Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009620.1 Hibiscus syriacus cultivar Beakdansim tig00117009_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: 1051670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:476971 original size:170 final size:170
Alignment explanation
Indices: 476592--477234 Score: 927
Period size: 170 Copynumber: 3.8 Consensus size: 170
476582 TTAATTACCA
* *
476592 TTACAGTTCCCCCAGATCCCTTTGCTGCGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTTCCTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-CCCCAGGTTCCTT
* * * * *
476657 TGTTGTGTGCAAAGGTAAGCCTTACAGTTT-CCCAGGTCCCTTTCCTGTGTGCAAGGGTAAGCCT
65 TGCTGTGTGCAAGGGTCAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCT
* *
476721 TACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
130 TACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
476763 TTACAGTTCCCCCAGGTCCCTTTACTGTGTGCAAGGGTAAGCTTTACAGTTCCCCCAGG-TCCCT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-CCCCAGGTTCCTT
*
476827 TGCTGTGTGCAAGCGT-AGGCCTTACAGTTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGC
65 TGCTGTGTGCAAGGGTCA-GCCTTACAGTTT-CCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGC
* * *
476891 CTTACAGTTTCCCAGGTTCCTTTACTATGTGCAAGGGTGAGCC
128 CTTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
476934 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCAGGTTCCTTT
*
476998 GCTGTGTGCAAGGGTCAGCCTTACAGTTTCCCCCAGGTTCCTTTACTGTGTGCAAGGGTAAGCCT
66 GCTGTGTGCAAGGGTCAGCCTTACAGTTT-CCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCT
*
477063 TACAGTTTCCCAGGTTCCTTTGCTGTGTGTAAGGGTAAGCC
130 TACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * * *
477104 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCATGTTCCTTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCAGGTTCCTTT
* * * *
477168 GCTGTGTGCAAGGGTCAGCCTTACAGTTTCCCCAGGCTCTTTTGCTATGTGCAAGGATAAGACCT
66 GCTGTGTGCAAGGGTCAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCT
477233 TA
130 TA
477235 TCATTTTTGC
Statistics
Matches: 433, Mismatches: 33, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
169 34 0.08
170 267 0.62
171 93 0.21
172 39 0.09
ACGTcount: A:0.17, C:0.27, G:0.24, T:0.32
Consensus pattern (170 bp):
TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCAGGTTCCTTT
GCTGTGTGCAAGGGTCAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTT
ACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:479279 original size:13 final size:13
Alignment explanation
Indices: 479257--479331 Score: 69
Period size: 13 Copynumber: 5.4 Consensus size: 13
479247 ACCCGACCTG
479257 ACCCGACCCGTTT
1 ACCCGACCCGTTT
*
479270 ACCTGACCCGTTT
1 ACCCGACCCGTTT
479283 ACCCGACCCGACCTGTT
1 ACCCGACCCG---T-TT
* *
479300 GACCCAACCCGTTG
1 -ACCCGACCCGTTT
*
479314 ACCCGACCCGTTG
1 ACCCGACCCGTTT
479327 ACCCG
1 ACCCG
479332 TTGACCGTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
13 38 0.73
14 1 0.02
15 1 0.02
16 1 0.02
17 2 0.04
18 9 0.17
ACGTcount: A:0.17, C:0.45, G:0.19, T:0.19
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:479291 original size:31 final size:31
Alignment explanation
Indices: 479251--479337 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
479241 GTCATAACCC
* * **
479251 GACCTGACCCGACCCGTTTACCTGACCCGTT
1 GACCCGACCCGACCCGTTGACCCAACCCGTT
* *
479282 TACCCGACCCGACCTGTTGACCCAACCCGTT
1 GACCCGACCCGACCCGTTGACCCAACCCGTT
479313 GACCCGACCCGTTGACCCGTTGACC
1 GACCCGACCC---GACCCGTTGACC
479338 GTTGACCACT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
31 34 0.76
34 11 0.24
ACGTcount: A:0.17, C:0.44, G:0.20, T:0.20
Consensus pattern (31 bp):
GACCCGACCCGACCCGTTGACCCAACCCGTT
Found at i:479317 original size:8 final size:8
Alignment explanation
Indices: 479306--479344 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
479296 TGTTGACCCA
479306 ACCCGTTG
1 ACCCGTTG
479314 ACCC---G
1 ACCCGTTG
479319 ACCCGTTG
1 ACCCGTTG
479327 ACCCGTTG
1 ACCCGTTG
479335 A-CCGTTG
1 ACCCGTTG
479342 ACC
1 ACC
479345 ACTGTTGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.19
7 7 0.26
8 15 0.56
ACGTcount: A:0.15, C:0.41, G:0.23, T:0.21
Consensus pattern (8 bp):
ACCCGTTG
Found at i:480666 original size:18 final size:18
Alignment explanation
Indices: 480640--480680 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
480630 ATTATTCGAA
* *
480640 AAGACTGAAGTAAATGAT
1 AAGATTGAAGTAAATAAT
*
480658 AAGATTGAATTAAATAAT
1 AAGATTGAAGTAAATAAT
480676 AAGAT
1 AAGAT
480681 CGGATGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (18 bp):
AAGATTGAAGTAAATAAT
Found at i:482386 original size:42 final size:42
Alignment explanation
Indices: 482140--482719 Score: 890
Period size: 42 Copynumber: 13.6 Consensus size: 42
482130 TTAATTACCG
* * * *
482140 TTACAGTTCCCCCATGTCCCTTTGGTGTGTGCAAGGGTAAGCC
1 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
482183 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTATGCC
1 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
482226 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
482269 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAGGCC
1 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
482312 TTACAGTTTACCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTT--CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
482356 TTACAGTTTCCCAGGTTCCTTTACTATGTGCAAGGGTAAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
482398 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
482440 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
482482 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTCAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
482524 TTACAGTTTCCCCCAGGTTCCTTTGCTGTGTACAAGGGTAAGCC
1 TTACAGTTT--CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
482568 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
482610 TTACAGTTTCTCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
482652 TTACAGTTTCCCAGGTTCATTTGCTGTGTGCAAGGGTCAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
482694 TTACAGTTTCCCCAGGCTCTTTTGCT
1 TTACAGTTT-CCCAGGTTCCTTTGCT
482720 ATGTACAAAG
Statistics
Matches: 510, Mismatches: 22, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
42 284 0.56
43 146 0.29
44 80 0.16
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.32
Consensus pattern (42 bp):
TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:482442 original size:84 final size:84
Alignment explanation
Indices: 482140--482719 Score: 890
Period size: 86 Copynumber: 6.8 Consensus size: 84
482130 TTAATTACCG
* * * * * *
482140 TTACAGTTCCCCCATGTCCCTTTGGTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTT
1 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-TCCCAGGTTCCTT
*
482205 TGCTGTGTGCAAGGGTATGCC
64 TGCTGTGTGCAAGGGTAAGCC
* * * *
482226 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTT
1 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-TCCCAGGTTCCTT
*
482291 TGCTGTGTGCAAGGGTAGGCC
64 TGCTGTGTGCAAGGGTAAGCC
482312 TTACAGTTTACCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTT
1 TTACAGTTT--CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTT
* *
482377 TACTATGTGCAAGGGTAAGCC
64 TGCTGTGTGCAAGGGTAAGCC
482398 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
482463 CTGTGTGCAAGGGTAAGCC
66 CTGTGTGCAAGGGTAAGCC
*
482482 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTCAGCCTTACAGTTTCCCCCAGGTTCCTT
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT--CCCAGGTTCCTT
*
482547 TGCTGTGTACAAGGGTAAGCC
64 TGCTGTGTGCAAGGGTAAGCC
*
482568 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCTCAGGTTCCTTTG
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
482633 CTGTGTGCAAGGGTAAGCC
66 CTGTGTGCAAGGGTAAGCC
* * * *
482652 TTACAGTTTCCCAGGTTCATTTGCTGTGTGCAAGGGTCAGCCTTACAGTTTCCCCAGGCTCTTTT
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCAGGTTCCTTT
482717 GCT
65 GCT
482720 ATGTACAAAG
Statistics
Matches: 467, Mismatches: 22, Indels: 11
0.93 0.04 0.02
Matches are distributed among these distances:
84 203 0.43
85 13 0.03
86 211 0.45
87 40 0.09
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.32
Consensus pattern (84 bp):
TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
CTGTGTGCAAGGGTAAGCC
Found at i:482540 original size:212 final size:212
Alignment explanation
Indices: 482167--482719 Score: 910
Period size: 212 Copynumber: 2.6 Consensus size: 212
482157 CCCTTTGGTG
* * *
482167 TGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTATGCCTTACAG
1 TGTGCAAGGGTAAGCCTTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG
* * * *
482232 TTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTTGCTGT
65 TT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-TCCCAGGTTCCTTTGCTGT
*
482297 GTGCAAGGGTAGGCCTTACAGTTTACCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG
128 GTGCAAGGGTAGGCCTTACAGTTTACCCCAGGTTCCTTTGCTGTGTACAAGGGTAAGCCTTACAG
482362 TTTCCCAGGTTCCTTTACTA
193 TTTCCCAGGTTCCTTTACTA
482382 TGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
482447 TTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGCTGTGTG
66 TTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGCTGTGTG
*
482512 CAAGGGTCA-GCCTTACAGTTTCCCCCAGGTTCCTTTGCTGTGTACAAGGGTAAGCCTTACAGTT
131 CAAGGGT-AGGCCTTACAGTTTACCCCAGGTTCCTTTGCTGTGTACAAGGGTAAGCCTTACAGTT
* *
482576 TCCCAGGTTCCTTTGCTG
195 TCCCAGGTTCCTTTACTA
*
482594 TGTGCAAGGGTAAGCCTTACAGTTTCTCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
* * * *
482659 TTCCCAGGTTCATTTGCTGTGTGCAAGGGTCAGCCTTACAGTTTCCCCAGGCTCTTTTGCT
66 TTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCAGGTTCCTTTGCT
482720 ATGTACAAAG
Statistics
Matches: 320, Mismatches: 16, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
212 202 0.63
213 55 0.17
214 39 0.12
215 24 0.08
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (212 bp):
TGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGT
TTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGCTGTGTG
CAAGGGTAGGCCTTACAGTTTACCCCAGGTTCCTTTGCTGTGTACAAGGGTAAGCCTTACAGTTT
CCCAGGTTCCTTTACTA
