Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 1 of 210
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--304 Score: 407
Period size: 7 Copynumber: 43.3 Consensus size: 7
1 AAACCCT
1 AAACCCT
8 AAACCCT
1 AAACCCT
15 AAACCCT
1 AAACCCT
22 AAACCCT
1 AAACCCT
29 AAACCCT
1 AAACCCT
36 AAACCCT
1 AAACCCT
43 AAACCCT
1 AAACCCT
50 AAACCCT
1 AAACCCT
57 AAACCCT
1 AAACCCT
64 AAACCCT
1 AAACCCT
71 AAACCCT
1 AAACCCT
78 AAACCCT
1 AAACCCT
85 AAACCCT
1 AAACCCT
92 AAACCCT
1 AAACCCT
99 AAACCCT
1 AAACCCT
106 AAACCCT
1 AAACCCT
113 AAACCCT
1 AAACCCT
120 AAACCCT
1 AAACCCT
127 AAACCCT
1 AAACCCT
134 AAAACCCT
1 -AAACCCT
142 AAACCCT
1 AAACCCT
149 AAACCCT
1 AAACCCT
156 AAACCCT
1 AAACCCT
*
163 AAACCCG
1 AAACCCT
*
170 AAACCCG
1 AAACCCT
*
177 AAACCCG
1 AAACCCT
*
184 AAACCCG
1 AAACCCT
*
191 AAACCCG
1 AAACCCT
*
198 AAACCCG
1 AAACCCT
*
205 AAACCCG
1 AAACCCT
*
212 AAAACCT
1 AAACCCT
219 -AACCC-
1 AAACCCT
*
224 AATCCCT
1 AAACCCT
231 -AACCCT
1 AAACCCT
237 AAACCCT
1 AAACCCT
244 AAAACCCT
1 -AAACCCT
252 AAACCCT
1 AAACCCT
*
259 AAACACCAA
1 AAAC-CC-T
*
268 AAACCTT
1 AAACCCT
*
275 AAACGCT
1 AAACCCT
* *
282 AAATCTT
1 AAACCCT
*
289 AAAACCT
1 AAACCCT
*
296 AAAACCT
1 AAACCCT
303 AA
1 AA
305 GAATGGGATA
Statistics
Matches: 274, Mismatches: 16, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
6 13 0.05
7 240 0.88
8 17 0.06
9 4 0.01
ACGTcount: A:0.45, C:0.40, G:0.03, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:340 original size:32 final size:32
Alignment explanation
Indices: 304--378 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
294 CTAAAACCTA
304 AGAATGGGATAAATCCAAACCGGGATAACCGC
1 AGAATGGGATAAATCCAAACCGGGATAACCGC
* * *
336 AGAATGGGATAAATCTAAACCGGGATATCCTC
1 AGAATGGGATAAATCCAAACCGGGATAACCGC
*
368 CGAATGGGATA
1 AGAATGGGATA
379 TCCCAACCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (32 bp):
AGAATGGGATAAATCCAAACCGGGATAACCGC
Found at i:589 original size:32 final size:32
Alignment explanation
Indices: 544--611 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
534 CTAAGTATAA
*
544 GATAATTCCAAACCGGGACAACCGCAGAATGG
1 GATAAATCCAAACCGGGACAACCGCAGAATGG
* * * * *
576 GATAAATCTAAACCGGGATATCCTCCGAATGG
1 GATAAATCCAAACCGGGACAACCGCAGAATGG
608 GATA
1 GATA
612 TCCCTACCTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.18
Consensus pattern (32 bp):
GATAAATCCAAACCGGGACAACCGCAGAATGG
Found at i:756 original size:235 final size:233
Alignment explanation
Indices: 311--769 Score: 756
Period size: 235 Copynumber: 2.0 Consensus size: 233
301 CTAAGAATGG
*
311 GATAAATCCAAACCGGGATAACCGCAGAATGGGATAAATCTAAACCGGGATATCCTCCGAATGGG
1 GATAAATCCAAACCGGGACAACCGCAGAATGGGATAAATCTAAACCGGGATATCCTCCGAATGGG
* * * * *
376 ATATCCCAACCTGGAATAACTACGGTAGGTTCCCCGGTCTAAACTCGATAAAATGATGAACCGGT
66 ATATCCCAACCTGGAATAACTACGGCAGATTCCCCGGTCTAAACTCGAAAAAACGATGAACCGGA
* * * *
441 GTCTAAACCATCTAAAACCGGCTATAGGATACTGAACCGGGACGGCATTTGAAAGGAATAACCGA
131 ATCTAAAACATCTAAAACCGGCTATAGGATACCGAACCGGGACGGCATTTAAAAGGAATAACCGA
*
506 GGAATAGCGTAATCCAGGTTGGGATATCCTAAGTATAA
196 GGAAAAGCGTAATCCAGGTTGGGATATCCTAAGTATAA
*
544 GATAATTCCAAACCGGGACAACCGCAGAATGGGATAAATCTAAACCGGGATATCCTCCGAATGGG
1 GATAAATCCAAACCGGGACAACCGCAGAATGGGATAAATCTAAACCGGGATATCCTCCGAATGGG
* *
609 ATATCCCTACCTGGAATAACTACGGCAGATTACTTCCGGTCTAAACTCGAAAAAACGATGAACCG
66 ATATCCCAACCTGGAATAACTACGGCAGATT-C-CCCGGTCTAAACTCGAAAAAACGATGAACCG
674 GAATCTAAAACATCTAAAACCGGCTATAGGATACCGAACCGGGACGGCATTTAAAAGGAATAACC
129 GAATCTAAAACATCTAAAACCGGCTATAGGATACCGAACCGGGACGGCATTTAAAAGGAATAACC
* *
739 GGGGAAAAGCTTAATCCAGGTTGGGATATCC
194 GAGGAAAAGCGTAATCCAGGTTGGGATATCC
770 CCGGGTTATC
Statistics
Matches: 208, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
233 91 0.44
234 1 0.00
235 116 0.56
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (233 bp):
GATAAATCCAAACCGGGACAACCGCAGAATGGGATAAATCTAAACCGGGATATCCTCCGAATGGG
ATATCCCAACCTGGAATAACTACGGCAGATTCCCCGGTCTAAACTCGAAAAAACGATGAACCGGA
ATCTAAAACATCTAAAACCGGCTATAGGATACCGAACCGGGACGGCATTTAAAAGGAATAACCGA
GGAAAAGCGTAATCCAGGTTGGGATATCCTAAGTATAA
Found at i:2060 original size:17 final size:17
Alignment explanation
Indices: 2034--2069 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2024 ACCTGAACTT
2034 ACTAACATTGTTAAAAA
1 ACTAACATTGTTAAAAA
*
2051 ACTAATATTGTTAAAAA
1 ACTAACATTGTTAAAAA
2068 AC
1 AC
2070 CGAAATCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (17 bp):
ACTAACATTGTTAAAAA
Found at i:3023 original size:19 final size:20
Alignment explanation
Indices: 2988--3035 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
2978 CAAACAACCC
*
2988 AAAACAGAAATGAATAAGCA
1 AAAACAAAAATGAATAAGCA
3008 AAAACAAAAATG-ATAAGCA
1 AAAACAAAAATGAATAAGCA
3027 AAAA-AAAAA
1 AAAACAAAAA
3036 ACACATAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 5 0.19
19 11 0.41
20 11 0.41
ACGTcount: A:0.73, C:0.08, G:0.10, T:0.08
Consensus pattern (20 bp):
AAAACAAAAATGAATAAGCA
Found at i:16997 original size:21 final size:21
Alignment explanation
Indices: 16973--17043 Score: 142
Period size: 21 Copynumber: 3.4 Consensus size: 21
16963 ACAAAAAATT
16973 TGAACCGGACACTAAAACACC
1 TGAACCGGACACTAAAACACC
16994 TGAACCGGACACTAAAACACC
1 TGAACCGGACACTAAAACACC
17015 TGAACCGGACACTAAAACACC
1 TGAACCGGACACTAAAACACC
17036 TGAACCGG
1 TGAACCGG
17044 GACGGGATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.41, C:0.32, G:0.17, T:0.10
Consensus pattern (21 bp):
TGAACCGGACACTAAAACACC
Found at i:18074 original size:45 final size:44
Alignment explanation
Indices: 18019--18104 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 44
18009 TACATTCAAT
*
18019 ATCTTTACCTGATTCAAAC-CACCTAATCAAGCTTTATTACATACA
1 ATCTCTACCTGATTC-AACTCACCTAATCAAGCTTTA-TACATACA
*
18064 ATCTCTACCTGATTCAGCTCACCTAATCAAGCTTTATACAT
1 ATCTCTACCTGATTCAACTCACCTAATCAAGCTTTATACAT
18105 TAGGTCTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 7 0.18
45 31 0.82
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.34
Consensus pattern (44 bp):
ATCTCTACCTGATTCAACTCACCTAATCAAGCTTTATACATACA
Found at i:30437 original size:7 final size:7
Alignment explanation
Indices: 30427--30457 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
30417 AAGCCTCAAG
30427 CCTAGAC
1 CCTAGAC
30434 CCTAGAC
1 CCTAGAC
30441 CCTAGAC
1 CCTAGAC
*
30448 CCTAAAC
1 CCTAGAC
30455 CCT
1 CCT
30458 TTTTCTCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.29, C:0.45, G:0.10, T:0.16
Consensus pattern (7 bp):
CCTAGAC
Found at i:34181 original size:47 final size:47
Alignment explanation
Indices: 34112--34201 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
34102 AATACAGTTG
*
34112 CATACAATATATTTACCTGATTCAAAC-CACCTAATCAAGCTTTATTA
1 CATACAATATATCTACCTGATTC-AACTCACCTAATCAAGCTTTATTA
* *
34159 CATACAATATCTCTACCTGATTCAGCTCACCTAATCAAGCTTT
1 CATACAATATATCTACCTGATTCAACTCACCTAATCAAGCTTT
34202 GTACATTAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
46 2 0.05
47 37 0.95
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (47 bp):
CATACAATATATCTACCTGATTCAACTCACCTAATCAAGCTTTATTA
Found at i:35622 original size:11 final size:11
Alignment explanation
Indices: 35606--35630 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35596 CGAAAACCTC
35606 AAACCGAAGCT
1 AAACCGAAGCT
35617 AAACCGAAGCT
1 AAACCGAAGCT
35628 AAA
1 AAA
35631 TCAAAACGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.24, G:0.16, T:0.08
Consensus pattern (11 bp):
AAACCGAAGCT
Found at i:39419 original size:46 final size:45
Alignment explanation
Indices: 39351--39584 Score: 217
Period size: 36 Copynumber: 5.6 Consensus size: 45
39341 TTTGAGTACT
* *
39351 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAATGATAAGTGGTAGC-TTAGCTACACTTA
39397 TCTGATCAAGTGACAAAATGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGACAAAATGATAAGTGGTAGCTTAGCTACACTTA
*
39433 TCTGATCAAGAT-ACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAG-TGACAAAATGATAAGTGGTAGC-TTAGCTACACTTA
39479 TCTGATCAAGTGA-AAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGACAAAA-TGATAAGTGGTAGCTTAGCTACACTTA
*
39515 TCTGATCAAGTGA-AAAAGTGATAAGTGGTAACTTAGCTACACTTA
1 TCTGATCAAGTGACAAAA-TGATAAGTGGTAGCTTAGCTACACTTA
*
39560 TCTGATC-AGGGAC-AAATGATAAGTG
1 TCTGATCAAGTGACAAAATGATAAGTG
39585 ATCATACGTA
Statistics
Matches: 159, Mismatches: 6, Indels: 49
0.74 0.03 0.23
Matches are distributed among these distances:
36 61 0.38
37 5 0.03
40 4 0.03
42 3 0.02
43 9 0.06
44 8 0.05
45 24 0.15
46 45 0.28
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAATGATAAGTGGTAGCTTAGCTACACTTA
Found at i:39488 original size:82 final size:82
Alignment explanation
Indices: 39351--39584 Score: 379
Period size: 82 Copynumber: 2.9 Consensus size: 82
39341 TTTGAGTACT
*
39351 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAAT
1 TCTGATCAAGATACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAAT
39416 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
39433 TCTGATCAAGATACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA-AAAAG
1 TCTGATCAAGATACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAA-
39497 TGATAAGTGCTACACTTA
65 TGATAAGTGCTACACTTA
* * *
39515 TCTGATCAAG-TGAAAAAGTGATAAGTGGTAAC-TTAGCTACACTTATCTGATC-AGGGAC-AAA
1 TCTGATCAAGAT-ACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAA
39576 TGATAAGTG
65 TGATAAGTG
39585 ATCATACGTA
Statistics
Matches: 145, Mismatches: 4, Indels: 9
0.92 0.03 0.06
Matches are distributed among these distances:
79 9 0.06
80 7 0.05
81 25 0.17
82 104 0.72
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (82 bp):
TCTGATCAAGATACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAAT
GATAAGTGCTACACTTA
Found at i:42935 original size:4 final size:4
Alignment explanation
Indices: 42926--42966 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
42916 ATCTCCCTCA
42926 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
42967 ACTGGATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:45897 original size:23 final size:24
Alignment explanation
Indices: 45866--45910 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
45856 TATTTCTTTT
*
45866 TTTATAAATAATTAATATTTATCG
1 TTTATAAATAATTAAAATTTATCG
*
45890 TTTA-AAATATTTAAAATTTAT
1 TTTATAAATAATTAAAATTTAT
45911 ATTTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTATAAATAATTAAAATTTATCG
Found at i:54992 original size:268 final size:261
Alignment explanation
Indices: 54504--55034 Score: 972
Period size: 268 Copynumber: 2.0 Consensus size: 261
54494 AGTTTAGTTG
54504 ATACATGGAAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCCC
1 ATACATGGAAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCCC
54569 TGGTCTGACGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGAGGTGAAGAGTTCAGCAAC
66 TGGTCTGACGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGAGGTGAAGAGTTCAGCAAC
*
54634 ACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGGAACCAAGTCTG
131 ACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACCAAGTCTG
54699 CTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAAGGCGCGG
196 CTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAAGGCGCGG
54764 A
261 A
54765 ATACATGGAAAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCC
1 ATACATGG-AAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCC
*
54830 CTGGTCTGATGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGAGGTTGCAGTGAAGAGTT
65 CTGGTCTGACGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGA----G--GTGAAGAGTT
*
54895 CAGCAACACAATTCTCTGCAACTAAAATTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACC
124 CAGCAACACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACC
54960 AAGTCTGCTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAA
189 AAGTCTGCTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAA
55025 GGCGCGGA
254 GGCGCGGA
55033 AT
1 AT
55035 GCTACTATTG
Statistics
Matches: 260, Mismatches: 3, Indels: 7
0.96 0.01 0.03
Matches are distributed among these distances:
261 8 0.03
262 103 0.40
266 1 0.00
268 148 0.57
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (261 bp):
ATACATGGAAAAAAAGAGTTCAGGTTGAGTTGGATGCTAAATACGGTCCAAATCAGTCTGTTCCC
TGGTCTGACGTTGCTAAATGTGGAATCAAGCACTATAGACCTTCTGAGGTGAAGAGTTCAGCAAC
ACAATTCTCTGCAACTAAAACTGGTTTTGTTAAGCTTTTTCAAGGAGGGACTGCAACCAAGTCTG
CTTCTGCAATGCCGGTACCTATGAAGGCATCAACATTGCCTGCTTCAGCCAGAACAAAGGCGCGG
A
Found at i:70835 original size:6 final size:6
Alignment explanation
Indices: 70826--70874 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
70816 TGGTCCTCAT
* * *
70826 CTCCAC CTCCAC CACCAC CTCCAC CTCCAA CTCCAC CTCCTC C-CCAC
1 CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC
70873 CT
1 CT
70875 TTCTTCAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.18, C:0.65, G:0.00, T:0.16
Consensus pattern (6 bp):
CTCCAC
Found at i:73901 original size:2 final size:2
Alignment explanation
Indices: 73894--73924 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
73884 AATAAGGAAG
73894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
73925 TGGTGAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:91063 original size:19 final size:19
Alignment explanation
Indices: 91023--91061 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
91013 TTTACTTCAC
91023 TTTCTTGTTTCTTTTCTTT
1 TTTCTTGTTTCTTTTCTTT
91042 TTTCTT-TTTCTTTT-TTT
1 TTTCTTGTTTCTTTTCTTT
91059 TTT
1 TTT
91062 TTTTTGGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 8 0.40
19 6 0.30
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (19 bp):
TTTCTTGTTTCTTTTCTTT
Found at i:94458 original size:26 final size:26
Alignment explanation
Indices: 94402--94458 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
94392 ACAAGTGGGA
*
94402 ATTTTAAGTAAAACGGAGAGTTTTGG
1 ATTTTAAGTAAAACGGAGAGTTTTGC
* * * * *
94428 GTTTTAAGTCATACGGGGCGTTTTGC
1 ATTTTAAGTAAAACGGAGAGTTTTGC
94454 ATTTT
1 ATTTT
94459 TGTTATAACT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.40
Consensus pattern (26 bp):
ATTTTAAGTAAAACGGAGAGTTTTGC
Found at i:99253 original size:26 final size:26
Alignment explanation
Indices: 99197--99253 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
99187 ACAAGTGGGA
*
99197 ATTTTAAGTAAAACGGAGAGTTTTGG
1 ATTTTAAGTAAAACGGAGAGTTTTGC
* * * * *
99223 GTTTTAAGTCATACGGGGCGTTTTGC
1 ATTTTAAGTAAAACGGAGAGTTTTGC
99249 ATTTT
1 ATTTT
99254 TGTTATAACT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.40
Consensus pattern (26 bp):
ATTTTAAGTAAAACGGAGAGTTTTGC
Found at i:102228 original size:22 final size:22
Alignment explanation
Indices: 102203--102259 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 22
102193 TCAATGGTTT
102203 ATTTTGCACACC-CTTAGTTTGC
1 ATTTTGCA-ACCACTTAGTTTGC
*
102225 ATTTTGCAACCAGTTTAGTTTGC
1 ATTTTGCAACCA-CTTAGTTTGC
102248 ATTTTGCAACCA
1 ATTTTGCAACCA
102260 GCTCAAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 3 0.09
22 8 0.25
23 21 0.66
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (22 bp):
ATTTTGCAACCACTTAGTTTGC
Found at i:102246 original size:23 final size:23
Alignment explanation
Indices: 102216--102260 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
102206 TTGCACACCC
102216 TTAGTTTGCATTTTGCAACCAGT
1 TTAGTTTGCATTTTGCAACCAGT
102239 TTAGTTTGCATTTTGCAACCAG
1 TTAGTTTGCATTTTGCAACCAG
102261 CTCAAAATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (23 bp):
TTAGTTTGCATTTTGCAACCAGT
Found at i:103905 original size:5 final size:5
Alignment explanation
