Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold93
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: 1685797
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 216 characters in sequence are not A, C, G, or T
File 3 of 14
Found at i:204982 original size:26 final size:26
Alignment explanation
Indices: 204953--205013 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
204943 ATTAAGGTAT
204953 ATTTTCTTTTAACTTCTTTTTGCTTG
1 ATTTTCTTTTAACTTCTTTTTGCTTG
204979 ATTTTCTTTTAACTTCTTTTTGCTTG
1 ATTTTCTTTTAACTTCTTTTTGCTTG
*
205005 ATTTCCTTT
1 ATTTTCTTT
205014 AATTTATTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.11, C:0.16, G:0.07, T:0.66
Consensus pattern (26 bp):
ATTTTCTTTTAACTTCTTTTTGCTTG
Found at i:206297 original size:150 final size:157
Alignment explanation
Indices: 206127--206410 Score: 384
Period size: 158 Copynumber: 1.8 Consensus size: 157
206117 TAGTCACCAA
* * **
206127 GTCTGTTTTTATGCCGAA-G-G-T-TTAGGATTGGTTCATCCCATTTCTAAT-C-TTTTTAAGTC
1 GTCTGCTTTTATGCCGAAGGTGATATTAGGATAGGTTCATCCCATTTAAAATCCTTTTTTAAGTC
* * * * *
206186 CTTTAGGGGTATCGAGCACTTTTATGTTGAAGGTATCCCCTAAGGACATTTTTATAATTTTT-TT
66 CTTTAAGGGTATCAAGCACTTTTATGTCGAAAGTATCCCCTAAGGAAATTTTTATAATTTTTCTT
206250 TAGAATCGAATCTTAGATTGTCATCGG
131 TAGAATCGAATCTTAGATTGTCATCGG
* *
206277 GTCTGCTTTTATGCCGAAGGTGAATATTAGGATAGGTTTATCCCTTTTAAAATCCTTTTTTTAAG
1 GTCTGCTTTTATGCCGAAGGTG-ATATTAGGATAGGTTCATCCCATTTAAAATCC-TTTTTTAAG
* *
206342 TCCTTTAAGGGTATCAAGTACTTTTATGTCGAAAGTATCCCCTAAGGAAATTTTTTTAATTTTTC
64 TCCTTTAAGGGTATCAAGCACTTTTATGTCGAAAGTATCCCCTAAGGAAATTTTTATAATTTTTC
206407 TTTA
129 TTTA
206411 AGGATAATTT
Statistics
Matches: 112, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
150 17 0.15
151 1 0.01
152 1 0.01
154 1 0.01
155 22 0.20
156 1 0.01
158 65 0.58
159 4 0.04
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (157 bp):
GTCTGCTTTTATGCCGAAGGTGATATTAGGATAGGTTCATCCCATTTAAAATCCTTTTTTAAGTC
CTTTAAGGGTATCAAGCACTTTTATGTCGAAAGTATCCCCTAAGGAAATTTTTATAATTTTTCTT
TAGAATCGAATCTTAGATTGTCATCGG
Found at i:208296 original size:98 final size:98
Alignment explanation
Indices: 208081--208298 Score: 230
Period size: 98 Copynumber: 2.2 Consensus size: 98
208071 TTTTTCGAGG
*
208081 GGATACTCCAACTCC-G-TTTTTAAACTTGTCAAGATTTAAATCTTATTTTCGTCTGAATTGTCA
1 GGATACTCCAAC-CCTGTTTTTTAAACTTATCAAGATTTAAATCTTATTTTCGTCTGAATTGTCA
* * * * **
208144 TCGTTAGGGACATTCCAACCCCATTCTTCTGAGA
65 TCGATAGGGACACTCAAACCCCATTCCTCCAAGA
* * *
208178 GGATCCTCCAACTCTGTTTTTTAAACTTATCAAGATTTAAATCTTATTTTCG-CTTAGATTGTCA
1 GGATACTCCAACCCTGTTTTTTAAACTTATCAAGATTTAAATCTTATTTTCGTCTGA-ATTGTCA
* * **
208242 TC-ATCGGAGATACTCAAACCTTATTCCTCCAAG-
65 TCGATAGG-GACACTCAAACCCCATTCCTCCAAGA
* *
208275 GGATACTCTAACCCTATTTTTTAA
1 GGATACTCCAACCCTGTTTTTTAA
208299 CCAAAATTGA
Statistics
Matches: 99, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
96 1 0.01
97 38 0.38
98 60 0.61
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.38
Consensus pattern (98 bp):
GGATACTCCAACCCTGTTTTTTAAACTTATCAAGATTTAAATCTTATTTTCGTCTGAATTGTCAT
CGATAGGGACACTCAAACCCCATTCCTCCAAGA
Found at i:210061 original size:27 final size:27
Alignment explanation
Indices: 210031--210083 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
210021 TCATTATAAC
210031 TATGTCTTCTTCCTCGGATAGACTCAT
1 TATGTCTTCTTCCTCGGATAGACTCAT
210058 TATGTCTTCTTCCTCGGATAGACTCA
1 TATGTCTTCTTCCTCGGATAGACTCA
210084 CCAATCTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (27 bp):
TATGTCTTCTTCCTCGGATAGACTCAT
Found at i:211034 original size:41 final size:41
Alignment explanation
Indices: 210980--211083 Score: 167
Period size: 41 Copynumber: 2.6 Consensus size: 41
210970 AGTCACATTT
210980 TTACCTAGATGTATCGATACATTTTTCAATGTATCGATACA
1 TTACCTAGATGTATCGATACATTTTTCAATGTATCGATACA
*
211021 TTACCTAGATGTATCGATACATCTTTCAATGTATCGATACA
1 TTACCTAGATGTATCGATACATTTTTCAATGTATCGATACA
*
211062 TT-CTTCA-ATGTATCGATACATT
1 TTACCT-AGATGTATCGATACATT
211084 CTGTCCTTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
40 16 0.27
41 43 0.73
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (41 bp):
TTACCTAGATGTATCGATACATTTTTCAATGTATCGATACA
Found at i:211084 original size:20 final size:20
Alignment explanation
Indices: 210988--211085 Score: 137
Period size: 20 Copynumber: 4.8 Consensus size: 20
210978 TTTTACCTAG
*
210988 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
*
211008 ATGTATCGATACATTACCT-A
1 ATGTATCGATACATT-CTTCA
211028 GATGTATCGATACA-TCTTTCA
1 -ATGTATCGATACATTC-TTCA
211049 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
211069 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
211086 GTCCTTTTAC
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.01
20 52 0.74
21 17 0.24
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:212049 original size:20 final size:20
Alignment explanation
Indices: 212011--212049 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
212001 TAGCCTTTGA
*
212011 TCATGCTTTTTCACTATGTT
1 TCATGCTTTTTAACTATGTT
212031 TCATGCATTTTTAAC-ATGT
1 TCATGC-TTTTTAACTATGT
212050 CTAGCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.51
Consensus pattern (20 bp):
TCATGCTTTTTAACTATGTT
Found at i:212850 original size:13 final size:13
Alignment explanation
Indices: 212832--212880 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
212822 ACATACAAGA
212832 TGTATCGATACAT
1 TGTATCGATACAT
212845 TGTATCGATACA-
1 TGTATCGATACAT
*
212857 TG-A-CCA-A-AT
1 TGTATCGATACAT
212866 TGTATCGATACAT
1 TGTATCGATACAT
212879 TG
1 TG
212881 GCTTGTAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 3 0.10
11 3 0.10
12 3 0.10
13 16 0.55
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:212875 original size:34 final size:32
Alignment explanation
Indices: 212812--212880 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
212802 CCTTAACTGT
212812 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
212844 TTGTATCGATACATGACCAA-ATTGTATCGATACA
1 TTGTATCGATACAT-A-CAAGA-TGTATCGATACA
212878 TTG
1 TTG
212881 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 14 0.41
33 2 0.06
34 18 0.53
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:218821 original size:8 final size:8
Alignment explanation
Indices: 218808--218838 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
218798 ATTTGATTAA
218808 ATTTTGTG
1 ATTTTGTG
218816 ATTTTGTG
1 ATTTTGTG
218824 ATTTTGTG
1 ATTTTGTG
218832 ATGTTTG
1 AT-TTTG
218839 ATGTTGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (8 bp):
ATTTTGTG
Found at i:218860 original size:22 final size:22
Alignment explanation
Indices: 218835--218887 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
218825 TTTTGTGATG
218835 TTTGATGTTGAAATTGAATGAA
1 TTTGATGTTGAAATTGAATGAA
218857 TTTGATGTTGAAATTGAATGAA
1 TTTGATGTTGAAATTGAATGAA
218879 TTTGATGTT
1 TTTGATGTT
218888 TGATTTTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (22 bp):
TTTGATGTTGAAATTGAATGAA
Found at i:219074 original size:13 final size:13
Alignment explanation
Indices: 219056--219094 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
219046 ACAACATTCT
219056 TTGTATCGATACA
1 TTGTATCGATACA
219069 TTGTATCGATACA
1 TTGTATCGATACA
*
219082 CTGTATCGATACA
1 TTGTATCGATACA
219095 AAGGGTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:220930 original size:13 final size:13
Alignment explanation
Indices: 220912--220936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
220902 ATAATGCACA
220912 GTATCGATACATT
1 GTATCGATACATT
220925 GTATCGATACAT
1 GTATCGATACAT
220937 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:220949 original size:20 final size:22
Alignment explanation
Indices: 220922--220977 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
220912 GTATCGATAC
**
220922 ATTGTATCGATACATG-ACCAA
1 ATTGTATCGATACATGCAAAAA
* *
220943 A-TGTATCAATACTTGCAAAAA
1 ATTGTATCGATACATGCAAAAA
220964 ATTGTATCGATACA
1 ATTGTATCGATACA
220978 GGTGATTGGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 12 0.44
21 5 0.19
22 10 0.37
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30
Consensus pattern (22 bp):
ATTGTATCGATACATGCAAAAA
Found at i:221070 original size:34 final size:32
Alignment explanation
Indices: 221007--221075 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
220997 CCTTAACTAT
221007 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
*
221039 TTGTATTGATACATGACCAA-ATTGTATCGATACA
1 TTGTATCGATACAT-A-CAAGA-TGTATCGATACA
221073 TTG
1 TTG
221076 GCTTGTAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 13 0.39
33 2 0.06
34 18 0.55
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:223305 original size:23 final size:23
Alignment explanation
Indices: 223275--223340 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
223265 GCGCATACGA
*
223275 AATTAAAACCTTTTATCAAATGG
1 AATTAAAACCTTTTATCAAACGG
*
223298 AATTAAAACCTTTTATCATACGG
1 AATTAAAACCTTTTATCAAACGG
*
223321 AATTAAAACTTTTTATCAAA
1 AATTAAAACCTTTTATCAAA
223341 ACCTAGATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (23 bp):
AATTAAAACCTTTTATCAAACGG
Found at i:232873 original size:1 final size:1
Alignment explanation
Indices: 232867--232953 Score: 57
Period size: 1 Copynumber: 87.0 Consensus size: 1
232857 TCCTTCGTAC
* ** * * * * * * *
232867 AAAAAAAAAACAAAAAAACCAAGAAAAAAAACAACAAAAAACAAAAAACAAAAAAAAAACAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
232932 CAAAAAAAAACAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
232954 GGGTCCAGAT
Statistics
Matches: 62, Mismatches: 24, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:232894 original size:24 final size:23
Alignment explanation
Indices: 232867--232953 Score: 99
Period size: 24 Copynumber: 3.8 Consensus size: 23
232857 TCCTTCGTAC
232867 AAAAAAAAAACAAAAAAACCAAGA
1 AAAAAAAAAACAAAAAAACCAA-A
*
232891 AAAAAAACAAC-AAAAAA-CAAA
1 AAAAAAAAAACAAAAAAACCAAA
*
232912 AAACAAAAAAA-AAACAAACACAAA
1 AAA-AAAAAAACAAAAAAAC-CAAA
*
232936 AAAAAACAAACAAAAAAA
1 AAAAAAAAAACAAAAAAA
232954 GGGTCCAGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
21 4 0.08
22 14 0.26
23 12 0.23
24 23 0.43
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAACAAAAAAACCAAA
Found at i:232909 original size:31 final size:30
Alignment explanation
Indices: 232865--232953 Score: 112
Period size: 31 Copynumber: 2.9 Consensus size: 30
232855 CATCCTTCGT
*
232865 ACAAAAAAAAAACAAAAAAACCAAGAAAAAAA
1 ACAAACAAAAAACAAAAAAA-CAA-AAAAAAA
232897 AC-AACAAAAAAC-AAAAAACAAAAAAAAA
