTTCCAAAAATTCCAT
23160 CCTCGACCCC
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
58 2 0.02
59 51 0.59
60 34 0.39
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.34
Consensus pattern (60 bp):
AAAATTCCATTTTTTACCCTGAAACTTCCAAAAATTCCATTTTTAACCACAAAACTTCCA
Found at i:23175 original size:89 final size:89
Alignment explanation
Indices: 23002--23168 Score: 217
Period size: 89 Copynumber: 1.9 Consensus size: 89
22992 AAACTGTTTG
* * *
23002 AAAATTACATTTGTACCCTTGAACTTCCAAAAATTCCATTTTTAACCACAAAACTTCCAAAAATT
1 AAAATTACATTTGTACCCTCGAACTTCCAAAAATTCAATTTTTAACCACAAAACTTCCAAAAACT
** **
23067 CCATTTTTTACCCTGAAACTTCCA
66 CCATCCTCGACCCTGAAACTTCCA
* * * * * *
23091 AAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCAATTTTTGATCTCGAAACTTCCAAAAACT
1 AAAATTACATTTGTACCCTCGAACTTCCAAAAATTCAATTTTTAACCACAAAACTTCCAAAAACT
23156 CCATCCTCGACCC
66 CCATCCTCGACCC
23169 CTAAACTCTC
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
89 65 1.00
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.32
Consensus pattern (89 bp):
AAAATTACATTTGTACCCTCGAACTTCCAAAAATTCAATTTTTAACCACAAAACTTCCAAAAACT
CCATCCTCGACCCTGAAACTTCCA
Found at i:35295 original size:205 final size:205
Alignment explanation
Indices: 34937--36210 Score: 1829
Period size: 205 Copynumber: 6.2 Consensus size: 205
34927 ACAAACAACA
* * * * *
34937 ACGCGATCATCTTTCTAATGAGATACTAAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAGC
1 ACGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
* * * *
35002 AAATCTTCGAACCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGTAATAAGCGGTTAGC
66 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
* * *
35067 TTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATATAAAGAAGCAGATT
131 TTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATT
35132 GAAACGAAA-G
196 GAAAC-AAATG
**
35142 ACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
1 ACGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
* * * *
35207 AAATCTTCGAACCCCAACTTCCTGATGAGACACTAAGAAACAGGTCGAAGCAATAAACAGTTAGC
66 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
* *
35272 TTCCTGATAAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCAGATT
131 TTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATT
*
35337 GAAACAAATA
196 GAAACAAATG
* * * *
35347 ACGTAATCATCTTCCTGATGAGATAATGAGAAGAAGACCAAATCAAACCCACGCTCGATGTAAGG
1 ACGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
* * * *
35412 AAATCTTTGAA-TCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAATGGTTAGC
66 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
* *
35476 TTCCTGATAAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATT
131 TTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATT
*
35541 GAAACGAATG
196 GAAACAAATG
* * *
35551 ACGCGATCATCTTTCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
1 ACGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
*
35616 AAATCTTCGAACCACAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
66 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
* *
35681 TTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAAAAGCAGATT
131 TTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATT
35746 GAAACAAATG
196 GAAACAAATG
* * *
35756 ACGCAGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACGTTCGATGTGAGC
1 ACGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
* * *
35821 AAATCTTCGAATCTCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACAGTTAGC
66 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
* *
35886 TTTCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGTTACAGAGAAGCAGATT
131 TTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATT
35951 GAAACAAATG
196 GAAACAAATG
* *
35961 ACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA--TGAAC
1 ACGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
* * * * **
36024 AAATCTTCAAACCCCAGCTTCCTGTTGAGATACTGAGAAGCGGGTCGAAATAATAAAACGGTTAG
