Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008532.1 Hibiscus syriacus cultivar Beakdansim tig00111410_pilon, whole genome shotgun sequence
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: 857509
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:179274 original size:30 final size:31
Alignment explanation
Indices: 179204--179275 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
179194 AACCATTGAT
* * * *
179204 AACTTTTCCAAAATTATTAAATTGGTTCCCT
1 AACTTTTCCAAAATTATCAAAATGGTCCCCA
179235 AACTTTTCCAAAATTA-CAAAATGGTCCCCA
1 AACTTTTCCAAAATTATCAAAATGGTCCCCA
*
179265 AATTTTTCCAA
1 AACTTTTCCAA
179276 GTCTTGTAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 20 0.56
31 16 0.44
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (31 bp):
AACTTTTCCAAAATTATCAAAATGGTCCCCA
Found at i:180888 original size:20 final size:20
Alignment explanation
Indices: 180859--180897 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
180849 AAAGCTCATA
180859 TAGGACCATATAGATGCATT
1 TAGGACCATATAGATGCATT
* *
180879 TAGGAGCATATAGTTGCAT
1 TAGGACCATATAGATGCAT
180898 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (20 bp):
TAGGACCATATAGATGCATT
Found at i:182282 original size:18 final size:19
Alignment explanation
Indices: 182241--182282 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
182231 GATTATTTTA
*
182241 CACATAATTCCTTTGCCAC
1 CACATAATTCATTTGCCAC
* *
182260 AACAT-ATTCATTTGCTAC
1 CACATAATTCATTTGCCAC
182278 CACAT
1 CACAT
182283 TGTCATCGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (19 bp):
CACATAATTCATTTGCCAC
Found at i:188015 original size:571 final size:571
Alignment explanation
Indices: 186933--188075 Score: 2268
Period size: 571 Copynumber: 2.0 Consensus size: 571
186923 TCAGCCAGGG
186933 CAAAAAAAAGGTTTCTGCATGATGTCGAGTTCTATTTTTCGGACGAGCCGTACTTGTTCAAGCAT
1 CAAAAAAAAGGTTTCTGCATGATGTCGAGTTCTATTTTTCGGACGAGCCGTACTTGTTCAAGCAT
186998 TGTACTGATCAAATGATTCGACGGTGTGTCCCCGAAGAGGAGCAACATGATATTTTACACCATTG
66 TGTACTGATCAAATGATTCGACGGTGTGTCCCCGAAGAGGAGCAACATGATATTTTACACCATTG
187063 CCACACAGCACCCTCTGGAGGGCATTTTGGAGGTGCAAGGATTGCTGCCAAGGTCTTTCAATTAG
131 CCACACAGCACCCTCTGGAGGGCATTTTGGAGGTGCAAGGATTGCTGCCAAGGTCTTTCAATTAG
187128 GCTTCTACTGGCCATCCCTATTTAAGGATGCCCACAAATATTTCAAGTCCTGCGATAGATGCCAG
196 GCTTCTACTGGCCATCCCTATTTAAGGATGCCCACAAATATTTCAAGTCCTGCGATAGATGCCAG
187193 CGTACTGAGAACATTTTGAGACGACACGAAATGCTGCTGCAAAATATTTTGGAGATAGAGCTATT
261 CGTACTGAGAACATTTTGAGACGACACGAAATGCTGCTGCAAAATATTTTGGAGATAGAGCTATT
187258 CGATGTTTGGGGCATAGATTTTATGGGACCGTTCCTATCTTCTTTTGGAAACTTATACATTTTAC
326 CGATGTTTGGGGCATAGATTTTATGGGACCGTTCCTATCTTCTTTTGGAAACTTATACATTTTAC
187323 TCGCGGTGGACTACGTATACAAGTGGGTTGAAGTGATTGCGACACCGATGAATGACTCAAAGACG
391 TCGCGGTGGACTACGTATACAAGTGGGTTGAAGTGATTGCGACACCGATGAATGACTCAAAGACG
*
187388 GTGCTCAAGTTCCTTCACAAGAACATTTTCACTCGATTTGGAGCACCAAGAGCCATTATCTGTGA
456 GTGCTCAAGTTCCTTCACAAAAACATTTTCACTCGATTTGGAGCACCAAGAGCCATTATCTGTGA
187453 CGAGGGCACCCACTTTGATAACAAACTAATTGCCAAGGCATTACAGAAATA
521 CGAGGGCACCCACTTTGATAACAAACTAATTGCCAAGGCATTACAGAAATA
187504 CAAAAAAAAGGTTTCTGCATGATGTCGAGTTCTATTTTTCGGACGAGCCGTACTTGTTCAAGCAT
1 CAAAAAAAAGGTTTCTGCATGATGTCGAGTTCTATTTTTCGGACGAGCCGTACTTGTTCAAGCAT
187569 TGTACTGATCAAATGATTCGACGGTGTGTCCCCGAAGAGGAGCAACATGATATTTTACACCATTG
66 TGTACTGATCAAATGATTCGACGGTGTGTCCCCGAAGAGGAGCAACATGATATTTTACACCATTG
*
187634 CCACACAGCACCCTCTGGAGGGCATTTTGGAGGTGCGAGGATTGCTGCCAAGGTCTTTCAATTAG
131 CCACACAGCACCCTCTGGAGGGCATTTTGGAGGTGCAAGGATTGCTGCCAAGGTCTTTCAATTAG
187699 GCTTCTACTGGCCATCCCTATTTAAGGATGCCCACAAATATTTCAAGTCCTGCGATAGATGCCAG
196 GCTTCTACTGGCCATCCCTATTTAAGGATGCCCACAAATATTTCAAGTCCTGCGATAGATGCCAG
187764 CGTACTGAGAACATTTTGAGACGACACGAAATGCTGCTGCAAAATATTTTGGAGATAGAGCTATT
261 CGTACTGAGAACATTTTGAGACGACACGAAATGCTGCTGCAAAATATTTTGGAGATAGAGCTATT
187829 CGATGTTTGGGGCATAGATTTTATGGGACCGTTCCTATCTTCTTTTGGAAACTTATACATTTTAC
326 CGATGTTTGGGGCATAGATTTTATGGGACCGTTCCTATCTTCTTTTGGAAACTTATACATTTTAC
187894 TCGCGGTGGACTACGTATACAAGTGGGTTGAAGTGATTGCGACACCGATGAATGACTCAAAGACG
391 TCGCGGTGGACTACGTATACAAGTGGGTTGAAGTGATTGCGACACCGATGAATGACTCAAAGACG
187959 GTGCTCAAGTTCCTTCACAAAAACATTTTCACTCGATTTGGAGCACCAAGAGCCATTATCTGTGA
456 GTGCTCAAGTTCCTTCACAAAAACATTTTCACTCGATTTGGAGCACCAAGAGCCATTATCTGTGA
188024 CGAGGGCACCCACTTTGATAACAAACTAATTGCCAAGGCATTACAGAAATA
521 CGAGGGCACCCACTTTGATAACAAACTAATTGCCAAGGCATTACAGAAATA
188075 C
1 C
188076 GGAGTGCGAT
Statistics
Matches: 570, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
571 570 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (571 bp):
CAAAAAAAAGGTTTCTGCATGATGTCGAGTTCTATTTTTCGGACGAGCCGTACTTGTTCAAGCAT
TGTACTGATCAAATGATTCGACGGTGTGTCCCCGAAGAGGAGCAACATGATATTTTACACCATTG
CCACACAGCACCCTCTGGAGGGCATTTTGGAGGTGCAAGGATTGCTGCCAAGGTCTTTCAATTAG
GCTTCTACTGGCCATCCCTATTTAAGGATGCCCACAAATATTTCAAGTCCTGCGATAGATGCCAG
CGTACTGAGAACATTTTGAGACGACACGAAATGCTGCTGCAAAATATTTTGGAGATAGAGCTATT
CGATGTTTGGGGCATAGATTTTATGGGACCGTTCCTATCTTCTTTTGGAAACTTATACATTTTAC
TCGCGGTGGACTACGTATACAAGTGGGTTGAAGTGATTGCGACACCGATGAATGACTCAAAGACG
GTGCTCAAGTTCCTTCACAAAAACATTTTCACTCGATTTGGAGCACCAAGAGCCATTATCTGTGA
CGAGGGCACCCACTTTGATAACAAACTAATTGCCAAGGCATTACAGAAATA
Found at i:189377 original size:13 final size:12
Alignment explanation
Indices: 189359--189392 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
189349 CCCACTTTGT
189359 AAAAAAAAGAGAA
1 AAAAAAAAGA-AA
189372 AAAAAAAAGAAA
1 AAAAAAAAGAAA
189384 AAAAGAAAA
1 AAAA-AAAA
189393 AATGAAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:190027 original size:20 final size:20
Alignment explanation
Indices: 189998--190035 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
189988 AAAGCTCATA
*
189998 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
190018 TAGGAGCATATAGTTGCA
1 TAGGAGCATATAGATGCA
190036 AGTGGTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:198587 original size:20 final size:20
Alignment explanation
Indices: 198558--198596 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
198548 AAAGCTCATA
*
198558 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
198578 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
198597 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:201269 original size:13 final size:13
Alignment explanation
Indices: 201237--201261 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
201227 CTTTTTTTCC
201237 TTTTTTTCCTCTA
1 TTTTTTTCCTCTA
201250 TTTTTTTCCTCT
1 TTTTTTTCCTCT
201262 TCTTTTTTTA
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:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTCCTCTA
Found at i:201276 original size:35 final size:35
Alignment explanation
Indices: 201226--201361 Score: 125
Period size: 35 Copynumber: 3.8 Consensus size: 35
201216 TCATCTCACA
** *
201226 TCTTTTTTTCCTTTTTTTCCTCTATT-TTTTTCCTCT
1 TCTTTTTTT-CTTTTTTTATTCT-TTCTTTTTCTTCT
* *
201262 TCTTTTTTTATTTTTTTATTCTTTCTTTTTCTTTT
1 TCTTTTTTTCTTTTTTTATTCTTTCTTTTTCTTCT
* *
201297 TCTTCTTTTCTTTTTTTTTTCTTTTCTTTTTCTTCT
1 TCTTTTTTTCTTTTTTTATTC-TTTCTTTTTCTTCT
*
201333 TCTTCTATTTCTATTTCTTT-TTC-TTCTTT
1 TCTT-TTTTTCT-TTT-TTTATTCTTTCTTT
201362 CTTTTTGTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
34 2 0.02
35 36 0.43
36 32 0.38
37 5 0.06
38 6 0.07
39 3 0.04
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (35 bp):
TCTTTTTTTCTTTTTTTATTCTTTCTTTTTCTTCT
Found at i:201277 original size:36 final size:37
Alignment explanation
Indices: 201226--201367 Score: 135
Period size: 36 Copynumber: 3.8 Consensus size: 37
201216 TCATCTCACA
** * * *
201226 TCTTTTTTTCCTTTTTTTCCTCTATTTTT-TTCCTCT
1 TCTTTTTTTATTTTTTTTCCTTTCTTTTTCTTCTTCT
* *
201262 TCTTTTTTTATTTTTTTATTCTTTCTTTTTCTTTTTCT
1 TCTTTTTTTATTTTTTT-TCCTTTCTTTTTCTTCTTCT
* *
201300 TCTTTTCTT-TTTTTTTTCTTTTCTTTTTCTTCTTCT
1 TCTTTTTTTATTTTTTTTCCTTTCTTTTTCTTCTTCT
* *
201336 TCTATTTCTATTTCTTTTTCTTCTTTCTTTTT
1 TCTTTTTTTATTT-TTTTTC--CTTTCTTTTT
201368 GTTTTTAGCT
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
36 38 0.45
37 19 0.22
38 19 0.22
40 9 0.11
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (37 bp):
TCTTTTTTTATTTTTTTTCCTTTCTTTTTCTTCTTCT
Found at i:201283 original size:19 final size:18
Alignment explanation
Indices: 201261--201374 Score: 70
Period size: 19 Copynumber: 6.0 Consensus size: 18
201251 TTTTTTCCTC
201261 TTCTTTTTTTATTTTTTTA
1 TTCTTTTTTT-TTTTTTTA
* *
201280 TTCTTTCTTTTTCTTTTTC
1 TTCTTT-TTTTTTTTTTTA
*
201299 TTC-TTTTCTTTTTTTT-
1 TTCTTTTTTTTTTTTTTA
* *
201315 TTCTTTTCTTTTTCTTCTTC
1 TTCTTTT-TTTTT-TTTTTA
* *
201335 TTCTATTTCTATTTCTTTTTC
1 TTCT-TTT-T-TTTTTTTTTA
*
201356 TTCTTTCTTTTTGTTTTTA
1 TTCTTT-TTTTTTTTTTTA
201375 GCTCTTATGC
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
16 3 0.04
17 12 0.16
18 6 0.08
19 27 0.35
20 11 0.14
21 15 0.19
22 3 0.04
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.79
Consensus pattern (18 bp):
TTCTTTTTTTTTTTTTTA
Found at i:201292 original size:6 final size:6
Alignment explanation
Indices: 201261--201373 Score: 90
Period size: 6 Copynumber: 18.3 Consensus size: 6
201251 TTTTTTCCTC
* *
201261 TTCTTT TT-TTA TT-TTT TTATTCT TTCTTT TTCTTT TTCTTCTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTT-T TTCTTT TTCTTT TTC-T-TT TTCTTT
* *
201310 TT-TTT TTC-TT TTCTTT TTCTTCTT CTTCTAT TTCTAT TTCTTT TTCTTCT
1 TTCTTT TTCTTT TTCTTT TTC-T-TT -TTCTTT TTCTTT TTCTTT TTCTT-T
*
201360 TTCTTT TTGTTT TT
1 TTCTTT TTCTTT TT
201374 AGCTCTTATG
Statistics
Matches: 91, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
5 18 0.20
6 47 0.52
7 15 0.16
8 8 0.09
9 3 0.03
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:204015 original size:45 final size:45
Alignment explanation
Indices: 203964--204498 Score: 921
Period size: 45 Copynumber: 11.9 Consensus size: 45
203954 AATTTCTTAT
203964 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
204009 CAATATACTTACCATTTATCACATAAGCTCGTAAGTTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
204054 CAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTAA
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
204099 TAATATACTTACCATTTATCCCATAATCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* * *
204144 TAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTAA
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
*
204189 TAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
*
204234 TAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
