Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold465
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: 646967
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 2 of 4
Found at i:165009 original size:28 final size:29
Alignment explanation
Indices: 164949--165032 Score: 143
Period size: 28 Copynumber: 2.9 Consensus size: 29
164939 AATATGATAT
* *
164949 TAATCTTTGTGATATTATTTTTAATTTAT
1 TAATCTTTGTGATATTATTTTTATTTTAA
164978 TAATCTTTGTGATATTA-TTTTATTTTAA
1 TAATCTTTGTGATATTATTTTTATTTTAA
165006 TAATCTTTGTGATATTATTTTTATTTT
1 TAATCTTTGTGATATTATTTTTATTTT
165033 TTCTTATATA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
28 26 0.50
29 26 0.50
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63
Consensus pattern (29 bp):
TAATCTTTGTGATATTATTTTTATTTTAA
Found at i:166161 original size:20 final size:21
Alignment explanation
Indices: 166138--166188 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
166128 TAATGCACAA
*
166138 TATCGATACATG-ACCA-AATG
1 TATCGATACATGTA-AAGAATG
*
166158 TATCGATACTTGTAAAGAATG
1 TATCGATACATGTAAAGAATG
166179 TATCGATACA
1 TATCGATACA
166189 GGTGATTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (21 bp):
TATCGATACATGTAAAGAATG
Found at i:166267 original size:13 final size:13
Alignment explanation
Indices: 166249--166274 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
166239 ACACACAATA
166249 TGTATCGATACAT
1 TGTATCGATACAT
166262 TGTATCGATACAT
1 TGTATCGATACAT
166275 CCCAAAATGT
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:166270 original size:32 final size:33
Alignment explanation
Indices: 166229--166296 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
166219 CCTTAACTGT
*
166229 TTGTATCGATACA-CACAATATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
* *
166261 TTGTATCGATACATCCCAAAATGTATCGATATA
1 TTGTATCGATACATCACAAAATGTATCGATACA
166294 TTG
1 TTG
166297 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:172457 original size:13 final size:13
Alignment explanation
Indices: 172439--172476 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
172429 CAGCATTCTC
*
172439 TGTATCGATACAT
1 TGTATCGATACAG
172452 TGTATCGATACAG
1 TGTATCGATACAG
172465 TGTATCGATACA
1 TGTATCGATACA
172477 AAGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:174367 original size:33 final size:32
Alignment explanation
Indices: 174302--174378 Score: 118
Period size: 33 Copynumber: 2.4 Consensus size: 32
174292 TAAATTTATG
* * *
174302 ATTAAGAGAGAGTAAGAAAATGTGATTGTTTT
1 ATTAAGGGGGAGTAAGAAAATGTGATTATTTT
174334 ATTAAGGGGGAGTAAGAAACATGTGATTATTTT
1 ATTAAGGGGGAGTAAGAAA-ATGTGATTATTTT
174367 ATTAAGGGGGAG
1 ATTAAGGGGGAG
174379 AAATTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 17 0.41
33 24 0.59
ACGTcount: A:0.38, C:0.01, G:0.30, T:0.31
Consensus pattern (32 bp):
ATTAAGGGGGAGTAAGAAAATGTGATTATTTT
Found at i:174954 original size:13 final size:13
Alignment explanation
Indices: 174936--174960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
174926 ACCTTCAACA
174936 GTATCGATACATT
1 GTATCGATACATT
174949 GTATCGATACAT
1 GTATCGATACAT
174961 GGCCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:175079 original size:13 final size:13
Alignment explanation
Indices: 175061--175086 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
175051 ACACACAATA
175061 TGTATCGATACAT
1 TGTATCGATACAT
175074 TGTATCGATACAT
1 TGTATCGATACAT
175087 CCCAAAATGT
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:175102 original size:33 final size:32
Alignment explanation
Indices: 175041--175108 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
175031 CCTTAACTGT
*
175041 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
175073 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
175106 TTG
1 TTG
175109 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:176592 original size:12 final size:12
Alignment explanation
Indices: 176575--176600 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
176565 ATCTTAGGAC
176575 AATATTTTTAAT
1 AATATTTTTAAT
176587 AATATTTTTAAT
1 AATATTTTTAAT
176599 AA
1 AA
176601 AATAGGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AATATTTTTAAT
Found at i:178503 original size:155 final size:152
Alignment explanation
Indices: 178292--178835 Score: 432
Period size: 155 Copynumber: 3.5 Consensus size: 152
178282 TATGCCAATG
* * * * * * * *
178292 GTGTGTTTAGAATAGGTTTATCCTTTACTTATCATTTTAGTGTATTGTAGGATTATCGGGATACT
1 GTGTGTTTAGGATAGGTTCATCATTTTCTTATCATTTTCGTGTCTT-TAGGGTTATCGAGATACT
*
178357 TTCATGTTGAAAGTATACCTAGATGCATTTTGATAATTTTCTCTAAAATTGAATCCTTGATAGTC
65 TTCATGTTGAAAGTATACCTAGA-GCATTTTGGTAATTTTCT-TAAAATTGAATCCTTGATAGTC
178422 ACTAGGTCGCTTTTATGCTAAAGGT
128 ACTAGGTCGCTTTTATGCTAAAGGT
**
178447 GTGTGTTTAGGATAAATTCATCATTTTCTTATCATTTTCGTGTCCTTTAGGGTTATCGAGATACT
1 GTGTGTTTAGGATAGGTTCATCATTTTCTTATCATTTTCGTGT-CTTTAGGGTTATCGAGATACT
* * *
178512 TTCATATT-AAAGGTATACCTTAGGAGTATTTTGGTAATTTT-TTAAAATCATG--TCC-TAAGT
65 TTCATGTTGAAA-GTATACC-TA-GAGCATTTTGGTAATTTTCTTAAAAT--TGAATCCTTGA-T
* * *
178572 AGTCAGC-AAGTCACTTTTATGCT-AATG-
124 AGTCA-CTAGGTCGCTTTTATGCTAAAGGT
** * * ** *
178599 GTGCATTTAGGATAGGTTCAT-TTTTTACTTATCATTTTCGTGTTCTTTAAGGCCA-CTAAGATA
1 GTGTGTTTAGGATAGGTTCATCATTTT-CTTATCATTTTCGTG-TCTTTAGGGTTATC-GAGATA
* * * * ** *
178662 CTTTCATGTCGAAGGTATACCTAAAGGCATTTTGGTAATTGTCTTAATAACCGAATCCTAGATAG
63 CTTTCATGTTGAAAGTATACCTAGA-GCATTTTGGTAATTTTCTTAA-AATTGAATCCTTGATAG
*
178727 TCACTAGGTCGCTTTTATGCCAAAGGT
126 TCACTAGGTCGCTTTTATGCTAAAGGT
* * * * * *
178754 GTG-GATTTAAGATGGGTTCATC-TCTTTATTTATC-GTTTCGTGTCCTTTAGGTTTA-CTAAGA
1 GTGTG-TTTAGGATAGGTTCATCAT-TTT-CTTATCATTTTCGTGT-CTTTAGGGTTATC-GAGA
* **
178815 TAGTTTCATGTCAAAAGTATA
61 TACTTTCATGTTGAAAGTATA
178836 TACCCTAAAG
Statistics
Matches: 312, Mismatches: 52, Indels: 50
0.75 0.13 0.12
Matches are distributed among these distances:
150 1 0.00
151 22 0.07
152 65 0.21
153 32 0.10
154 37 0.12
155 124 0.40
156 29 0.09
157 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (152 bp):
GTGTGTTTAGGATAGGTTCATCATTTTCTTATCATTTTCGTGTCTTTAGGGTTATCGAGATACTT
TCATGTTGAAAGTATACCTAGAGCATTTTGGTAATTTTCTTAAAATTGAATCCTTGATAGTCACT
AGGTCGCTTTTATGCTAAAGGT
Found at i:181306 original size:41 final size:41
Alignment explanation
Indices: 181249--181330 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
181239 AACATCCCTT
181249 GGTAGTCGCTCATTACTTATATTTCGAGGCACAATGACTAA
1 GGTAGTCGCTCATTACTTATATTTCGAGGCACAATGACTAA
*
181290 GGTAGTGGCTCATTACTTATATTTCGAGGCACAATGACTAA
1 GGTAGTCGCTCATTACTTATATTTCGAGGCACAATGACTAA
181331 ATGAAATTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (41 bp):
GGTAGTCGCTCATTACTTATATTTCGAGGCACAATGACTAA
Found at i:183889 original size:100 final size:97
Alignment explanation
Indices: 183756--183934 Score: 241
Period size: 100 Copynumber: 1.8 Consensus size: 97
183746 GAATGGGGTT
* * *
183756 GGAGTGTCCCCAACGATGGCAATCCAGATGAAAATAATATTTAAAATCTTGACAAGTTTTAAAAA
1 GGAGTGTCCCCAACGATGACAATCCAGACGAAAATAAGATTT-AAATCTTGACAAG-TTTAAAAA
183821 AAGGGATTGGAATATCCCCTCAAAAGAATGAGATC
64 AAGGG-TTGGAATATCCCCTCAAAAGAATGAGATC
* * * * * *
183856 GGAGTTTCCCTAATGATGACAATTCAGACGAAAATAAGATTTAAATTTTGACAAGTTTAAAAATA
1 GGAGTGTCCCCAACGATGACAATCCAGACGAAAATAAGATTTAAATCTTGACAAGTTTAAAAAAA
*
183921 GGGTTGGAGTATCC
66 GGGTTGGAATATCC
183935 TCTAGGGGTT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
97 10 0.14
98 12 0.17
99 12 0.17
100 35 0.51
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (97 bp):
GGAGTGTCCCCAACGATGACAATCCAGACGAAAATAAGATTTAAATCTTGACAAGTTTAAAAAAA
GGGTTGGAATATCCCCTCAAAAGAATGAGATC
Found at i:192501 original size:19 final size:20
Alignment explanation
Indices: 192472--192550 Score: 56
Period size: 19 Copynumber: 4.0 Consensus size: 20
192462 TCATACCTTA
*
192472 AAAAAACAAAAAAACAAAAC
1 AAAAGACAAAAAAACAAAAC
***
192492 AAAAGA-AAAAATTTAAAAC
1 AAAAGACAAAAAAACAAAAC
*
192511 AAAA-ACTAAAAAACAAAA-
1 AAAAGACAAAAAAACAAAAC
*
192529 AACCAAGAGAAAAATAACAAAA
1 AA--AAGACAAAAA-AACAAAA
192551 AAACAAAAAG
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
18 3 0.07
19 22 0.50
20 7 0.16
21 5 0.11
22 7 0.16
ACGTcount: A:0.78, C:0.11, G:0.04, T:0.06
Consensus pattern (20 bp):
AAAAGACAAAAAAACAAAAC
Found at i:192523 original size:14 final size:14
Alignment explanation
Indices: 192473--192529 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 14
192463 CATACCTTAA
*
192473 AAAAACAAAAAAAC
1 AAAAACTAAAAAAC
*
192487 -AAAAC-AAAAGA-
1 AAAAACTAAAAAAC
**
192498 AAAAA-TTTAAAAC
1 AAAAACTAAAAAAC
192511 AAAAACTAAAAAAC
1 AAAAACTAAAAAAC
192525 AAAAA
1 AAAAA
192530 ACCAAGAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
12 12 0.36
13 10 0.30
14 11 0.33
ACGTcount: A:0.81, C:0.11, G:0.02, T:0.07
Consensus pattern (14 bp):
AAAAACTAAAAAAC
Found at i:194022 original size:32 final size:32
Alignment explanation
Indices: 193979--194068 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
193969 TTTCAACAAT
*
193979 TTGTATCGATACAATGTATCGATAGATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
* *
194011 TTGTATTGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
194043 TTGTATCGATACAATGTATCGCTACA
1 TTGTATCGATACAATGTATCGATACA
194069 AAGCTACTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:196167 original size:21 final size:21
Alignment explanation
Indices: 196141--196189 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
196131 ATTTATCCCT
196141 CTCGGATTTCATCTCAAGGTA
1 CTCGGATTTCATCTCAAGGTA
*
196162 CTCGGATTTCATCTCGAGGTA
1 CTCGGATTTCATCTCAAGGTA
196183 CTCGGAT
1 CTCGGAT
196190 GCTTCTATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.33
Consensus pattern (21 bp):
CTCGGATTTCATCTCAAGGTA
Found at i:207734 original size:17 final size:15
Alignment explanation
Indices: 207657--207757 Score: 62
Period size: 18 Copynumber: 6.4 Consensus size: 15
207647 CATCCTCCGC
*
207657 CAAAAAACAAAAAAAA
1 CAAAAAA-AAAACAAA
*
207673 CAAGAAGAAGAAAAAAAA
1 CAA-AA-AA-AAAACAAA
* * *
207691 CAAACAATAAA-TAA
1 CAAAAAAAAAACAAA
*
207705 C-AAAAAAAAACAAC
1 CAAAAAAAAAACAAA
207719 CAAAAAAAAGAGACAAA
1 CAAAAAAAA-A-ACAAA
*
207736 CAAAACAAAAAAAAAA
1 CAAAA-AAAAAACAAA
207752 CAAAAA
1 CAAAAA
207758 GCGTCTGAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
13 7 0.10
14 5 0.07
15 11 0.16
16 15 0.22
17 13 0.19
18 17 0.25
ACGTcount: A:0.80, C:0.13, G:0.05, T:0.02
Consensus pattern (15 bp):
CAAAAAAAAAACAAA
Found at i:207751 original size:41 final size:43
Alignment explanation
Indices: 207657--207756 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 43
207647 CATCCTCCGC
*
207657 CAAAAAACAAAAAAAACAAGAAGAAGAAAAAAAACAAACAATAA
1 CAAAAAA-AAAAAAAACAACAAGAAGAAAAAAAACAAACAATAA
* * * *
207701 -ATAACAAAAAAAAACAACCAA-AA-AAAAGAGACAAACAA-AA
1 CAAAAAAAAAAAAAACAA-CAAGAAGAAAAAAAACAAACAATAA
207741 CAAAAAAAAAACAAAA
1 CAAAAAAAAAA-AAAA
207757 AGCGTCTGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
40 2 0.04
41 21 0.46
42 17 0.37
43 6 0.13
ACGTcount: A:0.80, C:0.13, G:0.05, T:0.02
Consensus pattern (43 bp):
CAAAAAAAAAAAAAACAACAAGAAGAAAAAAAACAAACAATAA
Found at i:209234 original size:30 final size:29
Alignment explanation
Indices: 209194--209279 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
209184 CACCCTATCA
*
209194 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTCC
* * * *
209224 GAAGTCCACAAGTTAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCTTTTCC
*
209253 AAAGCCCACAAGCCAGTGGCAACCTTT
1 AAAGCCCACAAGTCAGTGGC-ACCTTT
209280 AAAAGTCCAC
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
29 22 0.49
30 23 0.51
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCACCTTTTCC
Found at i:209261 original size:29 final size:30
Alignment explanation
Indices: 209194--209279 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 30
209184 CACCCTATCA
*
209194 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* * * *
209224 GAAGTCCACAAGTTAGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* *
209253 AAAGCCCACAAGCCAGTGGCAACCTTT
1 AAAGCCCACAAGTCAGTGGCACCCTTT
209280 AAAAGTCCAC
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
29 23 0.51
30 22 0.49
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTTCC
Found at i:209310 original size:59 final size:58
Alignment explanation
Indices: 209194--209307 Score: 149
Period size: 57 Copynumber: 2.0 Consensus size: 58
209184 CACCCTATCA
* * ** *
209194 AAAGCCCACAAGTCAGTGGCACCCTTTTTCGAAGTCCACAAGTTAGTGGCATCTTTTCC
1 AAAGCCCACAAGCCAGTGGCAACC-TTTTAAAAGTCCACAACTTAGTGGCATCTTTTCC
* *
209253 AAAGCCCACAAGCCAGTGGCAACC-TTTAAAAGTCCACAACTTCGTGGCACCTTTT
1 AAAGCCCACAAGCCAGTGGCAACCTTTTAAAAGTCCACAACTTAGTGGCATCTTTT
209308 TTCTTTTTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 26 0.54
59 22 0.46
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (58 bp):
AAAGCCCACAAGCCAGTGGCAACCTTTTAAAAGTCCACAACTTAGTGGCATCTTTTCC
Found at i:209431 original size:34 final size:35
Alignment explanation
Indices: 209281--209482 Score: 252
Period size: 35 Copynumber: 5.8 Consensus size: 35
209271 GCAACCTTTA
*
209281 AAAGTCCACAACT-TCGTGGCAC-CTTTTTTCTTTTT
1 AAAGCCCACAACTCT-GTGGCACTC-TTTTTCTTTTT
*
209316 AAAGCCCACAACTCCGTGGCAC-CTTTCTTCTTTTT
1 AAAGCCCACAACTCTGTGGCACTCTTT-TTCTTTTT
*
209351 AAAGCCCACAACTCTGTGGCACTATTTTTCCTTTTT
1 AAAGCCCACAACTCTGTGGCACTCTTTTT-CTTTTT
209387 AAAGCCCACAACTCTGTGGCACTCTTTTTCTTTTT
1 AAAGCCCACAACTCTGTGGCACTCTTTTTCTTTTT
* * *
209422 -AAGCCCACAACTCCGTGGCACTATTTTTCCTTTT
1 AAAGCCCACAACTCTGTGGCACTCTTTTTCTTTTT
* * *
209456 -AAGTCTACAACTCTGTGGCACCCTTTT
1 AAAGCCCACAACTCTGTGGCACTCTTTT
209483 AAGCCCACAA
Statistics
Matches: 150, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
34 56 0.37
35 57 0.38
36 37 0.25
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.38
Consensus pattern (35 bp):
AAAGCCCACAACTCTGTGGCACTCTTTTTCTTTTT
Found at i:209492 original size:27 final size:28
Alignment explanation
Indices: 209450--209534 Score: 91
Period size: 29 Copynumber: 3.0 Consensus size: 28
209440 CACTATTTTT
* * *
209450 CCTTTTAAGTCTACAACTCTGTGGC-AC
1 CCTTTTAAGCCCACAACTCAGTGGCAAC
*
209477 CCTTTTAAGCCCACAAGTCAGTGGCAAC
1 CCTTTTAAGCCCACAACTCAGTGGCAAC
* * *
209505 CCTTTCAAAGCCCATAAGTCAGTGGCAAC
1 CCTTT-TAAGCCCACAACTCAGTGGCAAC
209534 C
1 C
209535 TGCAAAAGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
27 21 0.42
28 7 0.14
29 22 0.44
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (28 bp):
CCTTTTAAGCCCACAACTCAGTGGCAAC
Found at i:209523 original size:29 final size:28
Alignment explanation
Indices: 209470--209534 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 28
209460 CTACAACTCT
*
209470 GTGGC-ACCCTTTTAAGCCCACAAGTCA
1 GTGGCAACCCTTTAAAGCCCACAAGTCA
*
209497 GTGGCAACCCTTTCAAAGCCCATAAGTCA
1 GTGGCAACCCTTT-AAAGCCCACAAGTCA
209526 GTGGCAACC
1 GTGGCAACC
209535 TGCAAAAGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 5 0.15
28 7 0.21
29 22 0.65
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.20
Consensus pattern (28 bp):
GTGGCAACCCTTTAAAGCCCACAAGTCA
Found at i:209551 original size:28 final size:29
Alignment explanation
Indices: 209483--209551 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
209473 GCACCCTTTT
* *
209483 AAGCCCACAAGTCAGTGGCAACCCTTTCA
1 AAGCACACAAGTCAGTGGCAACCCTTGCA
* *
209512 AAGCCCATAAGTCAGTGGCAA-CC-TGCAA
1 AAGCACACAAGTCAGTGGCAACCCTTGC-A
*
209540 AAGCATACAAGT
1 AAGCACACAAGT
209552 TGATGCAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 2 0.06
28 12 0.35
29 20 0.59
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.16
Consensus pattern (29 bp):
AAGCACACAAGTCAGTGGCAACCCTTGCA
Found at i:209891 original size:87 final size:87
Alignment explanation
Indices: 209736--209900 Score: 206
Period size: 87 Copynumber: 1.9 Consensus size: 87
209726 GGCATCGGCA
** * * *
209736 TCTTTAAGACCAATGTTGCTGGCCTTGAATCAACACATTGGCATAAGCCCAATATCACTGGCTTT
1 TCTTTAAGACCAATGTCACTGGCCTTGAATCAACACATCGGCACAAGCCCAATATCACTGGCTGT
*
209801 GAATCGGCATATTAGCACCTTG
66 GAATCAGCATATTAGCACCTTG
* ** * **
209823 TCTTTAAGTCCAATGTCACTGGCCTTGAATCAGTACATCGGCACAAGTCCAATATCTTTGG-TCG
1 TCTTTAAGACCAATGTCACTGGCCTTGAATCAACACATCGGCACAAGCCCAATATCACTGGCT-G
209887 TGAATCAGCATATT
65 TGAATCAGCATATT
209901 GGCATCTTTA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
86 1 0.02
87 64 0.98
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (87 bp):
TCTTTAAGACCAATGTCACTGGCCTTGAATCAACACATCGGCACAAGCCCAATATCACTGGCTGT
GAATCAGCATATTAGCACCTTG
Found at i:210779 original size:13 final size:13
Alignment explanation
Indices: 210761--210850 Score: 54
Period size: 13 Copynumber: 6.0 Consensus size: 13
210751 TTCAACAATT
210761 TGTATCGATACAA
1 TGTATCGATACAA
210774 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
210789 GTGTTGTATTGATACAA
1 ----TGTATCGATACAA
210806 TGTATCGATACATAA
1 TGTATCGATAC--AA
210821 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
210838 TGTATCGCTACAA
1 TGTATCGATACAA
210851 AGCTACAGCC
Statistics
Matches: 62, Mismatches: 3, Indels: 24
0.70 0.03 0.27
Matches are distributed among these distances:
13 33 0.53
15 4 0.06
17 4 0.06
19 21 0.34
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:210803 original size:32 final size:32
Alignment explanation
Indices: 210760--210849 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
210750 TTTCAACAAT
210760 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
* *
210792 TTGTATTGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
210824 TTGTATCGATACAATGTATCGCTACA
1 TTGTATCGATACAATGTATCGATACA
210850 AAGCTACAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:210830 original size:19 final size:18
Alignment explanation
Indices: 210774--210836 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
210764 ATCGATACAA
210774 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
*
210793 TGTATTGATAC--AA---
1 TGTATCGATACATAAGTT
210806 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
210825 TGTATCGATACA
1 TGTATCGATACA
210837 ATGTATCGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:212417 original size:21 final size:21
Alignment explanation
Indices: 212391--212431 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
212381 ATCCCTCTCG
212391 GATTTCATCTCGAGGTACTCA
1 GATTTCATCTCGAGGTACTCA
212412 GATTTCATCTCGAGGTACTC
1 GATTTCATCTCGAGGTACTC
212432 GGATGCTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (21 bp):
GATTTCATCTCGAGGTACTCA
Found at i:213666 original size:28 final size:28
Alignment explanation
Indices: 213626--214110 Score: 513
Period size: 28 Copynumber: 16.8 Consensus size: 28
213616 TCATCTCTTA
* *
213626 AAAGCCCATAAGTTAGTGGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
213654 AAAGCCCACAAGTCAGTGGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
*
213682 AAAGCCCACAAGTCAGTGGCACTCTTTTC
1 AAAGCCCACAAGTCAGTGGCAC-CCTTTC
* *
213711 AAAGCCCACAAGTTAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
* * *
213739 AAAGCCCACGAGTCGGTGGCAACTCTTTTC
1 AAAGCCCACAAGTCAGTGGC-AC-CCTTTC
* * *
213769 AAAGCCCATAACTCAGTCGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
* * *
213797 AATGCCCACAAGTCAGTGGCACTCTTTTT
1 AAAGCCCACAAGTCAGTGGCAC-CCTTTC
* *
213826 AAAGCCCACAAGTCAGTGGCATCCTCTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
*
213854 AAAGCCCACAAGTCAGTGGAACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
* * *
213882 AAAGCCCATAATTTAGTGGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
* * *
213910 AAAGCCAACAAGTTAGTGGCACTCTTCTC
1 AAAGCCCACAAGTCAGTGGCACCCTT-TC
* *
213939 AAAGCCCATAAGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
* * *
213967 AAAGCCCATAAGTCAGTGGCACTCATTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTC
*
213995 AAAGCCCACAAGTCAGTGGCACTCTTTTC
1 AAAGCCCACAAGTCAGTGGCAC-CCTTTC
* *
214024 AAAGCCCACAAG-CTAGTGGTAACTCTTTTC
1 AAAGCCCACAAGTC-AGTGG-CAC-CCTTTC
** *
214054 AAAGCCCACACGAGTTGGTGGCAACTCTTTTC
1 AAAGCCCACA--AGTCAGTGGC-AC-CCTTTC
*
214086 AAAGCCCAAACAAGTTAGTGGCACC
1 AAAGCCC--ACAAGTCAGTGGCACC
214111 TTTTTTTAAA
Statistics
Matches: 387, Mismatches: 56, Indels: 26
0.83 0.12 0.06
Matches are distributed among these distances:
28 216 0.56
29 95 0.25
30 40 0.10
31 2 0.01
32 31 0.08
34 3 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTC
Found at i:213722 original size:57 final size:57
Alignment explanation
Indices: 213626--214114 Score: 565
Period size: 57 Copynumber: 8.5 Consensus size: 57
213616 TCATCTCTTA
* * *
213626 AAAGCCCATAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
* *
213682 AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
* * * * *
213739 AAAGCCCACGAGTCGGTGGCAACTCTTTTCAAAGCCCATAACTCAGTCGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
* * * *
213797 AATGCCCACAAGTCAGTGGCACTCTTTTTAAAGCCCACAAGTCAGTGGCATCCTCTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
* * * * *
213854 AAAGCCCACAAGTCAGTGGAAC-CCTTTCAAAGCCCATAATTTAGTGGCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
* * * * *
213910 AAAGCCAACAAGTTAGTGGCACTCTTCTCAAAGCCCATAAGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
* * *
213967 AAAGCCCATAAGTCAGTGGCACTC-ATTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC
* ** *
214024 AAAGCCCACAAG-CTAGTGGTAACTCTTTTCAAAGCCCACACGAGTTGGTGGCAACTCTTTTC
1 AAAGCCCACAAGTC-AGTGG-CACTCTTTTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTC
*
214086 AAAGCCCAAACAAGTTAGTGGCAC-CTTTT
1 AAAGCCC--ACAAGTCAGTGGCACTCTTTT
214115 TTTAAAAAAA
Statistics
Matches: 367, Mismatches: 53, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
56 89 0.24
57 171 0.47
58 53 0.14
59 13 0.04
61 8 0.02
62 21 0.06
63 2 0.01
64 10 0.03
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
Found at i:213881 original size:85 final size:86
Alignment explanation
Indices: 213626--214114 Score: 562
Period size: 85 Copynumber: 5.7 Consensus size: 86
213616 TCATCTCTTA
* *
213626 AAAGCCCATAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCC
1 AAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCC
*
213689 ACAAGTCAGTGGCACTCTTTTC
66 ACAAGTCAGTGGCAC-CCTTTC
* *
213711 AAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCCACGAGTCGGTGGCAACTCTTTTCAAAGCC
1 AAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCC
* * *
213775 CATAACTCAGTCGCACCCTTTC
65 CACAAGTCAGTGGCACCCTTTC
* * * * * *
213797 AATGCCCACAAGTCAGTGGCACTCTTTTTAAAGCCCACAAGTCAGTGGCA-TCCTCTCAAAGCCC
1 AAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCC
*
213861 ACAAGTCAGTGGAACCCTTTC
66 ACAAGTCAGTGGCACCCTTTC
* * * * *
213882 AAAGCCCATAATTTAGTGGCAC-CCTTTCAAAGCCAACAAGTTAGTGGCACTCTTCTCAAAGCCC
1 AAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCC
* *
213946 ATAAGTCAGTGGCATCCTTTC
66 ACAAGTCAGTGGCACCCTTTC
* * *
213967 AAAGCCCATAAGTCAGTGGCACT-CATTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCC
1 AAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCC
* *
214031 ACAAG-CTAGTGGTAACTCTTTTC
66 ACAAGTC-AGTGG-CAC-CCTTTC
* * *
214054 AAAGCCCACACGAGTTGGTGGCAACTCTTTTCAAAGCCCAAACAAGTTAGTGGCAC-CTTTT
1 AAAGCCCACA--AGTTAGTGGC-ACTCCTTTCAAAGCCC--ACAAGTCAGTGGCACTCTTTT
214115 TTTAAAAAAA
Statistics
Matches: 341, Mismatches: 48, Indels: 23
0.83 0.12 0.06
Matches are distributed among these distances:
84 24 0.07
85 188 0.55