66 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAAT-AAACGGTTAG
* * * * * * **
36089 CTTCCTGATGAA-ATACGGGGAAGTAAACCAAAATCATCTTCCTGATGAAACACAGAGAAGTGGA
130 CTTCCTGAT-AAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGA
** *
36153 TCAAAACAAGTG
194 TTGAAACAAATG
***** * * *
36165 ATATGGTCATCTTCCAGATGAGATACTGAGAAGAAGGCCAAGTCAA
1 ACGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
36211 TGAAACCAGA
Statistics
Matches: 970, Mismatches: 95, Indels: 9
0.90 0.09 0.01
Matches are distributed among these distances:
203 50 0.05
204 298 0.31
205 622 0.64
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (205 bp):
ACGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
TTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATT
GAAACAAATG
Found at i:35702 original size:409 final size:409
Alignment explanation
Indices: 34936--36136 Score: 1859
Period size: 409 Copynumber: 2.9 Consensus size: 409
34926 CACAAACAAC
* * * *
34936 AACGCGATCATCTTTCTAATGAGATACTAAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAG
1 AACGCAATCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAG
* * * * *
35001 CAAATCTTCGAACCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGTAATAAGCGGTTAG
66 CAAATCTTCGAA-TCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAG
* * *
35066 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATATAAAGAAGCAGAT
130 CTTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGAT
* *
35131 TGAAACGAAAGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
195 TGAAACGAATGACGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* * *
35196 TCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTAAGAAACAGGTCGAAGCAAT
260 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAAT
* * * *
35261 AAACAGTTAGCTTCCTGATAAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAG
325 AAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAG
*
35326 AGAAGCAGATTGAAACAAAT
390 AAAAGCAGATTGAAACAAAT
* * * *
35346 AACGTAATCATCTTCCTGATGAGATAATGAGAAGAAGACCAAATCAAACCCACGCTCGATGTAAG
1 AACGCAATCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAG
* * * *
35411 GAAATCTTTGAATCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAATGGTTAGC
66 CAAATCTTCGAATCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
* *
35476 TTCCTGATAAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATT
131 TTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATT
* *
35541 GAAACGAATGACGCGATCATCTTTCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCT
196 GAAACGAATGACGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCT
*
35606 CGATGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATA
261 CGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATA
35671 AACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGA
326 AACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGA
35736 AAAGCAGATTGAAACAAAT
391 AAAGCAGATTGAAACAAAT
* * *
35755 GACGCAGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACGTTCGATGTGAG
1 AACGCAATCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAG
*
35820 CAAATCTTCGAATCTCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACAGTTAG
66 CAAATCTTCGAATC-CAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAG
* *
35885 CTTTCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGTTACAGAGAAGCAGAT
130 CTTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGAT
*
35950 TGAAACAAATGACGC-AGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
195 TGAAACGAATGACGCGA-TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
* * * * * **
36014 CTCGA--TGAACAAATCTTCAAACCCCAGCTTCCTGTTGAGATACTGAGAAGCGGGTCGAAATAA
259 CTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAA
* * * * *
36077 TAAAACGGTTAGCTTCCTGATGAAATACGGGGAAGTAAACCAAAATCATCTTCCTGATGA
324 T-AAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGA
36137 AACACAGAGA
Statistics
Matches: 721, Mismatches: 67, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