204279 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
204324 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
204369 CAATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
204413 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
204458 CAATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
204499 GCATGGTTAC
Statistics
Matches: 468, Mismatches: 21, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
44 68 0.15
45 400 0.85
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (45 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
Found at i:204726 original size:40 final size:40
Alignment explanation
Indices: 204601--204710 Score: 184
Period size: 40 Copynumber: 2.8 Consensus size: 40
204591 ACCGTAGTGC
*
204601 TACATATAAGGTCGTACCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTACCCACCATATACACCGAAGTGTAT
* *
204641 TACACATAAGGTTGTAACCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTACCCACCATATACACCGAAGTGTAT
*
204681 TACACATAAGGTCGTGCCCACCATATACAC
1 TACACATAAGGTCGTACCCACCATATACAC
204711 TTAGTGTTCT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTACCCACCATATACACCGAAGTGTAT
Found at i:205066 original size:24 final size:24
Alignment explanation
Indices: 205031--205076 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
205021 CTTCCTGGTG
*
205031 ATGTATAAAACATCTATTTACATA
1 ATGTATAAAACATCTATGTACATA
*
205055 ATGTATACAACATCTATGTACA
1 ATGTATAAAACATCTATGTACA
205077 ATGTCATGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (24 bp):
ATGTATAAAACATCTATGTACATA
Found at i:208275 original size:31 final size:31
Alignment explanation
Indices: 208240--208309 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
208230 GTAACATTTA
208240 ATAATTGAGAAACTCAACAAAGTAATACCCT
1 ATAATTGAGAAACTCAACAAAGTAATACCCT
208271 ATAATTGAGAAACTCAACAAAGTAATACCCT
1 ATAATTGAGAAACTCAACAAAGTAATACCCT
208302 ATAATTGA
1 ATAATTGA
208310 TGATCATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.24
Consensus pattern (31 bp):
ATAATTGAGAAACTCAACAAAGTAATACCCT
Found at i:216815 original size:51 final size:51
Alignment explanation
Indices: 216737--216834 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
216727 TTAGGGATTT
*
216737 TTTATGGTAAAGTACCTATTTGATCACTTATATATTATCTAATTTATCTAA
1 TTTATGGTAAACTACCTATTTGATCACTTATATATTATCTAATTTATCTAA
* *
216788 TTTATGGTAAACTATCTATTTGGTCACTTATATATTATCTAATTTAT
1 TTTATGGTAAACTACCTATTTGATCACTTATATATTATCTAATTTAT
216835 GTTTTGGTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (51 bp):
TTTATGGTAAACTACCTATTTGATCACTTATATATTATCTAATTTATCTAA
Found at i:216896 original size:68 final size:67
Alignment explanation
Indices: 216787--216988 Score: 261
Period size: 63 Copynumber: 3.1 Consensus size: 67
216777 AATTTATCTA
* *
216787 ATTTATGGTAAACTATCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATT
1 ATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGT-ACTCGATT
216852 ATT
65 ATT
** * ** *
216855 ATTTAGGGTAAACTACCTATTTGGTCGGTTATATATTATCTAATATAAT-TCAT-ATA-T--ATT
1 ATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAAT-TTATGTTTTGGTACTCGATT
*
216915 TTT
65 ATT
*
216918 ATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTACTCGCTTA
1 ATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTACTCGATTA
216983 TT
66 TT
216985 ATTT
1 ATTT
216989 TTTTTTAAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
62 3 0.03
63 49 0.44
64 2 0.02
65 2 0.02
66 1 0.01
67 9 0.08
68 42 0.38
69 3 0.03
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (67 bp):
ATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTACTCGATTA
TT
Found at i:218956 original size:14 final size:14
Alignment explanation
Indices: 218937--218981 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
218927 AGACTGAGAC
*
218937 AAAAATTTATATTA
1 AAAAATATATATTA
*
218951 AAAAATATAAACTTA
1 AAAAATATATA-TTA
218966 AAAAA-ATATATTA
1 AAAAATATATATTA
218979 AAA
1 AAA
218982 GTCTTCAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.22
14 13 0.48
15 8 0.30
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAATATATATTA
Found at i:220674 original size:11 final size:11
Alignment explanation
Indices: 220639--220691 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
220629 AAGAAATAAG
220639 AATAAAAAATAA
1 AATAAAAAA-AA
220651 AATTAAGATAAAAA
1 AA-TAA-A-AAAAA
220665 AATAAAAAAAA
1 AATAAAAAAAA
* *
220676 AATAATAATAA
1 AATAAAAAAAA
220687 AATAA
1 AATAA
220692 TAATAAAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
11 19 0.53
12 3 0.08
13 6 0.17
14 5 0.14
15 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
AATAAAAAAAA
Found at i:220677 original size:14 final size:14
Alignment explanation
Indices: 220639--220698 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
220629 AAGAAATAAG
220639 AATAAAAAATAAAAT
1 AATAAAAAA-AAAAT
* *
220654 --TAAGATAAAAA-
1 AATAAAAAAAAAAT
220665 AATAAAAAAAAAAT
1 AATAAAAAAAAAAT
* *
220679 AATAATAAAATAAT
1 AATAAAAAAAAAAT
220693 AATAAA
1 AATAAA
220699 GTGAAATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
12 4 0.11
13 14 0.40
14 17 0.49
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (14 bp):
AATAAAAAAAAAAT
Found at i:220680 original size:19 final size:19
Alignment explanation
Indices: 220642--220680 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
220632 AAATAAGAAT
** *
220642 AAAAAATAAAATTAAGATA
1 AAAAAATAAAAAAAAAATA
220661 AAAAAATAAAAAAAAAATA
1 AAAAAATAAAAAAAAAATA
220680 A
1 A
220681 TAATAAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (19 bp):
AAAAAATAAAAAAAAAATA
Found at i:220698 original size:11 final size:11
Alignment explanation
Indices: 220658--220694 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
220648 TAAAATTAAG
220658 ATAAAAAAATA
1 ATAAAAAAATA
*
220669 AAAAAAAAATA
1 ATAAAAAAATA
*
220680 ATAATAAAATA
1 ATAAAAAAATA
220691 ATAA
1 ATAA
220695 TAAAGTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAAAAATA
Found at i:220705 original size:16 final size:17
Alignment explanation
Indices: 220686--220724 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
220676 AATAATAATA
*
220686 AAATAATAATA-AAGTG
1 AAATAATAATACAAGAG
*
220702 AAATAATATTACAAGAG
1 AAATAATAATACAAGAG
220719 AAATAA
1 AAATAA
220725 ATAAAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.23
Consensus pattern (17 bp):
AAATAATAATACAAGAG
Found at i:220779 original size:24 final size:24
Alignment explanation
Indices: 220723--220770 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
220713 CAAGAGAAAT
220723 AAAT-AAAAATGAAGAAAATGTTA
1 AAATAAAAAATGAAGAAAATGTTA
220746 AAATAAAAAATGAAGAAAATGTTA
1 AAATAAAAAATGAAGAAAATGTTA
220770 A
1 A
220771 TTTTTAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (24 bp):
AAATAAAAAATGAAGAAAATGTTA
Found at i:220814 original size:22 final size:21
Alignment explanation
Indices: 220776--220816 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
220766 GTTAATTTTT
*
220776 AAAAGAAATAAAAATAAAATA
1 AAAAGAAAGAAAAATAAAATA
*
220797 AAAAGGAAAGAAATATAAAA
1 AAAA-GAAAGAAAAATAAAA
220817 ATTTAAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (21 bp):
AAAAGAAAGAAAAATAAAATA
Found at i:222186 original size:34 final size:35
Alignment explanation
Indices: 222112--222323 Score: 197
Period size: 36 Copynumber: 5.9 Consensus size: 35
222102 TAATATTATA
222112 TTTTCAAAACTATA-AATTATATATATTTTCAAAATTTG
1 TTTTCAAAACTATATAA-TATAT-T-TTTTCAAAA-TTG
222150 TTTTCAAAACTATATAATATATGTTTTTC-AAA-TG
1 TTTTCAAAACTATATAATATAT-TTTTTCAAAATTG
* * *
222184 TTTTCGAAACTATATACTATATATATATTTTCAAAAAACTA
1 TTTTCAAAACTATATA--ATATAT-T-TTTTC--AAAATTG
*
222225 TTTTCAAAA-TA-AT-ATATA-TTTTTCAAAAATCG
1 TTTTCAAAACTATATAATATATTTTTTC-AAAATTG
*
222257 TTTTCAAAACTATATAATATATATTTTCAAAAATTG
1 TTTTCAAAACTATATAATATATTTTTTC-AAAATTG
*
222293 TTTTCAAAACTATAT-ATATATATTTTCAAAA
1 TTTTCAAAACTATATAATATATTTTTTCAAAA
222324 ACCAATTTTT
Statistics
Matches: 152, Mismatches: 10, Indels: 28
0.80 0.05 0.15
Matches are distributed among these distances:
32 14 0.09
33 7 0.05
34 24 0.16
35 17 0.11
36 42 0.28
37 10 0.07
38 20 0.13
39 4 0.03
40 5 0.03
41 9 0.06
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (35 bp):
TTTTCAAAACTATATAATATATTTTTTCAAAATTG
Found at i:222430 original size:40 final size:38
Alignment explanation
Indices: 222184--222432 Score: 135
Period size: 36 Copynumber: 6.6 Consensus size: 38
222174 TTTTCAAATG
* * * *
222184 TTTTCGAAACTATATACTATATATATATTTTCAAAAAACTA
1 TTTTCAAAAATATATA-TAT-TATATGTTTTC-AAAAACCA
* *
222225 TTTTC--AAA-ATA-ATA-TATAT-TTTTCAAAAATCG
1 TTTTCAAAAATATATATATTATATGTTTTCAAAAACCA
* * ***
222257 TTTTCAAAACTATATA-A-TATATATTTTCAAAAATTG
1 TTTTCAAAAATATATATATTATATGTTTTCAAAAACCA
*
222293 TTTTCAAAACTATATATA-TATA--TTTTCAAAAACCAA
1 TTTTCAAAAATATATATATTATATGTTTTCAAAAACC-A
* * *
222329 TTTTTTTTTAAAAAAAGTATATATTATATGTTTTCAAAAACCG
1 ----TTTTCAAAAATA-TATATATTATATGTTTTCAAAAACCA
* * * *
222372 TTTTCTAAAATCTATATATTATATATTTTTCAAAAA-TA
1 TTTTCAAAAATATATATATTATAT-GTTTTCAAAAACCA
222410 TTTTCAAAAATTATACTATATTA
1 TTTTCAAAAA-TATA-TATATTA
222433 ATACATATAC
Statistics
Matches: 168, Mismatches: 22, Indels: 37
0.74 0.10 0.16
Matches are distributed among these distances:
32 10 0.06
33 5 0.03
34 7 0.04
35 19 0.11
36 31 0.18
37 6 0.04
38 24 0.14
39 23 0.14
40 16 0.10
41 11 0.07
42 4 0.02
44 12 0.07
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (38 bp):
TTTTCAAAAATATATATATTATATGTTTTCAAAAACCA
Found at i:230701 original size:16 final size:16
Alignment explanation
Indices: 230680--230713 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
230670 CAATGTATGC
230680 TCTAACTCTGACACTG
1 TCTAACTCTGACACTG
*
230696 TCTAACTCTGACATTG
1 TCTAACTCTGACACTG
230712 TC
1 TC
230714 GTAATTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (16 bp):
TCTAACTCTGACACTG
Found at i:231549 original size:21 final size:21
Alignment explanation
Indices: 231520--231561 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
231510 TCAAATGACT
231520 CATAATATATATTCTTAAGTC
1 CATAATATATATTCTTAAGTC
*
231541 CATACTATATATTCTTAAGTC
1 CATAATATATATTCTTAAGTC
231562 AAAGTACGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (21 bp):
CATAATATATATTCTTAAGTC
Found at i:234040 original size:4 final size:4
Alignment explanation
Indices: 234031--234065 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
234021 CAATGCATGT
234031 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
234066 CATAGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:236604 original size:27 final size:27
