Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007932.1 Hibiscus syriacus cultivar Beakdansim tig00110342_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: 1116633
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:292012 original size:6 final size:6
Alignment explanation
Indices: 291988--292073 Score: 73
Period size: 6 Copynumber: 14.3 Consensus size: 6
291978 AGCGGTCGCA
* * * * * *
291988 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * *
292036 GACGAT GAAGAT GATGAC GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
292074 TGATCCAAAC
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.38, C:0.08, G:0.34, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:292038 original size:36 final size:36
Alignment explanation
Indices: 291991--292069 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
291981 GGTCGCAGAA
*
291991 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* *
292027 GATGAAGCTGACGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
292063 GATGAAG
1 GATGAAG
292070 ATGATGATCC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.37, C:0.09, G:0.34, T:0.20
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:292077 original size:12 final size:12
Alignment explanation
Indices: 291991--292073 Score: 103
Period size: 12 Copynumber: 6.9 Consensus size: 12
291981 GGTCGCAGAA
*
291991 GATGAAGCTGAC
1 GATGAAGATGAC
292003 GATGAAGATGAC
1 GATGAAGATGAC
*
292015 GATGATGATGAC
1 GATGAAGATGAC
*
292027 GATGAAGCTGAC
1 GATGAAGATGAC
*
292039 GATGAAGATGAT
1 GATGAAGATGAC
* * *
292051 GACGATGATGAT
1 GATGAAGATGAC
292063 GATGAAGATGA
1 GATGAAGATGA
292074 TGATCCAAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 61 1.00
ACGTcount: A:0.37, C:0.08, G:0.34, T:0.20
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:293852 original size:183 final size:183
Alignment explanation
Indices: 293544--294252 Score: 1292
Period size: 183 Copynumber: 3.9 Consensus size: 183
293534 CTTTCAACAT
** * * * * * *
293544 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
293609 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
293674 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
293727 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
293792 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
293857 AATGTGTCGATACGATTTAAAAAAGTGTCGGCATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
293910 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTAAAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
293975 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
294040 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* * *
294093 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
294158 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
294223 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACGATTTAAAAAAGTGTCG
294253 TTAATTTTAA
Statistics
Matches: 510, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 510 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:296733 original size:23 final size:23
Alignment explanation
Indices: 296706--296764 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
296696 TAACTACAAG
* *
296706 TATATAATGTAATAGGTATCGTT
1 TATATAATGTAATAGGTAGCGCT
296729 TATATAATGTAATAGGTAGCGCT
1 TATATAATGTAATAGGTAGCGCT
296752 TATATAATGTAAT
1 TATATAATGTAAT
296765 TCGTTTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (23 bp):
TATATAATGTAATAGGTAGCGCT
Found at i:297225 original size:18 final size:18
Alignment explanation
Indices: 297204--297240 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
297194 GTAATTGAAG
297204 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
297222 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
297240 T
1 T
297241 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:297248 original size:24 final size:25
Alignment explanation
Indices: 297185--297248 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
297175 TTTCAAATTC
* *
297185 ATTTC-ATATGTAATTGAAGTTTGA
1 ATTTCAATATATATTTGAAGTTTGA
* *
297209 ATTTAAATTTCA-ATTTG-AGTTTGA
1 ATTTCAATAT-ATATTTGAAGTTTGA
297233 ATTTCAATATATATTT
1 ATTTCAATATATATTT
297249 CGGCTCCACT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
23 1 0.03
24 23 0.74
25 7 0.23
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (25 bp):
ATTTCAATATATATTTGAAGTTTGA
Found at i:297542 original size:39 final size:39
Alignment explanation
Indices: 297499--297583 Score: 134
Period size: 39 Copynumber: 2.2 Consensus size: 39
297489 CGATGCTCAT
*
297499 CAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAAG
1 CAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAAAG
* * *
297538 CAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAAAT
1 CAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAAAG
297577 CAAAATC
1 CAAAATC
297584 TACAACTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.16
Consensus pattern (39 bp):
CAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAAAG
Found at i:301910 original size:2 final size:2
Alignment explanation
Indices: 301903--301950 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
301893 ATATAAGGTT
301903 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
301945 TA TA TA
1 TA TA TA
301951 AAAGTTTATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:309210 original size:14 final size:14
Alignment explanation
Indices: 309191--309218 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
309181 AGATAATCGA
309191 TCATGCATGCCATG
1 TCATGCATGCCATG
309205 TCATGCATGCCATG
1 TCATGCATGCCATG
309219 AATCGTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (14 bp):
TCATGCATGCCATG
Found at i:312326 original size:11 final size:11
Alignment explanation
Indices: 312308--312336 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
312298 TTTGTTGTAC
312308 TATG-GCACTA
1 TATGTGCACTA
312318 TATGTGCACTA
1 TATGTGCACTA
312329 TATGTGCA
1 TATGTGCA
312337 AGGATAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (11 bp):
TATGTGCACTA
Found at i:314134 original size:20 final size:20
Alignment explanation
Indices: 314109--314160 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
314099 AAATTGTCCT
*
314109 GAATGACCTATGTATATCTC
1 GAATGACCTATGTATATCCC
* *
314129 GAATGACCTCTGTATTTCCC
1 GAATGACCTATGTATATCCC
314149 GAATGACCTATG
1 GAATGACCTATG
314161 AACCCTCGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (20 bp):
GAATGACCTATGTATATCCC
Found at i:319172 original size:20 final size:20
Alignment explanation
Indices: 319138--319189 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
319128 GAAATTGTCT
*
319138 CGAATGACCTATGTATATCC
1 CGAAGGACCTATGTATATCC
* * *
319158 TGAAGGACCTCTGTATGTCC
1 CGAAGGACCTATGTATATCC
319178 CGAAGGACCTAT
1 CGAAGGACCTAT
319190 AAACCCTCGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (20 bp):
CGAAGGACCTATGTATATCC
Found at i:320124 original size:7 final size:7
Alignment explanation
Indices: 320112--320136 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
320102 TCACATAACT
320112 TATTTCA
1 TATTTCA
320119 TATTTCA
1 TATTTCA
320126 TATTTCA
1 TATTTCA
320133 TATT
1 TATT
320137 ATTACCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (7 bp):
TATTTCA
Found at i:323177 original size:2 final size:2
Alignment explanation
Indices: 323170--323194 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
323160 TTCACATACC
323170 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
323195 AGTTAAAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:324408 original size:31 final size:31
Alignment explanation
Indices: 324363--324424 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
324353 ACTATTGAGA
324363 GACTAAACATGAACGGATCGATAAAGTTAGG
1 GACTAAACATGAACGGATCGATAAAGTTAGG
* *
324394 GACTAAA-ATCGAACGGATTGATAACGTTAGG
1 GACTAAACAT-GAACGGATCGATAAAGTTAGG
324425 AACCATTCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (31 bp):
GACTAAACATGAACGGATCGATAAAGTTAGG
Found at i:325848 original size:5 final size:5
Alignment explanation
Indices: 325838--326003 Score: 332
Period size: 5 Copynumber: 33.2 Consensus size: 5
325828 CATCGACAAC
325838 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
325888 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
325938 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
325988 ATATA ATATA ATATA A
1 ATATA ATATA ATATA A
326004 ATTTAGACAC
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 161 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:328214 original size:19 final size:19
Alignment explanation
Indices: 328186--328224 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
328176 TAATTAAATC
328186 AGAGTCCATCGATGCATGA
1 AGAGTCCATCGATGCATGA
* *
328205 AGAGTGCATCGGTGCATGA
1 AGAGTCCATCGATGCATGA
328224 A
1 A
328225 ATACATTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.21
Consensus pattern (19 bp):
AGAGTCCATCGATGCATGA