408 51 0.07
409 431 0.60
410 239 0.33
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (409 bp):
AACGCAATCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAG
CAAATCTTCGAATCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
TTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATT
GAAACGAATGACGCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCT
CGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATA
AACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGA
AAAGCAGATTGAAACAAAT
Found at i:36120 original size:614 final size:614
Alignment explanation
Indices: 34937--36148 Score: 1957
Period size: 614 Copynumber: 2.0 Consensus size: 614
34927 ACAAACAACA
*
34937 ACGCGATCATCTTTCTAATGAGATACTAAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAGC
1 ACGCGATCATCTTTCTAATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
* * * *
35002 AAATCTTCGAACCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGTAATAAGCGGTTAGC
66 AAATCTTCGAACCACAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
*
35067 TTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATATAAAGAAGCAGATT
131 TTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAAAGAAGCAGATT
* *
35132 GAAACGAAAGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCT
196 GAAACGAAAGACGCAGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCT
35197 CGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTAAGAAACAGGTCGAAGCAATA
261 CGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTAAGAAACAGGTCGAAGCAATA
* *
35262 AACAGTTAGCTTCCTGATAAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAGA
326 AACAGTTAGCTTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGA
*
35327 GAAGCAGATTGAAACAAATAACGTAATCATCTTCCTGATGAGATAATGAGAAGAAGACCAAATCA
391 GAAGCAGATTGAAACAAATAACGCAATCATCTTCCTGATGAGATAATGAGAAGAAGACCAAATCA
* ** *
35392 AACCCACGCTCGATGTAAGGAAATCTTTGAATCCAACTTCCTGATGAGACACTGAGAAGCAGGTC
456 AACCCACGCTCGATGTAAGCAAATCTTCAAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTC
* * * * * *
35457 GAAGCAATAAATGGTTAGCTTCCTGATAAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATG
521 GAAACAATAAACGGTTAGCTTCCTGATAAGATACGAAGAAGTAAACCAAAATCATCTTCCTGATG
* *
35522 AGATACAGAGAAGCAGATTGAAACGAATG
586 AAACACAGAGAAGCAGATTGAAACGAATG
*
35551 ACGCGATCATCTTTCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
1 ACGCGATCATCTTTCTAATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
*
35616 AAATCTTCGAACCACAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
66 AAATCTTCGAACCACAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
35681 TTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAA-AAGCAGAT
131 TTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACA-AAGAAGCAGAT
35745 TGAAAC-AAATGACGCAGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
195 TGAAACGAAA-GACGCAGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
* * * * * *
35809 TTCGATGTGAGCAAATCTTCGAATCTCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAA
259 CTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTAAGAAACAGGTCGAAGCAA
* *
35874 TAAACAGTTAGCTTTCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGTTACA
324 TAAACAGTTAGCTTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACA
* * *
35939 GAGAAGCAGATTGAAACAAATGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAAT
389 GAGAAGCAGATTGAAACAAATAACGCAATCATCTTCCTGATGAGATAATGAGAAGAAGACCAAAT
* * * *
36004 CAAACCCACGCTCGATG-AA-CAAATCTTCAAACCCCAGCTTCCTGTTGAGATACTGAGAAGCGG
454 CAAACCCACGCTCGATGTAAGCAAATCTTCAAA-CCCAACTTCCTGATGAGACACTGAGAAGCAG
* **
36067 GTCGAAATAATAAAACGGTTAGCTTCCTGATGAA-ATACGGGGAAGTAAACCAAAATCATCTTCC
518 GTCGAAACAAT-AAACGGTTAGCTTCCTGAT-AAGATACGAAGAAGTAAACCAAAATCATCTTCC
36131 TGATGAAACACAGAGAAG
581 TGATGAAACACAGAGAAG
36149 TGGATCAAAA
Statistics
Matches: 550, Mismatches: 43, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
612 9 0.02
613 40 0.07
614 497 0.90
615 4 0.01
