Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4541.1
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: 54806
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:4185 original size:40 final size:40
Alignment explanation
Indices: 4003--4225 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
3993 TCCTCGTTCA
* * * * *
4003 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
4042 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
4082 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
4122 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
4162 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
4202 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
4226 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:4234 original size:41 final size:41
Alignment explanation
Indices: 4157--4234 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
4147 TTAGTATCTC
* * *
4157 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
4198 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
4235 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:12190 original size:40 final size:40
Alignment explanation
Indices: 12010--12230 Score: 223
Period size: 40 Copynumber: 5.5 Consensus size: 40
12000 CTCGTTCAAG
* * * * *
12010 TGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
* * *
12049 TGCCTTCGGGACATAACCCGGATTCAACAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
12089 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
* * *
12129 TGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
* ** * * * *
12169 GGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-AA
1 TGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACGAA
* *
12209 AGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGACTTAACCCGGA
12231 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 34 0.22
40 114 0.73
41 8 0.05
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
Found at i:12239 original size:41 final size:41
Alignment explanation
Indices: 12162--12239 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
12152 TTAGTATCTC
* * *
12162 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
12203 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
12240 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:19267 original size:27 final size:26
Alignment explanation
Indices: 19223--19274 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
19213 CTCGCTACAA
*
19223 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
19250 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
19275 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:25044 original size:27 final size:27
Alignment explanation
Indices: 25014--25105 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
25004 ATTACCAAAG
* * *
25014 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCGTTT
*
25041 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACCGTTT
*
25068 TACCTTC-AGTTTACAAAATTACCGTTT
1 TACCCTCGA-TTTACAAAATTACCGTTT
25095 TACCCTCGATT
1 TACCCTCGATT
25106 GTGAAATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.02
27 54 0.96
28 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCGTTT
Found at i:25059 original size:54 final size:54
Alignment explanation
Indices: 25001--25105 Score: 131
Period size: 54 Copynumber: 1.9 Consensus size: 54
24991 CTTAACTTGT
* * *
25001 AAAATTACCAAAGTACCCTC-GATTTATAGAATTATCGTTTTACCCTCGATTTAC
1 AAAATTACCAAAGTACCCTCAG-TTTACAAAATTACCGTTTTACCCTCGATTTAC
*** *
25055 AAAATTACCATTTTACCTTCAGTTTACAAAATTACCGTTTTACCCTCGATT
1 AAAATTACCAAAGTACCCTCAGTTTACAAAATTACCGTTTTACCCTCGATT
25106 GTGAAATTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 42 0.98
55 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (54 bp):
AAAATTACCAAAGTACCCTCAGTTTACAAAATTACCGTTTTACCCTCGATTTAC
Found at i:25167 original size:27 final size:27
Alignment explanation
Indices: 25137--25205 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
25127 TGTAGGATAG
**
25137 AATTACCAAAATACCACT-GGTTTG-AGA
1 AATTACCAAAATACC-CTCAATTTGTA-A
*
25164 AATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCCTCAATTTGTAA
25191 AATTACCAAAATACC
1 AATTACCAAAATACC
25206 TTTGATTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.06