Alignment explanation
Indices: 236568--236630 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
236558 GAGAAAAAAT
236568 AAAAAA-ATTTGCATAATTGTTTTTTA
1 AAAAAATATTTGCATAATTGTTTTTTA
*
236594 AAAAAATATTTGCATAATTGTTTTTTT
1 AAAAAATATTTGCATAATTGTTTTTTA
236621 AAAAAATATT
1 AAAAAATATT
236631 GAATTTTAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (27 bp):
AAAAAATATTTGCATAATTGTTTTTTA
Found at i:236617 original size:25 final size:25
Alignment explanation
Indices: 236568--236627 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 25
236558 GAGAAAAAAT
236568 AAAAAAATTTGCATAATTGTTTTTTA
1 AAAAAAATTTGCATAATTG-TTTTTA
*
236594 AAAAAATATTTGCATAATTGTTTTTT
1 AAAAAA-ATTTGCATAATTGTTTTTA
*
236620 TAAAAAAT
1 AAAAAAAT
236628 ATTGAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 2 0.06
26 16 0.52
27 13 0.42
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (25 bp):
AAAAAAATTTGCATAATTGTTTTTA
Found at i:237124 original size:3 final size:3
Alignment explanation
Indices: 237116--237158 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
237106 AGGGCTAATT
237116 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
237159 ATATAACTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:237675 original size:2 final size:2
Alignment explanation
Indices: 237638--237667 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
237628 AATATGCATG
*
237638 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
237668 AAATATATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:238153 original size:2 final size:2
Alignment explanation
Indices: 238148--238180 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
238138 GGTTTAATCA
238148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
238181 AAAGGTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:250169 original size:20 final size:20
Alignment explanation
Indices: 250136--250175 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
250126 CTTCCCCTAG
* *
250136 CCCCTTCTCGTCCCCCTCCT
1 CCCCTTCCCCTCCCCCTCCT
*
250156 CCCCTTCCCCTCCCTCTCCT
1 CCCCTTCCCCTCCCCCTCCT
250176 ATTACTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.68, G:0.03, T:0.30
Consensus pattern (20 bp):
CCCCTTCCCCTCCCCCTCCT
Found at i:252799 original size:37 final size:37
Alignment explanation
Indices: 252746--252850 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 37
252736 CCTTTTCGTC
*
252746 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
252783 TTGCTAGGATTCAAACTCCTTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
252820 CTACTATGATAT-AAACTCCTAAAGATAGGAT
1 CTACTAGGAT-TCAAACTCCTAAAAATAGGAT
252851 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
37 56 0.98
38 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:253397 original size:19 final size:19
Alignment explanation
Indices: 253318--253406 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 19
253308 TTTTTTACAC
253318 TATATAT-TA-TTATTATCT
1 TATATATATATTTATTAT-T
* *
253336 ATACATATATATTTTTTATT
1 -TATATATATATTTATTATT
* *
253356 TATAT-TCATTTGGTTATTTTT
1 TATATAT-ATAT--TTATTATT
253377 TA-ATACTATATTTATTATT
1 TATATA-TATATTTATTATT
253396 TATATATATAT
1 TATATATATAT
253407 ATATACTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
18 1 0.02
19 27 0.50
20 8 0.15
21 17 0.31
22 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (19 bp):
TATATATATATTTATTATT
Found at i:253637 original size:18 final size:19
Alignment explanation
Indices: 253616--253666 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
253606 TTTTGGTTTT
253616 TTTTTATATTATATTA-TA
1 TTTTTATATTATATTATTA
*
253634 TTTTCATATTACTATTATTA
1 TTTTTATATTA-TATTATTA
*
253654 TTGTTATGATTAT
1 TTTTTAT-ATTAT
253667 TACTTTTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 5 0.19
20 8 0.30
21 4 0.15
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTTATATTATATTATTA
Found at i:254882 original size:19 final size:19
Alignment explanation
Indices: 254858--254894 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
254848 ACCTTACTAA
254858 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
254877 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
254895 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:258350 original size:16 final size:15
Alignment explanation
Indices: 258329--258405 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 15
258319 CAATCAAGAA
258329 CAAAAATGAAAAAAAG
1 CAAAAA-GAAAAAAAG
258345 CAAAAAAGCAAAAAAA-
1 C-AAAAAG-AAAAAAAG
*
258361 AAACAAAGAAAAAAGAG
1 CAA-AAAGAAAAAA-AG
*
258378 -AAACAAGAACAAAAAT
1 CAAA-AAGAA-AAAAAG
258394 CAAAAAGAAAAA
1 CAAAAAGAAAAA
258406 GGGACAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
15 12 0.24
16 20 0.39
17 19 0.37
ACGTcount: A:0.78, C:0.09, G:0.10, T:0.03
Consensus pattern (15 bp):
CAAAAAGAAAAAAAG
Found at i:258372 original size:9 final size:8
Alignment explanation
Indices: 258324--258380 Score: 53
Period size: 9 Copynumber: 6.8 Consensus size: 8
258314 AGATCCAATC
258324 AAGAACAAA
1 AAGAA-AAA
258333 AATGAAAAA
1 AA-GAAAAA
*
258342 AAGCAAAA
1 AAGAAAAA
258350 AAGCAAAAA
1 AAG-AAAAA
*
258359 AA-AAACA
1 AAGAAAAA
258366 AAGAAAAA
1 AAGAAAAA
258374 AGAGAAA
1 A-AGAAA
258381 CAAGAACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 6 0.15
8 13 0.32
9 18 0.45
10 3 0.08
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (8 bp):
AAGAAAAA
Found at i:259256 original size:22 final size:22
Alignment explanation
Indices: 259182--259258 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
259172 GCTACCCCAT
* *
259182 CAAACCGTTGAGCATCAACTGC
1 CAAACCTTTGAGCATCAAATGC
* *
259204 CAAACCTATGAGCATCAAATTC
1 CAAACCTTTGAGCATCAAATGC
259226 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
259248 CAAACCTTTGA
1 CAAACCTTTGA
259259 CCAAACATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.36, C:0.29, G:0.13, T:0.22
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:260217 original size:106 final size:106
Alignment explanation
Indices: 260060--261858 Score: 2734
Period size: 106 Copynumber: 17.0 Consensus size: 106
260050 ATATCGTGCC
* * * * * * * *
260060 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGATCGCTAGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
260125 AATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
260166 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAATAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
260231 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
260272 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACTGCTGGTTGTCAACAAACGACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
260337 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
260378 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
260443 AATTTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
260484 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGCCCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
260549 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
260590 ACTCAAGACAACGCAAGTTCAACTTCACGATGAAGGGCCCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
260655 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
260696 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
260761 AATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
260802 ACTCTAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
260867 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
260908 ACTCAAGACAACGCAAGTTCAACTTCACGACG-AGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
260972 AATTTCAGAGCCAATTTCAATTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
261013 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
261078 AATTTCAGAGCCAAATTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
261119 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
261184 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
261225 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGTACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
261290 AATTTCAGAGCCAATTTCAACTTTACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
261331 ACTCCATACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
261396 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
261437 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
261502 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
261543 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCAC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
261608 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
261649 AC-CCAAGACAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAA-CAA-AA-TT-T
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCC
*
261709 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
261749 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAATAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
** * *
261814 GGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
261855 ACTC
1 ACTC
261859 AGAACAATGC
Statistics
Matches: 1556, Mismatches: 127, Indels: 20
0.91 0.07 0.01
Matches are distributed among these distances:
100 79 0.05
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 104 0.07
106 1359 0.87
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:262634 original size:37 final size:37
Alignment explanation
Indices: 262581--262685 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
262571 CCTTTTCGTC
*
262581 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
262618 TTGCTAGGATTCAAACTCCTTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
262655 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
262686 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:263208 original size:22 final size:22
Alignment explanation
Indices: 263177--263242 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 22
263167 TATCTATACA
263177 TATATT-ATTTATTTATTTATT
1 TATATTCATTTATTTATTTATT
**
263198 TATATTCATTTGGTTATTT-TT
1 TATATTCATTTATTTATTTATT
* *
263219 TA-ATAC-TATATTTA-TTATT
1 TATATTCATTTATTTATTTATT
263238 TATAT
1 TATAT
263243 ATATATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 2 0.06
19 9 0.25
20 5 0.14
21 10 0.28
22 10 0.28
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (22 bp):
TATATTCATTTATTTATTTATT
Found at i:263239 original size:19 final size:19
Alignment explanation
