Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold312
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: 1822960
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 12
Found at i:214810 original size:61 final size:60
Alignment explanation
Indices: 214698--215257 Score: 571
Period size: 61 Copynumber: 9.4 Consensus size: 60
214688 AGGAGAGAGG
* ** *
214698 GAAAATGCGTCCTGCTCTTTGAGGACTAAAAAGTGTCCACCAACTCGTGTGGGCTTTGAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTG-CCACCAACTTGTGTGGGCTTT-AAAA
* * * * *
214760 GAAAAGGCATCTTGCTTTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * * *
214821 GAGAAA-GCATCTTGCTTTTTGAGGACTGGAAGGTGCCACCAACTTGTGTTGGCTTTAAAA
1 GA-AAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* * * *
214881 GGAAAAGGCTTCCTACTCTTTGAGGACT-AAAAGTGCCACCAACTTATGTGGGCTTTAAAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * * *
214942 GAAAAGGCGTCCTGCTCTTGGAGGACTAGAAGGTGCTACCAACTTGTGTGGGCTTTAGAAG
1 GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTA-AAA
* * * *
215003 GAAAAGGCATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCATTGTATGGGCTTT----
1 GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAAC-TTGTGTGGGCTTTAAAA
* *
215059 G-AAAGGCGTCATGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTTAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGC-TTTAAAA
* * *
215119 GGAAAAGGCTGTCCTGCTCTTTGAGGACTGAAAAGTACCACCAACTTATGTGGGCTTT----
1 -GAAAAGGC-GTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* * *
215177 G-AAAGGCGTCTTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT----
1 GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
*
215232 G-AAAGGCATCCTGCTCTTTGAGGACT
1 GAAAAGGCGTCCTGCTCTTTGAGGACT
215258 AAAGGGTGAA
Statistics
Matches: 433, Mismatches: 49, Indels: 39
0.83 0.09 0.07
Matches are distributed among these distances:
55 100 0.23
56 22 0.05
57 1 0.00
60 68 0.16
61 162 0.37
62 40 0.09
63 40 0.09
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (60 bp):
GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
Found at i:214935 original size:182 final size:181
Alignment explanation
Indices: 214697--215257 Score: 638
Period size: 182 Copynumber: 3.2 Consensus size: 181
214687 AAGGAGAGAG
* * * *
214697 GGAAAATGCGTCCTGCTCTTTGAGGACTAAAAAGTGTCCACCAACTCGTGTGGGCTTTGAAAAGA
1 GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTG-CCACCAACTTGTGTGGGCTTTAAAAAGA
* * *
214762 AAAGGCATCTTGCTTTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA
65 AAAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGAGAAA
* *
214827 GCATCTTGCTTTTTGAGGACTGGAAGGTGCCACCAACTTGTGTTGGCTTTAAAA
129 GCATCTTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AAA
* * *
214881 GGAAAAGGCTTCCTACTCTTTGAGGACT-AAAAGTGCCACCAACTTATGTGGGCTTTAAAAAGAA
1 GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAA
* * * *
214945 AAGGCGTCCTGCTCTTGGAGGACTAGAAGGTGCTACCAACTTGTGTGGGCTTTAGAAGGA-AAAG
66 AAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-GAAAGAGAAA-
* * *
215009 GCATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCATTGTATGGGCTTT---
129 GCATCTTGCTCTTTGAGGACTGGAAGGTGCCACCAAC-TTGTGTGGGCTTTAAA
* *
215059 -G-AAAGGCGTCATGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTTAAAAGG
1 GGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGC-TTTAAAAAG
* * * *
215121 AAAAGGCTGTCCTGCTCTTTGAGGACTGAAAAGTACCACCAACTTATGTGGGCTTTG-AA-AG--
64 AAAAGGC-GTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAA
* * **
215182 -GCGTCTTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT---
128 AGCATCTTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAA
*
215232 -G-AAAGGCATCCTGCTCTTTGAGGACT
1 GGAAAAGGCGTCCTGCTCTTTGAGGACT
215258 AAAGGGTGAA
Statistics
Matches: 328, Mismatches: 40, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
173 55 0.17
174 11 0.03
176 23 0.07
177 21 0.06
178 20 0.06
179 41 0.12
181 17 0.05
182 107 0.33
183 8 0.02
184 25 0.08
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (181 bp):
GGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAA
AAGGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAAGC
ATCTTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAA
Found at i:214966 original size:121 final size:117
Alignment explanation
Indices: 214698--215257 Score: 620
Period size: 121 Copynumber: 4.8 Consensus size: 117
214688 AGGAGAGAGG
* ** *
214698 GAAAATGCGTCCTGCTCTTTGAGGACTAAAAAGTGTCCACCAACTCGTGTGGGCTTTGAAAA-GA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTG-CCACCAACTTGTGTGGGCTTT-AAAAGGA
* * * * *
214762 AAAGGCATCTTGCTTTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT
64 AAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTATGTGGGCTTT
* * * * *
214816 GCAAAGAGAAAGCATCTTGCTTTTTGAGGACTGGAAGGTGCCACCAACTTGTGTTGGCTTTAAAA
1 G-AAA-AG---GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* *
214881 GGAAAAGGCTTCCTACTCTTTGAGGACT-AAAAGTGCCACCAACTTATGTGGGCTTT
61 GGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTATGTGGGCTTT
* * * * *
214937 AAAAAGAAAAGGCGTCCTGCTCTTGGAGGACTAGAAGGTGCTACCAACTTGTGTGGGCTTTAGAA
1 -----GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* * * *
215002 GGAAAAGGCATCCTGCTCTTTGAGGACTG-AAGGTGCCACCAGCATTGTATGGGCTTT
61 GGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAAC-TTATGTGGGCTTT
* *
215059 G-AAAGGCGTCATGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTTAAAAGGAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGC-TTTAAAAGGAA
* *
215123 AAGGCTGTCCTGCTCTTTGAGGACTGAAAAGTACCACCAACTTATGTGGGCTTT
65 AAGGC-ATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTATGTGGGCTTT
* * *
215177 G-AAAGGCGTCTTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-----G-AA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
215235 AGGCATCCTGCTCTTTGAGGACT
66 AGGCATCCTGCTCTTTGAGGACT
215258 AAAGGGTGAA
Statistics
Matches: 380, Mismatches: 46, Indels: 40
0.82 0.10 0.09
Matches are distributed among these distances:
110 18 0.05
111 6 0.02
112 1 0.00
116 45 0.12
117 19 0.05
118 81 0.21
119 14 0.04
120 1 0.00
121 113 0.30
122 53 0.14
123 23 0.06
124 2 0.01
125 3 0.01
126 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (117 bp):
GAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
AGGCATCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTATGTGGGCTTT
Found at i:215074 original size:55 final size:54
Alignment explanation
Indices: 214833--215261 Score: 374
Period size: 55 Copynumber: 7.4 Consensus size: 54
214823 GAAAGCATCT
* * * *
214833 TGCTTTTTGAGGACTGGAAGGTGCCACCAACTTGTGTTGGCTTTAAAAGGAAAAGGCTTCC
1 TGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCC
* * *
214894 TACTCTTTGAGGACTAAAAGTGCCACCAACTTATGTGGGCTTTAAAAAGAAAAGGCGTCC
1 TGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCC
* * * *
214954 TGCTCTTGGAGGACTAGAAGGTGCTACCAACTTGTGTGGGCTTTAGAAGGAAAAGGCATCC
1 TGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCC
* * * *
215015 TGCTCTTTGAGGACTGAAGGTGCCACCAGCATTGTATGGGCTTTGAAAGGCGTCA
1 TGCTCTTTGAGGACTGAAAGTGCCACCAAC-TTGTGTGGGCTTTGAAAGGCGTCC
*
215070 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTTAAAAGGAAAAGGCTGTCC
1 TGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGC-TTT-----G-AAAGGC-GTCC
* * *
215133 TGCTCTTTGAGGACTGAAAAGTACCACCAACTTATGTGGGCTTTGAAAGGCGTCT
1 TGCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
* *
215188 TGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCATCC
1 TGCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
215243 TGCTCTTTGAGGACT-AAAG
1 TGCTCTTTGAGGACTGAAAG
215262 GGTGAAAGGA
Statistics
Matches: 318, Mismatches: 38, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
53 3 0.01
55 100 0.31
56 22 0.07
57 1 0.00
60 65 0.20
61 78 0.25
62 10 0.03
63 39 0.12
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (54 bp):
TGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
Found at i:216353 original size:13 final size:12
Alignment explanation
Indices: 216337--216397 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
216327 CTTTTCTCTC
216337 TTTTTTTTATTGT
1 TTTTTTTTATT-T
* *
216350 TTTTTGTTGTTT
1 TTTTTTTTATTT
*
216362 TTTTGTTTTGTTT
1 TTTT-TTTTATTT
*
216375 TTTTGTTTTTTTGT
1 TTTT-TTTTATT-T
216389 TTTTTTTTA
1 TTTTTTTTA
216398 AAAAAGAAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
12 5 0.12
13 31 0.76
14 5 0.12
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.85
Consensus pattern (12 bp):
TTTTTTTTATTT
Found at i:216394 original size:8 final size:8
Alignment explanation
Indices: 216340--216394 Score: 69
Period size: 8 Copynumber: 6.9 Consensus size: 8
216330 TTCTCTCTTT
216340 TTTTTATTG
1 TTTTT-TTG
216349 -TTTTTTG
1 TTTTTTTG
216356 TTGTTTTT-
1 TT-TTTTTG
*
216364 TTGTTTTG
1 TTTTTTTG
216372 TTTTTTTG
1 TTTTTTTG
216380 TTTTTTTG
1 TTTTTTTG
216388 TTTTTTT
1 TTTTTTT
216395 TTAAAAAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
7 7 0.17
8 29 0.71
9 5 0.12
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (8 bp):
TTTTTTTG
Found at i:216396 original size:21 final size:21
Alignment explanation
Indices: 216338--216396 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
216328 TTTTCTCTCT
* *
216338 TTTTTTTATTGTTTTTTGTTG
1 TTTTTTTGTTTTTTTTTGTTG
216359 TTTTTTTGTTTTGTTTTT-TTG
1 TTTTTTTGTTTT-TTTTTGTTG
216380 TTTTTTTGTTTTTTTTT
1 TTTTTTTGTTTTTTTTT
216397 AAAAAAGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 5 0.14
21 25 0.71
22 5 0.14
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (21 bp):
TTTTTTTGTTTTTTTTTGTTG
Found at i:220932 original size:32 final size:33
Alignment explanation
Indices: 220895--220980 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 33
220885 TTTACCTTTG
*
220895 AGGCTAAGATAGAAACCTCCCTATCTTTTT-AT
1 AGGCTAAGATAGAAACCTCCCTATCTTTTTCAA
* *
220927 GGGCTAAGATAGAACTTCTCTCCCTATCTTTTTCAA
1 AGGCTAAGATAGAA--AC-CTCCCTATCTTTTTCAA
220963 AGGCTAAGATAG-AACCTC
1 AGGCTAAGATAGAAACCTC
220981 TCAATCACTT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
32 16 0.36
33 1 0.02
34 1 0.02
35 15 0.33
36 12 0.27
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.31
Consensus pattern (33 bp):
AGGCTAAGATAGAAACCTCCCTATCTTTTTCAA
Found at i:220975 original size:36 final size:34
Alignment explanation
Indices: 220895--220982 Score: 110
Period size: 36 Copynumber: 2.6 Consensus size: 34
220885 TTTACCTTTG
* *
220895 AGGCTAAGATAGAA-AC-CTCCCTATCTTTTTAT
1 AGGCTAAGATAGAACTCTCTCCCTATCTTTTTAA
*
220927 GGGCTAAGATAGAACTTCTCTCCCTATCTTTTTCAA
1 AGGCTAAGATAGAAC-TCTCTCCCTATCTTTTT-AA
220963 AGGCTAAGATAGAAC-CTCTC
1 AGGCTAAGATAGAACTCTCTC
220983 AATCACTTCG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
32 13 0.27
34 6 0.12
35 14 0.29
36 15 0.31
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (34 bp):
AGGCTAAGATAGAACTCTCTCCCTATCTTTTTAA
Found at i:221468 original size:10 final size:10
Alignment explanation
Indices: 221453--221505 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
221443 GTATCGATAC
221453 ATGAACAGTG
1 ATGAACAGTG
221463 ATGAACAGTG
1 ATGAACAGTG
* *
221473 ATGTATC-GATAC
1 ATG-AACAG-T-G
221485 ATGAACAGTG
1 ATGAACAGTG
221495 ATGAACAGTG
1 ATGAACAGTG
221505 A
1 A
221506 AAATGAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 25 0.71
11 6 0.17
12 4 0.11
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:221482 original size:32 final size:32
Alignment explanation
Indices: 221441--221505 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
221431 ACTATTCACA
221441 ATGTATCGATACATGAACAGTGATGAACAGTG
1 ATGTATCGATACATGAACAGTGATGAACAGTG
221473 ATGTATCGATACATGAACAGTGATGAACAGTG
1 ATGTATCGATACATGAACAGTGATGAACAGTG
221505 A
1 A
221506 AAATGAGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (32 bp):
ATGTATCGATACATGAACAGTGATGAACAGTG
Found at i:221551 original size:13 final size:13
Alignment explanation
Indices: 221533--221557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
221523 TGCTAGTTTT
221533 ATGTATCGATACA
1 ATGTATCGATACA
221546 ATGTATCGATAC
1 ATGTATCGATAC
221558 TAAGCAAAAT
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):
ATGTATCGATACA
Found at i:227065 original size:52 final size:51
Alignment explanation
Indices: 226987--227134 Score: 210
Period size: 52 Copynumber: 2.9 Consensus size: 51
226977 CGAAATATGA
226987 AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCT-GGC
* ** *
227039 AAATTTTCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGC
1 AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTGGC
*
227090 AAATTTGCCCGCATGTATCGATACA--AAGATTAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTAA-A-TAGTGTATCGATACA
227135 ATGTATTGAT
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
50 1 0.01
51 40 0.47
52 44 0.52
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTGGC
Found at i:227230 original size:13 final size:13
Alignment explanation
Indices: 227212--227236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
227202 AAAAAAAATA
227212 TGTATCGATACAT
1 TGTATCGATACAT
227225 TGTATCGATACA
1 TGTATCGATACA
227237 ACATTTTATG
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:228167 original size:55 final size:52
Alignment explanation
Indices: 228067--228359 Score: 213
Period size: 48 Copynumber: 5.9 Consensus size: 52
228057 GAAAAGTGAT
* ** * * *
228067 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATACTGATTCAAGGCCAACTATATTGGACTTAAAGATG-G-A
* * * *
228121 AAAGGATGTCAATGTACTGATTCAAGGCCAACTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATACTGATTCAAGGCCAACTATATTGGACTTAAAGATGGA