86 28 0.08
87 61 0.18
89 8 0.02
90 3 0.01
91 10 0.03
92 5 0.01
93 14 0.04
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (86 bp):
AAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCC
ACAAGTCAGTGGCACCCTTTC
Found at i:214988 original size:20 final size:20
Alignment explanation
Indices: 214965--215039 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
214955 AAGTACCCAG
214965 ATGTATCGATACATTTTTAA
1 ATGTATCGATACATTTTTAA
* * * *
214985 ATGTATCAATACATGTATGA
1 ATGTATCGATACATTTTTAA
* *
215005 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTAA
215025 ATGTATCGATACATT
1 ATGTATCGATACATT
215040 CTATCTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTAA
Found at i:221612 original size:33 final size:33
Alignment explanation
Indices: 221570--221634 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
221560 TTTGAGACAA
*
221570 TGTATCGATACAAT-TCTTCATGGATCGATACAT
1 TGTATCGATACAATGT-GTCATGGATCGATACAT
*
221603 TGTATCGATACAATGTGTCATGTATCGATACA
1 TGTATCGATACAATGTGTCATGGATCGATACA
221635 AATAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTGTCATGGATCGATACAT
Found at i:221687 original size:19 final size:19
Alignment explanation
Indices: 221663--221738 Score: 100
Period size: 19 Copynumber: 3.9 Consensus size: 19
221653 GCTGCCAGTT
221663 TCATGTATCGATACAATGA
1 TCATGTATCGATACAATGA
*
221682 TCATGTATCGATA-AATTTA
1 TCATGTATCGATACAA-TGA
*
221701 TGCAAGTATCGATACAATGA
1 T-CATGTATCGATACAATGA
*
221721 TCGTGTATCGATACAATG
1 TCATGTATCGATACAATG
221739 TATCGATACA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
18 2 0.04
19 31 0.63
20 14 0.29
21 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:221742 original size:13 final size:13
Alignment explanation
Indices: 221724--221749 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
221714 ACAATGATCG
221724 TGTATCGATACAA
1 TGTATCGATACAA
221737 TGTATCGATACAA
1 TGTATCGATACAA
221750 AGCATAATGT
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):
TGTATCGATACAA
Found at i:225699 original size:13 final size:13
Alignment explanation
Indices: 225681--225706 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
225671 ACATTTTATG
225681 ATGTATCGATACA
1 ATGTATCGATACA
225694 ATGTATCGATACA
1 ATGTATCGATACA
225707 TACTGGGTGT
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:225805 original size:20 final size:20
Alignment explanation
Indices: 225780--225829 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
225770 TCTTTTTCAA
*
225780 GTATCGATACAATGCAATCT
1 GTATCGATACAATGAAATCT
* * *
225800 GTATCGATACATTTAAATGT
1 GTATCGATACAATGAAATCT
225820 GTATCGATAC
1 GTATCGATAC
225830 TTTTCAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
GTATCGATACAATGAAATCT
Found at i:227814 original size:24 final size:24
Alignment explanation
Indices: 227784--227839 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 24
227774 GCTGCTAGTA
*
227784 TGGGTGCTGCCCGGTTGCGACCTG
1 TGGGTGCTGCCCGGTCGCGACCTG
227808 -GGG-G-TG-CCGGTCGCGACCTGG
1 TGGGTGCTGCCCGGTCGCGACCT-G
227829 TGGGTGCTGCC
1 TGGGTGCTGCC
227840 TAGGGGACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 9
0.72 0.03 0.25
Matches are distributed among these distances:
20 12 0.46
21 3 0.12
22 4 0.15
23 4 0.15
24 2 0.08
25 1 0.04
ACGTcount: A:0.04, C:0.29, G:0.46, T:0.21
Consensus pattern (24 bp):
TGGGTGCTGCCCGGTCGCGACCTG
Found at i:227823 original size:20 final size:21
Alignment explanation
Indices: 227794--227835 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
227784 TGGGTGCTGC
*
227794 CCGGTTGCGACCTGG-GGGTG
1 CCGGTCGCGACCTGGTGGGTG
227814 CCGGTCGCGACCTGGTGGGTG
1 CCGGTCGCGACCTGGTGGGTG
227835 C
1 C
227836 TGCCTAGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.05, C:0.29, G:0.48, T:0.19
Consensus pattern (21 bp):
CCGGTCGCGACCTGGTGGGTG
Found at i:234473 original size:31 final size:32
Alignment explanation
Indices: 234435--234513 Score: 133
Period size: 31 Copynumber: 2.5 Consensus size: 32
234425 GTTACAAGCC
*
234435 AATGTATCGATACATTTTATGATGTATCGAT-
1 AATGTATCGATACATTTTATGATATATCGATA
234466 AATGTATCGATACATTTTATGATATATCGATA
1 AATGTATCGATACATTTTATGATATATCGATA
234498 CAATGTATCGATACAT
1 -AATGTATCGATACAT
234514 ACTGGGTGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 30 0.67
33 15 0.33
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.39
Consensus pattern (32 bp):
AATGTATCGATACATTTTATGATATATCGATA
Found at i:234611 original size:20 final size:20
Alignment explanation
Indices: 234586--234635 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
234576 TCTTTTTCAA
*
234586 GTATCGATACAATGCAATCT
1 GTATCGATACAATGAAATCT
* * *
234606 GTATCGATACATTTAAATGT
1 GTATCGATACAATGAAATCT
234626 GTATCGATAC
1 GTATCGATAC
234636 TTTTCAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
GTATCGATACAATGAAATCT
Found at i:245151 original size:21 final size:21
Alignment explanation
Indices: 245118--245162 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
245108 TTGCAAGTTG
*
245118 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
245140 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
245160 AAA
1 AAA
245163 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:246986 original size:15 final size:15
Alignment explanation
Indices: 246966--246996 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
246956 TAAAAATGTC
*
246966 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
246981 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
246996 C
1 C
246997 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:249085 original size:13 final size:13
Alignment explanation
Indices: 249067--249092 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
249057 ACATTTTTCT
249067 TTGTATCGATACA
1 TTGTATCGATACA
249080 TTGTATCGATACA
1 TTGTATCGATACA
249093 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:251629 original size:13 final size:13
Alignment explanation
Indices: 251611--251636 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
251601 TACAGCAAGT
251611 ATGTATCGATACA
1 ATGTATCGATACA
251624 ATGTATCGATACA
1 ATGTATCGATACA
251637 CAAAAATTGT
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:251630 original size:32 final size:32
Alignment explanation
Indices: 251593--251655 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
251583 TAGCCAAACT
**
251593 TGTATCGATACAGCAAGTA-TGTATCGATACAA
1 TGTATCGATACA-CAAAAATTGTATCGATACAA
251625 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
251656 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAATTGTATCGATACAA
Found at i:256262 original size:61 final size:61
Alignment explanation
Indices: 256006--256609 Score: 451
Period size: 61 Copynumber: 9.6 Consensus size: 61
255996 ACCTTTTATT
* * * * *
256006 CTTTTAGTCCTCAAAGAGCAAGACACTTTCC-TTTCTCTTTTAAAGCCCATACAAGCTGGTGGCA
1 CTTTTAGTCCTCAAAGAGC-AG-GA--TGCCTTTTC-CTTTCAAAGCCCACACAAGCTAGTGGCA
256070 C
61 C
* * * * * * *
256071 CTTTTAGTCCTCAAAGGGCATGA--CATTTTCCTTTAAAAGCCTATATAAGCTAGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTAGTGGCAC
* * *** * *
256130 CTTTTAGTCCTTAAAGAGCATGACACTTTTTTTTTTTCTCTTTTAAAGCCCACACAGGCTAGTGG
1 CTTTTAGTCCTCAAAGAGCA-G-GA----TGCCTTTTC-CTTTCAAAGCCCACACAAGCTAGTGG
256195 CAC
59 CAC
* * * * *
256198 CTTTTAATCCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGCCCAGACAAGCTAATGCCAC
1 CTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTAGTGGCAC
** * * *
256259 CTTTTAGTCCTCAAAGAGCAGGAAACCTTTTCCTTTCAAAGCCCACACTAGTTGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTAGTGGCAC
* * * *
256320 CTTTTAGTCCTCAAAGAGCATGACACTTTG-ATTTTCTCTTTTAAAGCCCACATAAGCTAGTGGC
1 CTTTTAGTCCTCAAAGAGCA-G-GA---TGCCTTTTC-CTTTCAAAGCCCACACAAGCTAGTGGC
256384 AC
60 AC
* * * * * *
256386 GTTTTAATCCTTAAAGAGCAAGATGCCTTTTCCTTTTAAAGCTCACACAAGCTAGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTAGTGGCAC
* * * * * *
256447 CTTTTAGTCCTTAAAAAGCAAGATGCCTTTTCCTTTCAAAGCCCACATAAGTTGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTAGTGGCAC
* * * * * * * * *
256508 CTTTTAGTCCTCAAAGAGTAAGACACTTTCTTTTTTTCTTTTAAAGCCCACAAAAGCTGGTGACA
1 CTTTTAGTCCTCAAAGAG-CAG-GA--TGC-CTTTTCCTTTCAAAGCCCACACAAGCTAGTGGCA
256573 C
61 C
* * * *
256574 CTTTTAGTCCTCAAAGAGTAGGGTGTCTTTTTCTTT
1 CTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTT
256610 TTCTCTTTAA
Statistics
Matches: 433, Mismatches: 84, Indels: 48
0.77 0.15 0.08
Matches are distributed among these distances:
59 44 0.10
60 4 0.01
61 203 0.47
62 14 0.03
63 3 0.01
64 2 0.00
65 27 0.06
66 89 0.21
67 6 0.01
68 41 0.09
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (61 bp):
CTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTAGTGGCAC
Found at i:256364 original size:188 final size:187
Alignment explanation
Indices: 256037--256610 Score: 729
Period size: 188 Copynumber: 3.0 Consensus size: 187
256027 GACACTTTCC
* * * * *
256037 TTTCTCTTTTAAAGCCCATACAAGCTGGTGGCACCTTTTAGTCCTCAAAGGGCATG-ACATTTTC
1 TTTC-CTTTTAAAGCCCACACAAGCTAGTGGCACCTTTTAGTCCTCAAAGAGCAAGAACCTTTTC
* * * * * * *
256101 CTTTAAAAGCCTATATAAGCTAGTGGCACCTTTTAGTCCTTAAAGAGCATGACACTTTTTTTTTT
65 CTTTCAAAGCCCACATAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCATGACAC--TTTCTTTT
* *
256166 TCTCTTTTAAAGCCCACACAGGCTAGTGGCACCTTTTAATCCTCAAAGAGTAGGATGCCT
128 TCTCTTTTAAAGCCCACAAAAGCTAGTGGCACCTTTTAATCCTCAAAGAGTAGGATGCCT
* * * * *
256226 TTTCCTTTCAAAGCCCAGACAAGCTAATGCCACCTTTTAGTCCTCAAAGAGCAGGAAACCTTTTC
1 TTTCCTTTTAAAGCCCACACAAGCTAGTGGCACCTTTTAGTCCTCAAAGAGCAAG-AACCTTTTC
**
256291 CTTTCAAAGCCCACACT-AGTTGGTGGCACCTTTTAGTCCTCAAAGAGCATGACACTTTGATTTT
65 CTTTCAAAGCCCACA-TAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCATGACACTTTCTTTTT
* * * * *
256355 CTCTTTTAAAGCCCACATAAGCTAGTGGCACGTTTTAATCCTTAAAGAGCAAGATGCCT
129 CTCTTTTAAAGCCCACAAAAGCTAGTGGCACCTTTTAATCCTCAAAGAGTAGGATGCCT
* * * *
256414 TTTCCTTTTAAAGCTCACACAAGCTAGTGGCACCTTTTAGTCCTTAAAAAGCAAGATGCCTTTTC
1 TTTCCTTTTAAAGCCCACACAAGCTAGTGGCACCTTTTAGTCCTCAAAGAGCAAGA-ACCTTTTC
* * *
256479 CTTTCAAAGCCCACATAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAAGACACTTTCTTTTTT
65 CTTTCAAAGCCCACATAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCATGACACTTTCTTTTTC
* * * * *
256544 TCTTTTAAAGCCCACAAAAGCTGGTGACACCTTTTAGTCCTCAAAGAGTAGGGTGTCT
130 TCTTTTAAAGCCCACAAAAGCTAGTGGCACCTTTTAATCCTCAAAGAGTAGGATGCCT
*
256602 TTTTCTTTT
1 TTTCCTTTT
256611 TCTCTTTAAA
Statistics
Matches: 333, Mismatches: 47, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
187 2 0.01
188 272 0.82
189 4 0.01
190 54 0.16
191 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (187 bp):
TTTCCTTTTAAAGCCCACACAAGCTAGTGGCACCTTTTAGTCCTCAAAGAGCAAGAACCTTTTCC
TTTCAAAGCCCACATAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCATGACACTTTCTTTTTCT
CTTTTAAAGCCCACAAAAGCTAGTGGCACCTTTTAATCCTCAAAGAGTAGGATGCCT
Found at i:256604 original size:127 final size:126
Alignment explanation
Indices: 256006--256609 Score: 593
Period size: 127 Copynumber: 4.8 Consensus size: 126
255996 ACCTTTTATT
* *
256006 CTTTTAGTCCTCAAAGAGCAAGACACTTTCCTTTCTCTTTTAAAGCCCATACAAGCTGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAAGACACTTTCCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCAC
* * * * *
256071 CTTTTAGTCCTCAAAG-G--GCATGACATTTTCCTTTAAAAGCCTATATAAGCTAGTGGCAC
66 CTTTTAGTCCTCAAAGAGTAGGATG-CCTTTTCCTTTCAAAGCCCACATAAGCTAGTGGCAC
* * ** * *
256130 CTTTTAGTCCTTAAAGAGCATGACACTTTTTTTTTTTCTCTTTTAAAGCCCACACAGGCTAGTGG
1 CTTTTAGTCCTCAAAGAGCAAGACAC--TTTCCTTTT-TCTTTTAAAGCCCACACAAGCTGGTGG
* * * * *
256195 CACCTTTTAATCCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGCCCAGACAAGCTAATGCCAC
63 CACCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGCCCACATAAGCTAGTGGCAC
* * * * * *
256259 CTTTTAGTCCTCAAAGAGCAGGA-A---ACCTTTTCCTTTCAAAGCCCACACTAGTTGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAAGACACTTTCCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCAC
* * * *
256320 CTTTTAGTCCTCAAAGAGCATGACACTTTG-ATTTTCTCTTTTAAAGCCCACATAAGCTAGTGGC
66 CTTTTAGTCCTCAAAGAGTA-G-GA---TGCCTTTTC-CTTTCAAAGCCCACATAAGCTAGTGGC
256384 AC
125 AC
* * * * * * *
256386 GTTTTAATCCTTAAAGAGCAAG--A--TGCCTTTTCCTTTTAAAGCTCACACAAGCTAGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAAGACACTTTCCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCAC
* * * * * *
256447 CTTTTAGTCCTTAAAAAGCAAGATGCCTTTTCCTTTCAAAGCCCACATAAGTTGGTGGCAC
66 CTTTTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGCCCACATAAGCTAGTGGCAC
* * * *
256508 CTTTTAGTCCTCAAAGAGTAAGACACTTTCTTTTTTTCTTTTAAAGCCCACAAAAGCTGGTGACA
1 CTTTTAGTCCTCAAAGAGCAAGACACTTTC-CTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCA
* * *
256573 CCTTTTAGTCCTCAAAGAGTAGGGTGTCTTTTTCTTT
65 CCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTT
256610 TTCTCTTTAA
Statistics
Matches: 388, Mismatches: 73, Indels: 35
0.78 0.15 0.07
Matches are distributed among these distances:
122 88 0.23
123 10 0.03
124 26 0.07
125 1 0.00
126 14 0.04
127 193 0.50
128 2 0.01
129 50 0.13
130 4 0.01
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (126 bp):
CTTTTAGTCCTCAAAGAGCAAGACACTTTCCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCAC
CTTTTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGCCCACATAAGCTAGTGGCAC
Found at i:259469 original size:79 final size:79
Alignment explanation
Indices: 259385--259530 Score: 204
Period size: 79 Copynumber: 1.8 Consensus size: 79
259375 AATTTCAAGA
*
259385 GGATACTCCAACCCCGTTTTTATTTTCAAAACTATTAAATTTTT-ATCGCAAGGAAACTACAACC
1 GGATACTCCAACCCCGCTTTTATTTTCAAAA-TATTAAATTTTTCATCGCAAGGAAACTACAACC
259449 CTGTTATTTTCGAGG
65 CTGTTATTTTCGAGG
** * * * * *
259464 GGATACTCCAACCTTGCTTTTATTTTCAAAATATTAGATTTTTCATCTCGAGGATACTCCAACCC
1 GGATACTCCAACCCCGCTTTTATTTTCAAAATATTAAATTTTTCATCGCAAGGAAACTACAACCC
259529 TG
66 TG
259531 CTTTTATTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
78 11 0.19
79 47 0.81
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (79 bp):
GGATACTCCAACCCCGCTTTTATTTTCAAAATATTAAATTTTTCATCGCAAGGAAACTACAACCC
TGTTATTTTCGAGG
Found at i:259520 original size:51 final size:51
Alignment explanation
Indices: 259464--259581 Score: 191
Period size: 51 Copynumber: 2.3 Consensus size: 51
259454 ATTTTCGAGG
* *
259464 GGATACTCCAACCTTGCTTTTATTTTCAAAATATTAGATTTTTCATCTCGA
1 GGATACTCCAACCCTGCTTTTATTTCCAAAATATTAGATTTTTCATCTCGA
* *
259515 GGATACTCCAACCCTGCTTTTATTTCCAAAATATTAGATTTTTTATCTCGG
1 GGATACTCCAACCCTGCTTTTATTTCCAAAATATTAGATTTTTCATCTCGA
*
259566 GGATGCTCCAACCCTG
1 GGATACTCCAACCCTG
259582 TTATTTTCGA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (51 bp):
GGATACTCCAACCCTGCTTTTATTTCCAAAATATTAGATTTTTCATCTCGA
Found at i:259763 original size:77 final size:77
Alignment explanation
Indices: 259591--259816 Score: 252
Period size: 77 Copynumber: 2.9 Consensus size: 77
259581 GTTATTTTCG
* *
259591 AGGGAATACTCCAACCCCATCAA-TTCTAAAGGGATACTCTAACC-TGATTTTTATTTTC-AAAA
1 AGGG-ATACTTCAACCCCAT-AATTTCT-AAGGGATACTCTAGCCTTGATTTTTATTTTCAAAAA
*
259653 TATTAAACTTTTCTT
63 TATTAAATTTTTCTT
* * * *
259668 AGGGATAC-TCTAATCCCATTATTTCTAAGGGGATACTCCAGCCTTG-TTTTTATTTCCAAAAAT
1 AGGGATACTTC-AACCCCATAATTTCTAA-GGGATACTCTAGCCTTGATTTTTATTTTCAAAAAT
259731 ATTAAATTTTTCTT
64 ATTAAATTTTTCTT
*
259745 -GGAGATACTTCAACCCCATCAATTT-TGAAGGGATACTCTAG-CTCGATTTTTATTTTCAAAAA
1 AGG-GATACTTCAACCCCAT-AATTTCT-AAGGGATACTCTAGCCTTGATTTTTATTTTCAAAAA
259807 TATTAAATTT
63 TATTAAATTT
259817 ACCATTAGGG
Statistics
Matches: 127, Mismatches: 12, Indels: 20
0.80 0.08 0.13
Matches are distributed among these distances:
75 4 0.03
76 42 0.33
77 73 0.57
78 8 0.06
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (77 bp):
AGGGATACTTCAACCCCATAATTTCTAAGGGATACTCTAGCCTTGATTTTTATTTTCAAAAATAT
TAAATTTTTCTT
Found at i:262075 original size:19 final size:19
Alignment explanation
Indices: 262051--262101 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
262041 ACATTTATAA
262051 ATGTATCGATACATTACTT
1 ATGTATCGATACATTACTT
262070 ATGTATCGATACATTACTT
1 ATGTATCGATACATTACTT
262089 ATGTATCGATACA
1 ATGTATCGATACA
262102 ATTTTTGTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATTACTT
Found at i:265532 original size:20 final size:20
Alignment explanation
Indices: 265507--265600 Score: 120
Period size: 20 Copynumber: 4.7 Consensus size: 20
265497 TTTACCCAGA
*
265507 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
265527 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
*
265547 TGTATTGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
* *
265567 TGTATCGATACATT-TTACAG
1 TGTATCGATACATTGCT-CAT
265587 TGTATCGATACATT
1 TGTATCGATACATT
265601 CAGGCATTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.01
20 65 0.97
21 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:268168 original size:28 final size:29
Alignment explanation
Indices: 268129--268203 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
268119 TGTTTTCATA
*
268129 ATCGGGGGTACTCCAACCCTATTATTTC-
1 ATCGGGGATACTCCAACCCTATTATTTCG
*
268157 ATCGGGGATACTCCAATCCC-GTTATTTCG
1 ATCGGGGATACTCCAA-CCCTATTATTTCG
*
268186 A--AGGGATACTCCAACCCT
1 ATCGGGGATACTCCAACCCT
268204 GATTTTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 3 0.07
27 12 0.29
28 22 0.54
29 4 0.10
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCTATTATTTCG
Found at i:268285 original size:51 final size:51
Alignment explanation
Indices: 268188--268304 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
268178 TTATTTCGAA
* *
268188 GGGATACTCCAACCCTGATTTTATTTCTAAAATACCAAATTTTCACAATCG
1 GGGATACTCCAACCCTGATTTTATTTCCAAAACACCAAATTTTCACAATCG
* *
268239 GTGATACTCCAACTCC-GATTTTATTTCCAAAACATC-AATTTCTCACAATCG
1 GGGATACTCCAAC-CCTGATTTTATTTCCAAAACACCAAATTT-TCACAATCG
268290 GGGATACTCCAACCC
1 GGGATACTCCAACCC
268305 CGTTATTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
50 7 0.12
51 50 0.85
52 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.31
Consensus pattern (51 bp):
GGGATACTCCAACCCTGATTTTATTTCCAAAACACCAAATTTTCACAATCG
Found at i:268342 original size:79 final size:79
Alignment explanation
Indices: 268241--268457 Score: 238
Period size: 79 Copynumber: 2.7 Consensus size: 79
268231 CACAATCGGT
* * * * *
268241 GATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTCTCACAATCGGGGATACTCCAACCCC
1 GATACTCCAACCCCAATTTTATTTCCAAAACATCGATTTCTCATAATCGGGGATACTCCAAACCC
*
268306 GTTATTTTCGCGAG
66 GTTATTTTCGAGAG
* * * * *
268320 GATACTCTAACCCCAATTTTATTTTCAAAATATTGATTT-TCTATAATCAGGGATACTCCAAACC
1 GATACTCCAACCCCAATTTTATTTCCAAAACATCGATTTCTC-ATAATCGGGGATACTCCAAACC
* *
268384 TGTTATTTTCGAGGG
65 CGTTATTTTCGAGAG
* * * * * *
268399 GATACTCCAACCTCGATTTTTATTTCTAGAACATCGATTTCCCATAATCGAGGATACTC
1 GATACTCCAACC-CCAATTTTATTTCCAAAACATCGATTTCTCATAATCGGGGATACTC
268458 TAGCCTCATT
Statistics
Matches: 111, Mismatches: 24, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
78 2 0.02
79 74 0.67
80 34 0.31
81 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (79 bp):
GATACTCCAACCCCAATTTTATTTCCAAAACATCGATTTCTCATAATCGGGGATACTCCAAACCC
GTTATTTTCGAGAG
Found at i:280858 original size:1 final size:1
Alignment explanation
Indices: 280854--280933 Score: 70
Period size: 1 Copynumber: 80.0 Consensus size: 1
280844 ATTATTTTTC
* * * * * * *
280854 AAAAAAAAAACAAAAAAAACAAAAAAAAACAAAAAACAAAAAAACAAAAGAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
280919 CAATAAAAAACAAAA
1 AAAAAAAAAAAAAAA
280934 TAAAGAAAAG
Statistics
Matches: 59, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.88, C:0.10, G:0.01, T:0.01
Consensus pattern (1 bp):
A
Found at i:280870 original size:8 final size:8
Alignment explanation
Indices: 280857--280933 Score: 79
Period size: 8 Copynumber: 9.5 Consensus size: 8
280847 ATTTTTCAAA
280857 AAAAAAAC
1 AAAAAAAC
280865 AAAAAAAAC
1 -AAAAAAAC
*
280874 AAAAAAAA
1 AAAAAAAC
280882 ACAAAAAAC
1 A-AAAAAAC
280891 AAAAAAAC
1 AAAAAAAC
*
280899 ---AAAAG
1 AAAAAAAC
280904 AAAAAAAC
1 AAAAAAAC
280912 AAAAAAAC
1 AAAAAAAC
280920 AATAAAAAAC
1 -A-AAAAAAC
280930 AAAA
1 AAAA
280934 TAAAGAAAAG
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
5 4 0.07
8 30 0.52
9 17 0.29
10 7 0.12
ACGTcount: A:0.87, C:0.10, G:0.01, T:0.01
Consensus pattern (8 bp):
AAAAAAAC
Found at i:280897 original size:39 final size:39
Alignment explanation
Indices: 280854--280942 Score: 117
Period size: 38 Copynumber: 2.3 Consensus size: 39
280844 ATTATTTTTC
*
280854 AAAAAAAAAACAAAAAAAACAAAAAAA-AACAAAAAACA
1 AAAAAAAAAAAAAAAAAAACAAAAAAACAACAAAAAACA
* * *
280892 AAAAAACAAAAGAAAAAAACAAAAAAACAATAAAAAACA
1 AAAAAAAAAAAAAAAAAAACAAAAAAACAACAAAAAACA
* *
280931 AAATAAAGAAAA
1 AAAAAAAAAAAA
280943 GAGAGAAAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
38 24 0.57
39 18 0.43
ACGTcount: A:0.87, C:0.09, G:0.02, T:0.02
Consensus pattern (39 bp):
AAAAAAAAAAAAAAAAAAACAAAAAAACAACAAAAAACA
Found at i:280919 original size:21 final size:19
Alignment explanation
Indices: 280854--280933 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
280844 ATTATTTTTC
280854 AAAAAAAAAACAAAAAAAA
1 AAAAAAAAAACAAAAAAAA
*
280873 CAAAAAAAAACAAAAAACAA
1 AAAAAAAAAACAAAAAA-AA
* * *
280893 AAAAACAAAAGAAAAAAAC
1 AAAAAAAAAACAAAAAAAA
* *
280912 AAAAAAACAATAAAAAACAA
1 AAAAAAAAAACAAAAAA-AA
280932 AA
1 AA
280934 TAAAGAAAAG
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
19 31 0.62
20 19 0.38
ACGTcount: A:0.88, C:0.10, G:0.01, T:0.01
Consensus pattern (19 bp):
AAAAAAAAAACAAAAAAAA
Found at i:282045 original size:39 final size:39
Alignment explanation
Indices: 281986--282060 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
281976 GTTGGTGGCA
281986 CCTTCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCAC
1 CCTTCTAGTCCTCAAAGAGCAGGACGC-CTCTCCTTTCAC
*
282026 CCTT-TAGTCCTCAAAGAGCAGGACGCCTTTCCTTT
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTCTCCTTT
282061 TAAAGCCCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 8 0.24
39 22 0.65
40 4 0.12
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.29
Consensus pattern (39 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTCTCCTTTCAC
Found at i:282092 original size:99 final size:99
Alignment explanation
Indices: 281915--282202 Score: 417
Period size: 99 Copynumber: 2.9 Consensus size: 99
281905 ATTTAAACTT
* * *
281915 TCTCCTTTCA-CTTTTCAGTCCTCAAAAAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTT
1 TCTCCTTTCACCCTTT-AGTCCTCAAAGAGCAGGACGCC-TTTCCTTTTAAAGCCCACACAAGTT
281979 GGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCTC
64 GGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCTC
282015 TCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGG
1 TCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGG
* * * *
282080 TGGCACCCTCTAGTCCTCAAAGAGTAGGATGCTT
66 TGGCACCTTCTAGTCCTCAAAGAGCAGGACGCTC
* * *
282114 TCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTT-C----AACGCCTACACAAGTTTG
1 TCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGG
*
282174 TGGCACCTTTTAGTCCTCAAAGAGCAGGA
66 TGGCACCTTCTAGTCCTCAAAGAGCAGGA
282203 TGCCTTTTAA
Statistics
Matches: 174, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
94 41 0.24
98 1 0.01
99 98 0.56
100 30 0.17
101 4 0.02
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (99 bp):
TCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGG
TGGCACCTTCTAGTCCTCAAAGAGCAGGACGCTC
Found at i:282208 original size:55 final size:55
Alignment explanation
Indices: 282122--282615 Score: 341
Period size: 55 Copynumber: 8.5 Consensus size: 55
282112 TTTCTCCTTT
* * * * *
282122 CACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAACGCCTACACAAGTTTGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGG
* *
282177 CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACAGAAGTTGGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGG
* * * * * *
282232 CACTTTTTCTAGTCCTGAAAAAGCAAGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGGGG
1 CAC-CTTT-TAGTCCTCAAAGAGC-AG--G---ATGCCTTTCAAAGCCCACACAAGTTGGTGG
* * * **
282295 CA--TTTTCCAGTCCTCAAAGAGTAGGATGCTTTATTTTTTAAAGCCCACATGAGTTGGTGG
1 CACCTTTT--AGTCCTCAAAGAGCAGGATGC-----CTTTCAAAGCCCACACAAGTTGGTGG
* *
282355 CA--TTTTCCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTT--AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGG
** * *
282410 CATTTTTTTTTAGTCCTCAAAAAGCAGGATGCCTTTCGAAGCCCACACAAGTTGGTGG
1 CA---CCTTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGG
** * * *
282468 CA-CTTCCGAGTCCTCAAAGAGTAGGATGCTTTCTTTTTGCAAATCCTACACAAGTTGGTGG
1 CACCTT-TTAGTCCTCAAAGAGCAGGATGC---C--TTT-CAAAGCCCACACAAGTTGGTGG
** *
282529 CACCTTCCAGTCCTCAAAGAGCAGGATGCCTTTCTTTTTCAAAGCCCACACGAGTTGGTGG
1 CACCTTTTAGTCCTCAAAGAGCAGGATG-C---C--TTTCAAAGCCCACACAAGTTGGTGG
* * *
282590 CGCTTTTTTGTCCTCAAAGAGCAGGA
1 CACCTTTTAGTCCTCAAAGAGCAGGA
282616 CGCACTTTAT
Statistics
Matches: 356, Mismatches: 54, Indels: 52
0.77 0.12 0.11
Matches are distributed among these distances:
54 2 0.01
55 96 0.27
56 3 0.01
57 13 0.04
58 49 0.14
59 1 0.00
60 60 0.17
61 92 0.26
62 13 0.04
63 27 0.08
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (55 bp):
CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGG
Found at i:282482 original size:173 final size:176
Alignment explanation
Indices: 282163--282612 Score: 518
Period size: 178 Copynumber: 2.5 Consensus size: 176
282153 TTCAACGCCT
* ** * *
282163 ACACAAGTTTGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACAGAAGTTG
1 ACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTG
* * *
282228 GTGGCACTTTTTCTAGTCCTGAAAAAGCAAGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGG
66 GTGGCACTTTTTCTAGTCCTCAAAAAGCAAGA-G-C-ATGCCTTTCAAAGCCCACACAAGTTGGG
* *
282293 GGCATTTTCCAGTCCTCAAAGAGTAGGATGCTTTATTTTT-TAAAGCCC
128 GGCATCTTCCAGTCCTCAAAGAGTAGGATGCTTTATTTTTGCAAAGCCC
** ** * *
282341 ACATGAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTG
1 ACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTG
* * * *
282406 GTGGCATTTTTTTTTAGTCCTCAAAAAGC-AG-G-ATGCCTTTCGAAGCCCACACAAGTTGGTGG
66 GTGGCA-CTTTTTCTAGTCCTCAAAAAGCAAGAGCATGCCTTTCAAAGCCCACACAAGTTGGGGG
* * *
282468 CA-CTTCCGAGTCCTCAAAGAGTAGGATGCTTTCTTTTTGCAAATCCT
130 CATCTTCC-AGTCCTCAAAGAGTAGGATGCTTTATTTTTGCAAAGCCC
282515 ACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCCTTTCTTTTTCAAAGCCCACAC
1 ACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-C---C--TTTCAAAGCCCACAC
* * *
282580 GAGTTGGTGGCGCTTTTT-T-GTCCTCAAAGAGCA
60 AAGTTGGTGGCACTTTTTCTAGTCCTCAAAAAGCA
282613 GGACGCACTT
Statistics
Matches: 229, Mismatches: 33, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
172 4 0.02
173 57 0.25
174 41 0.18
175 1 0.00
176 1 0.00
177 12 0.05
178 64 0.28
179 24 0.10
180 25 0.11
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (176 bp):
ACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTG
GTGGCACTTTTTCTAGTCCTCAAAAAGCAAGAGCATGCCTTTCAAAGCCCACACAAGTTGGGGGC
ATCTTCCAGTCCTCAAAGAGTAGGATGCTTTATTTTTGCAAAGCCC
Found at i:282629 original size:61 final size:59
Alignment explanation
Indices: 282127--282629 Score: 403
Period size: 61 Copynumber: 8.6 Consensus size: 59
282117 CCTTTCACCC
* * * * *
282127 TTTAGTCCTCAAAGAGCAGGACGCC----TTTCAACGCCTACACAAGTTTGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCACTT
*
282182 TTTAGTCCTCAAAGAGCAGGATGCC---TTTT-AAAGCCCACAGAAGTTGGTGGCACTTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCAC-TT
* * * * *
282238 TTCTAGTCCTGAAAAAGCAAGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGGGGCA-TT
1 TT-TAGTCCTCAAAGAGCAGGATGCCTTTT--TTTCAAAGCCCACACAAGTTGGTGGCACTT
* * * * **
282299 TTCCAGTCCTCAAAGAGTAGGATGCTTTATTTTTTAAAGCCCACATGAGTTGGTGGCA-TT
1 TT-TAGTCCTCAAAGAGCAGGATGCCTT-TTTTTCAAAGCCCACACAAGTTGGTGGCACTT
* * * *
282359 TTCCAGTCCTCAAAGAGCAAGACGCC----TTTCAAAGCCCACACAAGTTGGTGGCATTTTTT
1 TT-TAGTCCTCAAAGAGCAGGATGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCA---CTT
* *
282418 TTTAGTCCTCAAAAAGCAGGATGCC----TTTCGAAGCCCACACAAGTTGGTGGCACTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCACTT
*** * * * * *
282473 CCGAGTCCTCAAAGAGTAGGATGCTTTCTTTTTGCAAATCCTACACAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTT-TTTTT-CAAAGCCCACACAAGTTGGTGGCACTT
** * *
282534 TCCAGTCCTCAAAGAGCAGGATGCCTTTCTTTTTCAAAGCCCACACGAGTTGGTGGCGCTT
1 TTTAGTCCTCAAAGAGCAGGATGCC-TT-TTTTTCAAAGCCCACACAAGTTGGTGGCACTT
* *
282595 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTC
1 TTTAGTCCTCAAAGAGCAGGATGC-CTTT-TTTTC
282630 CTCTCTCTTT
Statistics
Matches: 366, Mismatches: 59, Indels: 40
0.79 0.13 0.09
Matches are distributed among these distances:
55 89 0.24
56 6 0.02
57 19 0.05
58 45 0.12
59 4 0.01
60 52 0.14
61 116 0.32
62 14 0.04
63 21 0.06
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (59 bp):
TTTAGTCCTCAAAGAGCAGGATGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCACTT
Found at i:282658 original size:42 final size:42
Alignment explanation
Indices: 282595--282788 Score: 194
Period size: 42 Copynumber: 4.5 Consensus size: 42
282585 GGTGGCGCTT
* *
282595 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTC
1 TTTTGTCCTCAAAGAGCAGGACACACTTTATTTTCCTTTCTC
* * * **
282637 TTTTGTCCTCAAGGAGTAGGACACACTTCATTCCCTTATTTTCTC
1 TTTTGTCCTCAAAGAGCAGGACACACTTTATT---TTCCTTTCTC
* * *
282682 TTTTGTCCTCAAAGAGCAGGACACACTTTGTTTTCTTTTTTC
1 TTTTGTCCTCAAAGAGCAGGACACACTTTATTTTCCTTTCTC
* * *
282724 TTTTGTCCTCAAAAAGCAGGACGCA-TTTCATTTTCCTTTTTTC
1 TTTTGTCCTCAAAGAGCAGGACACACTTT-ATTTTCC-TTTCTC
*
282767 CTTTGTCCTCGAAA-AGCAGGAC
1 TTTTGTCCTC-AAAGAGCAGGAC
282789 GTACTCTTTT
Statistics
Matches: 128, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
41 3 0.02
42 64 0.50
43 23 0.18
44 3 0.02
45 35 0.27
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (42 bp):
TTTTGTCCTCAAAGAGCAGGACACACTTTATTTTCCTTTCTC
Found at i:282698 original size:87 final size:86
Alignment explanation
Indices: 282595--282789 Score: 243
Period size: 87 Copynumber: 2.3 Consensus size: 86
282585 GGTGGCGCTT
** *
282595 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTCTTTTGTCCTCAAGGAGTAGGACA
1 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTCTTTTGTCCTCAAAAAGCAGGACA
282660 CACTTCA-TTCCCTTATTTTCTC
66 CACTTCATTTCCCTT-TTTTC-C
* * * * * *
282682 TTTTGTCCTCAAAGAGCAGGACACACTTTGTTTTCTTTTTTCTTTTGTCCTCAAAAAGCAGGACG
1 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTCTTTTGTCCTCAAAAAGCAGGACA
* *
282747 CATTTCATTTTCCTTTTTTCC
66 CACTTCATTTCCCTTTTTTCC
282768 -TTTGTCCTCGAAA-AGCAGGACG
1 TTTTGTCCTC-AAAGAGCAGGACG
282790 TACTCTTTTT
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
85 17 0.18
86 4 0.04
87 67 0.71
88 6 0.06
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (86 bp):
TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTCTCTTTTGTCCTCAAAAAGCAGGACA
CACTTCATTTCCCTTTTTTCC
Found at i:283490 original size:13 final size:13
Alignment explanation
Indices: 283474--283499 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
283464 ATACATTGTT
283474 CATTGTATCGATA
1 CATTGTATCGATA
283487 CATTGTATCGATA
1 CATTGTATCGATA
283500 TATTATGAGT
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):
CATTGTATCGATA
Found at i:286136 original size:13 final size:13
Alignment explanation
Indices: 286118--286143 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
286108 AATTTTGTTG
286118 TGTATCGATACAT
1 TGTATCGATACAT
286131 TGTATCGATACAT
1 TGTATCGATACAT
286144 ACTTTGTGTA
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:293407 original size:13 final size:13
Alignment explanation
Indices: 293389--293414 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
293379 AATTTTTTTG
293389 TGTATCGATACAT
1 TGTATCGATACAT
293402 TGTATCGATACAT
1 TGTATCGATACAT
293415 ACTTTGTGTA
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:293426 original size:19 final size:19
Alignment explanation
Indices: 293402--293485 Score: 90
Period size: 19 Copynumber: 4.6 Consensus size: 19
293392 ATCGATACAT
293402 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
**
293421 TGTATCGATACAATTTTTTTG
1 TGTATCGATAC-A-TACTTTG
293442 TGTATCGATAC--A---T-
1 TGTATCGATACATACTTTG
293455 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
293474 TGTATCGATACA
1 TGTATCGATACA
293486 AGTTTGGCTA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
13 11 0.20
14 1 0.02
15 1 0.02
18 1 0.02
19 23 0.43
20 1 0.02
21 16 0.30
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATACTTTG
Found at i:293448 original size:53 final size:53
Alignment explanation
Indices: 293368--293486 Score: 229
Period size: 53 Copynumber: 2.2 Consensus size: 53
293358 TACAAGCCAA
*
293368 TGTATCAATACAATTTTTTTGTGTATCGATACATTGTATCGATACATACTTTG
1 TGTATCGATACAATTTTTTTGTGTATCGATACATTGTATCGATACATACTTTG
293421 TGTATCGATACAATTTTTTTGTGTATCGATACATTGTATCGATACATACTTTG
1 TGTATCGATACAATTTTTTTGTGTATCGATACATTGTATCGATACATACTTTG
293474 TGTATCGATACAA
1 TGTATCGATACAA
293487 GTTTGGCTAC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 65 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (53 bp):
TGTATCGATACAATTTTTTTGTGTATCGATACATTGTATCGATACATACTTTG
Found at i:293460 original size:13 final size:13
Alignment explanation
Indices: 293442--293467 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
293432 AATTTTTTTG
293442 TGTATCGATACAT
1 TGTATCGATACAT
293455 TGTATCGATACAT
1 TGTATCGATACAT
293468 ACTTTGTGTA
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:293889 original size:20 final size:20
Alignment explanation
Indices: 293861--294070 Score: 130
Period size: 20 Copynumber: 10.4 Consensus size: 20
293851 GATCCTAACA
*
293861 GATACATTGTTCATGGTATC
1 GATACATTGTTCATTGTATC
*
293881 GATATATTGTTCATTGTATC
1 GATACATTGTTCATTGTATC
*
293901 GATATA-TGTTGCATTGTATC
1 GATACATTGTT-CATTGTATC
*
293921 GATACATTGCTCATTGTATC
1 GATACATTGTTCATTGTATC
* *
293941 AATACATTG-T-ATCG-ATAC
1 GATACATTGTTCATTGTAT-C
* * *
293959 -AT-TATGGGTTTACCTAGATGTATC
1 GATACAT-TG-TT--C-A-TTGTATC
* *
293983 GATAAATT-TTGCATTGTATT
1 GATACATTGTT-CATTGTATC
* * *
294003 GATACATTGCTCATTGCATT
1 GATACATTGTTCATTGTATC
*
294023 GATACATTGCTCATTGTATC
1 GATACATTGTTCATTGTATC
*
294043 GATACATT-TTACAATGTATC
1 GATACATTGTT-CATTGTATC
294063 GATACATT
1 GATACATT
294071 CAGGCATTTT
Statistics
Matches: 152, Mismatches: 22, Indels: 32
0.74 0.11 0.16
Matches are distributed among these distances:
16 2 0.01
17 5 0.03
18 4 0.03
19 7 0.05
20 117 0.77
21 5 0.03
22 1 0.01
23 3 0.02
24 2 0.01
25 4 0.03
26 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (20 bp):
GATACATTGTTCATTGTATC
Found at i:293948 original size:13 final size:13
Alignment explanation
Indices: 293932--293961 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
293922 ATACATTGCT
293932 CATTGTATCAATA
1 CATTGTATCAATA
*
293945 CATTGTATCGATA
1 CATTGTATCAATA
293958 CATT
1 CATT
293962 ATGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:296640 original size:28 final size:28
Alignment explanation