Found at i:484765 original size:13 final size:13
Alignment explanation
Indices: 484765--484809 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
484755 CCGTTGACCC
*
484765 GACCCGACCTGTT
1 GACCCGACCCGTT
* *
484778 GACCCAACTCGTT
1 GACCCGACCCGTT
*
484791 GACCCGACCCATT
1 GACCCGACCCGTT
484804 GACCCG
1 GACCCG
484810 TTGACCGTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.20, C:0.42, G:0.20, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:484766 original size:18 final size:18
Alignment explanation
Indices: 484743--484782 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
484733 ACCGGTCATA
484743 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
484761 ACCCGACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
484779 ACCC
1 ACCC
484783 AACTCGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:484822 original size:15 final size:15
Alignment explanation
Indices: 484799--484848 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
484789 TTGACCCGAC
484799 CCATTGACCCGTTGA
1 CCATTGACCCGTTGA
* *
484814 CCGTTGACCTGTTGA
1 CCATTGACCCGTTGA
484829 CCATTGACCACTGTTGA
1 CCATTGACC-C-GTTGA
484846 CCA
1 CCA
484849 AAACTTTGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 21 0.72
17 8 0.28
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.28
Consensus pattern (15 bp):
CCATTGACCCGTTGA
Found at i:486158 original size:18 final size:18
Alignment explanation
Indices: 486132--486172 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
486122 ATTGTTCGAA
* *
486132 AAGACTGAAGTAAATGAT
1 AAGATTGAAGTAAATAAT
*
486150 AAGATTGAATTAAATAAT
1 AAGATTGAAGTAAATAAT
486168 AAGAT
1 AAGAT
486173 CGGATGGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (18 bp):
AAGATTGAAGTAAATAAT
Found at i:487749 original size:42 final size:42
Alignment explanation
Indices: 487631--488316 Score: 978
Period size: 42 Copynumber: 16.1 Consensus size: 42
487621 TTAATTACTG
* * *
487631 TTACAGTTCCCCCAGG-TCCGTTTGCTGTGTGTAAGGGTAATCC
1 TTACAGTT-TCCCAGGTTCC-TTTGCTGTGTGCAAGGGTAAGCC
* * * *
487674 TTACAGTTCCCCCAGGTTCCGTTGTTGTGTGCAAAGGTAAGCC
1 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
487717 TTACAGTTTCCCAGGTCCCTTTGCTGTATGCAAGGGTAAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
487759 TTACAGTTCCCCCAAGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
487802 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGCAAGCC
1 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * * * *
487845 TTACAGTTCCCCCAAGTCCCTTTGCTGTGTGCAAAGGTAGGCC
1 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
487888 TTACAGTTTCCCCCAGGTTCCTTTGATGTGTGCAAGGGTAAGCC
1 TTACAGTTT--CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
487932 TTACAGTTTCCTAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
487974 TTACAGTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
488016 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
488058 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTCAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
488100 TTACAGTTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTT--CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
488144 TTACAGTTTCCCAGGTTGCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
488186 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
488228 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTCAGCC
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * ** *
488270 TTACAGTTTCCCCAGGCTCTTTTGCAATGTGCAAGGATAAGACC
1 TTACAGTTT-CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CC
488314 TTA
1 TTA
488317 TCGTTTTTGC
Statistics
Matches: 593, Mismatches: 42, Indels: 15
0.91 0.06 0.02
Matches are distributed among these distances:
42 321 0.54
43 186 0.31
44 86 0.15
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (42 bp):
TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:488014 original size:84 final size:84
Alignment explanation
Indices: 487631--488316 Score: 978
Period size: 86 Copynumber: 8.0 Consensus size: 84
487621 TTAATTACTG
* * * * *
487631 TTACAGTTCCCCCAGG-TCCGTTTGCTGTGTGTAAGGGTAATCCTTACAGTTCCCCCAGGTTCCG
1 TTACAGTT-TCCCAGGTTCC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-TCCCAGGTTCCT
* *
487695 TTGTTGTGTGCAAAGGTAAGCC
63 TTGCTGTGTGCAAGGGTAAGCC
* * * * *
487717 TTACAGTTTCCCAGGTCCCTTTGCTGTATGCAAGGGTAAGCCTTACAGTTCCCCCAAGTCCCTTT
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-TCCCAGGTTCCTTT
487782 GCTGTGTGCAAGGGTAAGCC
65 GCTGTGTGCAAGGGTAAGCC
* * * * * *
487802 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGCAAGCCTTACAGTTCCCCCAAGTCCCTT
1 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-TCCCAGGTTCCTT
* *
487867 TGCTGTGTGCAAAGGTAGGCC
64 TGCTGTGTGCAAGGGTAAGCC
* *
487888 TTACAGTTTCCCCCAGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAGTTTCCTAGGTTCCTT
1 TTACAGTTT--CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTT
487953 TGCTGTGTGCAAGGGTAAGCC
64 TGCTGTGTGCAAGGGTAAGCC
*
487974 TTACAGTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
488039 CTGTGTGCAAGGGTAAGCC
66 CTGTGTGCAAGGGTAAGCC
*
488058 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTCAGCCTTACAGTTTCCCCCAGGTTCCTT
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT--CCCAGGTTCCTT
488123 TGCTGTGTGCAAGGGTAAGCC
64 TGCTGTGTGCAAGGGTAAGCC
*
488144 TTACAGTTTCCCAGGTTGCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
488209 CTGTGTGCAAGGGTAAGCC
66 CTGTGTGCAAGGGTAAGCC
* * *
488228 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTCAGCCTTACAGTTTCCCCAGGCTCTTTT
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCAGGTTCCTTT
** *
488293 GCAATGTGCAAGGATAAGACC
65 GCTGTGTGCAAGGGTAAG-CC
488314 TTA
1 TTA
488317 TCGTTTTTGC
Statistics
Matches: 554, Mismatches: 38, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
84 204 0.37
85 98 0.18
86 214 0.39
87 38 0.07
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (84 bp):
TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
CTGTGTGCAAGGGTAAGCC
Found at i:488149 original size:128 final size:126
Alignment explanation
Indices: 487631--488316 Score: 978
Period size: 128 Copynumber: 5.4 Consensus size: 126
487621 TTAATTACTG
* * * * *
487631 TTACAGTTCCCCCAGG-TCCGTTTGCTGTGTGTAAGGGTAATCCTTACAGTTCCCCCAGGTTCCG
1 TTACAGTT-TCCCAGGTTCC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-TCCCAGGTTCCT
* * * *
487695 TTGTTGTGTGCAAAGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTATGCAAGGGTAAGCC
63 TTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * * * *
487759 TTACAGTTCCCCCAAGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTT
1 TTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-TCCCAGGTTCCTT
* * * * * *
487824 TGCTGTGTGCAAGGGCAAGCCTTACAGTTCCCCCAAGTCCCTTTGCTGTGTGCAAAGGTAGGCC
64 TGCTGTGTGCAAGGGTAAGCCTTACAGTT-TCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
487888 TTACAGTTTCCCCCAGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAGTTTCCTAGGTTCCTT
1 TTACAGTTT--CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTT
*
487953 TGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
64 TGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
488016 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
*
488081 CTGTGTGCAAGGGTCAGCCTTACAGTTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
66 CTGTGTGCAAGGGTAAGCCTTACAGTTT--CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
488144 TTACAGTTTCCCAGGTTGCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
1 TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
*
488209 CTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTCAGCC
66 CTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * ** *
488270 TTACAGTTTCCCCAGGCTCTTTTGCAATGTGCAAGGATAAGACCTTA
1 TTACAGTTT-CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTA
488317 TCGTTTTTGC
Statistics
Matches: 509, Mismatches: 41, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
126 122 0.24
127 25 0.05
128 247 0.49
129 77 0.15
130 38 0.07
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (126 bp):
TTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTG
CTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:500149 original size:20 final size:21
Alignment explanation
Indices: 500126--500205 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 21
500116 TTGGTGCAGA
*
500126 GGGAATCGATACCCCCATGA-
1 GGGAACCGATACCCCCATGAG
* *
500146 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-ATG-AG
*
500169 GGGAACCGATTCCCCCCAT-AG
1 GGGAACCGA-TACCCCCATGAG
*
500190 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
500206 TGGGGTTCTA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 20 0.41
21 12 0.24
22 1 0.02
23 10 0.20
24 6 0.12
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAACCGATACCCCCATGAG
Found at i:500193 original size:21 final size:21
Alignment explanation
Indices: 500137--500205 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
500127 GGAATCGATA
500137 CCCCCAT-GAGGGAACCGATTC
1 CCCCCATAG-GGGAACCGATTC
**
500158 CCCCTTTGAAGGGGAACCGATTC
1 CCCCCAT--AGGGGAACCGATTC
* *
500181 CCCCCATAGGGGAATCGATAC
1 CCCCCATAGGGGAACCGATTC
500202 CCCC
1 CCCC
500206 TGGGGTTCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 21 0.54
23 17 0.44
24 1 0.03
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.16
Consensus pattern (21 bp):
CCCCCATAGGGGAACCGATTC
Found at i:504173 original size:22 final size:21
Alignment explanation
Indices: 504131--504170 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
504121 GAGTTTATTT
*
504131 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
504152 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
504171 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:506743 original size:14 final size:14
Alignment explanation
Indices: 506713--506757 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
506703 TCCATTTATA
506713 TTAGGGTTT-GTGAT
1 TTAGGGTTTAGTG-T
*
506727 TTAGGGTTTAATGT
1 TTAGGGTTTAGTGT
*
506741 TTAGTGTTTAGTGT
1 TTAGGGTTTAGTGT
506755 TTA
1 TTA
506758 TAGTTTAGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 25 0.93