* *
228174 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATACTGATTCAAGGCCAACTATATTGGACTTAAAGATGGA
* * * * * *
228217 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATAT-G-
1 AAAGGTGCCAATATACTGATTCAAGGCCAACTATATTGGACTTAAAGATGGA
* * * *
228267 -AAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT-AA-A-GG-
1 AAAGGTGCCAATATACTGATTCAAGGCCAACTATATTGGACTTAAAGATGGA
* * * *
228314 CAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 AAAGGTGCCAATATACTGATTCAAGGCCAACTATATTGGACTTAAA
228360 AGGAGACGCC
Statistics
Matches: 201, Mismatches: 27, Indels: 27
0.79 0.11 0.11
Matches are distributed among these distances:
43 38 0.19
44 1 0.00
46 1 0.00
47 2 0.01
48 41 0.20
49 40 0.20
51 1 0.00
52 30 0.15
53 6 0.03
54 5 0.02
55 36 0.18
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (52 bp):
AAAGGTGCCAATATACTGATTCAAGGCCAACTATATTGGACTTAAAGATGGA
Found at i:228235 original size:43 final size:43
Alignment explanation
Indices: 228174--228359 Score: 219
Period size: 43 Copynumber: 4.1 Consensus size: 43
228164 TAAAGATGGA
228174 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
228217 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T---T
* *
228264 ATGAAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT
1 A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
228309 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTT
1 --A---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
228357 AAA
1 AAA
228360 AGGAGACGCC
Statistics
Matches: 121, Mismatches: 13, Indels: 18
0.80 0.09 0.12
Matches are distributed among these distances:
43 40 0.33
44 1 0.01
45 1 0.01
46 1 0.01
47 3 0.02
48 40 0.33
49 35 0.29
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:228302 original size:92 final size:95
Alignment explanation
Indices: 228120--228359 Score: 306
Period size: 97 Copynumber: 2.5 Consensus size: 95
228110 AAAGATGAGA
* * * *
228120 AAAAGGATGTCAATGTACTGATTCAAGGCCAACTACATTGAACTTAAAGATGGAAAAGGTGCCAA
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG-AAAGGTGCCAA
*
228185 TATGCTGATTCAAGGCCAGCTATATTGGACTT
64 TATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
228217 -AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATAT-G-AAGGTGCCAATA
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATA
*
228279 TGCTGATTTAAGGCCAGCGATATTGGACTT
66 TGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
228309 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 -AA---AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
228360 AGGAGACGCC
Statistics
Matches: 126, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
92 40 0.32
94 2 0.02
95 38 0.30
96 5 0.04
97 41 0.33
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (95 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATA
TGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:228487 original size:30 final size:29
Alignment explanation
Indices: 228407--228502 Score: 133
Period size: 28 Copynumber: 3.3 Consensus size: 29
228397 TTGCATCAAA
* *
228407 TTGTGTGCTTTTG-AAGGTTGCTACTGAC
1 TTGTGGGCTTTTGAAAGGTTGCCACTGAC
228435 TTGTGGGCTTTT-AAAGGTTGCCACTGAC
1 TTGTGGGCTTTTGAAAGGTTGCCACTGAC
* *
228463 TTGTGGGCTTTTGAAAAGGGTGCCACTAAC
1 TTGTGGGCTTTTG-AAAGGTTGCCACTGAC
228493 TTGTGGGCTT
1 TTGTGGGCTT
228503 AAAAAGAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
28 37 0.61
30 24 0.39
ACGTcount: A:0.17, C:0.16, G:0.30, T:0.38
Consensus pattern (29 bp):
TTGTGGGCTTTTGAAAGGTTGCCACTGAC
Found at i:228563 original size:35 final size:34
Alignment explanation
Indices: 228476--228566 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 34
228466 TGGGCTTTTG
* * *
228476 AAAAGGGTGCCACTA-ACTTGTGGGCTTAAAAAGA
1 AAAAGAGTGCCAC-AGAGTTGTGAGCTTAAAAAGA
* * *
228510 AAAATAGTGCTATAGAGTTGTGAGCTTACAAAAGA
1 AAAAGAGTGCCACAGAGTTGTGAGCTTA-AAAAGA
*
228545 AAAAGAGTGCCACGGAGTTGTG
1 AAAAGAGTGCCACAGAGTTGTG
228567 GACTTTGGAA
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
33 1 0.02
34 20 0.44
35 24 0.53
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.22
Consensus pattern (34 bp):
AAAAGAGTGCCACAGAGTTGTGAGCTTAAAAAGA
Found at i:228580 original size:30 final size:30
Alignment explanation
Indices: 228545--228632 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 30
228535 TTACAAAAGA
* *
228545 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGAGTGCCACCGACTTGTGGACTTTGG
* *
228575 AAAAGA-TGCCACCGACTTGTGGGCTTCGG
1 AAAAGAGTGCCACCGACTTGTGGACTTTGG
* * * *
228604 AAAAGGGTGCCACTGATTTGTGGTCTTTG
1 AAAAGAGTGCCACCGACTTGTGGACTTTG
228633 ATGGGTGAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
29 24 0.50
30 24 0.50
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (30 bp):
AAAAGAGTGCCACCGACTTGTGGACTTTGG
Found at i:228594 original size:29 final size:29
Alignment explanation
Indices: 228545--228632 Score: 86
Period size: 30 Copynumber: 3.0 Consensus size: 29
228535 TTACAAAAGA
* *
228545 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACCGACTTGTGGACTTTGG
* *
228575 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACCGACTTGTGGACTTTGG
* * * *
228604 AAAAGGGTGCCACTGATTTGTGGTCTTTG
1 AAAA-GATGCCACCGACTTGTGGACTTTG
228633 ATGGGTGAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
29 23 0.48
30 25 0.52
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (29 bp):
AAAAGATGCCACCGACTTGTGGACTTTGG
Found at i:229743 original size:10 final size:10
Alignment explanation
Indices: 229728--229801 Score: 91
Period size: 10 Copynumber: 7.5 Consensus size: 10
229718 ATCCGGACCT
229728 TTTTTTTTTG
1 TTTTTTTTTG
229738 -TTTTTTTTG
1 TTTTTTTTTG
*
229747 TTTTTTTAT-
1 TTTTTTTTTG
*
229756 ATTTTTTTTG
1 TTTTTTTTTG
229766 TTTTTTTTTTG
1 -TTTTTTTTTG
229777 TTTTTTTTTG
1 TTTTTTTTTG
229787 TTTTGTTTTT-
1 TTTT-TTTTTG
229797 TTTTT
1 TTTTT
229802 GTGTTTTTGT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
9 17 0.30
10 25 0.45
11 14 0.25
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:229743 original size:11 final size:11
Alignment explanation
Indices: 229727--229811 Score: 79
Period size: 11 Copynumber: 7.8 Consensus size: 11
229717 CATCCGGACC
229727 TTTTTTT-TTT
1 TTTTTTTGTTT
* *
229737 GTTTTTT-TTG
1 TTTTTTTGTTT
* *
229747 TTTTTTTATAT
1 TTTTTTTGTTT
229758 TTTTTTTGTTT
1 TTTTTTTGTTT
229769 TTTTTTTG-TT
1 TTTTTTTGTTT
229779 TTTTTTTGTTT
1 TTTTTTTGTTT
229790 TGTTTTTT-TTT
1 T-TTTTTTGTTT
229801 TGTGTTTTTGT
1 T-T-TTTTTGT
229812 GGAGGACGCC
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
10 24 0.38
11 27 0.43
12 11 0.17
13 1 0.02
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.87
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:229781 original size:39 final size:39
Alignment explanation
Indices: 229727--229809 Score: 125
Period size: 39 Copynumber: 2.1 Consensus size: 39
229717 CATCCGGACC
*
229727 TTTTTTTTTTG-TTTTTTTTGTTTT-TTTATATTTTTTTTG
1 TTTTTTTTTTGTTTTTTTTTGTTTTGTTT-T-TTTTTTGTG
229766 TTTTTTTTTTGTTTTTTTTTGTTTTGTTTTTTTTTTGTG
1 TTTTTTTTTTGTTTTTTTTTGTTTTGTTTTTTTTTTGTG
229805 TTTTT
1 TTTTT
229810 GTGGAGGACG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
39 24 0.59
40 14 0.34
41 3 0.07
ACGTcount: A:0.02, C:0.00, G:0.10, T:0.88
Consensus pattern (39 bp):
TTTTTTTTTTGTTTTTTTTTGTTTTGTTTTTTTTTTGTG
Found at i:229809 original size:1 final size:1
Alignment explanation
Indices: 229727--229801 Score: 78
Period size: 1 Copynumber: 75.0 Consensus size: 1
229717 CATCCGGACC
* * * * * * * *
229727 TTTTTTTTTTGTTTTTTTTGTTTTTTTATATTTTTTTTGTTTTTTTTTTGTTTTTTTTTGTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
229792 TTTTTTTTTT
1 TTTTTTTTTT
229802 GTGTTTTTGT
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.89
Consensus pattern (1 bp):
T
Found at i:229809 original size:10 final size:9
Alignment explanation
Indices: 229729--229799 Score: 92
Period size: 9 Copynumber: 7.9 Consensus size: 9
229719 TCCGGACCTT
229729 TTTTTTTTG
1 TTTTTTTTG
229738 TTTTTTTTG
1 TTTTTTTTG
*
229747 TTTTTTTATA
1 TTTTTTT-TG
229757 TTTTTTTTG
1 TTTTTTTTG
229766 TTTTTTTT-
1 TTTTTTTTG
229774 TTGTTTTTT-
1 TT-TTTTTTG
*
229783 TTTGTTTTG
1 TTTTTTTTG
229792 TTTTTTTT
1 TTTTTTTT
229800 TTGTGTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.13
9 40 0.73
10 8 0.15
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.89
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:229810 original size:19 final size:19
Alignment explanation
Indices: 229738--229811 Score: 80
Period size: 19 Copynumber: 3.9 Consensus size: 19
229728 TTTTTTTTTG
* * *
229738 TTTTTTTTGTTTTTTTATA
1 TTTTTTTTGTGTTTTTGTT
*
229757 TTTTTTTTGT-TTTTTTTT
1 TTTTTTTTGTGTTTTTGTT
*
229775 TGTTTTTTTTTG-TTTTGTT
1 T-TTTTTTTGTGTTTTTGTT
229794 TTTTTTTTGTGTTTTTGT
1 TTTTTTTTGTGTTTTTGT
229812 GGAGGACGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
18 16 0.34
19 31 0.66
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (19 bp):
TTTTTTTTGTGTTTTTGTT
Found at i:248855 original size:78 final size:79
Alignment explanation
Indices: 248710--248884 Score: 210
Period size: 79 Copynumber: 2.2 Consensus size: 79
248700 GGAAAATCGG
* * * *
248710 TGTTCTAGAAATAAAATCAGGGTTGGAGTATCACCTTGATAATAACAAGGTTGGAGTATCCCTGA
1 TGTTCTAGAAATAAAATCAGGGTCGGAGTATCACCTCGAAAATAACAAGGTTGGAGTATCCCCGA
248775 TTGTGAAAAATCAA
66 TTGTGAAAAATCAA
* * **
248789 TGTTCTGGAAATAAAA-CTGGGGTCGGAGTATC-CCTCGAAAATAACGGGGTTGGAGTATCCCCG
1 TGTTCTAGAAATAAAATC-AGGGTCGGAGTATCACCTCGAAAATAACAAGGTTGGAGTATCCCCG
***
248852 ATTGTGAAAAGATTGG
65 ATTGTGAAAA-ATCAA
*
248868 TGTTTTAGAAATAAAAT
1 TGTTCTAGAAATAAAAT
248885 TGGTGTTGAA
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 37 0.46
79 43 0.54
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (79 bp):
TGTTCTAGAAATAAAATCAGGGTCGGAGTATCACCTCGAAAATAACAAGGTTGGAGTATCCCCGA
TTGTGAAAAATCAA
Found at i:251396 original size:49 final size:50
Alignment explanation
Indices: 251333--251466 Score: 198
Period size: 50 Copynumber: 2.7 Consensus size: 50
251323 AAAAATGCCT
* * * *
251333 GAATGTATCAATACATTGAAAAATGTATTGATACATCTAGG-TAAACCCA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTAGGTTAAACCCA
* *
251382 GAATGCATCGATACAATGAACAATGTATCGATACATCTGGGTTAAACCCA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTAGGTTAAACCCA
*
251432 GAATGTATCGATACAATGAACAATGTATCAATACA
1 GAATGTATCGATACAATGAACAATGTATCGATACA
251467 AATTGTGAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
49 35 0.46
50 41 0.54
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (50 bp):
GAATGTATCGATACAATGAACAATGTATCGATACATCTAGGTTAAACCCA
Found at i:252823 original size:81 final size:79
Alignment explanation
Indices: 252686--252975 Score: 296
Period size: 80 Copynumber: 3.6 Consensus size: 79
252676 AGATGATAGA
* * * * *
252686 GTTGGAGTGTCCCCAAAAAATGAAAAATTTGATATTTTAGAAGTTAAAATGAGGTTAGAGTATCC
1 GTTGGAGTATCCCC-AAAGATGGAAAATTTGATGTTTTTGAAG-TAAAATGAGGTTAGAGTATCC
* *
252751 TCTTGAAAATGGTGGG
64 TCTTGAAAATGGCGAG
* * **
252767 GTTGGAGTATCCCCATAGATGGAAAATTTGATGTTTTTGAAAGTAAAATTGGGGTTAGAGTATTT
1 GTTGGAGTATCCCCAAAGATGGAAAATTTGATGTTTTTG-AAGTAAAA-TGAGGTTAGAGTATCC
* * *
252832 TCTCGAAAATAGCAAG
64 TCTTGAAAATGGCGAG
* * * * * *
252848 ATTAGAATATCCCTAAAGAT-GAAAATTTTGATTTTTTTGAAGTAAAAATGAGGTTGGAGTATCC
1 GTTGGAGTATCCCCAAAGATGGAAAA-TTTGATGTTTTTGAAGT-AAAATGAGGTTAGAGTATCC
252912 -CTTCGAAAATGGCGAG
64 TCTT-GAAAATGGCGAG
* *
252928 GTTGGAGTATCCCTAAAGATGGAAAATTTTATGTTTTTGGAAGTAAAA
1 GTTGGAGTATCCCCAAAGATGGAAAATTTGATGTTTTT-GAAGTAAAA
252976 ACGGGATTGG
Statistics
Matches: 170, Mismatches: 32, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
79 2 0.01
80 87 0.51
81 81 0.48
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (79 bp):
GTTGGAGTATCCCCAAAGATGGAAAATTTGATGTTTTTGAAGTAAAATGAGGTTAGAGTATCCTC
TTGAAAATGGCGAG
Found at i:252921 original size:80 final size:81
Alignment explanation
Indices: 252707--252994 Score: 291
Period size: 81 Copynumber: 3.6 Consensus size: 81
252697 CCCAAAAAAT
* * * * * *
252707 GAAAAATTTGATATTTTAGAAGTTAAAATGAGGTTAGAGTATCCTCTT-GAAAATGGTGGGGTTG
1 GAAAATTTTGATTTTTTTGAAGTAAAAATGAGGTTAGAGTATCC-CTTCGAAAATGGCGAGGTTG
* *
252771 GAGTATCCCCATAGATG
65 GAGTATCCCTAAAGATG
* * * ** * * *
252788 GAAAA-TTTGATGTTTTTGAAAGTAAAATTGGGGTTAGAGTAT-TTTCTCGAAAATAGCAAGATT
1 GAAAATTTTGATTTTTTTG-AAGTAAAAATGAGGTTAGAGTATCCCT-TCGAAAATGGCGAGGTT
* *
252851 AGAATATCCCTAAAGAT-
64 GGAGTATCCCTAAAGATG
*
252868 GAAAATTTTGATTTTTTTGAAGTAAAAATGAGGTTGGAGTATCCCTTCGAAAATGGCGAGGTTGG
1 GAAAATTTTGATTTTTTTGAAGTAAAAATGAGGTTAGAGTATCCCTTCGAAAATGGCGAGGTTGG
252933 AGTATCCCTAAAGATG
66 AGTATCCCTAAAGATG
* * *
252949 GAAAATTTT-ATGTTTTTGGAAGTAAAAACG-GGATTGGAGTATCCCT
1 GAAAATTTTGAT-TTTTTTGAAGTAAAAATGAGG-TTAGAGTATCCCT
252995 CTTAATGTTT
Statistics
Matches: 170, Mismatches: 29, Indels: 16
0.79 0.13 0.07
Matches are distributed among these distances:
79 1 0.01
80 70 0.41
81 99 0.58
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33
Consensus pattern (81 bp):
GAAAATTTTGATTTTTTTGAAGTAAAAATGAGGTTAGAGTATCCCTTCGAAAATGGCGAGGTTGG
AGTATCCCTAAAGATG
Found at i:255398 original size:166 final size:167
Alignment explanation
Indices: 255226--255663 Score: 439
Period size: 166 Copynumber: 2.6 Consensus size: 167
255216 TAAATTTTTC
* * *
255226 ATTTTTTCCTTGAAATTTCTC-TATTTTCGA-AATTTAG-AGTTTTCTTCTCCAT-AATCTTTTC
1 ATTTTTTCCTTGAAATTTCCCTTA-TTTCGATAA-TGAGAAGTTTTCTACTCCATAAATCTTTTC
255287 GA-AGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAA
64 GAGAGGA-TTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAA
* * * * *