1 ACAAACAAAAAACAAAAAAACAAAAAAAAA
232925 ACAAACACAAAAA-AAAACAAACAAAAAAA
1 ACAAACA-AAAAACAAAA-AAACAAAAAAA
232954 GGGTCCAGAT
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
28 9 0.17
29 7 0.13
30 14 0.27
31 20 0.38
32 2 0.04
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.00
Consensus pattern (30 bp):
ACAAACAAAAAACAAAAAAACAAAAAAAAA
Found at i:232940 original size:45 final size:43
Alignment explanation
Indices: 232867--232952 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 43
232857 TCCTTCGTAC
*
232867 AAAAAAAAAACAAAAAAACCAAGAAAAAAAAC-AACAAAAAACA
1 AAAAAAAAAAAAAAAAAACC-AGAAAAAAAACAAACAAAAAACA
232910 AAAAACAAAAAAAAAACAAACACA-AAAAAAAACAAACAAAAAA
1 AAAAA-AAAAAAAAAA-AAAC-CAGAAAAAAAACAAACAAAAAA
232953 AGGGTCCAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
43 5 0.13
44 18 0.47
45 14 0.37
46 1 0.03
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (43 bp):
AAAAAAAAAAAAAAAAAACCAGAAAAAAAACAAACAAAAAACA
Found at i:232946 original size:16 final size:15
Alignment explanation
Indices: 232865--232953 Score: 103
Period size: 14 Copynumber: 5.9 Consensus size: 15
232855 CATCCTTCGT
232865 ACAAA-AAAAAAACAA
1 ACAAACAAAAAAA-AA
*
232880 AAAAACCAAGAAAAAAA
1 ACAAA-CAA-AAAAAAA
*
232897 AC-AACAAAAAACAA
1 ACAAACAAAAAAAAA
232911 A-AAACAAAAAAAAA
1 ACAAACAAAAAAAAA
232925 ACAAACACAAAAAAAA
1 ACAAACA-AAAAAAAA
232941 ACAAACAAAAAAA
1 ACAAACAAAAAAA
232954 GGGTCCAGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
14 19 0.30
15 18 0.28
16 17 0.27
17 5 0.08
18 5 0.08
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.00
Consensus pattern (15 bp):
ACAAACAAAAAAAAA
Found at i:234239 original size:28 final size:28
Alignment explanation
Indices: 234199--234554 Score: 376
Period size: 28 Copynumber: 12.5 Consensus size: 28
234189 CGTTCATCTC
234199 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
234227 TTCAAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCC-T
* * *
234256 TTCAAAGCCCACAAGTCAGTAGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
234284 TTCAAAGCCCAGAAGTCCGTGCCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCC-T
* * *
234313 TTCAAAGCCCCCAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
234341 TTCAAAGCCCACAAGTCAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCC-T
* *
234370 TTCAATGCCCACAAGTCAGTGGCA-TCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
234397 TTCCAAAGCCCACAAGTCAGTGGCATCCT
1 TT-CAAAGCCCACAAGTCAGTGGCACCCT
* * *
234426 TTCAAAGCCCATAAGTTAGTGGCA-TCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
234453 CTTCAAAACCCACAAGTTAGAGGCA-CCT
1 -TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
234481 TATCAAAACCCACAAGTCAGTGGCATCCT
1 T-TCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
234510 TTTAAAGCCCACACAAGTCGGTGGCAACTT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCCT
234540 TCTCTAAAGCCCACA
1 T-TC-AAAGCCCACA
234555 CAAGTTGGTG
Statistics
Matches: 277, Mismatches: 39, Indels: 22
0.82 0.12 0.07
Matches are distributed among these distances:
27 6 0.02
28 163 0.59
29 80 0.29
30 21 0.08
31 3 0.01
32 4 0.01
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:234287 original size:57 final size:57
Alignment explanation
Indices: 234199--234554 Score: 432
Period size: 57 Copynumber: 6.2 Consensus size: 57
234189 CGTTCATCTC
* * *
234199 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTT
* * * *
234256 TTCAAAGCCCACAAGTCAGTAGCATCTTTTCAAAGCCCAGAAGTCCGTGCCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTT
* * *
234313 TTCAAAGCCCCCAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTT
* * *
234370 TTCAATGCCCACAAGTCAGTGGCATCTTTCCAAAGCCCACAAGTCAGTGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTT
* * * * * *
234426 TTCAAAGCCCATAAGTTAGTGGCATCTCTTCAAAACCCACAAGTTAGAGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTT
* * * *
234482 ATCAAAACCCACAAGTCAGTGGCATCCTTTT-AAAGCCCACACAAGTCGGTGGCA-ACTT
1 TTCAAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAG-CC-CACAAGTCAGTGGCACCCTT
234540 TCTCTAAAGCCCACA
1 T-TC-AAAGCCCACA
234555 CAAGTTGGTG
Statistics
Matches: 253, Mismatches: 40, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
55 2 0.01
56 70 0.28
57 155 0.61
58 15 0.06
59 2 0.01
60 9 0.04
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.22
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTT
Found at i:234344 original size:85 final size:84
Alignment explanation
Indices: 234193--234554 Score: 427
Period size: 85 Copynumber: 4.2 Consensus size: 84
234183 CTAGAACGTT
* * *
234193 CATCTCTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACCCTTTT
1 CATCTCTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCC-TTT
*
234258 CAAAGCCCACAAGTCAGTAG
65 CAAAGCCCACAAGTCAGTGG
* * * * * *
234278 CATCTTTTCAAAGCCCAGAAGTCCGTGCCACCCTTTTCAAAGCCCCCAAGTTAGTGGCATCCTTT
1 CATCTCTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTT
234343 CAAAGCCCACAAGTCAGTGG
65 CAAAGCCCACAAGTCAGTGG
* * * * *
234363 CACCCTTTTCAATGCCCACAAGTCAGTGGCATCTTTCCAAAGCCCACAAGTCAGTGGCATCCTTT
1 CA-TCTCTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTT
* *
234428 CAAAGCCCATAAGTTAGTGG
65 CAAAGCCCACAAGTCAGTGG
* * * * * *
234448 CATCTCTTCAAAACCCACAAGTTAGAGGCACCTTATCAAAACCCACAAGTCAGTGGCATCCTTTT
1 CATCTCTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
*
234513 AAAGCCCACACAAGTCGGTGG
66 AAAG-CC-CACAAGTCAGTGG
* *
234534 CAACTTTCTCTAAAGCCCACA
1 CATCTCT-TC-AAAGCCCACA
234555 CAAGTTGGTG
Statistics
Matches: 233, Mismatches: 38, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
84 56 0.24
85 102 0.44
86 64 0.27
87 2 0.01
88 9 0.04
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.22
Consensus pattern (84 bp):
CATCTCTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
AAAGCCCACAAGTCAGTGG
Found at i:234948 original size:9 final size:10
Alignment explanation
Indices: 234935--234959 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
234925 GAAAAAATAC
234935 AAAAAAAAAG
1 AAAAAAAAAG
234945 AAAAAAAAAG
1 AAAAAAAAAG
234955 AAAAA
1 AAAAA
234960 TAGGGGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:235290 original size:21 final size:20
Alignment explanation
Indices: 235265--235369 Score: 97
Period size: 21 Copynumber: 5.1 Consensus size: 20
235255 AGTCACATTT
*
235265 TTACCCAGATGTATTGATACA
1 TTACCCA-ATGTATCGATACA
*
235286 TTACCCAAATGTATGGATACA
1 TTACCC-AATGTATCGATACA
*
235307 TTTTCCC-ATGTATCGATACA
1 -TTACCCAATGTATCGATACA
* *
235327 TTACCTAGATGAATCGATACA
1 TTACCCA-ATGTATCGATACA
*
235348 TCT-TCCAATGTATCGATACA
1 T-TACCCAATGTATCGATACA
235368 TT
1 TT
235370 CTGTCCTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
19 5 0.07
20 25 0.36
21 33 0.47
22 7 0.10
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
TTACCCAATGTATCGATACA
Found at i:235325 original size:41 final size:41
Alignment explanation
Indices: 235273--235369 Score: 131
Period size: 41 Copynumber: 2.4 Consensus size: 41
235263 TTTTACCCAG
* * * * *
235273 ATGTATTGATACATTACCCAAATGTATGGATACATTTTCCC
1 ATGTATCGATACATTACCCAAATGAATCGATACATCTTCCA
* *
235314 ATGTATCGATACATTACCTAGATGAATCGATACATCTTCCA
1 ATGTATCGATACATTACCCAAATGAATCGATACATCTTCCA
235355 ATGTATCGATACATT
1 ATGTATCGATACATT
235370 CTGTCCTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (41 bp):
ATGTATCGATACATTACCCAAATGAATCGATACATCTTCCA
Found at i:236334 original size:20 final size:20
Alignment explanation
Indices: 236296--236334 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
236286 TAGCCTTTGA
*
236296 TCATGCTTTTTCACTATGTT
1 TCATGCTTTTTAACTATGTT
236316 TCATGCATTTTTAAC-ATGT
1 TCATGC-TTTTTAACTATGT
236335 CCAGCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.51
Consensus pattern (20 bp):
TCATGCTTTTTAACTATGTT
Found at i:239213 original size:19 final size:20
Alignment explanation
Indices: 239189--239239 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
239179 TTATGCTCTA
**
239189 TATCGATACATGTTC-ATTG
1 TATCGATACATGGACAATTG
239208 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTG
239228 TATCGATACATG
1 TATCGATACATG
239240 AAACTGGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (20 bp):
TATCGATACATGGACAATTG
Found at i:247992 original size:13 final size:13
Alignment explanation
Indices: 247974--247998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
247964 ATTATGCTTG
247974 GTATCGATACATT
1 GTATCGATACATT
247987 GTATCGATACAT
1 GTATCGATACAT
247999 GTTCATTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:248035 original size:20 final size:19
Alignment explanation
Indices: 247982--248038 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
247972 TGGTATCGAT
*
247982 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
248001 TCATTATATCGATACATGG
1 ACATTGTATCGATACATGG
*
248020 ACAATTGTATCAATACATG
1 AC-ATTGTATCGATACATG
248039 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:254662 original size:129 final size:132
Alignment explanation
Indices: 254500--254878 Score: 456
Period size: 129 Copynumber: 2.8 Consensus size: 132
254490 TAATTTTTAT
* *
254500 TTAATTTTTAATTTTC--AAATTCATTTCATACCTTAATAGAGAACCGAAAAGATACAAAAAGTT
1 TTAATTTTTAATTTTCAAAAATTCATTTCGTACCTTAATAGAGAACCAAAAAGATACAAAAAGTT
254563 TTGAAAATTTCTATACCCCTACGAAAAACCATAGGAATATTAGAAATCTTGAAAAATTAAG-AT-
66 TTGAAAATTTCTATACCCCTACGAAAAACCATAGGAATATTAGAAAT-TTGAAAAATTAAGAATA
254626 A-A
130 ATA
*
254628 -TAATTTTT-ATTTTCCAAAAATTCATTTCGTACCTTAATAGAG-ACTCAAAAAGATAAAAAAGA
1 TTAATTTTTAATTTT-CAAAAATTCATTTCGTACCTTAATAGAGAAC-CAAAAAGATACAAAA-A
* *
254690 GTTTTGAAGATTTCTATACCCCTA-GGAAAACCATAGGAATATTAGAAAATTTGAAAAATTAAGA
63 GTTTTGAAAATTTCTATACCCCTACGAAAAACCATAGGAATATTAG-AAATTTGAAAAATTAAG-
254754 AAATAATTTTTA
126 -AATAA----TA
* * *
254766 TTTAATTTTTAATTTTTAAAAATTCATTTCGTACCTTAATAGAGAACCAAAAATATTCAAAAAGT
1 -TTAATTTTTAATTTTCAAAAATTCATTTCGTACCTTAATAGAGAACCAAAAAGATACAAAAAGT
* * *
254831 TTT-AAATATTTCTAT-GCCCTAACGAAAAACCATAAGAATAATAGAAAT
65 TTTGAAA-ATTTCTATACCCCT-ACGAAAAACCATAGGAATATTAGAAAT
254879 ATATAAAAAT
Statistics
Matches: 215, Mismatches: 14, Indels: 33
0.82 0.05 0.13
Matches are distributed among these distances:
126 5 0.02
127 9 0.04
128 2 0.01
129 70 0.33
130 28 0.13
132 2 0.01
133 1 0.00
138 7 0.03
139 19 0.09
140 65 0.30
141 7 0.03
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (132 bp):
TTAATTTTTAATTTTCAAAAATTCATTTCGTACCTTAATAGAGAACCAAAAAGATACAAAAAGTT
TTGAAAATTTCTATACCCCTACGAAAAACCATAGGAATATTAGAAATTTGAAAAATTAAGAATAA
TA