15 2 0.07
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (14 bp):
TTAGGGTTTAGTGT
Found at i:506750 original size:21 final size:21
Alignment explanation
Indices: 506718--506770 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
506708 TTATATTAGG
506718 GTTT-GTGATTTAGGGTTTA-A
1 GTTTAGTG-TTTAGGGTTTATA
*
506738 TGTTTAGTGTTTAGTGTTTATA
1 -GTTTAGTGTTTAGGGTTTATA
*
506760 GTTTAGGGTTT
1 GTTTAGTGTTT
506771 CTATAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (21 bp):
GTTTAGTGTTTAGGGTTTATA
Found at i:506863 original size:20 final size:20
Alignment explanation
Indices: 506840--506892 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
506830 ATAAGTAATT
*
506840 TACTTTATATAGTTTATATA
1 TACTTTATATAGTTTATACA
* * *
506860 TACTATACATGGTTTATACA
1 TACTTTATATAGTTTATACA
506880 TACATATTATATA
1 TAC-T-TTATATA
506893 AAATTATTTA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 19 0.79
21 1 0.04
22 4 0.17
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (20 bp):
TACTTTATATAGTTTATACA
Found at i:507245 original size:14 final size:14
Alignment explanation
Indices: 507227--507287 Score: 68
Period size: 14 Copynumber: 4.4 Consensus size: 14
507217 TAGAGTTTGT
507227 GATTTAGGGTTTAA
1 GATTTAGGGTTTAA
* * *
507241 TATTTAGTGTTTAG
1 GATTTAGGGTTTAA
*
507255 GGTTTAGGGTTTAA
1 GATTTAGGGTTTAA
* *
507269 GATTTAGGTTTTAG
1 GATTTAGGGTTTAA
507283 GATTT
1 GATTT
507288 CTATAAACTA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
GATTTAGGGTTTAA
Found at i:507252 original size:28 final size:27
Alignment explanation
Indices: 507227--507287 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
507217 TAGAGTTTGT
*
507227 GATTTAGGGTTTAATATTTAGTGTTTAG
1 GATTTAGGGTTTAAGATTTAG-GTTTAG
*
507255 GGTTTAGGGTTTAAGATTTAGGTTTTAG
1 GATTTAGGGTTTAAGATTTAGG-TTTAG
507283 GATTT
1 GATTT
507288 CTATAAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (27 bp):
GATTTAGGGTTTAAGATTTAGGTTTAG
Found at i:507267 original size:21 final size:22
Alignment explanation
Indices: 507216--507282 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 22
507206 TCCATTTACA
507216 TTAGAGTTT-GTGATTTAGGGT
1 TTAGAGTTTAGTGATTTAGGGT
*
507237 TTA-ATATTTAGTG-TTTAGGGT
1 TTAGA-GTTTAGTGATTTAGGGT
* * *
507258 TTAGGGTTTA-AGATTTAGGTT
1 TTAGAGTTTAGTGATTTAGGGT
507279 TTAG
1 TTAG
507283 GATTTCTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 2 0.05
21 32 0.86
22 3 0.08
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.49
Consensus pattern (22 bp):
TTAGAGTTTAGTGATTTAGGGT
Found at i:507390 original size:2 final size:2
Alignment explanation
Indices: 507322--507375 Score: 67
Period size: 2 Copynumber: 27.0 Consensus size: 2
507312 TTATATAGTT
*
507322 TA TA TA TA TA TA TA TA TA TGA -A TA TA TA TA TA TA AA CTA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA -TA TA TA
507365 TA TA TA -A TA TA
1 TA TA TA TA TA TA
507376 CATGGTTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
1 2 0.04
2 42 0.91
3 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:507901 original size:14 final size:14
Alignment explanation
Indices: 507884--507935 Score: 86
Period size: 14 Copynumber: 3.7 Consensus size: 14
507874 GGTTTTGTGA
507884 TTTAGGGTTTAAAG
1 TTTAGGGTTTAAAG
507898 TTTAGGGTTTAAAG
1 TTTAGGGTTTAAAG
**
507912 TTTAGGGTTTAGGG
1 TTTAGGGTTTAAAG
507926 TTTAGGGTTT
1 TTTAGGGTTT
507936 CTATAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (14 bp):
TTTAGGGTTTAAAG
Found at i:507921 original size:7 final size:7
Alignment explanation
Indices: 507884--507935 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
507874 GGTTTTGTGA
507884 TTTAGGG
1 TTTAGGG
**
507891 TTTAAAG
1 TTTAGGG
507898 TTTAGGG
1 TTTAGGG
**
507905 TTTAAAG
1 TTTAGGG
507912 TTTAGGG
1 TTTAGGG
507919 TTTAGGG
1 TTTAGGG
507926 TTTAGGG
1 TTTAGGG
507933 TTT
1 TTT
507936 CTATAAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:508028 original size:13 final size:13
Alignment explanation
Indices: 508010--508039 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
508000 TAATTTACTT
508010 TATATAGTTTATA
1 TATATAGTTTATA
508023 TATATAGTTTATA
1 TATATAGTTTATA
508036 TATA
1 TATA
508040 CTATACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:508044 original size:20 final size:21
Alignment explanation
Indices: 508020--508070 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
508010 TATATAGTTT
*
508020 ATATATATAGTTTATATATAC
1 ATATATATAGTTTATACATAC
* *
508041 -TATACATGGTTTATACATAC
1 ATATATATAGTTTATACATAC
508061 ATATTATATA
1 ATA-TATATA
508071 AAATTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (21 bp):
ATATATATAGTTTATACATAC
Found at i:508415 original size:14 final size:14
Alignment explanation
Indices: 508393--508453 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
508383 TCCATTTACA
* *
508393 TTAGAGTTTTTGAT
1 TTAGGGTTTATGAT
508407 TTAGGGTTTAATG-T
1 TTAGGGTTT-ATGAT
* *
508421 TTAGGGTTTAGGGT
1 TTAGGGTTTATGAT
*
508435 TTAGGGTTTAGGAT
1 TTAGGGTTTATGAT
508449 TTAGG
1 TTAGG
508454 ATTTTTATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
13 2 0.05
14 37 0.90
15 2 0.05
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.48
Consensus pattern (14 bp):
TTAGGGTTTATGAT
Found at i:508457 original size:7 final size:7
Alignment explanation
Indices: 508406--508453 Score: 69
Period size: 7 Copynumber: 6.9 Consensus size: 7
508396 GAGTTTTTGA
508406 TTTAGGG
1 TTTAGGG
**
508413 TTTAATG
1 TTTAGGG
508420 TTTAGGG
1 TTTAGGG
508427 TTTAGGG
1 TTTAGGG
508434 TTTAGGG
1 TTTAGGG
*
508441 TTTAGGA
1 TTTAGGG
508448 TTTAGG
1 TTTAGG
508454 ATTTTTATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:508770 original size:15 final size:14
Alignment explanation
Indices: 508733--508761 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
508723 TACCTATTAT
508733 ATAAAATTA-TTTA
1 ATAAAATTATTTTA
508746 ATAAAATTATTTTA
1 ATAAAATTATTTTA
508760 AT
1 AT
508762 GTAAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAAAATTATTTTA
Found at i:509119 original size:21 final size:22
Alignment explanation
Indices: 509069--509120 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
509059 TCCATTTACA
509069 TTAGGGTTT-GTGATTTAGGGT
1 TTAGGGTTTAGTGATTTAGGGT
** * *
509090 TTAATGTTTAGT-TTTTATGGT
1 TTAGGGTTTAGTGATTTAGGGT
509111 TTAGGGTTTA
1 TTAGGGTTTA
509121 TGGTTTACAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (22 bp):
TTAGGGTTTAGTGATTTAGGGT
Found at i:509121 original size:14 final size:14
Alignment explanation
Indices: 509069--509127 Score: 66
Period size: 14 Copynumber: 4.2 Consensus size: 14
509059 TCCATTTACA
* *
509069 TTAGGGTTTGTGAT
1 TTAGGGTTTATGGT
509083 TTAGGGTTTAAT-GT
1 TTAGGGTTT-ATGGT
**
509097 TTAGTTTTTATGGT
1 TTAGGGTTTATGGT
509111 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
509125 TTA
1 TTA
509128 CATTTTAGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
13 2 0.05
14 34 0.92
15 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:509648 original size:7 final size:7
Alignment explanation
Indices: 509623--509677 Score: 65
Period size: 7 Copynumber: 7.9 Consensus size: 7
509613 GAGTTTTTGA
509623 TTTAGGG
1 TTTAGGG
**
509630 TTTAATG
1 TTTAGGG
*
509637 TTTAGTG
1 TTTAGGG
509644 TTTAGGG
1 TTTAGGG
509651 TTTAGGG
1 TTTAGGG
*
509658 TTTATGG
1 TTTAGGG
*
509665 TTTAGGT
1 TTTAGGG
509672 TTTAGG
1 TTTAGG
509678 ATTTCTATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (7 bp):
TTTAGGG
Found at i:509783 original size:49 final size:47
Alignment explanation
Indices: 509682--509783 Score: 116
Period size: 49 Copynumber: 2.1 Consensus size: 47
509672 TTTAGGATTT
* * * *
509682 CTATAAACTATATAATTTATTACTTTATATAGTTTATGCATAATGTTT
1 CTATAAACTATATAAGTAATTACTTTATATAGTTTAT-CATAATATTA
*
509730 CTATAAACTATATAAGTAATTTGCTTTATATAGTTTAT-ATATATATATA
1 CTATAAACTATATAAGTAA-TTACTTTATATAGTTTATCATA-ATAT-TA
509779 CTATA
1 CTATA
509784 CATGGTTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
47 3 0.07
48 20 0.43
49 23 0.50
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (47 bp):
CTATAAACTATATAAGTAATTACTTTATATAGTTTATCATAATATTA
Found at i:509982 original size:15 final size:14
Alignment explanation
Indices: 509945--509973 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
509935 GACCTATTAT
509945 ATAAAATTA-TTTA
1 ATAAAATTATTTTA
509958 ATAAAATTATTTTA
1 ATAAAATTATTTTA
509972 AT
1 AT
509974 GTAAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAAAATTATTTTA
Found at i:510398 original size:2 final size:2
Alignment explanation
Indices: 510393--510441 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
510383 TAATTTACTT
510393 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
510435 TA CTA TA
1 TA -TA TA
510442 CATGGTTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:510829 original size:14 final size:15
Alignment explanation
Indices: 510810--510870 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 15
510800 TCCGTTTATA
*
510810 TTAGGGTTT-GTGAT
1 TTAGGGTTTAATGAT
510824 TTAGGGTTTAATG-T
1 TTAGGGTTTAATGAT
* * *
510838 TTTGGGTTT-AGGGT
1 TTAGGGTTTAATGAT
510852 TTAGGGTTT-ATGAT
1 TTAGGGTTTAATGAT
510866 TTAGG
1 TTAGG
510871 ATTCTATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
13 2 0.05
14 35 0.90
15 2 0.05
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.49
Consensus pattern (15 bp):
TTAGGGTTTAATGAT
Found at i:510839 original size:21 final size:20
Alignment explanation
Indices: 510814--510870 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
510804 TTTATATTAG
510814 GGTTTGTGATTTAGGGTTTAA
1 GGTTT-TGATTTAGGGTTTAA
* * *
510835 TGTTTTGGGTTTAGGGTTTAG
1 GGTTTT-GATTTAGGGTTTAA
510856 GGTTTATGATTTAGG
1 GGTTT-TGATTTAGG
510871 ATTCTATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (20 bp):
GGTTTTGATTTAGGGTTTAA
Found at i:510846 original size:7 final size:7
Alignment explanation
Indices: 510810--510861 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
510800 TCCGTTTATA
510810 TTAGGGT
1 TTAGGGT
*
510817 TT-GTGAT
1 TTAG-GGT
510824 TTAGGGT
1 TTAGGGT
**
510831 TTAATGT
1 TTAGGGT
*
510838 TTTGGGT
1 TTAGGGT
510845 TTAGGGT
1 TTAGGGT