255351 TTCTGTTTTCAAAAAATGCATTCATTTTCA-CGAGTTTTTAA
128 ATCAGTTCTC-AAAAATGCACTCATTCTCATC-AGTTTTTAA
* * * * *
255392 ATTTTTT-CTTCAAA-TTCCCTTATTTCTATAATGCGAAGTTTTCTACTTCATAAATGTTTTCGA
1 ATTTTTTCCTTGAAATTTCCCTTATTTCGATAATGAGAAGTTTTCTACTCCATAAATCTTTTCGA
* * *
255455 GGGGATTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAATTCATGTTAAATC
66 GAGGATTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATC
*
255520 AGTTCTCAAAAATTCACTCATTCTCATCAGTTTTTAA
131 AGTTCTCAAAAATGCACTCATTCTCATCAGTTTTTAA
* * * * *** *
255557 AGTTTTTCCTTGAAATTTCCTTTTTTTTTCGAAAAACTGAA-TTTTCTAAC-CCATAAATATTTT
1 ATTTTTTCCTTGAAATTTCC--CTTATTTCGATAATGAGAAGTTTTCT-ACTCCATAAATCTTTT
* * ** * *
255620 CGAG-GGGTTTTCTTTGGTTTACAATTTTTATAATTCATCTAATA
63 CGAGAGGATTTTC-TTAGTTTTTAATTTTTAAAATTCATCAAATA
255664 ATGTCATGGA
Statistics
Matches: 227, Mismatches: 33, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
164 11 0.05
165 54 0.24
166 86 0.38
167 14 0.06
168 48 0.21
169 14 0.06
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (167 bp):
ATTTTTTCCTTGAAATTTCCCTTATTTCGATAATGAGAAGTTTTCTACTCCATAAATCTTTTCGA
GAGGATTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATC
AGTTCTCAAAAATGCACTCATTCTCATCAGTTTTTAA
Found at i:256412 original size:10 final size:10
Alignment explanation
Indices: 256397--256442 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
256387 AAGTGGGAAG
256397 AAAAAGAAAA
1 AAAAAGAAAA
256407 AAAAAGGAGAAA
1 AAAAA-GA-AAA
*
256419 AAAAAGAGAA
1 AAAAAGAAAA
256429 AAAAAGAAGAA
1 AAAAAGAA-AA
256440 AAA
1 AAA
256443 TCAAGCCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 14 0.45
11 9 0.29
12 8 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:256419 original size:11 final size:11
Alignment explanation
Indices: 256405--256442 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
256395 AGAAAAAGAA
256405 AAAAAAAGGAG
1 AAAAAAAGGAG
*
256416 AAAAAAAAGAG
1 AAAAAAAGGAG
*
256427 AAAAAAAGAAG
1 AAAAAAAGGAG
256438 AAAAA
1 AAAAA
256443 TCAAGCCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAAAGGAG
Found at i:256419 original size:13 final size:12
Alignment explanation
Indices: 256397--256442 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
256387 AAGTGGGAAG
256397 AAAA-AGAAAAA
1 AAAAGAGAAAAA
256408 AAAAG-GAGAAAA
1 AAAAGAGA-AAAA
256420 AAAAGAGAAAAA
1 AAAAGAGAAAAA
*
256432 AAGA-AGAAAAA
1 AAAAGAGAAAAA
256443 TCAAGCCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 13 0.42
12 16 0.52
13 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAGAGAAAAA
Found at i:256425 original size:22 final size:22
Alignment explanation
Indices: 256397--256442 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
256387 AAGTGGGAAG
*
256397 AAAAAGAAAAAAAAAGGAGAAA
1 AAAAAGAAAAAAAAAGAAGAAA
*
256419 AAAAAGAGAAAAAAAGAAGAAA
1 AAAAAGAAAAAAAAAGAAGAAA
256441 AA
1 AA
256443 TCAAGCCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAGAAGAAA
Found at i:257494 original size:11 final size:11
Alignment explanation
Indices: 257478--257503 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
257468 AAAAATAAAA
257478 AAATAACAAAT
1 AAATAACAAAT
257489 AAATAACAAAT
1 AAATAACAAAT
257500 AAAT
1 AAAT
257504 TCCTTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATAACAAAT
Found at i:260416 original size:20 final size:20
Alignment explanation
Indices: 260391--260511 Score: 100
Period size: 20 Copynumber: 5.8 Consensus size: 20
260381 TTTTACCCAG
260391 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
260411 ATGTATCGATACATTCTATC-
1 ATGTATCGATACATT-TTTCA
* * *
260431 TTTTACCCAGATGTATCAATTTTTCA
1 ATGTA-TC-GA--TA-C-ATTTTTCA
* * *
260457 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
260477 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
260497 ATGTATCGATACATT
1 ATGTATCGATACATT
260512 CATAGTTAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 16
0.72 0.14 0.15
Matches are distributed among these distances:
20 54 0.69
21 5 0.06
22 4 0.05
24 4 0.05
25 5 0.06
26 6 0.08
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:263930 original size:22 final size:23
Alignment explanation
Indices: 263894--263936 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
263884 ATTTGATTTA
*
263894 TTTATTTAACCAATT-ATGATAC
1 TTTATTTAAACAATTCATGATAC
*
263916 TTTATTTAAATAATTCATGAT
1 TTTATTTAAACAATTCATGAT
263937 TATCTTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (23 bp):
TTTATTTAAACAATTCATGATAC
Found at i:267432 original size:7 final size:7
Alignment explanation
Indices: 267415--267462 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
267405 CTCCGTTGTG
*
267415 GAAAGAA
1 GAAAAAA
*
267422 GAAAAAT
1 GAAAAAA
267429 GAAAAAA
1 GAAAAAA
*
267436 GAAAATA
1 GAAAAAA
267443 GAAAAAA
1 GAAAAAA
267450 -AACAAAA
1 GAA-AAAA
267457 GAAAAA
1 GAAAAA
267463 TCAAGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
6 2 0.06
7 30 0.88
8 2 0.06
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (7 bp):
GAAAAAA
Found at i:267451 original size:16 final size:15
Alignment explanation
Indices: 267430--267482 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
267420 AAGAAAAATG
267430 AAAAAAGAAAATAGAA
1 AAAAAAGAAAA-AGAA
*
267446 AAAAAA-CAAAAGAA
1 AAAAAAGAAAAAGAA
*
267460 AAATCAAGAAAAAGACA
1 AAA-AAAGAAAAAGA-A
267477 AAAAAA
1 AAAAAA
267483 AGGGCATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.23
15 5 0.17
16 14 0.47
17 4 0.13
ACGTcount: A:0.81, C:0.06, G:0.09, T:0.04
Consensus pattern (15 bp):
AAAAAAGAAAAAGAA
Found at i:271413 original size:13 final size:13
Alignment explanation
Indices: 271395--271422 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
271385 ATACAAAGAT
271395 CAATGTATCGATA
1 CAATGTATCGATA
271408 CAATGTATCGATA
1 CAATGTATCGATA
271421 CA
1 CA
271423 TTAAGTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:271419 original size:33 final size:32
Alignment explanation
Indices: 271377--271581 Score: 120
Period size: 32 Copynumber: 6.4 Consensus size: 32
271367 AGATTCCCAG
271377 ATGTATCGATACA-AAGATCAATGTATCGATACA
1 ATGTATCGATACATAAG-T-AATGTATCGATACA
*
271410 ATGTATCGATACATTAAGTAATGTATCGATA-T
1 ATGTATCGATACA-TAAGTAATGTATCGATACA
* * * * *
271442 AT-TTTC-TTGGCAGT-AGT-TTCGTAGCGATACA
1 ATGTATCGAT-ACA-TAAGTAAT-GTATCGATACA
* * *
271473 TTGTATCGATACAAAACTAATGTATCGATACA
1 ATGTATCGATACATAAGTAATGTATCGATACA
* * *
271505 TTGTATCGATACA-ACACTTATGTATCGATACA
1 ATGTATCGATACATA-AGTAATGTATCGATACA
* * * * *
271537 TTGTATCGATACA-ACACTTATGTTTCAATACA
1 ATGTATCGATACATA-AGTAATGTATCGATACA
*
271569 TTGTATCGATACA
1 ATGTATCGATACA
271582 AATTGTTGAA
Statistics
Matches: 143, Mismatches: 19, Indels: 21
0.78 0.10 0.11
Matches are distributed among these distances:
29 1 0.01
30 12 0.08
31 8 0.06
32 91 0.64
33 27 0.19
34 1 0.01
35 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (32 bp):
ATGTATCGATACATAAGTAATGTATCGATACA
Found at i:271498 original size:19 final size:17
Alignment explanation
Indices: 271474--271583 Score: 64
Period size: 13 Copynumber: 6.8 Consensus size: 17
271464 AGCGATACAT
271474 TGTATCGATACAAAACTAA
1 TGTATCGATAC-AAACT-A
271493 TGTATCGATAC--A-T-
1 TGTATCGATACAAACTA
271506 TGTATCGATACAACACTTA
1 TGTATCGATACAA-AC-TA
271525 TGTATCGATAC--A-T-
1 TGTATCGATACAAACTA
271538 TGTATCGATACAACACTTA
1 TGTATCGATACAA-AC-TA
* *
271557 TGTTTCAATAC--A-T-
1 TGTATCGATACAAACTA
271570 TGTATCGATACAAA
1 TGTATCGATACAAA
271584 TTGTTGAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 32
0.67 0.04 0.29
Matches are distributed among these distances:
13 31 0.42
14 2 0.03
15 2 0.03
16 5 0.07
18 2 0.03
19 31 0.42
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (17 bp):
TGTATCGATACAAACTA
Found at i:271507 original size:32 final size:32
Alignment explanation
Indices: 271466--271583 Score: 191
Period size: 32 Copynumber: 3.7 Consensus size: 32
271456 AGTTTCGTAG
*
271466 CGATACATTGTATCGATACAAAACTAATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
271498 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
271530 CGATACATTGTATCGATACAACACTTATGTTT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
271562 CAATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
271584 TTGTTGAAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 81 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:271645 original size:21 final size:20
Alignment explanation
Indices: 271619--271657 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
271609 GTTGGGACCT
271619 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
271640 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
271658 CAAAAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:272494 original size:60 final size:59
Alignment explanation
Indices: 272339--273132 Score: 412
Period size: 60 Copynumber: 13.3 Consensus size: 59
272329 CTTGCTTTCG
* * * * *
272339 GTCAAGACTATCTTCATTTGACTGTATTTGGTTAAATTTCACCC-TCGGTTAACTGTATTCA
1 GTCAAGACTATCCTCATTTGACTGTATTCGGTCAAATTT-ACCCTTC--TTGACTATATTCA
* * * * *
272400 GTCAAGTCTTTCCTTATTTGACTGTACTT-GGTCAAATCTTACCCTTCTTGACTACATTCG
1 GTCAAGACTATCCTCATTTGACTGTA-TTCGGTCAAAT-TTACCCTTCTTGACTATATTCA
* * * * * *
272460 GTGAAGACTATCCTCATTTGACTGTATTCAGTCAAATTTCACCATTGCTTGATTGT-TTTA
1 GTCAAGACTATCCTCATTTGACTGTATTCGGTCAAATTT-ACCCTT-CTTGACTATATTCA
* * * * * * * * * *
272520 GTTAAGTCTTTCCTTATTTGACTGTACTCGATCAAATTTTACCCCTCTTGCCTGTATTCG
1 GTCAAGACTATCCTCATTTGACTGTATTCGGTCAAA-TTTACCCTTCTTGACTATATTCA
* ** * *
272580 GTCAAGACTATCCTCATTTGATTGTATTCAATCAAA--T-CGCTTGATTG--TAT-TT-A
1 GTCAAGACTATCCTCATTTGACTGTATTCGGTCAAATTTACCCTT-CTTGACTATATTCA
* ** * * * * * *
272633 GTCACGTTTTTTCTCATTTGATTGTACTCGGTCAAATTTTACCCCTCTTGACTGTATTCA
1 GTCAAGACTATCCTCATTTGACTGTATTCGGTCAAA-TTTACCCTTCTTGACTATATTCA
* * * * * *
272693 GTTAAGATTATCCTCATTTGGCTTTATTCGGTCAAATTTTACCCTCACTTGACTCTATTCA
1 GTCAAGACTATCCTCATTTGACTGTATTCGGTCAAA-TTTACCCT-TCTTGACTATATTCA
* * * * * * *
272754 GTCAAGCCTTTCCTCATTTGATTATACTCGGTCAAATTTTACCCCTCTTGACTATATT-T
1 GTCAAGACTATCCTCATTTGACTGTATTCGGTCAAA-TTTACCCTTCTTGACTATATTCA
* * *
272813 GATCAAAACTATCCTCATTTGACTATATTCGATCAAATTTCACCCTTGCTTGACTATATTCA
1 G-TCAAGACTATCCTCATTTGACTGTATTCGGTCAAATTT-ACCCTT-CTTGACTATATTCA
* * * * ** * ** **
272875 GTCAAGTCTTTCCTCATTTAACTGTACTCAATCAAATCTTACCCTGCTCAACTATATTTT
1 GTCAAGACTATCCTCATTTGACTGTATTCGGTCAAAT-TTACCCTTCTTGACTATATTCA
* * * * * **
272935 GTCAACATTATCCTCATTTGATTGTACTTGGGTCAAATCTTACCCTGT-TCGACCGTATTC-
1 GTCAAGACTATCCTCATTTGACTGTA-TTCGGTCAAAT-TTACCCT-TCTTGACTATATTCA
* * * * * ** * **
272995 GATCAAGTCTTTCTTCACTTGACTGTACTCGACCAAATTTTACCATGATTGACTATATTCA
1 G-TCAAGACTATCCTCATTTGACTGTATTCGGTCAAA-TTTACCCTTCTTGACTATATTCA
* * * * * * * *
273056 GTCAAGTCTTTCTTCATTTGACTATATTTGATCAAATCTTA-CCTCGCTTGATTATATTC-
1 GTCAAGACTATCCTCATTTGACTGTATTCGGTCAAAT-TTACCCT-TCTTGACTATATTCA
* *
273115 GATCAAGCCTTTCCTCAT
1 G-TCAAGACTATCCTCAT
273133 CTACTTACAT
Statistics
Matches: 559, Mismatches: 142, Indels: 65
0.73 0.19 0.08
Matches are distributed among these distances:
53 28 0.05
54 2 0.00
55 2 0.00
56 7 0.01
57 7 0.01
58 2 0.00
59 21 0.04
60 301 0.54
61 180 0.32
62 9 0.02
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (59 bp):
GTCAAGACTATCCTCATTTGACTGTATTCGGTCAAATTTACCCTTCTTGACTATATTCA
Found at i:272739 original size:31 final size:31
Alignment explanation
Indices: 272704--272797 Score: 77
Period size: 31 Copynumber: 3.1 Consensus size: 31
272694 TTAAGATTAT
272704 CCTCATTTGGCTTTATTCGGTCAAATTTTAC
1 CCTCATTTGGCTTTATTCGGTCAAATTTTAC
* * * * **
272735 CCTCACTTGACTCTATTCAGTCAAGCCTTT--
1 CCTCATTTGGCTTTATTCGGTCAA-ATTTTAC
* *
272765 CCTCATTT-GATTATACTCGGTCAAATTTTAC
1 CCTCATTTGGCTT-TATTCGGTCAAATTTTAC
272796 CC
1 CC
272798 CTCTTGACTA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
29 4 0.09
30 16 0.36
31 22 0.49
32 3 0.07
ACGTcount: A:0.21, C:0.28, G:0.11, T:0.40
Consensus pattern (31 bp):
CCTCATTTGGCTTTATTCGGTCAAATTTTAC
Found at i:272795 original size:121 final size:121
Alignment explanation
Indices: 272335--273132 Score: 696
Period size: 121 Copynumber: 6.7 Consensus size: 121
272325 CATCCTTGCT
* * * * *
272335 TTCGGTCAAGACTATCTTCATTTGACTGTATTTGGTTAAATTTCACCCTCGGTTAACTGTATTCA
1 TTCGGTCAAGACTATCCTCATTTGACTGTATTCGGTCAAATTTCACCCTCGCTTGACTGTATTCA
* * * * *
272400 GTCAAGTCTTTCCTTATTTGACTGTACTTGGTCAAATCTTACCCTTCTTGACTACA
66 GTCAAGTCTTTCCTCATTTGACTGTACTCGGTCAAATTTTACCCCTCTTGACTATA
* * * * * *
272456 TTCGGTGAAGACTATCCTCATTTGACTGTATTCAGTCAAATTTCACCATTGCTTGATTGT-TTTA
1 TTCGGTCAAGACTATCCTCATTTGACTGTATTCGGTCAAATTTCACCCTCGCTTGACTGTATTCA
* * * * *
272520 GTTAAGTCTTTCCTTATTTGACTGTACTCGATCAAATTTTACCCCTCTTGCCTGTA
66 GTCAAGTCTTTCCTCATTTGACTGTACTCGGTCAAATTTTACCCCTCTTGACTATA
* ** * *
272576 TTCGGTCAAGACTATCCTCATTTGATTGTA-T---TC-AA--TCA-AATCGCTTGATTGTATTTA
1 TTCGGTCAAGACTATCCTCATTTGACTGTATTCGGTCAAATTTCACCCTCGCTTGACTGTATTCA
* * * * *
272633 GTCACGTTTTTTCTCATTTGATTGTACTCGGTCAAATTTTACCCCTCTTGACTGTA
66 GTCAAGTCTTTCCTCATTTGACTGTACTCGGTCAAATTTTACCCCTCTTGACTATA
* * * * * * * *
272689 TTCAGTTAAGATTATCCTCATTTGGCTTTATTCGGTCAAATTTTACCCTCACTTGACTCTATTCA
1 TTCGGTCAAGACTATCCTCATTTGACTGTATTCGGTCAAATTTCACCCTCGCTTGACTGTATTCA
* * *
272754 GTCAAGCCTTTCCTCATTTGATTATACTCGGTCAAATTTTACCCCTCTTGACTATA
66 GTCAAGTCTTTCCTCATTTGACTGTACTCGGTCAAATTTTACCCCTCTTGACTATA
* * * * * * *
272810 TTTGATCAAAACTATCCTCATTTGACTATATTCGATCAAATTTCACCCTTGCTTGACTATATTCA
1 TTCGGTCAAGACTATCCTCATTTGACTGTATTCGGTCAAATTTCACCCTCGCTTGACTGTATTCA
* ** * **
272875 GTCAAGTCTTTCCTCATTTAACTGTACTCAATCAAATCTTA-CCCTGCTCAACTATA
66 GTCAAGTCTTTCCTCATTTGACTGTACTCGGTCAAATTTTACCCCT-CTTGACTATA