Found at i:254887 original size:140 final size:140
Alignment explanation
Indices: 254438--254888 Score: 419
Period size: 140 Copynumber: 3.3 Consensus size: 140
254428 ATAAAAACCT
* * * * * *
254438 TACCCCTATGAAAAGCCATAGGCAGAATAG-AAATCTAGAAAAATTAAGATAATAATTTTTATTT
1 TACCCCTA-GAAAAACCATAAGAATAATAGAAAATAT-GAAAAATTAAGAAAATAATTTTTATTT
* * *
254502 AATTTTTAATTTT-C--AAATTCATTTCATACCTTAATAGAGAAC-CGAAAAGATACAAAA-AGT
64 AATTTTT-ATTTTCCAAAAATTCATTTCGTACCTTAATAGAG-ACTCAAAAAGATAAAAAAGAGT
254562 TTTGAAA-ATTTCTA
127 TTT-AAAGATTTCTA
* * *
254576 TACCCCTACGAAAAACCATAGGAATATTAG-AAATCTTGAAAAATTAAG---AT-A-----A--T
1 TACCCCTA-GAAAAACCATAAGAATAATAGAAAAT-ATGAAAAATTAAGAAAATAATTTTTATTT
254629 AATTTTTATTTTCCAAAAATTCATTTCGTACCTTAATAGAGACTCAAAAAGATAAAAAAGAGTTT
64 AATTTTTATTTTCCAAAAATTCATTTCGTACCTTAATAGAGACTCAAAAAGATAAAAAAGAGTTT
*
254694 TGAAGATTTCTA
129 TAAAGATTTCTA
* * * *
254706 TACCCCTAGGAAAACCATAGGAATATTAGAAAATTTGAAAAATTAAGAAAATAATTTTTATTTAA
1 TACCCCTAGAAAAACCATAAGAATAATAGAAAATATGAAAAATTAAGAAAATAATTTTTATTTAA
* * **
254771 TTTTTAATTTT-TAAAAATTCATTTCGTACCTTAATAGAGAAC-CAAAAATATTCAAAA-AGTTT
66 TTTTT-ATTTTCCAAAAATTCATTTCGTACCTTAATAGAG-ACTCAAAAAGATAAAAAAGAGTTT
*
254833 TAAATATTTCTA
129 TAAAGATTTCTA
*
254845 T-GCCCTAACGAAAAACCATAAGAATAATAGAAATATAT-AAAAAT
1 TACCCCT-A-GAAAAACCATAAGAATAATAGAAA-ATATGAAAAAT
254889 GATTAAAATA
Statistics
Matches: 267, Mismatches: 22, Indels: 46
0.80 0.07 0.14
Matches are distributed among these distances:
126 5 0.02
127 9 0.03
128 2 0.01
129 73 0.27
130 25 0.09
132 2 0.01
133 1 0.00
134 1 0.00
135 2 0.01
138 45 0.17
139 18 0.07
140 74 0.28
141 10 0.04
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.33
Consensus pattern (140 bp):
TACCCCTAGAAAAACCATAAGAATAATAGAAAATATGAAAAATTAAGAAAATAATTTTTATTTAA
TTTTTATTTTCCAAAAATTCATTTCGTACCTTAATAGAGACTCAAAAAGATAAAAAAGAGTTTTA
AAGATTTCTA
Found at i:255653 original size:11 final size:11
Alignment explanation
Indices: 255636--255676 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
255626 AGCTAGGTTT
255636 TTCTTTTTTCA
1 TTCTTTTTTCA
* *
255647 CTCTTTTTTCT
1 TTCTTTTTTCA
255658 TTCTTTTTT-A
1 TTCTTTTTTCA
255668 TTCTTTTTT
1 TTCTTTTTT
255677 TTCCACTTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (11 bp):
TTCTTTTTTCA
Found at i:255677 original size:22 final size:22
Alignment explanation
Indices: 255635--255676 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
255625 TAGCTAGGTT
255635 TTTCTTTTTTCACTCTTTTTTC
1 TTTCTTTTTTCACTCTTTTTTC
*
255657 TTTCTTTTTT-ATTCTTTTTT
1 TTTCTTTTTTCACTCTTTTTT
255677 TTCCACTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTCACTCTTTTTTC
Found at i:257910 original size:85 final size:83
Alignment explanation
Indices: 257818--258083 Score: 277
Period size: 84 Copynumber: 3.1 Consensus size: 83
257808 ATCAGGGTTA
* * *
257818 AACCGATAAG-CAAATAAAGGATAAAAAGATTTATATGGGACTAAGCCGATAGGTAAACAAGGGA
1 AACCGATAAGTC-AACAAAGGATAAAAAGATTTAT-CGGGACTAAGCCGATAGGTAAACAAAGGA
*
257882 TGAAAAAGTTGA-TTGGAATTG
64 T-AAAAAGTTGACTAGG-ATTG
* * **
257903 AACCGATAAGTCAACAAAGGATAAAAGGATTTACTCGGGACTAAGCTGGCAGGTAAACAAAGGAT
1 AACCGATAAGTCAACAAAGGATAAAAAGATTTA-TCGGGACTAAGCCGATAGGTAAACAAAGGAT
257968 AAAAAGGTTGACTAGGATTG
65 AAAAA-GTTGACTAGGATTG
* * * ** *
257988 AA-CGACAAGTCAACAAAGGATGAAAAGATTTACCCAAGACTAAGCCGATTGGTAAACAAAGGAT
1 AACCGATAAGTCAACAAAGGATAAAAAGATTTA-TCGGGACTAAGCCGATAGGTAAACAAAGGAT
* *
258052 AAAAAGTTTGACCAGGAATG
65 AAAAAG-TTGACTAGGATTG
* *
258072 AATCGACAAGTC
1 AACCGATAAGTC
258084 GACCAATTAA
Statistics
Matches: 155, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
83 1 0.01
84 75 0.48
85 74 0.48
86 5 0.03
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.19
Consensus pattern (83 bp):
AACCGATAAGTCAACAAAGGATAAAAAGATTTATCGGGACTAAGCCGATAGGTAAACAAAGGATA
AAAAGTTGACTAGGATTG
Found at i:258218 original size:39 final size:41
Alignment explanation
Indices: 258110--258247 Score: 113
Period size: 41 Copynumber: 3.4 Consensus size: 41
258100 GGCCAGAGCG
*** * ** *
258110 AAACCGATAAAGCCAACTGGGTTAGAAGGGTTAATTAGGGCA
1 AAACCGATAAAGCCAAC-CAATTAGAAGGGTTGACCAAGGCA
* *
258152 AAACCGATAAAGTCAACCAATTGGAA-GGTTG-CC-AGTGCA
1 AAACCGATAAAGCCAACCAATTAGAAGGGTTGACCAAG-GCA
* *
258191 AAACCGATAAAGCCAA-TAGTTTAGAAGGGTTGACCAAGGCA
1 AAACCGATAAAGCCAACCA-ATTAGAAGGGTTGACCAAGGCA
*
258232 AAACCAATAAAGCCAA
1 AAACCGATAAAGCCAA
258248 ACGAGAATGA
Statistics
Matches: 77, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
38 2 0.03
39 23 0.30
40 9 0.12
41 25 0.32
42 18 0.23
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (41 bp):
AAACCGATAAAGCCAACCAATTAGAAGGGTTGACCAAGGCA
Found at i:258297 original size:46 final size:46
Alignment explanation
Indices: 258245--258451 Score: 197
Period size: 46 Copynumber: 4.5 Consensus size: 46
258235 CCAATAAAGC
*
258245 CAAACGAGAATGAAAAGGGTTTGACCAGGATGGTAACCGATATAGT
1 CAAACGAGAATGAAAAGGGTTTGACCAGGATGGTAACCGATACAGT
* * * * *
258291 CAAACGAGAATGAAAAAGGTTTGACCA-AAGTGATGACCAATACAGT
1 CAAACGAGAATGAAAAGGGTTTGACCAGGA-TGGTAACCGATACAGT
* * * *
258337 CAAACGAGCATGAAAAGGGTTTGACTAGGGTGGTAATCGATACAGT
1 CAAACGAGAATGAAAAGGGTTTGACCAGGATGGTAACCGATACAGT
* * ** *
258383 C-AACCATAGATGAAAAGGGTTTGACCAAGG-TGGTATTCAATACAGT
1 CAAACGAGA-ATGAAAAGGGTTTGACC-AGGATGGTAACCGATACAGT
* *
258429 TAAAC-ATAGATGAAAAGGGTTTG
1 CAAACGAGA-ATGAAAAGGGTTTG
258452 TTTGCTAAAG
Statistics
Matches: 134, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
45 5 0.04
46 123 0.92
47 6 0.04
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (46 bp):
CAAACGAGAATGAAAAGGGTTTGACCAGGATGGTAACCGATACAGT
Found at i:258350 original size:92 final size:90
Alignment explanation
Indices: 258234--258451 Score: 249
Period size: 92 Copynumber: 2.4 Consensus size: 90
258224 CCAAGGCAAA
* * * *
258234 ACCAATAAAGCCAAACGAGAATGAAAAGGGTTTGACCAGGATGGTAACCGATATAGTCAAAC-GA
1 ACCAATACAGTCAAACGAG-ATGAAAAGGGTTTGACCAGGATGGTAACCGATACAGTCAACCAGA
258298 GAATGAAAAAGGTTTGACCAAAGTGAT
65 G-ATGAAAAAGGTTTGACCAAAGTGAT
* * * *
258325 GACCAATACAGTCAAACGAGCATGAAAAGGGTTTGACTAGGGTGGTAATCGATACAGTCAACCAT
1 -ACCAATACAGTCAAACGAG-ATGAAAAGGGTTTGACCAGGATGGTAACCGATACAGTCAACCAG
* * *
258390 AGATGAAAAGGGTTTGACCAAGGTGGT
64 AGATGAAAAAGGTTTGACCAAAGTGAT
* * *
258417 ATTCAATACAGTTAAACATAGATGAAAAGGGTTTG
1 A-CCAATACAGTCAAAC-GAGATGAAAAGGGTTTG
258452 TTTGCTAAAG
Statistics
Matches: 108, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
91 1 0.01
92 103 0.95
93 4 0.04
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (90 bp):
ACCAATACAGTCAAACGAGATGAAAAGGGTTTGACCAGGATGGTAACCGATACAGTCAACCAGAG
ATGAAAAAGGTTTGACCAAAGTGAT
Found at i:259271 original size:93 final size:92
Alignment explanation
Indices: 259003--259491 Score: 463
Period size: 93 Copynumber: 5.3 Consensus size: 92
258993 ATGGCAGAAT
* * * * * *
259003 AAAAGAGATATGATTAGGAATGTGTGGTTGAGACATCTTAGCCACGAGAAAACCAGGCTTTGTGA
1 AAAAAAGATATGATTGGGAATGTGTGGTTGAGACATCTTGGCCGCGAGAAAACTAGGCTTTGTAA
259068 TGCATCGATACCATCTAGTGGTTGAGG
66 TGCATCGATACCATCTAGTGGTTGAGG
* * * * * * * * * *
259095 AAAAAGGATATGGTT-GGAATATGTGGTTGGGATATCCTT-GCC-CTG-GAGATCTTGGACTATA
1 AAAAAAGATATGATTGGGAATGTGTGGTTGAGACAT-CTTGGCCGC-GAGAAAACTAGG-CTTTG
* * *
259156 TGATGCAT-TAGTACCATCTAGTGGTTGAGA
63 TAATGCATCGA-TACCATCTAGTGGTTGAGG
* * *
259186 AAAAAAGATATGATTGGGGAATGTATGGTTGAGACATCTTGGCTGTGAGAAAACTAGGCTTTGTA
1 AAAAAAGATATGATT-GGGAATGTGTGGTTGAGACATCTTGGCCGCGAGAAAACTAGGCTTTGTA
*
259251 ATGCATCGATACCATCTAGTGGTTAAGG
65 ATGCATCGATACCATCTAGTGGTTGAGG
* * * * * * * * *
259279 AAAAAAGATATGATTGGGAATGTGTGGTTGGGATATCCTT-GTC-CTAGAGATCTTGGATTATAT
1 AAAAAAGATATGATTGGGAATGTGTGGTTGAGACAT-CTTGGCCGCGAGAAAACTAGGCTT-TGT
*
259342 GAA-GCATCAATACCATCTAGTGGTTGAGG
64 -AATGCATCGATACCATCTAGTGGTTGAGG
* * * * *
259371 AAAAAGGATATGATTGGGGAATCTGTGGTCGAGACATCCTGGCCGCAAGAAAACTAGGCTTTGTA
1 AAAAAAGATATGATT-GGGAATGTGTGGTTGAGACATCTTGGCCGCGAGAAAACTAGGCTTTGTA
* *
259436 ATGCATCGATACCATCTACTGGTTTAGG
65 ATGCATCGATACCATCTAGTGGTTGAGG
* *
259464 AAAAAGGATATGATTTGGAATGTGTGGT
1 AAAAAAGATATGATTGGGAATGTGTGGT
259492 CAGGATATCC
Statistics
Matches: 317, Mismatches: 63, Indels: 34
0.77 0.15 0.08
Matches are distributed among these distances:
90 8 0.03
91 73 0.23
92 92 0.29
93 125 0.39
94 19 0.06
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (92 bp):
AAAAAAGATATGATTGGGAATGTGTGGTTGAGACATCTTGGCCGCGAGAAAACTAGGCTTTGTAA
TGCATCGATACCATCTAGTGGTTGAGG
Found at i:259359 original size:92 final size:93
Alignment explanation
Indices: 259069--259584 Score: 465
Period size: 93 Copynumber: 5.6 Consensus size: 93
259059 GCTTTGTGAT
* * * *
259069 GCATCGATACCATCTAGTGGTTGAGGAAAAAGGATATGGTT--GGAATATGTGGTTGGGATATCC
1 GCATCAATACCATCTAGTGGTTGAGGAAAAAAGATATGATTGGGGAATGTGTGGTTGGGATATCC
* * *
259132 TTGCCCTGGAGATCTTGGACTATATGAT
66 TTGCCCTAGAGATCTTGGATTATATGAA
* * * * * *
259160 GCATTAGTACCATCTAGTGGTTGAGAAAAAAAGATATGATTGGGGAATGTATGGTTGAGACAT-C
1 GCATCAATACCATCTAGTGGTTGAGGAAAAAAGATATGATTGGGGAATGTGTGGTTGGGATATCC
** * * * * *
259224 TTGGCTGTGAGAAAACTAGGCTT-TGT-AA
66 TT-GCCCT-AGAGATCTTGGATTATATGAA
* *
259252 TGCATCGATACCATCTAGTGGTTAAGGAAAAAAGATATGATT-GGGAATGTGTGGTTGGGATATC
1 -GCATCAATACCATCTAGTGGTTGAGGAAAAAAGATATGATTGGGGAATGTGTGGTTGGGATATC
*
259316 CTTGTCCTAGAGATCTTGGATTATATGAA
65 CTTGCCCTAGAGATCTTGGATTATATGAA
* * * * *
259345 GCATCAATACCATCTAGTGGTTGAGGAAAAAGGATATGATTGGGGAATCTGTGGTCGAGACATCC
1 GCATCAATACCATCTAGTGGTTGAGGAAAAAAGATATGATTGGGGAATGTGTGGTTGGGATATCC
* * * * * * *
259410 TGGCCGCAAGAAAACTAGGCTT-TGT-AA
66 TTGCC-CTAGAGATCTTGGATTATATGAA
* * * * * **
259437 TGCATCGATACCATCTACTGGTTTAGGAAAAAGGATATGATT-TGGAATGTGTGGTCAGGATATC
1 -GCATCAATACCATCTAGTGGTTGAGGAAAAAAGATATGATTGGGGAATGTGTGGTTGGGATATC
* * * * *
259501 CTTTCCTTGGAGATCTTGGATTAAATGAT
65 CTTGCCCTAGAGATCTTGGATTATATGAA
* * **
259530 GCATCAGTACCATCTAGTGGTTAAGGAAAAAAGATATGATTAAGGAATGTGTGGT
1 GCATCAATACCATCTAGTGGTTGAGGAAAAAAGATATGATTGGGGAATGTGTGGT
259585 CAGTGCCTCC
Statistics
Matches: 334, Mismatches: 77, Indels: 26
0.76 0.18 0.06
Matches are distributed among these distances:
91 54 0.16
92 124 0.37
93 137 0.41
94 19 0.06
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCAATACCATCTAGTGGTTGAGGAAAAAAGATATGATTGGGGAATGTGTGGTTGGGATATCC
TTGCCCTAGAGATCTTGGATTATATGAA
Found at i:259392 original size:185 final size:184
Alignment explanation
Indices: 259003--259584 Score: 826
Period size: 185 Copynumber: 3.2 Consensus size: 184
258993 ATGGCAGAAT
* * * * *
259003 AAAAGAGATATGATT-AGGAATGTGTGGTTGAGACATCTTAGCCACGAGAAAACCAGGCTTTGTG