Indices: 296609--296674 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
296599 TAATCGGGGG
*
296609 TACTCCAACCCCGTTATTTCAT-CGGGAA
1 TACTCCAACCCCGTTATTTC-TGAGGGAA
* *
296637 TACTCCAATCCCGTTATTTCTGAGGGGA
1 TACTCCAACCCCGTTATTTCTGAGGGAA
296665 TACTCCAACC
1 TACTCCAACC
296675 TCGATTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (28 bp):
TACTCCAACCCCGTTATTTCTGAGGGAA
Found at i:296732 original size:51 final size:51
Alignment explanation
Indices: 296661--296776 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 51
296651 TATTTCTGAG
* * *
296661 GGGATACTCCAACCTCGATTTTATTTTTAAAATACCAATTTGC-CGCAATCA
1 GGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTT-CTCACAATCA
* *
296712 GTGATACTCCAA-CTCTGATTTTATTTTCAAAACACCAATTTCTCACAATCG
1 GGGATACTCCAACCTC-GATTTTATTTTCAAAACACCAATTTCTCACAATCA
296763 GGGATACTCCAACC
1 GGGATACTCCAACC
296777 CTGTTATTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 4 0.07
51 51 0.91
52 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTCTCACAATCA
Found at i:296846 original size:79 final size:80
Alignment explanation
Indices: 296714--296883 Score: 247
Period size: 79 Copynumber: 2.1 Consensus size: 80
296704 CGCAATCAGT
*
296714 GATACTCCAA-CTCTGATTTTATTTTCAAAACACCAATTTCTCACAATCGGGGATACTCCAACCC
1 GATACTCCAACCTCTGATTTTATTTTCAAAACACCAATTTCTCACAATCAGGGATACTCCAACCC
* *
296778 TGTTATTTTCGCGGG
66 TATTATTTTCGAGGG
* * *
296793 GATACTCCAACCTC-GATTTTATTTTCAAAATACTAATTT-TCTATAATCAGGGATACTCCAACC
1 GATACTCCAACCTCTGATTTTATTTTCAAAACACCAATTTCTC-ACAATCAGGGATACTCCAACC
*
296856 CTATTATTTTTGAGGG
65 CTATTATTTTCGAGGG
296872 GATACTCCAACC
1 GATACTCCAACC
296884 CCAACTTTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
78 2 0.02
79 77 0.94
80 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (80 bp):
GATACTCCAACCTCTGATTTTATTTTCAAAACACCAATTTCTCACAATCAGGGATACTCCAACCC
TATTATTTTCGAGGG
Found at i:305825 original size:25 final size:25
Alignment explanation
Indices: 305778--305826 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
305768 AAATTCAAGA
*
305778 AGAAACAAGGCTGGAGTGTCCCCTC
1 AGAAACAAGGCTGGAGTGACCCCTC
*
305803 AGAATACAAGGTTGGAGT-ACCCCT
1 AGAA-ACAAGGCTGGAGTGACCCCT
305827 AATGGTGACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (25 bp):
AGAAACAAGGCTGGAGTGACCCCTC
Found at i:306302 original size:79 final size:79
Alignment explanation
Indices: 305991--306412 Score: 362
Period size: 79 Copynumber: 5.4 Consensus size: 79
305981 TCCCTAATGG
* ** * * *
305991 TGAAAATTTTGATATTTTTGGAAAT-AAAACCGTGGTTAAAGTACCCCCTCAAAAATAATGAGGT
1 TGAAAATTTTAATA-TTTTGGAAATAAAAATAG-GGTTAGAGTATCCCCTCAAAAATAACGAGGT
*
306055 TGGAGTATCCCC-A-T
64 TGGAGTATCCCCGAGA
* * * * * *
306069 TGGTAAA-TTTAATATTTTTGGAAATAAAAATGGGGCTAGATTATCCTCTCATAAATAAC-ACGG
1 T-GAAAATTTTAATA-TTTTGGAAATAAAAATAGGGTTAGAGTATCCCCTCAAAAATAACGA-GG
*
306132 TTGGAGTATCCTCGAGA
63 TTGGAGTATCCCCGAGA
* * * * * * * *
306149 --AAAA-TTTAATATTTTGAAAATAAAAATA-GGTTAGAATATCCCCTTAGAATTTATGGGGTTG
1 TGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTAGAGTATCCCCTCAAAAATAACGAGGTTG
* * *
306210 CAATATCCTCGAGA
66 GAGTATCCCCGAGA
* *
306224 TGAAAATTTTAACATTTTGGAAATAAAAATAGGGTTAGAGTATCCCCTCAAAAATAACAAGGTTG
1 TGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTAGAGTATCCCCTCAAAAATAACGAGGTTG
306289 GAGTATCCCCGAGA
66 GAGTATCCCCGAGA
* * * ** * * *
306303 TAAAAAATCTAATATTTTGGAAAT-AAAAGCGGATTTGCAGTATCCCCTCAAAAATAACGGGGTT
1 TGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTAG-AGTATCCCCTCAAAAATAACGAGGTT
*
306367 AGAGTATCCCCGTA-A
65 GGAGTATCCCCG-AGA
*
306382 TGAAAATTTTAATGTTTTTGGAAATAAAAAT
1 TGAAAATTTTAAT-ATTTTGGAAATAAAAAT
306413 GAGACTGAAG
Statistics
Matches: 274, Mismatches: 56, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
75 35 0.13
76 15 0.05
77 15 0.05
78 82 0.30
79 112 0.41
80 11 0.04
81 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (79 bp):
TGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTAGAGTATCCCCTCAAAAATAACGAGGTTG
GAGTATCCCCGAGA
Found at i:307124 original size:10 final size:9
Alignment explanation
Indices: 307109--307134 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
307099 CCTTTAAGAG
307109 AAAAAAATC
1 AAAAAAATC
307118 AAAAAAATC
1 AAAAAAATC
307127 AAAAAAAT
1 AAAAAAAT
307135 TGTTTCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATC
Found at i:318369 original size:13 final size:13
Alignment explanation
Indices: 318351--318440 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
318341 TTCAACAATT
318351 TGTATCGATACAA
1 TGTATCGATACAA
318364 TGTATCGATACATAA
1 TGTATCGATAC--AA
318379 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
318396 TGTATCGATACATAA
1 TGTATCGATAC--AA
318411 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
318428 TGTATCGCTACAA
1 TGTATCGATACAA
318441 AGCTATTGCC
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:318388 original size:19 final size:18
Alignment explanation
Indices: 318364--318426 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
318354 ATCGATACAA
318364 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
318383 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
318396 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
318415 TGTATCGATACA
1 TGTATCGATACA
318427 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:318391 original size:32 final size:32
Alignment explanation
Indices: 318350--318439 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
318340 TTTCAACAAT
318350 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
318382 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
318414 TTGTATCGATACAATGTATCGCTACA
1 TTGTATCGATACAATGTATCGATACA
318440 AAGCTATTGC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:320743 original size:24 final size:25
Alignment explanation
Indices: 320716--320766 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
320706 ATCAAAATTT
320716 ATTCATCC-GGGACACTCCAACCCC
1 ATTCATCCGGGGACACTCCAACCCC
*
320740 ATTCCTCCGAGGGGACACTCCAACCCC
1 ATTCATCC--GGGGACACTCCAACCCC
320767 GTTTTCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
27 16 0.70
ACGTcount: A:0.24, C:0.45, G:0.16, T:0.16
Consensus pattern (25 bp):
ATTCATCCGGGGACACTCCAACCCC
Found at i:325405 original size:51 final size:51
Alignment explanation
Indices: 325327--325427 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
325317 ATTGTTTTCG
* *
325327 ATTATGAAAAATTGGTGTTTTGAAAATAACA-TCGGAGTTGGAGTATCCCCA
1 ATTATGAAAAATTCGTGTTTTGAAAATAAAACT-GGAGTTGGAGTATCCCCA
* * *
325378 ATTATGGAGAATTCGTGTTTT-AGAAATAAAACTGGGGTTGGAGTATCCCC
1 ATTATGAAAAATTCGTGTTTTGA-AAATAAAACTGGAGTTGGAGTATCCCC
325428 TCGAAAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
50 1 0.02
51 41 0.95
52 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.32
Consensus pattern (51 bp):
ATTATGAAAAATTCGTGTTTTGAAAATAAAACTGGAGTTGGAGTATCCCCA
Found at i:327850 original size:13 final size:13
Alignment explanation
Indices: 327832--327861 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
327822 GTAAATTCAG
327832 AATGTATCGATAC
1 AATGTATCGATAC
*
327845 AATGTATTGATAC
1 AATGTATCGATAC
327858 AATG
1 AATG
327862 AGCAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:327872 original size:33 final size:33
Alignment explanation
Indices: 327832--327914 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
327822 GTAAATTCAG
*
327832 AATGTATCGATACAATGTATTGATACAATGAGC
1 AATGTATCGATACAATGTATTAATACAATGAGC
*
327865 AATGTATCGATACATTGTATTAATACAATGAGC
1 AATGTATCGATACAATGTATTAATACAATGAGC
*
327898 AATGTATCGATATAATG
1 AATGTATCGATACAATG
327915 AATAATGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.33
Consensus pattern (33 bp):
AATGTATCGATACAATGTATTAATACAATGAGC
Found at i:328512 original size:41 final size:41
Alignment explanation
Indices: 328433--328776 Score: 143
Period size: 41 Copynumber: 8.1 Consensus size: 41
328423 GGAAGAGGAA
* ** *
328433 AAAAAGGAAGAGGGCGTCCTGCTCTTTGAGGATTAAGGAAAAGG
1 AAAAA-GAA-AGGG-GTCCTGCTCCTTGAGGACAAAGGAAAAAG
* * *
328477 AGAATGAAAGGGGTCATGCTCCTTGAGGACAAAGGAAGAAAG
1 AAAAAGAAAGGGGTCCTGCTCCTTGAGGACAAAGGAA-AAAG
* * *
328519 AAAAAGAAA-GTGTCCTGTTTCTTGAGGACAAAGTGAAAAAG
1 AAAAAGAAAGGGGTCCTGCTCCTTGAGGACAAAG-GAAAAAG
* *
328560 ----AG-TA--CGTCCTGCT--TTAAGAGGACAAAGGAAAAAAGG
1 AAAAAGAAAGGGGTCCTGCTCCTT--GAGGACAAAGG-AAAAA-G
* ** * * * *
328596 GAAGCGAAATGCGTCCTGCTCTTTGAGGACAAAAGAAAAAG
1 AAAAAGAAAGGGGTCCTGCTCCTTGAGGACAAAGGAAAAAG
* * * *
328637 GAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAG
1 AAAAAGAAAG-GGGTCCTGCTCCTTGAGGAC-AAA-GG-AAA-AAG
* * * *
328683 GAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGGGAAAAA-
1 AAAAAGAAAG-GGGTCCTGCTCCTTGAGGAC-AAA-GGAAAAAG
* * * *
328726 AAGGAAATGAAATGTGTCCTGCTCTTTGAGGGCAAAGGAGAAAAG
1 AA--AAA-GAAAGGGGTCCTGCTCCTTGAGGACAAAGGA-AAAAG
328771 AAAAAG
1 AAAAAG
328777 GCGTCCTGCT
Statistics
Matches: 246, Mismatches: 29, Indels: 52
0.75 0.09 0.16
Matches are distributed among these distances:
33 2 0.01
34 1 0.00
35 22 0.09
36 2 0.01
37 2 0.01
40 1 0.00
41 53 0.22
42 43 0.17
43 32 0.13
44 13 0.05
45 31 0.13
46 44 0.18
ACGTcount: A:0.41, C:0.12, G:0.29, T:0.18
Consensus pattern (41 bp):
AAAAAGAAAGGGGTCCTGCTCCTTGAGGACAAAGGAAAAAG
Found at i:328651 original size:42 final size:44
Alignment explanation
Indices: 328564--328775 Score: 233
Period size: 46 Copynumber: 4.8 Consensus size: 44
328554 AAAAAGAGTA
* ***
328564 CGTCCTGCT-TTAAGAGGAC-AAAGGAAAAAAGGGAAGCGAAA-TG
1 CGTCCTGCTCTT-TGAGGACAAAAGGAAAAAA-GGAAAATAAAGTG
328607 CGTCCTGCTCTTTGAGGACAAAA-G-AAAAAGGAAAATAAAGTG
1 CGTCCTGCTCTTTGAGGACAAAAGGAAAAAAGGAAAATAAAGTG
328649 CGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAAATAAAGTG
1 CGTCCTGCTCTTTGAGGACAAAA-GGAAAA-AAGGAAAATAAAGTG
328695 CGTCCTGCTCTTTGAGGACAAAAGGGAAAAAAAGG-AAATGAAA-TG
1 CGTCCTGCTCTTTGAGGACAAAA-GG-AAAAAAGGAAAAT-AAAGTG
* * * *
328740 TGTCCTGCTCTTTGAGGGC-AAAGGAGAAAAGAAAAA
1 CGTCCTGCTCTTTGAGGACAAAAGGAAAAAAGGAAAA
328776 GGCGTCCTGC
Statistics
Matches: 151, Mismatches: 8, Indels: 20
0.84 0.04 0.11
Matches are distributed among these distances:
41 7 0.05
42 36 0.24
43 21 0.14
44 9 0.06
45 26 0.17
46 48 0.32
47 4 0.03
ACGTcount: A:0.42, C:0.14, G:0.27, T:0.17
Consensus pattern (44 bp):
CGTCCTGCTCTTTGAGGACAAAAGGAAAAAAGGAAAATAAAGTG
Found at i:328701 original size:46 final size:46
Alignment explanation
Indices: 328605--328772 Score: 242
Period size: 46 Copynumber: 3.8 Consensus size: 46
328595 GGAAGCGAAA
328605 TGCGTCCTGCTCTTTGAGGACAAAA--G-AAA-AAGGAAAATAAAG
1 TGCGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAAATAAAG
328647 TGCGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAAATAAAG
1 TGCGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAAATAAAG
*
328693 TGCGTCCTGCTCTTTGAGGACAAAAGGGAAAAAAAGG-AAATGAAA-
1 TGCGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAAAT-AAAG
* *
328738 TGTGTCCTGCTCTTTGAGGGC-AAAGGAGAAAAGAA
1 TGCGTCCTGCTCTTTGAGGACAAAAGG-GAAAAGAA
328773 AAAGGCGTCC
Statistics
Matches: 116, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
42 25 0.22
44 6 0.05
45 33 0.28
46 52 0.45
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.19
Consensus pattern (46 bp):
TGCGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGAAAATAAAG
Found at i:328769 original size:91 final size:88
Alignment explanation
Indices: 328605--328772 Score: 243
Period size: 91 Copynumber: 1.9 Consensus size: 88
328595 GGAAGCGAAA
328605 TGCGTCCTGCTCTTTGAGGACAAAAGAAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAA
1 TGCGTCCTGCTCTTTGAGGACAAAAGAAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAA
328670 AAGGGAAAAGAAGGAAAATAAAG
66 AAGGGAAAAGAAGGAAAATAAAG
*
328693 TGCGTCCTGCTCTTTGAGGACAAAAGGGAAAAAAAGG-AAATGAAA-TGTGTCCTGCTCTTTGAG
1 TGCGTCCTGCTCTTTGAGGACAAAA--G--AAAAAGGAAAAT-AAAGTGCGTCCTGCTCTTTGAG
*
328756 GGC-AAAGGAGAAAAGAA
61 GACAAAAGG-GAAAAGAA
328773 AAAGGCGTCC
Statistics
Matches: 72, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
88 25 0.35
90 6 0.08
91 31 0.43
92 10 0.14
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.19
Consensus pattern (88 bp):
TGCGTCCTGCTCTTTGAGGACAAAAGAAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAA
AAGGGAAAAGAAGGAAAATAAAG
Found at i:328784 original size:38 final size:38
Alignment explanation
Indices: 328741--328862 Score: 167
Period size: 37 Copynumber: 3.3 Consensus size: 38
328731 AATGAAATGT
** *
328741 GTCCTGCTCTTTGAGGGCAAAGGAGAAAAGAAAAAGGC
1 GTCCTGCTCTAAGAGGGCAAAGGAGAAAAGGAAAAGGC
*
328779 GTCCTGCTC-AAGAGGGCAAAGGAGAAAGGGAAAAGGC
1 GTCCTGCTCTAAGAGGGCAAAGGAGAAAAGGAAAAGGC
* * *
328816 ATCATGC-CCAAGAGGGCAAAGGAGAAAAGGAAAAGGC
1 GTCCTGCTCTAAGAGGGCAAAGGAGAAAAGGAAAAGGC
328853 GTCCTGCTCT
1 GTCCTGCTCT
328863 TTGAGGACTA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
36 1 0.01
37 61 0.85
38 10 0.14
ACGTcount: A:0.37, C:0.18, G:0.33, T:0.12
Consensus pattern (38 bp):
GTCCTGCTCTAAGAGGGCAAAGGAGAAAAGGAAAAGGC
Found at i:328798 original size:37 final size:37
Alignment explanation
Indices: 328753--328861 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
328743 CCTGCTCTTT
*
328753 GAGGGCAAAGGAGAAAAGAAAAAGGCGTCCTGCTCAA
1 GAGGGCAAAGGAGAAAAGGAAAAGGCGTCCTGCTCAA
* * * *
328790 GAGGGCAAAGGAGAAAGGGAAAAGGCATCATGCCCAA
1 GAGGGCAAAGGAGAAAAGGAAAAGGCGTCCTGCTCAA
328827 GAGGGCAAAGGAGAAAAGGAAAAGGCGTCCTGCTC
1 GAGGGCAAAGGAGAAAAGGAAAAGGCGTCCTGCTC
328862 TTTGAGGACT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.41, C:0.17, G:0.35, T:0.07
Consensus pattern (37 bp):
GAGGGCAAAGGAGAAAAGGAAAAGGCGTCCTGCTCAA
Found at i:329009 original size:60 final size:61
Alignment explanation
Indices: 328840--329137 Score: 373
Period size: 61 Copynumber: 5.0 Consensus size: 61
328830 GGCAAAGGAG
*
328840 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTG-GAGGCTTT
1 AAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTG-GGCTTT
*
328901 AAAAGGAAAAGGCGTCCTACTTTTTGAGGACTGAAAAAGTGCCACCAACTTGTGT-GGCTTT
1 AAAAGGAAAAGGCGTCCTACTCTTTGAGGACT-AAAAAGTGCCACCAACTTGTGTGGGCTTT
* * ** * *
328962 AAAAGAAAAAGGCATCCGGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTATGGGCTTT
1 AAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
329023 AAAAGGAGAAGGCGTCCTACTCTTTGAGGACT-AAAGGTGCCACCAGCTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
329083 ------AAAAGGCGTCCTACTTTTTGAGGACTCGAAAA-TGCCACCAACTTATGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTACTCTTTGAGGACT-AAAAAGTGCCACCAACTTGTGTGGGCTTT
329138 GAGAGGTGTC
Statistics
Matches: 209, Mismatches: 23, Indels: 16
0.84 0.09 0.06
Matches are distributed among these distances:
54 24 0.11
55 21 0.10
56 3 0.01
60 44 0.21
61 96 0.46
62 21 0.10
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (61 bp):
AAAAGGAAAAGGCGTCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:329297 original size:60 final size:60
Alignment explanation
Indices: 329172--329467 Score: 330
Period size: 55 Copynumber: 5.1 Consensus size: 60
329162 CTAAAGGGTG
* * * * *
329172 AAAGGAG-AGAGCGTCCTACTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGTTTT
1 AAAGGAGAAG-GCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT
* *
329232 AAAAGGAGAAGGCGTCCTGCTCTCTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT
1 -AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT
329292 ----GA-AAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *
329347 AAAAGGAGAAGGCGTCCAGCTCTCTGAGGACT-GAAGGTGCCACTAGCTTGTGTGGGCTTT
1 -AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
329407 ----GA-AAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTATGTGGGCTTT
1 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT
329462 GAAAGG
1 -AAAGG
329468 CATCCTACTT
Statistics
Matches: 200, Mismatches: 21, Indels: 29
0.80 0.08 0.12
Matches are distributed among these distances:
54 44 0.22
55 54 0.27
60 53 0.26
61 47 0.23
62 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (60 bp):
AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:329303 original size:154 final size:148
Alignment explanation
Indices: 329024--329318 Score: 362
Period size: 154 Copynumber: 2.0 Consensus size: 148
329014 ATGGGCTTTA
* *
329024 AAAGGAGAAGGCGTCCTACTCTTTGAGGACTAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGG
1 AAAGGAGAAGGCGTCCTACTCTTTAAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
* * * * *
329089 CGTCCTACTTTTTGAGGACTCGAAAATGCCACCAACTTATGTGGGCTTTGAGAGGTGTCCTGCTT
66 CGTCCTACTCTCTGAGGACTCGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGCGTCCTGCTC
329154 TTTGAAGACTAAAGGGTG
131 TTTGAAGACTAAAGGGTG
* *
329172 AAAGGAG-AGAGCGTCCTACTCTTTAAGGACTGGGAA-GTGCCACCAACTTGTGTGGGTTTTAAA
1 AAAGGAGAAG-GCGTCCTACTCTTTAAGGACT--AAAGGTGCCACCAACTTGTGTGGGCTTT---
* ** *
329235 AGGAGAAGGCGTCCTGCTCTCTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
60 A--A-AAGGCGTCCTACTCTCTGAGGACTCGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGC
*
329299 GTCCTGCTCTTTGAGGACTA
122 GTCCTGCTCTTTGAAGACTA
329319 GAAAGTGCCA
Statistics
Matches: 124, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
147 2 0.02
148 27 0.22
149 22 0.18
150 2 0.02
152 1 0.01
154 49 0.40
155 21 0.17
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.26
Consensus pattern (148 bp):
AAAGGAGAAGGCGTCCTACTCTTTAAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
CGTCCTACTCTCTGAGGACTCGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGCGTCCTGCTC
TTTGAAGACTAAAGGGTG
Found at i:329384 original size:115 final size:115
Alignment explanation
Indices: 329182--329467 Score: 464
Period size: 115 Copynumber: 2.5 Consensus size: 115
329172 AAAGGAGAGA
* * * * *
329182 GCGTCCTACTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGTTTTAAAAGGAGAAGGCGT
1 GCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGT
*
329247 CCTGCTCTCTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
66 CCAGCTCTCTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
329297 GCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGT
1 GCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGT
* *
329362 CCAGCTCTCTGAGGACTGAAGGTGCCACTAGCTTGTGTGGGCTTTGAAAG
66 CCAGCTCTCTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
* * * *
329412 GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTATGTGGGCTTTGAAAGG
1 GCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
329468 CATCCTACTT
Statistics
Matches: 159, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
115 159 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (115 bp):
GCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGT
CCAGCTCTCTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
Found at i:329447 original size:324 final size:323
Alignment explanation
Indices: 328851--329675 Score: 1224
Period size: 324 Copynumber: 2.5 Consensus size: 323
328841 AAAGGAAAAG
**
328851 GCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTG-GAGGCTTTAAAAGGAAAAGGCG
1 GCGTCCTGCTCTTTGAGGACT-GGAAGTGCCACCAACTTGTGTG-GGCTTTAAAAGGAAAAGGCG
* * * *
328915 TCCTACTTTTTGAGGACTGAAAAAGTGCCACCAACTTGTGT-GGCTTTAAAAGAAAAAGGCATCC
64 TCCTGCTCTTTGAGGACTG--AAGGTGCCACCAACTTGTGTGGGCTTT----G--AAAGGCGTCC
* *
328979 GGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGAGAAGGCGTCCTACT
121 TGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTACT
* * *
329044 CTTTGAGGACTAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGCGTCCTACTTTTTGAGGACT
186 CTCTGAGGACTAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAGGACT
* * ** *
329109 CGAAAATGCCACCAACTTATGTGGGCTTTGAGAGGTGTCCTGCTTTTTGAAGACTAAAGGGTGAA
251 AGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGCATCCTACTTTTTGAAGACTAAAGGGTGAA
329174 AGGAGAGA
316 AGGAGAGA
* * * *
329182 GCGTCCTACTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGTTTTAAAAGGAGAAGGCGT
1 GCGTCCTGCTCTTTGAGGACT-GGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
*
329247 CCTGCTCTCTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTG
65 CCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTG
329312 AGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCC-AGCTCTCTGAGG
130 AGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTA-CTCTCTGAGG
* * * *
329376 ACTGAAGGTGCCACTAGCTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTAGAAAATG
194 ACTAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAGGACTAGAAAATG
329441 CCACCAACTTATGTGGGCTTTGAAAGGCATCCTACTTTTTGAAGACTAAAGGGTGAAAGGAGAGA
259 CCACCAACTTATGTGGGCTTTGAAAGGCATCCTACTTTTTGAAGACTAAAGGGTGAAAGGAGAGA
* * *
329506 GCATCCTGCTCTTTGAGGACTGGAAGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCATC
1 GCGTCCTGCTCTTTGAGGACTGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
* *
329571 CTGCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGCCGTCCTGCTCTTTGA
66 CTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGA
* * *
329636 GGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG
131 GGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
329676 CATCCTACTT
Statistics
Matches: 452, Mismatches: 39, Indels: 14
0.90 0.08 0.03
Matches are distributed among these distances:
323 140 0.31
324 214 0.47
326 1 0.00
329 19 0.04
330 6 0.01
331 71 0.16
332 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (323 bp):
GCGTCCTGCTCTTTGAGGACTGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
CTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGA
GGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTACTCTCTGAGGAC
TAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAGGACTAGAAAATGCC
ACCAACTTATGTGGGCTTTGAAAGGCATCCTACTTTTTGAAGACTAAAGGGTGAAAGGAGAGA
Found at i:329572 original size:60 final size:58
Alignment explanation
Indices: 329496--329675 Score: 217
Period size: 60 Copynumber: 3.1 Consensus size: 58
329486 CTAAAGGGTG
* *
329496 AAAGGAGAGAGCATCCTGCTCTTTGAGGACTGGAAGTGCCACCAACTTGTGTAGGCTTT
1 AAAGGAAAG-GCATCCTGCTCTTTGAGGACTGGAAGTGCCACCAACTTGTGTGGGCTTT
*
329555 AAAAGGAAAAGGCATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTT
1 -AAAGG-AAAGGCATCCTGCTCTTTGAGGACTGGAA-GTGCCACCAACTTGTGTGGGCTTT
* * *
329615 ----GAAAGCCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT
1 AAAGGAAAGGCATCCTGCTCTTTGAGGACTGG-AAGTGCCACCAACTTGTGTGGGCTTT
329670 GAAAGG
1 -AAAGG
329676 CATCCTACTT
Statistics
Matches: 104, Mismatches: 7, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
54 23 0.22
55 24 0.23
56 2 0.02
59 3 0.03
60 49 0.47
61 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (58 bp):
AAAGGAAAGGCATCCTGCTCTTTGAGGACTGGAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:329666 original size:55 final size:55
Alignment explanation
Indices: 329507--329695 Score: 220
Period size: 55 Copynumber: 3.4 Consensus size: 55
329497 AAGGAGAGAG
* *
329507 CATCCTGCTCTTTGAGGACTGG-AAGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGG
1 CATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGC
* *
329567 CATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGC
1 CATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGC
* * *
329621 CGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG
1 CATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGC
* * *
329676 CATCCTACTTTTTGAAGACT
1 CATCCTGCTCTTTGAGGACT