** * * * * *
272931 TTTTGTCAACATTATCCTCATTTGATTGTACTTGGGTCAAATCTT-ACCCT-G-TTCGACCGTAT
1 TTCGGTCAAGACTATCCTCATTTGACTGTA-TTCGGTCAAAT-TTCACCCTCGCTT-GACTGTAT
* * ** * *
272993 TC-GATCAAGTCTTTCTTCACTTGACTGTACTCGACCAAATTTTA-CCATGATTGACTATA
63 TCAG-TCAAGTCTTTCCTCATTTGACTGTACTCGGTCAAATTTTACCCCT-CTTGACTATA
* * * * * * * * *
273052 TTCAGTCAAGTCTTTCTTCATTTGACTATATTTGATCAAATCTT-A-CCTCGCTTGATTATATTC
1 TTCGGTCAAGACTATCCTCATTTGACTGTATTCGGTCAAAT-TTCACCCTCGCTTGACTGTATTC
*
273115 -GATCAAGCCTTTCCTCAT
65 AG-TCAAGTCTTTCCTCAT
273133 CTACTTACAT
Statistics
Matches: 552, Mismatches: 109, Indels: 33
0.80 0.16 0.05
Matches are distributed among these distances:
112 12 0.02
113 79 0.14
114 1 0.00
115 2 0.00
116 2 0.00
117 2 0.00
118 2 0.00
119 4 0.01
120 124 0.22
121 308 0.56
122 14 0.03
123 2 0.00
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (121 bp):
TTCGGTCAAGACTATCCTCATTTGACTGTATTCGGTCAAATTTCACCCTCGCTTGACTGTATTCA
GTCAAGTCTTTCCTCATTTGACTGTACTCGGTCAAATTTTACCCCTCTTGACTATA
Found at i:274555 original size:168 final size:171
Alignment explanation
Indices: 274304--274688 Score: 470
Period size: 168 Copynumber: 2.3 Consensus size: 171
274294 AATTAGTTTG
* ** * *
274304 CAAAAATTCACATATTTTCAT-AAATTTT-ACATTTTTTTCCTCGAAATT-CCTTGGTTTTAGAA
1 CAAAAATTCATATATTTTCATGAGTTTTTGA-ATTTTTTTCCTTGAAATTCCCTTGATTTTAGAA
* * * *
274366 ATATGGAGTTTTCTTCTCCATAATTTTTTTC-AGAGGGATTTTTCTTT-GTTTTTAA-TTTTTAA
65 ATATAGAGTTTTCTACTCCATAAATGTTTTCGAG-GGGATTTTT-TTTAGTTTTTAATTTTTTAA
* *
274428 AATTCATCAAATATTATTATTTAATTAATTTTAAATCAATT-TT
128 AATTCATCAAATATAATTATTTAATTAATATTAAATCAATTCTT
* *
274471 CAAAAATTCATACATTTTCATGAGTTTTTGAATTTTTTTCCTTGAAATTCCCTT-ATTTTCGAAA
1 CAAAAATTCATATATTTTCATGAGTTTTTGAATTTTTTTCCTTGAAATTCCCTTGATTTTAGAAA
*
274535 TGTAGAGTTTTCTACTCCATAAATGTTTTCGAGGGGATTTTTTTTAGTTTTTAATTTTTTAAAAT
66 TATAGAGTTTTCTACTCCATAAATGTTTTCGAGGGGATTTTTTTTAGTTTTTAATTTTTTAAAAT
* * *
274600 TCATCAAGTATAATTATTTAATTCATATTAAATCAGTTCTT
131 TCATCAAATATAATTATTTAATTAATATTAAATCAATTCTT
* * * *
274641 ---AAGTTCATTTATTCTCATGAGTTTTTGAATTTTTTT-CTTAAAATTCCC
1 CAAAAATTCATATATTTTCATGAGTTTTTGAATTTTTTTCCTTGAAATTCCC
274689 CTTTTTCTGA
Statistics
Matches: 189, Mismatches: 22, Indels: 15
0.84 0.10 0.07
Matches are distributed among these distances:
166 11 0.06
167 54 0.29
168 72 0.38
169 50 0.26
170 2 0.01
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (171 bp):
CAAAAATTCATATATTTTCATGAGTTTTTGAATTTTTTTCCTTGAAATTCCCTTGATTTTAGAAA
TATAGAGTTTTCTACTCCATAAATGTTTTCGAGGGGATTTTTTTTAGTTTTTAATTTTTTAAAAT
TCATCAAATATAATTATTTAATTAATATTAAATCAATTCTT
Found at i:277291 original size:21 final size:20
Alignment explanation
Indices: 277265--277341 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 20
277255 TTTTACAATT
*
277265 TGTATCGATATAAACAGTAAA
1 TGTATCGATACAAA-AGTAAA
* * *
277286 TGTATCCATACATAGGTAAA
1 TGTATCGATACAAAAGTAAA
****
277306 TGTATCGATACATGCCTAAAA
1 TGTATCGATACAAAAGT-AAA
277327 TGTATCGATACAAAA
1 TGTATCGATACAAAA
277342 TCACCTTGCA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 18 0.41
21 26 0.59
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAAAAGTAAA
Found at i:277325 original size:20 final size:20
Alignment explanation
Indices: 277282--277338 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
277272 ATATAAACAG
* *
277282 TAAATGTATCCATACATAGG
1 TAAATGTATCGATACATAGC
277302 TAAATGTATCGATACAT-GCC
1 TAAATGTATCGATACATAG-C
277322 TAAAATGTATCGATACA
1 T-AAATGTATCGATACA
277339 AAATCACCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 1 0.03
20 17 0.52
21 15 0.45
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
TAAATGTATCGATACATAGC
Found at i:279528 original size:28 final size:27
Alignment explanation
Indices: 279474--279548 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
279464 AATAAAGCCG
*** *
279474 GGGTTGGAGTATCCCCTCGGAAGTAAC
1 GGGTTGGAGTATCCCCGATGAAATAAC
279501 AGGGTTGGAGTATCCCCGATGAAATAAC
1 -GGGTTGGAGTATCCCCGATGAAATAAC
* *
279529 GAGGTTAGAGTATCCTCGAT
1 G-GGTTGGAGTATCCCCGAT
279549 TGTGAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.24
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGATGAAATAAC
Found at i:279595 original size:52 final size:51
Alignment explanation
Indices: 279531--279754 Score: 216
Period size: 52 Copynumber: 4.3 Consensus size: 51
279521 GAAATAACGA
* * * * *
279531 GGTTAGAGTATCCTCGATTGTGAAAAATTTGTGTTTTTGTAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTTG-AAATAAAACCGG
* * * *
279583 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG-TTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTTG-AAATAAAACCGG
* * *
279635 GGTTGGAGTATCCCCGATTGTGAAAAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATG---AAAAATTAGTGTTTTTGAAATAAAACCGG
* * * * ** *
279689 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCAG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTTGAAATAAAACCGG
279740 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
279755 TCAGAAATAA
Statistics
Matches: 142, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
51 37 0.26
52 50 0.35
53 10 0.07
54 41 0.29
55 4 0.03
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTTGAAATAAAACCGG
Found at i:279682 original size:54 final size:54
Alignment explanation
Indices: 279531--279715 Score: 204
Period size: 54 Copynumber: 3.5 Consensus size: 54
279521 GAAATAACGA
* * * * *
279531 GGTTAGAGTATCCTCGATTGTG---AAAAATTTGTGTTTTTGTAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAAAATTAGTG-TTTTGAAAATAAAACCGG
* * *
279583 AGTTGGAGTATCCCCGA-T-T-AAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGAAA-AAAAATTAGTGTTTTGAAAATAAAACCGG
*
279635 GGTTGGAGTATCCCCGATTGTGAAAAAAAATTAGTGTTTT-AGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAAAATTAGTGTTTTGA-AAATAAAACCGG
*
279689 GGTTGGAGTATCCCCGATTATGAAAAA
1 GGTTGGAGTATCCCCGATTGTGAAAAA
279716 TCAATATTTT
Statistics
Matches: 113, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 46 0.41
53 11 0.10
54 51 0.45
55 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (54 bp):
GGTTGGAGTATCCCCGATTGTGAAAAAAAATTAGTGTTTTGAAAATAAAACCGG
Found at i:279800 original size:27 final size:28
Alignment explanation
Indices: 279739--279808 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
279729 AATAAAGTCA
279739 GGGTTGGAGTATCCCCTCAGAAATAACG
1 GGGTTGGAGTATCCCCTCAGAAATAACG
* *
279767 GGGTTGGAGTATCCCC-GATG-ATTAACG
1 GGGTTGGAGTATCCCCTCA-GAAATAACG
279794 GGGTTGGAGTATCCC
1 GGGTTGGAGTATCCC
279809 TGATTGTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCTCAGAAATAACG
Found at i:279896 original size:51 final size:51
Alignment explanation
Indices: 279536--279914 Score: 199
Period size: 51 Copynumber: 7.3 Consensus size: 51
279526 AACGAGGTTA
* * * *
279536 GAGTATCCTCGATTGT-GAAAAATTTGTGTTTTTGTAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATAG-AAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
* * * *
279588 GAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTG
1 GAGTATCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
* * * * *
279640 GAGTATCCCCGATTGTGAAAAAAAATTAGTGTTTT-AGCAATAAAACCGGGGTTG
1 GAGTATCCCCGA-T-T-ATAGAAAATTAGTGTTTTGA-AAATAAAATCGGAGTTG
* * * * *
279694 GAGTATCCCCGATTAT-GAAAAATCAATATTTTGGAAATAAAGTCAGG-GTTG
1 GAGTATCCCCGATTATAG-AAAATTAGTGTTTTGAAAATAAAATC-GGAGTTG
* * * * * * * *
279745 GAGTATCCCC---T-CAG-AAATAACGGGGTTGGAGTATCCCCGATGATTAA-CGGGGTTG
1 GAGTATCCCCGATTATAGAAAATTA-GTGTTTTGA--A-----AAT-A-AAATCGGAGTTG
* * * *
279800 GAGTATCCCTGATTGT-GAAGAAATT-G-GTGTTGGAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATAG-A-AAATTAGTGTTTTGAAAATAAAATCGGAGTTG
279850 GAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
*
279901 GAATATCCCCGATT
1 GAGTATCCCCGATT
279915 GTGGAGAATT
Statistics
Matches: 250, Mismatches: 45, Indels: 65
0.69 0.12 0.18
Matches are distributed among these distances:
46 5 0.02
47 3 0.01
48 2 0.01
49 8 0.03
50 24 0.10
51 71 0.28
52 48 0.19
53 12 0.05
54 47 0.19
55 18 0.07
56 2 0.01
58 5 0.02
59 1 0.00
61 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
Found at i:282277 original size:20 final size:20
Alignment explanation
Indices: 282247--282301 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
282237 TAAAATTTCC
* *
282247 AAATCTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
282267 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
282287 AAATGTATCGATACA
1 AAATGTATCGATACA
282302 TTTCCTTGGC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:282345 original size:19 final size:19
Alignment explanation
Indices: 282321--282375 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
282311 CAGTAGCTAA
*
282321 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
282340 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
*
282359 TTATCTATCGATACAAA
1 TTATGTATCGATACAAA
282376 TTGTTGAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:282437 original size:21 final size:21
Alignment explanation
Indices: 282411--282466 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
282401 GTTGGGACCC
*
282411 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTACACAAA
*
282432 TGTATCGATACATTATACAAA
1 TGTATCGATACATTACACAAA
282453 TGTATCGATACATT
1 TGTATCGATACATT
282467 TGGATAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATTACACAAA
Found at i:283440 original size:59 final size:59
Alignment explanation
Indices: 283231--284541 Score: 2086
Period size: 59 Copynumber: 22.2 Consensus size: 59
283221 AGTGTATCCT
* * * * *
283231 GCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGTGTCCT
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
283286 GCTCTTTGAGGACTGATAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCT
1 GCTCTTTGAGGACTGA-AGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
**
283341 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
*
283401 ACTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
** * * *
283460 GCTCTTTGAGGACTCGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCC
*
283521 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
283580 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCTC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
283639 GCTCTTTGAGGACTGAAGGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAGGCTTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
283698 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
283757 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
** ** * **
283816 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAACATCAT
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCC
283877 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
283936 ACTCTTTGAGAACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
283995 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
284054 GCACTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
284113 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCC
* * *
284173 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCC
*
284233 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
*
284292 GCTCTTTGAGGACTGAAGGTGTCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
284351 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
284410 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-AAAAGGGCGTCCC
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAA-GGCGTCCC
*
284469 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCT
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
284528 GCTCTTTGAGGACT
1 GCTCTTTGAGGACT
284542 AAAAAGCAGA
Statistics
Matches: 1177, Mismatches: 63, Indels: 28
0.93 0.05 0.02
Matches are distributed among these distances:
54 1 0.00
55 85 0.07
56 2 0.00
57 4 0.00
58 4 0.00
59 784 0.67
60 243 0.21
61 54 0.05
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (59 bp):
GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
Found at i:283687 original size:297 final size:295
Alignment explanation
Indices: 283226--284541 Score: 2098
Period size: 297 Copynumber: 4.5 Consensus size: 295
283216 AATAAAGTGT
* * * * * *
283226 ATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGTGTCCT
1 ATCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
*
283286 GCTCTTTGAGGACTGATAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCTGCTCT
65 GCTCTTTGAGGACTGA-AGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCT
** *
283346 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCACTCTTTGAG
129 TTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAG
283411 GACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTCG
193 GACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-G
** *
283476 AAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
257 AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGC
* *
283516 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCCG
1 ATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCG
*
283581 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCAT-CTCGCTCTT
66 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCT-GCTCTT
* *
283645 TGAGGACTGAAGGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAGGCTTCCCGCTCTTTGAGGA
130 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGA
283710 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
195 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
283775 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
260 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
* ** ** * *