1 AAAAAAGATATGATTGAGGAATGTGTGGTTGAGACATCTTGGCCGCGAGAAAACTAGGCTTTGTA
* * *
259067 ATGCATCGATACCATCTAGTGGTTGAGGAAAAAGGATATGGTTGGAATATGTGGTTGGGATATCC
66 ATGCATCGATACCATCTAGTGGTTAAGGAAAAAGGATATGATTGGAATGTGTGGTTGGGATATCC
* * * *
259132 TTGCCCTGGAGATCTTGGACTATATGATGCATTAGTACCATCTAGTGGTTGAGA
131 TTGTCCTGGAGATCTTGGATTATATGATGCATCAGTACCATCTAGTGGTTGAGG
* * * *
259186 AAAAAAGATATGATTGGGGAATGTATGGTTGAGACATCTTGGCTGTGAGAAAACTAGGCTTTGTA
1 AAAAAAGATATGATTGAGGAATGTGTGGTTGAGACATCTTGGCCGCGAGAAAACTAGGCTTTGTA
*
259251 ATGCATCGATACCATCTAGTGGTTAAGGAAAAAAGATATGATTGGGAATGTGTGGTTGGGATATC
66 ATGCATCGATACCATCTAGTGGTTAAGGAAAAAGGATATGATT-GGAATGTGTGGTTGGGATATC
* * *
259316 CTTGTCCTAGAGATCTTGGATTATATGAAGCATCAATACCATCTAGTGGTTGAGG
130 CTTGTCCTGGAGATCTTGGATTATATGATGCATCAGTACCATCTAGTGGTTGAGG
* * * * * *
259371 AAAAAGGATATGATTGGGGAATCTGTGGTCGAGACATCCTGGCCGCAAGAAAACTAGGCTTTGTA
1 AAAAAAGATATGATTGAGGAATGTGTGGTTGAGACATCTTGGCCGCGAGAAAACTAGGCTTTGTA
* * **
259436 ATGCATCGATACCATCTACTGGTTTAGGAAAAAGGATATGATTTGGAATGTGTGGTCAGGATATC
66 ATGCATCGATACCATCTAGTGGTTAAGGAAAAAGGATATGA-TTGGAATGTGTGGTTGGGATATC
* *
259501 CTT-TCCTTGGAGATCTTGGATTAAATGATGCATCAGTACCATCTAGTGGTTAAGG
130 CTTGTCC-TGGAGATCTTGGATTATATGATGCATCAGTACCATCTAGTGGTTGAGG
*
259556 AAAAAAGATATGATTAAGGAATGTGTGGT
1 AAAAAAGATATGATTGAGGAATGTGTGGT
259585 CAGTGCCTCC
Statistics
Matches: 353, Mismatches: 42, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
183 14 0.04
184 84 0.24
185 253 0.72
186 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (184 bp):
AAAAAAGATATGATTGAGGAATGTGTGGTTGAGACATCTTGGCCGCGAGAAAACTAGGCTTTGTA
ATGCATCGATACCATCTAGTGGTTAAGGAAAAAGGATATGATTGGAATGTGTGGTTGGGATATCC
TTGTCCTGGAGATCTTGGATTATATGATGCATCAGTACCATCTAGTGGTTGAGG
Found at i:266743 original size:13 final size:13
Alignment explanation
Indices: 266725--266750 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
266715 TATACCAAGT
266725 ATGTATCGATACA
1 ATGTATCGATACA
266738 ATGTATCGATACA
1 ATGTATCGATACA
266751 CGAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:268999 original size:21 final size:21
Alignment explanation
Indices: 268966--269010 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
268956 TTGCAAGTTG
*
268966 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
268988 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
269008 AAA
1 AAA
269011 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:270834 original size:15 final size:15
Alignment explanation
Indices: 270814--270844 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
270804 TAAAAATGTC
*
270814 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
270829 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
270844 C
1 C
270845 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:273236 original size:20 final size:20
Alignment explanation
Indices: 273211--273264 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
273201 AAAACCCTTA
273211 AAAGTATCGATACACAATT-C
1 AAAGTATCGATACAC-ATTGC
*
273231 AAAGTATCGATACACGTTGC
1 AAAGTATCGATACACATTGC
*
273251 AATGTATCGATACA
1 AAAGTATCGATACA
273265 TGAAAAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (20 bp):
AAAGTATCGATACACATTGC
Found at i:273343 original size:13 final size:13
Alignment explanation
Indices: 273325--273350 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
273315 TACACCAAAT
273325 ATGTATCGATACA
1 ATGTATCGATACA
273338 ATGTATCGATACA
1 ATGTATCGATACA
273351 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:273348 original size:32 final size:33
Alignment explanation
Indices: 273307--273370 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
273297 TAGCCAAACT
* *
273307 TGTATCGATACACCAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
273339 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
273371 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:275378 original size:16 final size:17
Alignment explanation
Indices: 275357--275388 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
275347 GTGTATAGAC
275357 ATGTATATGA-ATGAAG
1 ATGTATATGATATGAAG
275373 ATGTATATGATATGAA
1 ATGTATATGATATGAA
275389 AATTATGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (17 bp):
ATGTATATGATATGAAG
Found at i:277396 original size:54 final size:54
Alignment explanation
Indices: 277294--277399 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 54
277284 GGAGTTGCTG
* * *
277294 CACCACTCTCTACATGGTAAAACCAATGGAAATAAGAGTAGCCGAGCATAGTGC
1 CACCACTCTCTACATGGCAAAACCAATAGAAATAAGAGTAGCCAAGCATAGTGC
* * *
277348 CACCACTGTTCTACATGGCATAACCAATAG-AATGAA-AGTAGCTAAGCATAGT
1 CACCACT-CTCTACATGGCAAAACCAATAGAAAT-AAGAGTAGCCAAGCATAGT
277400 ACTTGGAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
54 24 0.55
55 20 0.45
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (54 bp):
CACCACTCTCTACATGGCAAAACCAATAGAAATAAGAGTAGCCAAGCATAGTGC
Found at i:279555 original size:10 final size:11
Alignment explanation
Indices: 279534--279567 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
279524 AAAAAGTAGC
279534 AATAATAAATAA
1 AATAA-AAATAA
279546 AAT-AAAATAA
1 AATAAAAATAA
279556 AATAAAAATAA
1 AATAAAAATAA
279567 A
1 A
279568 TATCCTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.43
11 9 0.43
12 3 0.14
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:285298 original size:13 final size:13
Alignment explanation
Indices: 285280--285306 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
285270 TGAAAAACTA
285280 TTTGATAAATCGC
1 TTTGATAAATCGC
285293 TTTGATAAATCGC
1 TTTGATAAATCGC
285306 T
1 T
285307 CATCCTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTGATAAATCGC
Found at i:288541 original size:51 final size:52
Alignment explanation
Indices: 288411--288549 Score: 190
Period size: 51 Copynumber: 2.7 Consensus size: 52
288401 AATTGCTTAC
* * *
288411 ATGTATCGATACATTGAAGAATGTATCGATACATTTGGGTCAAAAACTTAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAAACCTAGA
* * *
288463 ATGTATCGATATAATGAATAATGTATCGATACATTTGGGT-TAAAACCTAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAAACCTAGA
* * *
288514 ATGTATCGATACAATAAAAAATTTATCGATATATTT
1 ATGTATCGATACAATGAAAAATGTATCGATACATTT
288550 TCTTTCCAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 40 0.52
52 37 0.48
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (52 bp):
ATGTATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAAACCTAGA
Found at i:289448 original size:47 final size:47
Alignment explanation
Indices: 289389--289759 Score: 244
Period size: 47 Copynumber: 7.9 Consensus size: 47
289379 TTTATCTATT
* * *
289389 TTTGACTGTATTAGCGTTAGGACTAGGTCAAACTCTTTTCACCCTCG
1 TTTGACTATATTGGCGTTAGGACTAGGTCAAACTCTTTTCACCCTCA
* * * * * * * *
289436 TTTGATTATATTAGAGTAAAGACTTGGTCAAACTCTTTTTATCCTCA
1 TTTGACTATATTGGCGTTAGGACTAGGTCAAACTCTTTTCACCCTCA
* * * **
289483 TTTGACTGTATTGGCGTTA-GTCTTA-GTCATACTCTTGTTCACCCTTG
1 TTTGACTATATTGGCGTTAGGAC-TAGGTCAAACTCTT-TTCACCCTCA
* * *
289530 TTTGACTGTATTGGCGTTAAGACCTA-GTCAAACTCCTTTT-ACCATCA
1 TTTGACTATATTGGCGTTAGGA-CTAGGTCAAACT-CTTTTCACCCTCA
** *
289577 TTTGACTATATTGGCAG-TAGTCCT-GGTAAAACTCTTTTTTCACCCTCA
1 TTTGACTATATTGGC-GTTAGGACTAGGTCAAACTC--TTTTCACCCTCA
* * * * * *
289625 TTTGAATGTATTGGTGTTAGGACCT-GCTCAAACTTTTTCTCACCCTCG
1 TTTGACTATATTGGCGTTAGGA-CTAGGTCAAACTCTTT-TCACCCTCA
* *
289673 TTTGAC-AGTATTGGCGTTAGGACTTA-GTCATACGT-TTTCTCACTCTCA
1 TTTGACTA-TATTGGCGTTAGGAC-TAGGTCAAAC-TCTTT-TCACCCTCA
* *
289721 TTTGACTGTATTGGCATTAGGACCTA-GTCAAACT-TTTTC
1 TTTGACTATATTGGCGTTAGGA-CTAGGTCAAACTCTTTTC
289760 CATTCTTGTT
Statistics
Matches: 254, Mismatches: 51, Indels: 39
0.74 0.15 0.11
Matches are distributed among these distances:
45 1 0.00
46 23 0.09
47 111 0.44
48 104 0.41
49 15 0.06
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (47 bp):
TTTGACTATATTGGCGTTAGGACTAGGTCAAACTCTTTTCACCCTCA
Found at i:289589 original size:94 final size:93
Alignment explanation
Indices: 289389--289758 Score: 299
Period size: 94 Copynumber: 3.9 Consensus size: 93
289379 TTTATCTATT
* * * * * * *
289389 TTTGACTGTATTAGCGTTAGGAC-TAGGTCAAACTCTTTTCACCCTCGTTTGATTATATTAGAGT
1 TTTGACTATATTGGCGTTAGGACTTA-GTCAAACTCTTTTCACCCTCATTTGACTGTATTGGCGT
* * *
289453 AAAGACTTGGTCAAACTCTTTTTATCCTCA
65 TAAGACCTAGTCAAACTCTTTTTA-CCTCA
* * * **
289483 TTTGACTGTATTGGCGTTA-GTCTTAGTCATACTCTTGTTCACCCTTGTTTGACTGTATTGGCGT
1 TTTGACTATATTGGCGTTAGGACTTAGTCAAACTCTT-TTCACCCTCATTTGACTGTATTGGCGT
*
289547 TAAGACCTAGTCAAACTCCTTTTACCATCA
65 TAAGACCTAGTCAAACTCTTTTTACC-TCA
* * * * * *
289577 TTTGACTATATTGGCAG-TA-GTCCTGGTAAAACTCTTTTTTCACCCTCATTTGAATGTATTGGT
1 TTTGACTATATTGGC-GTTAGGACTTAGTCAAACTC--TTTTCACCCTCATTTGACTGTATTGGC
* *
289640 GTTAGGACCT-GCTCAAACT-TTTTCTCACCCTCG
63 GTTAAGACCTAG-TCAAACTCTTTT-T-A-CCTCA
* *
289673 TTTGAC-AGTATTGGCGTTAGGACTTAGTCATACGT-TTTCTCACTCTCATTTGACTGTATTGGC
1 TTTGACTA-TATTGGCGTTAGGACTTAGTCAAAC-TCTTT-TCACCCTCATTTGACTGTATTGGC
* *
289736 ATTAGGACCTAGTCAAACT-TTTT
63 GTTAAGACCTAGTCAAACTCTTTT
289759 CCATTCTTGT
Statistics
Matches: 227, Mismatches: 33, Indels: 30
0.78 0.11 0.10
Matches are distributed among these distances:
93 14 0.06
94 96 0.42
95 44 0.19
96 61 0.27
97 11 0.05
98 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (93 bp):
TTTGACTATATTGGCGTTAGGACTTAGTCAAACTCTTTTCACCCTCATTTGACTGTATTGGCGTT
AAGACCTAGTCAAACTCTTTTTACCTCA
Found at i:289759 original size:48 final size:49
Alignment explanation
Indices: 289389--289759 Score: 304
Period size: 48 Copynumber: 7.8 Consensus size: 49
289379 TTTATCTATT
* *
289389 TTTGACTGTATTAGCGTTAGGA-CTAGGTCAAACTC-TTT-TCACCCTCG
1 TTTGACTGTATTGGCGTTAGGACCTA-GTCAAACTCTTTTCTCACCCTCA
* * * * * * * * *
289436 TTTGATTATATTAGAGTAAAGACTTGGTCAAACTCTTTT-T-ATCCTCA
1 TTTGACTGTATTGGCGTTAGGACCTAGTCAAACTCTTTTCTCACCCTCA
* * * * **
289483 TTTGACTGTATTGGCGTTA-GTCTTAGTCATACTCTTGT-TCACCCTTG
1 TTTGACTGTATTGGCGTTAGGACCTAGTCAAACTCTTTTCTCACCCTCA
* * *
289530 TTTGACTGTATTGGCGTTAAGACCTAGTCAAACTCCTTT-T-ACCATCA
1 TTTGACTGTATTGGCGTTAGGACCTAGTCAAACTCTTTTCTCACCCTCA
* * * * *
289577 TTTGACTATATTGGCAG-TA-GTCCTGGTAAAACTCTTTTTTCACCCTCA
1 TTTGACTGTATTGGC-GTTAGGACCTAGTCAAACTCTTTTCTCACCCTCA
* * *
289625 TTTGAATGTATTGGTGTTAGGACCT-GCTCAAACT-TTTTCTCACCCTCG
1 TTTGACTGTATTGGCGTTAGGACCTAG-TCAAACTCTTTTCTCACCCTCA
* * * * *
289673 TTTGACAGTATTGGCGTTAGGACTTAGTCATAC-GTTTTCTCACTCTCA
1 TTTGACTGTATTGGCGTTAGGACCTAGTCAAACTCTTTTCTCACCCTCA
*
289721 TTTGACTGTATTGGCATTAGGACCTAGTCAAACT-TTTTC
1 TTTGACTGTATTGGCGTTAGGACCTAGTCAAACTCTTTTC
289760 CATTCTTGTT
Statistics