Indices: 263211--263248 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
263201 ATTCATTTGG
*
263211 TTATTTTTTA-ATACTATAT
1 TTATTATTTATATA-TATAT
263230 TTATTATTTATATATATAT
1 TTATTATTTATATATATAT
263249 ATATATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATTATTTATATATATAT
Found at i:263488 original size:19 final size:17
Alignment explanation
Indices: 263454--263517 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
263444 TTTTTGGTTT
*
263454 TTTTTTATATTATATTA
1 TTTTTCATATTATATTA
263471 TATTTTCATATTACTATTA
1 T-TTTTCATATTA-TATTA
** *
263490 TTTTTGTTATGATTATTA
1 TTTTTCATATTA-TATTA
263508 TTTTTC-TATT
1 TTTTTCATATT
263518 TTACTCATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
17 4 0.11
18 28 0.74
19 6 0.16
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTTCATATTATATTA
Found at i:263509 original size:21 final size:18
Alignment explanation
Indices: 263453--263505 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
263443 GTTTTTGGTT
263453 TTTTTTTATATTATATTA
1 TTTTTTTATATTATATTA
* *
263471 TATTTTCATATTACTATTA
1 TTTTTTTATATTA-TATTA
263490 TTTTTGTTATGATTAT
1 TTTTT-TTAT-ATTAT
263506 TATTTTTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.39
19 9 0.32
20 4 0.14
21 4 0.14
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTTTTTATATTATATTA
Found at i:263534 original size:2 final size:2
Alignment explanation
Indices: 263527--263551 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
263517 TTTACTCATT
263527 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
263552 TAATATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:263589 original size:12 final size:12
Alignment explanation
Indices: 263574--263606 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
263564 TATTTATTTA
263574 TTTATTTTTCCT
1 TTTATTTTTCCT
263586 TTTATTTTTCCT
1 TTTATTTTTCCT
263598 TTTATTTTT
1 TTTATTTTT
263607 TTTTACTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTTTTCCT
Found at i:274079 original size:13 final size:12
Alignment explanation
Indices: 274062--274107 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 12
274052 AAAAGTAATG
274062 AAAATAAAGAAA
1 AAAATAAAGAAA
274074 ACAAATAAAGAAA
1 A-AAATAAAGAAA
*
274087 AAAATGAAATAAA
1 AAAAT-AAAGAAA
274100 TAAAATAA
1 -AAAATAA
274108 GATAAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.17
13 20 0.67
14 5 0.17
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (12 bp):
AAAATAAAGAAA
Found at i:274102 original size:4 final size:4
Alignment explanation
Indices: 274076--274640 Score: 77
Period size: 4 Copynumber: 137.5 Consensus size: 4
274066 TAAAGAAAAC
* * *
274076 AAAT AAAG AAAA AAAT GAAAT AAAT AAAAT AAGAT AAAG AAA- AAA- AAAT
1 AAAT AAAT AAAT AAAT -AAAT AAAT -AAAT AA-AT AAAT AAAT AAAT AAAT
* *
274125 AAAGT CGAGAT AGAA- AAGT AAAT AAAAT AAAT AAAAT AAAAT AAAT AAAT
1 AAA-T --AAAT A-AAT AAAT AAAT -AAAT AAAT -AAAT -AAAT AAAT AAAT
* **
274175 AAAT ATA- AAAT ATAAT AAA- ATAAT AGTAA- AAAT AATAT ATGT ATAAT
1 AAAT AAAT AAAT A-AAT AAAT A-AAT A--AAT AAAT AA-AT AAAT A-AAT
* * *
274222 AAAT AAAT AAAT AAAA ACAAGG AGA- AAAT -AA- AAAT AAAT AAAT AAACT
1 AAAT AAAT AAAT AAAT A-AA-T AAAT AAAT AAAT AAAT AAAT AAAT AAA-T
* * *
274270 AAAT --AT AAAG AAA- ATAA- AAAC AAAT GAAAT -AAT AAAAA AAAT AAAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT
* * * *
274316 AAAGAT AAAG AAAA AAAT AAAT AAAGA AAAT AAA- AAGAGG AAAT AATAGT
1 -AA-AT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AA-A-T AAAT AA-A-T
* * * * * *
274366 AAAA ATAAT ATAT ATAT ATAT ATAT ATAAT AAAT AAA- ACACT AAA- AAAT
1 AAAT A-AAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT A-AAT AAAT AAAT
* *
274415 -AAT -AAT -AAT AAA- ACAAGG AGAA- AATAC AAAT AAAT AAAT AAA-
1 AAAT AAAT AAAT AAAT A-AA-T A-AAT AA-AT AAAT AAAT AAAT AAAT
* * *
274457 ATAT AAAG AAA- ATAA- AAAC AAAT GAAAT -AA- AAAT AAGGA- AAAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT -AAAT AAAT AAAT AA--AT AAAT
* * *
274500 AAAA AAAT AAA- AAA- AAGAT AAAG GAA- AAAT AAAT AAAT AAAAT AAA-
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT
* * * *
274546 AAGAGG AAAT AATAGT AAAA ATAAT ATAT ATAAT AAAT AAAT AAAT AAAA
1 AA-A-T AAAT AA-A-T AAAT A-AAT AAAT A-AAT AAAT AAAT AAAT AAAT
* *
274596 ACAAGG AAA- AAAG AAAT -AAT AAAT -AAT AAAT -AAT AAAT AATAT AA
1 A-AA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AA
274641 TTATATATAT
Statistics
Matches: 430, Mismatches: 53, Indels: 155
0.67 0.08 0.24
Matches are distributed among these distances:
2 2 0.00
3 72 0.17
4 233 0.54
5 99 0.23
6 22 0.05
7 2 0.00
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:274105 original size:5 final size:5
Alignment explanation
Indices: 274087--274350 Score: 68
Period size: 5 Copynumber: 53.8 Consensus size: 5
274077 AATAAAGAAA
* * * * *
274087 AAAAT GAAAT -AAAT AAAAT AAGAT AAAGA- AAAA- AAAAT AAAGT CGAGAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT -AAAAT
274136 AGAAAAGT AAA-T AAAAT -AAAT AAAAT AAAAT -AAAT -AAAT AAATAT
1 A--AAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT
* * * ** *
274181 AAAAT ATAAT AAAAT AATAGT AAAA- ATAAT ATATGT ATAAT -AAAT -AAAT
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT
* *
274230 -AAAT AAAA- ACAAGGAG AAAAT AAAA- ATAAAT -AAAT AAACT -AAAT
1 AAAAT AAAAT A-AA--AT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT
* *
274274 ATAAAG AAAAT AAAA- ACAAAT GAAAT --AAT AAAA- AAAAT -AAAT AAAGAT
1 A-AAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT
* *
274322 AAAGA- AAAAA ATAAAT -AAAG AAAAT AAAA
1 AAA-AT AAAAT A-AAAT AAAAT AAAAT AAAA
274351 AGAGGAAATA
Statistics
Matches: 195, Mismatches: 30, Indels: 68
0.67 0.10 0.23
Matches are distributed among these distances:
3 3 0.02
4 61 0.31
5 93 0.48
6 30 0.15
7 5 0.03
8 3 0.02
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:274113 original size:31 final size:31
Alignment explanation
Indices: 274058--274121 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
274048 GAAAAAAAGT
274058 AATGAAAATAAAGAAAACAAATAAAGAAAAA
1 AATGAAAATAAAGAAAACAAATAAAGAAAAA
* *
274089 AATG-AAATAAATAAAATAAGATAAAGAAAAA
1 AATGAAAATAAAGAAAACAA-ATAAAGAAAAA
274120 AA
1 AA
274122 AATAAAGTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (31 bp):
AATGAAAATAAAGAAAACAAATAAAGAAAAA
Found at i:274258 original size:35 final size:33
Alignment explanation
Indices: 274219--274351 Score: 123
Period size: 31 Copynumber: 4.1 Consensus size: 33
274209 ATATATGTAT
274219 AATAAATAAATAAATAAAAACAAGGAGAAAATAAA
1 AATAAATAAATAAATAAAAACAA--AGAAAATAAA
* *
274254 AATAAATAAATAAACTAAATATAAAGAAAATAAA
1 AATAAATAAATAAA-TAAAAACAAAGAAAATAAA
* *
274288 AACAAATGAAAT-AATAAAAA-AAA-TAAATAAA
1 AATAAAT-AAATAAATAAAAACAAAGAAAATAAA
* * * *
274319 GATAAAGAAA-AAA-ATAAATAAAGAAAATAAA
1 AATAAATAAATAAATAAAAACAAAGAAAATAAA
274350 AA
1 AA
274352 GAGGAAATAA
Statistics
Matches: 82, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
29 4 0.05
30 8 0.10
31 19 0.23
32 3 0.04
33 5 0.06
34 18 0.22
35 18 0.22
36 7 0.09
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (33 bp):
AATAAATAAATAAATAAAAACAAAGAAAATAAA
Found at i:274263 original size:164 final size:167
Alignment explanation
Indices: 274086--274403 Score: 386
Period size: 164 Copynumber: 1.9 Consensus size: 167
274076 AAATAAAGAA
* * **
274086 AAAAATGAAATAAATAAAAT-AAGATAAAGAAAA-AAAAATAAAGTCGAGATAGA-AAAGTAAAT
1 AAAAATGAAATAAATAAAATAAAGATAAAGAAAATAAAAACAAA-T-GAAATA-ATAAAAAAAAT
* * *
274148 AAA-ATAA-AT-AA-AATAAAATAAATAAATAAATATAAAATATAATAAAATAATAGTAAAAATA
63 AAATA-AAGATAAAGAAAAAAATAAATAAAGAAA-ATAAAA-A-AAGAAAATAATAGTAAAAATA
*
274209 ATATATGTATA-ATAAATA-AATAAATAAAAACAAGGAGAAAAT
124 ATATATATATATATAAATATAATAAATAAAAACAAGGAGAAAAT
* *
274251 AAAAAT-AAATAAATAAACTAAATATAAAGAAAATAAAAACAAATGAAATAATAAAAAAAATAAA
1 AAAAATGAAATAAATAAAATAAAGATAAAGAAAATAAAAACAAATGAAATAATAAAAAAAATAAA
* *
274315 TAAAGATAAAGAAAAAAATAAATAAAGAAAATAAAAAGAGGAAATAATAGTAAAAATAATATATA
66 TAAAGATAAAGAAAAAAATAAATAAAGAAAATAAAAAAAGAAAATAATAGTAAAAATAATATATA
*
274380 TATATATATATATAATAAATAAAA
131 TATATATAAATATAATAAATAAAA
274404 CACTAAAAAA
Statistics
Matches: 131, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
163 1 0.01
164 57 0.44
165 29 0.22
166 27 0.21
167 17 0.13
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.21
Consensus pattern (167 bp):
AAAAATGAAATAAATAAAATAAAGATAAAGAAAATAAAAACAAATGAAATAATAAAAAAAATAAA
TAAAGATAAAGAAAAAAATAAATAAAGAAAATAAAAAAAGAAAATAATAGTAAAAATAATATATA
TATATATAAATATAATAAATAAAAACAAGGAGAAAAT
Found at i:274325 original size:46 final size:50
Alignment explanation
Indices: 274230--274351 Score: 139
Period size: 47 Copynumber: 2.5 Consensus size: 50
274220 ATAAATAAAT
*
274230 AAATAAAAACAAGGAGAAAATAAAAATAAATAAATAAACTAAATATAAAGA
1 AAATAAAAACAA-GAGAAAATAAAAATAAATAAATAAACTAAAGATAAAGA
*
274281 AAATAAAAACAA-ATG-AAATAATAA-AAA-AAATAAA-TAAAGATAAAGA
1 AAATAAAAACAAGA-GAAAATAAAAATAAATAAATAAACTAAAGATAAAGA
* *
274327 AAAAAATAAATAA-AGAAAATAAAAA
1 AAATAA-AAACAAGAGAAAATAAAAA
274352 GAGGAAATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
46 17 0.27
47 21 0.33
48 3 0.05
49 9 0.14
50 1 0.02
51 12 0.19
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (50 bp):
AAATAAAAACAAGAGAAAATAAAAATAAATAAATAAACTAAAGATAAAGA
Found at i:274349 original size:185 final size:178
Alignment explanation
Indices: 274144--274630 Score: 500
Period size: 185 Copynumber: 2.7 Consensus size: 178
274134 ATAGAAAAGT
*
274144 AAATAAAATAAATAAAATAAAATAAATAAATAAATATAAAATATAATAAAATAATAGTAAAAATA
1 AAAT-AAATAAAGAAAATAAAATAAATAAATAAATATAAAA-ATAATAAAATAATAGTAAAAATA
274209 ATATATGTATAATAAATAAATAAATAAAAACAAGGAGAAAATAAAAATAAATAAATAAACTAAAT
64 ATATAT-TATAATAAATAAATAAATAAAAACAAGGAGAAAATAAAAATAAATAAATAAA--AAAT
274274 ATAAAGAAAATAAAAACAAATGAAATAATAAA-AAAAATAAATAAAGATAAAGAAAA
126 ATAAAGAAAATAAAAACAAATGAAATAA-AAATAAAAA-AAATAAA-A-AAAGAAAA
** * * *
274330 AAATAAATAAAGAAAATAAAA-AGAGGAAAT-AATAGTAAAAATAATATATATATATA-TATATA
1 AAATAAATAAAGAAAATAAAATA-AATAAATAAATA-TAAAAATAATA-AAATA-ATAGTAAAAA
* * * *
274392 TAATAAATAAAACACTAAA-AAATAATAATAATAAAACAAGGAGAAAATACAAATAAATAAAT--
62 TAATATATTATA-A-TAAATAAAT-A-AAT-A-AAAACAAGGAGAAAATAAAAATAAATAAATAA
** *
274454 AAAATATAAAGAAAATAAAAACAAATGAAATAAAAATAAGGAAAATAAAAAAATAAAA
121 AAAATATAAAGAAAATAAAAACAAATGAAATAAAAATAAAAAAAATAAAAAAAGAAAA
* * * **
274512 AAA-AGATAAAG--GA-AAAATAAATAAATAAA-ATAAAAA-GAGGAAATAATAGTAAAAATAAT
1 AAATAAATAAAGAAAATAAAATAAATAAATAAATATAAAAATAATAAAATAATAGTAAAAATAAT
* * *