Found at i:330908 original size:24 final size:23
Alignment explanation
Indices: 330837--330940 Score: 124
Period size: 24 Copynumber: 4.5 Consensus size: 23
330827 CATGATCTTG
*
330837 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
330860 TGCATCGGTG--CA-TCATGTGGA
1 TGCATCGATGCACATTCAAG-GGA
330881 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
330905 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
*
330929 TACATCGATGCA
1 TGCATCGATGCA
330941 TTGTTAAGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.06
21 13 0.19
23 11 0.16
24 40 0.57
25 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:336951 original size:21 final size:21
Alignment explanation
Indices: 336927--336966 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
336917 CAATTTATTC
336927 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
336948 ATTGATGCATCGATGCATG
1 ATTGATGCATCGATGCATG
336967 CCTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:339951 original size:26 final size:26
Alignment explanation
Indices: 339896--339978 Score: 75
Period size: 26 Copynumber: 3.3 Consensus size: 26
339886 ATTTAACTCA
*
339896 AATTTAAAAAATTTCAAATCAAATTG
1 AATTTAAAAAATTACAAATCAAATTG
* * *
339922 AATTTAAAAAATTACGAGTCGAATAT-
1 AATTTAAAAAATTACAAATCAAAT-TG
* *
339948 AATTT-AAAATTTA-AAATAAAATT-
1 AATTTAAAAAATTACAAATCAAATTG
339971 AATTTAAA
1 AATTTAAA
339979 TTAAAATTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
23 6 0.13
24 7 0.15
25 7 0.15
26 25 0.54
27 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (26 bp):
AATTTAAAAAATTACAAATCAAATTG
Found at i:339976 original size:16 final size:16
Alignment explanation
Indices: 339955--339986 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
339945 TATAATTTAA
339955 AATTTAAAATAAAATT
1 AATTTAAAATAAAATT
*
339971 AATTTAAATTAAAATT
1 AATTTAAAATAAAATT
339987 TTCAAATGAG
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAAATAAAATT
Found at i:340200 original size:20 final size:20
Alignment explanation
Indices: 340175--340220 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
340165 CAGTTAAGTA
340175 AATATTTTATTAAAAATATT
1 AATATTTTATTAAAAATATT
*
340195 AATATTTTATTGAAAATATT
1 AATATTTTATTAAAAATATT
340215 AATATT
1 AATATT
340221 CTTTTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AATATTTTATTAAAAATATT
Found at i:340254 original size:12 final size:12
Alignment explanation
Indices: 340237--340261 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
340227 ATATTTTTAG
340237 TAAAATATTATT
1 TAAAATATTATT
340249 TAAAATATTATT
1 TAAAATATTATT
340261 T
1 T
340262 TTTTTACTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:343962 original size:17 final size:18
Alignment explanation
Indices: 343942--343975 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
343932 TAGTTATTGT
343942 AATTA-TTGTCCTATTAA
1 AATTACTTGTCCTATTAA
*
343959 AATTACTTGTCTTATTA
1 AATTACTTGTCCTATTA
343976 GTTCTGTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (18 bp):
AATTACTTGTCCTATTAA
Found at i:361758 original size:23 final size:23
Alignment explanation
Indices: 361732--361811 Score: 115
Period size: 23 Copynumber: 3.5 Consensus size: 23
361722 CTTGTATGGA
361732 ACTACGATGCAATTCTACGTGGC
1 ACTACGATGCAATTCTACGTGGC
* *
361755 ACTACGGTGCAATTCTACGCGGC
1 ACTACGATGCAATTCTACGTGGC
* *
361778 ACTACGGTGCAATTCTACGTGAC
1 ACTACGATGCAATTCTACGTGGC
*
361801 ACTTCGATGCA
1 ACTACGATGCA
361812 TTTATACGAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (23 bp):
ACTACGATGCAATTCTACGTGGC
Found at i:369074 original size:17 final size:18
Alignment explanation
Indices: 369052--369085 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
369042 TCAGCCGGTC
369052 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
369069 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
369086 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:369439 original size:26 final size:26
Alignment explanation
Indices: 369403--369454 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
369393 CATATGGGTT
369403 GAGAAGCTCAAGATTTGAAAGATAAA
1 GAGAAGCTCAAGATTTGAAAGATAAA
369429 GAGAAGCTCAAGATTTGAAAGATAAA
1 GAGAAGCTCAAGATTTGAAAGATAAA
369455 ACTATCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.19
Consensus pattern (26 bp):
GAGAAGCTCAAGATTTGAAAGATAAA
Found at i:380256 original size:359 final size:359
Alignment explanation
Indices: 379597--380315 Score: 1251
Period size: 359 Copynumber: 2.0 Consensus size: 359
379587 ATTAGGGGAG
* *
379597 AGTTGTAACTCATCAAATCCCAGGTTAGGAGTTTTAGGATAAACTGATATAGGCCTTAGATTAAT
1 AGTTGTAACTCATCAAATCCCAGGTTAGGAGTTTTAGGATAAACCGAGATAGGCCTTAGATTAAT
* *
379662 TCTCTAGCTTGTATGAAGACTTGACCCAATTTGAGGTGAATTTGGGCTTGAGTTAAGCCCAATAG
66 TCTCTAGCTTGTACGAAGACTTGACCCAATTTGAGGTGAATTTAGGCTTGAGTTAAGCCCAATAG
*
379727 AGAGTAAAAAGGGGTGTTTTCAGCTGTAGCTAAAATAAGAACGATCCAGAGTGTAATTAGATCAC
131 AGAGTAAAAAGGGGTGTTTTCAGCTGTAGCTAAAATAAGAACGACCCAGAGTGTAATTAGATCAC
* * * *
379792 TTTTCAAAATAAATGATGAATACCATTAAAATTTGGTGATCTTACGTCTGTACAAGTCCCTCTTT
196 TATTCAAAATAAATGATGAATACAATTAAAATTTGGTAATCTTACATCTGTACAAGTCCCTCTTT
379857 TTCTCCACAACTATTATCTTCTACTCTTCTCATCTCTTCAACCTATCTTTCTTTAAGCCAAACTT
261 TTCTCCACAACTATTATCTTCTACTCTTCTCATCTCTTCAACCTATCTTTCTTTAAGCCAAACTT
379922 AAAGGTAGAACCTTTAGAGATTTCAGTTGTTACC
326 AAAGGTAGAACCTTTAGAGATTTCAGTTGTTACC
* * *
379956 AGTTGTAACTCCTCAAATCCCAGGTTAGGAGTTTTAGGATAACCCGAGATAGGTCTTAGATTAAT
1 AGTTGTAACTCATCAAATCCCAGGTTAGGAGTTTTAGGATAAACCGAGATAGGCCTTAGATTAAT
*
380021 TCTCTAGCTTGTACGAAG-CTTTGACCTAATTTGAGGTGAATTTAGGCTTGAGTTAAGCCCAATA
66 TCTCTAGCTTGTACGAAGAC-TTGACCCAATTTGAGGTGAATTTAGGCTTGAGTTAAGCCCAATA
* *
380085 GAGAGTAAAAAGGGGTGTTTTCAGTTGTAGCTAAAATAAGAAGGACCCAGAGTGTAATTAGATCA
130 GAGAGTAAAAAGGGGTGTTTTCAGCTGTAGCTAAAATAAGAACGACCCAGAGTGTAATTAGATCA
*
380150 CTATTCAAAATAAATGTTGAATACAATTAAAATTTGGTAATCTTACATCTGTACAAGTCCCTCTT
195 CTATTCAAAATAAATGATGAATACAATTAAAATTTGGTAATCTTACATCTGTACAAGTCCCTCTT
* *
380215 TTTCTCCACAACTATTGTCTTCTACTCTTCTCCTCTCTTCAACCTATCTTTCTTTAAGCCAAACT
260 TTTCTCCACAACTATTATCTTCTACTCTTCTCATCTCTTCAACCTATCTTTCTTTAAGCCAAACT
*
380280 TAAAGGTAGAACCTTTATAGATTTCAGTTGTTACC
325 TAAAGGTAGAACCTTTAGAGATTTCAGTTGTTACC
380315 A
1 A
380316 AGAGAAGTTA
Statistics
Matches: 340, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
358 1 0.00
359 339 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (359 bp):
AGTTGTAACTCATCAAATCCCAGGTTAGGAGTTTTAGGATAAACCGAGATAGGCCTTAGATTAAT
TCTCTAGCTTGTACGAAGACTTGACCCAATTTGAGGTGAATTTAGGCTTGAGTTAAGCCCAATAG
AGAGTAAAAAGGGGTGTTTTCAGCTGTAGCTAAAATAAGAACGACCCAGAGTGTAATTAGATCAC
TATTCAAAATAAATGATGAATACAATTAAAATTTGGTAATCTTACATCTGTACAAGTCCCTCTTT
TTCTCCACAACTATTATCTTCTACTCTTCTCATCTCTTCAACCTATCTTTCTTTAAGCCAAACTT
AAAGGTAGAACCTTTAGAGATTTCAGTTGTTACC
Found at i:383984 original size:24 final size:23
Alignment explanation
Indices: 383939--383987 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
383929 ATGTTTTACC
*
383939 TTAAATATTATGTTGTAGTTGAT
1 TTAAATATTATGTTGTACTTGAT
383962 TTAAATCATTATGTT-TCACTTGAT
1 TTAAAT-ATTATGTTGT-ACTTGAT
383986 TT
1 TT
383988 TATGGTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (23 bp):
TTAAATATTATGTTGTACTTGAT
Found at i:396442 original size:21 final size:22
Alignment explanation
Indices: 396418--396474 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
396408 GGGGTACCGA
396418 TTCCCCT-ATGGGGGGAATCGG
1 TTCCCCTCATGGGGGGAATCGG
**
396439 TTCCCCTTCAAAGGGGGAATCGG
1 TTCCCC-TCATGGGGGGAATCGG
396462 TT-CCCTCATGGGG
1 TTCCCCTCATGGGG
396475 TATCGATTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 12 0.40
22 4 0.13
23 14 0.47
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (22 bp):
TTCCCCTCATGGGGGGAATCGG
Found at i:398633 original size:3 final size:3
Alignment explanation
Indices: 398625--398673 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
398615 TTTTTTATAT
* *
398625 TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA ATA TTT TTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT-A TTA
398672 TT
1 TT
398674 TTTTGCAGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:398646 original size:19 final size:19
Alignment explanation
Indices: 398622--398673 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
398612 TACTTTTTTA
*
398622 TATTTATTATTATTATTAT
1 TATTTATTATTATTAATAT
398641 TATTTATTATTATTAATAT
1 TATTTATTATTATTAATAT
398660 T-TTTATTAATTATT
1 TATTTATT-ATTATT
398674 TTTTGCAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTATTATTATTAATAT
Found at i:398653 original size:22 final size:22
Alignment explanation
Indices: 398625--398673 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
398615 TTTTTTATAT
* *
398625 TTATTATTATTATTATTATTTA
1 TTATTATTAATATTATTATTAA
*
398647 TTATTATTAATATTTTTATTAA
1 TTATTATTAATATTATTATTAA
398669 TTATT
1 TTATT
398674 TTTTGCAGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATTATTAATATTATTATTAA
Found at i:404053 original size:43 final size:42