Indices: 103897--103922 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
103887 GTATCCTATC
103897 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
103923 GCTAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:105236 original size:93 final size:93
Alignment explanation
Indices: 105077--105262 Score: 354
Period size: 93 Copynumber: 2.0 Consensus size: 93
105067 TCAAATGTAA
105077 ACAGCATATGTTAAGTCAAAATGGAACTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
1 ACAGCATATGTTAAGTCAAAATGGAACTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
105142 TTAAGATTCATCAATTAAACAAAAATTC
66 TTAAGATTCATCAATTAAACAAAAATTC
*
105170 ACAGCATATGTTAAGTCAAAATGGATCTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
1 ACAGCATATGTTAAGTCAAAATGGAACTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
*
105235 TTGAGATTCATCAATTAAACAAAAATTC
66 TTAAGATTCATCAATTAAACAAAAATTC
105263 CAAGAAACTA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.24
Consensus pattern (93 bp):
ACAGCATATGTTAAGTCAAAATGGAACTAAAAGCATCACAAAACCACTTAAGCATCTCAACAATA
TTAAGATTCATCAATTAAACAAAAATTC
Found at i:108691 original size:10 final size:11
Alignment explanation
Indices: 108678--108707 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
108668 TTTTCATATG
108678 TTTTATTTTC-
1 TTTTATTTTCA
108688 TTTTATTTTCA
1 TTTTATTTTCA
108699 TTTTATTTT
1 TTTTATTTT
108708 GTTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:121327 original size:2 final size:2
Alignment explanation
Indices: 121320--121373 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
121310 TTTCTCACTA
121320 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
121361 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
121374 ACCTTAGGCA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:124188 original size:22 final size:22
Alignment explanation
Indices: 124161--124204 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
124151 TAGATAACTT
124161 TGTTGAAGATAAAATTTTAAAA
1 TGTTGAAGATAAAATTTTAAAA
124183 TGTTGAAGATAAAATTTTAAAA
1 TGTTGAAGATAAAATTTTAAAA
124205 GTCAATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (22 bp):
TGTTGAAGATAAAATTTTAAAA
Found at i:125526 original size:27 final size:27
Alignment explanation
Indices: 125491--125543 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
125481 CATACAATAC
*
125491 AAAAAAATTAACAAATATTAATATATA
1 AAAAAAATTAACAAATACTAATATATA
125518 AAAAAAATTAACAAATACTAATATAT
1 AAAAAAATTAACAAATACTAATATAT
125544 GTTTGGTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (27 bp):
AAAAAAATTAACAAATACTAATATATA
Found at i:136339 original size:4 final size:4
Alignment explanation
Indices: 136326--136355 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
136316 AGTTGATGTT
136326 TTTC -TTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
136356 TTTTTTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:139168 original size:33 final size:33
Alignment explanation
Indices: 139126--139189 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
139116 TTTTATTTTG
139126 ACATTGTTTTGGACTGTAAATATGCTACTCTTA
1 ACATTGTTTTGGACTGTAAATATGCTACTCTTA
*
139159 ACATTGTTTTGGACTGTAAATATTCTACTCT
1 ACATTGTTTTGGACTGTAAATATGCTACTCT
139190 CTTTTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (33 bp):
ACATTGTTTTGGACTGTAAATATGCTACTCTTA
Found at i:142268 original size:13 final size:13
Alignment explanation
Indices: 142250--142278 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
142240 TTTCTTTGTG
142250 TTAAATTCACTAA
1 TTAAATTCACTAA
142263 TTAAATTCACTAA
1 TTAAATTCACTAA
142276 TTA
1 TTA
142279 GGATCCTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAATTCACTAA
Found at i:143495 original size:13 final size:14
Alignment explanation
Indices: 143469--143498 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
143459 GTATTCTTCC
143469 TTTATTTTTCCTCA
1 TTTATTTTTCCTCA
143483 TTTATTTTT-CTCA
1 TTTATTTTTCCTCA
143496 TTT
1 TTT
143499 CTTTATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTTTTCCTCA
Found at i:157159 original size:5 final size:5
Alignment explanation
Indices: 157149--157173 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
157139 CTAACGTCAA
157149 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
157174 TTGCTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:175397 original size:21 final size:24
Alignment explanation
Indices: 175348--175397 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
175338 TATATTATAA
*
175348 TATATTTTTTAATTTTCACATTAT
1 TATATTTTTTAATATTCACATTAT
*
175372 AATATTTTTTAA-ATT-A-ATTAT
1 TATATTTTTTAATATTCACATTAT
175393 TATAT
1 TATAT
175398 AATATTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 9 0.39
22 1 0.04
23 2 0.09
24 11 0.48
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
TATATTTTTTAATATTCACATTAT
Found at i:175731 original size:3 final size:3
Alignment explanation
Indices: 175723--175773 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
175713 AGAACAAAAC
* * * *
175723 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCG TCT TCA TCT TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
175771 TCA
1 TCA
175774 CCCAATTGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.25, C:0.33, G:0.02, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:187858 original size:7 final size:7
Alignment explanation
Indices: 187840--187873 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
187830 GCCTGCTGTG
187840 TATATG-
1 TATATGA
187846 TATATGA
1 TATATGA
187853 TATATGA
1 TATATGA
187860 TATATGA
1 TATATGA
187867 TATATGA
1 TATATGA
187874 ACATGGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (7 bp):
TATATGA
Found at i:194043 original size:22 final size:22
Alignment explanation
Indices: 194015--194079 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
194005 TTTATTGTTC
194015 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
194037 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
194059 AGCCATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
194080 AAATTAATGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:202055 original size:15 final size:15
Alignment explanation
Indices: 202021--202055 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
202011 CCTCCATCCG
*
202021 GATCCCTCGCATTTA
1 GATCTCTCGCATTTA
*
202036 GATCTCTCGGATTTA
1 GATCTCTCGCATTTA
202051 GATCT
1 GATCT
202056 GACCATAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (15 bp):
GATCTCTCGCATTTA
Found at i:210118 original size:12 final size:12
Alignment explanation
Indices: 210101--210133 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
210091 ATGTTGAGAT
210101 ACAGAAGAAAAG
1 ACAGAAGAAAAG
210113 ACAGAAGAAAAG
1 ACAGAAGAAAAG
210125 ACAGAAGAA
1 ACAGAAGAA
210134 TTTTAAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.09, G:0.24, T:0.00
Consensus pattern (12 bp):
ACAGAAGAAAAG
Found at i:211055 original size:8 final size:8
Alignment explanation
Indices: 211042--211096 Score: 60
Period size: 8 Copynumber: 6.9 Consensus size: 8
211032 AAAAATTATT
211042 TTTATGTA
1 TTTATGTA
211050 TTTATGTA
1 TTTATGTA
*
211058 TTTATGATT
1 TTTATG-TA
211067 TTTAT-T-
1 TTTATGTA
*
211073 TTTATCTA
1 TTTATGTA
211081 TTTTATGTA
1 -TTTATGTA
211090 TTTATGT
1 TTTATGT
211097 GTATACATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 5 0.12
7 2 0.05
8 21 0.51
9 13 0.32
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (8 bp):
TTTATGTA
Found at i:211093 original size:23 final size:23
Alignment explanation
Indices: 211050--211094 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
211040 TTTTTATGTA
* *
211050 TTTATGTATTTATGATTTTTATT
1 TTTATCTATTTATGATATTTATT
211073 TTTATCTATTTTATG-TATTTAT
1 TTTATCTA-TTTATGATATTTAT