Matches: 258, Mismatches: 53, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
46 31 0.12
47 90 0.35
48 126 0.49
49 11 0.04
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (49 bp):
TTTGACTGTATTGGCGTTAGGACCTAGTCAAACTCTTTTCTCACCCTCA
Found at i:289813 original size:45 final size:46
Alignment explanation
Indices: 289764--289891 Score: 114
Period size: 46 Copynumber: 2.8 Consensus size: 46
289754 TTTTTCCATT
* * * * *
289764 CTTGTTTGACTATATT-TTTACCACCTTGGTCAAACCCATTTCAGC
1 CTTGTCTGAATATATTGGTTACCACCCTAGTCAAACCCATTTCAGC
* * **
289809 CTTGTCTGAATGTATTGGTTACCACCCTAGTCAAACCCTTTTCATT
1 CTTGTCTGAATATATTGGTTACCACCCTAGTCAAACCCATTTCAGC
** * * * *
289855 CTCATTTGACTGTATGGGTTACCACCCTAGTCAAACC
1 CTTGTCTGAATATATTGGTTACCACCCTAGTCAAACC
289892 TTTTTGTTCT
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
45 13 0.19
46 55 0.81
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (46 bp):
CTTGTCTGAATATATTGGTTACCACCCTAGTCAAACCCATTTCAGC
Found at i:289842 original size:46 final size:46
Alignment explanation
Indices: 289781--289891 Score: 132
Period size: 46 Copynumber: 2.4 Consensus size: 46
289771 GACTATATTT
* * ** *
289781 TTACCACCTTGGTCAAACCCATTTCAGCCTTGTCTGAATGTATTGG
1 TTACCACCCTAGTCAAACCCATTTCAGCCTCATCTGAATGTATGGG
* ** * *
289827 TTACCACCCTAGTCAAACCCTTTTCATTCTCATTTGACTGTATGGG
1 TTACCACCCTAGTCAAACCCATTTCAGCCTCATCTGAATGTATGGG
289873 TTACCACCCTAGTCAAACC
1 TTACCACCCTAGTCAAACC
289892 TTTTTGTTCT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (46 bp):
TTACCACCCTAGTCAAACCCATTTCAGCCTCATCTGAATGTATGGG
Found at i:289920 original size:91 final size:92
Alignment explanation
Indices: 289825--290054 Score: 261
Period size: 91 Copynumber: 2.5 Consensus size: 92
289815 TGAATGTATT
*
289825 GGTTACCACCCTAGTCAAACCCTTTTCATTCTCATTTGACTGTATGGGTTACCACCCTAGTCAAA
1 GGTTATCACCCTAGTCAAACCCTTTTCATTCTCATTTGACTGTATGGGTTACCACCCTAGTCAAA
* *
289890 -CCTTTTTGTTCTTGA-TTGACTATAGC
66 CCCTTTTTGTTC-TCATTTAACTATAGC
* * * ** *
289916 GGTTATCACCCCTA-TCAAACCTTTTTCATTCTCGTTTAACTGTATCAGTTATCACCCTAGTCAA
1 GGTTATCA-CCCTAGTCAAACCCTTTTCATTCTCATTTGACTGTATGGGTTACCACCCTAGTCAA
**
289980 ACCCTTTTTGTTCTCATTTAACTATATT
65 ACCCTTTTTGTTCTCATTTAACTATAGC
* * * * *
290008 GGTTATCACCCTGGTCAAGCTCTTTTCATCCTTATTTGA-TGTGATGG
1 GGTTATCACCCTAGTCAAACCCTTTTCATTCTCATTTGACTGT-ATGG
290055 TTTAGCCTTG
Statistics
Matches: 113, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
91 61 0.54
92 52 0.46
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (92 bp):
GGTTATCACCCTAGTCAAACCCTTTTCATTCTCATTTGACTGTATGGGTTACCACCCTAGTCAAA
CCCTTTTTGTTCTCATTTAACTATAGC
Found at i:290033 original size:46 final size:45
Alignment explanation
Indices: 289825--290025 Score: 199
Period size: 46 Copynumber: 4.4 Consensus size: 45
289815 TGAATGTATT
* * * * *
289825 GGTTACCACCCTAGTCAAACCCTTTTCATTCTCATTTGACTGTATG
1 GGTTATCACCCTAGTCAAA-CCTTTTTATTCTCATTTAACTATATC
* * * * *
289871 GGTTACCACCCTAGTCAAACCTTTTTGTTCTTGA-TTGACTATAGC
1 GGTTATCACCCTAGTCAAACCTTTTTATTC-TCATTTAACTATATC
* *
289916 GGTTATCACCCCTA-TCAAACCTTTTTCATTCTCGTTTAACTGTATC
1 GGTTATCA-CCCTAGTCAAACCTTTTT-ATTCTCATTTAACTATATC
* * *
289962 AGTTATCACCCTAGTCAAACCCTTTTTGTTCTCATTTAACTATATT
1 GGTTATCACCCTAGTCAAA-CCTTTTTATTCTCATTTAACTATATC
*
290008 GGTTATCACCCTGGTCAA
1 GGTTATCACCCTAGTCAA
290026 GCTCTTTTCA
Statistics
Matches: 129, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
45 42 0.33
46 80 0.62
47 7 0.05
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (45 bp):
GGTTATCACCCTAGTCAAACCTTTTTATTCTCATTTAACTATATC
Found at i:290376 original size:84 final size:84
Alignment explanation
Indices: 290138--290421 Score: 322
Period size: 84 Copynumber: 3.3 Consensus size: 84
290128 TGTCGACTTC
* * *
290138 GTATCCTTTGTTTACCTGTCAGGCTTAGTCCTCGGTAAATCTTTTTTAT-CTTTGTTGGCTTGTC
1 GTATCCTTTGTTTACCTGTCA-GCTTAGTCCTAGGTAAATC-CTTTTATCCTTTGTTGACTTGT-
*
290202 TGTTTAATCCCGATCAACTTTT
63 TGTTCAATCCCGATCAACTTTT
* * * *
290224 GTATACTTTGTTTACCTATCAGCTTAGTCCCAAGTAAATCCTTTTATCCTTTGTTGACTTGTTAG
1 GTATCCTTTGTTTACCTGTCAGCTTAGTCCTAGGTAAATCCTTTTATCCTTTGTTGACTTGTT-G
* *
290289 TTCAATCCCGGTAAACCTTTT
65 TTCAATCCCGATCAA-CTTTT
* * * *
290310 -TATCCTTTGTTTACCTGTCAGTTTAGT-CTAGGTATATCCTTTTCTCCCTTGTTGACTTGTTGG
1 GTATCCTTTGTTTACCTGTCAGCTTAGTCCTAGGTAAATCCTTTTATCCTTTGTTGACTTGTT-G
* *
290373 TTCATTCCTGATCAACTTTT
65 TTCAATCCCGATCAACTTTT
* **
290393 GTCTCCTTCATTTACCTGTCAGCTTAGTC
1 GTATCCTTTGTTTACCTGTCAGCTTAGTC
290422 TCGGTTAACT
Statistics
Matches: 166, Mismatches: 27, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
83 5 0.03
84 71 0.43
85 66 0.40
86 24 0.14
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.46
Consensus pattern (84 bp):
GTATCCTTTGTTTACCTGTCAGCTTAGTCCTAGGTAAATCCTTTTATCCTTTGTTGACTTGTTGT
TCAATCCCGATCAACTTTT
Found at i:291793 original size:164 final size:165
Alignment explanation
Indices: 291598--291910 Score: 438
Period size: 164 Copynumber: 1.9 Consensus size: 165
291588 ATTTTTAATG
*
291598 GTTTATAATTTTTAAAATTCATCAAATATCATCATTTAATT-ATTATT-AAATCAATTTTAAAAA
1 GTTTAAAATTTTTAAAATTCATCAAATATCATCATTTAATTCA-TATTAAAAT-AATTTT-AAAA
*
291661 ATTCATTTATTTTCATGAGTTTTTCATTTTTTCCTTAAAATTCCC-TA-TTTAT-AAAAAGCTGA
63 ATTCATTTATTTTCATGAGTTTTTCATTTTTTCCTTAAAATGCCCATATTTTATGAAAAA-CTGA
* *
291723 CTTTTCTATTCCATAAAGGTTTTCGCGGAGTTTTTCACA
127 ATTTTCTATCCCATAAAGGTTTTCGCGGAGTTTTTCACA
* * * **
291762 GTTTAAAATTTTTTAAATTCATCAAATATCATCATTTAATTCATATTAAAATAGTTTTGAATTTT
1 GTTTAAAATTTTTAAAATTCATCAAATATCATCATTTAATTCATATTAAAATAATTTTAAAAATT
* *
291827 CATTTATTTTCATGAGTTTTTCATTTTTTCTTTAAAATGCCCATATTTTCTGAAAAACTGAATTT
66 CATTTATTTTCATGAGTTTTTCATTTTTTCCTTAAAATGCCCATATTTTATGAAAAACTGAATTT
* *
291892 TTTATCCCATAAATGTTTT
131 TCTATCCCATAAAGGTTTT
291911 TGGGGTGGAT
Statistics
Matches: 131, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
163 44 0.34
164 50 0.38
165 32 0.24
166 5 0.04
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (165 bp):
GTTTAAAATTTTTAAAATTCATCAAATATCATCATTTAATTCATATTAAAATAATTTTAAAAATT
CATTTATTTTCATGAGTTTTTCATTTTTTCCTTAAAATGCCCATATTTTATGAAAAACTGAATTT
TCTATCCCATAAAGGTTTTCGCGGAGTTTTTCACA
Found at i:292552 original size:13 final size:13
Alignment explanation
Indices: 292508--292566 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
292498 GGCAAGTGAG
*
292508 AAAAAAAAAGGAA
1 AAAAAAAAAAGAA
* *
292521 AGAAAATAAAGAGAG
1 A-AAAA-AAAAAGAA
292536 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
292549 AAAAGAAAAATAGAA
1 AAAA-AAAAA-AGAA
292564 AAA
1 AAA
292567 CTAGTTAGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
13 11 0.30
14 13 0.35
15 13 0.35
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:292552 original size:26 final size:28
Alignment explanation
Indices: 292505--292566 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 28
292495 CTTGGCAAGT
* * *
292505 GAGAAAAAAAAAGGAAAGAAAATAAAGA
1 GAGAAAAAAAAAAGAAAGAAAAGAAAAA
292533 GAGAAAAAAAAAAG-AA-AAAAGAAAAA
1 GAGAAAAAAAAAAGAAAGAAAAGAAAAA
*
292559 TAGAAAAA
1 GAGAAAAA
292567 CTAGTTAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 15 0.50
27 2 0.07
28 13 0.43
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (28 bp):
GAGAAAAAAAAAAGAAAGAAAAGAAAAA
Found at i:293730 original size:141 final size:141
Alignment explanation
Indices: 293462--293832 Score: 466
Period size: 141 Copynumber: 2.6 Consensus size: 141
293452 TATTTATCAC
* *
293462 TAAATAAAAATTATTTTCTTAATTTTTCAAGATTTCTAACATTCCTATGCCTATCCATAGGGGTA
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAACATTCCTATGCCTAGCCATAGGGGTA
* * *
293527 TAGAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACAAAATGATTTTTTTTT
66 TAGAAATCTTCAAAACTTTTCATATATTTTCAGTTCTCCATTAAGGTACAAAATGA--ATTTTTT
*
293592 GGAAATAAAAAAAT
129 GAAAAT-AAAAAAT
* * * * **
293606 T-AA-ACAAATTATTATCTTAACTTTT-AGGATTTCTAATATTCCTATGGTTAGCCATAGGGGTA
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAACATTCCTATGCCTAGCCATAGGGGTA
*
293668 TAGAAATCTTCAAAACTTTTCGTATATTTTCAGTTCTCCATTAAGGTACAAAATGAATTTTTTGA
66 TAGAAATCTTCAAAACTTTTCATATATTTTCAGTTCTCCATTAAGGTACAAAATGAATTTTTTGA
*
293733 AAATGAAAAAT
131 AAATAAAAAAT
* * * * * * *
293744 TAAATAAAAATTATTATCTTAATTTTTCAAGACTTCTATCATTTCTATG-GTCGTCCGTAAGGGT
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAACATTCCTATGCCTAG-CCATAGGGGT
293808 ATAGAAATC--CACAAACTTTTCATAT
65 ATAGAAATCTTCA-AAACTTTTCATAT
293833 CCCCTCAGTT
Statistics
Matches: 196, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
138 7 0.04
139 15 0.08
140 34 0.17
141 118 0.60
142 19 0.10
143 2 0.01
144 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Consensus pattern (141 bp):
TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAACATTCCTATGCCTAGCCATAGGGGTA
TAGAAATCTTCAAAACTTTTCATATATTTTCAGTTCTCCATTAAGGTACAAAATGAATTTTTTGA
AAATAAAAAAT
Found at i:293862 original size:140 final size:141
Alignment explanation
Indices: 293462--293876 Score: 463
Period size: 141 Copynumber: 2.9 Consensus size: 141
293452 TATTTATCAC
* * * *
293462 TAAATAAAAATTATTTTCTTAATTTTTCAAGATTTCTAACATTCCTAT-GCCTATCCATAGGGGT
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTATCATTCCTATGGTC-GTCCATAGGGGT
*
293526 ATAGAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACAAAATGATTTTTTTT
65 ATAGAAATC-TCAAAACTTTTCATATCTTTTCAGTTCTCCATTAAGGTACAAAATGA--TTTTTT
*
293591 TGGAAATAAAAAAAT
127 TGAAAATAAAAAAAT
* * * *
293606 T-AA-ACAAATTATTATCTTAACTTTT-AGGATTTCTAAT-ATTCCTATGGTTAG-CCATAGGGG
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCT-ATCATTCCTATGG-TCGTCCATAGGGG
* * *
293666 TATAGAAATCTTCAAAACTTTTCGTATATTTTCAGTTCTCCATTAAGGTACAAAATGAATTTTTT
64 TATAGAAATC-TCAAAACTTTTCATATCTTTTCAGTTCTCCATTAAGGTACAAAATGATTTTTTT
*
293731 GAAAAT-GAAAAAT
128 GAAAATAAAAAAAT
* * * *
293744 TAAATAAAAATTATTATCTTAATTTTTCAAGACTTCTATCATTTCTATGGTCGTCCGTAAGGGTA
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTATCATTCCTATGGTCGTCCATAGGGGTA
*** * *
293809 TAGAAATC-CACAAACTTTTCATATCCCCTCAGTTCTCCA-AAAGGGTACGAAATG-TTTTTTTG
66 TAGAAATCTCA-AAACTTTTCATATCTTTTCAGTTCTCCATTAA-GGTACAAAATGATTTTTTTG
293871 CAAAAT
129 -AAAAT
293877 TTAGAGACTT
Statistics
Matches: 230, Mismatches: 30, Indels: 26
0.80 0.10 0.09
Matches are distributed among these distances:
138 7 0.03
139 24 0.10
140 62 0.27
141 113 0.49
142 21 0.09
143 2 0.01
144 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (141 bp):
TAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTATCATTCCTATGGTCGTCCATAGGGGTA
TAGAAATCTCAAAACTTTTCATATCTTTTCAGTTCTCCATTAAGGTACAAAATGATTTTTTTGAA
AATAAAAAAAT
