Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 17
Found at i:12378 original size:27 final size:27
Alignment explanation
Indices: 12347--12399 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
12337 AATAAATTTA
*
12347 ATTTAAATGAAAAATATATATTTATAT
1 ATTTAAATGAAAAATATATATATATAT
* * *
12374 ATTTAATTTAAATATATATATATATA
1 ATTTAAATGAAAAATATATATATATA
12400 CCCGGCCCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTTAAATGAAAAATATATATATATAT
Found at i:12432 original size:12 final size:12
Alignment explanation
Indices: 12417--12451 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
12407 CGATTCTAGG
12417 CCCAATACCCGA
1 CCCAATACCCGA
*
12429 CCCAATACCCGG
1 CCCAATACCCGA
12441 CCCAATACCCG
1 CCCAATACCCG
12452 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:13469 original size:20 final size:20
Alignment explanation
Indices: 13427--13470 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
13417 GTTTTACTCT
***
13427 TATATTTATTAATTTAGTTA
1 TATATTTATTAATTTAACCA
*
13447 TATATTTTTTAATTTAACCA
1 TATATTTATTAATTTAACCA
13467 TATA
1 TATA
13471 CTTAAATTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (20 bp):
TATATTTATTAATTTAACCA
Found at i:14710 original size:21 final size:21
Alignment explanation
Indices: 14693--14751 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 21
14683 CAATATAACC
14693 ACTACCTATTACATTATATAAA
1 ACTACCTATTACATTATA-AAA
**
14715 ACGATACCTATTACATTATAAGG
1 AC--TACCTATTACATTATAAAA
*
14738 GCTACCTATTACAT
1 ACTACCTATTACAT
14752 CATATGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 12 0.38
22 2 0.06
23 2 0.06
24 16 0.50
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (21 bp):
ACTACCTATTACATTATAAAA
Found at i:15827 original size:22 final size:23
Alignment explanation
Indices: 15796--15838 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
15786 TTCCACAGTG
15796 AAAAAAGTATAGACAC-TTTTAT
1 AAAAAAGTATAGACACATTTTAT
* *
15818 AAAAAGGTATCGACACATTTT
1 AAAAAAGTATAGACACATTTT
15839 TATACCGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (23 bp):
AAAAAAGTATAGACACATTTTAT
Found at i:16296 original size:181 final size:181
Alignment explanation
Indices: 15834--16510 Score: 1080
Period size: 178 Copynumber: 3.8 Consensus size: 181
15824 GTATCGACAC
*
15834 ATTTTTATACCGGTTATATACAAAATTATCTATTACCTTATAAATCTGGGTTCCGATGTGTAAAT
1 ATTTTTATACCGGTTATATACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAAT
*
15899 GTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACACA
66 GTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACA
*
15964 ATATTAGAAAGTGTCGATA-AGGTGTAGACCTATTCACTCATAAAACCGGT
131 ATATTAGAAAGTGTCGATATAGGTGTAGACCTATTCGCTCATAAAACCGGT
* *
16014 A-TTTT-TACCGATTATATTACAAAATTATCTA-TACA-T-TAAATATGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATA-TACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
16074 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
65 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
16139 -ATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
130 AATATTAGAAAGTGTCGATATAGG-TGTAGACCTATTCGCTCATAAAACCGGT
16191 ATTTTTATA-CGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATA-TACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
16255 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCC-ATCTGGACATAAAGTACCGACAC
65 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
16319 AATATTAGAAAGTGTCGATATAGGT-T-GACCTATTCGCTCATAAAACCGGT
130 AATATTAGAAAGTGTCGATATAGGTGTAGACCTATTCGCTCATAAAACCGGT
* * *
16369 ATATTTATACCGGTTATATACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTTTTTTC
1 ATTTTTATACCGGTTATATACAAAATTATCTATTACATTATAAATCTGGGTTCCGATG---TGTA
* **
16434 AA--TCGACAC-TTTTTAAATGGTATCGACACATTTTTCTT-CATTCTGGACAT-AAGTACAAAC
63 AATGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGAC
*
16494 ACAATATTAAAAAGTGT
128 ACAATATTAGAAAGTGT
16511 GAAAACTTTG
Statistics
Matches: 469, Mismatches: 14, Indels: 31
0.91 0.03 0.06
Matches are distributed among these distances:
175 19 0.04
176 90 0.19
177 54 0.12
178 149 0.32
179 40 0.09
180 26 0.06
181 91 0.19
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (181 bp):
ATTTTTATACCGGTTATATACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAAT
GTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACA
ATATTAGAAAGTGTCGATATAGGTGTAGACCTATTCGCTCATAAAACCGGT
Found at i:17703 original size:3 final size:3
Alignment explanation
Indices: 17695--17769 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
17685 ACTTGTTTGG
* * * * **
17695 ATC ATC ATC TTC ATC ATC ATC AAC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
17743 AGC TTC ATC GTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
17770 GTCGCTTCAT
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.27, C:0.35, G:0.05, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:19943 original size:395 final size:397
Alignment explanation
Indices: 19215--20306 Score: 2081
Period size: 395 Copynumber: 2.8 Consensus size: 397
19205 TTTAAATTAG
19215 TATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
19278 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
19342 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTAATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
19406 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGT
19471 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
19536 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
19601 AAAAAAA
391 AAAAAAA
19608 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA-TCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
19671 ATTGTACC-GTTAGATTGAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTG-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
19735 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
19800 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
19865 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
19930 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGG
325 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
19995 AAAAAAAA
390 AAAAAAAA
*
20003 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