27 33 0.92
28 1 0.03
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (27 bp):
AATTACCAAAATACCCTCAATTTGTAA
Found at i:25213 original size:27 final size:27
Alignment explanation
Indices: 25137--25213 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 27
25127 TGTAGGATAG
* *
25137 AATTACCAAAATACCACTGGTTTGAGA
1 AATTACCAAAATACCATTGATTTGAGA
* * **
25164 AATTACCGAAATACCCTCAATTTGTA-A
1 AATTACCAAAATACCATTGATTTG-AGA
*
25191 AATTACCAAAATACCTTTGATTT
1 AATTACCAAAATACCATTGATTT
25214 ACAAAGTTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCATTGATTTGAGA
Found at i:25278 original size:27 final size:26
Alignment explanation
Indices: 25242--25297 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
25232 CCTTGACTTT
*
25242 TTTAAAAATTA-TAGGAATACCATTGG
1 TTTAAAAATTACT-GAAATACCATTGG
*
25268 TTTACAAAATTACTGAAATACCCTTGG
1 TTTA-AAAATTACTGAAATACCATTGG
25295 TTT
1 TTT
25298 GTAGATTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (26 bp):
TTTAAAAATTACTGAAATACCATTGG
Found at i:26174 original size:16 final size:16
Alignment explanation
Indices: 26153--26183 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26143 CAAATATGGG
*
26153 CATGACATTTTGCATA
1 CATGACATATTGCATA
26169 CATGACATATTGCAT
1 CATGACATATTGCAT
26184 GGGATATGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (16 bp):
CATGACATATTGCATA
Found at i:26254 original size:25 final size:24
Alignment explanation
Indices: 26216--26285 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 24
26206 AGAAAGTGCT
*
26216 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
26240 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
26265 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
26286 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 1 0.02
25 41 0.98
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:26298 original size:24 final size:24
Alignment explanation
Indices: 26215--26298 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
26205 GAGAAAGTGC
* *
26215 TAAAAGGGCTCTGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
*
26240 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
26264 CAGAAAGGGCTTTGCCCCAG-TTAT
1 TA-AAAGGGCTTTGCCCCAGTTTAT
26288 TAAAAGAGGCT
1 TAAAAG-GGCT
26299 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:26492 original size:42 final size:42
Alignment explanation
Indices: 26433--26521 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
26423 TAGTCTCCCC
* ** *
26433 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
26475 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
26517 AAATG
1 AAATG
26522 AGCCTAAGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:30719 original size:27 final size:27
Alignment explanation
Indices: 30689--30886 Score: 263
Period size: 27 Copynumber: 7.3 Consensus size: 27
30679 TACTGAAATG
* * *
30689 CCCTCGATTTGTAGATTTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* *
30716 CCCTCGATTTATAGAATTACCATTTCA
1 CCCTCGATTTATAAAATTACCATTTTA
* *
30743 CCCTCGATTTACAAAATTACCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
*
30770 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
**
30797 CCCTCGATTTATAAAATTACTGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
30824 CCCTCGATTTATAAAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* **
30851 CCCTC-AGTTTACAAAATTACTGTTTTA
1 CCCTCGA-TTTATAAAATTACCATTTTA
30878 CCCTCGATT
1 CCCTCGATT
30887 GCAAAATTAC
Statistics
Matches: 151, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 149 0.99
28 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTATAAAATTACCATTTTA
Found at i:30763 original size:54 final size:54
Alignment explanation
Indices: 30705--30886 Score: 294
Period size: 54 Copynumber: 3.4 Consensus size: 54
30695 ATTTGTAGAT
* *
30705 TTACCATTTTACCCTCGATTTATAGAATTACCATTTCACCCTCGATTTACAAAA
1 TTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAA
*
30759 TTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAAAA
1 TTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAA
* *
30813 TTACTGTTTTACCCTCGATTTATAAAATTACCATTTTACCCTC-AGTTTACAAAA
1 TTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGA-TTTACAAAA
*
30867 TTACTGTTTTACCCTCGATT
1 TTACCGTTTTACCCTCGATT