510852 TTAGGGT
1 TTAGGGT
510859 TTA
1 TTA
510862 TGATTTAGGA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
6 1 0.03
7 33 0.94
8 1 0.03
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (7 bp):
TTAGGGT
Found at i:510974 original size:18 final size:19
Alignment explanation
Indices: 510951--510986 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
510941 ATATAGTTTA
510951 TATATATATATAG-GTATG
1 TATATATATATAGTGTATG
510969 TATATATATATAGTGTAT
1 TATATATATATAGTGTAT
510987 ATATTGTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (19 bp):
TATATATATATAGTGTATG
Found at i:511145 original size:2 final size:2
Alignment explanation
Indices: 511138--511281 Score: 81
Period size: 2 Copynumber: 73.5 Consensus size: 2
511128 CTATAAACTA
* *
511138 AT AT AT AT AT AT AT AT AT A- AT CT AT AG AT -T ACT -T AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
511177 AGT -T AT AC AT AC AT AT AT AT AT AT A- AT AT AA AT -T AT A- AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
511216 TT AT AA ACT AT AT AT TT AT AT AGT -T GAT AC AT AT AT AGT TT AT
1 AT AT AT A-T AT AT AT AT AT AT A-T AT -AT AT AT AT AT A-T AT AT
511259 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
511282 ATTAAAAGTA
Statistics
Matches: 107, Mismatches: 20, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
1 9 0.08
2 92 0.86
3 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:511250 original size:15 final size:15
Alignment explanation
Indices: 511232--511267 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
511222 ACTATATATT
511232 TATATAGTTGATACA
1 TATATAGTTGATACA
* *
511247 TATATAGTTTATATA
1 TATATAGTTGATACA
511262 TATATA
1 TATATA
511268 TATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (15 bp):
TATATAGTTGATACA
Found at i:511515 original size:20 final size:19
Alignment explanation
Indices: 511490--511534 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
511480 AAATTTTCTA
*
511490 TTCCCTCTAAATTTCTCAAT
1 TTCCCTCTAAA-TTCCCAAT
511510 TTCCCTCTAAATTCCCAAT
1 TTCCCTCTAAATTCCCAAT
511529 TTCCCT
1 TTCCCT
511535 ATATTCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.22, C:0.36, G:0.00, T:0.42
Consensus pattern (19 bp):
TTCCCTCTAAATTCCCAAT
Found at i:511530 original size:19 final size:20
Alignment explanation
Indices: 511490--511568 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 20
511480 AAATTTTCTA
*
511490 TTCCCTCTAAATTTCTCAAT
1 TTCCCTCTAAATTTCCCAAT
511510 TTCCCTCTAAA-TTCCCAAT
1 TTCCCTCTAAATTTCCCAAT
511529 TTCCCTATATTCTTAAAATTTCCCAAT
1 TTCCC-----TC-T-AAATTTCCCAAT
511556 TTCCCTCTAAATT
1 TTCCCTCTAAATT
511569 CTCAAATAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
19 12 0.24
20 16 0.32
21 1 0.02
22 2 0.04
24 2 0.04
25 1 0.02
26 3 0.06
27 13 0.26
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (20 bp):
TTCCCTCTAAATTTCCCAAT
Found at i:511652 original size:2 final size:2
Alignment explanation
Indices: 511645--511697 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
511635 ACTTTGAATA
* * * *
511645 AT AT AT AT AT AT AT AT AT AT AT A- AA AGT AT AT AC AT AA AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
511687 AT AT AT AT AT A
1 AT AT AT AT AT A
511698 ATTAAACATA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.95
3 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:512212 original size:2 final size:2
Alignment explanation
Indices: 512202--512285 Score: 159
Period size: 2 Copynumber: 42.0 Consensus size: 2
512192 TTTTATAGTT
*
512202 TA TA CA 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
512244 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
512286 AATTATAGTT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:512299 original size:28 final size:27
Alignment explanation
Indices: 512207--512461 Score: 116
Period size: 28 Copynumber: 9.5 Consensus size: 27
512197 TAGTTTATAC
* *
512207 ATATATATATATATATATATATATATAT
1 ATATTTATATATATATATATATAAAT-T
* *
512235 ATATATATATATATATATATATATATAT
1 ATATTTATATATATATATATATAAAT-T
*
512263 ATATATATATATATATATATATAAATT
1 ATATTTATATATATATATATATAAATT
512290 ATAGTTTATA-A-ACTATAT-T-T---TT
1 ATA-TTTATATATA-TATATATATAAATT
* * *
512312 ATAGTTTATACATATATAGT-T-TACATAC
1 ATA-TTTATATATATATA-TATATAAAT-T
* *
512340 ATAGTTTTTATATATAGT-TCATATAAA-C
1 ATA-TTTATATATATA-TAT-ATATAAATT
**
512368 ATAATTTATATATATAGCT-TAT-AA-T
1 AT-ATTTATATATATATATATATAAATT
512393 A-A-TTATATAGTATATA-ATATAAA-T
1 ATATTTATATA-TATATATATATAAATT
512417 ATAGTTTATATATATAGTTTATATATAAACTT
1 ATA-TTTATATATATA---TATATATAAA-TT
512449 ATA-TTATATATAT
1 ATATTTATATATAT
512462 TATGTTTTTC
Statistics
Matches: 189, Mismatches: 11, Indels: 52
0.75 0.04 0.21
Matches are distributed among these distances:
22 19 0.10
23 13 0.07
24 8 0.04
25 5 0.03
26 9 0.05
27 19 0.10
28 87 0.46
29 5 0.03
30 20 0.11
32 4 0.02
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (27 bp):
ATATTTATATATATATATATATAAATT
Found at i:512334 original size:22 final size:22
Alignment explanation
Indices: 512208--512334 Score: 64
Period size: 22 Copynumber: 5.8 Consensus size: 22
512198 AGTTTATACA
* * *
512208 TATATATATATATATATATA-TA
1 TATAAATATATA-ATTTATAGTT
* * *
512230 TATATATATATATATATATA-TA
1 TATAAATATATA-ATTTATAGTT
* * *
512252 TATATATATATATATATATA-TA
1 TATAAATATATA-ATTTATAGTT
* *
512274 TATATATATATAAATTATAGTT
1 TATAAATATATAATTTATAGTT
*
512296 TATAAACTATAT-TTTTATAGTT
1 TATAAA-TATATAATTTATAGTT
* *
512318 TATACATATATAGTTTA
1 TATAAATATATAATTTA
512335 CATACATAGT
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
21 10 0.11
22 79 0.84
23 5 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TATAAATATATAATTTATAGTT
Found at i:512336 original size:13 final size:13
Alignment explanation
Indices: 512320--512358 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
512310 TTATAGTTTA
512320 TACATATATAGTT
1 TACATATATAGTT
*
512333 TACATACATAGTT
1 TACATATATAGTT
**
512346 TTTATATATAGTT
1 TACATATATAGTT
512359 CATATAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (13 bp):
TACATATATAGTT
Found at i:512418 original size:18 final size:19
Alignment explanation
Indices: 512397--512432 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
512387 TATAATAATT
512397 ATATAGTATATA-ATATAA
1 ATATAGTATATATATATAA
*
512415 ATATAGTTTATATATATA
1 ATATAGTATATATATATA
512433 GTTTATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATAGTATATATATATAA
Found at i:512429 original size:11 final size:13
Alignment explanation
Indices: 512195--512443 Score: 133
Period size: 12 Copynumber: 20.2 Consensus size: 13
512185 TTAATTTTTT
*
512195 TATAGTTTATACA
1 TATAGTTTATATA
512208 TATA---TATATA
1 TATAGTTTATATA
*
512218 TATA-TATATATA
1 TATAGTTTATATA
*
512230 TATA-TATATATA
1 TATAGTTTATATA
*
512242 TATA-TATATATA
1 TATAGTTTATATA
*
512254 TATA-TATATATA
1 TATAGTTTATATA
*
512266 TATA-TATATATA
1 TATAGTTTATATA
* *
512278 TATA-TATAAAT-
1 TATAGTTTATATA
*
512289 TATAGTTTATAAA
1 TATAGTTTATATA
512302 CTATA--TT-T-T-
1 -TATAGTTTATATA
512311 TATAGTTTATACATA
1 TATAGTTTAT--ATA
*
512326 TATAGTTTACATA
1 TATAGTTTATATA
* *
512339 CATAGTTTTTATA
1 TATAGTTTATATA
*
512352 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
512367 CATAATTTATATA
1 TATAGTTTATATA
*
512380 TATAGCTTATA-A
1 TATAGTTTATATA
512392 TA-A--TTATATA
1 TATAGTTTATATA
* *
512402 GTATA-TAATATAAA
1 -TATAGT-TTATATA
512416 TATAGTTTATATA
1 TATAGTTTATATA
512429 TATAGTTTATATA
1 TATAGTTTATATA
512442 TA
1 TA
512444 AACTTATATT
Statistics
Matches: 193, Mismatches: 23, Indels: 40
0.75 0.09 0.16
Matches are distributed among these distances:
8 4 0.02
9 5 0.03
10 12 0.06
11 9 0.05
12 74 0.38
13 60 0.31
14 11 0.06
15 18 0.09
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:522796 original size:31 final size:31
Alignment explanation
Indices: 522761--522831 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
522751 TTTCAATAAA
* *
522761 GTCCCATAACATTTAGTTCGTTTGCAATATG
1 GTCCCACAACATTTAGTCCGTTTGCAATATG
*
522792 GTCCCCCAACATTTAGTCCGTTTGCAATATG
1 GTCCCACAACATTTAGTCCGTTTGCAATATG
522823 GTCCC-CAAC
1 GTCCCACAAC
522832 GTAAATATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 4 0.11
31 33 0.89
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.32
Consensus pattern (31 bp):
GTCCCACAACATTTAGTCCGTTTGCAATATG
Found at i:522831 original size:30 final size:31
Alignment explanation
Indices: 522768--522828 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
522758 AAAGTCCCAT
*
522768 AACATTTAGTTCGTTTGCAATATGGTCCCCC
1 AACATTTAGTCCGTTTGCAATATGGTCCCCC
522799 AACATTTAGTCCGTTTGCAATATGGTCCCC
1 AACATTTAGTCCGTTTGCAATATGGTCCCC
522829 AACGTAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.34
Consensus pattern (31 bp):
AACATTTAGTCCGTTTGCAATATGGTCCCCC
Found at i:526608 original size:12 final size:12
Alignment explanation
Indices: 526593--526652 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
526583 CAGAAATAAA
526593 AACAGAATTCAG
1 AACAGAATTCAG
526605 AACAG-ATATCAG
1 AACAGAAT-TCAG
* *
526617 AACAAAATCCAG
1 AACAGAATTCAG
* *
526629 ATCAGAAATCAG
1 AACAGAATTCAG
*
526641 AACAAAATTCAG
1 AACAGAATTCAG
526653 GTCATGTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.53, C:0.18, G:0.13, T:0.15
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:526610 original size:24 final size:24
Alignment explanation
Indices: 526583--526652 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
526573 ACGGAGATAT
* * *
526583 CAGAAATAAAAACAGAATTCAGAA
1 CAGAAATCAGAACAAAATTCAGAA
* * *
526607 CAGATATCAGAACAAAATCCAGAT
1 CAGAAATCAGAACAAAATTCAGAA
526631 CAGAAATCAGAACAAAATTCAG
1 CAGAAATCAGAACAAAATTCAG
526653 GTCATGTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.56, C:0.17, G:0.13, T:0.14
Consensus pattern (24 bp):
CAGAAATCAGAACAAAATTCAGAA
Found at i:526663 original size:24 final size:24
Alignment explanation
Indices: 526593--526675 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
526583 CAGAAATAAA
* *
526593 AACAGAATTCAGAACAGATATCAG
1 AACAAAATTCAGATCAGATATCAG
* *
526617 AACAAAATCCAGATCAGAAATCAG
1 AACAAAATTCAGATCAGATATCAG
* *
526641 AACAAAATTCAGGTCATG-TATCAT