Alignment explanation
Indices: 403992--404241 Score: 131
Period size: 43 Copynumber: 5.5 Consensus size: 42
403982 ATTTCCCAAT
403992 TTCAACTTCACAACGAAGGATATTGGGATCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGG-TCCAGACAACGCAAG
* *** * * * *
404035 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG--GTC--CAGACAA---CGCAAG
404086 TTCAACTTCACAACGAAGGATATTGGGCTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGG-TCCAGACAACGCAAG
* * *** * * * *
404129 TTAAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG--GTC--CAGACAA---CGCAAG
* * *
404180 TTCAACTTCACAACGAAGGATATTGGACTCCGGACAACACAAG
1 TTCAACTTCACAACGAAGGATATTGG-GTCCAGACAACGCAAG
404223 TTCAACTTCACAACGAAGG
1 TTCAACTTCACAACGAAGG
404242 GACCGCTGGT
Statistics
Matches: 151, Mismatches: 37, Indels: 38
0.67 0.16 0.17
Matches are distributed among these distances:
43 58 0.38
44 6 0.04
45 6 0.04
46 13 0.09
47 3 0.02
48 14 0.09
49 6 0.04
50 6 0.04
51 39 0.26
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (42 bp):
TTCAACTTCACAACGAAGGATATTGGGTCCAGACAACGCAAG
Found at i:404057 original size:94 final size:94
Alignment explanation
Indices: 403896--404787 Score: 1174
Period size: 94 Copynumber: 9.0 Consensus size: 94
403886 TTCAGAGTCT
* * * * *
403896 ATTTCAACTTCGCAGCGAAGGATATTGGACTCCGGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
403961 ACCGCTGGTTGTCAATAAACAATTTCCCA
66 ACCGCTGGTTGTCAATAAACAATTTCCCA
403990 ATTTCAACTTCACAACGAAGGATATTGGGA-TCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAACGAAGGATATT-GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
404054 GACCGCTGGTTGTCAATAAACAATTTCCCA
65 GACCGCTGGTTGTCAATAAACAATTTCCCA
* *
404084 ATTTCAACTTCACAACGAAGGATATTGGGCTCCAGACAACGCAAGTTAAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
404149 ACCGCTGGTTGTCAATAAACAATTTCCCA
66 ACCGCTGGTTGTCAATAAACAATTTCCCA
* * *
404178 ATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
404243 ACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAAC-A-------ATTTC----CCA
*
404284 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
404349 ACCGCTGGTTGTCAACAAACAATTTCCCGATTTTAGAGCCA
66 ACCGCTGGTTGTCAATAAACAATTT--C----------CCA
*
404390 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
404455 ACCGCTGGTTGTCAACAAAAAATTTCCCGATTTCAGAGCCA
66 ACCGCTGGTTGT---CAATAAA-----CAATTTC----CCA
* **
404496 ATTTCAACGTCACAACGAAGGATATTGGACTCCAGATGACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
404561 ACCGCTGGTTGTCAATAAACAATTTTTCGATTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAAC-A-------ATTTC----CCA
404602 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
404667 ACCGCTGGTTGTCAATAAACAATTTCCCA
66 ACCGCTGGTTGTCAATAAACAATTTCCCA
404696 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
404761 ACCGCTGGTTGTCAATAAACAATTTCC
66 ACCGCTGGTTGTCAATAAACAATTTCC
404788 TAGTTCCAGA
Statistics
Matches: 732, Mismatches: 28, Indels: 76
0.88 0.03 0.09
Matches are distributed among these distances:
93 2 0.00
94 349 0.48
95 4 0.01
98 10 0.01
100 1 0.00
102 5 0.01
103 6 0.01
105 2 0.00
106 341 0.47
109 6 0.01
112 1 0.00
114 5 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (94 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAATAAACAATTTCCCA
Found at i:404360 original size:106 final size:106
Alignment explanation
Indices: 404175--404832 Score: 1038
Period size: 106 Copynumber: 6.3 Consensus size: 106
404165 AAACAATTTC
* * *
404175 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACACAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
404240 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
*
404281 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
404346 GGGACCGCTGGTTGTCAACAAACAATTTCCCGATTTTAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
*
404387 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
404452 GGGACCGCTGGTTGTCAACAAAAAATTTCCCGATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
* **
404493 CCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGATGACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
**
404558 GGGACCGCTGGTTGTCAATAAACAATTTTTCGATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
404599 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
404664 GGGACCGCTGGTTGTCAATAAAC-A-------ATTTC----
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
404693 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
404758 GGGACCGCTGGTTGTCAATAAACAATTT-CCTAGTTCCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCGA-TTTCAGAG
**
404799 CCAATTTCAACTTCACGGC-AGAGGATATTGGACT
1 CCAATTTCAACTTCACAACGA-AGGATATTGGACT
404833 TGGAACAATA
Statistics
Matches: 517, Mismatches: 22, Indels: 26
0.92 0.04 0.05
Matches are distributed among these distances:
94 88 0.17
95 1 0.00
98 5 0.01
101 1 0.00
102 3 0.01
105 2 0.00
106 417 0.81
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
Found at i:404665 original size:43 final size:43
Alignment explanation
Indices: 404604--404759 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 43
404594 CAGAGCCAAT
404604 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
404647 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
404698 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
404741 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
404760 GACCGCTGGT
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
43 38 0.45
44 3 0.04
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 3 0.04
51 20 0.24
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:405559 original size:249 final size:248
Alignment explanation
Indices: 405013--405643 Score: 951
Period size: 249 Copynumber: 2.5 Consensus size: 248
405003 TCCAACTCAA
* *
405013 AGAAGGAG-TGTCTACCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAATGACACATCA
1 AGAAGG-GTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCA
* * ** *
405076 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAATACCCCCTAGTTCGATTACACTCAG
64 TTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAG
* * *
405141 CTTCGAGGGCATATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATTTGCAACCAAAGACCTT
129 CTTCGAGGGCACATCATTTACAGTATAACTCAAGGCGAGAAGGGTTATCTGCAACCAAAGACCTT
* * *
405206 CGAATTCGACTATGCTCAGCTTCAAGGCATATCATTTGCAGTACAACTTAAGTTT
194 CGAATTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTCT
*
405261 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCGAGGCACATCATT
1 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
405326 TGCAGTATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTTGATTACACTCAGCT
66 TGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCT
* * *
405391 TCGAGGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTC
131 TCGAGGGCACATCATTTACAGTATAACTCAAGGCGAGAAGGGTTATCTG-CAACCAAAGACCTTC
*
405456 GAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTCT
195 GAATTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTCT
* * * *
405510 ATAGGGGTTGTCTGCCAACAAAAGGCCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
405575 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCGAAGACTTTCGAGTTCGATTACACTC
66 TGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC-A---AAGACCTTCGAGTTCGATTACACTC
405640 AGCT
127 AGCT
405644 CAGAGGCAAA
Statistics
Matches: 347, Mismatches: 29, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
247 1 0.00
248 158 0.46
249 160 0.46
250 1 0.00
253 27 0.08
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (248 bp):
AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCT
TCGAGGGCACATCATTTACAGTATAACTCAAGGCGAGAAGGGTTATCTGCAACCAAAGACCTTCG
AATTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTCT
Found at i:405644 original size:84 final size:84
Alignment explanation
Indices: 405027--405644 Score: 680
Period size: 84 Copynumber: 7.4 Consensus size: 84
405017 GGAGTGTCTA
* * * * * *
405027 CCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAATGACACATCATTTGCAGCATAGCTT
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTGCAGTATAACTT
*
405091 AAGTCGAGAAGGGCTATCTG
65 AAGTCGAGAAGGGTTATCTG
* ** * * * * * * *
405111 ----CCAAATACCCCCTAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGTATAACTC
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGTATAACTT
* * *
405172 AAGGCTAGAAGGGTTATTTG
65 AAGTCGAGAAGGGTTATCTG
* * * *
405192 -CAACCAAAGACCTTCGAATTCGACTATGCTCAGCTTCAAGGCATATCATTTGCAGTACAACTTA
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTA
** *
405256 AGTTTAGAAGGGTTGTCTG
66 AGTCGAGAAGGGTTATCTG
* * * *
405275 CCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCGAGGCACATCATTTGCAGTATAACTTA
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTA
*
405340 AGTCGAGAAGGGCTATCTG
66 AGTCGAGAAGGGTTATCTG
* * * * * *
405359 ----CCAAAGACCTTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTGCAGTATAACTT
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGTATAACTT
405420 AAGTCGAGAAGGGTTATCTG
65 AAGTCGAGAAGGGTTATCTG
*
405440 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAACTTA
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTA
* * * *
405505 AGTCTATAGGGGTTGTCTG
66 AGTCGAGAAGGGTTATCTG
* * * *
405524 CCAACAAAAGGCCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTA
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTA
405589 AGTCGAGAAGGGTTATCTG
66 AGTCGAGAAGGGTTATCTG
* * * *
405608 CCAACCGAAGACTTTCGAGTTCGATTACACTCAGCTC
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
405645 AGAGGCAAAC
Statistics
Matches: 437, Mismatches: 86, Indels: 22
0.80 0.16 0.04
Matches are distributed among these distances:
80 49 0.11
81 80 0.18
82 1 0.00
83 39 0.09
84 240 0.55
85 28 0.06
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.26
Consensus pattern (84 bp):
CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTA
AGTCGAGAAGGGTTATCTG
Found at i:406405 original size:3 final size:3
Alignment explanation
Indices: 406397--406442 Score: 65
Period size: 3 Copynumber: 14.7 Consensus size: 3
406387 TTTTTTATAT
*
406397 TTA TTA TTA TTA TTA TTTA TTA TTA TTA ATA TTA TTA TTAA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT-A TTA TT
406443 TTTTGTAGGC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:406415 original size:22 final size:22
Alignment explanation
Indices: 406397--406442 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
406387 TTTTTTATAT
*
406397 TTATTATTATTATTATTTATTA
1 TTATTAATATTATTATTTATTA
*
406419 TTATTAATATTATTATTAATTA
1 TTATTAATATTATTATTTATTA
406441 TT
1 TT
406443 TTTTGTAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTAATATTATTATTTATTA
Found at i:409978 original size:22 final size:21
Alignment explanation
Indices: 409936--409975 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
409926 GAGTTTATTT
*
409936 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
409957 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
409976 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:413208 original size:57 final size:57
Alignment explanation
Indices: 413144--413257 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
413134 GCATGTCAGG
**
413144 AAGTTGAGTAAAGCTCAAGTTAAGTTAAGTTATGGTACATTCGTGTACATTATATAT
1 AAGTTGAGTAAAGCTCAAGTTAAGTTAAGTTATAATACATTCGTGTACATTATATAT
*
413201 AAGTTGAGTAAAGCTCAAGTTAGGTTAAGTTATAATACATTCGTGTACATTATATAT
1 AAGTTGAGTAAAGCTCAAGTTAAGTTAAGTTATAATACATTCGTGTACATTATATAT
413258 GGCACCGTTG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (57 bp):
AAGTTGAGTAAAGCTCAAGTTAAGTTAAGTTATAATACATTCGTGTACATTATATAT
Found at i:414982 original size:20 final size:20
Alignment explanation
Indices: 414957--415009 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
414947 TAATACAAAA
*
414957 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
414977 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
414997 TCGCAACGCGATA
1 TCGCAACGCGATA
415010 ATACATAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:415225 original size:22 final size:22
Alignment explanation
Indices: 415197--415240 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
415187 CACTCTCTCA
415197 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
415219 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
415241 TATCTCCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:416228 original size:64 final size:63
Alignment explanation
Indices: 416146--416283 Score: 170
Period size: 64 Copynumber: 2.2 Consensus size: 63
416136 TTTAAGGTGC
* * *
416146 ATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTATGA
1 ATCGATGCATAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTATGA
* * * *
416210 ATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGC
1 ATCGATGCATAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTATGA
*
416274 ATCAATGCAT
1 ATCGATGCAT
416284 GGTGTAGTGC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 56 0.88
65 7 0.11
66 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (63 bp):
ATCGATGCATAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTATGA
Found at i:417877 original size:149 final size:147
Alignment explanation
Indices: 417609--417910 Score: 568
Period size: 149 Copynumber: 2.0 Consensus size: 147
417599 GAGTCGAGGG
417609 TTCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
1 TTCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
*
417674 CTTGATCCCTAGTATATGTATATTATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
*
417739 ATGGCACTATGGTGCAA
131 ATGGCACTACGGTGCAA
417756 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
1 TTCTACGCGGTCCTTCGGG--ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
417821 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
64 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
417886 ATATGGCACTACGGTGCAA
129 ATATGGCACTACGGTGCAA
417905 TTCTAC
1 TTCTAC
417911 ATGGCACTTC
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
147 19 0.13
149 132 0.87
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (147 bp):
TTCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAA
Found at i:421262 original size:64 final size:63
Alignment explanation
Indices: 421177--421317 Score: 185
Period size: 64 Copynumber: 2.2 Consensus size: 63
421167 TTATTTAAGG
* *
421177 TGCATCGATGCACATGCAGTGCATCGATGCAT-AAATTTAAATAGAAAACATCAAATAGGATTTA
1 TGCATCGATGCATAAGCAGTGCATCGATGCATCAAA-TTAAATA-AAAACATCAAATAGGATTTA
* ** * *
421241 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGCAGTGCATCGATGCAT-CAAATTAAATAAAAACATCAAATAGGATTTA
421305 TGCATCGATGCAT
1 TGCATCGATGCAT
421318 GGTGTAGTGC
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 60 0.88
65 7 0.10
66 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGCAGTGCATCGATGCATCAAATTAAATAAAAACATCAAATAGGATTTA
Found at i:421686 original size:18 final size:18
Alignment explanation
Indices: 421652--421686 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
421642 AAATGGGTAT
* *
421652 ATATGTTATATGTATTGC
1 ATATGTTACATGAATTGC
421670 ATATGTTACATGAATTG
1 ATATGTTACATGAATTG
421687 AATGAATATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (18 bp):
ATATGTTACATGAATTGC
Found at i:422981 original size:149 final size:149
Alignment explanation
Indices: 422666--422970 Score: 592
Period size: 149 Copynumber: 2.0 Consensus size: 149
422656 GAGTCGAGGG
422666 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
1 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
*
422731 TACTTGATCCCTAATATATGTATATTATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
422796 ATATGGCACTACGGTGCAA
131 ATATGGCACTACGGTGCAA
422815 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
1 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
*
422880 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
422945 ATATGGCACTACGGTGCAA
131 ATATGGCACTACGGTGCAA
422964 TTCTACG
1 TTCTACG
422971 TGGCACTTCG
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (149 bp):
TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
ATATGGCACTACGGTGCAA
Found at i:422982 original size:23 final size:23
Alignment explanation
Indices: 422948--422993 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
422938 CATTATTATA
*
422948 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
422971 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
422994 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:423842 original size:20 final size:20
Alignment explanation
Indices: 423789--423846 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
423779 CGATTCTCTC
**
423789 GTTGCGATAGTCAAATTCGT
1 GTTGCGATAGTCATTTTCGT
423809 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
423829 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
423847 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.45
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:424036 original size:25 final size:24
Alignment explanation
Indices: 423982--424036 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
423972 TGTTTATTAT
* *
423982 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
424006 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
424032 TGTTT
1 TGTTT
424037 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:425184 original size:18 final size:18
Alignment explanation
Indices: 425163--425207 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
425153 TCCACTTCGG
*
425163 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
425181 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
425199 GAGCCATCA
1 GAGCCATCA
425208 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:425714 original size:20 final size:20
Alignment explanation
Indices: 425689--425734 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
425679 TAGTTTACTT
425689 TCGCAACAC-GAAACTGACTA
1 TCGCAACACGGAAA-TGACTA
* *
425709 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTA
425729 TCGCAA
1 TCGCAA
425735 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGGAAATGACTA
Found at i:425743 original size:19 final size:20
Alignment explanation
Indices: 425706--425743 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
425696 ACGAAACTGA
425706 CTATCGCAACGCGGAAATGG
1 CTATCGCAACGCGGAAATGG
*
425726 CTATCGCAATGC-GAAATG
1 CTATCGCAACGCGGAAATG
425744 AAAATCGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGGAAATGG
Found at i:425763 original size:14 final size:14
Alignment explanation
Indices: 425744--425801 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
425734 ATGCGAAATG
425744 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
425758 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
425774 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
425790 AAAATCGCAACG
1 AAAATCGCAACG
425802 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:425770 original size:33 final size:33
Alignment explanation
Indices: 425728--425818 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
425718 GGAAATGGCT
425728 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
425761 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
425793 ATCGCAACGCGAAATGAAAATTGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
425819 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:425905 original size:33 final size:32
Alignment explanation
Indices: 425842--425905 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
425832 TCGCGTTGTG
*
425842 ATTTTGTCGTTGCGATTTCATTTCTAATTGCA
1 ATTTTGTCGTTGCGATTTCATTTCGAATTGCA
*
425874 ATTTTGTCGTTGCGATTTTCATTTCGCATTGC
1 ATTTTGTCGTTGCGA-TTTCATTTCGAATTGC
425906 GATAGCCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.16, C:0.17, G:0.17, T:0.50
Consensus pattern (32 bp):
ATTTTGTCGTTGCGATTTCATTTCGAATTGCA
Found at i:425927 original size:20 final size:19
Alignment explanation
Indices: 425893--425948 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
425883 TTGCGATTTT
*
425893 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
425912 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
425932 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
425949 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:426407 original size:42 final size:42
Alignment explanation
Indices: 426310--426398 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
426300 GACTCACCTG
* * *
426310 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
* * *
426352 TCCTCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
426394 TCATC
1 TCATC
426399 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.44, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
Found at i:427827 original size:14 final size:14
Alignment explanation
Indices: 427808--427843 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
427798 ATTGTTTAAT
427808 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
427822 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
427836 TGATTTGT
1 TGATTTGT
427844 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:428004 original size:19 final size:19
Alignment explanation
Indices: 427980--428047 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
427970 ATCGCAACGA
427980 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
427999 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
428018 GAAAATTGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
428032 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
428048 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 2 0.05
17 2 0.05
19 29 0.66
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:428137 original size:20 final size:19
Alignment explanation
Indices: 428074--428140 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
428064 CGATTTTCTA
*
428074 GTTGTGATACCATTTTCGC
1 GTTGCGATACCATTTTCGC
** *
428093 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA--TACCATTTTCGC
*
428113 ATTGCGATAGCCATTTTCGC
1 GTTGCGATA-CCATTTTCGC
428133 GTTGCGAT
1 GTTGCGAT
428141 TTCCCCGTTG
Statistics
Matches: 35, Mismatches: 9, Indels: 7
0.69 0.18 0.14
Matches are distributed among these distances:
18 1 0.03
19 8 0.23
20 23 0.66
21 3 0.09
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.42
Consensus pattern (19 bp):
GTTGCGATACCATTTTCGC
Found at i:429498 original size:12 final size:12
Alignment explanation
Indices: 429481--429505 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
429471 ATATAATCCT
429481 GAAGAAGAAAAA
1 GAAGAAGAAAAA
429493 GAAGAAGAAAAA
1 GAAGAAGAAAAA
429505 G
1 G
429506 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:431814 original size:19 final size:19
Alignment explanation
Indices: 431792--431850 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
431782 GGAAATTACT
431792 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
431811 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
431825 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
431844 ATCGCAA
1 ATCGCAA
431851 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:433527 original size:42 final size:42
Alignment explanation
Indices: 433429--433606 Score: 203
Period size: 42 Copynumber: 4.2 Consensus size: 42
433419 CCTCTTCAAC
* * * *
433429 GATGACAGTGGCCTCTTGAACGGGTGGGAGGGGACTCTCGAGG
1 GATGACAGGGGCCTCTTCAAC-GATAGGAGGGGACTCTCGAGG
* * * *
433472 AATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGG
1 GATGACAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
* * * *
433514 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGG
1 GATGACAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
* * * *
433556 AATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGG
1 GATGACAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
433598 GATGACAGG
1 GATGACAGG
433607 CGAGTCGGGC
Statistics
Matches: 109, Mismatches: 26, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
42 92 0.84
43 17 0.16
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
Found at i:433550 original size:21 final size:21
Alignment explanation
Indices: 433399--433550 Score: 51
Period size: 21 Copynumber: 7.2 Consensus size: 21
433389 GTGAATCGGG
*
433399 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
433419 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
433441 CTCTTGAACGGGTGGGAGGGGA
1 CTCTTGAAC-GGTGGGAGGGGA
* ** *
433463 CTCTCG-A-GGAATGATAGGGGC
1 CTCTTGAACGG--TGGGAGGGGA
* * * *
433484 CTCTTCAACGATAGGAGTGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** * *
433505 CTCTTG-AGGGATGACAGTGGC
1 CTCTTGAACGG-TGGGAGGGGA
433526 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
433547 CTCT
1 CTCT
433551 CGAGGAATGA
Statistics
Matches: 86, Mismatches: 37, Indels: 16
0.62 0.27 0.12
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 63 0.73
22 18 0.21
23 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:433567 original size:84 final size:85
Alignment explanation
Indices: 433429--433605 Score: 347
Period size: 84 Copynumber: 2.1 Consensus size: 85
433419 CCTCTTCAAC
433429 GATGACAGTGGCCTCTTGAACGGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACG
1 GATGACAGTGGCCTCTTGAACGGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACG
433494 ATAGGAGTGGACTCTTGAGG
66 ATAGGAGTGGACTCTTGAGG
433514 GATGACAGTGGCCTCTTGAAC-GGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACG
1 GATGACAGTGGCCTCTTGAACGGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACG
433578 ATAGGAGTGGACTCTTGAGG
66 ATAGGAGTGGACTCTTGAGG
433598 GATGACAG
1 GATGACAG
433606 GCGAGTCGGG
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 71 0.77
85 21 0.23
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (85 bp):
GATGACAGTGGCCTCTTGAACGGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACG
ATAGGAGTGGACTCTTGAGG
Found at i:433998 original size:91 final size:89
Alignment explanation
Indices: 433824--434007 Score: 280
Period size: 91 Copynumber: 2.0 Consensus size: 89
433814 ATTTCAAACT
*
433824 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATGTT--A-AATAAACAGTTTAGC
433889 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAAT-AATTTAC
*
433917 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAATGTTAAATAAACAGTTTAGCA
*
433981 GTATTGGCAGCAACCGAATAATTTAC
64 GAATTGGCAGCAACCGAATAATTTAC
434007 T
1 T
434008 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
90 8 0.09
91 33 0.38
93 19 0.22
95 26 0.30
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (89 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAATTTAC
Found at i:435704 original size:20 final size:19
Alignment explanation
Indices: 435673--435794 Score: 75
Period size: 20 Copynumber: 6.8 Consensus size: 19
435663 TCTTTTGGTT
435673 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
435692 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
435713 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