30887 GCAAAATTAC
Statistics
Matches: 121, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
53 1 0.01
54 120 0.99
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.41
Consensus pattern (54 bp):
TTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAA
Found at i:30948 original size:27 final size:26
Alignment explanation
Indices: 30889--31042 Score: 166
Period size: 27 Copynumber: 5.7 Consensus size: 26
30879 CCTCGATTGC
* *
30889 AAAATTACAAAAATACCTCT-GTATGAT
1 AAAATTACCAAAATACC-CTAGTTTG-T
*
30916 AGAATTACCAAAATACTCCTAGTTTGT
1 AAAATTACCAAAATAC-CCTAGTTTGT
30943 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATA-CCCTAGTTTGT
* * *
30970 AAAATTACCGAAATACCACTGGTTTAT
1 AAAATTACCAAAATACC-CTAGTTTGT
* * *
30997 AAAATTACCGAAATACCTTCAATTTGT
1 AAAATTACCAAAATACCCT-AGTTTGT
31024 AAAATTACCAAAATACCCT
1 AAAATTACCAAAATACCCT
31043 TGATTTACAA
Statistics
Matches: 109, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
26 3 0.03
27 100 0.92
28 6 0.06
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (26 bp):
AAAATTACCAAAATACCCTAGTTTGT
Found at i:31005 original size:81 final size:81
Alignment explanation
Indices: 30888--31067 Score: 213
Period size: 81 Copynumber: 2.2 Consensus size: 81
30878 CCCTCGATTG
* * * * *
30888 CAAAATTACAAAAATACCTCT-GTATGATAGAATTACCAAAATACTCCT-AGTTTGTAAAATTAC
1 CAAAATTACAGAAATACCACTGGT-TTATAAAATTACCAAAATAC-CCTCAATTTGTAAAATTAC
*
30951 CAAAATACCCCTAG-TTTG
64 CAAAATA-CCCTAGATTTA
* * * *
30969 TAAAATTACCGAAATACCACTGGTTTATAAAATTACCGAAATACCTTCAATTTGTAAAATTACCA
1 CAAAATTACAGAAATACCACTGGTTTATAAAATTACCAAAATACCCTCAATTTGTAAAATTACCA
*
31034 AAATACCCTTGATTTA
66 AAATACCCTAGATTTA
31050 CAAAATTACAGAAATACC
1 CAAAATTACAGAAATACC
31068 TTTGACTTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
80 7 0.08
81 74 0.89
82 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.29
Consensus pattern (81 bp):
CAAAATTACAGAAATACCACTGGTTTATAAAATTACCAAAATACCCTCAATTTGTAAAATTACCA
AAATACCCTAGATTTA
Found at i:31048 original size:27 final size:27
Alignment explanation
Indices: 30876--31154 Score: 162
Period size: 27 Copynumber: 10.3 Consensus size: 27
30866 ATTACTGTTT
* * *
30876 TACCCTCGA-TTGCAAAATTACAAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* *
30902 TA-CCTCTG-TATGATAGAATTACCAAAA
1 TACCCT-TGATTTG-TAAAATTACCAAAA
*
30929 TACTCCTAG-TTTGTAAAATTACCAAAA
1 TAC-CCTTGATTTGTAAAATTACCAAAA
* *
30956 TACCCCT-AGTTTGTAAAATTACCGAAA
1 TACCCTTGA-TTTGTAAAATTACCAAAA
* * *
30983 TACCAC-TGGTTTATAAAATTACCGAAA
1 TACC-CTTGATTTGTAAAATTACCAAAA
*
31010 TA-CCTTCAATTTGTAAAATTACCAAAA
1 TACCCTT-GATTTGTAAAATTACCAAAA
**
31037 TACCCTTGATTTACAAAATTA-CAGAAA
1 TACCCTTGATTTGTAAAATTACCA-AAA
* * *
31064 TACCTTTGACTTTTTAAAAATTA-TAGAAA
1 TACCCTTGA-TTTGT-AAAATTACCA-AAA
* * ** **
31093 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* * *
31120 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
*
31147 CACCCTTG
1 TACCCTTG
31155 TAGGATGAAA
Statistics
Matches: 200, Mismatches: 37, Indels: 31
0.75 0.14 0.12
Matches are distributed among these distances:
25 4 0.02
26 11 0.05
27 147 0.74
28 16 0.08
29 22 0.11
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (27 bp):
TACCCTTGATTTGTAAAATTACCAAAA
Found at i:31069 original size:54 final size:54
Alignment explanation
Indices: 30888--31154 Score: 197
Period size: 54 Copynumber: 4.9 Consensus size: 54
30878 CCCTCGATTG
* * * * * *
30888 CAAAATTACAAAAATACC-TCTGTATGATAGAATTACCAAAATACTCC-TAGTTTG
1 CAAAATTACAGAAATACCTTCAGTTTG-TAAAATTACCAAAATAC-CCTTGGTTTA
* * *
30942 TAAAATTACCA-AAATACC-CCTAGTTTGTAAAATTACCGAAATACCAC-TGGTTTA
1 CAAAATTA-CAGAAATACCTTC-AGTTTGTAAAATTACCAAAATACC-CTTGGTTTA
* * * *
30996 TAAAATTACCGAAATACCTTCAATTTGTAAAATTACCAAAATACCCTTGATTTA
1 CAAAATTACAGAAATACCTTCAGTTTGTAAAATTACCAAAATACCCTTGGTTTA
* * * * *
31050 CAAAATTACAGAAATACCTTTGACTTTTTAAAAATTA-TAGAAATACCATTGGTTTA
1 CAAAATTACAGAAATACC-TTCAGTTTGT-AAAATTACCA-AAATACCCTTGGTTTA
* * * * *
31106 CAAAATTACTGAAATACCCTT-GGTTTGTAGATTTACCAAAACACCCTTG
1 CAAAATTACAGAAATA-CCTTCAGTTTGTAAAATTACCAAAATACCCTTG
31155 TAGGATGAAA
Statistics
Matches: 172, Mismatches: 30, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
53 3 0.02
54 109 0.63
55 20 0.12
56 38 0.22
57 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (54 bp):