1 AACAAAATTCAGATCA-GATATCAG
*
526665 AACAGAATTCA
1 AACAAAATTCA
526676 AGTCGGAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 48 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.19
Consensus pattern (24 bp):
AACAAAATTCAGATCAGATATCAG
Found at i:528509 original size:36 final size:36
Alignment explanation
Indices: 528456--528528 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
528446 GATAAATTAT
528456 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
**
528492 AATCTACATATTGATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
528528 A
1 A
528529 TTCCAGAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:529224 original size:18 final size:18
Alignment explanation
Indices: 529198--529237 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
529188 ACGGTCAACG
*
529198 GGTCGGGTCAACGGGTCA
1 GGTCAGGTCAACGGGTCA
529216 GGTCAGGTCAACGGGTCA
1 GGTCAGGTCAACGGGTCA
529234 GGTC
1 GGTC
529238 GGGTTGTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.23, G:0.42, T:0.17
Consensus pattern (18 bp):
GGTCAGGTCAACGGGTCA
Found at i:529237 original size:13 final size:13
Alignment explanation
Indices: 529190--529220 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
529180 GTCGGTCAAC
*
529190 GGTCAACGGGTCG
1 GGTCAACGGGTCA
529203 GGTCAACGGGTCA
1 GGTCAACGGGTCA
529216 GGTCA
1 GGTCA
529221 GGTCAACGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:531316 original size:12 final size:12
Alignment explanation
Indices: 531291--531383 Score: 73
Period size: 12 Copynumber: 7.8 Consensus size: 12
531281 ACAGAGATAT
* *
531291 CAGAAATCAAAA
1 CAGAATTCAGAA
531303 CAGAATTCAGAA
1 CAGAATTCAGAA
531315 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
531327 CAGAATCCATAT
1 CAGAATTCAGAA
*
531339 CAGAAATCAGAA
1 CAGAATTCAGAA
**
531351 CAGAATTCAGGT
1 CAGAATTCAGAA
*
531363 CATGTA-TCAGAA
1 CA-GAATTCAGAA
531375 CAGAATTCA
1 CAGAATTCA
531384 AGTCGGAAAT
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
11 4 0.07
12 53 0.87
13 4 0.07
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:531323 original size:24 final size:24
Alignment explanation
Indices: 531289--531397 Score: 114
Period size: 24 Copynumber: 4.5 Consensus size: 24
531279 AAACAGAGAT
*
531289 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
531313 AACAGATATCAGAACAGAATCCAT
1 ATCAGAAATCAGAACAGAATTCAG
531337 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
531361 GTCATG-TATCAGAACAGAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
*
531384 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
531398 TAAAATATTT
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
23 1 0.01
24 66 0.97
25 1 0.01
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:531353 original size:48 final size:48
Alignment explanation
Indices: 531287--531397 Score: 145
Period size: 48 Copynumber: 2.3 Consensus size: 48
531277 GTAAACAGAG
*
531287 ATATCAGAAATCAAAACAGAATTCAGAACA-GATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGAACATG-TATCAGAACAGAATCC
** *
531335 ATATCAGAAATCAGAACAGAATTCAGGTCATGTATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTCAGAACATGTATCAGAACAGAATCC
*
531383 A-AGTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
531398 TAAAATATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 1 0.02
48 54 0.96
49 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.19
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGAACATGTATCAGAACAGAATCC
Found at i:532554 original size:18 final size:18
Alignment explanation
Indices: 532508--532545 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
532498 CTTCCGTCTG
532508 ATCTTACTATTAAACTCA
1 ATCTTACTATTAAACTCA
*
532526 ATCTTACTATTAAATTCA
1 ATCTTACTATTAAACTCA
532544 AT
1 AT
532546 TTTATTATTT
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:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (18 bp):
ATCTTACTATTAAACTCA
Found at i:533214 original size:36 final size:36
Alignment explanation
Indices: 533167--533239 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
533157 GATAAATTAT
533167 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
*
533203 AATCTACATATCGATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
533239 A
1 A
533240 TTCCAGAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.41
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:533910 original size:13 final size:13
Alignment explanation
Indices: 533892--533921 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
533882 GGTCAACGCC
533892 GGTCAACGGGACA
1 GGTCAACGGGACA
*
533905 GGTCAACGGGTCA
1 GGTCAACGGGACA
533918 GGTC
1 GGTC
533922 GGGTCAACGG
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:0.23, C:0.23, G:0.40, T:0.13
Consensus pattern (13 bp):
GGTCAACGGGACA
Found at i:533928 original size:18 final size:18
Alignment explanation
Indices: 533905--533943 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
533895 CAACGGGACA
533905 GGTCAACGGGTCAGGTCG
1 GGTCAACGGGTCAGGTCG
533923 GGTCAACGGGTCAGGTCG
1 GGTCAACGGGTCAGGTCG
533941 GGT
1 GGT
533944 TGTAACCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCAGGTCG
Found at i:536037 original size:17 final size:17
Alignment explanation
Indices: 536015--536048 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
536005 AAACAGAATT
*
536015 CAGAATAGATATCAGAA
1 CAGAATACATATCAGAA
*
536032 CAGAATCCATATCAGAA
1 CAGAATACATATCAGAA
536049 ATCAGAACAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.18
Consensus pattern (17 bp):
CAGAATACATATCAGAA
Found at i:536059 original size:12 final size:12
Alignment explanation
Indices: 535996--536065 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
535986 ACGGAGATAT
*
535996 CAGAAATCAAAA
1 CAGAAATCAGAA
*
536008 CAGAATTCAGAA
1 CAGAAATCAGAA
* *
536020 TAGATATCAGAA
1 CAGAAATCAGAA
* *
536032 CAG-AATCCATAT
1 CAGAAAT-CAGAA
536044 CAGAAATCAGAA
1 CAGAAATCAGAA
*
536056 CAGAATTCAG
1 CAGAAATCAG
536066 GTCATGTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.89
13 3 0.07
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:536100 original size:24 final size:25
Alignment explanation
Indices: 535995--536102 Score: 100
Period size: 24 Copynumber: 4.5 Consensus size: 25
535985 AACGGAGATA
* *
535995 TCAGAAATCAAAACAGAATTCAGAA
1 TCAGAAATCAGAACAGAATTCAGAG
* * *
536020 T-AGATATCAGAACAGAATCCATA-
1 TCAGAAATCAGAACAGAATTCAGAG
536043 TCAGAAATCAGAACAGAATTCAG-G
1 TCAGAAATCAGAACAGAATTCAGAG
* *
536067 TCATG-TATCATAACAGAATTCA-AG
1 TCA-GAAATCAGAACAGAATTCAGAG
*
536091 TCGGAAATCAGA
1 TCAGAAATCAGA
536103 TAAAATATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
23 2 0.03
24 62 0.94
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (25 bp):
TCAGAAATCAGAACAGAATTCAGAG
Found at i:537236 original size:18 final size:18
Alignment explanation
Indices: 537213--537250 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
537203 CTTCCGTCTG
537213 ATCTTACTATTAAACTCA
1 ATCTTACTATTAAACTCA
*
537231 ATCTTACTATTAAATTCA
1 ATCTTACTATTAAACTCA
537249 AT
1 AT
537251 TTTATTGTTT
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:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (18 bp):
ATCTTACTATTAAACTCA
Found at i:537921 original size:36 final size:36
Alignment explanation
Indices: 537874--537946 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
537864 GATAAATTAT
537874 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
*
537910 AATCTACATATCGATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
537946 A
1 A
537947 TTTCAGAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.41
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:538618 original size:13 final size:13
Alignment explanation
Indices: 538600--538629 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
538590 GGTCAACGCC
*
538600 GGTCAACGGGTGA
1 GGTCAACGGGTCA
538613 GGTCAACGGGTCA
1 GGTCAACGGGTCA
538626 GGTC
1 GGTC
538630 GGGTCAACGG
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:0.20, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:538636 original size:18 final size:18
Alignment explanation
Indices: 538613--538651 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
538603 CAACGGGTGA
538613 GGTCAACGGGTCAGG-TCG
1 GGTCAACGGGTC-GGATCG
538631 GGTCAACGGGTCGGATCG
1 GGTCAACGGGTCGGATCG
538649 GGT
1 GGT
538652 TGTAACTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGATCG
Found at i:550592 original size:18 final size:19
Alignment explanation
Indices: 550556--550599 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
550546 CAAAATAATC
550556 CAATTTCACATCTTAACAT
1 CAATTTCACATCTTAACAT
550575 CAATTTCAACA-C-TAACAT
1 CAATTTC-ACATCTTAACAT
*
550593 TAATTTC
1 CAATTTC
550600 CAGCATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 12 0.52
19 8 0.35
20 3 0.13
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (19 bp):
CAATTTCACATCTTAACAT
Found at i:552194 original size:15 final size:15
Alignment explanation
Indices: 552161--552194 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
552151 TATATTTATT
* *
552161 TATTATTGTTATTAT
1 TATTATTGTTAATAA
552176 TATTATTGTTAATAA
1 TATTATTGTTAATAA
552191 TATT
1 TATT
552195 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TATTATTGTTAATAA
Found at i:553629 original size:20 final size:20
Alignment explanation
Indices: 553604--553644 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
553594 GTCTTTTTTA
553604 TTTA-TTTATTTATTTTATAC
1 TTTATTTTATTT-TTTTATAC
*
553624 TTTATTTTATTTTTTTTTAC
1 TTTATTTTATTTTTTTATAC
553644 T
1 T
553645 AACTTATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTTATTTTTTTATAC
Found at i:553710 original size:17 final size:19
Alignment explanation
Indices: 553665--553722 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
553655 TTCTTTGTTA
553665 TTTATT-AT-TTATTTTTC
1 TTTATTAATATTATTTTTC
553682 TTATATTAATATT-TTTTTC
1 TT-TATTAATATTATTTTTC
* *
553701 TTT-TTCATATTATTTTAC
1 TTTATTAATATTATTTTTC
553719 TTTA
1 TTTA
553723 CAATCTAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
17 9 0.26
18 13 0.38
19 10 0.29
20 2 0.06
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTATTAATATTATTTTTC
Found at i:555336 original size:26 final size:25
Alignment explanation
Indices: 555305--555361 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
555295 AGACATGTTG
*
555305 TGCATTTTG-TTACTTTTCTTTACAT
1 TGCATTATGATTACTTTT-TTTACAT
* *
555330 TCGCATTATGATTCCTTTTTTTTCAT
1 T-GCATTATGATTACTTTTTTTACAT
555356 TGCATT
1 TGCATT
555362 CACATATGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 6 0.22
26 14 0.52
27 7 0.26
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.58
Consensus pattern (25 bp):
TGCATTATGATTACTTTTTTTACAT
Found at i:555832 original size:12 final size:11
Alignment explanation
Indices: 555815--555844 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
555805 TAACATGTTT
555815 AAAAAAAATAA
1 AAAAAAAATAA
555826 AAAAAAAATAA
1 AAAAAAAATAA
555837 AAAAAAAA
1 AAAAAAAA
555845 GACTTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:557478 original size:105 final size:105
Alignment explanation
Indices: 557333--557956 Score: 1131
Period size: 105 Copynumber: 5.9 Consensus size: 105
557323 CGCTCAAGAT
*
557333 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAGAG
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTCAGAG
557398 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
66 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
* *
557438 AATGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTCAGAG
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTCAGAG
557503 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
66 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
*
557543 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAGAG
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTCAGAG
**
557608 CCAATTTCGTCTTCACAACGAAGGATATTGGACTCCAGAC
66 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
557648 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTCAGAG
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTCAGAG
557713 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
66 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
* *
557753 AACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAG
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTCAGAG
557818 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
66 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
*
557858 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC-ATTTCTCAATTTCAGA
** *
557923 GCCAATTTCAACTTCACGGCGGAGGATATTGGAC
65 GCCAATTTCAACTTCACAACGAAGGATATTGGAC
557957 CTGGAACAAT
Statistics
Matches: 499, Mismatches: 19, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 453 0.91
106 46 0.09
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (105 bp):
AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTTCAGAG
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
Found at i:558200 original size:83 final size:83
Alignment explanation
Indices: 558061--558265 Score: 266
Period size: 83 Copynumber: 2.4 Consensus size: 83
558051 AACTTCACGA
*
558061 AGAAGGGATATCTGCCAACAAAAACCTTCGAGTTCGACCACGCTCAGCTCAAAGGCACATCATTT
1 AGAAGGGATATCTGCCAACAAAGACCTTCGAGTTCGACCACGCTCAGCTCAAAGGCACATCATTT
* ** * * *
558126 GCGGCATAGCTTAAGTCG
66 ACAACATAACTCAAGGCG
* * *
558144 AGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGATATCTGCCAACAAAGACCTTCGAGTTCGACCACGCTCAGCTCAAAGGCACATCATTT
*
558209 ACAACATAACTCAAGGCT
66 ACAACATAACTCAAGGCG
* * *
558227 AGAAGGGTTATCTGTCAACTAAAGACCTGACGAGTTCGA
1 AGAAGGGATATCTGCCAAC-AAAGACCT-TCGAGTTCGA
558266 TTTCATTCAG
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
83 89 0.84
84 8 0.08
85 9 0.08
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (83 bp):
AGAAGGGATATCTGCCAACAAAGACCTTCGAGTTCGACCACGCTCAGCTCAAAGGCACATCATTT
ACAACATAACTCAAGGCG
Found at i:558547 original size:15 final size:15
Alignment explanation
Indices: 558514--558547 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
558504 TATATTTATT
* *
558514 TATTATTGTTATTAT
1 TATTATTGTTAATAA
558529 TATTATTGTTAATAA
1 TATTATTGTTAATAA
558544 TATT
1 TATT
558548 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TATTATTGTTAATAA
Found at i:559994 original size:4 final size:4
Alignment explanation
Indices: 559985--560027 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
559975 TTTGGTCTTT
559985 TTTA TTTA TTTA TTTA TTTA TTT- TATTA CTTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA -TTTA TTTA TTTA TTT
560028 TTTTTACTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 4 0.11
4 27 0.77
5 3 0.09
6 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:560010 original size:21 final size:21
Alignment explanation
Indices: 559984--560073 Score: 69
Period size: 21 Copynumber: 4.2 Consensus size: 21
559974 TTTTGGTCTT
559984 TTTTATTTATTTATTTATTTA
1 TTTTATTTATTTATTTATTTA
560005 TTTTA-TTACTTTATTTA-TTA
1 TTTTATTTA-TTTATTTATTTA
* * * *
560025 TTTTTTTTACTAACTTATGTT-
1 TTTTATTTATTTATTTAT-TTA
*
560046 TTTCTTTGTTATTTATTATATTTA
1 TTT-TAT-TTATTTATT-TATTTA
560070 TTTT
1 TTTT
560074 TCTTATATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
20 15 0.28
21 19 0.35
22 5 0.09
23 9 0.17
24 6 0.11
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTATTTATTTATTTATTTA
Found at i:560118 original size:21 final size:20
Alignment explanation
Indices: 560057--560119 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 20
560047 TTCTTTGTTA
560057 TTTATT-ATATTTATTTTTC
1 TTTATTAATATTTATTTTTC
560076 TTATATTAATA-TT-TTTTTC
1 TT-TATTAATATTTATTTTTC
* *
560095 TTTTTTCATATTTATTTTTAC
1 TTTATTAATATTTATTTTT-C
560116 TTTA
1 TTTA
560120 CAATCTAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 6 0.17
19 12 0.33
20 11 0.31
21 7 0.19
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTAATATTTATTTTTC
Found at i:560733 original size:2 final size:2
Alignment explanation
Indices: 560726--560774 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
560716 ACACATACAA
560726 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
560768 AT AT AT A
1 AT AT AT A
560775 CATAAAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:566664 original size:32 final size:32
Alignment explanation
Indices: 566614--566674 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
566604 TGGGTTTTAA
*
566614 TGAATGGGGCATCCTAGGGAACATGCCTCCCT
1 TGAATGGCGCATCCTAGGGAACATGCCTCCCT
* * *
566646 TGAATGGCGTATCGTAGGGAACGTGCCTC
1 TGAATGGCGCATCCTAGGGAACATGCCTC
566675 TCATGATCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (32 bp):
TGAATGGCGCATCCTAGGGAACATGCCTCCCT
Found at i:577000 original size:20 final size:20
Alignment explanation
Indices: 576975--577012 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
576965 TTTGGTTCAC
*
576975 GGAATATAAGATTACCAGCG
1 GGAATAAAAGATTACCAGCG
576995 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
577013 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.18
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGCG
Found at i:577015 original size:18 final size:19
Alignment explanation
Indices: 576975--577018 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
576965 TTTGGTTCAC
*
576975 GGAATATAAGATTACCAGCG
1 GGAATAAAAGATTACCA-CG
576995 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCACG
577013 GGAATA
1 GGAATA
577019 GGATTACTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.11, G:0.25, T:0.18
Consensus pattern (19 bp):
GGAATAAAAGATTACCACG
Found at i:581747 original size:81 final size:80
Alignment explanation
Indices: 581634--581951 Score: 304
Period size: 81 Copynumber: 4.0 Consensus size: 80
581624 TATAATTCCT
* * * * *
581634 TTATT-TTTTACCTCAA-AGTATTTAGCTTTTCATTTAACTTGCATATTTGACCCTTTTCTGTCA
1 TTATTCTTTTA-CTCAACAGTATTTAACTGTTCATATAACTTGCATAATTGACCCTTTTCTGCCA
* * * *
581697 AATACACAGCTAATCCA
65 ATTGCACAGTTAA-CTA
* *
581714 TTATTCTTTTACTCAACGGTATTTAACTGTTCATATAACTGGCATAATTGACACC-TTTCTGCCA
1 TTATTCTTTTACTCAACAGTATTTAACTGTTCATATAACTTGCATAATTGAC-CCTTTTCTGCCA
581778 ATTGCACAGTTAGACTA
65 ATTGCACAGTTA-ACTA
* * * ** * *
581795 TTATTCTTTTACTCAACAATGTTTAACCGTTCACCTAA-TTGACATAATTGACACTTTTCTACCA
1 TTATTCTTTTACTCAACAGTATTTAACTGTTCATATAACTTG-CATAATTGACCCTTTTCTGCCA
*
581859 ATTGCACAGTTAGGCTA
65 ATTGCACAGTTA-ACTA
* ** * ** *
581876 TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTCACATAATTGACACC-TTTCTACCA
1 TTATTCTTTTACTCAACAGTATTTAACTGTTCATATAACTTGCATAATTGAC-CCTTTTCTGCCA
581940 ATTGCACAGTTA
65 ATTGCACAGTTA
581952 GGCCTCAAAG
Statistics
Matches: 201, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
80 13 0.06
81 183 0.91
82 5 0.02
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (80 bp):
TTATTCTTTTACTCAACAGTATTTAACTGTTCATATAACTTGCATAATTGACCCTTTTCTGCCAA
TTGCACAGTTAACTA
Found at i:581952 original size:81 final size:81
Alignment explanation
Indices: 581713--581954 Score: 367
Period size: 81 Copynumber: 3.0 Consensus size: 81
581703 CAGCTAATCC
* * * *
581713 ATTATTCTTTTACTCAACGGTATTTAACTGTTCATATAACTGGCATAATTGACACCTTTCTGCCA
1 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGACATAATTGACACCTTTCTACCA
*
581778 ATTGCACAGTTAGACT
66 ATTGCACAGTTAGGCT
** * * * *
581794 ATTATTCTTTTACTCAACAATGTTTAACCGTTCACCTAATTGACATAATTGACACTTTTCTACCA
1 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGACATAATTGACACCTTTCTACCA
581859 ATTGCACAGTTAGGCT
66 ATTGCACAGTTAGGCT
* *
581875 ATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTCACATAATTGACACCTTTCTACCA
1 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGACATAATTGACACCTTTCTACCA
581940 ATTGCACAGTTAGGC
66 ATTGCACAGTTAGGC
581955 CTCAAAGGAA
Statistics
Matches: 142, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 142 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (81 bp):
ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGACATAATTGACACCTTTCTACCA
ATTGCACAGTTAGGCT
Found at i:581996 original size:68 final size:68
Alignment explanation
Indices: 581905--582364 Score: 708
Period size: 68 Copynumber: 6.8 Consensus size: 68
581895 TATTTAACCA
** * ** *
581905 TTCATCTAACTCACATAATTGACACCTTTCTACCAATTGCACAGTTAGGCCTCAAAGGAACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
*