Found at i:309881 original size:79 final size:78
Alignment explanation
Indices: 309750--310044 Score: 285
Period size: 79 Copynumber: 3.7 Consensus size: 78
309740 ACACCGAGGG
* * * * * *
309750 TGGAGTGTCCCCGATTATGGAAAATCAGTGTTCTGAAAATAAAATTGGGGTTGGAGTATTCCCTC
1 TGGAGTATCCCTGATTATAG-AAATTAGTGTTTTGAAAATAAAATCGGGGTTGGAGTATTCCCTC
* *
309815 GGAAATAACAGGAT
65 GGAAATAACGGGGT
309829 TGGAGTATCCCTGATTATAGCAAATTAGTGTTTTGAAAATAAAATCGGGGTTGGAGTATTCCCTC
1 TGGAGTATCCCTGATTATAG-AAATTAGTGTTTTGAAAATAAAATCGGGGTTGGAGTATTCCCTC
*
309894 GAAAATAACGGGGT
65 GGAAATAACGGGGT
* * * * * * *** *
309908 TGGAGTATCCTTGATTGTGGAAAATCGATGCTTT-AGAAATAAGGCCAGGGTTGGAGTA-TCCC-
1 TGGAGTATCCCTGATTATAGAAATTAG-TGTTTTGA-AAATAAAATCGGGGTTGGAGTATTCCCT
309970 CGTGATAATAACGGGGT
64 CG-GA-AATAACGGGGT
* * *
309987 TGGAGTAT-CCTCGATTGTAAGAAATTGGTGTTTTG-AAATAAAATCGGAGTTGGAGTAT
1 TGGAGTATCCCT-GATTAT-AGAAATTAGTGTTTTGAAAATAAAATCGGGGTTGGAGTAT
310045 CCCGATTGTG
Statistics
Matches: 177, Mismatches: 31, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
77 2 0.01
78 30 0.17
79 139 0.79
80 6 0.03
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (78 bp):
TGGAGTATCCCTGATTATAGAAATTAGTGTTTTGAAAATAAAATCGGGGTTGGAGTATTCCCTCG
GAAATAACGGGGT
Found at i:310061 original size:49 final size:50
Alignment explanation
Indices: 309984--310097 Score: 162
Period size: 50 Copynumber: 2.3 Consensus size: 50
309974 ATAATAACGG
* *
309984 GGTTGGAGTATCCTCGATTGTAAGAAATTGGTGTTTT-GAAATAAAATCG-
1 GGTTGGAGTATCC-CGATTGTAAGAAATTAGTATTTTAGAAATAAAATCGA
310033 GAGTTGGAGTATCCCGATTGTGAA-AAATTAGTATTTTAGAAATAAAATCGA
1 G-GTTGGAGTATCCCGATTGT-AAGAAATTAGTATTTTAGAAATAAAATCGA
310084 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
310098 CTCGAAAATA
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
49 19 0.32
50 39 0.66
51 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.32
Consensus pattern (50 bp):
GGTTGGAGTATCCCGATTGTAAGAAATTAGTATTTTAGAAATAAAATCGA
Found at i:310229 original size:28 final size:29
Alignment explanation
Indices: 310189--310262 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 29
310179 GACATAGAGC
*
310189 CGGGGTTAGAGTATCCCCTCG-GAAATAA
1 CGGGGTTGGAGTATCCCCTCGAGAAATAA
310217 CGGGGTTGGAGTAT--CCTCGATGAAATAA
1 CGGGGTTGGAGTATCCCCTCGA-GAAATAA
*
310245 CGAGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
310263 AATTATGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
26 5 0.12
28 33 0.82
30 2 0.05
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (29 bp):
CGGGGTTGGAGTATCCCCTCGAGAAATAA
Found at i:310392 original size:51 final size:51
Alignment explanation
Indices: 310249--310392 Score: 148
Period size: 51 Copynumber: 2.8 Consensus size: 51
310239 AAATAACGAG
* * *
310249 GTTGGAGTATCCCCAATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGAAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAATCGGA
* * ** * *
310300 GTTGAAGTATCCCCGATTGCTG-TAAATCAATGCTTTAGAAATAAAA-CTGGA
1 GTTGAAGTATCCCCGATT-ATGAAAAATTGATGTTTTGGAAATAAAATC-GGA
* * *
310351 GTTGAATTATCCTCGATTAAGAAAAATTGATGTTTTGGAAAT
1 GTTGAAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAAT
310393 GGAACCAGGA
Statistics
Matches: 72, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
50 2 0.03
51 68 0.94
52 2 0.03
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (51 bp):
GTTGAAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAATCGGA
Found at i:312810 original size:20 final size:20
Alignment explanation
Indices: 312785--312835 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
312775 GATACAACAC
312785 ATCGATACATTGAGCAATGT
1 ATCGATACATTGAGCAATGT
*
312805 ATCGATACAATGAGCAATGT
1 ATCGATACATTGAGCAATGT
312825 ATCGATACATT
1 ATCGATACATT
312836 TGGGTAAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (20 bp):
ATCGATACATTGAGCAATGT
Found at i:312874 original size:20 final size:20
Alignment explanation
Indices: 312849--312903 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
312839 GTAAACCCAG
*
312849 AATGTATTGATACAATGAAA
1 AATGTATCGATACAATGAAA
*
312869 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAA
312889 AATGTATCGATACAA
1 AATGTATCGATACAA
312904 ATTGTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAAA
Found at i:316316 original size:21 final size:22
Alignment explanation
Indices: 316270--316314 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
316260 TTGCAAGATG
316270 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
316292 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
316312 AAA
1 AAA
316315 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:318152 original size:16 final size:16
Alignment explanation
Indices: 318116--318152 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
318106 GATAAAAATG
318116 TCCAAAATGAGAAAGC
1 TCCAAAATGAGAAAGC
318132 T-CAAAATGA-AGAAGC
1 TCCAAAATGAGA-AAGC
318147 TCCAAA
1 TCCAAA
318153 CGAAATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.05
15 13 0.68
16 5 0.26
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (16 bp):
TCCAAAATGAGAAAGC
Found at i:320245 original size:13 final size:13
Alignment explanation
Indices: 320227--320252 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
320217 ACATTTTTCC
320227 TTGTATCGATACA
1 TTGTATCGATACA
320240 TTGTATCGATACA
1 TTGTATCGATACA
320253 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:322083 original size:20 final size:20
Alignment explanation
Indices: 322058--322098 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
322048 TGATATGAAT
322058 TACTTGATTAAGGGGGAGAA
1 TACTTGATTAAGGGGGAGAA
322078 TACTTGATTAAGGGGGAGAA
1 TACTTGATTAAGGGGGAGAA
322098 T
1 T
322099 TATTAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.27
Consensus pattern (20 bp):
TACTTGATTAAGGGGGAGAA
Found at i:322769 original size:20 final size:19
Alignment explanation
Indices: 322714--322769 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
322704 AAAACCCTTA
*
322714 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
*
322734 AAAGTATCAATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
322754 AATGTATCGATACATG
1 AAAGTATCGATACATG
322770 AAAAAGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:322846 original size:13 final size:13
Alignment explanation
Indices: 322828--322853 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
322818 TACAGCAAGT
322828 ATGTATCGATACA
1 ATGTATCGATACA
322841 ATGTATCGATACA
1 ATGTATCGATACA
322854 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:323777 original size:38 final size:39
Alignment explanation
Indices: 323637--323781 Score: 143
Period size: 37 Copynumber: 3.6 Consensus size: 39
323627 AGAGGAAAAT
* * *
323637 AAAGTGCGTCCTGCTCTTTGAAGACAAAAGGGAAAAGAAGGGA
1 AAAGTGCGTCCTACTCTTTGAGGAC-AAA-GGAGAA-AA-GGA
* * *
323680 ATGAAGTGTGTCCTACTCTTTGAGGACAAAAGAGAAAATG-
1 A--AAGTGCGTCCTACTCTTTGAGGACAAAGGAGAAAAGGA
*
323720 AAA-TGTGTCCTACTCTTTGAGGACAAAGGAGAAAAGGA
1 AAAGTGCGTCCTACTCTTTGAGGACAAAGGAGAAAAGGA
*
323758 AAAG-GCGTCCTGCTCTTTGAGGAC
1 AAAGTGCGTCCTACTCTTTGAGGAC
323782 TAAAAAGTGC
Statistics
Matches: 88, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
37 32 0.36
38 23 0.26
40 1 0.01
41 1 0.01
42 2 0.02
43 5 0.06
44 3 0.03
45 21 0.24
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (39 bp):
AAAGTGCGTCCTACTCTTTGAGGACAAAGGAGAAAAGGA
Found at i:323853 original size:61 final size:61
Alignment explanation
Indices: 323751--324021 Score: 369
Period size: 61 Copynumber: 4.5 Consensus size: 61
323741 GACAAAGGAG
* **
323751 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTCATGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTT
* **
323812 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
** *
323873 GCAAAGAGAAA-GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT
1 AAAAAGA-AAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
323934 ------AAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
* *
323989 AAAAGGAAAAGGCATCCTGCTCTTTGAGGACTA
1 AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTA
324022 AAGGGTGAAA
Statistics
Matches: 189, Mismatches: 12, Indels: 18
0.86 0.05 0.08
Matches are distributed among these distances:
54 3 0.02
55 50 0.26
61 131 0.69
62 5 0.03
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (61 bp):
AAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
Found at i:323985 original size:116 final size:117
Alignment explanation
Indices: 323751--324023 Score: 374
Period size: 116 Copynumber: 2.3 Consensus size: 117
323741 GACAAAGGAG
323751 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTAAAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTT----
* **
323816 AGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT
62 A-AAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
* * **
323873 GCAAA-GAGAAA-GCGTCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT-
1 -AAAAGGA-AAAGGCGTCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCATGTGGGCTTTA
323934 AAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
63 AAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
*
323989 AAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAA
324024 GGGTGAAAGG
Statistics
Matches: 136, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
115 8 0.06
116 74 0.54
122 44 0.32
123 10 0.07
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (117 bp):
AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCATGTGGGCTTTAAAA
AGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
Found at i:323992 original size:27 final size:27
Alignment explanation
Indices: 323907--323992 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
323897 TGAGGACTGG
323907 AAAATGCCACCAACTTGTGTGGGCTTT
1 AAAATGCCACCAACTTGTGTGGGCTTT
* ** ** * * * **
323934 AAAAGGCGTCCTGCTCTTTGAGGACTAG
1 AAAATGCCACCAACT-TGTGTGGGCTTT
323962 AAAATGCCACCAACTTGTGTGGGCTTT
1 AAAATGCCACCAACTTGTGTGGGCTTT
323989 AAAA
1 AAAA
323993 GGAAAAGGCA
Statistics
Matches: 38, Mismatches: 20, Indels: 2
0.63 0.33 0.03
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (27 bp):
AAAATGCCACCAACTTGTGTGGGCTTT
Found at i:324112 original size:100 final size:100
Alignment explanation
Indices: 323939--324120 Score: 301
Period size: 100 Copynumber: 1.8 Consensus size: 100
323929 GCTTTAAAAG
*
323939 GCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCAT
1 GCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCAT
*
324004 CCTGCTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