274571 ATA-TATAATAAATAAATAAATAAAAACAAGGAAAAAAGAAATAATAAAT-AATAAATAATA
66 ATATTATAATAAATAAATAAATAAAAACAAGGAGAAAATAAA-AATAAATAAATAAAAAATA
274631 AATAATATAA
Statistics
Matches: 253, Mismatches: 30, Indels: 51
0.76 0.09 0.15
Matches are distributed among these distances:
169 19 0.08
170 8 0.03
171 8 0.03
172 5 0.02
173 5 0.02
174 5 0.02
175 14 0.06
176 1 0.00
177 6 0.02
178 10 0.04
179 4 0.02
181 7 0.03
182 10 0.04
183 1 0.00
184 23 0.09
185 81 0.32
186 12 0.05
187 4 0.02
188 1 0.00
189 29 0.11
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (178 bp):
AAATAAATAAAGAAAATAAAATAAATAAATAAATATAAAAATAATAAAATAATAGTAAAAATAAT
ATATTATAATAAATAAATAAATAAAAACAAGGAGAAAATAAAAATAAATAAATAAAAAATATAAA
GAAAATAAAAACAAATGAAATAAAAATAAAAAAAATAAAAAAAGAAAA
Found at i:274456 original size:30 final size:31
Alignment explanation
Indices: 274433--274546 Score: 96
Period size: 30 Copynumber: 3.8 Consensus size: 31
274423 TAAAACAAGG
* * *
274433 AGAAAATACAAATAAAT-AAATAAAATATAA
1 AGAAAATAAAAACAAATGAAATAAAACATAA
274463 AGAAAATAAAAACAAATGAAATAAAA-ATAA
1 AGAAAATAAAAACAAATGAAATAAAACATAA
* * *
274493 GGAAAAT-AAAA-AAAT-AAAAAAAAGATAA
1 AGAAAATAAAAACAAATGAAATAAAACATAA
* * *
274521 AGGAAAA-ATAAATAAATAAAATAAAA
1 A-GAAAATAAAAACAAATGAAATAAAA
274547 AGAGGAAATA
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
27 7 0.10
28 8 0.11
29 12 0.17
30 29 0.41
31 15 0.21
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (31 bp):
AGAAAATAAAAACAAATGAAATAAAACATAA
Found at i:274485 original size:35 final size:33
Alignment explanation
Indices: 274442--274632 Score: 85
Period size: 32 Copynumber: 5.6 Consensus size: 33
274432 GAGAAAATAC
*
274442 AAATAAATAAATAAAATATAAAGAAAATAAAAAC
1 AAATAAATAAATAAAA-ATAAAGAAAATAAAAAT
*
274476 AAATGAAATAAAAATAAGGAAAATAAA-AAAATAAAAAA
1 AAAT-AAAT--AAAT-A--AAAATAAAGAAAATAAAAAT
* *
274514 AAGATAAAGGAAA-AATAAATAAATAAAATAAAAA-
1 AA-ATAAA-TAAATAA-AAATAAAGAAAATAAAAAT
* ** * * *
274548 GAGGAAATAATAGTAAAAAT-AA-TATAT-ATAAT
1 AAATAAATAA-A-TAAAAATAAAGAAAATAAAAAT
* *
274580 AAATAAATAAATAAAAACAAGGAAAA-AAGAAAT
1 AAATAAATAAATAAAAATAAAGAAAATAA-AAAT
274613 -AATAAAT-AATAAATAATAAA
1 AAATAAATAAATAAA-AATAAA
274633 TAATATAATT
Statistics
Matches: 119, Mismatches: 19, Indels: 40
0.67 0.11 0.22
Matches are distributed among these distances:
30 6 0.05
31 11 0.09
32 26 0.22
33 10 0.08
34 16 0.13
35 17 0.14
37 7 0.06
38 16 0.13
39 7 0.06
40 3 0.03
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (33 bp):
AAATAAATAAATAAAAATAAAGAAAATAAAAAT
Found at i:274486 original size:15 final size:15
Alignment explanation
Indices: 274436--274547 Score: 76
Period size: 15 Copynumber: 7.6 Consensus size: 15
274426 AACAAGGAGA
*
274436 AAATACAAATAAAT-
1 AAATAAAAATAAATG
274450 AAATAAAATATAAA-G
1 AAATAAAA-ATAAATG
*
274465 AAAATAAAAACAAATG
1 -AAATAAAAATAAATG
*
274481 AAATAAAAAT-AAGG
1 AAATAAAAATAAATG
274495 AAA-ATAAAA-AAAT-
1 AAATA-AAAATAAATG
* *
274508 AAAAAAAAGATAAAGG
1 AAATAAAA-ATAAATG
*
274524 AAA-AATAAATAAATA
1 AAATAA-AAATAAATG
274539 AAATAAAAA
1 AAATAAAAA
274548 GAGGAAATAA
Statistics
Matches: 78, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
13 7 0.09
14 21 0.27
15 34 0.44
16 16 0.21
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (15 bp):
AAATAAAAATAAATG
Found at i:274543 original size:58 final size:60
Alignment explanation
Indices: 274217--274547 Score: 155
Period size: 58 Copynumber: 5.4 Consensus size: 60
274207 TAATATATGT
* * * *
274217 ATAATAAATAAAT-AAATAAAAACAAGGAGAAAATAAAAATAAATAAATAAACTAAATATAAAGA
1 ATAA-AAACAAATAAAATAAAAATAA-G-GAAAATACAAATAAAT-AA-AAA--AAAGATAAAGA
274281 AA
59 AA
* ** * *
274283 ATAAAAACAAATGAAATAATAAA-AAAAATAAATA-AAGATAAAGAAAAAAATAAATAAAGAAA
1 ATAAAAACAAATAAAATAA-AAATAAGGA-AAATACAA-ATAAATAAAAAAA-AGATAAAGAAA
* * * * * * * * * *
274345 ATAAAAAGAGGAAATAATAGTAAAAATAA--TATATATATATATATATATAATAA-ATAAA-ACA
1 AT-AAAA-A-CAAATAA-AATAAAAATAAGGAAAATACAAATAAATA-AAAAAAAGATAAAGAAA
* * * *
274406 CTAAAAA-ATAATAATAATAAAACA-AGGAGAAAATACAAATAAATAAATAAAATATAAAGAAA
1 ATAAAAACA-AATAA-AATAAAA-ATAAG-GAAAATACAAATAAATAAAAAAAAGATAAAGAAA
*
274468 ATAAAAACAAATGAAATAAAAATAAGGAAAATA-AAA-AAATAAAAAAAAGATAAAGGAAA
1 ATAAAAACAAATAAAATAAAAATAAGGAAAATACAAATAAATAAAAAAAAGATAAA-GAAA
* *
274527 A-ATAAATAAATAAAATAAAAA
1 ATAAAAACAAATAAAATAAAAA
274548 GAGGAAATAA
Statistics
Matches: 207, Mismatches: 36, Indels: 52
0.70 0.12 0.18
Matches are distributed among these distances:
57 1 0.00
58 46 0.22
59 10 0.05
60 16 0.08
61 30 0.14
62 29 0.14
63 18 0.09
64 11 0.05
65 25 0.12
66 18 0.09
67 3 0.01
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (60 bp):
ATAAAAACAAATAAAATAAAAATAAGGAAAATACAAATAAATAAAAAAAAGATAAAGAAA
Found at i:274603 original size:50 final size:49
Alignment explanation
Indices: 274527--274640 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 49
274517 ATAAAGGAAA
* *
274527 AATAAATAAATAAAATAAAAAGAGGAAATAATAGTAAA-AAT-AAT-ATATAT
1 AATAAATAAAT-AAATAAAAAAAGGAAA-AA-AG-AAATAATAAATAATAAAT
274577 AATAAATAAATAAATAAAAACAAGGAAAAAAGAAATAATAAATAATAAAT
1 AATAAATAAATAAATAAAAA-AAGGAAAAAAGAAATAATAAATAATAAAT
274627 AATAAATAATATAA
1 AATAAATAA-ATAA
274641 TTATATATAT
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
47 3 0.05
48 5 0.09
49 14 0.25
50 31 0.54
51 4 0.07
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (49 bp):
AATAAATAAATAAATAAAAAAAGGAAAAAAGAAATAATAAATAATAAAT
Found at i:275797 original size:2 final size:2
Alignment explanation
Indices: 275790--275855 Score: 93
Period size: 2 Copynumber: 34.0 Consensus size: 2
275780 AACAAACAAA
275790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CA- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
275832 AT A- AT AT AT AA AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
275856 GGTGAGATAA
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 3 0.05
2 54 0.93
3 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:276905 original size:29 final size:30
Alignment explanation
Indices: 276873--276938 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
276863 TCCTCAATTA
276873 TAAAAAAAT-ATAAAATAATT-ATT-TGATTT
1 TAAAAAAATAATAAAATAATTCATTATG--TT
*
276902 TAAAAAAATAATAAATTAATTCATTATGTT
1 TAAAAAAATAATAAAATAATTCATTATGTT
276932 TAAAAAA
1 TAAAAAA
276939 TTAAACAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
29 9 0.27
30 19 0.58
31 3 0.09
32 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (30 bp):
TAAAAAAATAATAAAATAATTCATTATGTT
Found at i:280284 original size:134 final size:134
Alignment explanation
Indices: 280112--280533 Score: 605
Period size: 134 Copynumber: 3.1 Consensus size: 134
280102 TTGATGTTCT
* * *
280112 TCAGGGAAGATTGAATTGCGGCAGACTTGTTCCACTGTTACTTATGGAATATCAAATCTTG-AAA
1 TCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTTAGGGAATATCAAAT-TTGAAAA
*
280176 GAGAGGGATCAGTTTTGCTTCTTCTTGAAGGAAAATCAAATCTGGGGACGTTTATTCATTCCACT
65 GAGAGGGATCAGTTTTGCTTCTTCTTGAAGGAAAATCAAATCTGGGGACGTTGATTCATTCCACT
*
280241 TTTAC
130 GTTAC
* * *
280246 TCAGGGAAGATTGAATCGAGGTAGACTTGTTCCTCTGTTACTTAGGGAACATCAAATTTGAAAAG
1 TCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTTAGGGAATATCAAATTTGAAAAG
* * * * * * * *
280311 AGATGGATCTA-TTATGTTTTTTCTTGAGGGAAAATTAGATTTGGGGACGTTGATTCATTCCACT
66 AGAGGGATC-AGTTTTGCTTCTTCTTGAAGGAAAATCAAATCTGGGGACGTTGATTCATTCCACT
280375 GTTAC
130 GTTAC
* * *
280380 TCAAGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATAAAATTTGAAAAG
1 TCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTTAGGGAATATCAAATTTGAAAAG
* * * *
280445 AGAGGGATCTGTTTCGCTTCTTATTGAAGGAAAATCACATCTGGGGACGTTGATTCATTCCACTG
66 AGAGGGATCAGTTTTGCTTCTTCTTGAAGGAAAATCAAATCTGGGGACGTTGATTCATTCCACTG
280510 TTAC
131 TTAC
280514 TCAGGGAAGATTGAATCGAG
1 TCAGGGAAGATTGAATCGAG
280534 TTAGATTTGC
Statistics
Matches: 251, Mismatches: 34, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
133 3 0.01
134 247 0.98
135 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32
Consensus pattern (134 bp):
TCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTTAGGGAATATCAAATTTGAAAAG
AGAGGGATCAGTTTTGCTTCTTCTTGAAGGAAAATCAAATCTGGGGACGTTGATTCATTCCACTG
TTAC
Found at i:281719 original size:8 final size:7
Alignment explanation
Indices: 281696--281784 Score: 69
Period size: 7 Copynumber: 12.9 Consensus size: 7
281686 ATTTTGTTTA
281696 TTCTATTT
1 TTCT-TTT
281704 TTC-TTT
1 TTCTTTT
281710 TTCTTCTT
1 TTCTT-TT
*
281718 TTATTTAT
1 TTCTTT-T
281726 TTCTTTT
1 TTCTTTT
281733 TTCTTTT
1 TTCTTTT
*
281740 TT-TCTT
1 TTCTTTT
281746 TTCTTTT
1 TTCTTTT
**
281753 TT-TCAT
1 TTCTTTT
281759 TT-TTTT
1 TTCTTTT
*
281765 TTATTTT
1 TTCTTTT
*
281772 TTCATTT
1 TTCTTTT
281779 TTCTTT
1 TTCTTT
281785 ATTATATATT
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
6 19 0.29
7 31 0.48
8 15 0.23
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (7 bp):
TTCTTTT
Found at i:281722 original size:20 final size:19
Alignment explanation
Indices: 281701--281772 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 19
281691 GTTTATTCTA
281701 TTTTTCTTTTTCTTCTTTTAT
1 TTTTTCTTTTTCTTC-TTT-T
281722 TTATTTCTTTTTTCTT-TTTT
1 TT-TTTC-TTTTTCTTCTTTT
281742 TCTTTTCTTTTT-TTCATTTT
1 T-TTTTCTTTTTCTTC-TTTT
*
281762 TTTTTATTTTT
1 TTTTTCTTTTT
281773 TCATTTTTCT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
18 2 0.04
19 14 0.31
20 11 0.24
21 6 0.13
22 4 0.09
23 8 0.18
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTCTTTTTCTTCTTTT
Found at i:281733 original size:29 final size:28
Alignment explanation
Indices: 281687--281772 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 28
281677 TGAACCCCCA
*
281687 TTTTGTTTA-TTCTATTTTTCTTTTTCTTC
1 TTTTATTTATTTCT-TTTTTCTTTTT-TTC
281716 TTTTATTTATTTCTTTTTTCTTTTTTTC
1 TTTTATTTATTTCTTTTTTCTTTTTTTC
* * *
281744 TTTTCTTTTTTTCATTTTTTTTTATTTTT
1 TTTTATTTATTTC-TTTTTTCTT-TTTTT
281773 TCATTTTTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
28 14 0.28
29 27 0.54
30 9 0.18
ACGTcount: A:0.07, C:0.10, G:0.01, T:0.81
Consensus pattern (28 bp):
TTTTATTTATTTCTTTTTTCTTTTTTTC
Found at i:281747 original size:13 final size:13
Alignment explanation
Indices: 281702--281784 Score: 73
Period size: 13 Copynumber: 6.2 Consensus size: 13
281692 TTTATTCTAT
281702 TTTTCTTTTTCTTC
1 TTTTCTTTTT-TTC
* *
281716 TTTTATTTATTTCTT
1 TTTTCTTT-TTT-TC
281731 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
281744 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
281757 ATTTT-TTTTTATT-
1 -TTTTCTTTTT-TTC
*