435732 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
435746 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
435765 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
435779 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
435795 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
14 19 0.24
16 4 0.05
17 4 0.05
19 20 0.26
20 29 0.37
21 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:435755 original size:33 final size:33
Alignment explanation
Indices: 435698--435794 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
435688 ACGAGATAAT
435698 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
435732 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
435765 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
435795 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:435822 original size:19 final size:19
Alignment explanation
Indices: 435795--435860 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 19
435785 AAAATCGCAA
**
435795 TGCGATTTTGGTTTCGCG-
1 TGCGATTTTTATTTCGCGT
435813 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
435832 TGCGATAGTAATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
435852 TGCGATTTT
1 TGCGATTTT
435861 CATTCTCGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.41
19 11 0.28
20 12 0.31
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:436419 original size:20 final size:20
Alignment explanation
Indices: 436394--436447 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
436384 GATTTTGTAT
436394 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
436414 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
436434 TATCGCATTGCGAT
1 TATCGCATTGCGAT
436448 TTTCTCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:436480 original size:20 final size:21
Alignment explanation
Indices: 436436--436487 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
436426 ATAGTCAGTA
*
436436 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACTCAAT
* *
436457 TCGCGTTGCGATTTACT-TAT
1 TCGCATTGCGATTTACTCAAT
436477 TCGCATTGCGA
1 TCGCATTGCGA
436488 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTACTCAAT
Found at i:436558 original size:21 final size:21
Alignment explanation
Indices: 436518--436558 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
436508 ACTGTAGATC
**
436518 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
436539 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
436559 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:437707 original size:2 final size:2
Alignment explanation
Indices: 437700--437741 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
437690 TATTTGTTTG
437700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
437742 TATTAGCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:441607 original size:12 final size:12
Alignment explanation
Indices: 441590--441620 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
441580 TATAGTCATC
441590 AAAATTTTTGAG
1 AAAATTTTTGAG
441602 AAAATTTTTGAG
1 AAAATTTTTGAG
441614 AAAATTT
1 AAAATTT
441621 GTTTTTGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (12 bp):
AAAATTTTTGAG
Found at i:447260 original size:166 final size:170
Alignment explanation
Indices: 446986--447318 Score: 606
Period size: 166 Copynumber: 2.0 Consensus size: 170
446976 AAATTAAATC
446986 TCGAAACAAAACTGACTTCTGTGAACAGTGAGAATTTAATAAAACCGAGAACAGTAGTATAATCT
1 TCGAAACAAAACTGACTTCTGTGAACAGTGAGAATTTAATAAAACCGAGAACAGTAGTATAATCT
447051 CAATGTATAAATATTAACAAGAAATATTGAATGGCACACATACC-TTTTGATTTC-TGATT-ATA
66 CAATGTATAAATATTAACAAGAAATATTGAATGGCACACATACCTTTTTGATTTCTTGATTAATA
447113 TTATAAATTCGTTGCCAACC-ATCTCGAACCATCAATGTG
131 TTATAAATTCGTTGCCAACCAATCTCGAACCATCAATGTG
447152 TCGAAACAAAACTGACTTCTGTGAACAGTGAGAATTTAATAAAACCGAGAACAGTAGTATAATCT
1 TCGAAACAAAACTGACTTCTGTGAACAGTGAGAATTTAATAAAACCGAGAACAGTAGTATAATCT
447217 CAATGTAT-AA-ATTATACAAGAAATATTGAATGGTCACACATACCTTTTTGATTTCTTGATTAA
66 CAATGTATAAATATTA-ACAAGAAATATTGAATGG-CACACATACCTTTTTGATTTCTTGATTAA
447280 TATTATAAATTCGTTGCCAACCAATCTCGAACCATCAAT
129 TATTATAAATTCGTTGCCAACCAATCTCGAACCATCAAT
447319 ATGTGGGTTC
Statistics
Matches: 161, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
164 4 0.02
165 20 0.12
166 83 0.52
167 10 0.06
168 5 0.03
169 23 0.14
170 16 0.10
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (170 bp):
TCGAAACAAAACTGACTTCTGTGAACAGTGAGAATTTAATAAAACCGAGAACAGTAGTATAATCT
CAATGTATAAATATTAACAAGAAATATTGAATGGCACACATACCTTTTTGATTTCTTGATTAATA
TTATAAATTCGTTGCCAACCAATCTCGAACCATCAATGTG
Found at i:448235 original size:36 final size:36
Alignment explanation
Indices: 448184--448319 Score: 159
Period size: 36 Copynumber: 3.8 Consensus size: 36
448174 GCAACACCTT
448184 CTTCCGTTC-ATCTTGAATCAAAAGTGCCGATGCTTC
1 CTTCCGTTCGA-CTTGAATCAAAAGTGCCGATGCTTC
* *
448220 TTTCCGTTCGACTTGAAT-AGGAAGTGCCGATGCTTC
1 CTTCCGTTCGACTTGAATCA-AAAGTGCCGATGCTTC
* ** * *
448256 CTTCCGTTCGACTTGAATCGAAAGTGATGTTGTTTC
1 CTTCCGTTCGACTTGAATCAAAAGTGCCGATGCTTC
**
448292 CTTCCGTTCGACTTGAATCGGAAGTGCC
1 CTTCCGTTCGACTTGAATCAAAAGTGCC
448320 TATGAAATCA
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
35 1 0.01
36 83 0.98
37 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (36 bp):
CTTCCGTTCGACTTGAATCAAAAGTGCCGATGCTTC
Found at i:448280 original size:72 final size:72
Alignment explanation
Indices: 448184--448319 Score: 193
Period size: 72 Copynumber: 1.9 Consensus size: 72
448174 GCAACACCTT
* *
448184 CTTCCGTTCATCTTGAATCAAAAGTGCCGATGCTTCTTTCCGTTCGACTTGAATAGGAAGTGCCG
1 CTTCCGTTCATCTTGAATCAAAAGTGACGATGCTTCCTTCCGTTCGACTTGAATAGGAAGTGCCG
448249 ATGCTTC
66 ATGCTTC
* * * * *
448256 CTTCCGTTCGA-CTTGAATCGAAAGTGATGTTGTTTCCTTCCGTTCGACTTGAATCGGAAGTGCC
1 CTTCCGTTC-ATCTTGAATCAAAAGTGACGATGCTTCCTTCCGTTCGACTTGAATAGGAAGTGCC
448320 TATGAAATCA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 55 0.98
73 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (72 bp):
CTTCCGTTCATCTTGAATCAAAAGTGACGATGCTTCCTTCCGTTCGACTTGAATAGGAAGTGCCG
ATGCTTC
Found at i:449565 original size:32 final size:32
Alignment explanation
Indices: 449529--449593 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
449519 TACATCAGCT
449529 GGCATTATGTACACACTTGCACAGCTAACAAA
1 GGCATTATGTACACACTTGCACAGCTAACAAA
449561 GGCATTATGTACACACTTGCACAGCTAACAAA
1 GGCATTATGTACACACTTGCACAGCTAACAAA
449593 G
1 G
449594 CTGTCTGCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (32 bp):
GGCATTATGTACACACTTGCACAGCTAACAAA
Found at i:450621 original size:13 final size:13
Alignment explanation
Indices: 450600--450629 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
450590 ACTTTGTGAA
*
450600 TTGTGTCTCAAAG
1 TTGTCTCTCAAAG
450613 TTGTCTCTCAAAG
1 TTGTCTCTCAAAG
450626 TTGT
1 TTGT
450630 TTCTAAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (13 bp):
TTGTCTCTCAAAG
Found at i:455391 original size:21 final size:21
Alignment explanation
Indices: 455328--455379 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
455318 GCAAACATAA
455328 TGAAGTTAAACAAAACGAAAG
1 TGAAGTTAAACAAAACGAAAG
455349 TGAAGTTAAACAAAACGAAAG
1 TGAAGTTAAACAAAACGAAAG
455370 TGAAGTTAAA
1 TGAAGTTAAA
455380 AATACTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.17
Consensus pattern (21 bp):
TGAAGTTAAACAAAACGAAAG
Found at i:457129 original size:14 final size:14
Alignment explanation
Indices: 457107--457150 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
457097 AAATTAATTA
457107 AAATT-TTTAAAAT
1 AAATTATTTAAAAT
457120 AAATTATTTAAAAT
1 AAATTATTTAAAAT
457134 AAATTATTTAAAAT
1 AAATTATTTAAAAT
457148 AAA
1 AAA
457151 GGGTAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 5 0.17
14 25 0.83
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTATTTAAAAT
Found at i:458036 original size:24 final size:24
Alignment explanation
Indices: 458005--458050 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
457995 ACGTTCGGTA
*
458005 TTATCTTCGTTTATATTCGTTAGT
1 TTATCTTCATTTATATTCGTTAGT
*
458029 TTATCTTCATTTATGTTCGTTA
1 TTATCTTCATTTATATTCGTTA
458051 ATATTTTAAA
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:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (24 bp):
TTATCTTCATTTATATTCGTTAGT
Found at i:458339 original size:23 final size:22
Alignment explanation
Indices: 458309--458415 Score: 80
Period size: 23 Copynumber: 4.7 Consensus size: 22
458299 GTAAAATAAA
458309 TTCATTTATGCTCGTTTGTTTTG
1 TTCATTTATG-TCGTTTGTTTTG
* *
458332 TTCATTTATGTTCGTTT-ATGTG
1 TTCATTTATG-TCGTTTGTTTTG
458354 ATT-ATTGT-TGT--TTTAGTTTATG
1 -TTCATT-TATGTCGTTT-GTTT-TG
*
458376 TTCATTTATGTCCATTTGTTTTG
1 TTCATTTATGT-CGTTTGTTTTG
458399 TTCATTTATGTTCGTTT
1 TTCATTTATG-TCGTTT
458416 ACATTCGTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
19 3 0.04
21 5 0.07
22 16 0.24
23 35 0.52
24 5 0.07
25 3 0.04
ACGTcount: A:0.13, C:0.09, G:0.16, T:0.62
Consensus pattern (22 bp):