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (614 bp):
ACGCGATCATCTTTCTAATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGC
AAATCTTCGAACCACAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
TTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAAAGAAGCAGATT
GAAACGAAAGACGCAGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCT
CGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGACACTAAGAAACAGGTCGAAGCAATA
AACAGTTAGCTTCCTGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGA
GAAGCAGATTGAAACAAATAACGCAATCATCTTCCTGATGAGATAATGAGAAGAAGACCAAATCA
AACCCACGCTCGATGTAAGCAAATCTTCAAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTC
GAAACAATAAACGGTTAGCTTCCTGATAAGATACGAAGAAGTAAACCAAAATCATCTTCCTGATG
AAACACAGAGAAGCAGATTGAAACGAATG
Found at i:36543 original size:17 final size:17
Alignment explanation
Indices: 36518--36565 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
36508 CTGGGCCCAA
36518 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
36535 TAAAATTAAGTTTATTT
1 TAAATTTAAATTTATTT
36552 TAAATTTAAATTTA
1 TAAATTTAAATTTA
36566 AAATATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:36569 original size:7 final size:6
Alignment explanation
Indices: 36518--36567 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
36508 CTGGGCCCAA
* * * *
36518 TAAATT TAAATT T-ATTT TAAAAT TAAGTT T-ATTT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
36564 TAAA
1 TAAA
36568 ATATATTTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
5 8 0.23
6 27 0.77
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:38358 original size:30 final size:29
Alignment explanation
Indices: 38300--38487 Score: 236
Period size: 30 Copynumber: 6.4 Consensus size: 29
38290 CTAAACTGTT
** * *
38300 CAAAAATTATATTTTTACCCCTAAACTTC
1 CAAAAATTCCATTTTTACCTCGAAACTTC
* *
38329 TAAAAATTCCATTTTTAACCTCAAAACTTC
1 CAAAAATTCCATTTTT-ACCTCGAAACTTC
*
38359 TAAAAATTCCATTTTTACCCTC-AAACTTC
1 CAAAAATTCCATTTTTA-CCTCGAAACTTC
38388 CAAAAAATTCCATTTTTACCTCGAAACTTC
1 C-AAAAATTCCATTTTTACCTCGAAACTTC
* *
38418 CAAAAGTTCCATTTTTACCCCG-AACTTC
1 CAAAAATTCCATTTTTACCTCGAAACTTC
38446 CAAAAATTCCATTTTTGACCTCGAAACTTC
1 CAAAAATTCCATTTTT-ACCTCGAAACTTC
*
38476 CAAAAACTCCAT
1 CAAAAATTCCAT
38488 CTTCGACCCC
Statistics
Matches: 142, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
28 21 0.15
29 49 0.35
30 72 0.51
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCTCGAAACTTC
Found at i:38393 original size:59 final size:57
Alignment explanation
Indices: 38300--38487 Score: 259
Period size: 59 Copynumber: 3.2 Consensus size: 57
38290 CTAAACTGTT
** * *
38300 CAAAAATTATATTTTTACCCCTAAACTTCTAAAAATTCCATTTTTAACCTCAAAACTTC
1 CAAAAATTCCATTTTTACCCC-AAACTTCCAAAAATTCCATTTTT-ACCTCGAAACTTC
*
38359 TAAAAATTCCATTTTTACCCTCAAACTTCCAAAAAATTCCATTTTTACCTCGAAACTTC
1 CAAAAATTCCATTTTTACCC-CAAACTTCC-AAAAATTCCATTTTTACCTCGAAACTTC
* *
38418 CAAAAGTTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
1 CAAAAATTCCATTTTTACCCCAAACTTCCAAAAATTCCATTTTT-ACCTCGAAACTTC
*
38476 CAAAAACTCCAT
1 CAAAAATTCCAT
38488 CTTCGACCCC
Statistics
Matches: 116, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
57 15 0.13
58 31 0.27
59 54 0.47
60 16 0.14
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (57 bp):
CAAAAATTCCATTTTTACCCCAAACTTCCAAAAATTCCATTTTTACCTCGAAACTTC
Found at i:38503 original size:30 final size:29
Alignment explanation
Indices: 38288--38504 Score: 222
Period size: 30 Copynumber: 7.3 Consensus size: 29
38278 CCCTGGAGGT
* **
38288 CCCTAAACTGTTCAAAAATTATATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
*
38318 CCCTAAACTTCTAAAAATTCCATTTTTAAC
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * *
38348 CTCAAAACTTCTAAAAATTCCATTTTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
38376 CCCTCAAACTTCCAAAAAATTCCATTTTTAC
1 CCCT-AAACTTCC-AAAAATTCCATTTTTAC
* * *
38407 CTCGAAACTTCCAAAAGTTCCATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
*
38436 CCC-GAACTTCCAAAAATTCCATTTTTGAC