281770 TTTTC-ATTTTTC
1 TTTTCTTTTTTTC
281782 TTT
1 TTT
281785 ATTATATATT
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
11 2 0.03
12 10 0.17
13 19 0.33
14 17 0.29
15 10 0.17
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:281784 original size:33 final size:33
Alignment explanation
Indices: 281699--281773 Score: 91
Period size: 32 Copynumber: 2.2 Consensus size: 33
281689 TTGTTTATTC
*
281699 TATTTTTCTTTTTCTTCTTTTATTTATTTCTTTTT
1 TATTTTT-TTCTT-TTCTTTTATTTATTTCTTTTT
*
281734 TCTTTTTTTCTTTTCTTTT-TTTCATTT-TTTTT
1 TATTTTTTTCTTTTCTTTTATTT-ATTTCTTTTT
281766 TATTTTTT
1 TATTTTTT
281774 CATTTTTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 15 0.42
33 11 0.31
34 4 0.11
35 6 0.17
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.83
Consensus pattern (33 bp):
TATTTTTTTCTTTTCTTTTATTTATTTCTTTTT
Found at i:281785 original size:18 final size:18
Alignment explanation
Indices: 281750--281787 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
281740 TTTCTTTTCT
*
281750 TTTTTTCATTTTTTTTTA
1 TTTTTTCATTTTTCTTTA
281768 TTTTTTCATTTTTCTTTA
1 TTTTTTCATTTTTCTTTA
281786 TT
1 TT
281788 ATATATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTCATTTTTCTTTA
Found at i:285315 original size:22 final size:20
Alignment explanation
Indices: 285267--285316 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
285257 ATCTCATATA
285267 AAAAAATAAAATGAAGTAAT
1 AAAAAATAAAATGAAGTAAT
*
285287 AATAAATGATAAATGAA-TAAT
1 AAAAAAT-A-AAATGAAGTAAT
285308 GAAAAAATA
1 -AAAAAATA
285317 TACACGGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 6 0.24
21 6 0.24
22 13 0.52
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (20 bp):
AAAAAATAAAATGAAGTAAT
Found at i:294751 original size:3 final size:3
Alignment explanation
Indices: 294743--294782 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
294733 GCCTGAAAGA
*
294743 AAT AAT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
294783 TAAAAACAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:295005 original size:5 final size:5
Alignment explanation
Indices: 294955--294986 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
294945 GCAAAAAAAC
294955 CCGAT CCGA- CCGAT CCGAT CCGAT CCGAT CCG
1 CCGAT CCGAT CCGAT CCGAT CCGAT CCGAT CCG
294987 TTGATCCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.44, G:0.22, T:0.16
Consensus pattern (5 bp):
CCGAT
Found at i:295939 original size:21 final size:21
Alignment explanation
Indices: 295906--295946 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
295896 TCGGATTCGG
*
295906 ATCCGGATATTCGGATATCCA
1 ATCCGAATATTCGGATATCCA
*
295927 ATCCGAATTTTCGGATATCC
1 ATCCGAATATTCGGATATCC
295947 GATTTTTCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (21 bp):
ATCCGAATATTCGGATATCCA
Found at i:295948 original size:16 final size:16
Alignment explanation
Indices: 295927--295958 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
295917 CGGATATCCA
295927 ATCCGAATTTTCGGAT
1 ATCCGAATTTTCGGAT
*
295943 ATCCGATTTTTCGGAT
1 ATCCGAATTTTCGGAT
295959 TGGATACGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (16 bp):
ATCCGAATTTTCGGAT
Found at i:296012 original size:16 final size:17
Alignment explanation
Indices: 295982--296015 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
295972 TTATTTTAGG
*
295982 TATCCGAAATTTTCGGA
1 TATCCGAAATATTCGGA
295999 TATCCGAAA-ATTCGGA
1 TATCCGAAATATTCGGA
296015 T
1 T
296016 CGGATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (17 bp):
TATCCGAAATATTCGGA
Found at i:303209 original size:149 final size:149
Alignment explanation
Indices: 302934--303236 Score: 570
Period size: 149 Copynumber: 2.0 Consensus size: 149
302924 AGGCATAAAA
*
302934 TATTTGACAACAGAATTCCATGAGTAATTTACATTATGGGTCATTATTAAACATGACATTAACTT
1 TATTTGACAACAGAATTCCACGAGTAATTTACATTATGGGTCATTATTAAACATGACATTAACTT
*
302999 TCACATAGGTGACTTATGCTAAAACCGTTAAGTAATTTTAATGGAAAAGTTGAGTTTGCATGCAT
66 TCACATAGGTGACTTATGCTAAAACCGTTAAGTAATTTTAATGGAAAAGTTGAGTTCGCATGCAT
303064 AAGAACTAAGAACATGGAT
131 AAGAACTAAGAACATGGAT
303083 TATTTGACAACAGAATTCCACGAGTAATTTACATTATGGGTCATTATTAAACATGACATTAACTT
1 TATTTGACAACAGAATTCCACGAGTAATTTACATTATGGGTCATTATTAAACATGACATTAACTT
*
303148 TCACATAGGTGACTTATGCTAACACCGTTAAGTAATTTTAATGGAAAAGTTGAGTTCGCATGCAT
66 TCACATAGGTGACTTATGCTAAAACCGTTAAGTAATTTTAATGGAAAAGTTGAGTTCGCATGCAT
*
303213 AAGAACTAAGAATATGGAT
131 AAGAACTAAGAACATGGAT
303232 TATTT
1 TATTT
303237 TATACATTGT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (149 bp):
TATTTGACAACAGAATTCCACGAGTAATTTACATTATGGGTCATTATTAAACATGACATTAACTT
TCACATAGGTGACTTATGCTAAAACCGTTAAGTAATTTTAATGGAAAAGTTGAGTTCGCATGCAT
AAGAACTAAGAACATGGAT
Found at i:305313 original size:28 final size:30
Alignment explanation
Indices: 305272--305338 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
305262 TATCAATTAT
*
305272 ATATTTTTAAATAAA-ATAAAATAATTTTA
1 ATATTTTTAAATAAATATAAAATAAATTTA
* * *
305301 ATATTTTT-TATAAATTTAAATTAAATTTA
1 ATATTTTTAAATAAATATAAAATAAATTTA
*
305330 TTATTTTTA
1 ATATTTTTA
305339 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
ATATTTTTAAATAAATATAAAATAAATTTA
Found at i:305339 original size:28 final size:28
Alignment explanation
Indices: 305305--305358 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
305295 ATTTTAATAT
305305 TTTTTATAAATTTAAATTAAATTTATTA
1 TTTTTATAAATTTAAATTAAATTTATTA
**
305333 TTTTTATATTTTTAAATTAAATTTAT
1 TTTTTATAAATTTAAATTAAATTTAT
305359 AGAAGAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTTATAAATTTAAATTAAATTTATTA
Found at i:307253 original size:11 final size:11
Alignment explanation
Indices: 307237--307299 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
307227 AAAATTACAT
307237 TATTAAAAATA
1 TATTAAAAATA
*
307248 TATTAAAACTA
1 TATTAAAAATA
* ***
307259 CATTATTGATA
1 TATTAAAAATA
307270 -ATTATAAAAT-
1 TATTA-AAAATA
307280 T-TTAAAAATA
1 TATTAAAAATA
307290 TATTAAAAAT
1 TATTAAAAAT
307300 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 8 0.21
11 26 0.67
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:315133 original size:30 final size:30
Alignment explanation
Indices: 315074--315133 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
315064 GTTCGAGCCC
* * * *
315074 TTTCGAGTTCGAGTTGAGTTTCAATATTTT
1 TTTCGAGTTCGAGTCGAGCTACAAAATTTT
*
315104 TTTCGAGTTCGAGTCGAGCTAGAAAATTTT
1 TTTCGAGTTCGAGTCGAGCTACAAAATTTT
315134 AGGCTCGCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (30 bp):
TTTCGAGTTCGAGTCGAGCTACAAAATTTT
Found at i:316517 original size:16 final size:16
Alignment explanation
Indices: 316498--316536 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
316488 AATAAGTTTT
*
316498 AATAAAATAATATAAA
1 AATAAAATAAAATAAA
*
316514 AATAAGATAAAATAAA
1 AATAAAATAAAATAAA
*
316530 ATTAAAA
1 AATAAAA
316537 AGAATTTGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AATAAAATAAAATAAA
Found at i:322774 original size:14 final size:15
Alignment explanation
Indices: 322755--322783 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
322745 ATTCCTCCAC
322755 AGTAATCGA-GTTAA
1 AGTAATCGATGTTAA
322769 AGTAATCGATGTTAA
1 AGTAATCGATGTTAA
322784 TGATCACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (15 bp):
AGTAATCGATGTTAA
Found at i:326244 original size:16 final size:16
Alignment explanation
Indices: 326223--326254 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
326213 GATTTTTTCG
326223 CAGGGTTTTATTTGCA
1 CAGGGTTTTATTTGCA
326239 CAGGGTTTTATTTGCA
1 CAGGGTTTTATTTGCA
326255 GGGATTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (16 bp):
CAGGGTTTTATTTGCA
Found at i:327601 original size:60 final size:60
Alignment explanation
Indices: 327535--327657 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 60
327525 GCCTCATATG
* *
327535 TCCTCAAATTATAACCCTCATT-TTAAATTGATT-CTTAAACTTTTAAATACTCTAATTTCA
1 TCCTCAAACTATAACCCTCATTCTAAAATT--TTCCTTAAACTTTTAAATACTCTAATTTCA
* * * * *
327595 TCCTCAAACTATCACTCTTATTCTAAAATTTTCCTTAAACTTTTGAATATTCTAATTTCA
1 TCCTCAAACTATAACCCTCATTCTAAAATTTTCCTTAAACTTTTAAATACTCTAATTTCA
327655 TCC
1 TCC
327658 CTAAATGATA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 2 0.04
60 46 0.85
61 6 0.11
ACGTcount: A:0.33, C:0.22, G:0.02, T:0.44
Consensus pattern (60 bp):
TCCTCAAACTATAACCCTCATTCTAAAATTTTCCTTAAACTTTTAAATACTCTAATTTCA
Found at i:327679 original size:60 final size:60
Alignment explanation
Indices: 327558--327718 Score: 143
Period size: 60 Copynumber: 2.7 Consensus size: 60
327548 ACCCTCATTT
* * * * *
327558 TAAATTGATTCTTAAACTTTTAAATACTCTAATTTCAT-CCTCAAACTATCACTCTTATTC
1 TAAATT-AGTCTTAAACTTTTGAATATTCTAATTTCATCCCTCAAACTATCAATATTATTC
* *
327618 TAAAATT-TTCCTTAAACTTTTGAATATTCTAATTTCATCCCT-AAA-TGAT-AATATTCTTTC
1 T-AAATTAGT-CTTAAACTTTTGAATATTCTAATTTCATCCCTCAAACT-ATCAATATT-ATTC
* * *
327678 TAAATTAGTCTCTAAACTATTGAATATTCCAAATTCATCCC
1 TAAATTAGTCT-TAAACTTTTGAATATTCTAATTTCATCCC
327719 CAAGTTCATC
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
59 14 0.16
60 63 0.74
61 8 0.09
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.43
Consensus pattern (60 bp):
TAAATTAGTCTTAAACTTTTGAATATTCTAATTTCATCCCTCAAACTATCAATATTATTC
Found at i:334488 original size:41 final size:41
Alignment explanation
Indices: 334418--334581 Score: 138
Period size: 41 Copynumber: 4.0 Consensus size: 41
334408 CACAAACGCC
*
334418 AAGTACGAGTCTT-TAGCGACAATTT-TATAAAAATGCCACTA
1 AAGTACGA-TTTTATAGCGAC-ATTTGTATAAAAATGCCACTA
* * * *
334459 AAGTACGATTTTATAGCAATATTTGTATAAAAACGCCACTG
1 AAGTACGATTTTATAGCGACATTTGTATAAAAATGCCACTA
* * * * * **
334500 ATGTCCGAGTATATAGCGACGTTTGTATAAAAATTTCACTA
1 AAGTACGATTTTATAGCGACATTTGTATAAAAATGCCACTA
* * *
334541 AAGTAC-AGTTTT-TAGCGGCATTTGTATACAAGTGCCACTA
1 AAGTACGA-TTTTATAGCGACATTTGTATAAAAATGCCACTA
334581 A
1 A
334582 TGTATTGATA
Statistics
Matches: 94, Mismatches: 26, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
40 31 0.33
41 63 0.67
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (41 bp):
AAGTACGATTTTATAGCGACATTTGTATAAAAATGCCACTA
Found at i:334776 original size:82 final size:82
Alignment explanation
Indices: 334680--334840 Score: 202
Period size: 82 Copynumber: 2.0 Consensus size: 82
334670 TCCTATTAAA
* * ** *
334680 ACTTTTGTATAAAAACGCTACTAAAGTA-TGAGTC-ATTAGTGGTGTTTGTATAAAAACGA-CAC
1 ACTTTTGTATAAAAACACCACTAAAGTACT-AGTCTA-TAACGGCGTTTGTATAAAAAC-ACCAC
334742 TAAAGTACAAGTCTTTAGAC
63 TAAAGTACAAGTCTTTAGAC
*
334762 ACTTTTGTATAAAAACACCACTAAAGTACTAGTCTATAACGGCGTTTGTATGAAAACACCACTAA