TTCATTTATGTCGTTTGTTTTG
Found at i:461070 original size:20 final size:20
Alignment explanation
Indices: 461045--461089 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
461035 AGGTAAGAGA
461045 AGTATCGATACTCTTTAGGT
1 AGTATCGATACTCTTTAGGT
461065 AGTATCGATACTCTTTAGGT
1 AGTATCGATACTCTTTAGGT
461085 AGTAT
1 AGTAT
461090 TGTTGAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (20 bp):
AGTATCGATACTCTTTAGGT
Found at i:467016 original size:38 final size:38
Alignment explanation
Indices: 466974--467050 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
466964 AAATGAAAAA
466974 TGCTTATAATAGTAATTTTTGATTGCATTCATTGCTAT
1 TGCTTATAATAGTAATTTTTGATTGCATTCATTGCTAT
467012 TGCTTATAATAGTAATTTTTGATTGCATTCATTGCTAT
1 TGCTTATAATAGTAATTTTTGATTGCATTCATTGCTAT
467050 T
1 T
467051 AGTTAGTGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (38 bp):
TGCTTATAATAGTAATTTTTGATTGCATTCATTGCTAT
Found at i:467280 original size:23 final size:21
Alignment explanation
Indices: 467227--467288 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
467217 TTTTGGTGTA
*
467227 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
467247 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
467268 GAAGAGGAACCGATTCCCCCC
1 G-AG-GGAACCGATTCCCCCC
467289 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 2 0.06
23 15 0.42
ACGTcount: A:0.23, C:0.35, G:0.24, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:470429 original size:18 final size:18
Alignment explanation
Indices: 470405--470453 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
470395 AATACAAAAT
470405 AGGTACCGATACTCAAAG
1 AGGTACCGATACTCAAAG
*
470423 GGGTACCGATACTCAAAG
1 AGGTACCGATACTCAAAG
*
470441 AGGTATCGATACT
1 AGGTACCGATACT
470454 ACTCTACACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.20
Consensus pattern (18 bp):
AGGTACCGATACTCAAAG
Found at i:470477 original size:21 final size:24
Alignment explanation
Indices: 470442--470500 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
470432 TACTCAAAGA
*
470442 GGTATCGATACTACTCTACACAGT
1 GGTATCAATACTACTCTACACAGT
470466 GGTATCAATACTACTCTACACAGT
1 GGTATCAATACTACTCTACACAGT
470490 GGTATCAATAC
1 GGTATCAATAC
470501 CATGATCATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (24 bp):
GGTATCAATACTACTCTACACAGT
Found at i:471761 original size:20 final size:20
Alignment explanation
Indices: 471728--471775 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
471718 AATGATTTTC
* *
471728 TTTTG-AAAGAAAAATTAGA
1 TTTTGAAAAGAAAAATGAAA
*
471747 TTTTGAAAAGTAAAATGAAA
1 TTTTGAAAAGAAAAATGAAA
471767 TTTTGAAAA
1 TTTTGAAAA
471776 ATGATTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (20 bp):
TTTTGAAAAGAAAAATGAAA
Found at i:494702 original size:21 final size:21
Alignment explanation
Indices: 494673--494725 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
494663 ATTCTGACTA
494673 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
494694 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
494715 TCGCAATGCGA
1 TCGCATTGCGA
494726 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:494740 original size:20 final size:20
Alignment explanation
Indices: 494715--494848 Score: 196
Period size: 20 Copynumber: 6.7 Consensus size: 20
494705 TTTTCCTAAT
494715 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
494735 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
494756 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
494776 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
494796 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
494816 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
494836 TCGCAACGCGAAT
1 TCGCAATGCGAAT
494849 CTAACTATCA
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 85 0.85
21 15 0.15
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:494862 original size:20 final size:20
Alignment explanation
Indices: 494839--494877 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
494829 ACGTAAATCG
*
494839 CAACGCGAATCTAACTATCA
1 CAACGAGAATCTAACTATCA
* *
494859 CAACGAGATTCTGACTATC
1 CAACGAGAATCTAACTATC
494878 GCAATACTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (20 bp):
CAACGAGAATCTAACTATCA
Found at i:498204 original size:20 final size:20
Alignment explanation
Indices: 498179--498272 Score: 102
Period size: 20 Copynumber: 4.7 Consensus size: 20
498169 GACATTCATT
*
498179 TGACTATCACAACGC-AAATA
1 TGACTATCGCAACGCGAAA-A
* *
498199 TGACTATCGTAACAC-AGAAA
1 TGACTATCGCAACGCGA-AAA
* *
498219 TGACTATCGCAACGCGGAAT
1 TGACTATCGCAACGCGAAAA
*
498239 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGAAAA
498259 TGACTATCGCAACG
1 TGACTATCGCAACG
498273 AGAGAATCGC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGAAAA
Found at i:498243 original size:40 final size:40
Alignment explanation
Indices: 498179--498272 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
498169 GACATTCATT
* *
498179 TGACTATCACAACGCAAATATGACTATCGTAACACAGAAA
1 TGACTATCGCAACGCAAATATGACTATCGCAACACAGAAA
* * *
498219 TGACTATCGCAACGCGGAAT-TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGC-AAATATGACTATCGCAACACAGAAA
498259 TGACTATCGCAACG
1 TGACTATCGCAACG
498273 AGAGAATCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 45 0.94
41 3 0.06
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (40 bp):
TGACTATCGCAACGCAAATATGACTATCGCAACACAGAAA
Found at i:498294 original size:33 final size:33
Alignment explanation
Indices: 498244--498372 Score: 204
Period size: 33 Copynumber: 3.8 Consensus size: 33
498234 GGAATTGACT
* ** *
498244 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGTGA
498278 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
498311 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
498344 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
498373 CGAATTTAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
33 64 0.71
34 26 0.29
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
Found at i:498574 original size:14 final size:14
Alignment explanation
Indices: 498555--498591 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
498545 CATCAATTAA
498555 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
498569 ACAAATCATCTTTT
1 ACAAATCAACATTT
498583 ACAAATCAA
1 ACAAATCAA
498592 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:500056 original size:24 final size:24
Alignment explanation
Indices: 499996--500057 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 24
499986 CGATGAAAGT
* *
499996 GGCCTCTTGAACGGTGGGAGGGGA
1 GGCCTCTTGAACGATGAGAGGGGA
** *
500020 ---CTCTTGAGGGATGATAGGGGA
1 GGCCTCTTGAACGATGAGAGGGGA
500041 GGCCTCTTGAACGATGA
1 GGCCTCTTGAACGATGA
500058 CAAAGTGAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
21 16 0.57
24 12 0.43
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21
Consensus pattern (24 bp):
GGCCTCTTGAACGATGAGAGGGGA
Found at i:500562 original size:20 final size:20
Alignment explanation
Indices: 500539--500645 Score: 151
Period size: 20 Copynumber: 5.3 Consensus size: 20
500529 GAAACTTAAA
*
500539 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
500559 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
500579 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* **
500599 ATCGCAATACGAATTTGACT
1 ATCGCAATGCGAAAATGACT
* **
500619 ATCACAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
500639 ATCGCAA
1 ATCGCAA
500646 CGAGAGAATT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:500717 original size:20 final size:20
Alignment explanation
Indices: 500692--500888 Score: 197
Period size: 20 Copynumber: 10.5 Consensus size: 20
500682 AATTCTTTCG
** *
500692 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCATTTTCGCA
500712 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
500732 TTACGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
500752 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
500772 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
500792 TTGCGAT--T--TTATT-G--
1 TTGCGATAGTCATT-TTCGCA
**
500806 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
500825 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
* *
500839 TTGTGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
500859 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
500879 TTGCGATAGT
1 TTGCGATAGT
500889 AAACTATTCT
Statistics
Matches: 152, Mismatches: 11, Indels: 28
0.80 0.06 0.15
Matches are distributed among these distances:
14 13 0.09
16 12 0.08
17 6 0.04
18 5 0.03
19 7 0.05
20 109 0.72
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:500810 original size:34 final size:34
Alignment explanation
Indices: 500735--500865 Score: 120
Period size: 33 Copynumber: 3.7 Consensus size: 34
500725 TTTCGCATTA
* *
500735 CGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCGTTGCGAT--TC--TATCG--TTG
* *
500775 CGATAGTCATTTTCGCGTTGCGATTTTATTGTTG