283811 GTCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAACATCA
1 ATCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCC
* **
283876 TGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCACTCT
64 CGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCT
*
283941 TTGAGAACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGG
129 TTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGG
* * *
284006 ACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCCCGCACTTTGAGGACTGAA
194 ACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAA
284071 GGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
259 GGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
* *
284108 ATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCC
1 ATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCC
* *
284173 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCT
65 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCTGCTCT
*
284238 TTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGG
129 TTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGG
*
284303 ACTGAAGGTGTCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAA
194 ACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAA
284368 GGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
259 GGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
*
284405 GTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-AAAAGGGCGTCCC
1 ATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAA-GGCGTCCC
284469 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTT
65 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTT
284534 TGAGGACT
130 TGAGGACT
284542 AAAAAGCAGA
Statistics
Matches: 954, Mismatches: 56, Indels: 27
0.92 0.05 0.03
Matches are distributed among these distances:
289 24 0.03
290 19 0.02
293 27 0.03
294 25 0.03
295 64 0.07
296 186 0.19
297 590 0.62
298 19 0.02
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (295 bp):
ATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCG
CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTT
GAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGAC
TGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGG
TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
Found at i:283752 original size:356 final size:355
Alignment explanation
Indices: 283231--284546 Score: 2215
Period size: 356 Copynumber: 3.7 Consensus size: 355
283221 AGTGTATCCT
* * * * *
283231 GCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGTGTCCTGCTCT
1 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCT
*
283291 TTGAGGACTGATAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGG-TGTCCTGCTCTTTGA
65 TTGAGGACTGA-AGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCT-TCCCGCTCTTTGA
** *
283350 GGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCACTCTTTGAGGACT
128 GGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT
283415 GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTCGAAAA
192 GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAAA
283480 TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCA
256 TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCA
283545 CCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCC
321 CCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
283580 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCTCGCTCTT
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTT
*
283645 TGAGGACTGAAGGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAGGCTTCCCGCTCTTTGAGGA
66 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCTTCCCGCTCTTTGAGGA
283710 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
131 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
283775 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGGAAAATGCC
196 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAAATGCC
* *
283840 ACCAACTTGTGTGGGCTTTGAAAAGAAAAAACATCATGCTCTTTGAGGACTGAAGGTGCCACCAA
260 ACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAA
*
283905 CTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
325 CTTGGGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
283936 ACTCTTTGAGAACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTT
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTT
* * *
284001 TGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCATCCCGCACTTTGAGGA
66 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCTTCCCGCTCTTTGAGGA
*
284066 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAG
131 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
* * **
284131 GTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCCGCTCTTTGAGGACTGAAGGTGCC
196 GTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAATGCC
284196 ACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAA
260 ACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAA
284261 CTTGGGTGGGCTTTAAAAGAAAAGGCGTCCC
325 CTTGGGTGGGCTTTAAAAGAAAAGGCGTCCC
*
284292 GCTCTTTGAGGACTGAAGGTGTCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTT
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTT
*
284357 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGA
66 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCTTCCCGCTCTTTGAGGA
284422 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-AAAAGGGCGTCCCGCTCTTTGAGGACTGAA
131 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAA-GGCGTCCCGCTCTTTGAGGACTGAA
* *
284486 GGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAA
195 GGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAA
284547 GCAGAAGGAG
Statistics
Matches: 909, Mismatches: 45, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
348 25 0.03
349 14 0.02
352 26 0.03
353 23 0.03
354 3 0.00
355 34 0.04
356 734 0.81
357 49 0.05
358 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (355 bp):
GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTT
TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCTTCCCGCTCTTTGAGGA
CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAG
GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAATGCCA
CCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAAC
TTGGGTGGGCTTTAAAAGAAAAGGCGTCCC
Found at i:289980 original size:33 final size:33
Alignment explanation
Indices: 289938--290002 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
289928 TAGCCAAACT
* **
289938 TGTATCGATACACCAAAGTTTATATCGATACAA
1 TGTATCGATACACAAAAAATTATATCGATACAA
*
289971 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTATATCGATACA
290003 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTATATCGATACAA
Found at i:296166 original size:13 final size:13
Alignment explanation
Indices: 296148--296184 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
296138 ACATTTTTCT
296148 TTGTATCGATACA
1 TTGTATCGATACA
296161 TTGTATCGATACA
1 TTGTATCGATACA
*
296174 CTGTATCGATA
1 TTGTATCGATA
296185 TAGGGGGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:298783 original size:33 final size:33
Alignment explanation
Indices: 298741--298805 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
298731 TAGCCAAACT
* **
298741 TGTATCGATACACCAAAGTTTATATCGATACAA
1 TGTATCGATACACAAAAAATTATATCGATACAA
*
298774 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTATATCGATACA
298806 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTATATCGATACAA
Found at i:307781 original size:80 final size:79
Alignment explanation
Indices: 307648--307799 Score: 195
Period size: 79 Copynumber: 1.9 Consensus size: 79
307638 ATATTTCCCG
* * *
307648 ATGAGAAATTTAATATTTTGGAGATAATAACGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGTT
1 ATGAGAAATTCAATATTTTGGAGATAATAACGGGGTTGGAGTGATCCCTTG-AAATAACGAGGTT
307713 GGAGTATCTCCAATT
65 GGAGTATCTCCAATT
*
307728 ATGAGAAA-TCAATATTTTGG-GAATAA-AGCTGGGGTTGGAGT-ATCCCTGATGAAATAACGAG
1 ATGAGAAATTCAATATTTTGGAG-ATAATAAC-GGGGTTGGAGTGATCCCT--TGAAATAACGAG
307789 GTTGGAGTATC
62 GTTGGAGTATC
307800 CTCGATTGTG
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
78 8 0.12
79 46 0.72
80 10 0.16
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (79 bp):
ATGAGAAATTCAATATTTTGGAGATAATAACGGGGTTGGAGTGATCCCTTGAAATAACGAGGTTG
GAGTATCTCCAATT
Found at i:307858 original size:52 final size:52
Alignment explanation
Indices: 307789--308134 Score: 219
Period size: 51 Copynumber: 6.6 Consensus size: 52
307779 AAATAACGAG
* * *
307789 GTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTTGGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTTGGAAATAAAATCGGA
* * * ** * *
307841 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTG-TTTTAAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGATGTTTTTGGAAATAAAATCGGA
** * * *
307893 GTTGGAGTATCCCCGATTATGAAAAATCAAT-ATTTTGGAAATAAAGTCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTTGGAAATAAAATCGGA
* * * *** * *
307944 GTTGGAGTATCCCC---T-TGGAAAA-TAACGGGGTTGGAGTATCCCCGATGATTAA-CGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTTGGA--A------AT-A-AAATCGGA
* *
308000 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTGTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAA-AAATTGATGTTT-TTGGAAATAAAATCGGA
*
308054 GTTGGAGTATCCCCGATTAT-AGAAAATT-A-GTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTGATGT-TTTTGGAAATAAAATCGGA
* * *
308105 GTTGGAATATCCCCGATTATGGAGAATTGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGA
308135 GAAACTCAAC
Statistics
Matches: 227, Mismatches: 42, Indels: 50
0.71 0.13 0.16
Matches are distributed among these distances:
46 2 0.01
47 11 0.05
48 1 0.00
49 1 0.00
51 79 0.35
52 52 0.23
53 18 0.08
54 24 0.11
55 4 0.02
56 19 0.08
57 1 0.00
59 1 0.00
60 3 0.01
61 4 0.02
62 2 0.01
63 5 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTTGGAAATAAAATCGGA
Found at i:308004 original size:27 final size:27
Alignment explanation
Indices: 307940--308016 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
307930 GAAATAAAGT
307940 CGGGGTTGGAGTATCCCCTTGGA-AAATAA
1 CGGGGTTGGAGTATCCCC---GATAAATAA
* *
307969 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGATAAATAA
307996 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
308017 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.04
27 25 0.56
29 18 0.40
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATAAATAA
Found at i:310499 original size:13 final size:13
Alignment explanation
Indices: 310481--310506 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
310471 ACAAAGATCC
310481 ATGTATCGATACA
1 ATGTATCGATACA
310494 ATGTATCGATACA
1 ATGTATCGATACA
310507 CAGAAAAATG
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:310568 original size:18 final size:18
Alignment explanation
Indices: 310545--310611 Score: 90
Period size: 18 Copynumber: 3.9 Consensus size: 18
310535 CAGTAGCTAA
310545 TTATGTATCGATACAAAC
1 TTATGTATCGATACAAAC
310563 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
310578 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
310595 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
310612 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 18 0.42
19 11 0.26
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:310584 original size:13 final size:13
Alignment explanation
Indices: 310566--310590 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
310556 TACAAACTTA
310566 TGTATCGATACAT
1 TGTATCGATACAT
310579 TGTATCGATACA
1 TGTATCGATACA
310591 AAACTTATGT
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:310586 original size:31 final size:32
Alignment explanation
Indices: 310548--310609 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
310538 TAGCTAATTA
310548 TGTATCGATAC-AAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
310579 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
310610 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:310673 original size:21 final size:21
Alignment explanation
Indices: 310647--310730 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
310637 GTTGGGACCC
310647 TGTATCGATACATTTGTATAA
1 TGTATCGATACATTTGTATAA
* **
310668 TGTATCAATACATTTGTGGAA
1 TGTATCGATACATTTGTATAA
* *
310689 TGTATCGATACA-TTATACAAA
1 TGTATCGATACATTTGTA-TAA
*
310710 TGTATCGATACATTTGGATAA
1 TGTATCGATACATTTGTATAA
310731 ATTTTTTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
20 3 0.06
21 45 0.88
22 3 0.06
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTATAA
Found at i:316714 original size:470 final size:470
Alignment explanation
Indices: 315828--316768 Score: 1375
Period size: 470 Copynumber: 2.0 Consensus size: 470
315818 TGCACCAAAT
* *
315828 AATCTAGGTGCTAACCAGCGAAGGTAGCAATTCGACCATATCCCTGTGACATACAAGGAGCTTTA
1 AATCTAGGTGCTAACCAGCAAAGGTAGCAATTCGACCATATCCCTATGACATACAAGGAGCTTTA
* * * * *
315893 CCAGACTCACTTCAAAGCCATTTAGTGGCCCTTGAGTATGTCCCAGATAGGAAGCTTCCATACCC
66 CCAGACTCACTCCAAAGCCATCTAGTGGCCCCTGAATATGTCCCAGATAGGAAGCCTCCATACCC
* * * * *
315958 TCATTGATATAACCCCAATGCCCATTGTGATTACCATGCTGGGGTAGCGGGACATGATATCGAGA
131 TCACTGATATAACCCCAATGCCCATTGCGATTACCATGCTAGGGTAGCAGGACATGATATCGAAA
* * * * * *
316023 ATTTCTTCCTATTCAAGCGAAGGGTACAGGGGCTGCTTGATTCAAAGGTCCAATAGTTTGGGGCA
196 ATTACTTCCTATTCAAGCAAAGGGTACAAGGCCTACTTGATTCAAAGGTCCAACAGTTTGGGGCA
* ** * * *
316088 AGTCAAGGGTCGAATGTTGCAGCAAACCCCTTGGCAAGCCGTGCTGAGCCTGTAAACCAATGACC
261 AGTCAAGGGTCGAATGTTGCAGCAAACCCCCTACCAAACCATGCTGAGCCCGTAAACCAATGACC
* * *
316153 TTGAGCAAAGAATCCATCTCCATCCAGCAGAGTCGGCTTTTAACAATGGAGTCATGTGGGAAATC