1 ACTTTTGTATAAAAACACCACTAAAGTACTAGTCTATAACGGCGTTTGTATAAAAACACCACTAA
* *
334827 AGTTCTAGTCTTTA
66 AGTACAAGTCTTTA
334841 TCGGCGTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
81 1 0.01
82 65 0.96
83 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (82 bp):
ACTTTTGTATAAAAACACCACTAAAGTACTAGTCTATAACGGCGTTTGTATAAAAACACCACTAA
AGTACAAGTCTTTAGAC
Found at i:334846 original size:41 final size:41
Alignment explanation
Indices: 334683--334849 Score: 153
Period size: 41 Copynumber: 4.1 Consensus size: 41
334673 TATTAAAACT
* * ** *
334683 TTTGTATAAAAACGCTACTAAAGTA-TGAGTC-ATTAGTGGTG
1 TTTGTATAAAAACACCACTAAAGTACT-AGTCTA-TAACGGCG
* * * *
334724 TTTGTATAAAAACGA-CACTAAAGTACAAGTCTTTAGAC-ACT
1 TTTGTATAAAAAC-ACCACTAAAGTACTAGTCTATA-ACGGCG
334765 TTTGTATAAAAACACCACTAAAGTACTAGTCTATAACGGCG
1 TTTGTATAAAAACACCACTAAAGTACTAGTCTATAACGGCG
* * * *
334806 TTTGTATGAAAACACCACTAAAGTTCTAGTCTTTATCGGCG
1 TTTGTATAAAAACACCACTAAAGTACTAGTCTATAACGGCG
334847 TTT
1 TTT
334850 TTGCTTAAAA
Statistics
Matches: 103, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
40 3 0.03
41 100 0.97
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (41 bp):
TTTGTATAAAAACACCACTAAAGTACTAGTCTATAACGGCG
Found at i:337167 original size:21 final size:21
Alignment explanation
Indices: 337125--337168 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
337115 AAAAATTCTC
*
337125 TTTATGAAAAGATTAAATCCT
1 TTTATGAAAAGATTAAACCCT
* *
337146 TTTATGAAAAGGTTAAGCCCT
1 TTTATGAAAAGATTAAACCCT
337167 TT
1 TT
337169 CACCGAAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (21 bp):
TTTATGAAAAGATTAAACCCT
Found at i:344213 original size:441 final size:431
Alignment explanation
Indices: 343496--344378 Score: 1358
Period size: 441 Copynumber: 2.0 Consensus size: 431
343486 TCAATTTGTG
* *
343496 CTTACTTTTCATAAAGAACAACAACAAATGGGGTTGGGATAGGAAGCCATTTATTGAGATATGCT
1 CTTAATTTTCATAAAGAACAACAACAAATGGGGCTGGGATAGGAAGCCA-TTATTGAGATATGCT
343561 CTCGAATGCTTTTGCAGCATTGGCTGGCTTGTTCATGCAGATCTCTTCTTCCTCCTATAGTTCTT
65 CTCGAATGCTTTTGCAGCATTGGCTGGCTTGTTCATGCAGA---CTTCTTCCTCCTATAGTTCTT
* *
343626 CACCATTATGGAATTTAACTGTTTGTTTCAATTGAGTTCCCTATTCTCGCTTCCGGTGGTGGGTC
127 CACCATAATGGAATTTAACTGTTTGTTTCAATTGAGTTCCCTATTCTAGCTTCCGGTGGTGGGTC
343691 AGTAAAAGTCATTGTTCAATGAAGCTGGTACTTAGATTTGCTTTGCCTCTTTCGGTTCTTTGGAA
192 AGTAAAAGTCATTGTTCAATGAAGCTGGTACTTAGATTTGCTTTGCCTCTTTCGGTTCTTTGGAA
* * *
343756 CAGTGAGATCAATTTTCCTTATTTCAGGCAATCTACAGCTTCAGCAAACTAATATAATTATCTCC
257 CAATGAGATAAATTTTCCTTATTTCAGGCAATCT--AGCTTCAACAAACTAATATAATTATCTCC
343821 TAGTCCTAAGTTCCTAACCATTTCTAATATAGAGCTCTTCATCCGCT-CAATCTAATGTCAGGAT
320 TAGTCCTAA----CT----ATTTCTAATATAGAG--C-TCATCCGCTCCAATCTAAT-TCAGGAT
343885 CTGGAATAACACAATGAACACTCTGGCATTTAGTAGAACTAAAACTGTCACA-TGATGGATT
373 CTGGAATAACACAATGAACACTCTGGCA-TTAGTAGAACTAAAA-T-TCACATTGATGGATT
*
343946 CTTAATTTTCATAAAGAACAACAACAAAT-GGGCTGGGATAGGAAGCCA-TATTGAGATATGTTC
1 CTTAATTTTCATAAAGAACAACAACAAATGGGGCTGGGATAGGAAGCCATTATTGAGATATGCTC
*
344009 TCGATTGCTTTTGCCA-CATTGGCTGGCTTGTTCATGCAGA-TTCTTCCT-CTATAGTTCTTCAC
66 TCGAATGCTTTTG-CAGCATTGGCTGGCTTGTTCATGCAGACTTCTTCCTCCTATAGTTCTTCAC
*
344071 CATAATGGAA-TTAACTGTTTGTTTCAATTGAAGTT-CCTATTCTAGTTTCCGGTGGATGGGTC-
130 CATAATGGAATTTAACTGTTTGTTTCAATTG-AGTTCCCTATTCTAGCTTCCGGTGG-TGGGTCA
344133 GATAAAAGTCATTG-TCAATGAAGCTGGTACTCTAGATTTGCTTTGCCTCTTTCGGTTC-TTGGA
193 G-TAAAAGTCATTGTTCAATGAAGCTGGTACT-TAGATTTGCTTTGCCTCTTTCGGTTCTTTGGA
344196 ACAATGAGATAAATTTTCCTTATTTCAGGCAATCTAGCTTCAACAAACTAATATAATTATCTCCT
256 ACAATGAGATAAATTTTCCTTATTTCAGGCAATCTAGCTTCAACAAACTAATATAATTATCTCCT
344261 AGTCCTAACTATTTCTAATATAGAGCTCATCCGCTCCAATCTAATTCAGGATCTGGAATAACACA
321 AGTCCTAACTATTTCTAATATAGAGCTCATCCGCTCCAATCTAATTCAGGATCTGGAATAACACA
344326 ATGAACACTCTGGCATTAGTAGAACTAAAATTCACATTGATGGATT
386 ATGAACACTCTGGCATTAGTAGAACTAAAATTCACATTGATGGATT
344372 CTTAATT
1 CTTAATT
344379 CTAATAAGGA
Statistics
Matches: 416, Mismatches: 10, Indels: 38
0.90 0.02 0.08
Matches are distributed among these distances:
425 5 0.01
426 17 0.04
427 15 0.04
428 44 0.11
429 10 0.02
431 15 0.04
435 2 0.00
439 37 0.09
441 94 0.23
442 71 0.17
443 8 0.02
447 50 0.12
448 2 0.00
449 18 0.04
450 28 0.07
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (431 bp):
CTTAATTTTCATAAAGAACAACAACAAATGGGGCTGGGATAGGAAGCCATTATTGAGATATGCTC
TCGAATGCTTTTGCAGCATTGGCTGGCTTGTTCATGCAGACTTCTTCCTCCTATAGTTCTTCACC
ATAATGGAATTTAACTGTTTGTTTCAATTGAGTTCCCTATTCTAGCTTCCGGTGGTGGGTCAGTA
AAAGTCATTGTTCAATGAAGCTGGTACTTAGATTTGCTTTGCCTCTTTCGGTTCTTTGGAACAAT
GAGATAAATTTTCCTTATTTCAGGCAATCTAGCTTCAACAAACTAATATAATTATCTCCTAGTCC
TAACTATTTCTAATATAGAGCTCATCCGCTCCAATCTAATTCAGGATCTGGAATAACACAATGAA
CACTCTGGCATTAGTAGAACTAAAATTCACATTGATGGATT
Found at i:344551 original size:62 final size:61
Alignment explanation
Indices: 344449--344570 Score: 208
Period size: 62 Copynumber: 2.0 Consensus size: 61
344439 ATAAAACATA
*
344449 CTTTATAAGCTCTTAAAGCTGAAAACATGAGTATAAGGTTTATATGATAGGGATAAGTAATC
1 CTTTATAAGCTCTGAAAGCTGAAAACATGAGTATAAGGTTT-TATGATAGGGATAAGTAATC
* *
344511 CTTTATAAGCTCTGAAAGCTGAAAACATGAGTATATGGTTTTATGATAGGGGTAAGTAAT
1 CTTTATAAGCTCTGAAAGCTGAAAACATGAGTATAAGGTTTTATGATAGGGATAAGTAAT
344571 TCTCTATTGT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
61 18 0.32
62 39 0.68
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (61 bp):
CTTTATAAGCTCTGAAAGCTGAAAACATGAGTATAAGGTTTTATGATAGGGATAAGTAATC
Found at i:348539 original size:28 final size:28
Alignment explanation
Indices: 348499--348553 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
348489 TTCTGGAAAA
348499 TGATTTACATTTCTGTAAAAC-ATTTTCC
1 TGATTTACATTTCTGT-AAACTATTTTCC
348527 TGATTT-CATTTTCTGTAAACTATTTTC
1 TGATTTACA-TTTCTGTAAACTATTTTC
348554 AGTAAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.51
Consensus pattern (28 bp):
TGATTTACATTTCTGTAAACTATTTTCC
Found at i:349849 original size:43 final size:44
Alignment explanation
Indices: 349788--349878 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 44
349778 TCTTTTTTTG
*
349788 TGGCGTTTTGTCCCAAAAACACCGCTAAATATTTTGACATATAA
1 TGGCGTTTTGTCCCAAAAACACCGCTAAATATTATGACATATAA
** * * *
349832 TGGCGTTTT-TCCCAAAAATGCCGCTAAATGTTATGTCATATAG
1 TGGCGTTTTGTCCCAAAAACACCGCTAAATATTATGACATATAA
349875 TGGC
1 TGGC
349879 ATTTGTGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 32 0.78
44 9 0.22
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
TGGCGTTTTGTCCCAAAAACACCGCTAAATATTATGACATATAA
Found at i:350126 original size:21 final size:21
Alignment explanation
Indices: 350100--350158 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
350090 ATTATCCAAT
*
350100 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* * *
350121 AAACTTCAAATCTATAACAAG
1 AAACTTGAAATCCATAACAAC
350142 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
350159 TAATAAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:353105 original size:41 final size:40
Alignment explanation
Indices: 353060--353495 Score: 178
Period size: 41 Copynumber: 10.7 Consensus size: 40
353050 TAAAGTTTAC
*
353060 AAACGCAACTAAAGTACGAGTCTTTAGCA-GTTTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCACG--TTTGTATAA
* * * * * * *
353101 AAACGCCACTGAAGCACAATTCTATAGTGACGTATGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAG-CACGTTTGTATAA
* *
353142 AAACACCACTAAAGTACGAGT-TTATTGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTT-TAGC-ACGTTTGTATAA
* * * * * *
353183 AAATGACACTAACGTATGAGTCTTTAGCGGCTTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGC-ACGTTTGTATAA
* * ** * *
353224 AAGCGCCACTAATGTACTGA-TAAATTA-CAACATTTAT-TCAAA
1 AAACGCCACTAAAGTAC-GAGT-CTTTAGC-ACGTTTGTAT--AA
* * * * *
353266 AAAAGCCATTACAA-TATGAATCTCTTA-CAGCGTTT-TTTCAA
1 AAACGCCACTA-AAGTACGAGTCT-TTAGCA-CGTTTGTAT-AA
* * * * ** *
353307 AAATGCCATTATA-TATGTTTCTTATTA-CGATGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTC-T-TTAGC-ACGTTTGTATAA
* * ** *
353348 AAACGCCACTAAAGTTCGAGT-ATTAGCGGTGTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGC-ACGTTTGTATAA
* *
353388 AAACGGCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGC-ACGTTTGTATAA
* * *
353429 AAACGCCACTAAAGTACTAGTCTATATTG-GCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCT-T-TAGCACGTTTGTATAA
353470 AAACGCCACTAAAGT-CTGAGTCTTTA
1 AAACGCCACTAAAGTAC-GAGTCTTTA
353496 CTGGCTTTTT
Statistics
Matches: 300, Mismatches: 72, Indels: 48
0.71 0.17 0.11
Matches are distributed among these distances:
39 4 0.01
40 42 0.14
41 213 0.71
42 37 0.12
43 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (40 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCACGTTTGTATAA
Found at i:353387 original size:40 final size:40
Alignment explanation
Indices: 353338--353484 Score: 195
Period size: 41 Copynumber: 3.6 Consensus size: 40
353328 TTATTACGAT
* *
353338 GTTTGTATAAAAACGCCACTAAAGTTCGAGTATTAGCGGT
1 GTTTGTATAAAAACGCCACTAAAGTACGAGTATTAGCGGC
* * *
353378 GTTTATATAAAAACGGCACTAAAGTACGAGTCTTTAGCGGC
1 GTTTGTATAAAAACGCCACTAAAGTACGAGT-ATTAGCGGC
* * **
353419 GTTTGTATAAAAACGCCACTAAAGTACTAGTCTATATTGGC
1 GTTTGTATAAAAACGCCACTAAAGTACGAGTAT-TAGCGGC
353460 GTTTGTATAAAAACGCCACTAAAGT
1 GTTTGTATAAAAACGCCACTAAAGT
353485 CTGAGTCTTT
Statistics
Matches: 94, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
40 29 0.31
41 65 0.69
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (40 bp):
GTTTGTATAAAAACGCCACTAAAGTACGAGTATTAGCGGC
Found at i:353492 original size:82 final size:81
Alignment explanation
Indices: 353338--353495 Score: 219
Period size: 82 Copynumber: 1.9 Consensus size: 81
353328 TTATTACGAT
* * *
353338 GTTTGTATAAAAACGCCACTAAAGTTCGAGTATTAGCGGTGTTTATATAAAAACGGCACTAAAGT
1 GTTTGTATAAAAACGCCACTAAAGTACGAGTATTAGCGGCGTTTATATAAAAACGCCACTAAAGT
353403 ACGAGTCTTTAGCGGC
66 ACGAGTCTTTAGCGGC
* * ** *
353419 GTTTGTATAAAAACGCCACTAAAGTACTAGTCTATATTGGCGTTTGTATAAAAACGCCACTAAAG
1 GTTTGTATAAAAACGCCACTAAAGTACGAGTAT-TAGCGGCGTTTATATAAAAACGCCACTAAAG
353484 T-CTGAGTCTTTA
65 TAC-GAGTCTTTA
353496 CTGGCTTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 31 0.46
82 36 0.54
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (81 bp):
GTTTGTATAAAAACGCCACTAAAGTACGAGTATTAGCGGCGTTTATATAAAAACGCCACTAAAGT
ACGAGTCTTTAGCGGC
Found at i:356963 original size:21 final size:21
Alignment explanation
Indices: 356939--356984 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
356929 AATAATTCTC
* *
356939 TTCATGAAAAGTTTAAATCCT
1 TTCATGAAAAGGTTAAACCCT
*