211095 GTGTATACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (23 bp):
TTTATCTATTTATGATATTTATT
Found at i:211320 original size:30 final size:28
Alignment explanation
Indices: 211286--211358 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
211276 AGCCAGTGCT
*
211286 CAAATAAAACAATTTTGAAGCA-TTAATAAC
1 CAAATAAAAC-ATTTT-AA-AATTTAATAAC
*
211316 CAAATTATAACATTTTAAAATTTAATAAC
1 CAAA-TAAAACATTTTAAAATTTAATAAC
211345 CAAAATAAAA-ATTT
1 C-AAATAAAACATTT
211359 AAGTATGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 5 0.14
29 15 0.41
30 12 0.32
31 5 0.14
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (28 bp):
CAAATAAAACATTTTAAAATTTAATAAC
Found at i:212143 original size:14 final size:15
Alignment explanation
Indices: 212083--212143 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
212073 TTTATACTAC
* *
212083 AAAACATTTATTATT
1 AAAATATTTAATATT
* *
212098 AATATATTTATATAGT
1 AAAATATTTA-ATATT
*
212114 ATAAATATTTAGTATT
1 A-AAATATTTAATATT
212130 AAAATA-TTAATATT
1 AAAATATTTAATATT
212144 GATATTTTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
14 7 0.19
15 13 0.36
16 8 0.22
17 8 0.22
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (15 bp):
AAAATATTTAATATT
Found at i:213464 original size:22 final size:22
Alignment explanation
Indices: 213439--213480 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
213429 TTTATAATTC
*
213439 AATCAATTGAATTAATTAAAAA
1 AATCAATTAAATTAATTAAAAA
* *
213461 AATCGATTAAATTCATTAAA
1 AATCAATTAAATTAATTAAA
213481 TTCGTATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (22 bp):
AATCAATTAAATTAATTAAAAA
Found at i:234494 original size:31 final size:31
Alignment explanation
Indices: 234456--234516 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
234446 GATGCTTTTA
* *
234456 ATTTGACTATTAAGGCCTTTTTACCAAAAAT
1 ATTTGACTATTAAGGCCCTCTTACCAAAAAT
234487 ATTTGACTATTAAGGCCCTCTTACCAAAAA
1 ATTTGACTATTAAGGCCCTCTTACCAAAAA
234517 AAGTCCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (31 bp):
ATTTGACTATTAAGGCCCTCTTACCAAAAAT
Found at i:235078 original size:123 final size:122
Alignment explanation
Indices: 234866--235103 Score: 390
Period size: 123 Copynumber: 1.9 Consensus size: 122
234856 TTATTTCGAG
* **
234866 TTGACGTTTCTAGTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATCAGAGAAGAAATTGTG
1 TTGACGTTTCTAGTCAAATAGTATAAAATAGCTGATACCAGGATGCTATCAGAGAAGAAATTGTG
* *
234931 AAATCGTGCCCTCGTGGACGCGATTTCGGTACAGTTGGTCATGTAAGAAAAAAAAAT
66 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAAAAAAAAT
234988 TTGACGTTTTCTGAG-CAAATAGTATAAAATAGCTGATACCAGGATGCTAT-ATGAGAAGAAATT
1 TTGACG-TTTCT-AGTCAAATAGTATAAAATAGCTGATACCAGGATGCTATCA-GAGAAGAAATT
235051 GTGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAA
63 GTGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAA
235104 TAATTATTTT
Statistics
Matches: 108, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
122 7 0.06
123 99 0.92
124 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (122 bp):
TTGACGTTTCTAGTCAAATAGTATAAAATAGCTGATACCAGGATGCTATCAGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAAAAAAAAT
Found at i:237654 original size:17 final size:16
Alignment explanation
Indices: 237634--237666 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
237624 AAAACTTTTG
237634 TTAATTAAAATAGGGTT
1 TTAATTAAAAT-GGGTT
237651 TTAATTAAAATGGGTT
1 TTAATTAAAATGGGTT
237667 AGGGTTAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (16 bp):
TTAATTAAAATGGGTT
Found at i:237686 original size:29 final size:29
Alignment explanation
Indices: 237665--238087 Score: 587
Period size: 29 Copynumber: 14.9 Consensus size: 29
237655 TTAAAATGGG
**
237665 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
* **
237694 TTAGGGTTTAAGG-TTTTAATTAAATTAGG
1 TTAGGG-TTAGGGTTTTTAATTAAATTAAA
237723 TTAGGGTTTAGGG-TTTTAATTAAATTAAA
1 TTAGGG-TTAGGGTTTTTAATTAAATTAAA
* *
237752 CTAGGGTTAGTGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
*
237781 CTAGGGTTAGGGTTTTTAATT--A--AAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
237806 -T-GGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
237833 TTAGGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
* * ***
237862 CTAGGGTTAGGGTTTTTAATTAAAATGGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
237891 TTAGGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
237920 TTAGGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
* * **
237949 CTAGGGTTAGGGTTTTTAATTAAAATAGG
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
237978 TTAGGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
238007 TTAGGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
*
238036 TTA-GGTTTGGGTTTTTAATTAAATTAAA
1 TTAGGGTTAGGGTTTTTAATTAAATTAAA
*
238064 TTA-GGTTAGGGTTTTTAATCAAAT
1 TTAGGGTTAGGGTTTTTAATTAAAT
238088 AATATCAAAA
Statistics
Matches: 358, Mismatches: 28, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
23 18 0.05
24 1 0.00
25 4 0.01
27 4 0.01
28 52 0.15
29 274 0.77
30 5 0.01
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.44
Consensus pattern (29 bp):
TTAGGGTTAGGGTTTTTAATTAAATTAAA
Found at i:238416 original size:24 final size:24
Alignment explanation
Indices: 238367--238422 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
238357 TGTATGTGGA
*
238367 GGTGTTTGCATCATGAACGGCAAC
1 GGTGTTTGCATCATGAACGACAAC
*
238391 GGTGTTTGCATCATGAACGACGAC
1 GGTGTTTGCATCATGAACGACAAC
*
238415 GGAGTTTG
1 GGTGTTTG
238423 AAAGCCATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (24 bp):
GGTGTTTGCATCATGAACGACAAC
Found at i:238750 original size:22 final size:21
Alignment explanation
Indices: 238722--238772 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
238712 AAATATGGAT
*
238722 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
*
238744 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGA-GATTTTGGAAGGAAA
238766 TTGAGAG
1 TTGAGAG
238773 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:242024 original size:4 final size:4
Alignment explanation
Indices: 242017--242051 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
242007 AATGAATGAT
242017 TAAC TAAC TAAC TAAC -AGAC TAAC TAAC TAAC TAA
1 TAAC TAAC TAAC TAAC TA-AC TAAC TAAC TAAC TAA
242052 TATATCCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 1 0.03
4 27 0.93
5 1 0.03
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (4 bp):
TAAC
Found at i:246652 original size:26 final size:26
Alignment explanation
Indices: 246623--246674 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
246613 GAGCCCCGCA
246623 TGAGCATCATTCCCACCAAAATCGTC
1 TGAGCATCATTCCCACCAAAATCGTC
246649 TGAGCATCATTCCCACCAAAATCGTC
1 TGAGCATCATTCCCACCAAAATCGTC
246675 ATTCAAGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.23
Consensus pattern (26 bp):
TGAGCATCATTCCCACCAAAATCGTC
Found at i:252549 original size:37 final size:35
Alignment explanation
Indices: 252474--252549 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
252464 ATCATTGTGC
* * *
252474 CTTCATGTATTTTGTTGTGTTACTCTTGATCGTGT
1 CTTCATGTAGTTTGTTGTGTTACCCTTGATCGTAT
*
252509 CTTCATGTAGTTTGTTGTGCATTACCCTTGATTGTAT
1 CTTCATGTAGTTTGTTGTG--TTACCCTTGATCGTAT
252546 CTTC
1 CTTC
252550 GTTAATCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 18 0.51
37 17 0.49
ACGTcount: A:0.13, C:0.17, G:0.18, T:0.51
Consensus pattern (35 bp):
CTTCATGTAGTTTGTTGTGTTACCCTTGATCGTAT
Found at i:256296 original size:25 final size:26
Alignment explanation
Indices: 256248--256296 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
256238 TTGGACTTAT
* * *
256248 TTGATCCTTTTTAATAGTATAGGGAA
1 TTGATCCTATTTAATAATAGAGGGAA
256274 TTGATCC-ATTTAATAATAGAGGG
1 TTGATCCTATTTAATAATAGAGGG