326 TTGAGCAAAGAATCCATCTCCATCCAGCAAAGTCAGCTTTTAACAATGGAATCATGTGGGAAATC
* * *
316218 TTTGCACTTTTCTTGCTTGTTTTGTGTAAATCATGAAAATCTACTTGCCTTTGCCTGATGGCATG
391 CTTGCACTTTTCTTGCTTGTTTTGTGTAAATCAAGAAAATCTACTTGCCTTTGCCCGATGGCATG
*
316283 TAGGAATCTTATGCA
456 TAGAAATCTTATGCA
*
316298 AATCTGGGTGCTAACCAGCAAAGGTAGCAATT-GAACCA-ATCCCTATGACATACAAGGAGCTTT
1 AATCTAGGTGCTAACCAGCAAAGGTAGCAATTCG-ACCATATCCCTATGACATACAAGGAGCTTT
* *
316361 ACCAGACTCTGCTCCAAAGCCATCTAGTGGCCCCTGAATATGTCCTAGATAGGAAGCCTCCATAC
65 ACCAGACTC-ACTCCAAAGCCATCTAGTGGCCCCTGAATATGTCCCAGATAGGAAGCCTCCATAC
*
316426 CCTCACTGGTATAACCCCAATGCCCATTGCGATTACCATGCTAGGGTAGCAGGA-ATTGATATCG
129 CCTCACTGATATAACCCCAATGCCCATTGCGATTACCATGCTAGGGTAGCAGGACA-TGATATCG
* * **
316490 AAAATTACTTCCTATTTAAGCAAAGGGTACAAGGCCTACTTGATTCAAATGTCTTACAGTTTGGG
193 AAAATTACTTCCTATTCAAGCAAAGGGTACAAGGCCTACTTGATTCAAAGGTCCAACAGTTTGGG
* * * *
316555 GTAAGTCAAGGGTCGAATGTTGTAGCAAACCCCCTACCAAACTATGCTGAGCCCGTAAACCATTG
258 GCAAGTCAAGGGTCGAATGTTGCAGCAAACCCCCTACCAAACCATGCTGAGCCCGTAAACCAATG
* * * * * **
316620 ATCTTGAGCAAAGAATCCGTCTCCATCCATCAAAGTTAGCTTTTGACAATGGAATTGTGTGGGAA
323 ACCTTGAGCAAAGAATCCATCTCCATCCAGCAAAGTCAGCTTTTAACAATGGAATCATGTGGGAA
*
316685 ATCCTTGCACTTTTCTTGTTTGTTTTGTGTAAATCAAGAAAATCTACTTGCCTTTGCCCGATGGC
388 ATCCTTGCACTTTTCTTGCTTGTTTTGTGTAAATCAAGAAAATCTACTTGCCTTTGCCCGATGGC
316750 ATGTAGAAATCTTATGCA
453 ATGTAGAAATCTTATGCA
316768 A
1 A
316769 CGAGCCCTTT
Statistics
Matches: 417, Mismatches: 51, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
469 35 0.08
470 382 0.92
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (470 bp):
AATCTAGGTGCTAACCAGCAAAGGTAGCAATTCGACCATATCCCTATGACATACAAGGAGCTTTA
CCAGACTCACTCCAAAGCCATCTAGTGGCCCCTGAATATGTCCCAGATAGGAAGCCTCCATACCC
TCACTGATATAACCCCAATGCCCATTGCGATTACCATGCTAGGGTAGCAGGACATGATATCGAAA
ATTACTTCCTATTCAAGCAAAGGGTACAAGGCCTACTTGATTCAAAGGTCCAACAGTTTGGGGCA
AGTCAAGGGTCGAATGTTGCAGCAAACCCCCTACCAAACCATGCTGAGCCCGTAAACCAATGACC
TTGAGCAAAGAATCCATCTCCATCCAGCAAAGTCAGCTTTTAACAATGGAATCATGTGGGAAATC
CTTGCACTTTTCTTGCTTGTTTTGTGTAAATCAAGAAAATCTACTTGCCTTTGCCCGATGGCATG
TAGAAATCTTATGCA
Found at i:317462 original size:37 final size:38
Alignment explanation
Indices: 317389--317462 Score: 87
Period size: 37 Copynumber: 1.9 Consensus size: 38
317379 AAAAATGGCC
* * **
317389 AAAAAAAAAGAGAAGTCAAAAGCAAAAGCATGAAAAATG
1 AAAAAAAAAGAAAAG-CAAAAACAAAAGCACAAAAAATG
*
317428 AAAAAAAAAGAAAAG-AAAAACAAAAGGACAAAAAA
1 AAAAAAAAAGAAAAGCAAAAACAAAAGCACAAAAAA
317463 ATGTGCAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 16 0.53
39 14 0.47
ACGTcount: A:0.74, C:0.07, G:0.15, T:0.04
Consensus pattern (38 bp):
AAAAAAAAAGAAAAGCAAAAACAAAAGCACAAAAAATG
Found at i:318764 original size:31 final size:31
Alignment explanation
Indices: 318705--318764 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
318695 CCAAATCTTT
* ** *
318705 TTCTTTCTTCATAGTCCATGACATAGTGGTA
1 TTCTTTCTTCAAAGTCCACAACACAGTGGTA
*
318736 TTCTTTCTTCAAAGTCCACAACCCAGTGG
1 TTCTTTCTTCAAAGTCCACAACACAGTGG
318765 CACCTCTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (31 bp):
TTCTTTCTTCAAAGTCCACAACACAGTGGTA
Found at i:318797 original size:29 final size:29
Alignment explanation
Indices: 318746--319039 Score: 204
Period size: 29 Copynumber: 9.8 Consensus size: 29
318736 TTCTTTCTTC
318746 AAAGTCCACAAC-CCAGTGGCACCTCTTTT
1 AAAGTCCACAACTCC-GTGGCACCTCTTTT
* * *
318775 AAAGTCCACGACTCCGTGACACCTTTTTT
1 AAAGTCCACAACTCCGTGGCACCTCTTTT
* **
318804 TAAG-CTCACAACTCTATGGCATCCT-TTTT
1 AAAGTC-CACAACTCCGTGGCA-CCTCTTTT
* *
318833 AAAGTCCACAACTCAGTGGCACCCCTTTT
1 AAAGTCCACAACTCCGTGGCACCTCTTTT
* * *
318862 AAAGTCCACAACTCCATGGCACATTTTTT
1 AAAGTCCACAACTCCGTGGCACCTCTTTT
* * *
318891 TAAGCCCACAATTCCGTGGCATCC-CTTTT
1 AAAGTCCACAACTCCGTGGCA-CCTCTTTT
* **
318920 CAAAGTCCACAACTCCATGGTGCCTCTTTTCTTT
1 -AAAGTCCACAACTCCGTGGCACCTC---T-TTT
* * *
318954 TAAGTCCATAACTCCATGGCACCTTTTCCTTTT
1 AAAGTCCACAACTCCGTGGCACC---T-CTTTT
318987 -AAGTCCACAACTCCGTGGCATCC-CTTTTT
1 AAAGTCCACAACTCCGTGGCA-CCTC-TTTT
* * *
319016 AAAGTCTACAACTCCATAGCACCT
1 AAAGTCCACAACTCCGTGGCACCT
319040 TTTCCTTTTA
Statistics
Matches: 207, Mismatches: 38, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
28 4 0.02
29 114 0.55
30 40 0.19
32 18 0.09
33 25 0.12
34 4 0.02
36 1 0.00
37 1 0.00
ACGTcount: A:0.25, C:0.32, G:0.12, T:0.31
Consensus pattern (29 bp):
AAAGTCCACAACTCCGTGGCACCTCTTTT
Found at i:318892 original size:87 final size:88
Alignment explanation
Indices: 318746--319029 Score: 306
Period size: 87 Copynumber: 3.2 Consensus size: 88
318736 TTCTTTCTTC
* * * * * *
318746 AAAGTCCACAACCCAGTGGCACCTCTTTTAAAGTCCACGACTCCGTGACACCTTTTTTTAAGCTC
1 AAAGTCCACAACTCAGTGGCACCCCTTTTAAAGTCCACAACTCCATGGCACATTTTTTTAAGCTC
**
318811 ACAACTCTATGGCAT-CCTTTTT
66 ACAACTCCGTGGCATCCCTTTTT
*
318833 AAAGTCCACAACTCAGTGGCACCCCTTTTAAAGTCCACAACTCCATGGCACATTTTTTTAAGCCC
1 AAAGTCCACAACTCAGTGGCACCCCTTTTAAAGTCCACAACTCCATGGCACATTTTTTTAAGCTC
* *
318898 ACAATTCCGTGGCATCCCTTTTC
66 ACAACTCCGTGGCATCCCTTTTT
** * *
318921 AAAGTCCACAACTCCA-TGGTGCCTCTTTTCTTTT-AAGTCCATAACTCCATGGCACCTTTTCCT
1 AAAGTCCACAACT-CAGTGGCACC-C----CTTTTAAAGTCCACAACTCCATGGCA-CATTT--T
318984 TTTAAG-TCCACAACTCCGTGGCATCCCTTTTT
57 TTTAAGCT-CACAACTCCGTGGCATCCCTTTTT
*
319016 AAAGTCTACAACTC
1 AAAGTCCACAACTC
319030 CATAGCACCT
Statistics
Matches: 167, Mismatches: 19, Indels: 15
0.83 0.09 0.07
Matches are distributed among these distances:
87 70 0.42
88 24 0.14
89 3 0.02
92 19 0.11
93 9 0.05
94 1 0.01
95 41 0.25
ACGTcount: A:0.25, C:0.32, G:0.12, T:0.31
Consensus pattern (88 bp):
AAAGTCCACAACTCAGTGGCACCCCTTTTAAAGTCCACAACTCCATGGCACATTTTTTTAAGCTC
ACAACTCCGTGGCATCCCTTTTT
Found at i:319007 original size:95 final size:91
Alignment explanation
Indices: 318743--319058 Score: 285
Period size: 87 Copynumber: 3.5 Consensus size: 91
318733 GTATTCTTTC
* ** * * *
318743 TTCAAAGTCCACAAC-CCAGTGGCACC---T-CTTTTAAAGTCCACGACTCCGTGACACCTTTTT
1 TTCAAAGTCCACAACTCCA-TAGCACCTTTTCCTTTT-AAGTCCATAACTCCATGGCACATTTTT
* **
318803 TTAAGCTCACAACTCTATGGCAT-CCTT
64 TTAAGCCCACAACTCCGTGGCATCCCTT
* * *
318830 TTTAAAGTCCACAACT-CAGTGGCACC----CCTTTTAAAGTCCACAACTCCATGGCACATTTTT
1 TTCAAAGTCCACAACTCCA-TAGCACCTTTTCCTTTT-AAGTCCATAACTCCATGGCACATTTTT
*
318890 TTAAGCCCACAATTCCGTGGCATCCCTT
64 TTAAGCCCACAACTCCGTGGCATCCCTT
* ** * *
318918 TTCAAAGTCCACAACTCCATGGTGCCTCTTTTCTTTTAAGTCCATAACTCCATGGCACCTTTTCC
1 TTCAAAGTCCACAACTCCATAGCACCT-TTTCCTTTTAAGTCCATAACTCCATGGCA-CATTT--
*
318983 TTTTAAGTCCACAACTCCGTGGCATCCCTT
62 TTTTAAGCCCACAACTCCGTGGCATCCCTT
* * *
319013 TTTAAAGTCTACAACTCCATAGCACCTTTTCCTTTTAAATCCATAA
1 TTCAAAGTCCACAACTCCATAGCACCTTTTCCTTTTAAGTCCATAA
319059 TTTTGTGGCA
Statistics
Matches: 193, Mismatches: 24, Indels: 17
0.82 0.10 0.07
Matches are distributed among these distances:
87 72 0.37
88 24 0.12
89 2 0.01
92 19 0.10
93 9 0.05
94 17 0.09
95 50 0.26
ACGTcount: A:0.25, C:0.31, G:0.11, T:0.32
Consensus pattern (91 bp):
TTCAAAGTCCACAACTCCATAGCACCTTTTCCTTTTAAGTCCATAACTCCATGGCACATTTTTTT
AAGCCCACAACTCCGTGGCATCCCTT
Found at i:319039 original size:62 final size:59
Alignment explanation
Indices: 318951--319087 Score: 175
Period size: 62 Copynumber: 2.3 Consensus size: 59
318941 GCCTCTTTTC
* * * *
318951 TTTTAAGTCCATAACTCCATGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCATCCCT
1 TTTTAAGTCTACAACTCCATAGCACCTTTTCCTTTTAAATCCACAACTCCGTGGCA--CCT
* * **
319012 TTTTAAAGTCTACAACTCCATAGCACCTTTTCCTTTTAAATCCATAATTTTGTGGCACCT
1 TTTT-AAGTCTACAACTCCATAGCACCTTTTCCTTTTAAATCCACAACTCCGTGGCACCT
319072 TTTTAAGTCTACAACT
1 TTTTAAGTCTACAACT
319088 TCGTGGCTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 12 0.18
60 7 0.10
61 4 0.06
62 44 0.66
ACGTcount: A:0.25, C:0.28, G:0.09, T:0.38
Consensus pattern (59 bp):
TTTTAAGTCTACAACTCCATAGCACCTTTTCCTTTTAAATCCACAACTCCGTGGCACCT
Found at i:319158 original size:32 final size:32
Alignment explanation
Indices: 319122--319701 Score: 520
Period size: 32 Copynumber: 18.1 Consensus size: 32
319112 CACAACTCCA
*
319122 TGGC-ACCATTTTCTAAGGCCCACACAAGTTGG
1 TGGCAACC-TTTTCTAAAGCCCACACAAGTTGG
** ** * **
319154 TGGCAACCCCCTTC-AAAAACC-CATAAGTCAG
1 TGGCAA-CCTTTTCTAAAGCCCACACAAGTTGG
* * *
319185 TGGTAACCCTTTTCTAAAACCCACGCAAGTTGG
1 TGGCAA-CCTTTTCTAAAGCCCACACAAGTTGG
* *
319218 TGGCAA-CTTCTTCTAAAACCCATACAAGTTGG
1 TGGCAACCTT-TTCTAAAGCCCACACAAGTTGG
**
319250 TGGCAACCTCTTT-TAAAGCCCACACAAGTCAG
1 TGGCAACCT-TTTCTAAAGCCCACACAAGTTGG
*
319282 T-GCAACCCTTCTCTAAAGCCCACACAAGTTGG
1 TGGCAA-CCTTTTCTAAAGCCCACACAAGTTGG
*
319314 TGGCAACCTTTTCTAAAGCCCACACAAGTTAG
1 TGGCAACCTTTTCTAAAGCCCACACAAGTTGG
* *
319346 TGGCAACCTCTTT-AAAAGTCCACACAAGTTGG
1 TGGCAACCT-TTTCTAAAGCCCACACAAGTTGG
* *
319378 TGGCAACCCTTCTCTAAAGCCCACACAACTTGG
1 TGGCAA-CCTTTTCTAAAGCCCACACAAGTTGG
*
319411 TGGCAACCTCTTCTAAAGCCCACACAAGTTGG
1 TGGCAACCTTTTCTAAAGCCCACACAAGTTGG
* * * * *
319443 TGACAACCTCTTT-AAAAGCCCATACAAGTCGA
1 TGGCAACCT-TTTCTAAAGCCCACACAAGTTGG
319475 TGGCAACCCTTTTCTAAAGCCCACACAAGTTGG
1 TGGCAA-CCTTTTCTAAAGCCCACACAAGTTGG
* * * *
319508 TGGC-A--TCTTCTAAAGCCAACACAAGTCGA
1 TGGCAACCTTTTCTAAAGCCCACACAAGTTGG
* **
319537 TGGCAACC-CTTCTCAAAGCCCACACAAGTCAG
1 TGGCAACCTTTTCT-AAAGCCCACACAAGTTGG
* **
319569 TGGCAAACCTTCTCTAAAGCCCACACAAGTTAA
1 TGGC-AACCTTTTCTAAAGCCCACACAAGTTGG
* * * *
319602 TGGCAACC-CTTCTAAGGCCCACACAAGGTAG
1 TGGCAACCTTTTCTAAAGCCCACACAAGTTGG
* * * *
319633 TAGCAACTCTTCTCTAAAGCCCACACAAGTCGA
1 TGGCAAC-CTTTTCTAAAGCCCACACAAGTTGG
* *
319666 TGGCAACCCTCTTCAAAAGCCCACACAAGTTGG
1 TGGCAA-CCTTTTCTAAAGCCCACACAAGTTGG
319699 TGG
1 TGG
319702 AATCTCCTTT
Statistics
Matches: 444, Mismatches: 79, Indels: 49
0.78 0.14 0.09
Matches are distributed among these distances:
29 24 0.05
30 1 0.00
31 56 0.13
32 213 0.48
33 143 0.32
34 7 0.02
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (32 bp):
TGGCAACCTTTTCTAAAGCCCACACAAGTTGG
Found at i:319418 original size:97 final size:97
Alignment explanation
Indices: 319132--319701 Score: 678
Period size: 97 Copynumber: 5.9 Consensus size: 97
319122 TGGCACCATT
* * * * * *
319132 TTCTAAGGCCCACACAAGTTGGTGGCAACCCCCTTCAAAA-ACC-CATAAGTCAGTGGTAACCCT
1 TTCTAAAGCCCACACAAGTTGGTGGCAA-CCTCTTTAAAAGCCCACACAAGTCAGTGGCAACCCT
* * * *
319195 TTTCTAAAACCCACGCAAGTTGGTGGCAACTTC
65 TCTCTAAAGCCCACACAAGTTGGTGGCAACCTC
* * *
319228 TTCTAAAACCCATACAAGTTGGTGGCAACCTCTTTTAAAGCCCACACAAGTCAGT-GCAACCCTT
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTCTTTAAAAGCCCACACAAGTCAGTGGCAACCCTT
*
319292 CTCTAAAGCCCACACAAGTTGGTGGCAACCTT
66 CTCTAAAGCCCACACAAGTTGGTGGCAACCTC
* * **
319324 TTCTAAAGCCCACACAAGTTAGTGGCAACCTCTTTAAAAGTCCACACAAGTTGGTGGCAACCCTT
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTCTTTAAAAGCCCACACAAGTCAGTGGCAACCCTT
*
319389 CTCTAAAGCCCACACAACTTGGTGGCAACCTC
66 CTCTAAAGCCCACACAAGTTGGTGGCAACCTC
* *
319421 TTCTAAAGCCCACACAAGTTGGTGACAACCTCTTTAAAAGCCCATACAAGTC-GATGGCAACCCT
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTCTTTAAAAGCCCACACAAGTCAG-TGGCAACCCT
*
319485 TTTCTAAAGCCCACACAAGTTGGTGGC-A--TC
65 TCTCTAAAGCCCACACAAGTTGGTGGCAACCTC
* * * * *
319515 TTCTAAAGCCAACACAAGTCGATGGCAACC-CTTCTCAAAGCCCACACAAGTCAGTGGCAAACCT
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTCTT-TAAAAGCCCACACAAGTCAGTGGCAACCCT
**
319579 TCTCTAAAGCCCACACAAGTTAATGGCAACC-C
65 TCTCTAAAGCCCACACAAGTTGGTGGCAACCTC
* * * * *
319611 TTCTAAGGCCCACACAAGGTAGTAGCAA-CTCTTCTCTAAAGCCCACACAAGTC-GATGGCAACC
1 TTCTAAAGCCCACACAAGTTGGTGGCAACCTCTT-T-AAAAGCCCACACAAGTCAG-TGGCAACC
*
319674 C-TCTTCAAAAGCCCACACAAGTTGGTGG
63 CTTC-TCTAAAGCCCACACAAGTTGGTGG
319702 AATCTCCTTT
Statistics
Matches: 409, Mismatches: 52, Indels: 25
0.84 0.11 0.05
Matches are distributed among these distances:
93 3 0.01
94 77 0.19
95 11 0.03
96 142 0.35
97 176 0.43
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (97 bp):
TTCTAAAGCCCACACAAGTTGGTGGCAACCTCTTTAAAAGCCCACACAAGTCAGTGGCAACCCTT
CTCTAAAGCCCACACAAGTTGGTGGCAACCTC
Found at i:319961 original size:52 final size:52
Alignment explanation
Indices: 319878--320268 Score: 214
Period size: 52 Copynumber: 7.2 Consensus size: 52
319868 ATCATTCTTC
* * **
319878 TCATCTTTAAGTCTAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTG
1 TCATCTTTAAGCCTAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTG
* * * * *
319930 TCATCTTTAAGCCTAATATCACTAGCTTTGAATCAACACATTGGCACCTTTA
1 TCATCTTTAAGCCTAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTG
* * * *
319982 TCATCTTTGAGCCTAATATCGCTGGCCTTGAATTAGCATATCGGCATTTTTATCATTCTTT-
1 TCATCTTTAAGCCTAATATCACTGGCCTTGAATCAGCATATTGGC------A-C---CTTTG
* * ** * * *
320043 TCATCTTTAAGTCC-ATTTTCGTTGGCCTTGAATCAACACATTGGCACCTTAG
1 TCATCTTTAAG-CCTAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTG
* * * ** * *
320095 TCATCTTTAAG-CTCAATATCACTAGCCGTCAATCAGCATATCAGCACTTTTATTATTCTTC
1 TCATCTTTAAGCCT-AATATCACTGGCCTTGAATCAGCATATTGGCAC--------CT-TTG
* * * * * *
320156 TCATCTTCAAGTCC-AATGTCACTAGCCTTGAATCAACACATTGGCACTTTTG
1 TCATCTTTAAG-CCTAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTG
* * * *
320208 TCATTTTTAAGCCTAATATCACTGGCTTTGAATCAGCATATTGGCATCTTTA
1 TCATCTTTAAGCCTAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTG
320260 TCATACTTT
1 TCAT-CTTT
320269 TCATCTTCAA
Statistics
Matches: 252, Mismatches: 60, Indels: 53
0.69 0.16 0.15
Matches are distributed among these distances:
50 1 0.00
51 5 0.02
52 158 0.63
53 5 0.02
54 1 0.00
55 1 0.00
58 1 0.00
59 1 0.00
60 1 0.00
61 71 0.28
62 6 0.02
63 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (52 bp):
TCATCTTTAAGCCTAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTG
Found at i:320088 original size:165 final size:166
Alignment explanation
Indices: 319800--320120 Score: 459
Period size: 165 Copynumber: 1.9 Consensus size: 166
319790 CTTTAATTAG
* * * *
319800 CACATTGGCATATTTGTCATCTTTAAGCCCAATATCGTTTGCCTTGAATCAGCATATCGACAATT
1 CACATTGGCACATTTATCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATCGACAATT
* * *
319865 TTTATCATTCTTCTCATCTTTAAGTCTAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTG
66 TTTATCATTCTTCTCATCTTTAAGTCTAATGTTGCTGGCCTTGAATCAACACATTGGCACCTTAG
319930 TCATCTTTAAGC-CTAATATCACTAGCTTTGAATCAA
131 TCATCTTTAAGCTC-AATATCACTAGCTTTGAATCAA
* * * * *
319966 CACATTGGCACCTTTATCATCTTTGAGCCTAATATCGCTGGCCTTGAATTAGCATATCGGC-ATT
1 CACATTGGCACATTTATCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATCGACAATT
* * * *
320030 TTTATCATTCTTTTCATCTTTAAGTC-CATTTTCGTTGGCCTTGAATCAACACATTGGCACCTTA
66 TTTATCATTCTTCTCATCTTTAAGTCTAATGTT-GCTGGCCTTGAATCAACACATTGGCACCTTA
320094 GTCATCTTTAAGCTCAATATCACTAGC
130 GTCATCTTTAAGCTCAATATCACTAGC
320121 CGTCAATCAG
Statistics
Matches: 137, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
164 4 0.03
165 80 0.58
166 53 0.39
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.38
Consensus pattern (166 bp):
CACATTGGCACATTTATCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATCGACAATT
TTTATCATTCTTCTCATCTTTAAGTCTAATGTTGCTGGCCTTGAATCAACACATTGGCACCTTAG
TCATCTTTAAGCTCAATATCACTAGCTTTGAATCAA
Found at i:320133 original size:113 final size:113
Alignment explanation
Indices: 319925--320306 Score: 419
Period size: 113 Copynumber: 3.4 Consensus size: 113
319915 ATATTGGCAC
* * *
319925 CTTTGTCATCTTTAAG-CCTAATATCACTAGCTTTGAATCAACACATTGGCACCTTTA-TCATCT
1 CTTT-TCATCTTCAAGTCC-AATGTCACTAGCCTTGAATCAACACATTGGCACC-TTAGTCATCT
* * *
319988 TTGAGCCTAATATCGCTGGCCTTGAATTAGCATATCGGCATTTTTATCATT
63 TTAAGCCTAATATCACTGGCCTTGAATCAGCATATCGGCATTTTTATCATT
* * * ** *
320039 CTTTTCATCTTTAAGTCCATTTTCGTTGGCCTTGAATCAACACATTGGCACCTTAGTCATCTTTA
1 CTTTTCATCTTCAAGTCCAATGTCACTAGCCTTGAATCAACACATTGGCACCTTAGTCATCTTTA
* * * * * *
320104 AG-CTCAATATCACTAGCCGTCAATCAGCATATCAGCACTTTTATTATT
66 AGCCT-AATATCACTGGCCTTGAATCAGCATATCGGCATTTTTATCATT
* * * *
320152 CTTCTCATCTTCAAGTCCAATGTCACTAGCCTTGAATCAACACATTGGCACTTTTGTCATTTTTA
1 CTTTTCATCTTCAAGTCCAATGTCACTAGCCTTGAATCAACACATTGGCACCTTAGTCATCTTTA
* * * *
320217 AGCCTAATATCACTGGCTTTGAATCAGCATATTGGCATCTTTATCATA
66 AGCCTAATATCACTGGCCTTGAATCAGCATATCGGCATTTTTATCATT
* * * * * *
320265 CTTTTCATCTTCAAGCCCGATATCGCTAACCATGAATCAACA
1 CTTTTCATCTTCAAGTCCAATGTCACTAGCCTTGAATCAACA
320307 TAGTGGCGCC
Statistics
Matches: 222, Mismatches: 42, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
112 5 0.02
113 209 0.94
114 8 0.04
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (113 bp):
CTTTTCATCTTCAAGTCCAATGTCACTAGCCTTGAATCAACACATTGGCACCTTAGTCATCTTTA
AGCCTAATATCACTGGCCTTGAATCAGCATATCGGCATTTTTATCATT
Found at i:321127 original size:20 final size:21
Alignment explanation
Indices: 321085--321133 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
321075 TATAAATAGT
321085 AAATGTATCGATACATAGGTG
1 AAATGTATCGATACATAGGTG
*
321106 -AATGTATCGATACAT-GCTTG
1 AAATGTATCGATACATAG-GTG
321126 AAATGTAT
1 AAATGTAT
321134 TGACACAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 1 0.04
20 17 0.68
21 7 0.28
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (21 bp):
AAATGTATCGATACATAGGTG
Found at i:321233 original size:20 final size:21
Alignment explanation
Indices: 321188--321242 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
321178 CATAAGTAAA
*
321188 TGTATTGATACATTTACTATT
1 TGTATCGATACATTTACTATT
321209 TGTATCGATACA-TTATCTA-T
1 TGTATCGATACATTTA-CTATT
321229 TGTATCGATACATT
1 TGTATCGATACATT
321243 CTGAGTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (21 bp):
TGTATCGATACATTTACTATT
Found at i:324561 original size:13 final size:13
Alignment explanation
Indices: 324543--324568 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
324533 TCACTATTCA
324543 TGTATCGATACAT
1 TGTATCGATACAT
324556 TGTATCGATACAT
1 TGTATCGATACAT
324569 CATAAATAGT
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):
TGTATCGATACAT
Found at i:328126 original size:21 final size:21
Alignment explanation
Indices: 328074--328146 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
328064 TTTATTCAAT
* *
328074 ATAAAAAATAATAATAAGTAGAA
1 ATAAAAATTAATAA-AAATA-AA
328097 ATCAAAAATTAA-AAAAATAAAA
1 AT-AAAAATTAATAAAAAT-AAA
* *
328119 ATAAAAATTAATAGAAATCAA
1 ATAAAAATTAATAAAAATAAA
328140 ATAAAAA
1 ATAAAAA
328147 AAATCATGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 18 0.42
22 12 0.28
23 5 0.12
24 8 0.19
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.21
Consensus pattern (21 bp):
ATAAAAATTAATAAAAATAAA
Found at i:328149 original size:38 final size:38
Alignment explanation
Indices: 328077--328150 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
328067 ATTCAATATA
* *
328077 AAAAATAATAATAAGTAGAAATCAAAAATTAAAAAAAT
1 AAAAATAAAAATAAGTAGAAATCAAAAATAAAAAAAAT
328115 AAAAATAAAAATTAA-TAGAAATC--AAATAAAAAAAAT
1 AAAAATAAAAA-TAAGTAGAAATCAAAAATAAAAAAAAT
328151 CATGAAATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 12 0.36
38 18 0.55
39 3 0.09
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.20
Consensus pattern (38 bp):
AAAAATAAAAATAAGTAGAAATCAAAAATAAAAAAAAT
Found at i:328836 original size:82 final size:82
Alignment explanation
Indices: 328699--329060 Score: 508
Period size: 82 Copynumber: 4.4 Consensus size: 82
328689 AAACTCTAGC
* * *
328699 AGCTTCAGGCAGCAGCAGCATCCATCAACACCGACAGCAGCTCGAGCCTCTTCCAGTCCACGAAC
1 AGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGCAGCTCGAGCCTCTTCCAGCCCACGAAC
328764 ACGGCAGCAGCTCCAGT
66 ACGGCAGCAGCTCCAGT
* * * *
328781 AGCTTCAGGCAGCAGCTGCATCCATCAACACCGGCAGTAGCTCGAGCCTCTTCCAGTCCACGAAC
1 AGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGCAGCTCGAGCCTCTTCCAGCCCACGAAC
*
328846 ACGGCAGCAGCTCAAGT
66 ACGGCAGCAGCTCCAGT
* *
328863 AGCTTCAGGCAGCAGCTGCATCCATCAATACCTGCAGCAGCTCGAGCCTCTTCCAGCCCACGAAC
1 AGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGCAGCTCGAGCCTCTTCCAGCCCACGAAC
* *
328928 ACGGTAGCAGCTCTAGT
66 ACGGCAGCAGCTCCAGT
* * * * * * * *
328945 AGCTTTAAGCAGCAGCAACATCCATCAATACCAGTAGCAGCTCAAGCCTTTTCTAGCCCACGAAC
1 AGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGCAGCTCGAGCCTCTTCCAGCCCACGAAC
* *
329010 ACGGCCGCAGCTCCAGC
66 ACGGCAGCAGCTCCAGT
* *
329027 AGCTTCAGGCAGTAGCAACATCCATCAATACCGG
1 AGCTTCAGGCAGCAGCAGCATCCATCAATACCGG
329061 TACTGACCAA
Statistics
Matches: 253, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 253 1.00
ACGTcount: A:0.27, C:0.35, G:0.21, T:0.16
Consensus pattern (82 bp):
AGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGCAGCTCGAGCCTCTTCCAGCCCACGAAC
ACGGCAGCAGCTCCAGT
Found at i:331566 original size:82 final size:82
Alignment explanation
Indices: 331429--331625 Score: 243
Period size: 82 Copynumber: 2.4 Consensus size: 82
331419 CTGGGGTTGG
* * * *
331429 TGGATGCTGGTGCTG-CTGGAAACTGCTAGAGCTGCTGCCGTGTTCGTGGGCTGGAAAAGGCTCG
1 TGGATGCTGCTGCTGCCT-GAAGCTGCTAGAGCTACTACCGTGTTCGTGGGCTGGAAAAGGCTCG
* * * *
331493 CGCTGCTGCTGGTATTGA
65 AGCTGCTACCGATATTGA
* * * *
331511 TGGATGCTGCTGCTGCCTGAAGCTACTAGAGCTACTATCGTGTTGGTGGGCTGGAAGAGGCTCGA
1 TGGATGCTGCTGCTGCCTGAAGCTGCTAGAGCTACTACCGTGTTCGTGGGCTGGAAAAGGCTCGA
331576 GCTGCTACCGATATTGA
66 GCTGCTACCGATATTGA
** *
331593 TGGATGCTATTGCTGCCTGAAGCTGCTCGAGCT
1 TGGATGCTGCTGCTGCCTGAAGCTGCTAGAGCT
331626 GCTGCTGGTA
Statistics
Matches: 98, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
82 96 0.98
83 2 0.02
ACGTcount: A:0.17, C:0.21, G:0.35, T:0.27
Consensus pattern (82 bp):
TGGATGCTGCTGCTGCCTGAAGCTGCTAGAGCTACTACCGTGTTCGTGGGCTGGAAAAGGCTCGA
GCTGCTACCGATATTGA
Found at i:331624 original size:47 final size:47
Alignment explanation
Indices: 331570--331672 Score: 134
Period size: 47 Copynumber: 2.2 Consensus size: 47
331560 GCTGGAAGAG
* *
331570 GCTCGAGCTGCTACCGATATTGATGGATGCTATTGCTGCCTGAAGCT
1 GCTCGAGCTGCTACCGATATTGATAGATGCTACTGCTGCCTGAAGCT
* * * * *
331617 GCTCGAGCTGCTGCTGGTATTGATAGATGTTGCTGCTGCCTGAAGCT
1 GCTCGAGCTGCTACCGATATTGATAGATGCTACTGCTGCCTGAAGCT
*
331664 GCTGGAGCT
1 GCTCGAGCT
331673 ACTGTCGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.17, C:0.22, G:0.31, T:0.30
Consensus pattern (47 bp):
GCTCGAGCTGCTACCGATATTGATAGATGCTACTGCTGCCTGAAGCT
Found at i:331754 original size:129 final size:129
Alignment explanation
Indices: 331488--331743 Score: 361
Period size: 129 Copynumber: 2.0 Consensus size: 129
331478 GCTGGAAAAG
* *
331488 GCTCGCGCTGCTGCTGGTATTGATGGATGCTGCTGCTGCCTGAAGCTACTAGAGCTACTATCGTG
1 GCTCGAGCTGCTGCTGGTATTGATAGATGCTGCTGCTGCCTGAAGCTACTAGAGCTACTATCGTG
* * * * *
331553 TTGGTGGGCTGGAAGAGGCTCGAGCTGCTACCGATATTGATGGATGCTATTGCTGCCTGAAGCT
66 TTCGTGGACTGGAAGAGGCTCGAGCTGCTACAGATATTGATGGATGCTACTGCTACCTGAAGCT
* * * *
331617 GCTCGAGCTGCTGCTGGTATTGATAGATGTTGCTGCTGCCTGAAGCTGCTGGAGCTACTGTCGTG
1 GCTCGAGCTGCTGCTGGTATTGATAGATGCTGCTGCTGCCTGAAGCTACTAGAGCTACTATCGTG
* ** *
331682 TTCGTGGACTGGAAGAGGCTTGAGCTGCTGTTAG-TATTGATGGATGCTGCTGCTACCTGAAG
66 TTCGTGGACTGGAAGAGGCTCGAGCTGCT-ACAGATATTGATGGATGCTACTGCTACCTGAAG
331744 TTGTTGGAGC
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
129 110 0.99
130 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (129 bp):
GCTCGAGCTGCTGCTGGTATTGATAGATGCTGCTGCTGCCTGAAGCTACTAGAGCTACTATCGTG
TTCGTGGACTGGAAGAGGCTCGAGCTGCTACAGATATTGATGGATGCTACTGCTACCTGAAGCT
Found at i:338942 original size:20 final size:20
Alignment explanation
Indices: 338917--338971 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
338907 CTGCCAAGGA
338917 AATGTATCGATACATT-ATTC
1 AATGTATCGATACATTGA-TC
338937 AATGTATCGATACATTGATC
1 AATGTATCGATACATTGATC
**
338957 TTTGTATCGATACAT
1 AATGTATCGATACAT
338972 CTAGGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:339899 original size:13 final size:13
Alignment explanation
Indices: 339881--339937 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
339871 CATAAAGTGT
339881 TGTATCGATACAA
1 TGTATCGATACAA
339894 TGTATCGATACATAA
1 TGTATCGATAC--AA
339909 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
339926 TGTATCGATACA
1 TGTATCGATACA
339938 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:339916 original size:32 final size:32
Alignment explanation
Indices: 339864--339958 Score: 172
Period size: 32 Copynumber: 2.9 Consensus size: 32
339854 AACGATTTGC
339864 ATCGATACATAAAGTGTTGTATCGATACAATGT
1 ATCGATACAT-AAGTGTTGTATCGATACAATGT
339897 ATCGATACATAAGTGTTGTATCGATACAATGT
1 ATCGATACATAAGTGTTGTATCGATACAATGT
*
339929 ATCGATACATAAGTTTTGTATCGATACAAT
1 ATCGATACATAAGTGTTGTATCGATACAAT
339959 TTAAGCTACT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.84
33 10 0.16
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
ATCGATACATAAGTGTTGTATCGATACAATGT
Found at i:339918 original size:19 final size:18
Alignment explanation
Indices: 339859--339956 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
339849 ATTTCAACGA
*
339859 TTTGCATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
339878 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
339894 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
339910 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
339926 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
339942 TTTTGTATCGATACA
1 -TTTGTATCGATACA
339957 ATTTAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 24 0.37
20 11 0.17
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:340017 original size:13 final size:13
Alignment explanation
Indices: 339999--340023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
339989 ATTACTCAAA
339999 TGTATCGATACAT
1 TGTATCGATACAT
340012 TGTATCGATACA
1 TGTATCGATACA
340024 CTGATCTTTG
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:342262 original size:24 final size:26
Alignment explanation
Indices: 342235--342285 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
342225 TATCAAAATT
342235 TATTCAT-CG-GGGACACTCCAACCC
1 TATTCATCCGAGGGACACTCCAACCC
*
342259 TATTCCTCCGAAGGGACACTCCAACCC
1 TATTCATCCG-AGGGACACTCCAACCC
342286 CGTTTTCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 2 0.09
27 15 0.65
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (26 bp):
TATTCATCCGAGGGACACTCCAACCC
Found at i:346990 original size:8 final size:8
Alignment explanation
Indices: 346977--347023 Score: 78
Period size: 8 Copynumber: 5.9 Consensus size: 8
346967 AGTTCCCTTA
346977 AAAAAAAC
1 AAAAAAAC
346985 AAAAAAAC
1 AAAAAAAC
346993 -AAAAAAC
1 AAAAAAAC
347000 AAAAAAAC
1 AAAAAAAC
347008 AAAAAAAAC
1 -AAAAAAAC
347017 AAAAAAA
1 AAAAAAA
347024 ACACAGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.19
8 22 0.59
9 8 0.22
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:346990 original size:9 final size:9
Alignment explanation
Indices: 346976--347026 Score: 74
Period size: 9 Copynumber: 6.1 Consensus size: 9
346966 GAGTTCCCTT
346976 AAAAAAAAC
1 AAAAAAAAC
346985 -AAAAAAAC
1 AAAAAAAAC
346993 --AAAAAAC
1 AAAAAAAAC
347000 -AAAAAAAC
1 AAAAAAAAC
347008 AAAAAAAAC
1 AAAAAAAAC
347017 AAAAAAAAC
1 AAAAAAAAC
347026 A
1 A
347027 CAGAAAAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.17
8 15 0.38
9 18 0.45
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:346998 original size:15 final size:16
Alignment explanation
Indices: 346977--347023 Score: 78
Period size: 15 Copynumber: 2.9 Consensus size: 16
346967 AGTTCCCTTA
346977 AAAAAAACAAAAAAAC
1 AAAAAAACAAAAAAAC
346993 -AAAAAACAAAAAAAC