CAAAATTACAGAAATACCTTCAGTTTGTAAAATTACCAAAATACCCTTGGTTTA
Found at i:35013 original size:24 final size:24
Alignment explanation
Indices: 34931--35013 Score: 96
Period size: 25 Copynumber: 3.4 Consensus size: 24
34921 AAGAAATGCT
* *
34931 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTATC
34955 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTATC
* *
34980 AGAAAGGGCTTTGCCCTAG-TTATT
1 A-AAAGGGCTTTGCCCCAGTTTATC
35004 AAAAGAGGCT
1 AAAAG-GGCT
35014 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATC
Found at i:35200 original size:42 final size:42
Alignment explanation
Indices: 35141--35223 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
35131 CCCAAATAGG
*
35141 CTTGCTTACATTCATTGACATTACATATGATATTGAAATGGA
1 CTTGCATACATTCATTGACATTACATATGATATTGAAATGGA
*
35183 CTTGCATACA-TCTATTGACATTACATGTGATATTGAAATGG
1 CTTGCATACATTC-ATTGACATTACATATGATATTGAAATGG
35224 GCTTAAGGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 2 0.05
42 36 0.95
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (42 bp):
CTTGCATACATTCATTGACATTACATATGATATTGAAATGGA
Found at i:35288 original size:31 final size:31
Alignment explanation
Indices: 35249--35353 Score: 167
Period size: 31 Copynumber: 3.4 Consensus size: 31
35239 CGTTTACAGT
35249 AAAA-GCTTCGGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
* *
35279 AAAAGGCTTCTGCCCAGTGATAAGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
*
35310 AAAAGGCTTCGGCCCAGTGATATAATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
*
35341 GAAAGGCTTCGGC
1 AAAAGGCTTCGGC
35354 TTAGTATATG
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
30 4 0.06
31 64 0.94
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (31 bp):
AAAAGGCTTCGGCCCAGTGATATGATTTATG
Found at i:37685 original size:54 final size:54
Alignment explanation
Indices: 37636--37810 Score: 271
Period size: 54 Copynumber: 3.2 Consensus size: 54
37626 GAATTATAAA
* *
37636 TTTACCATCGATTTATAGAATTACCATTTCACCCTCGATTTACAAAATTACCGT
1 TTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGT
*
37690 TTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGT
1 TTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGT
* * * *
37744 TTTACCCTCGATTTACAAAATTACCATTTTACCCTC-AGTTTAAAAAATTACTGT
1 TTTACCCTCGATTTATAGAATTACCATTTTACCCTCGA-TTTACAAAATTACCGT
37798 TTTACCCTCGATT
1 TTTACCCTCGATT
37811 GTCAAATTAT
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
53 1 0.01
54 111 0.99
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (54 bp):
TTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGT
Found at i:37728 original size:81 final size:81
Alignment explanation
Indices: 37611--37810 Score: 267
Period size: 81 Copynumber: 2.5 Consensus size: 81
37601 ATTACTGAAA
* * * * *
37611 TACCCTCGATTTGTAGAATTATAAATTTACCATCGATTTATAGAATTACCATTTCACCCTCGATT
1 TACCCTCGATTTATAGAATTACAATTTTACCCTCGATTTACAGAATTACCATTTCACCCTCGATT
*
37676 TACAAAATTACCGTTT
66 TACAAAATTACCATTT
* * *
37692 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATT
1 TACCCTCGATTTATAGAATTACAATTTTACCCTCGATTTACAGAATTACCATTTCACCCTCGATT
37757 TACAAAATTACCATTT
66 TACAAAATTACCATTT
* * **
37773 TACCCTC-AGTTTAAAAAATTACTGTTTTACCCTCGATT
1 TACCCTCGA-TTTATAGAATTACAATTTTACCCTCGATT
37811 GTCAAATTAT
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
80 1 0.01
81 104 0.99
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (81 bp):
TACCCTCGATTTATAGAATTACAATTTTACCCTCGATTTACAGAATTACCATTTCACCCTCGATT
TACAAAATTACCATTT
Found at i:37741 original size:27 final size:27
Alignment explanation
Indices: 37611--37810 Score: 231
Period size: 27 Copynumber: 7.4 Consensus size: 27
37601 ATTACTGAAA
** ** *
37611 TACCCTCGATTTGTAGAATTATAAATT
1 TACCCTCGATTTACAGAATTACCATTT
* *
37638 TACCATCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
37665 CACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
*
37692 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
37719 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
*
37746 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * **
37773 TACCCTC-AGTTTAAAAAATTACTGTTT
1 TACCCTCGA-TTTACAGAATTACCATTT
37800 TACCCTCGATT
1 TACCCTCGATT
37811 GTCAAATTAT
Statistics