256297 GCCAATTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (26 bp):
TTGATCCTATTTAATAATAGAGGGAA
Found at i:258803 original size:72 final size:70
Alignment explanation
Indices: 258596--258879 Score: 383
Period size: 72 Copynumber: 4.0 Consensus size: 70
258586 ATATAGTATT
* * * * *
258596 TTAAACATGCAAAAAATTTAAAACTTTTTAAATTTATTTATACCAATTACACATTTAAAATATTT
1 TTAAACATGCAAAAAATTAAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATATTT
258661 ATATA
66 ATATA
* *
258666 TTAAATATGCAAAAAAATTAAAAAC--ATTAAATTTATTCATACCTATCACACATTTTAAATATT
1 TTAAACATGC-AAAAAATTAAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATATT
258729 TATATA
65 TATATA
* * *
258735 TTAAACATGCAAAAAATTAAAAAAACTTATTGAATTTATTCATACCAACCACACATTTTTAATAT
1 TTAAACATGCAAAAAATT--AAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATAT
258800 TTATATA
64 TTATATA
* * * *
258807 TTAAAAATACAAAAAAAATTAAAAACTTATTAAATTTATTCAAACCAAGCACACATTTTAAATAT
1 TTAAACATGC--AAAAAATTAAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATAT
258872 TTATATA
64 TTATATA
258879 T
1 T
258880 ACATACATAC
Statistics
Matches: 189, Mismatches: 18, Indels: 12
0.86 0.08 0.05
Matches are distributed among these distances:
68 8 0.04
69 48 0.25
70 15 0.08
71 13 0.07
72 97 0.51
74 8 0.04
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (70 bp):
TTAAACATGCAAAAAATTAAAAACTTATTAAATTTATTCATACCAATCACACATTTTAAATATTT
ATATA
Found at i:258958 original size:27 final size:27
Alignment explanation
Indices: 258920--258973 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
258910 ATACATCGAG
258920 ACCTTTGTTTCATGTTTAAAGTTTAAT
1 ACCTTTGTTTCATGTTTAAAGTTTAAT
258947 ACCTTTGTTTCATGTTTAAAGTTTAAT
1 ACCTTTGTTTCATGTTTAAAGTTTAAT
258974 GATGACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (27 bp):
ACCTTTGTTTCATGTTTAAAGTTTAAT
Found at i:259625 original size:23 final size:22
Alignment explanation
Indices: 259585--259635 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
259575 GATTTTTTTT
259585 TTTGTTAATATATCTTTTTAGTA
1 TTTGTTAATATATCTTTTTA-TA
* * * *
259608 TTTGTTAATGTTTTTTTTTATC
1 TTTGTTAATATATCTTTTTATA
259630 TTTGTT
1 TTTGTT
259636 TTTCCTCGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.18, C:0.04, G:0.10, T:0.69
Consensus pattern (22 bp):
TTTGTTAATATATCTTTTTATA
Found at i:264885 original size:31 final size:31
Alignment explanation
Indices: 264850--264914 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
264840 GAATTTTTTA
*
264850 AAAGGATAAACTTCAACTTGATTTAATCTAT
1 AAAGGATAAACTTCAACCTGATTTAATCTAT
*
264881 AAAGGATAAACTTTAACCTGATTTAATCTAT
1 AAAGGATAAACTTCAACCTGATTTAATCTAT
264912 AAA
1 AAA
264915 CACCTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (31 bp):
AAAGGATAAACTTCAACCTGATTTAATCTAT
Found at i:267935 original size:113 final size:113
Alignment explanation
Indices: 267634--267937 Score: 322
Period size: 112 Copynumber: 2.8 Consensus size: 113
267624 ACACAATTCA
* * *
267634 TTAACTTATCCAAAGTTCTATAAATATAAAATACCTTAAG--C----ACAATACGAGAAGATACA
1 TTAACTTATCAAAAGTTCTATAAACATAAAATACCGTAAGCACAATTACAATACGAGAAGATACA
* *
267693 CAAATACG-AAAAGAATACATGTATAACCAAATAAATCCAATACATTG
66 CAAATACGAAAAAGAATACATATATAACCAAATAAATCCAATACACTG
* * * * ** * *
267740 TTAACTTATCAAAAGTTCTATAAATATAAAATATCGTAAGTACGATTATTATACGAAAATATACA
1 TTAACTTATCAAAAGTTCTATAAACATAAAATACCGTAAGCACAATTACAATACGAGAAGATACA
* *
267805 CAAATAC-AAGAAGAATACATATATAAACCAAGTAAATCCAAT-CGACTG
66 CAAATACGAAAAAGAATACATATAT-AACCAAATAAATCCAATAC-ACTG
* * * * * *
267853 TTAACTTATCAAAAGTTGTA-AAACATAGAATACCTTAAGCGCAATTACAACACGAGAAGATGCA
1 TTAACTTATCAAAAGTTCTATAAACATAAAATACCGTAAGCACAATTACAATACGAGAAGATACA
*
267917 CAAATACGAAAAACAATACAT
66 CAAATACGAAAAAGAATACAT
267938 GATAAGTTCT
Statistics
Matches: 161, Mismatches: 27, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
106 37 0.23
108 1 0.01
112 74 0.46
113 49 0.30
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.25
Consensus pattern (113 bp):
TTAACTTATCAAAAGTTCTATAAACATAAAATACCGTAAGCACAATTACAATACGAGAAGATACA
CAAATACGAAAAAGAATACATATATAACCAAATAAATCCAATACACTG
Found at i:271579 original size:25 final size:25
Alignment explanation
Indices: 271545--271631 Score: 165
Period size: 25 Copynumber: 3.5 Consensus size: 25
271535 GTGCAAGACC
*
271545 AATTTTTAACCGTAGAAATGAGTGA
1 AATTTTTAACAGTAGAAATGAGTGA
271570 AATTTTTAACAGTAGAAATGAGTGA
1 AATTTTTAACAGTAGAAATGAGTGA
271595 AATTTTTAACAGTAGAAATGAGTGA
1 AATTTTTAACAGTAGAAATGAGTGA
271620 AATTTTTAACAG
1 AATTTTTAACAG
271632 AAGGATCAGG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (25 bp):
AATTTTTAACAGTAGAAATGAGTGA
Found at i:272506 original size:21 final size:22
Alignment explanation
Indices: 272473--272515 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
272463 TAATTATTTA
*
272473 AAACATATTTTTAATATATAAT
1 AAACATATATTTAATATATAAT
*
272495 AAACAT-TATTTAATATTTAAT
1 AAACATATATTTAATATATAAT
272516 GATTTAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
AAACATATATTTAATATATAAT
Found at i:287296 original size:21 final size:21
Alignment explanation
Indices: 287272--287351 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
287262 TAAGATCTTG
* *
287272 AATTTAATGTGAAATTGATCA
1 AATTTTATGCGAAATTGATCA
* * *
287293 AATTTTAT-TG-ATTTG-T-T
1 AATTTTATGCGAAATTGATCA
287310 AATTTTATGCGAAATTGATCA
1 AATTTTATGCGAAATTGATCA
*
287331 AATTCTATGCGAAATTGATCA
1 AATTTTATGCGAAATTGATCA
287352 TGAATTCGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
17 8 0.17
18 2 0.04
19 8 0.17
20 3 0.06
21 27 0.56
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (21 bp):
AATTTTATGCGAAATTGATCA
Found at i:300964 original size:4 final size:4
Alignment explanation
Indices: 300955--300985 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
300945 ATGTATAATA
*
300955 ATTT ATTT ATTT GTTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
300986 AATATAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:304906 original size:18 final size:18
Alignment explanation
Indices: 304883--304917 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
304873 ATTAAAGCTG
304883 TGTATAATAAA-ATTAAAA
1 TGTATAA-AAATATTAAAA
304901 TGTATAAAAATATTAAA
1 TGTATAAAAATATTAAA
304918 TAAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
TGTATAAAAATATTAAAA
Found at i:316741 original size:15 final size:15
Alignment explanation
Indices: 316721--316771 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
316711 TGGAATGGGA
316721 TATCCCCGACCGGCG
1 TATCCCCGACCGGCG
*
316736 TATCCCGCGA-TGG-G
1 TATCCC-CGACCGGCG
316750 ATATCCCCGACCGGCG
1 -TATCCCCGACCGGCG
316766 TATCCC
1 TATCCC
316772 GCGATGGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 4 0.13
15 22 0.73
16 4 0.13
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (15 bp):
TATCCCCGACCGGCG
Found at i:316751 original size:30 final size:30
Alignment explanation
Indices: 316715--316785 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
316705 TATGCTTGGA
316715 ATGGGATATCCCCGACCGGCGTATCCCGCG
1 ATGGGATATCCCCGACCGGCGTATCCCGCG
316745 ATGGGATATCCCCGACCGGCGTATCCCGCG
1 ATGGGATATCCCCGACCGGCGTATCCCGCG
316775 ATGGGATATCC
1 ATGGGATATCC
316786 TCCAGCCGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.18, C:0.34, G:0.30, T:0.18
Consensus pattern (30 bp):
ATGGGATATCCCCGACCGGCGTATCCCGCG
Found at i:316784 original size:15 final size:14
Alignment explanation
Indices: 316715--316785 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 14
316705 TATGCTTGGA
316715 ATGGGATATCCCCG
1 ATGGGATATCCCCG
*
316729 ACCGGCG-TATCCCGCG
1 A-TGG-GATATCCC-CG
316745 ATGGGATATCCCCG
1 ATGGGATATCCCCG
*
316759 ACCGGCG-TATCCCGCG
1 A-TGG-GATATCCC-CG
316775 ATGGGATATCC
1 ATGGGATATCC
316786 TCCAGCCGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