1 AAAAAAACAAAAAAAC
347008 AAAAAAAACAAAAAAA
1 -AAAAAAACAAAAAAA
347024 ACACAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.52
17 14 0.48
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAAAAAC
Found at i:347034 original size:1 final size:1
Alignment explanation
Indices: 346976--347024 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
346966 GAGTTCCCTT
* * * * *
346976 AAAAAAAACAAAAAAACAAAAAACAAAAAAACAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
347025 CACAGAAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:347308 original size:26 final size:25
Alignment explanation
Indices: 347273--347335 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
347263 GTTCTTTGCC
*
347273 AAAAAAAGAAACA-AAACAAAAAAGGA
1 AAAAAAAGAAAAACAAACAAAAAA--A
*
347299 AAAAAAAGAAGAAACAAACAAACAAA
1 AAAAAAAGAA-AAACAAACAAAAAAA
347325 AAAAAAAGAAA
1 AAAAAAAGAAA
347336 GGAAAAACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 1 0.03
26 21 0.64
27 2 0.06
28 9 0.27
ACGTcount: A:0.83, C:0.08, G:0.10, T:0.00
Consensus pattern (25 bp):
AAAAAAAGAAAAACAAACAAAAAAA
Found at i:347312 original size:29 final size:26
Alignment explanation
Indices: 347273--347334 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 26
347263 GTTCTTTGCC
347273 AAAAA-AAGAAACAAAACAAAAAAGGAAA
1 AAAAAGAAGAAAC-AAACAAAAAA--AAA
*
347301 AAAAAGAAGAAACAAACAAACAAAAA
1 AAAAAGAAGAAACAAACAAAAAAAAA
347327 AAAAAGAA
1 AAAAAGAA
347335 AGGAAAAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 11 0.34
28 14 0.44
29 7 0.22
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (26 bp):
AAAAAGAAGAAACAAACAAAAAAAAA
Found at i:347343 original size:26 final size:26
Alignment explanation
Indices: 347273--347343 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 26
347263 GTTCTTTGCC
*
347273 AAAAAAAGAAA-CAAAACAAAAAAGGA
1 AAAAAAAGAAAGAAAAACAAAAAA-GA
*
347299 AAAAAAAG-AAGAAACAAACAAACAA-A
1 AAAAAAAGAAAG-AA-AAACAAAAAAGA
347325 AAAAAAAGAAAGGAAAAAC
1 AAAAAAAGAAA-GAAAAAC
347344 CCCTTTTCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
25 2 0.05
26 21 0.55
27 5 0.13
28 10 0.26
ACGTcount: A:0.80, C:0.08, G:0.11, T:0.00
Consensus pattern (26 bp):
AAAAAAAGAAAGAAAAACAAAAAAGA
Found at i:348179 original size:16 final size:17
Alignment explanation
Indices: 348154--348191 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
348144 TTGTGCTGTA
* *
348154 ATCATGACATC-ATGAC
1 ATCATAACATCAATAAC
348170 ATCATAACATCAATAAC
1 ATCATAACATCAATAAC
348187 ATCAT
1 ATCAT
348192 TATTTGCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (17 bp):
ATCATAACATCAATAAC
Found at i:348331 original size:30 final size:30
Alignment explanation
Indices: 348290--348526 Score: 179
Period size: 31 Copynumber: 7.9 Consensus size: 30
348280 CTTCAAATAC
* *
348290 CTTTTCAAAGTCCACAATTCAGTGGCATCT
1 CTTTTCAAAGTCCACGACTCAGTGGCATCT
* *
348320 CTTTCCAAAGTCCACGACTCAGTGGCATTTT
1 CTTTTCAAAGTCCACGACTCAGTGGCA-TCT
348351 CTTTTCAAAGTCCACGACTCAGTGGCA---
1 CTTTTCAAAGTCCACGACTCAGTGGCATCT
* *
348378 ----TCAAAGTCCACAACCTC-GTGGCACCTT
1 CTTTTCAAAGTCCACGA-CTCAGTGGCATC-T
* ** *
348405 ATTCCTTTTAAGTCCATGACTCAGTGGCATCCT
1 CTT--TTCAAAGTCCACGACTCAGTGGCAT-CT
* *
348438 TTTCTTCAAAGTCCACGACTCAGGGGCAT-T
1 CTT-TTCAAAGTCCACGACTCAGTGGCATCT
*
348468 -TTGTCTCAAAGTCCACGACTCAGTGGCATTT
1 CTT-T-TCAAAGTCCACGACTCAGTGGCATCT
* *
348499 TTTCTTCAAAGTCCACGACTCCGTGGCA
1 CTT-TTCAAAGTCCACGACTCAGTGGCA
348527 CCCTTTTAAG
Statistics
Matches: 170, Mismatches: 20, Indels: 33
0.76 0.09 0.15
Matches are distributed among these distances:
23 18 0.11
24 3 0.02
29 3 0.02
30 48 0.28
31 51 0.30
32 28 0.16
33 18 0.11
34 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (30 bp):
CTTTTCAAAGTCCACGACTCAGTGGCATCT
Found at i:348360 original size:31 final size:30
Alignment explanation
Indices: 348291--348526 Score: 204
Period size: 30 Copynumber: 7.9 Consensus size: 30
348281 TTCAAATACC
* * * *
348291 TTTTCAAAGTCCACAATTCAGTGGCATCTC
1 TTTTCAAAGTCCACGACTCAGTGGCATTTT
*
348321 TTTCCAAAGTCCACGACTCAGTGGCATTTT
1 TTTTCAAAGTCCACGACTCAGTGGCATTTT
348351 CTTTTCAAAGTCCACGACTCAGTGGCA----
1 -TTTTCAAAGTCCACGACTCAGTGGCATTTT
*
348378 ---TCAAAGTCCACAACCTC-GTGGCACCTTATT
1 TTTTCAAAGTCCACGA-CTCAGTGGCA--TT-TT
*
348408 CCTTTT--AAGTCCATGACTCAGTGGCATCCTTT
1 --TTTTCAAAGTCCACGACTCAGTGGCAT--TTT
* *
348440 TCTTCAAAGTCCACGACTCAGGGGCATTTT
1 TTTTCAAAGTCCACGACTCAGTGGCATTTT
* *
348470 GTCTCAAAGTCCACGACTCAGTGGCATTTT
1 TTTTCAAAGTCCACGACTCAGTGGCATTTT
*
348500 TTCTTCAAAGTCCACGACTCCGTGGCA
1 TT-TTCAAAGTCCACGACTCAGTGGCA
348527 CCCTTTTAAG
Statistics
Matches: 167, Mismatches: 19, Indels: 39
0.74 0.08 0.17
Matches are distributed among these distances:
23 18 0.11
24 3 0.02
30 58 0.35
31 48 0.29
32 24 0.14
33 15 0.09
35 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (30 bp):
TTTTCAAAGTCCACGACTCAGTGGCATTTT
Found at i:348398 original size:23 final size:23
Alignment explanation
Indices: 348355--348400 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
348345 CATTTTCTTT
*
348355 TCAAAGTCCACGACTCAGTGGCA
1 TCAAAGTCCACAACTCAGTGGCA
348378 TCAAAGTCCACAACCTC-GTGGCA
1 TCAAAGTCCACAA-CTCAGTGGCA
348401 CCTTATTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (23 bp):
TCAAAGTCCACAACTCAGTGGCA
Found at i:348432 original size:33 final size:32
Alignment explanation
Indices: 348378--348533 Score: 162
Period size: 32 Copynumber: 4.9 Consensus size: 32
348368 CTCAGTGGCA
*
348378 TCAAAGTCCACAACCTC-GTGGCA-CCTTATTCCT
1 TCAAAGTCCACGA-CTCAGTGGCATCCTT-TT-CT
** *
348411 TTTAAGTCCATGACTCAGTGGCATCCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCCTTTTCT
*
348443 TCAAAGTCCACGACTCAGGGGCAT--TTTGTC-
1 TCAAAGTCCACGACTCAGTGGCATCCTTT-TCT
*
348473 TCAAAGTCCACGACTCAGTGGCAT-TTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCCTTTTCT
* *
348504 TCAAAGTCCACGACTCCGTGGCACCCTTTT
1 TCAAAGTCCACGACTCAGTGGCATCCTTTT
348534 AAGCCCACAA
Statistics
Matches: 105, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
30 28 0.27
31 27 0.26
32 29 0.28
33 17 0.16
34 4 0.04
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.31
Consensus pattern (32 bp):
TCAAAGTCCACGACTCAGTGGCATCCTTTTCT
Found at i:348573 original size:34 final size:34
Alignment explanation
Indices: 348534--348829 Score: 305
Period size: 34 Copynumber: 8.8 Consensus size: 34
348524 GCACCCTTTT
* *
348534 AAGCCCACAACTCCGTGGCACCTTCTCCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
* * **
348568 AAGCCCAAAACTTCGTGGCACCTTTTTCTTTTTG
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
* **
348602 AAGCCCACAACTCCATGGCACCTTTTTCTTTTTG
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
*
348636 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
* *
348670 AAGCCCACAACTCTGTGGTACCTTTTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
* ** *
348704 AAGCCCACCACTCTATGGCACCTTTTT-TTTT-T
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
* * * * *
348736 AAGTCCACGACCCCGTGGCACCTTGTTCCTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
* * * *
348770 AAGTCCACAACTTCGTGGCA---TCTCCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
* *
348801 AAGCCCATAACTCTGTGGCACTCTTTTTC
1 AAGCCCACAACTCCGTGGCAC-CTTTTTC
348830 CCTTTTAAGT
Statistics
Matches: 218, Mismatches: 38, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
31 24 0.11
32 21 0.10
33 7 0.03
34 163 0.75
35 3 0.01
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
Found at i:348614 original size:68 final size:67
Alignment explanation
Indices: 348530--348907 Score: 325
Period size: 68 Copynumber: 5.7 Consensus size: 67
348520 CGTGGCACCC
* *
348530 TTTTAAGCCCACAACTCCGTGGCACCTTCTCCTTTTCAAAGCCCAAAACTTCGTGGCACCTTTTT
1 TTTTAAGCCCACAACTCCGTGGCACCTTTTCCTTTTCAAAGCCCACAACTTCGTGGCACCTTTTT
348595 CT
66 CT
* * ** *
348597 TTTTGAAGCCCACAACTCCATGGCACCTTTTTCTTTTTGAAGCCCACAACTCCGTGGCACCTTTT
1 TTTT-AAGCCCACAACTCCGTGGCACCTTTTCCTTTTCAAAGCCCACAACTTCGTGGCACCTTTT
348662 TCT
65 TCT
* * * * *
348665 TTTTAAAGCCCACAACTCTGTGGTACCTTTTTCTTTTCAAAGCCCACCAC-TCTATGGCACCTTT
1 TTTT-AAGCCCACAACTCCGTGGCACCTTTTCCTTTTCAAAGCCCACAACTTC-GTGGCACCTTT
348729 TT-T
64 TTCT
* * * * *
348732 TTTTAAGTCCACGACCCCGTGGCACCTTGTTCC-TTTCAAAGTCCACAACTTCGTGGCA---TCT
1 TTTTAAGCCCACAACTCCGTGGCACCTT-TTCCTTTTCAAAGCCCACAACTTCGTGGCACCTTTT
*
348793 CCT
65 TCT
* * * * *
348796 TTTCAAAGCCCATAACTCTGTGGCACTCTTTTTCCCTTTT--AAGTCCACAATTTCGTGGCACC-
1 TTT-TAAGCCCACAACTCCGTGGCAC-C-TTTT-CCTTTTCAAAGCCCACAACTTCGTGGCACCT
348858 ----C-
62 TTTTCT
* * * *
348859 TTTTAAGTCTACAACTCTGTGGCATCTTTCTCCTTTTCAAAAGCCCACA
1 TTTTAAGCCCACAACTCCGTGGCACCTTT-TCCTTTTC-AAAGCCCACA
348908 CAAGTCGGTG
Statistics
Matches: 255, Mismatches: 40, Indels: 36
0.77 0.12 0.11
Matches are distributed among these distances:
60 9 0.04
61 2 0.01
62 17 0.07
63 13 0.05
64 5 0.02
65 16 0.06
66 60 0.24
67 19 0.07
68 114 0.45
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.35
Consensus pattern (67 bp):
TTTTAAGCCCACAACTCCGTGGCACCTTTTCCTTTTCAAAGCCCACAACTTCGTGGCACCTTTTT
CT
Found at i:348710 original size:102 final size:100
Alignment explanation
Indices: 348530--348862 Score: 368
Period size: 102 Copynumber: 3.3 Consensus size: 100
348520 CGTGGCACCC
* * *
348530 TTTTAAGCCCACAACTCCGTGGCACCTTCTCCTTTTCAAAGCCCAAAACTTCGTGGCACCTTTTT
1 TTTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTTCGTGG-ACCTTTTT
** *
348595 CTTTTTGAAGCCCACAACTCCATGGCACCTTTTTCT
65 CTTTTCAAAGCCCACAACTCTATGGCACCTTTTTCT
*
348631 TTTTGAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAAC-TCTGTGGTACCTTT
1 TTTT-AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTTC-GTGG-ACCTTT
*
348695 TTCTTTTCAAAGCCCACCACTCTATGGCACCTTTTT-T
63 TTCTTTTCAAAGCCCACAACTCTATGGCACCTTTTTCT
* * * * * * * * *
348732 TTTTAAGTCCACGACCCCGTGGCACCTTGTTCCTTTCAAAGTCCACAACTTCGTGG--CATCTCC
1 TTTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTTCGTGGACCTTTTTC
* * *
348795 TTTTCAAAGCCCATAACTCTGTGGCACTCTTTTTCCC
66 TTTTCAAAGCCCACAACTCTATGGCAC-CTTTTT-CT
* * * *
348832 TTTTAAGTCCACAATTTCGTGGCACCCTTTT
1 TTTTAAGCCCACAACTCCGTGGCACCTTTTT
348863 AAGTCTACAA
Statistics
Matches: 197, Mismatches: 29, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
97 28 0.14
98 6 0.03
100 67 0.34
101 13 0.07
102 83 0.42
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (100 bp):
TTTTAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTTCGTGGACCTTTTTC
TTTTCAAAGCCCACAACTCTATGGCACCTTTTTCT
Found at i:348803 original size:31 final size:30
Alignment explanation
Indices: 348765--348829 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
348755 ACCTTGTTCC
*
348765 TTTCAAAGTCCACAACT-TCGTGGCATCTCCT
1 TTTCAAAGCCCACAACTCT-GTGGCA-CTCCT
* *
348796 TTTCAAAGCCCATAACTCTGTGGCACTCTT
1 TTTCAAAGCCCACAACTCTGTGGCACTCCT
348826 TTTC
1 TTTC
348830 CCTTTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 8 0.27
31 21 0.70
32 1 0.03
ACGTcount: A:0.22, C:0.31, G:0.12, T:0.35
Consensus pattern (30 bp):
TTTCAAAGCCCACAACTCTGTGGCACTCCT
Found at i:348880 original size:27 final size:27
Alignment explanation
Indices: 348829--348882 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
348819 CACTCTTTTT
*
348829 CCCTTTTAAGTCCACAATTTCGTGGCA
1 CCCTTTTAAGTCCACAATCTCGTGGCA
*
348856 CCCTTTTAAGTCTACAA-CTCTGTGGCA
1 CCCTTTTAAGTCCACAATCTC-GTGGCA
348883 TCTTTCTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (27 bp):
CCCTTTTAAGTCCACAATCTCGTGGCA
Found at i:348940 original size:33 final size:33
Alignment explanation
Indices: 348898--349122 Score: 352
Period size: 33 Copynumber: 6.9 Consensus size: 33
348888 CTCCTTTTCA
348898 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCC
* *
348931 AAAGCCCACACAAGTCGGTGGCAACCCTTTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCC
*
348964 AAAGCCCACACAAGTCGGTGGCAACCC-CCT-C
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCC
*
348995 AAAGCCCACACAAGTCGGTGGCAA-CCTTCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTC-TCC
349028 AAAGCCCACACAAGTCGGTGGCAACCCTTCT-C
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCC
* *
349060 AAAGCCCACACAAGTTGGTGGCAACCC-TCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCC
349092 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
349123 AAGCCCAATA
Statistics
Matches: 175, Mismatches: 11, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.01
31 28 0.16
32 54 0.31
33 86 0.49
34 5 0.03
ACGTcount: A:0.28, C:0.36, G:0.19, T:0.17
Consensus pattern (33 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTCC
Found at i:349010 original size:97 final size:97
Alignment explanation
Indices: 348898--349122 Score: 382
Period size: 97 Copynumber: 2.3 Consensus size: 97
348888 CTCCTTTTCA
*
348898 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCCAAAGCCCACACAAGTCGGTGGCAACCCTTTTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCCAAAGCCCACACAAGTCGGTGGCAACCCTTCTC
348963 TAAAGCCCACACAAGTCGGTGGCAACCCCCTC-
66 -AAAGCCCACACAAGTCGGTGGCAACCCCCTCT
*
348995 AAAGCCCACACAAGTCGGTGGCAA-CCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTC-TCCAAAGCCCACACAAGTCGGTGGCAACCCTTCT
* *
349059 CAAAGCCCACACAAGTTGGTGGCAACCCTCTCT
65 CAAAGCCCACACAAGTCGGTGGCAACCCCCTCT
349092 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
349123 AAGCCCAATA
Statistics
Matches: 121, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
96 34 0.28
97 82 0.68
98 5 0.04
ACGTcount: A:0.28, C:0.36, G:0.19, T:0.17
Consensus pattern (97 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTCCAAAGCCCACACAAGTCGGTGGCAACCCTTCTC
AAAGCCCACACAAGTCGGTGGCAACCCCCTCT
Done.