Matches: 150, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 148 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCATTT
Found at i:37993 original size:27 final size:27
Alignment explanation
Indices: 37839--38105 Score: 272
Period size: 27 Copynumber: 9.8 Consensus size: 27
37829 CCCTGTAGGA
*
37839 TAAAATTACCAAAATACCCCTAGTTTG
1 TAAAATTACCAAAATACCCTTAGTTTG
37866 TAAAATTACCAAAATACCCTTAGTTTG
1 TAAAATTACCAAAATACCCTTAGTTTG
37893 TAAAATTACCAAAATACCCTTAGTTTG
1 TAAAATTACCAAAATACCCTTAGTTTG
* *
37920 TAAAATTACCGAAATACCAC-TGGTTTG
1 TAAAATTACCAAAATACC-CTTAGTTTG
* *
37947 TAAAATTACCAAAATACCCTCAATTTG
1 TAAAATTACCAAAATACCCTTAGTTTG
*
37974 TAAAATTACCAAAATACCCTT-GATTTA
1 TAAAATTACCAAAATACCCTTAG-TTTG
* * *
38001 CAAAATTA-CAGAAATACCCTTGACTTTC
1 TAAAATTACCA-AAATACCCTT-AGTTTG
* * * *
38029 TAAAAATTA-TAGAAATACCATTGGTTTA
1 T-AAAATTACCA-AAATACCCTTAGTTTG
* ** *
38057 CAAAATTACTGAAATACCCTTGGTTTG
1 TAAAATTACCAAAATACCCTTAGTTTG
* * *
38084 TAGATTTACCAAAACACCCTTA
1 TAAAATTACCAAAATACCCTTA
38106 TAGGATAAAA
Statistics
Matches: 202, Mismatches: 30, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
26 3 0.01
27 173 0.86
28 8 0.04
29 18 0.09
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTTAGTTTG
Found at i:38946 original size:25 final size:24
Alignment explanation
Indices: 38908--38977 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 24
38898 AGGAAGTGCT
*
38908 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
38932 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
38957 ATAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
38978 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 1 0.02
25 41 0.98
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:38990 original size:24 final size:24
Alignment explanation
Indices: 38907--38990 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
38897 GAGGAAGTGC
* *
38907 TAAAAGGGCTCTGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
*
38932 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
38956 CATAAAGGGCTTTGCCCCAG-TTAT
1 TA-AAAGGGCTTTGCCCCAGTTTAT
38980 TAAAAGAGGCT
1 TAAAAG-GGCT
38991 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:39184 original size:42 final size:42
Alignment explanation
Indices: 39125--39216 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
39115 TAGTCTCCCC
*
39125 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
*
39167 AAATGGTCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
39209 AAATGGGC
1 AAATGGGC
39217 CTAAGGGCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:39285 original size:31 final size:31
Alignment explanation
Indices: 39240--39354 Score: 171
Period size: 31 Copynumber: 3.8 Consensus size: 31
39230 CGTTTACAGT
* *
39240 AAAA-GCTTCAGCCCAATGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
*
39270 AAAAGGCTTTGGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
*
39301 AAAAGGCTTCGGCTCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
*
39332 GAAAGGCTTCGGCCCAGT-ATATG
1 AAAAGGCTTCGGCCCAGTGATATG
39355 TGAAGACTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
30 9 0.12
31 68 0.88
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (31 bp):
AAAAGGCTTCGGCCCAGTGATATGATTTATG
Found at i:41569 original size:24 final size:24
Alignment explanation
Indices: 41536--41601 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
41526 CCGATATATC
*
41536 AGCTCGTAAGAGCTTACTG-TTCTT
1 AGCTCATAAGAGCTTACTGTTTC-T
*
41560 AGCTTATAAGAGCTTACTGTTTCT
1 AGCTCATAAGAGCTTACTGTTTCT
41584 AGCTCA-ATAGAGCTTACT
1 AGCTCATA-AGAGCTTACT
41602 ACTCATTAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 1 0.03
24 33 0.89
25 3 0.08
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (24 bp):
AGCTCATAAGAGCTTACTGTTTCT
Found at i:43072 original size:19 final size:19
Alignment explanation
Indices: 43048--43111 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
43038 TCAAGAATTC
43048 TTTATCACCAACCTACAAT
1 TTTATCACCAACCTACAAT
* * * *
43067 TTTATCA-CTATCAAGAATT
1 TTTATCACCAACCTACAA-T
43086 CTTTATCACCAACCTACAAT
1 -TTTATCACCAACCTACAAT
43106 TTTATC
1 TTTATC
43112 TCTTTTCGCT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 6 0.18
19 14 0.41
20 8 0.24
21 6 0.18
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.38