356960 TTCATGAAAAGGTTAAGCCCT
1 TTCATGAAAAGGTTAAACCCT
356981 TTCA
1 TTCA
356985 CCGAAAGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (21 bp):
TTCATGAAAAGGTTAAACCCT
Found at i:359496 original size:42 final size:42
Alignment explanation
Indices: 359442--359540 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 42
359432 TTTTCGGATG
*
359442 CAAACGCCACAAAAGGTGT-GATATATAGCAACGTTTTTCATA
1 CAAACGCCACAAAAGGTCTCG-TATATAGCAACGTTTTTCATA
* * **
359484 CAAACGCTACAAAAGGTCTCGTATATAGCGACGTTTTTTGTTA
1 CAAACGCCACAAAAGGTCTCGTATATAGCAACG-TTTTTCATA
*
359527 CAAACGTCACAAAA
1 CAAACGCCACAAAA
359541 TATCTACATT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 28 0.58
43 20 0.42
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.26
Consensus pattern (42 bp):
CAAACGCCACAAAAGGTCTCGTATATAGCAACGTTTTTCATA
Found at i:369034 original size:42 final size:42
Alignment explanation
Indices: 368945--369026 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
368935 ATTGTCGTTT
* *
368945 ACAAACGTAACTAAAGGTTATGTTTTTTTAGCGGCATTTTTA
1 ACAAACGTAACTAAAGGTTATGTATATTTAGCGGCATTTTTA
** *
368987 ACAAACGTCGCTAAAGGTTATG-ATATTTAGTGGCATTTTT
1 ACAAACGTAACTAAAGGTTATGTATATTTAGCGGCATTTTT
369027 TCCCAAACAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 15 0.43
42 20 0.57
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (42 bp):
ACAAACGTAACTAAAGGTTATGTATATTTAGCGGCATTTTTA
Found at i:369041 original size:42 final size:42
Alignment explanation
Indices: 368955--369041 Score: 95
Period size: 42 Copynumber: 2.1 Consensus size: 42
368945 ACAAACGTAA
* * **
368955 CTAAAGGTTATGTTTTTTTAGCGGCATTTTTAACAAACGTCG
1 CTAAAGGTTATGTATATTTAGCGGCATTTTTAACAAACAACG
* **
368997 CTAAAGGTTATG-ATATTTAGTGGCATTTTTTCCCAAACAACG
1 CTAAAGGTTATGTATATTTAGCGGCA-TTTTTAACAAACAACG
369039 CTA
1 CTA
369042 TTTATCTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
41 10 0.27
42 27 0.73
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (42 bp):
CTAAAGGTTATGTATATTTAGCGGCATTTTTAACAAACAACG
Found at i:369407 original size:21 final size:20
Alignment explanation
Indices: 369375--369432 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
369365 TTATCCAATG
*
369375 AACTTAACATCCGTAACAACA
1 AACTTAA-ATCCATAACAACA
*
369396 AACTTCAAATCCATAACAAGA
1 AACTT-AAATCCATAACAACA
369417 AACTTGAAATCCATAA
1 AACTT-AAATCCATAA
369433 TAATAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.50, C:0.24, G:0.05, T:0.21
Consensus pattern (20 bp):
AACTTAAATCCATAACAACA
Found at i:370827 original size:69 final size:67
Alignment explanation
Indices: 370707--370842 Score: 209
Period size: 69 Copynumber: 2.0 Consensus size: 67
370697 AGCAGCAAAT
* *
370707 GAGTTTGTGTAAACGACGAGAATGAAAAGATAGGTCAAGGGGAAAAATGAAAAATGGTTAAAGGG
1 GAGTTTGGGTAAACGACGAGAATGAAAAGATAGGTCAAGGGGAAAAATGAAAAAGGGTTAAAGGG
370772 GC
66 GC
* * *
370774 GAGTTTGGGTAAACGGCGGGAATGAAAAAATATAGGTCAAGGGGAAAAATGAAAAAGGGTTAAAG
1 GAGTTTGGGTAAACGACGAGAATG--AAAAGATAGGTCAAGGGGAAAAATGAAAAAGGGTTAAAG
370839 GGGC
64 GGGC
370843 ACGAGACTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 21 0.34
69 41 0.66
ACGTcount: A:0.43, C:0.06, G:0.35, T:0.17
Consensus pattern (67 bp):
GAGTTTGGGTAAACGACGAGAATGAAAAGATAGGTCAAGGGGAAAAATGAAAAAGGGTTAAAGGG
GC
Found at i:371014 original size:41 final size:41
Alignment explanation
Indices: 370913--371022 Score: 116
Period size: 41 Copynumber: 2.7 Consensus size: 41
370903 TCTATTGAGA
* *
370913 CGTTTGTATAAAAACACCACTAAAGTACGAGCTTATAGCGG
1 CGTTTGTATAAAATCGCCACTAAAGTACGAGCTTATAGCGG
* * *
370954 CATTTATATAAAAAT-GCCACTAAAGTATGAGTCTT-TAGCGG
1 CGTTTGTAT-AAAATCGCCACTAAAGTACGAG-CTTATAGCGG
* * *
370995 TGTTTGTATACAATCGCCACTAATGTAC
1 CGTTTGTATAAAATCGCCACTAAAGTAC
371023 TGATAAATTA
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
40 4 0.07
41 44 0.80
42 7 0.13
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (41 bp):
CGTTTGTATAAAATCGCCACTAAAGTACGAGCTTATAGCGG
Found at i:371276 original size:82 final size:82
Alignment explanation
Indices: 371121--371288 Score: 216
Period size: 82 Copynumber: 2.0 Consensus size: 82
371111 CTATTATGGA
* * *
371121 GTTTGTATTAAAAAGCCACTAAAGTACTAGTCTTTACTAGCGTTTGTATAAAAATGACACTAATG
1 GTTTGTATTAAAAAGCCACTAAAGTACTAGTCTATACGAGCGTTTGTATAAAAATGACACTAAAG
* **
371186 TATGAGTCTTTTGCGGC
66 TATAAGTCTTTACCGGC
* *
371203 GTTTGTA-TAAAAACGCCGCTAAAGTACTAGTCTATAGCGA-CGTTTGTATAAAAATGCCACTAA
1 GTTTGTATTAAAAA-GCCACTAAAGTACTAGTCTATA-CGAGCGTTTGTATAAAAATGACACTAA
371266 AGT-TCAAGTCTTTACCGGC
64 AGTAT-AAGTCTTTACCGGC
371285 GTTT
1 GTTT
371289 TCCCTTAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
81 7 0.09
82 66 0.88
83 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (82 bp):
GTTTGTATTAAAAAGCCACTAAAGTACTAGTCTATACGAGCGTTTGTATAAAAATGACACTAAAG
TATAAGTCTTTACCGGC
Found at i:371288 original size:41 final size:41
Alignment explanation
Indices: 371121--371288 Score: 187
Period size: 41 Copynumber: 4.1 Consensus size: 41
371111 CTATTATGGA
**
371121 GTTTGTATTAAAAA-GCCACTAAAGTACTAGTCTTTACTAGC
1 GTTTGTA-TAAAAATGCCACTAAAGTACTAGTCTTTACCGGC
* * **
371162 GTTTGTATAAAAATGACACTAATGTA-TGAGTCTTTTGCGGC
1 GTTTGTATAAAAATGCCACTAAAGTACT-AGTCTTTACCGGC
* * * * *
371203 GTTTGTATAAAAACGCCGCTAAAGTACTAGTCTATAGCGAC
1 GTTTGTATAAAAATGCCACTAAAGTACTAGTCTTTACCGGC
* *
371244 GTTTGTATAAAAATGCCACTAAAGTTCAAGTCTTTACCGGC
1 GTTTGTATAAAAATGCCACTAAAGTACTAGTCTTTACCGGC
371285 GTTT
1 GTTT
371289 TCCCTTAAAA
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
40 7 0.07
41 96 0.92
42 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (41 bp):
GTTTGTATAAAAATGCCACTAAAGTACTAGTCTTTACCGGC
Found at i:373026 original size:21 final size:21
Alignment explanation
Indices: 373002--373053 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
372992 AACAATTCTC
*
373002 TTCATGAAAAGATTAAATCCT
1 TTCATGAAAAGATTAAACCCT
* *
373023 TTCATGAAAAGGTTAAGCCCT
1 TTCATGAAAAGATTAAACCCT
373044 TTCATTGAAA
1 TTCA-TGAAA
373054 GGTCTTAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (21 bp):
TTCATGAAAAGATTAAACCCT
Found at i:374294 original size:19 final size:20
Alignment explanation
Indices: 374266--374304 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
374256 TCTATAAAAA
*
374266 TAAAAATATTTAT-TATTTT
1 TAAAAATATTGATATATTTT
*
374285 TAAAATTATTGATATATTTT
1 TAAAAATATTGATATATTTT
374305 AAGGAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TAAAAATATTGATATATTTT
Found at i:374513 original size:12 final size:12
Alignment explanation
Indices: 374457--374515 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
374447 TAATAGTATC
374457 ATATATTATTAT
1 ATATATTATTAT
*
374469 ATA-ATTGAGTAT
1 ATATATT-ATTAT
*
374481 ATAT-TGTAATA-
1 ATATAT-TATTAT
374492 ATATTATTATTAT
1 ATA-TATTATTAT
374505 ATATATTATTA
1 ATATATTATTA
374516 ATAATTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
11 6 0.16
12 27 0.71
13 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (12 bp):
ATATATTATTAT
Found at i:374517 original size:24 final size:25
Alignment explanation
Indices: 374443--374518 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 25
374433 TGAAAATAAG
374443 AATATAA-T-AGTATCATATATTATT
1 AATATAATTGAGTAT-ATATATTATT
*
374467 -ATATAATTGAGTATATAT-TGTAAT
1 AATATAATTGAGTATATATAT-TATT
* *
374491 AATATTATT-ATTATATATATTATT
1 AATATAATTGAGTATATATATTATT
374515 AATA
1 AATA
374519 ATTAATAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
23 7 0.16
24 23 0.53
25 13 0.30
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (25 bp):
AATATAATTGAGTATATATATTATT
Found at i:375211 original size:68 final size:67
Alignment explanation
Indices: 375073--375207 Score: 195
Period size: 68 Copynumber: 2.0 Consensus size: 67
375063 AGCAGCAAAT
*
375073 GAGTTTGGGTAAACGGCGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGGAAAAAGGTTAAAGA
1 GAGTTTGGGTAAACGACGGGAATGAAAAAATAGGTCAAGGGG-AAAAATGGAAAAAGGTTAAAGA
375138 GGC
65 GGC
* *
375141 GAGTTTGGGTAAACGACGGGAATGAAAAAAACTAGGTCAAGGTG-AAAAT-GAAAAGGGTTAAAG
1 GAGTTTGGGTAAACGACGGGAATG-AAAAAA-TAGGTCAAGGGGAAAAATGGAAAAAGGTTAAAG
375204 -GGC
64 AGGC
375207 G
1 G
375208 CGAGACTTAG
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
66 4 0.06
67 13 0.21
68 28 0.45
69 6 0.10
70 11 0.18
ACGTcount: A:0.43, C:0.07, G:0.35, T:0.16
Consensus pattern (67 bp):
GAGTTTGGGTAAACGACGGGAATGAAAAAATAGGTCAAGGGGAAAAATGGAAAAAGGTTAAAGAG
GC
Found at i:375328 original size:41 final size:41
Alignment explanation
Indices: 375248--375385 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
375238 TTGTTAACCT
* * * * *
375248 AAACGCCACTAA-ATACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAATGTATGAGTCTATAGCGGCATTTGTATAA
* *
375288 AAACGCCACTAATGTATGAGTCTATAGTGGCATTTATATAA
1 AAACGCCACTAATGTATGAGTCTATAGCGGCATTTGTATAA
* * *
375329 AAATGCCACTAAAT-TATGAGTCTTTAGCGGCATTTGTATAC
1 AAACGCCACT-AATGTATGAGTCTATAGCGGCATTTGTATAA
*
375370 AATCGCCACTAATGTA
1 AAACGCCACTAATGTA
375386 CTGATAAATT
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
40 15 0.19
41 63 0.78
42 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (41 bp):
AAACGCCACTAATGTATGAGTCTATAGCGGCATTTGTATAA
Found at i:376179 original size:3 final size:3
Alignment explanation
Indices: 376173--376198 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
376163 TAATATATGC
376173 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
376199 TATCTCGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:380511 original size:49 final size:50
Alignment explanation
Indices: 380438--380537 Score: 193
Period size: 49 Copynumber: 2.0 Consensus size: 50
380428 ATGATGATCC
380438 TCCTATTATTAGAGAGGATGAGAAAACATTGTTTCCATATCCACCGTTGT
1 TCCTATTATTAGAGAGGATGAGAAAACATTGTTTCCATATCCACCGTTGT
380488 TCCTATTATTA-AGAGGATGAGAAAACATTGTTTCCATATCCACCGTTGT
1 TCCTATTATTAGAGAGGATGAGAAAACATTGTTTCCATATCCACCGTTGT
380537 T
1 T
380538 GAAAATTTGG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 39 0.78
50 11 0.22
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (50 bp):
TCCTATTATTAGAGAGGATGAGAAAACATTGTTTCCATATCCACCGTTGT
Found at i:381728 original size:21 final size:21
Alignment explanation
Indices: 381696--381742 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
381686 CAACAACTAT
*
381696 CTTT-ATGAAAAGATTAAATC
1 CTTTCATGAAAAGATTAAACC
* * *
381716 CTTTCATGTAAAGGTTAAGCC
1 CTTTCATGAAAAGATTAAACC
381737 CTTTCA
1 CTTTCA
381743 CCGAAAGGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (21 bp):
CTTTCATGAAAAGATTAAACC
Done.