66 CCTACTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
* * * * *
324039 GCGTCCTACTTTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGT
1 GCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCAT
324104 CCTACTCTTTGAGGACT
66 CCTACTCTTTGAGGACT
324121 GGGAAGTGCC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 75 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (100 bp):
GCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCAT
CCTACTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
Found at i:324186 original size:55 final size:56
Alignment explanation
Indices: 324034--324280 Score: 306
Period size: 55 Copynumber: 4.4 Consensus size: 56
324024 GGGTGAAAGG
*
324034 AGAGAGCGTCCTACTTTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAA
1 AGAG-GCGTCCTACTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT--AA
*
324093 GGAGAAGGCGTCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT-A
1 --AG-AGGCGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAA
* * * *
324151 AGAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTAGGCTTTGA
1 AGAGGCGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAA
*
324207 A-AGGCGTCCTACTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGA
1 AGAGGCGTCCTACTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAA
* *
324262 A-AGGCATCCTGCTCTTTGA
1 AGAGGCGTCCTACTCTTTGA
324281 AGACCAACGG
Statistics
Matches: 172, Mismatches: 10, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
54 4 0.02
55 111 0.65
56 4 0.02
58 1 0.01
60 2 0.01
61 48 0.28
62 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (56 bp):
AGAGGCGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAA
Found at i:325223 original size:167 final size:165
Alignment explanation
Indices: 325043--325360 Score: 401
Period size: 167 Copynumber: 1.9 Consensus size: 165
325033 ATAGTAAATA
* *
325043 AGTTTTGAAAAATTCATTCATTTT-TATGAGTTTTTCATTTTTTTTCTTGAAATTTCTCTAT-TT
1 AGTTTTGAAAAATTCATTCATTTTATATG-G-TTTTCATTTTTTTCCTTGAAA-TAC-CTATGTT
* * * *
325106 T-CAAAAAACTAAATTTTCTATTCCATAAATATTTT-TGGGGGAATTTTTCTCGCCTTAAAATTT
62 TCCAAAAAACTAAATTTTCTATCCCAAAAATATTTTAT-GGGGAATTTCT-TCGACTTAAAATTT
* *
325169 TTAAAATTCGTCTAACATTATCATTGGACACCCTTTAAACC
125 TCAAAATTCATCTAACATTATCATTGGACACCCTTTAAACC
*
325210 AGTTTTGAAAAATTCATTTATTTTCATATGGTTTTCATTTTTTTCCTTGAAATACCTATGTTTCC
1 AGTTTTGAAAAATTCATTCATTTT-ATATGGTTTTCATTTTTTTCCTTGAAATACCTATGTTTCC
* * * *
325275 AAAAAACTGAATTTTCTATCCCAAAAATGTTTTCATGGGGACTTTCTTCGATTTAAAATTTTCAA
65 AAAAAACTAAATTTTCTATCCCAAAAATATTTT-ATGGGGAATTTCTTCGACTTAAAATTTTCAA
* *
325340 AATTCATCTAATATTGTCATT
129 AATTCATCTAACATTATCATT
325361 AAACTCCCAT
Statistics
Matches: 130, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
165 4 0.03
166 5 0.04
167 106 0.82
168 10 0.08
169 5 0.04
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (165 bp):
AGTTTTGAAAAATTCATTCATTTTATATGGTTTTCATTTTTTTCCTTGAAATACCTATGTTTCCA
AAAAACTAAATTTTCTATCCCAAAAATATTTTATGGGGAATTTCTTCGACTTAAAATTTTCAAAA
TTCATCTAACATTATCATTGGACACCCTTTAAACC
Found at i:326833 original size:12 final size:13
Alignment explanation
Indices: 326816--326848 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
326806 AAATTTTTGA
326816 AAATAAA-AAAAT
1 AAATAAATAAAAT
326828 AAATAAATAAAAT
1 AAATAAATAAAAT
326841 -AATAAATA
1 AAATAAATA
326849 TTATTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:326837 original size:16 final size:16
Alignment explanation
Indices: 326816--326848 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
326806 AAATTTTTGA
326816 AAATAAAAAAATAAAT
1 AAATAAAAAAATAAAT
*
326832 AAATAAAATAATAAAT
1 AAATAAAAAAATAAAT
326848 A
1 A
326849 TTATTTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATAAAAAAATAAAT
Found at i:327121 original size:141 final size:141
Alignment explanation
Indices: 326859--327233 Score: 515
Period size: 141 Copynumber: 2.7 Consensus size: 141
326849 TTATTTTATC
* *
326859 ACTAAATGAAAATTATTAT-TTAATTTCTCAAGATTTTCTAATATTCCTATGGTTTTTTGTAGGG
1 ACTAAATAAAAATTATTATCTTAATTTCTCAAGA-TTTCTAATATTCCTATGGTTTTCTGTAGGG
* *
326923 GTATAGAAATCTTCAAAACATTTCGTACCTTTTCAATTCTCCAATAAAGTATCAAATGAATTTTC
65 GTATAGAAATCTTCAAAACTTTTCGTATCTTTTCAATTCTCCAATAAAGTATCAAATGAATTTT-
326988 TTAAAAATTAAAA
129 TTAAAAATTAAAA
* * * *
327001 ATTAAAT-AAAATTATTATCTTAATTTCTCAAGATTTCTAATATTCTTATGGTTTTCCGTAGGGA
1 ACTAAATAAAAATTATTATCTTAATTTCTCAAGATTTCTAATATTCCTATGGTTTTCTGTAGGGG
** * * *
327065 TATAGAAATCTTCAAAACTTTTCGTATCTTTTCGGTTCTCTATTAAGGTA-CGAAATGAATTTTT
66 TATAGAAATCTTCAAAACTTTTCGTATCTTTTCAATTCTCCAATAAAGTATC-AAATGAATTTTT
*
327129 TGAAAATTAAAA
130 TAAAAATTAAAA
* * * *
327141 ACTAAATAAAAATTATTATCTTAATTTTTTAAAATTTCTAATATTCCTATGGTTTTCTATAGGGG
1 ACTAAATAAAAATTATTATCTTAATTTCTCAAGATTTCTAATATTCCTATGGTTTTCTGTAGGGG
*
327206 TATAGAAATTTTCAAAA-TGTTTCGTATC
66 TATAGAAATCTTCAAAACT-TTTCGTATC
327234 CCATGTTTTT
Statistics
Matches: 207, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
140 20 0.10
141 167 0.81
142 20 0.10
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (141 bp):
ACTAAATAAAAATTATTATCTTAATTTCTCAAGATTTCTAATATTCCTATGGTTTTCTGTAGGGG
TATAGAAATCTTCAAAACTTTTCGTATCTTTTCAATTCTCCAATAAAGTATCAAATGAATTTTTT
AAAAATTAAAA
Found at i:327804 original size:153 final size:154
Alignment explanation
Indices: 327525--327813 Score: 395
Period size: 153 Copynumber: 1.9 Consensus size: 154
327515 TTTTCAGTCC
* *
327525 TTTAGGGGTGCCAAGCACTTCTATGTCGAAGATATCCCCTAGGGACATTTTTATAATTTTTTAGA
1 TTTAGAGGTGCCAAGCACTTCTACGTCGAAGATATCCCCTAGGGACATTTTTATAATTTTTTAGA
* * * **
327590 ACCGAGTCTTAAGTTGTCACCAGGTCTATTTTTATGTCGAAAGTGGGTATTTAGGATAGGTTCAT
66 ACCAAGTCCTAAGTTGTCACCAGGTCTAGTTTTATACCGAAAGTGGGTATTTAGGATAGGTTCAT
327655 CCCATCATTTTACCTTTTAGGCTT
131 CCCATCATTTTACCTTTTAGGCTT
* * * *
327679 TTTAGAGGTGCTAGGCACTTCTACGTCGAA-AGTATCCCTTAGAGG-CATTTTTGTAA-TTTTTA
1 TTTAGAGGTGCCAAGCACTTCTACGTCGAAGA-TATCCCCTAG-GGACATTTTTATAATTTTTTA
* * * * *
327741 GAACCAAGTCCTAGGTTGTCACCGGGTCTGGTTTTATACCGAAGGTGGGTATTTAGGATAGGTTT
64 GAACCAAGTCCTAAGTTGTCACCAGGTCTAGTTTTATACCGAAAGTGGGTATTTAGGATAGGTTC
327806 ATCCCATC
129 ATCCCATC
327814 TATAATATTT
Statistics
Matches: 117, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
153 70 0.60
154 45 0.38
155 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (154 bp):
TTTAGAGGTGCCAAGCACTTCTACGTCGAAGATATCCCCTAGGGACATTTTTATAATTTTTTAGA
ACCAAGTCCTAAGTTGTCACCAGGTCTAGTTTTATACCGAAAGTGGGTATTTAGGATAGGTTCAT
CCCATCATTTTACCTTTTAGGCTT
Found at i:327865 original size:153 final size:151
Alignment explanation
Indices: 327540--327888 Score: 389
Period size: 153 Copynumber: 2.3 Consensus size: 151
327530 GGGTGCCAAG
* * * *
327540 CACTTCTATGTCGAAGATATCCCCTAGGGACATTTTTATAATTTTTTAGAACCGAGTCTTAAGTT
1 CACTTCTACGTCGAAG-TATCCCCTAGGG-CATTTTTGTAA-TTTTTAGAACCAAGTCCTAAGTT
* ** **
327605 GTCACCAGGTCTATTTTTATGTCGAAAGTGGGTATTTAGGATAGGTTCATCCCATCATTTTACCT
63 GTCACCAGGTCTAGTTTTATACCGAAAGTGGGTATTTAGGATAGGTTCATCCCATCATAATACCT
* *
327670 TTTAGGCTTTTTAGAGGTGCTAGG
128 TTTAGGCTCTTTAGAGGTGCTAGC
* *
327694 CACTTCTACGTCGAAAGTATCCCTTAGAGGCATTTTTGTAATTTTTAGAACCAAGTCCTAGGTTG
1 CACTTCTACGTCG-AAGTATCCCCTAG-GGCATTTTTGTAATTTTTAGAACCAAGTCCTAAGTTG
* * * * **
327759 TCACCGGGTCTGGTTTTATACCGAAGGTGGGTATTTAGGATAGGTTTATCCCATCTATAATATTT
64 TCACCAGGTCTAGTTTTATACCGAAAGTGGGTATTTAGGATAGGTTCATCCCATC-ATAATACCT
* * *
327824 TTTAAG-TCCTTTA-AGCGTGTTTGC
128 TTTAGGCT-CTTTAGAG-GTGCTAGC
* *
327848 CACTTTTACGTCGAAGTA-CCCCTAGGGCATATTTGTAATTT
1 CACTTCTACGTCGAAGTATCCCCTAGGGCATTTTTGTAATTT
327889 CTATAATAGA
Statistics
Matches: 165, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
151 15 0.09
152 6 0.04
153 77 0.47
154 62 0.38
155 5 0.03
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (151 bp):
CACTTCTACGTCGAAGTATCCCCTAGGGCATTTTTGTAATTTTTAGAACCAAGTCCTAAGTTGTC
ACCAGGTCTAGTTTTATACCGAAAGTGGGTATTTAGGATAGGTTCATCCCATCATAATACCTTTT
AGGCTCTTTAGAGGTGCTAGC
Found at i:337228 original size:13 final size:13
Alignment explanation
Indices: 337210--337234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
337200 ACACAAAGTA
337210 TGTATCGATACAT
1 TGTATCGATACAT
337223 TGTATCGATACA
1 TGTATCGATACA
337235 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:337231 original size:32 final size:33
Alignment explanation
Indices: 337190--337257 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
337180 GTAGCCAAAC
*
337190 TTGTATCGATACA-CA-AAGTATGTATCGATACA
1 TTGTATCGATACACCATAA-AATGTATCGATACA
337222 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
337255 TTG
1 TTG
337258 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:343225 original size:20 final size:20
Alignment explanation
Indices: 343153--343232 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
343143 AATTTCCAAA
*
343153 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATCTTTCT
* *
343173 GTGTATCGATACATCTGGAAAATTCA
1 ATGTATCGATACATCT------TTCT
343199 ATGTATCGATACATCTTTCT
1 ATGTATCGATACATCTTTCT
*
343219 TTGTATCGATACAT
1 ATGTATCGATACAT
343233 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
20 30 0.62
26 18 0.38
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATCTTTCT
Found at i:343237 original size:13 final size:13
Alignment explanation
Indices: 343219--343257 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
343209 ACATCTTTCT
343219 TTGTATCGATACA
1 TTGTATCGATACA
343232 TTGTATCGATACA
1 TTGTATCGATACA
*
343245 CTGTATCGATACA
1 TTGTATCGATACA
343258 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:345812 original size:13 final size:13
Alignment explanation
Indices: 345794--345818 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
345784 ACACAAAGTA
345794 TGTATCGATACAT
1 TGTATCGATACAT
345807 TGTATCGATACA
1 TGTATCGATACA
345819 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:347199 original size:32 final size:32
Alignment explanation
Indices: 347158--347348 Score: 152
Period size: 32 Copynumber: 6.0 Consensus size: 32
347148 TTTTTTAAAA
347158 TCCTCAAAGAGCAGGACGCTTACCTACCTCAG
1 TCCTCAAAGAGCAGGACGCTTACCTACCTCAG
* * *
347190 TCTTCAAAGAGCA-GAGCGCTTACCAACCTTAG
1 TCCTCAAAGAGCAGGA-CGCTTACCTACCTCAG
* *
347222 TCCTCAAAGAACAGGGCGCTTA-CTAACCTCAG
1 TCCTCAAAGAGCAGGACGCTTACCT-ACCTCAG
* ** ** * *
347254 TCCTCAAAGAGTAGGGTGCTTACGAAGCTTAG
1 TCCTCAAAGAGCAGGACGCTTACCTACCTCAG
* * * * * *
347286 TCCTCAATGAGCAGGGCACTTACCAATCTTAG
1 TCCTCAAAGAGCAGGACGCTTACCTACCTCAG
* * * *
347318 TCCTCAAAGAGTAGGACACTAACTTACCTCA
1 TCCTCAAAGAGCAGGACGCTTACCTACCTCA