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * * **
38465 CTCGAAACTTCCAAAAACTCCATCTTCGAC
1 CCCTAAACTTCCAAAAATTCCAT-TTTTAC
38495 CCCTAAACTT
1 CCCTAAACTT
38505 TCGAAATTAC
Statistics
Matches: 158, Mismatches: 22, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
28 23 0.15
29 44 0.28
30 87 0.55
31 4 0.03
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:38541 original size:87 final size:87
Alignment explanation
Indices: 38316--38504 Score: 220
Period size: 87 Copynumber: 2.1 Consensus size: 87
38306 TTATATTTTT
* * * **
38316 ACCCCTAAACTTCTAAAAATTCCATTTTTAACCTCAAAACTTCTAAAAATTCCATTTTTACCCTC
1 ACCCCGAAACTTCCAAAAGTTCCATTTTT-ACC-CCGAACTTCTAAAAATTCCATTTTTACCCTC
* **
38381 AAACTTCCAAAAAATTCCATTTTT
64 AAACTTCCAAAAAACTCCATTTCG
* *
38405 ACCTCGAAACTTCCAAAAGTTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTGA-CCTCG
1 ACCCCGAAACTTCCAAAAGTTCCATTTTTACCCCGAACTTCTAAAAATTCCATTTTT-ACCCTC-
38469 AAACTTCC-AAAAACTCCATCTTCG
64 AAACTTCCAAAAAACTCCAT-TTCG
*
38493 ACCCCTAAACTT
1 ACCCCGAAACTT
38505 TCGAAATTAC
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
87 36 0.42
88 24 0.28
89 25 0.29
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.32
Consensus pattern (87 bp):
ACCCCGAAACTTCCAAAAGTTCCATTTTTACCCCGAACTTCTAAAAATTCCATTTTTACCCTCAA
ACTTCCAAAAAACTCCATTTCG
Found at i:39941 original size:19 final size:17
Alignment explanation
Indices: 39904--39943 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
39894 TTAATCACTC
*
39904 AAAATATAATATTAATT
1 AAAATATAATATCAATT
39921 AAAATATAATAATGCAATT
1 AAAATATAAT-AT-CAATT
39940 AAAA
1 AAAA
39944 AAGTACTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 2 0.10
19 8 0.40
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATATAATATCAATT
Found at i:46648 original size:151 final size:151
Alignment explanation
Indices: 46374--46662 Score: 481
Period size: 151 Copynumber: 1.9 Consensus size: 151
46364 CCATTAACTC
*
46374 AAAGATTCAATATCTTTGATTCCGATATCTTCTTCCCGTTAAGTTTTTTTGGGTTAATGGGTTTC
1 AAAGATTCAATATCTTTGATTCCAATATCTTCTTCCCGTTAAGTTTTTTTGGGTTAATGGGTTTC
*
46439 AAATATTCAAACTTTGAGACAAATTTGTAACAAAAGATATTGTAATCAAAAGGGAAGAAAATGAA
66 AAAGATTCAAACTTTGAGACAAATTTGTAACAAAAGATATTGTAATCAAAAGGGAAGAAAATGAA
46504 AATGAAGAAGAGAGGTGTGTG
131 AATGAAGAAGAGAGGTGTGTG
*
46525 AAAGATTCAATATCTTTGATTCCAATATCTTCTTCCCGTTAAGTTTTTTTGGGTTAATGGGTTTT
1 AAAGATTCAATATCTTTGATTCCAATATCTTCTTCCCGTTAAGTTTTTTTGGGTTAATGGGTTTC
* * * * *
46590 AAAGATTCAAGCTTTGAGACAGATTTGTAACTAAAGATATTAG-AATCAGAAGGGAAGAATATGA
66 AAAGATTCAAACTTTGAGACAAATTTGTAACAAAAGATATT-GTAATCAAAAGGGAAGAAAATGA
*
46654 AGATGAAGA
130 AAATGAAGA
46663 TGAAGATGAG
Statistics
Matches: 128, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
151 127 0.99
152 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (151 bp):
AAAGATTCAATATCTTTGATTCCAATATCTTCTTCCCGTTAAGTTTTTTTGGGTTAATGGGTTTC
AAAGATTCAAACTTTGAGACAAATTTGTAACAAAAGATATTGTAATCAAAAGGGAAGAAAATGAA
AATGAAGAAGAGAGGTGTGTG
Found at i:47724 original size:17 final size:17
Alignment explanation
Indices: 47702--47736 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
47692 TCAGGGTTAA
47702 ATTATAAAAATTTAATT
1 ATTATAAAAATTTAATT
**
47719 ATTATAAATTTTTAATT
1 ATTATAAAAATTTAATT
47736 A
1 A
47737 GAAAAAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATAAAAATTTAATT
Found at i:53118 original size:3 final size:3
Alignment explanation
Indices: 53110--53182 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
53100 TCAAACAGAA
53110 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53158 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
53183 TTTACTTGTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53950 original size:3 final size:3
Alignment explanation
Indices: 53942--53968 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53932 ACACTCCCTT
53942 CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC
53969 ATCACTGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:56802 original size:97 final size:96