581970 CAT
66 CCT
* *
581973 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAAGCCT-AAAAGACACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGA-ACTTA
*
582037 ACCT
65 GCCT
** * * *
582041 TTCATCTAACTGGCATAAATGACACCTTTCTAACAAATGCATAGTTAGGTCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
582106 CCT
66 CCT
*
582109 TTCATCTAACTGGCATAAATGACAGCTTTCTGTCAAATGCACAGTTAGGCCTCAAA-GACACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGA-ACTTA
582173 GCCT
65 GCCT
* *
582177 TTCATCTAACTGGCATAAATGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
582242 CCT
66 CCT
*
582245 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
582310 CCT
66 CCT
*
582313 TTCATCTAACTGGCATAAATGACACCTTTCTGTTAAATGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCT
582365 ATAATCTTTT
Statistics
Matches: 359, Mismatches: 29, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
67 6 0.02
68 348 0.97
69 5 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
CCT
Found at i:582709 original size:59 final size:59
Alignment explanation
Indices: 582614--582792 Score: 256
Period size: 59 Copynumber: 3.1 Consensus size: 59
582604 TCTTATTTCA
* * *
582614 CACACATAGTGCCC-ATATGAAAACTCATACACTTAGTATGAATTTCTTAACATTTTAG
1 CACACAAAGTGCCCAATAAGAAAAATCATACACTTAGTATGAATTTCTTAACATTTTAG
* * * *
582672 CACACAAAGTTCCCAATACA-TAAATTCATACACTTAGTATGAATTTCTTAACCTTTTAG
1 CACACAAAGTGCCCAATA-AGAAAAATCATACACTTAGTATGAATTTCTTAACATTTTAG
*
582731 CACACATAGTGCCCAATAAGAAAAATCATACACTTAGTATGAATTTCTTAACATTTTA-
1 CACACAAAGTGCCCAATAAGAAAAATCATACACTTAGTATGAATTTCTTAACATTTTAG
582789 CACA
1 CACA
582793 TTAGTGCCAT
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
58 17 0.16
59 90 0.84
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (59 bp):
CACACAAAGTGCCCAATAAGAAAAATCATACACTTAGTATGAATTTCTTAACATTTTAG
Found at i:582765 original size:118 final size:111
Alignment explanation
Indices: 582581--582792 Score: 318
Period size: 118 Copynumber: 1.8 Consensus size: 111
582571 TACCATACGG
* *
582581 AAATTCATACATTGATATGAATTTCTTATTTCACACACATAGTGCCCATATGAAAACTCATACAC
1 AAATTCATACATTGATATGAATTTCTTATTTCACACACATAGTGCCCATAAGAAAAATCATACAC
582646 TTAGTATGAATTTCTTAACATTTTAGCACACAAAGTTCCCAATACAT
66 TTAGTATGAATTTCTTAACATTTTA-CACACAAAGTTCCCAATACAT
*
582693 AAATTCATACACTT-AGTATGAATTTCTTAACCTTTTAGCACACATAGTGCCCAATAAGAAAAAT
1 AAATTCATACA-TTGA-TATGAATTTCTT-A--TTTCA-CACACATAGTGCCC-ATAAGAAAAAT
582757 CATACACTTAGTATGAATTTCTTAACATTTTACACA
59 CATACACTTAGTATGAATTTCTTAACATTTTACACA
582793 TTAGTGCCAT
Statistics
Matches: 90, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
112 12 0.13
113 14 0.16
114 1 0.01
116 4 0.04
117 18 0.20
118 41 0.46
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (111 bp):
AAATTCATACATTGATATGAATTTCTTATTTCACACACATAGTGCCCATAAGAAAAATCATACAC
TTAGTATGAATTTCTTAACATTTTACACACAAAGTTCCCAATACAT
Found at i:583289 original size:94 final size:96
Alignment explanation
Indices: 583157--583337 Score: 276
Period size: 95 Copynumber: 1.9 Consensus size: 96
583147 ACTTCTATAA
* *
583157 TATGGTACAAATACCCCCTTTTGGTATCGATACCAATTTTAGTTTCGATG-TTGCCTGGTATCAA
1 TATGGTACAAATACCCCCTTTTGGTATAGATACCAATTTTAGATTCGATGTTTGCCTGGTATCAA
*
583221 TATCCTTACCATGGTATCGATATTACCATAC
66 TACCCTTACCATGGTATCGATATTACCATAC
** * * *
583252 TATGGTACTGATA-CCCCTTTTGGTATAGATACCAATTTTAGATTCGATGTTTTCTTGGTATCGA
1 TATGGTACAAATACCCCCTTTTGGTATAGATACCAATTTTAGATTCGATGTTTGCCTGGTATCAA
583316 TACCCTTACCATGGTATCGATA
66 TACCCTTACCATGGTATCGATA
583338 CTATCTCGTC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 34 0.44
95 43 0.56
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (96 bp):
TATGGTACAAATACCCCCTTTTGGTATAGATACCAATTTTAGATTCGATGTTTGCCTGGTATCAA
TACCCTTACCATGGTATCGATATTACCATAC
Found at i:583351 original size:20 final size:20
Alignment explanation
Indices: 583328--583381 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
583318 CCCTTACCAT
*
583328 GGTATCGATACTATCTC-GTC
1 GGTATCGATACTAT-TCAATC
583348 GGTATCGATACTGATTCAATC
1 GGTATCGATACT-ATTCAATC
*
583369 AGTATCGATACTA
1 GGTATCGATACTA
583382 CTCAGTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (20 bp):
GGTATCGATACTATTCAATC
Found at i:589996 original size:12 final size:12
Alignment explanation
Indices: 589969--590008 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
589959 ATTTACTATT
*
589969 ATTATATATTTA
1 ATTATATATTAA
589981 ATTAT-TATTAA
1 ATTATATATTAA
589992 TATTATATATTAA
1 -ATTATATATTAA
590005 ATTA
1 ATTA
590009 AAGTAAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 5 0.20
12 14 0.56
13 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTATATATTAA
Found at i:592867 original size:29 final size:29
Alignment explanation
Indices: 592822--592906 Score: 161
Period size: 29 Copynumber: 2.9 Consensus size: 29
592812 AAGGTCCAAG
*
592822 GATCGTAGCTTTGCTTGAAACGAGGACTA
1 GATCGTAGCTTTACTTGAAACGAGGACTA
592851 GATCGTAGCTTTACTTGAAACGAGGACTA
1 GATCGTAGCTTTACTTGAAACGAGGACTA
592880 GATCGTAGCTTTACTTGAAACGAGGAC
1 GATCGTAGCTTTACTTGAAACGAGGAC
592907 CAGCTGTAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (29 bp):
GATCGTAGCTTTACTTGAAACGAGGACTA
Found at i:596822 original size:16 final size:16
Alignment explanation
Indices: 596801--596832 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
596791 TGAGAAAAAT
596801 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
*
596817 TTAATTTAATTTTAAA
1 TTAATTTAAATTTAAA
596833 ATAACATTAA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:597058 original size:16 final size:16
Alignment explanation
Indices: 597037--597067 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
597027 TCGCATTTTA
597037 TCGATATTGCGTCGCG
1 TCGATATTGCGTCGCG
*
597053 TCGATATTGTGTCGC
1 TCGATATTGCGTCGC
597068 TGTAACCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.29, T:0.35
Consensus pattern (16 bp):
TCGATATTGCGTCGCG
Found at i:602179 original size:23 final size:21
Alignment explanation
Indices: 602129--602180 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
602119 GGTTATTGGT
*
602129 ATAATTTACCTTTTATTTCAA
1 ATAATTTACCTTTAATTTCAA
*
602150 ATGATTTACCTTTAAATTTTCAA
1 ATAATTTACCTTT-AA-TTTCAA
*
602173 CTAATTTA
1 ATAATTTA
602181 TAATTATACG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 12 0.48
22 1 0.04
23 12 0.48
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (21 bp):
ATAATTTACCTTTAATTTCAA
Found at i:602308 original size:2 final size:2
Alignment explanation
Indices: 602301--602327 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
602291 CATATGTATG
602301 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
602328 TGTATTGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:603376 original size:23 final size:23
Alignment explanation
Indices: 603313--603376 Score: 94
Period size: 22 Copynumber: 2.8 Consensus size: 23
603303 TCAATTTTGC
*
603313 AGCTGCCAATTTGGACTTCAACA
1 AGCTGCCAATTTGGACTTTAACA
603336 AGCT-CCAATTTGGACTTTAACA
1 AGCTGCCAATTTGGACTTTAACA
* *
603358 AGCTGTCAATTTAGACTTT
1 AGCTGCCAATTTGGACTTT
603377 TTTTTAACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 21 0.57
23 16 0.43
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (23 bp):
AGCTGCCAATTTGGACTTTAACA
Found at i:635926 original size:37 final size:37
Alignment explanation
Indices: 635849--635949 Score: 170
Period size: 37 Copynumber: 2.8 Consensus size: 37
635839 CAAGTCAATC
*
635849 AAGCCTTCAC-AAAAGAGTAGTGAAG-GATGCAAATT
1 AAGCCTTCACAAAAAGAGTAGTGAAGCAATGCAAATT
635884 AAGCCTTCACAAAAAGAGTAGTGAAGCAATGCAAATT
1 AAGCCTTCACAAAAAGAGTAGTGAAGCAATGCAAATT
*
635921 CAGCCTTCACAAAAAGAGTAGTGAAGCAA
1 AAGCCTTCACAAAAAGAGTAGTGAAGCAA
635950 GATCAGATCA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 10 0.16
36 15 0.24
37 37 0.60
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.18
Consensus pattern (37 bp):
AAGCCTTCACAAAAAGAGTAGTGAAGCAATGCAAATT
Found at i:652705 original size:551 final size:548
Alignment explanation
Indices: 651661--652755 Score: 1430
Period size: 551 Copynumber: 2.0 Consensus size: 548
651651 AAGGATTACA
*** *
651661 CCATGTTTAATGATGCATTATTAAATGGCTTAGGGTATATATTAATGCAAGAATGGAAGGATTTG
1 CCATGTTTAATGATGCATTATTAAACAACTTAGGGTATATATTAATGCAAGAAAGGAAGGATTTG
* * * ** *
651726 GCCTTTGCATCCCGACAACTCAAGCCGTTTGAGCATACTTATCTTACCCATGATTTGGAACTTGT
66 GCCTATGCATCCCGACAACTCAAGCCGTATGAGCATACCTATCCCACCCATGATTTAGAACTTGT
* * * * * *
651791 TGCAGTAGTCTTCACTTTAAAGATTTGGTGGCGCTACTTATTTGGGTAGAAATTCTACATCTTCA
131 TACAGTAGTCTTCACCTTAAAGATTTAGAGGCACTACTTATTTGGGTAGAAATGCTACATCTTCA
* *
651856 CATACCACAAGAGCCTCAAGTACCTACTCACGCTAAAAGAGTTGAATTTAAGACCGTGTAGGTGA
196 CATACCACAAGAGCCTCAAGTACCTACTCACACAAAAAGAGTTGAATTTAAGACCGTGTAGGTGA
* * * * ** *
651921 GTAGAACATTCGAAGAATTACGACTATGTTATCAACTATCATCTTGAGAATGCTAGTGTTGTTGC
261 GTAGAACATTCGAAGAATTACAACTATGTTATCAACTATCATCCTGAGAAAGCTAATGCGGTTGA
** * * * **
651986 TTATGATCTACGTCAGAAGTTGATAAATGAGTTACGAGCTTTGTTAGCATGTTTGAGCTTGACAG
326 TTATGATCTAAATCAGAAGTTGATAAACGAGTTACAAGCTTTGCTAGCACATTTGAGCTTGACAG
* ** * * *
652051 TAGAGGGAAGTTTACTAGCTTAGTTGATGGTAGAGCCCAGATTTGTAAGCACAACAAAGGATTAG
391 TAGAAGGAAGTTTACTAGCAGAGTTCAGGGTAGAGCCCAGATTGGTAAGCACAACAAAGGATTAG
* *
652116 CACCCAATTTTGAGCTAAAATATGGGGACGTGTTGTACTTTAGGAGTAATTTATTCGTCCCATAA
456 CACCCAATTTTGAGCTAAAATATGGGGACGTCTTGTACTTTA-G-G-AATTTATACGTCCCATAA
*
652181 GATGAATAGTTACGTAGTAAGATTTTTCATC
518 GATGAATAGTTACATAGTAAGATTTTTCATC
*
652212 CCATGTTTAATGATGCATTATTAAACAACTTAGGGTATGTATTAATGCAAGAAAGGAAGG-TTGT
1 CCATGTTTAATGATGCATTATTAAACAACTTAGGGTATATATTAATGCAAGAAAGGAAGGATT-T
* * *
652276 GGCCTATGGATCCCAGA-AACTCAAGCTGTATGAGCGTACCTATCCCACCCATGATTTAGAACTT
65 GGCCTATGCATCCC-GACAACTCAAGCCGTATGAGCATACCTATCCCACCCATGATTTAGAACTT
* *
652340 GTTACAGTAGTCTTCACCTTAAAGATTTAGAGGTATTACTTATTCT-GGTAGAAATGCTACATCT
129 GTTACAGTAGTCTTCACCTTAAAGATTTAGAGGCACTACTTATT-TGGGTAGAAATGCTACATCT
* *
652404 TCACATACCACAAGAGTCTCAAGTACCTACTCACACAAAAAGAGTTGAATTTAATACCGTGTAGG
193 TCACATACCACAAGAGCCTCAAGTACCTACTCACACAAAAAGAGTTGAATTTAAGACCGTGTAGG
* * * * * * * *
652469 TGATTAGATCTTTGGAAGGATTACAACTGTGTTATCGACTATCATCCTGGGAAAGCTAATGCGGT