329696 AAAGGGTGAA
Statistics
Matches: 114, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
54 23 0.20
55 47 0.41
59 1 0.01
60 43 0.38
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.28
Consensus pattern (55 bp):
CATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGC
Found at i:329679 original size:208 final size:209
Alignment explanation
Indices: 329300--329798 Score: 865
Period size: 208 Copynumber: 2.4 Consensus size: 209
329290 TTGAAAGGCG
* *
329300 TCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCA
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCT
* * *
329365 GCTCTCTGAGGACTGAAGGTGCCACTAGCTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGG
66 GCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGCCATCCTGCTCTTTGAGG
329430 ACTAGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGCATCCTACTTTTTGAAGACTAAAGGGT
131 ACTAGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGCATCCTACTTTTTGAAGACTAAAGGGT
329495 GAAAGGAGAGAGCA
196 GAAAGGAGAGAGCA
* * *
329509 TCCTGCTCTTTGAGGACT-GGAAGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCATCCT
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCT
*
329573 GCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGCCGTCCTGCTCTTTGAGG
66 GCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGCCATCCTGCTCTTTGAGG
* *
329638 ACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTACTTTTTGAAGACTAAAGGGT
131 ACTAGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGCATCCTACTTTTTGAAGACTAAAGGGT
*
329703 GAAAGGAGAGAGCG
196 GAAAGGAGAGAGCA
* *
329717 TCTTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCT
329782 GCTCTTTGAGGACTGAA
66 GCTCTTTGAGGACTGAA
329799 AAGTGAAAGG
Statistics
Matches: 273, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
208 195 0.71
209 78 0.29
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (209 bp):
TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCT
GCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAGCCATCCTGCTCTTTGAGG
ACTAGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGCATCCTACTTTTTGAAGACTAAAGGGT
GAAAGGAGAGAGCA
Found at i:330783 original size:1 final size:1
Alignment explanation
Indices: 330777--330850 Score: 67
Period size: 1 Copynumber: 74.0 Consensus size: 1
330767 CTTTTCTCTC
* * * * * * * * *
330777 TTTTTTTTTTGTTTTTGTTTTTTTGTTTTGTTTTGTTTTTATTTTTTTTTTGTTTTGTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
330842 TTTTTTTTT
1 TTTTTTTTT
330851 AAAAAGAATA
Statistics
Matches: 55, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.01, C:0.00, G:0.11, T:0.88
Consensus pattern (1 bp):
T
Found at i:330791 original size:6 final size:6
Alignment explanation
Indices: 330777--330849 Score: 84
Period size: 6 Copynumber: 12.8 Consensus size: 6
330767 CTTTTCTCTC
* *
330777 TTTTT- TTTTTG TTTTTG TTTTTT TGTTTTG -TTTTG TTTTTA TTTTT-
1 TTTTTG TTTTTG TTTTTG TTTTTG T-TTTTG TTTTTG TTTTTG TTTTTG
330823 TTTTTG -TTTTG TTTTTG TTTTT- TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
330850 TAAAAAGAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
5 25 0.42
6 31 0.52
7 4 0.07
ACGTcount: A:0.01, C:0.00, G:0.11, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:335275 original size:20 final size:20
Alignment explanation
Indices: 335222--335276 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
335212 AAATTCCCAG
** *
335222 ATGTATCGATACAAAGATTA
1 ATGTATCGATACATTGAATA
*
335242 ATGTATTGATACATTGAATA
1 ATGTATCGATACATTGAATA
335262 ATGTATCGATACATT
1 ATGTATCGATACATT
335277 TTCTTGGCAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:335364 original size:19 final size:19
Alignment explanation
Indices: 335306--335364 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
335296 AGCGATACAC
* *
335306 TGTATCGATACAACACT-TA
1 TGTATCGATACAA-ATTGTT
*
335325 TGTATCGATACATTTATTGTT
1 TGTATCGATACA--AATTGTT
335346 TGTATCGATACAAATTGTT
1 TGTATCGATACAAATTGTT
335365 GAAATTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 18 0.55
20 2 0.06
21 13 0.39
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (19 bp):
TGTATCGATACAAATTGTT
Found at i:344146 original size:4 final size:4
Alignment explanation
Indices: 344137--344167 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
344127 ACAAAAAACA
344137 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
344168 CACCTCGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:346326 original size:79 final size:79
Alignment explanation
Indices: 346230--346553 Score: 330
Period size: 79 Copynumber: 4.1 Consensus size: 79
346220 ACAACGGGGC
* *
346230 TGGAGTATCCCCGATTATGGAAAATCGGTGTTTTGGAAATAAAATCGGGGTTAGAGTATCCCCTC
1 TGGAGTATCCCCGATTATGGAAAATCGATGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTC
* * *
346295 GGAAAGAACAAGGT
66 GAAAATAACAGGGT
* * * * * *
346309 TGGAGTATCCCTGATTATAGAAAATTGGTGTTTT-GAAAATAAAATCGGGGTTGGAGTATCCCTT
1 TGGAGTATCCCCGATTATGGAAAATCGATGTTTTAG-AAATAAAATCGGGGTTAGAGTATCCCCT
*
346373 CGAAAATAACGGGGT
65 CGAAAATAACAGGGT
* * * * ** * *
346388 TGGAGTATCCCTGATTATGAAAAATTGATGCTTTAGAAAT-AAGGCTGGGGTTGGAGTATCCCCG
1 TGGAGTATCCCCGATTATGGAAAATCGATGTTTTAGAAATAAAATC-GGGGTTAGAGTATCCCCT
* *
346452 CAAAAATAACGGGGT
65 CGAAAATAACAGGGT
* * * ** * *
346467 TGGAGTATCCCCGATTGT-GAGAAATCAATATTTTAGAAATAAAGCCGGGGCTAGAGTATCCCGT
1 TGGAGTATCCCCGATTATGGA-AAATCGATGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCT
*
346531 CGAAAATAATAGGGT
65 CGAAAATAACAGGGT
346546 TGGAGTAT
1 TGGAGTAT
346554 TCCCAATGAA
Statistics
Matches: 207, Mismatches: 33, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
78 5 0.02
79 197 0.95
80 5 0.02
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (79 bp):
TGGAGTATCCCCGATTATGGAAAATCGATGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTC
GAAAATAACAGGGT
Found at i:346642 original size:51 final size:51
Alignment explanation
Indices: 346572--346845 Score: 180
Period size: 51 Copynumber: 5.3 Consensus size: 51
346562 AAATACCGGG
* *
346572 GTTGGAGTATCGCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAGAATTGATGTTTTGGAAATAAAATCGGA
* * * * * * * *
346623 GTTGGAATATCCCCAATTGTGGAGAATTGGTGTTTTAGATATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGAAGAATTGATGTTTTGGAAATAAAATCGGA
* * *** ** * *
346674 GTTAGAGTATCCCCTCAAAAAT-AACGGGGTTGGA-GTATCCCTGATGAAAT--AATAGG-
1 GTTGGAGTAT-CCC-CGATTGTGAA--GAATT-GATGT-T--TTG--GAAATAAAATCGGA
* * * *
346730 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTGTGAAGAATTGATGTTTTGGAAATAAAATCGGA
* * * *
346781 GTTGGAGTATCCCCGATTGTGGAGAATTGATGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGAAGAATTGATGTTTTGGAAATAAAATCGGA
346832 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
346846 TCGAAAATAA
Statistics
Matches: 165, Mismatches: 43, Indels: 30
0.69 0.18 0.13
Matches are distributed among these distances:
48 5 0.03
50 6 0.04
51 106 0.64
52 6 0.04
53 8 0.05
54 9 0.05
55 7 0.04
56 9 0.05
57 5 0.03
59 4 0.02
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAGAATTGATGTTTTGGAAATAAAATCGGA
Found at i:346723 original size:28 final size:27
Alignment explanation
Indices: 346670--346742 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
346660 GATATAAAAC
*
346670 CGGGGTTAGAGTATCCCCTCAAAAATAA
1 CGGGGTTGGAGTAT-CCCTCAAAAATAA
* *
346698 CGGGGTTGGAGTATCCCTGATGAAATAA
1 CGGGGTTGGAGTATCCCTCA-AAAATAA
**
346726 TAGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
346743 CGATTATGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.13
28 34 0.87
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCTCAAAAATAA
Found at i:346870 original size:158 final size:156
Alignment explanation
Indices: 346465--346872 Score: 566
Period size: 158 Copynumber: 2.6 Consensus size: 156
346455 AAATAACGGG
** * * *
346465 GTTGGAGTATCCCCGATTGT-GAGAAATCAATATTTTAGAAATAAAGCCGGGGCTAGAGTATCCC
1 GTTGGAGTATCCCCGATTGTGGAG-AATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCC
* * * * * *
346529 GTCGAAAATAATAGGGTTGGAGTATTCCCAATGAAATACCGGGGTTGGAGTATCGCCGATTGTGA
65 CTCGAAAATAA-CGGGTTGGAGTA-TCCCAATGAAATAACAGGGTTGGAGTATCCCCGATTATGA
*
346594 AAAATTGATGTTTTGGAAATAAAATCGGA
128 AAAATTGATGTTTTGGAAATAAAATCGAA
* * * *
346623 GTTGGAATATCCCCAATTGTGGAGAATTGGTGTTTTAGATATAAAACCGGGGTTAGAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGGAGAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCCC
* * *
346688 TCAAAAATAACGGGGTTGGAGTATCCCTGATGAAATAATAGGGTTGGAGTATCCCCGATTATGAA
66 TCGAAAATAAC-GGGTTGGAGTATCCC-AATGAAATAACAGGGTTGGAGTATCCCCGATTATGAA
*
346753 AAATTGGTGTTTTGGAAATAAAATCGAA
129 AAATTGATGTTTTGGAAATAAAATCGAA
*
346781 GTTGGAGTATCCCCGATTGTGGAGAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGGAGAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCCC
346846 TCGAAAATAACGGGATTGGAGTATCCC
66 TCGAAAATAACGGG-TTGGAGTATCCC
346873 CGATTATGAA
Statistics
Matches: 220, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
157 7 0.03
158 210 0.95
159 3 0.01
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (156 bp):
GTTGGAGTATCCCCGATTGTGGAGAATTGATGTTTTAGAAATAAAACCGGGGTTAGAGTATCCCC
TCGAAAATAACGGGTTGGAGTATCCCAATGAAATAACAGGGTTGGAGTATCCCCGATTATGAAAA
ATTGATGTTTTGGAAATAAAATCGAA
Found at i:349271 original size:21 final size:20
Alignment explanation
Indices: 349225--349277 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
349215 GTAGCCAAAC
**
349225 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
349245 -TGTATCGATACACCAAAAAA
1 TTGTATCGATACACC-AAAAA
349265 TTGTATCGATACA
1 TTGTATCGATACA
349278 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 12 0.41
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:357729 original size:52 final size:52
Alignment explanation
Indices: 357644--357768 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
357634 ATATGAAAAG
* *
357644 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
357696 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
357748 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
357769 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:357781 original size:52 final size:51
Alignment explanation
Indices: 357644--357789 Score: 213
Period size: 52 Copynumber: 2.8 Consensus size: 51
357634 ATATGAAAAG
*
357644 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
357696 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
357748 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACAT
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACAT
357790 GTGAGTAATG
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:357870 original size:33 final size:33
Alignment explanation
Indices: 357828--357930 Score: 170
Period size: 33 Copynumber: 3.1 Consensus size: 33
357818 GGCAGTAGCT
* ***
357828 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAACATTTTATGTATCGA
357861 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAACATTTTATGTATCGA
357894 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAACATTTTATGTATCGA
357927 TACA
1 TACA
357931 AATCGTTGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.36
Consensus pattern (33 bp):
TACATTGTATCGATACAACATTTTATGTATCGA
Found at i:357871 original size:13 final size:13
Alignment explanation
Indices: 357853--357910 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
357843 CAAAAAAATA
357853 TGTATCGATACAT
1 TGTATCGATACAT
357866 TGTATCGATACAACATTTT
1 TGTATCGAT---ACA---T
357885 ATGTATCGATACAT
1 -TGTATCGATACAT
357899 TGTATCGATACA
1 TGTATCGATACA
357911 ACATTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 9 0.24
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Done.