Alignment explanation
Indices: 56617--56809 Score: 255
Period size: 97 Copynumber: 2.0 Consensus size: 96
56607 TTTTTGGGAA
* * * *
56617 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTTGCTCCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTCA
*
56682 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAGCAAACATTGCCTCGATT
* * *
56713 AAGGGTATTCGATTATTTTGATTTGAAGAAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTC
1 AAGGATATTCGATTATCTCGATTTGAAG-AAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTC
* *
56778 -GAAACTCGAA-ATAATCAAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAGCAAACATTGCCTCGATT
56810 TTAAAGTTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
96 26 0.31
97 53 0.63
98 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTCA
GAATCGAAGATAAGCAAACATTGCCTCGATT
Found at i:57056 original size:29 final size:28
Alignment explanation
Indices: 57024--57086 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
57014 AAAATGAGAC
57024 TTTTCGGATACCTAG-GGGCAAAATGGTAA
1 TTTT-GGAT-CCTAGAGGGCAAAATGGTAA
* *
57053 TTTTGGATTCTCGAGGGCAAAATGGTAA
1 TTTTGGATCCTAGAGGGCAAAATGGTAA
57081 TTTTGG
1 TTTTGG
57087 GAAAGTTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 3 0.10
28 24 0.77
29 4 0.13
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.33
Consensus pattern (28 bp):
TTTTGGATCCTAGAGGGCAAAATGGTAA
Found at i:57140 original size:59 final size:60
Alignment explanation
Indices: 57063--57353 Score: 264
Period size: 59 Copynumber: 5.0 Consensus size: 60
57053 TTTTGGATTC
* *
57063 TCGAGGG-CAAAATGGTAATTTTGGGAAAG-TTCGAGGTTAAAAATGGAATTTTTAGACAT
1 TCGAGGGTAAAAATGGTAATTTT-GGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACAT
* * * * ** ** *
57122 TTGGGGGT-AAAAGGGTAATTTT-GAGAGTTTTAAGGTCGAAAATGGAGTTTTTGGACAT
1 TCGAGGGTAAAAATGGTAATTTTGGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACAT
* * * **
57180 CCGAGGGT-AAAATGGTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAAATTTTGGAGGT
1 TCGAGGGTAAAAATGGTAATTTTGGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACAT
* *
57239 TC-AGGGGTAAAAATGG-AATTTTTGAAAG-TTCGAGGGTAAAAATGGAATTTTTGGA-AGTT
1 TCGA-GGGTAAAAATGGTAATTTTGGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACA--T
* *
57298 TC-AAGGTAAAAAATGG-AATTTTTGG-AAGTTTCGAGGTCAAAAATGGAATTTTTGGA
1 TCGAGGGT-AAAAATGGTAA-TTTTGGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGA
57354 AGTTTCGGGA
Statistics
Matches: 191, Mismatches: 31, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
57 4 0.02
58 71 0.37
59 79 0.41
60 37 0.19
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (60 bp):
TCGAGGGTAAAAATGGTAATTTTGGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGACAT
Found at i:57355 original size:30 final size:29
Alignment explanation
Indices: 57071--57360 Score: 231
Period size: 30 Copynumber: 9.8 Consensus size: 29
57061 TCTCGAGGGC
*
57071 AAAATGGTAATTTTGGGAAAG-TTCGAGGTTA
1 AAAATGG-AATTTTTGG-AAGTTTCGAGG-TA
* * *
57102 AAAATGGAATTTTTAGACA-TTTGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTTCGAGGTA
* ** *
57130 AAAAGGGTAA-TTTT-GAGAGTTTTAAGGTCG
1 AAAATGG-AATTTTTGGA-AGTTTCGAGGT-A
* *
57160 AAAATGGAGTTTTTGGACA--TCCGAGGGT-
1 AAAATGGAATTTTTGGA-AGTTTCGA-GGTA
*
57188 AAAATGGTAATTTTTGAAAGTTTCGAGGTTA
1 AAAATGG-AATTTTTGGAAGTTTCGAGG-TA
* * *
57219 AAAATGGAAATTTTGG-AGGTTCAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GAGGTA
*
57248 AAAATGGAATTTTTGAAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTA
*
57277 AAAATGGAATTTTTGGAAGTTTCAAGGTAA
1 AAAATGGAATTTTTGGAAGTTTCGAGGT-A
57307 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGT-A
57337 AAAATGGAATTTTTGGAAGTTTCG
1 AAAATGGAATTTTTGGAAGTTTCG
57361 GGACCTCCAG
Statistics
Matches: 211, Mismatches: 29, Indels: 39
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.01
28 25 0.12
29 66 0.31
30 100 0.47
31 17 0.08
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTA
Done.