14 6 0.13
15 31 0.69
16 8 0.18
ACGTcount: A:0.18, C:0.34, G:0.30, T:0.18
Consensus pattern (14 bp):
ATGGGATATCCCCG
Found at i:325955 original size:34 final size:34
Alignment explanation
Indices: 325903--325974 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
325893 TTTAAATTAA
* * *
325903 AAAATTTATATTACATTAGTG-ATGAGTAGTTATG
1 AAAAGTTATACTACATTAG-GAATGAGTAATTATG
* *
325937 AAAAGTTATACTATATTAGGAATTAGTAATTATG
1 AAAAGTTATACTACATTAGGAATGAGTAATTATG
325971 AAAA
1 AAAA
325975 TGATTAGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 1 0.03
34 31 0.97
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38
Consensus pattern (34 bp):
AAAAGTTATACTACATTAGGAATGAGTAATTATG
Found at i:326613 original size:34 final size:30
Alignment explanation
Indices: 326574--326636 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
326564 CAAAAATTAA
*
326574 TAAAATTTTAAGTATATATTTTATAATTAAATTT
1 TAAAATTTT-ACTAT-TA-TTTA-AATTAAATTT
326608 TAAAATTTTACTATTATTTAAATTAAATT
1 TAAAATTTTACTATTATTTAAATTAAATT
326637 CAGAGCAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 9 0.32
31 4 0.14
32 2 0.07
33 4 0.14
34 9 0.32
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
TAAAATTTTACTATTATTTAAATTAAATTT
Found at i:342734 original size:15 final size:14
Alignment explanation
Indices: 342716--342749 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
342706 AGAGGAAAGG
342716 GAGAGGGAAAGAGAA
1 GAGAGGGAAAGAG-A
342731 GAGAGGGAAAGAGA
1 GAGAGGGAAAGAGA
342745 GAGAG
1 GAGAG
342750 AAAGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (14 bp):
GAGAGGGAAAGAGA
Found at i:342739 original size:27 final size:27
Alignment explanation
Indices: 342701--342756 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
342691 AAGGCGGAGG
* *
342701 GAAGAAGAGGAAAGGGAGAGGGAAAGA
1 GAAGAAGAGGAAAGAGAGAGAGAAAGA
342728 GAAG-AGAGGGAAAGAGAGAGAGAAAGA
1 GAAGAAGA-GGAAAGAGAGAGAGAAAGA
342755 GA
1 GA
342757 TTTCAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (27 bp):
GAAGAAGAGGAAAGAGAGAGAGAAAGA
Found at i:342754 original size:12 final size:12
Alignment explanation
Indices: 342702--342756 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
342692 AGGCGGAGGG
342702 AAGA-AGAG-GA
1 AAGAGAGAGAGA
* *
342712 AAGGGAGAGGGA
1 AAGAGAGAGAGA
342724 AAGAGAAGAGAGGGA
1 AAGAG-AGAGA--GA
342739 AAGAGAGAGAGA
1 AAGAGAGAGAGA
342751 AAGAGA
1 AAGAGA
342757 TTTCAATGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 3 0.08
11 4 0.11
12 14 0.38
13 4 0.11
14 5 0.14
15 7 0.19
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (12 bp):
AAGAGAGAGAGA
Found at i:355802 original size:15 final size:16
Alignment explanation
Indices: 355772--355810 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
355762 TGATAAATAT
355772 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
355789 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
355804 ATAATTT
1 ATAATTT
355811 TAAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:355820 original size:26 final size:24
Alignment explanation
Indices: 355766--355816 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
355756 TTATGATGAT
* *
355766 AAATATATAATTTTATTATTTTAA
1 AAATTTATAATTTTATAATTTTAA
* *
355790 TAATTTATATTTTTATAATTTTAA
1 AAATTTATAATTTTATAATTTTAA
355814 AAA
1 AAA
355817 AATTAAATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AAATTTATAATTTTATAATTTTAA
Found at i:355841 original size:30 final size:30
Alignment explanation
Indices: 355800--355874 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
355790 TAATTTATAT
*
355800 TTTTATAATTTTAAAAAAATTAAATTAAAA
1 TTTTATAATTTTAAAAAAATTAAAGTAAAA
* * * *
355830 TTTTATCATTTTTAAAAAGTTAAAGTACAA
1 TTTTATAATTTTAAAAAAATTAAAGTAAAA
*
355860 TTTTATTATTATTAA
1 TTTTATAATT-TTAA
355875 TTTAAAATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 34 0.92
31 3 0.08
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTTATAATTTTAAAAAAATTAAAGTAAAA
Found at i:358960 original size:2 final size:2
Alignment explanation
Indices: 358953--358991 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
358943 CATAAACTTC
358953 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
358992 TTACTATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:377687 original size:60 final size:60
Alignment explanation
Indices: 377623--377747 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
377613 TCAAGTTTAG
* * * * *
377623 GTACCTAATCGAGCCAAAA-TAAACTTTAGGTATCAAATTAAACCTTAAAGCCAATTTCAA
1 GTACCTAAT-GAGACAAAAGAAAACTTTAGGTACCAAATTAAACCTTAAAGCCAAATACAA
* * * *
377683 GTACCTAATTAGACAAAAGAAAATTTTAGGTACCAATTTAAACTTTAAAGCCAAATACAA
1 GTACCTAATGAGACAAAAGAAAACTTTAGGTACCAAATTAAACCTTAAAGCCAAATACAA
377743 GTACC
1 GTACC
377748 AAAATGTATA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 7 0.13
60 48 0.87
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.26
Consensus pattern (60 bp):
GTACCTAATGAGACAAAAGAAAACTTTAGGTACCAAATTAAACCTTAAAGCCAAATACAA
Found at i:380536 original size:18 final size:19
Alignment explanation
Indices: 380513--380548 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
380503 TTTTCCTAGA
380513 TAAAAGTATTA-GGATAGG
1 TAAAAGTATTAGGGATAGG
380531 TAAAAGTATTAGGGATAG
1 TAAAAGTATTAGGGATAG
380549 AGATAGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (19 bp):
TAAAAGTATTAGGGATAGG
Found at i:408570 original size:17 final size:18
Alignment explanation
Indices: 408550--408656 Score: 53
Period size: 18 Copynumber: 6.1 Consensus size: 18
408540 AATAAATATA
* *
408550 TTTATTTTTTAAAT-TTT
1 TTTAATTTTAAAATATTT
408567 TTTAATTTTAAAATATTT
1 TTTAATTTTAAAATATTT
* * ** *
408585 TTCAA--AT-ACTTTTTT
1 TTTAATTTTAAAATATTT
408600 TTTAATTTTAAAATATTT
1 TTTAATTTTAAAATATTT
** **
408618 TAAAATACTTTTTAAT-TTT
1 TTTAAT--TTTAAAATATTT
*
408637 TTTATTTTTAAAATATTT
1 TTTAATTTTAAAATATTT
408655 TT
1 TT
408657 AAAATACTTT
Statistics
Matches: 62, Mismatches: 21, Indels: 13
0.65 0.22 0.14
Matches are distributed among these distances:
15 9 0.15
16 1 0.02
17 19 0.31
18 21 0.34
19 6 0.10
20 6 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAATTTTAAAATATTT
Found at i:408586 original size:11 final size:11
Alignment explanation
Indices: 408572--408668 Score: 59
Period size: 11 Copynumber: 9.4 Consensus size: 11
408562 ATTTTTTTAA
408572 TTTTAAAATAT
1 TTTTAAAATAT
*
408583 TTTTCAAATACT
1 TTTTAAAATA-T
*** *
408595 TTTT-TTTTAA
1 TTTTAAAATAT
408605 TTTTAAAATA-
1 TTTTAAAATAT
408615 TTTTAAAATACT
1 TTTTAAAATA-T
408627 TTTT--AAT-T
1 TTTTAAAATAT
408635 TTTT----TAT
1 TTTTAAAATAT
408642 TTTTAAAATAT
1 TTTTAAAATAT
408653 TTTTAAAATACT
1 TTTTAAAATA-T
408665 TTTT
1 TTTT
408669 TAATTTTTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
6 1 0.01
7 5 0.07
8 5 0.07
10 17 0.25
11 26 0.38
12 14 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:408688 original size:20 final size:20
Alignment explanation
Indices: 408651--408689 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
408641 TTTTTAAAAT
**
408651 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATAAATTTTTA
408671 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
408690 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTTA
Found at i:408696 original size:22 final size:20
Alignment explanation
Indices: 408650--408707 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
408640 ATTTTTAAAA
*
408650 TATTTTTAAAAT-ACTTTTT
1 TATTTTTAAAATAAATTTTT
408669 TAATTTTTAAAATAAATTTTT
1 T-ATTTTTAAAATAAATTTTT
408690 GGTATTTATTAAAA-AAAT
1 --TATTT-TTAAAATAAAT
408708 GAGCCCGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 1 0.03
20 11 0.33
21 6 0.18
22 8 0.24
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTTTAAAATAAATTTTT
Found at i:408750 original size:16 final size:16
Alignment explanation
Indices: 408710--408751 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
408700 AAAAAAATGA
408710 GCCCGGCCCAAACTCG
1 GCCCGGCCCAAACTCG
* *
408726 GCCCAGCCCAAATTCG
1 GCCCGGCCCAAACTCG
*
408742 GCCTGGCCCA
1 GCCCGGCCCA
408752 GCCCATGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.19, C:0.48, G:0.24, T:0.10
Consensus pattern (16 bp):
GCCCGGCCCAAACTCG
Found at i:409233 original size:21 final size:20
Alignment explanation
Indices: 409207--409271 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 20
409197 GTGTATCTTA
*
409207 TTTTAACATACAAAGACTATT
1 TTTTAACATA-AAAGACTAAT
*
409228 TTTTAACAATAAAAATGAATAAT
1 TTTTAAC-AT-AAAA-GACTAAT
409251 TTTTAACA-AAAAGACTAAT
1 TTTTAACATAAAAGACTAAT
409270 TT
1 TT
409272 GATCTTTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 8 0.21
20 4 0.11
21 7 0.18
22 6 0.16
23 13 0.34
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (20 bp):
TTTTAACATAAAAGACTAAT
Found at i:416616 original size:16 final size:16
Alignment explanation
Indices: 416597--416627 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
416587 AATCATTCGA
416597 TTTGAATATTATTAAG
1 TTTGAATATTATTAAG
*
416613 TTTGAATTTTATTAA
1 TTTGAATATTATTAA
416628 TTCGATCAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
TTTGAATATTATTAAG
Found at i:417549 original size:20 final size:21
Alignment explanation
Indices: 417524--417563 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
417514 CGAGTGCATG
417524 AAAATCCAAAAAT-TTAATAT
1 AAAATCCAAAAATATTAATAT
* *
417544 AAAATCTAATAATATTAATA
1 AAAATCCAAAAATATTAATA
417564 CACACAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATCCAAAAATATTAATAT
Found at i:423803 original size:22 final size:21
Alignment explanation
Indices: 423773--423813 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
423763 TTTTGTGAAC
*
423773 TTTTTATATGTTTTAATTTTTA
1 TTTTGATAT-TTTTAATTTTTA
*
423795 TTTTGATATTTTTTATTTT
1 TTTTGATATTTTTAATTTT
423814 CATAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTTGATATTTTTAATTTTTA
Found at i:423807 original size:15 final size:15
Alignment explanation
Indices: 423786--423824 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
423776 TTATATGTTT
*
423786 TAATTTTTATTTTGA
1 TAATTTTTATTTTCA
*
423801 TATTTTTTATTTTCA
1 TAATTTTTATTTTCA
423816 TAATTTTTA
1 TAATTTTTA
423825 AATTATTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (15 bp):
TAATTTTTATTTTCA
Found at i:425156 original size:25 final size:25
Alignment explanation
Indices: 425105--425158 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
425095 TCATTATGCC
** *
425105 AATTTTAAATAAAAATAGTTTTGAA
1 AATTTTAAATAAAAATAAATATGAA
425130 AATTTTAAATAAAAATTAAATAT-AA
1 AATTTTAAATAAAAA-TAAATATGAA
425155 AATT
1 AATT
425159 ATAGGGCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
AATTTTAAATAAAAATAAATATGAA
Found at i:430563 original size:22 final size:22
Alignment explanation
Indices: 430529--430572 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
430519 TTAACAACTT
*
430529 AATGACTTAAATAAATTTTTTTA
1 AATGACTTAAAT-AATTATTTTA
*
430552 AATGA-TTTAATAATTATTTTA
1 AATGACTTAAATAATTATTTTA
430573 TAATTTTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 5 0.26
23 5 0.26
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
AATGACTTAAATAATTATTTTA
Found at i:437810 original size:23 final size:22
Alignment explanation
Indices: 437764--437810 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
437754 TTTCTTTCAA
* **
437764 TTGTTTTTTTTGGTGATATTGT
1 TTGTTTTTTTTGGTGAGAAAGT
437786 TTGTTTTTTTTGGTTGAGAAAGT
1 TTGTTTTTTTTGG-TGAGAAAGT
437809 TT
1 TT
437811 TGATATTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.13, C:0.00, G:0.23, T:0.64
Consensus pattern (22 bp):
TTGTTTTTTTTGGTGAGAAAGT
Found at i:445281 original size:14 final size:14
Alignment explanation
Indices: 445256--445283 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
445246 AATTATTTTC
445256 TTACAAATATTATG
1 TTACAAATATTATG
445270 TTACAAATATTATG
1 TTACAAATATTATG
445284 AGGGCACGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TTACAAATATTATG
Found at i:453653 original size:2 final size:2
Alignment explanation
Indices: 453646--453699 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
453636 AGACATATTC
*
453646 AT AT AT AT AT AT AT A- AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
453687 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
453700 ATTATAATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:455382 original size:41 final size:41
Alignment explanation
Indices: 455254--455383 Score: 156
Period size: 41 Copynumber: 3.2 Consensus size: 41
455244 TCTGATTTAT
* * * * *
455254 TGCCAGTGAAATAATTCAGACTTTATGTCTAGCAGGCTTTA
1 TGCCGGTGAAATTATTCAGACTATAAGTCTAGCAGGCTTAA
*
455295 TGCCGGTGAAATTATTCAGACTATACGTCTAGCAGGCTTAA
1 TGCCGGTGAAATTATTCAGACTATAAGTCTAGCAGGCTTAA
*
455336 TGCCGGTGATACA-T-TTCAGACTATAAGTCTAGCAGGCTAAA
1 TGCCGGTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAA
*
455377 AGCCGGT
1 TGCCGGT
455384 CTACCGAATC
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
41 76 0.96
42 2 0.03
43 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (41 bp):
TGCCGGTGAAATTATTCAGACTATAAGTCTAGCAGGCTTAA
Found at i:455586 original size:13 final size:13
Alignment explanation
Indices: 455570--455594 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
455560 ATATTAAATA
455570 TATATGCATTTGG
1 TATATGCATTTGG
455583 TATATGCATTTG
1 TATATGCATTTG
455595 ATAAGCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
TATATGCATTTGG
Found at i:455613 original size:2 final size:2
Alignment explanation
Indices: 455606--455672 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
455596 TAAGCAATTG
*
455606 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
455648 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
455673 ATAGTTTACA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:458061 original size:20 final size:20
Alignment explanation
Indices: 458022--458063 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
458012 ATGTTAGAGT
*
458022 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
458042 TAATATAGTCAAAACTGTTG
1 TAATATAGTCAAAACAGTTG
458062 TA
1 TA
458064 CCGTTGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:458092 original size:15 final size:15
Alignment explanation
Indices: 458072--458102 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
458062 TACCGTTGTA
458072 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
458087 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
458102 A
1 A
458103 AAGATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:462780 original size:20 final size:20
Alignment explanation
Indices: 462741--462782 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
462731 ATGTTAGAGT
*
462741 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
462761 TAATATAGTCAAAACTGTTG
1 TAATATAGTCAAAACAGTTG
462781 TA
1 TA
462783 CCGTTGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:462811 original size:15 final size:15
Alignment explanation
Indices: 462791--462821 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
462781 TACCGTTGTA
462791 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
462806 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
462821 A
1 A
462822 AAGATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:470196 original size:9 final size:9
Alignment explanation
Indices: 470182--470213 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
470172 AACTTGGTGC
470182 ATTTTGTTT
1 ATTTTGTTT
470191 ATTTTGTTT
1 ATTTTGTTT
470200 ATTTTGTTT
1 ATTTTGTTT
470209 ATTTT