258 TGAGTAGAACATTCGAAGAATTACAACTATGTTATCAACTATCATCCTGAGAAAGCTAATGCGGT
*
652534 T-ATTAATGCTCTAAATCAGAAGTTGATAAACGAGTTACAAGCTTTGCTAGCACATTTGAGCTTG
323 TGATT-ATGATCTAAATCAGAAGTTGATAAACGAGTTACAAGCTTTGCTAGCACATTTGAGCTTG
** * *
652598 ACTA-TAGAAGGAAGTTTACTAGCAGAGTTCAGGGTAGAGCCC-GAATTGGTGGGCATAATGAAA
387 AC-AGTAGAAGGAAGTTTACTAGCAGAGTTCAGGGTAGAGCCCAG-ATTGGTAAGCACAA-CAAA
* * * *
652661 GGGTTAGCACCCGATTTTGAGCTAAAA-ATGGGGATGTCTTGTACTTTAGGCATTTATACGTCCC
449 GGATTAGCACCCAATTTTGAGCTAAAATATGGGGACGTCTTGTACTTTAGGAATTTATACGTCCC
* * *
652725 ATTAGATGAATAGTTGCATAGTAATATTTTT
514 ATAAGATGAATAGTTACATAGTAAGATTTTT
652756 TGTAGTCTAT
Statistics
Matches: 468, Mismatches: 69, Indels: 17
0.84 0.12 0.03
Matches are distributed among these distances:
548 39 0.08
549 1 0.00
550 6 0.01
551 390 0.83
552 32 0.07
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (548 bp):
CCATGTTTAATGATGCATTATTAAACAACTTAGGGTATATATTAATGCAAGAAAGGAAGGATTTG
GCCTATGCATCCCGACAACTCAAGCCGTATGAGCATACCTATCCCACCCATGATTTAGAACTTGT
TACAGTAGTCTTCACCTTAAAGATTTAGAGGCACTACTTATTTGGGTAGAAATGCTACATCTTCA
CATACCACAAGAGCCTCAAGTACCTACTCACACAAAAAGAGTTGAATTTAAGACCGTGTAGGTGA
GTAGAACATTCGAAGAATTACAACTATGTTATCAACTATCATCCTGAGAAAGCTAATGCGGTTGA
TTATGATCTAAATCAGAAGTTGATAAACGAGTTACAAGCTTTGCTAGCACATTTGAGCTTGACAG
TAGAAGGAAGTTTACTAGCAGAGTTCAGGGTAGAGCCCAGATTGGTAAGCACAACAAAGGATTAG
CACCCAATTTTGAGCTAAAATATGGGGACGTCTTGTACTTTAGGAATTTATACGTCCCATAAGAT
GAATAGTTACATAGTAAGATTTTTCATC
Found at i:653365 original size:21 final size:20
Alignment explanation
Indices: 653317--653365 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
653307 TAGTCCCAAA
*
653317 TCAACATTCTAAATCAAAAT
1 TCAACATTCAAAATCAAAAT
* * *
653337 TTAGCATTCAACAATTAAAAT
1 TCAACATTCAA-AATCAAAAT
653358 TCAACATT
1 TCAACATT
653366 GAATACCCAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (20 bp):
TCAACATTCAAAATCAAAAT
Found at i:662560 original size:22 final size:23
Alignment explanation
Indices: 662519--662567 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
662509 GAATATTCAG
662519 TTTAAATAATTATTAGAAATA-A
1 TTTAAATAATTATTAGAAATATA
662541 TTTAAATAA-T-TTAGATAAATATA
1 TTTAAATAATTATTAG--AAATATA
662564 TTTA
1 TTTA
662568 TTTATATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.17
21 1 0.04
22 14 0.58
23 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
TTTAAATAATTATTAGAAATATA
Found at i:662622 original size:22 final size:23
Alignment explanation
Indices: 662596--662644 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
662586 AGAAAAAGTC
*
662596 TTTTAACATATATTAAA-TAATT
1 TTTTAACATATATTAAAGAAATT
* *
662618 TTTTAATATATTTTAAAGAAATT
1 TTTTAACATATATTAAAGAAATT
662641 TTTT
1 TTTT
662645 TTTGGATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTAACATATATTAAAGAAATT
Found at i:683842 original size:15 final size:15
Alignment explanation
Indices: 683822--683852 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
683812 TTTAAAACAT
683822 CCATGAAAAATATTC
1 CCATGAAAAATATTC
683837 CCATGAAAAATATTC
1 CCATGAAAAATATTC
683852 C
1 C
683853 AAACAATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.26
Consensus pattern (15 bp):
CCATGAAAAATATTC
Found at i:687431 original size:57 final size:57
Alignment explanation
Indices: 687340--687606 Score: 310
Period size: 57 Copynumber: 4.8 Consensus size: 57
687330 ATGGCACTGA
* ** * *
687340 GTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATGGGAACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCCGTATGGGAACTAT
* * * *
687397 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTAT
1 GTGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCCGTATGGGAACTAT
* ** *
687454 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCACTAT
1 GTGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCCGTATGGGAACTAT
* * * *
687511 GTGTGC--AAA-CTAAGAAATTCATACTAAGTGTGTGAATTTTCGTATGGAAACTAT
1 GTGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCCGTATGGGAACTAT
* * * *
687565 ATGTGCAAACA--TAAGAAATTCATAATAAGTATGTGAATTTCC
1 GTGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCC
687607 ATATTGGCAG
Statistics
Matches: 190, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
54 46 0.24
55 31 0.16
56 2 0.01
57 111 0.58
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (57 bp):
GTGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCCGTATGGGAACTAT
Found at i:693614 original size:19 final size:21
Alignment explanation
Indices: 693590--693640 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
693580 TGCAAAAATG
*
693590 GTATCGATAC-TGTAATAG-A
1 GTATCGATACATATAATAGTA
*
693609 GTATCGATATCATATTATAGTA
1 GTATCGATA-CATATAATAGTA
693631 GTATCGATAC
1 GTATCGATAC
693641 CATGGTAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 9 0.33
20 1 0.04
21 7 0.26
22 10 0.37
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (21 bp):
GTATCGATACATATAATAGTA
Found at i:694127 original size:57 final size:57
Alignment explanation
Indices: 693983--694426 Score: 480
Period size: 57 Copynumber: 8.0 Consensus size: 57
693973 ATTACCAAAT
*
693983 GGCACTGA-GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTAT-
1 GGCACT-ATGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* *
694039 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATG
1 GGCACTATGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* * *
694096 GGCACTTTGTGTGCAATAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATG
1 GGCACTATGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* * * * *
694153 GGTACTTTGTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCATATG
1 GGCACTATGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* * * * * * * *
694210 GACAC--TGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTGTGAATTTCCATAAG
1 GGCACTATGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* * * * * *
694265 GGCACTATGTGTGC--AAA-CTAAGAAATTCATACTAAGTGTGTGAATTTACGTAAG
1 GGCACTATGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* * * *
694319 GGCACTATGTGTGC--AAA-CTAAGAAATTCATACTAAGTGTGTGAATTTTCGTATG
1 GGCACTATGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* * * ***
694373 GGAACTATATGTGCAAACA--TAAGAAATTCATAATAAGTAGGTGAATTTTCGTAT
1 GGCACTATGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
694427 TAGTAGTGGG
Statistics
Matches: 357, Mismatches: 25, Indels: 13
0.90 0.06 0.03
Matches are distributed among these distances:
54 99 0.28
55 83 0.23
56 56 0.16
57 119 0.33
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (57 bp):
GGCACTATGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
Found at i:694298 original size:27 final size:27
Alignment explanation
Indices: 694268--694358 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 27
694258 CCATAAGGGC
694268 ACTATGTGTGCAAACTAAGAAATTCAT
1 ACTATGTGTGCAAACTAAGAAATTCAT
** * ***
694295 ACTAAGTGTGTG-AATTTACGTAAGGGC--
1 ACT-A-TGTGTGCAAACTAAG-AAATTCAT
694322 ACTATGTGTGCAAACTAAGAAATTCAT
1 ACTATGTGTGCAAACTAAGAAATTCAT
*
694349 ACTAAGTGTG
1 ACTATGTGTG
694359 TGAATTTTCG
Statistics
Matches: 45, Mismatches: 13, Indels: 12
0.64 0.19 0.17
Matches are distributed among these distances:
25 9 0.20
26 6 0.13
27 15 0.33
28 6 0.13
29 9 0.20
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (27 bp):
ACTATGTGTGCAAACTAAGAAATTCAT
Found at i:694443 original size:55 final size:54
Alignment explanation
Indices: 694228--694426 Score: 188
Period size: 54 Copynumber: 3.7 Consensus size: 54
694218 GTGCAAAAAG
* * * * * * *
694228 CTAAGAAATTCATACTAAGTGTGTGAATTTCCATAAGGGCACTATG-TGTGCAAA
1 CTAAGAAATTCATAATAAGTGTGTGAATTTTCGTATGAGAACTA-GATATGCAAA
* * * * * *
694282 CTAAGAAATTCATACTAAGTGTGTGAATTTACGTAAGGGCACTATG-TGTGCAAA
1 CTAAGAAATTCATAATAAGTGTGTGAATTTTCGTATGAGAACTA-GATATGCAAA
* * * *
694336 CTAAGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGAACTATATGTGCAAA
1 CTAAGAAATTCATAATAAGTGTGTGAATTTTCGTATGAGAACTAGATATGCAAA
694390 CATAAGAAATTCATAATAAGTAG-GTGAATTTTCGTAT
1 C-TAAGAAATTCATAATAAGT-GTGTGAATTTTCGTAT
694427 TAGTAGTGGG
Statistics
Matches: 135, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
54 102 0.76
55 32 0.24
56 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (54 bp):
CTAAGAAATTCATAATAAGTGTGTGAATTTTCGTATGAGAACTAGATATGCAAA
Found at i:695595 original size:20 final size:20
Alignment explanation
Indices: 695570--695610 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
695560 CCAAACCACC
*
695570 AAATGCAACTATATGATCCT
1 AAATGCAACTAAATGATCCT
*
695590 AAATGCATCTAAATGATCCT
1 AAATGCAACTAAATGATCCT
695610 A
1 A
695611 CATGTGCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATGCAACTAAATGATCCT
Found at i:696690 original size:18 final size:18
Alignment explanation
Indices: 696667--696705 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
696657 TTACAATTAC
696667 AATCCTAATTTGATTAAA
1 AATCCTAATTTGATTAAA
*
696685 AATCCTAGTTTGATTAAA
1 AATCCTAATTTGATTAAA
696703 AAT
1 AAT
696706 AGATAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (18 bp):
AATCCTAATTTGATTAAA
Found at i:702470 original size:39 final size:39
Alignment explanation
Indices: 702404--702526 Score: 149
Period size: 39 Copynumber: 3.2 Consensus size: 39
702394 GGAATACCAA
* *
702404 CCATCCACT-CCATGCATGTGAACACCAACCGTACACTT
1 CCATGCACTACCATGCATGTGAACACCAACCATACACTT
* * *
702442 CCATGCACTGCCCTGCATGTGAACACCAACCATCCACTT
1 CCATGCACTACCATGCATGTGAACACCAACCATACACTT
* * * * *
702481 CCGTGAACTACCATGCTTGTGAACACCAACCATGCACTA
1 CCATGCACTACCATGCATGTGAACACCAACCATACACTT
702520 CCATGCA
1 CCATGCA
702527 TGTGAACTGG
Statistics
Matches: 71, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
38 8 0.11
39 63 0.89
ACGTcount: A:0.28, C:0.38, G:0.13, T:0.20
Consensus pattern (39 bp):
CCATGCACTACCATGCATGTGAACACCAACCATACACTT
Found at i:708952 original size:19 final size:19
Alignment explanation
Indices: 708915--708958 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
708905 CGATATTGAC
**
708915 GTAGCACCCTACATTCAATA
1 GTAG-ACCCTACAACCAATA
708935 GTAGACCCTACAACCAATA
1 GTAGACCCTACAACCAATA
*
708954 TTAGA
1 GTAGA
708959 TTTCTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (19 bp):
GTAGACCCTACAACCAATA
Done.