Consensus pattern (19 bp):
TTTATCACCAACCTACAAT
Found at i:43076 original size:39 final size:39
Alignment explanation
Indices: 43033--43111 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
43023 TCCAAGGTGA
43033 CACTATCAAGAATTCTTTATCACCAACCTACAATTTTAT
1 CACTATCAAGAATTCTTTATCACCAACCTACAATTTTAT
43072 CACTATCAAGAATTCTTTATCACCAACCTACAATTTTAT
1 CACTATCAAGAATTCTTTATCACCAACCTACAATTTTAT
43111 C
1 C
43112 TCTTTTCGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (39 bp):
CACTATCAAGAATTCTTTATCACCAACCTACAATTTTAT
Found at i:43092 original size:20 final size:20
Alignment explanation
Indices: 43033--43094 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
43023 TCCAAGGTGA
43033 CACTATCAAGAATTCTTTAT
1 CACTATCAAGAATTCTTTAT
* * * *
43053 CACCAACCTACAA-T-TTTAT
1 CA-CTATCAAGAATTCTTTAT
43072 CACTATCAAGAATTCTTTAT
1 CACTATCAAGAATTCTTTAT
43092 CAC
1 CAC
43095 CAACCTACAA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
18 6 0.19
19 8 0.26
20 11 0.35
21 6 0.19
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (20 bp):
CACTATCAAGAATTCTTTAT
Found at i:49025 original size:37 final size:37
Alignment explanation
Indices: 48975--49053 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
48965 TTATTACGAA
* * *
48975 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
49012 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
49049 GTCTT
1 GTCTT
49054 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:49277 original size:24 final size:24
Alignment explanation
Indices: 49249--49326 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
49239 TCACATTCAT
*
49249 CATATCGGCCATTAGGCCTTATCA
1 CATATCAGCCATTAGGCCTTATCA
** *** *
49273 CATAT-ATACACTTTCACATTCATCA
1 CATATCAGCCA-TTAGGCCTT-ATCA
49298 CATATCAGCCATTAGGCCTTATCA
1 CATATCAGCCATTAGGCCTTATCA
49322 CATAT
1 CATAT
49327 ATACACTTTC
Statistics
Matches: 38, Mismatches: 13, Indels: 6
0.67 0.23 0.11
Matches are distributed among these distances:
23 2 0.05
24 19 0.50
25 14 0.37
26 3 0.08
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (24 bp):
CATATCAGCCATTAGGCCTTATCA
Found at i:49298 original size:25 final size:25
Alignment explanation
Indices: 49269--49349 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
49259 ATTAGGCCTT
49269 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** *** *
49294 ATCACATATCAGCCA-TTAGGCCTT-
1 ATCACATAT-ATACACTTTCACATTC
49318 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
49343 ATCACAT
1 ATCACAT
49350 CGGCGCCATT
Statistics
Matches: 41, Mismatches: 12, Indels: 6
0.69 0.20 0.10
Matches are distributed among these distances:
23 3 0.07
24 14 0.34
25 21 0.51
26 3 0.07
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:49309 original size:49 final size:48
Alignment explanation
Indices: 49172--49741 Score: 873
Period size: 49 Copynumber: 11.8 Consensus size: 48
49162 CCCTTCGGGA
* * * * * *
49172 CTTATCAC-ATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
49219 CTTGTCAC-ATATATACACTTTCACATTCATCATATCGGCCATTAGGC
1 CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49266 CTTATCAC-ATATATACACTTTCACATTCATCACATATCAGCCATTAGGC
1 CTTATCACAATATATACACTTTCACATTCATCAC--ATCGGCCATTAGGC
49315 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCGCCATTAGGC
1 CTTATCACAATATATACACTTTCACATTCATCACATC-G-GCCATTAGGC
49364 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49413 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49462 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49511 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49560 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
49609 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
49658 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
49707 CTTATCTC-ATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACAATATATACACT-TTCACATTCATCACAT
49742 AGAATCCTAA
Statistics
Matches: 500, Mismatches: 16, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
46 1 0.00
47 96 0.19
49 374 0.75
50 1 0.00
51 28 0.06
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (48 bp):
CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:51498 original size:41 final size:41
Alignment explanation
Indices: 51453--51583 Score: 92