1 CGATAGTCATTTTCGCGTTGCGATTCTATCGTTG
** * *
500809 CGATTTTCA-TTTCGCATTGCGATTCTCTCGTTG
1 CGATAGTCATTTTCGCGTTGCGATTCTATCGTTG
*
500842 TGATAGTCATTTTCGCGTTGCGAT
1 CGATAGTCATTTTCGCGTTGCGAT
500866 AGTCATTTTC
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
33 26 0.34
34 23 0.30
36 3 0.04
38 1 0.01
40 23 0.30
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (34 bp):
CGATAGTCATTTTCGCGTTGCGATTCTATCGTTG
Found at i:502741 original size:20 final size:20
Alignment explanation
Indices: 502718--502807 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
502708 TCTGAAACTT
502718 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
502738 AAAATCGCAACACAAAAATG
1 AAAATCGCAACACGAAAATG
** * **
502758 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
502778 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
502797 AAAATTGCAAC
1 AAAATCGCAAC
502808 GACAGAATCG
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
19 11 0.19
20 47 0.81
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:503406 original size:20 final size:20
Alignment explanation
Indices: 503383--503496 Score: 165
Period size: 20 Copynumber: 5.7 Consensus size: 20
503373 CGATAGTCAG
*
503383 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
503403 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
503423 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
503443 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
503464 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
503484 ATTCGCATTGCGA
1 ATTCGCATTGCGA
503497 ATTAGGAAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 67 0.82
21 15 0.18
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:503517 original size:21 final size:21
Alignment explanation
Indices: 503493--503538 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
503483 TATTCGCATT
*
503493 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCACAAC
* *
503514 GCGAATTTGGAAAATCACAAT
1 GCGAATTAGGAAAATCACAAC
503535 GCGA
1 GCGA
503539 TAGCCAGAAT
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:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCACAAC
Found at i:504717 original size:26 final size:25
Alignment explanation
Indices: 504683--504748 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
504673 TAGAGTAATT
*
504683 AAATTAAACTTCAATTAAATTAAAA
1 AAATAAAACTTCAATTAAATTAAAA
* **
504708 ATATAAAAACATT-TTTTAAATTAAAA
1 AAAT-AAAAC-TTCAATTAAATTAAAA
*
504734 AAATTAAACTTCAAT
1 AAATAAAACTTCAAT
504749 GACCAACAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
24 2 0.07
25 8 0.27
26 18 0.60
27 2 0.07
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (25 bp):
AAATAAAACTTCAATTAAATTAAAA
Found at i:505108 original size:5 final size:5
Alignment explanation
Indices: 505098--505141 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
505088 GTCCGTCCGT
* * *
505098 CTCGG CTCGG CTCGG CACGG CACGG CTCGG CTCGG TTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
505142 TGGTTGTGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.05, C:0.39, G:0.39, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:511042 original size:6 final size:6
Alignment explanation
Indices: 511031--511060 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
511021 TCGGCTCGGC
511031 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
511061 ATGGTAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:511366 original size:22 final size:22
Alignment explanation
Indices: 511341--511395 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
511331 TCAGGAGTTA
* *
511341 CATGAGTTATTTGATTTAATTC
1 CATGAGTTATATGATATAATTC
* * *
511363 CATGGGTTACATGATATAATTT
1 CATGAGTTATATGATATAATTC
*
511385 CAGGAGTTATA
1 CATGAGTTATA
511396 ACAGTTGAAC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (22 bp):
CATGAGTTATATGATATAATTC
Found at i:512044 original size:21 final size:21
Alignment explanation
Indices: 512018--512132 Score: 90
Period size: 21 Copynumber: 5.5 Consensus size: 21
512008 GTTTCCAGAT
*
512018 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGAATTTGGACTA
* * *
512039 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAATTTGGACTA
* * * *
512059 TCGCAATGCGATAGTCGAAGT-
1 TCGCAATGCGA-ATTTGGACTA
* *
512080 TCGCAATGCAAACTTGGACTA
1 TCGCAATGCGAATTTGGACTA
* *
512101 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAATTTGGACTA
*
512122 TCGCATTGCGA
1 TCGCAATGCGA
512133 TTTACATATT
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
20 17 0.23
21 57 0.77
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGACTA
Found at i:512295 original size:12 final size:11
Alignment explanation
Indices: 512278--512313 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
512268 GACACGTATT
512278 ACCACGACCACG
1 ACCACGACC-CG
512290 ACCACGACCCG
1 ACCACGACCCG
512301 ACC-CGACCCG
1 ACCACGACCCG
512311 ACC
1 ACC
512314 CGAGACGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.28, C:0.56, G:0.17, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:512304 original size:5 final size:5
Alignment explanation
Indices: 512282--512316 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
512272 CGTATTACCA
512282 CGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
512317 GACGAGACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.26, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:512814 original size:5 final size:5
Alignment explanation
Indices: 512800--512830 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
512790 CCGCCGCCGC
512800 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
512831 GGTCGTGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:512979 original size:20 final size:20
Alignment explanation
Indices: 512954--513026 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
512944 ATTTTGGACT
512954 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
512974 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
512995 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
513015 ATCGCAATGCGA
1 ATCGCAATGCGA
513027 TAGTCGAAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
19 3 0.07
20 24 0.52
21 12 0.26
22 3 0.07
23 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:512985 original size:41 final size:41
Alignment explanation
Indices: 512950--513089 Score: 169
Period size: 41 Copynumber: 3.4 Consensus size: 41
512940 TGCGATTTTG
512950 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
512991 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
* * * * *
513032 GAAGT-TCGCATTGCG-ATA-GTCCAAGTTCGCATTACGATAGTC
1 G-ACTATCGCAATGCGAATATGT--AA-ATCGCAATGCGATAGTC
*
513074 GACTATCGCATTGCGA
1 GACTATCGCAATGCGA
513090 TTTACATATT
Statistics
Matches: 87, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 55 0.63
42 27 0.31
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (41 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
Found at i:513000 original size:21 final size:21
Alignment explanation
Indices: 512974--513172 Score: 146
Period size: 21 Copynumber: 9.6 Consensus size: 21
512964 GAATATGTAA
*
512974 ATCGCAATGCGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
* *
512995 ATCGCAATGCGAATA-T-GTA-A
1 ATCGCATTGCG-ATAGTCG-ACT
* *
513015 ATCGCAATGCGATAGTCGAAGT
1 ATCGCATTGCGATAGTCG-ACT
* *
513037 -TCGCATTGCGATAGTCCAAGT
1 ATCGCATTGCGATAGT-CGACT
*
513058 -TCGCATTACGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
*
513078 ATCGCATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
* *
513097 ATTCGCATTGCGATAGTCCAAGT
1 A-TCGCATTGCGATAGT-CGACT
513120 -TCGCATTGCGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
* **
513140 ATCGCATTGCGATAGTCCAAA
1 ATCGCATTGCGATAGTCGACT
513161 ATCGCATTGCGA
1 ATCGCATTGCGA
513173 ATCTGGAAAC
Statistics
Matches: 147, Mismatches: 17, Indels: 28
0.77 0.09 0.15
Matches are distributed among these distances:
18 2 0.01
19 6 0.04
20 31 0.21
21 101 0.69
22 5 0.03
23 1 0.01
24 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (21 bp):
ATCGCATTGCGATAGTCGACT
Found at i:513062 original size:62 final size:62
Alignment explanation
Indices: 512996--513172 Score: 159
Period size: 62 Copynumber: 2.8 Consensus size: 62
512986 TAGTCGACTA
*
512996 TCGCAATGCGAATATGT-A-AATCGCAATGCGATAGT-CGA-AGTTCGCATTGCGATAGTCCAAG
1 TCGCATTGCGAATA-GTCACAATCGCAATGCGAT-GTAC-ATA-TTCGCATTGCGATAGTCCAAG
513057 T
62 T
* * * *
513058 TCGCATTACG-ATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGAATAGTC-ACAATCGCAATGCGATGTACATATTCGCATTGCGATAGTCCAAGT
* * * * *
513120 TCGCATTGCG-ATAGTCGACTATCGCATTGCGATAGTCCAAAATCGCATTGCGA
1 TCGCATTGCGAATAGTC-ACAATCGCAATGCGAT-GTACATATTCGCATTGCGA
513173 ATCTGGAAAC
Statistics
Matches: 99, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
60 2 0.02
61 3 0.03
62 65 0.66
63 29 0.29
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (62 bp):
TCGCATTGCGAATAGTCACAATCGCAATGCGATGTACATATTCGCATTGCGATAGTCCAAGT
Done.