347349 ATTCATGATG
Statistics
Matches: 126, Mismatches: 29, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
31 3 0.02
32 122 0.97
33 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (32 bp):
TCCTCAAAGAGCAGGACGCTTACCTACCTCAG
Found at i:347329 original size:64 final size:64
Alignment explanation
Indices: 347158--347332 Score: 224
Period size: 64 Copynumber: 2.7 Consensus size: 64
347148 TTTTTTAAAA
* * * * *
347158 TCCTCAAAGAGCAGGACGCTTACCTACCTCAGTCTTCAAAGAGCAGAGCGCTTACCAACCTTAG
1 TCCTCAAAGAGCAGGGCGCTTACCAACCTCAGTCCTCAAAGAGTAGGGCGCTTACCAACCTTAG
* * * * *
347222 TCCTCAAAGAACAGGGCGCTTACTAACCTCAGTCCTCAAAGAGTAGGGTGCTTACGAAGCTTAG
1 TCCTCAAAGAGCAGGGCGCTTACCAACCTCAGTCCTCAAAGAGTAGGGCGCTTACCAACCTTAG
* * * *
347286 TCCTCAATGAGCAGGGCACTTACCAATCTTAGTCCTCAAAGAGTAGG
1 TCCTCAAAGAGCAGGGCGCTTACCAACCTCAGTCCTCAAAGAGTAGG
347333 ACACTAACTT
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 95 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (64 bp):
TCCTCAAAGAGCAGGGCGCTTACCAACCTCAGTCCTCAAAGAGTAGGGCGCTTACCAACCTTAG
Found at i:351902 original size:48 final size:49
Alignment explanation
Indices: 351839--351948 Score: 177
Period size: 48 Copynumber: 2.3 Consensus size: 49
351829 ATGCCTTAAA
*
351839 TGTATCAATACAAGGTCCTAATAGTCAAAGATTTCAAAA-TTTAAAATT
1 TGTATCAATACAAGGTCCCAATAGTCAAAGATTTCAAAATTTTAAAATT
* * *
351887 TGTATCAATGCAAGGTCCCAATAGTCAGAGATTTCAAAATTTTACAATT
1 TGTATCAATACAAGGTCCCAATAGTCAAAGATTTCAAAATTTTAAAATT
351936 TGTATCAATACAA
1 TGTATCAATACAA
351949 CAAGTTAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 36 0.64
49 20 0.36
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (49 bp):
TGTATCAATACAAGGTCCCAATAGTCAAAGATTTCAAAATTTTAAAATT
Found at i:351978 original size:20 final size:20
Alignment explanation
Indices: 351936--351989 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
351926 TTTTACAATT
* * *
351936 TGTATCAATACAACAAGTTAA
1 TGTATCGATAC-ATAAGTGAA
351957 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
*
351977 TGCATCGATACAT
1 TGTATCGATACAT
351990 TCTAGGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:355467 original size:3 final size:3
Alignment explanation
Indices: 355459--355491 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
355449 TCAAAAACAT
355459 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
355492 CACAATCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:357623 original size:27 final size:27
Alignment explanation
Indices: 357587--357643 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
357577 ATATTTATTT
* * *
357587 TTTTATTTAAAAAATTTTAAATTTAGA
1 TTTTACTTAAAAAATATTAAATTTAAA
*
357614 TTTTACTTAAAAGATATTAAATTTAAA
1 TTTTACTTAAAAAATATTAAATTTAAA
357641 TTT
1 TTT
357644 AATTAGTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (27 bp):
TTTTACTTAAAAAATATTAAATTTAAA
Found at i:358167 original size:16 final size:17
Alignment explanation
Indices: 358148--358185 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
358138 TATTTGTTAT
358148 ATAATTTTAAAA-AAAA
1 ATAATTTTAAAACAAAA
358164 ATAATTTTAAAACAAAA
1 ATAATTTTAAAACAAAA
358181 A-AATT
1 ATAATT
358186 ATGATAGCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATTTTAAAACAAAA
Found at i:360859 original size:21 final size:21
Alignment explanation
Indices: 360826--360866 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
360816 CTAAGTAAAA
360826 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
360847 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
360867 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:361028 original size:53 final size:53
Alignment explanation
Indices: 360946--361082 Score: 220
Period size: 53 Copynumber: 2.6 Consensus size: 53
360936 AGATTGCATA
* * *
360946 GTATCGATACGCACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAAGACACTGGCAGTAGCCAAATTT
*
361000 GTATCGATACACACAATATGTATCGATACAAGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAAGACACTGGCAGTAGCCAAATTT
*
361053 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
361083 TTGGTAGTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAAGACACTGGCAGTAGCCAAATTT
Found at i:361125 original size:10 final size:10
Alignment explanation
Indices: 361106--361136 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
361096 AATCTTATTT
361106 TCACTGTTCA
1 TCACTGTTCA
*
361116 TCACTATTCA
1 TCACTGTTCA
361126 TCACTGTTCA
1 TCACTGTTCA
361136 T
1 T
361137 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:361158 original size:21 final size:22
Alignment explanation
Indices: 361124--361179 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
361114 CATCACTATT
361124 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
361146 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
361167 CATCACTGTTCAT
1 CATCACTGTTCAT
361180 AGGTCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:361216 original size:38 final size:35
Alignment explanation
Indices: 361148--361217 Score: 95
Period size: 38 Copynumber: 1.9 Consensus size: 35
361138 TATCGATACA
* *
361148 TCACTTTCATGTATCGATACATCACTGTTCATAGG
1 TCACTTTCATGTATCGAAAAATCACTGTTCATAGG
361183 TCACTGTTCATGTATCGTTAAAAATCACTGTTCAT
1 TCACT-TTCATGTATCG--AAAAATCACTGTTCAT
361218 CACTATTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 5 0.17
36 11 0.37
38 14 0.47
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (35 bp):
TCACTTTCATGTATCGAAAAATCACTGTTCATAGG
Found at i:361245 original size:13 final size:13
Alignment explanation
Indices: 361227--361265 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
361217 TCACTATTCA
361227 TGTATCGATACAT
1 TGTATCGATACAT
*
361240 TGTATCGATACAG
1 TGTATCGATACAT
361253 TGTATCGATACAT
1 TGTATCGATACAT
361266 CATAAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:361798 original size:34 final size:35
Alignment explanation
Indices: 361735--361801 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
361725 CTAAGTGATT
361735 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
361771 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
361802 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:364999 original size:13 final size:13
Alignment explanation
Indices: 364981--365005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
364971 TTTTCCAGAT
364981 TGTATCGATACAA
1 TGTATCGATACAA
364994 TGTATCGATACA
1 TGTATCGATACA
365006 TTACTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:366640 original size:21 final size:21
Alignment explanation
Indices: 366607--366647 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
366597 CTAAGTAAAA
366607 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
366628 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
366648 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:366809 original size:53 final size:53
Alignment explanation
Indices: 366727--366863 Score: 220
Period size: 53 Copynumber: 2.6 Consensus size: 53
366717 AGATTGCATA
* * *
366727 GTATCGATACGCACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAAGACACTGGCAGTAGCCAAATTT
*
366781 GTATCGATACACACAATATGTATCGATACAAGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAAGACACTGGCAGTAGCCAAATTT
*
366834 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
366864 TTGGTAGTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAAGACACTGGCAGTAGCCAAATTT
Found at i:366906 original size:10 final size:10
Alignment explanation
Indices: 366887--366917 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
366877 AATCTTATTT
366887 TCACTGTTCA
1 TCACTGTTCA
*
366897 TCACTATTCA
1 TCACTGTTCA
366907 TCACTGTTCA
1 TCACTGTTCA
366917 T
1 T
366918 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:366939 original size:21 final size:22
Alignment explanation
Indices: 366905--366960 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
366895 CATCACTATT
366905 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
366927 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
366948 CATCACTGTTCAT
1 CATCACTGTTCAT
366961 AGGTCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:366997 original size:38 final size:35
Alignment explanation
Indices: 366929--366998 Score: 95
Period size: 38 Copynumber: 1.9 Consensus size: 35
366919 TATCGATACA
* *
366929 TCACTTTCATGTATCGATACATCACTGTTCATAGG
1 TCACTTTCATGTATCGAAAAATCACTGTTCATAGG
366964 TCACTGTTCATGTATCGTTAAAAATCACTGTTCAT
1 TCACT-TTCATGTATCG--AAAAATCACTGTTCAT
366999 CACTATTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 5 0.17
36 11 0.37
38 14 0.47
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (35 bp):
TCACTTTCATGTATCGAAAAATCACTGTTCATAGG
Found at i:367028 original size:13 final size:13
Alignment explanation
Indices: 367010--367058 Score: 89
Period size: 13 Copynumber: 3.8 Consensus size: 13
367000 ACTATTCATA
*
367010 TATCGATACATTG
1 TATCGATACAGTG
367023 TATCGATACAGTG
1 TATCGATACAGTG
367036 TATCGATACAGTG
1 TATCGATACAGTG
367049 TATCGATACA
1 TATCGATACA
367059 TCATAAATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (13 bp):
TATCGATACAGTG
Found at i:367173 original size:20 final size:20
Alignment explanation
Indices: 367130--367173 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
367120 TTCAAATGCA
* **
367130 TGTATCGATACATTATAATT
1 TGTATCGATACATTAGAACG
*
367150 TGTATCGATACATTAGAGCG
1 TGTATCGATACATTAGAACG
367170 TGTA
1 TGTA
367174 AGAGCGGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTAGAACG
Found at i:367592 original size:34 final size:35
Alignment explanation
Indices: 367529--367595 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
367519 CTAAGTGATT
367529 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
367565 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
367596 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:370793 original size:13 final size:13
Alignment explanation
Indices: 370775--370799 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
370765 TTTTCCAGAT
370775 TGTATCGATACAA
1 TGTATCGATACAA
370788 TGTATCGATACA
1 TGTATCGATACA
370800 TTACTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:372434 original size:21 final size:21
Alignment explanation
Indices: 372401--372441 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
372391 CTAAGTAAAA
372401 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
372422 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
372442 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Done.