1 ATTTT
470214 TAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:470294 original size:23 final size:23
Alignment explanation
Indices: 470264--470315 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
470254 TGCAACTTGG
470264 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
470287 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
470310 TTTCAT
1 TTTCAT
470316 CTTTTGCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:470327 original size:59 final size:59
Alignment explanation
Indices: 470264--470379 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 59
470254 TGCAACTTGG
*
470264 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTATAATGCTTTCATCTTTTGC
1 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTTGC
* * *
470323 TTTCATAATCATAGCTAATATGCTTTCATAATGGTAGTTACAATGCTTTCATCTTTT
1 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTT
470380 TAATTATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (59 bp):
TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTTGC
Found at i:471847 original size:21 final size:23
Alignment explanation
Indices: 471803--471847 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
471793 AATAAGCCAG
*
471803 ATAATATATCCAAATATTCGAATA
1 ATAATATATCCAAAGATTC-AATA
471827 ATAA-ATATCCAAAGATT-AATA
1 ATAATATATCCAAAGATTCAATA
471848 TCTGTATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (23 bp):
ATAATATATCCAAAGATTCAATA
Found at i:474410 original size:44 final size:44
Alignment explanation
Indices: 474347--474435 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
474337 TGAAGATAAG
474347 TGGCATTGTAAAGAACGTTTACATTACGAGAAAGATAACTTACT
1 TGGCATTGTAAAGAACGTTTACATTACGAGAAAGATAACTTACT
474391 TGGCATTGTAAAGAACGTTTACATTACGAGAAAGATAACTTACT
1 TGGCATTGTAAAGAACGTTTACATTACGAGAAAGATAACTTACT
474435 T
1 T
474436 CAGTAGATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (44 bp):
TGGCATTGTAAAGAACGTTTACATTACGAGAAAGATAACTTACT
Found at i:483742 original size:22 final size:24
Alignment explanation
Indices: 483716--483759 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
483706 GAAAAATATT
483716 AAATAT-AT-ATTTTTTATTTTTA
1 AAATATAATAATTTTTTATTTTTA
483738 AAATATAATAATTTTTTATTTT
1 AAATATAATAATTTTTTATTTT
483760 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 2 0.10
24 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
AAATATAATAATTTTTTATTTTTA
Found at i:483870 original size:9 final size:9
Alignment explanation
Indices: 483856--483883 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
483846 TTTTGTTACA
483856 ACAATTAAT
1 ACAATTAAT
483865 ACAATTAAT
1 ACAATTAAT
483874 ACAATTAAT
1 ACAATTAAT
483883 A
1 A
483884 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:483905 original size:68 final size:68
Alignment explanation
Indices: 483826--484035 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
483816 TCAAATTTGT
*
483826 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
483891 AAA
66 AAA
483894 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
483959 AAA
66 AAA
483962 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
484025 AAT
66 AAA
484028 TTTACTAA
1 TTTACTAA
484036 CAATTAATTT
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 27 0.19
67 1 0.01
68 112 0.80
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:483936 original size:9 final size:9
Alignment explanation
Indices: 483924--483951 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
483914 TTTTATTACA
483924 ACAATTAAT
1 ACAATTAAT
483933 ACAATTAAT
1 ACAATTAAT
483942 ACAATTAAT
1 ACAATTAAT
483951 A
1 A
483952 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:484045 original size:16 final size:16
Alignment explanation
Indices: 484024--484065 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
484014 AATAATTTGA
*
484024 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
484040 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
484056 TAGTTTTAAT
1 TAATTTTAAT
484066 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:484049 original size:22 final size:22
Alignment explanation
Indices: 484039--484093 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
484029 TTACTAACAA
* * *
484039 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
484061 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
484083 TTAATTTTAAT
1 TTAATTTTAAT
484094 TTTAATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:484087 original size:6 final size:6
Alignment explanation
Indices: 484078--484106 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
484068 TATTAAAAAA
484078 TAATTT TAATTT TAATTT TAATTT TAATT
1 TAATTT TAATTT TAATTT TAATTT TAATT
484107 AAAAACGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TAATTT
Found at i:494596 original size:2 final size:2
Alignment explanation
Indices: 494589--494634 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
494579 CTCATTTCGG
494589 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
494631 TA TA
1 TA TA
494635 ACAAACTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:504205 original size:30 final size:30
Alignment explanation
Indices: 504169--504230 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
504159 AGGGGGAGGC
*
504169 GGCATTCCAGGGCGTGGGGGTGGTGGAGCA
1 GGCATTCCAGGGCGTGGGGGTGGTGGACCA
*
504199 GGCATTCCAGGGCGTGGTGGTGGTGGACCA
1 GGCATTCCAGGGCGTGGGGGTGGTGGACCA
504229 GG
1 GG
504231 AGGTCCTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.13, C:0.18, G:0.52, T:0.18
Consensus pattern (30 bp):
GGCATTCCAGGGCGTGGGGGTGGTGGACCA
Found at i:509313 original size:26 final size:27
Alignment explanation
Indices: 509275--509326 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
509265 AATGAGTAGA
* *
509275 TTTGAATACAAAAGA-AGAGAAAAAGC
1 TTTGAATAAAAAAAAGAGAGAAAAAGC
509301 TTTGAATAAAAAAAAGAGAGAAAAAG
1 TTTGAATAAAAAAAAGAGAGAAAAAG
509327 AGGTGATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.62, C:0.04, G:0.19, T:0.15
Consensus pattern (27 bp):
TTTGAATAAAAAAAAGAGAGAAAAAGC
Found at i:517659 original size:18 final size:19
Alignment explanation
Indices: 517625--517666 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
517615 ATCACATGTT
*
517625 TAAAATGAAAAT-TAAAAA
1 TAAAATGAAAATGAAAAAA
517643 TAAAAT-AAAATCGAAAAAA
1 TAAAATGAAAAT-GAAAAAA
517662 TAAAA
1 TAAAA
517667 ATGCGCTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 6 0.29
19 10 0.48
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (19 bp):
TAAAATGAAAATGAAAAAA
Found at i:528188 original size:6 final size:6
Alignment explanation
Indices: 528177--528207 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
528167 TTTCACTTAG
528177 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT A
1 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT A
528208 ATTTAACGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (6 bp):
ATTTGT
Found at i:531250 original size:3 final size:3
Alignment explanation
Indices: 531242--531270 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
531232 CCTAGTTGTT
531242 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
531271 TTTTCAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:536409 original size:45 final size:45
Alignment explanation
Indices: 536358--536448 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
536348 TTTTGCTCTT
536358 ATGCTTTGAATGATCATATATTTACCTACAGTTGATGATAAGACA
1 ATGCTTTGAATGATCATATATTTACCTACAGTTGATGATAAGACA
536403 ATGCTTTGAATGATCATATATTTACCTACAGTTGATGATAAGACA
1 ATGCTTTGAATGATCATATATTTACCTACAGTTGATGATAAGACA
536448 A
1 A
536449 AAGAGGGCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (45 bp):
ATGCTTTGAATGATCATATATTTACCTACAGTTGATGATAAGACA
Done.