Period size: 41 Copynumber: 3.1 Consensus size: 41
51443 TTAATCCTTA
51453 CATAATGCACTACTCCAACATGTTTATGACATGTTTTTAGC
1 CATAATGCACTACTCCAACATGTTTATGACATGTTTTTAGC
** * *** *
51494 CATAA--CATCTTGTCCACCCATGCTCTTTATTTTAT-TAATCCTTA-C
1 CATAATGCA-CTACTCCA-ACATG---TTTATGACATGT--T-TTTAGC
51539 -ATAATGCACTACTCCAACATGTTTATGACATGTTTTTAGC
1 CATAATGCACTACTCCAACATGTTTATGACATGTTTTTAGC
51579 CATAA
1 CATAA
51584 CATCTTGTCC
Statistics
Matches: 63, Mismatches: 14, Indels: 26
0.61 0.14 0.25
Matches are distributed among these distances:
39 5 0.08
40 8 0.13
41 20 0.32
42 1 0.02
43 1 0.02
44 15 0.24
45 8 0.13
46 5 0.08
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (41 bp):
CATAATGCACTACTCCAACATGTTTATGACATGTTTTTAGC
Found at i:51554 original size:85 final size:85
Alignment explanation
Indices: 51425--52368 Score: 1861
Period size: 85 Copynumber: 11.1 Consensus size: 85
51415 TATTTTATTG
* *
51425 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACTCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
51490 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
*
51510 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACTCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
51575 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
51595 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
51660 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
51680 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
51745 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
51765 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
51830 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
51850 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
51915 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
51935 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
52000 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
52020 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
52085 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
52105 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
52170 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
52190 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
52255 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
52275 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
52340 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
52360 CCCATGCTC
1 CCCATGCTC
52369 ATGGCCGGCC
Statistics
Matches: 857, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 857 1.00
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.39
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:54124 original size:40 final size:40
Alignment explanation
Indices: 54094--54443 Score: 522
Period size: 40 Copynumber: 8.8 Consensus size: 40
54084 AGCATGATTA
* * *
54094 CTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* ** *
54134 CTCTTTGGGGTTTAGCACGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* *
54174 CTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* *
54214 CTCCTCGGGACTTAGCCCAGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
*
54254 CTCCTTC-GGACTTAGCCCGGATACATCACTAGCACGAATG
1 CT-CTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* * *
54294 CTCCTCGGGACTTAGCCCGGATATAACACCAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* *
54334 CTCTTTGGGACTTAGCCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
*
54374 CTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
54414 CTCTTCGGGACTTAGCCCGGATATATCACT
1 CTCTTCGGGACTTAGCCCGGATATATCACT
54444 CTCAATTCTC
Statistics
Matches: 275, Mismatches: 33, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
39 3 0.01
40 269 0.98
41 3 0.01
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
Found at i:54632 original size:40 final size:40
Alignment explanation
Indices: 54588--54667 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
54578 TAGTCATAAC
*
54588 ACTCTTTCAAAATTGCGTCACTTATACCCTTATAATTCAA
1 ACTCTTTCAAAATTGCATCACTTATACCCTTATAATTCAA
54628 ACTCTTTCAAAATTGCATCACTTATACCCTTATAATTCAA
1 ACTCTTTCAAAATTGCATCACTTATACCCTTATAATTCAA
54668 TCCAAATCGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (40 bp):
ACTCTTTCAAAATTGCATCACTTATACCCTTATAATTCAA
Done.