20068 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
20133 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
20198 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
20263 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATA
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATA
20307 TGGATCGACA
Statistics
Matches: 686, Mismatches: 4, Indels: 13
0.98 0.01 0.02
Matches are distributed among these distances:
392 9 0.01
393 59 0.09
394 87 0.13
395 276 0.40
396 8 0.01
397 126 0.18
398 121 0.18
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (397 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
AAAAAAA
Found at i:20038 original size:199 final size:199
Alignment explanation
Indices: 19215--20306 Score: 2058
Period size: 199 Copynumber: 5.5 Consensus size: 199
19205 TTTAAATTAG
*
19215 TATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
19278 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
19342 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTAATTCTGG--AA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
19405 AAAA
196 AAAA
19409 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
19474 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
19539 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
19604 AAAA
196 AAAA
19608 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATAT-CTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
19671 ATTGTACC-GTTAGATTGAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTG-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
19735 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
19799 AAAAA
195 AAAAA
19804 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
19869 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
19934 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
19999 AAAA
196 AAAA
* *
20003 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
20068 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
20133 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
20198 AAAA
196 AAAA
20202 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
20267 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATA
20307 TGGATCGACA
Statistics
Matches: 881, Mismatches: 7, Indels: 15
0.98 0.01 0.02
Matches are distributed among these distances:
194 13 0.01
196 155 0.18
197 213 0.24
198 133 0.15
199 367 0.42
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:20480 original size:18 final size:18
Alignment explanation
Indices: 20454--20501 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
20444 TTATATTCAC
*
20454 ATACAAAAATATAAATCGT
1 ATACAAAATTAT-AATCGT
*
20473 ATACAAAATTATAATCTT
1 ATACAAAATTATAATCGT
20491 ATACAAAATTA
1 ATACAAAATTA
20502 ACTCGACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (18 bp):
ATACAAAATTATAATCGT
Found at i:22324 original size:33 final size:33
Alignment explanation
Indices: 22287--22352 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
22277 CATCTTAATA
*
22287 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
22320 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
22353 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:24673 original size:17 final size:18
Alignment explanation
Indices: 24651--24693 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
24641 ATATATCCGG
24651 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
24668 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
24688 TATCAT
1 TATCAT
24694 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:24711 original size:20 final size:19
Alignment explanation
Indices: 24656--24702 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
24646 TCCGGTATCA
24656 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
24675 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
24696 TTTTACC
1 TTTTACC
24703 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:24850 original size:20 final size:20
Alignment explanation
Indices: 24825--24884 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
24815 ACTTTTAAAT
24825 TTACCGGTTTTATCATTTTG
1 TTACCGGTTTTATCATTTTG
24845 TTACCGGTTTTATCATATTT-
1 TTACCGGTTTTATCAT-TTTG
*
24865 TTACCTGG-TATATCATTTTG
1 TTACC-GGTTTTATCATTTTG
24885 GATCGATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 3 0.08
20 28 0.78
21 5 0.14
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.53
Consensus pattern (20 bp):
TTACCGGTTTTATCATTTTG
Found at i:25336 original size:229 final size:228
Alignment explanation
Indices: 24935--25383 Score: 799
Period size: 229 Copynumber: 2.0 Consensus size: 228
24925 TTAAAACTGC
24935 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
25000 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* * *
25065 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATGA
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAA
*
25130 GTATGGACACTTTTATAAAAATGATATATACTTT
195 GTATGGACACTTTTATAAAAAGGATATATACTTT
*
25164 TTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
*
25229 TTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
25294 TTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
25359 TATGGACACTTTTATAAAAAGGATA
196 TATGGACACTTTTATAAAAAGGATA
25384 GATAATTTAC
Statistics
Matches: 210, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
228 36 0.17
229 174 0.83
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (228 bp):
TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATATACTTT
Found at i:28575 original size:2 final size:2
Alignment explanation
Indices: 28568--28618 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
28558 GACCGTTTAA
28568 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
28610 AT AT AT AT A
1 AT AT AT AT A
28619 GAGAGAGAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40894 original size:21 final size:21
Alignment explanation
Indices: 40870--40944 Score: 64
Period size: 23 Copynumber: 3.5 Consensus size: 21
40860 CCCAGGGGGT
40870 ATCGATTCCCTAAAGGAGGGA
1 ATCGATTCCCTAAAGGAGGGA
*
40891 ATCGGTTCCCATTCAAAGG-GGGA
1 ATCGATTCCC--T-AAAGGAGGGA
* * * *
40914 ATCGGTTCCCT-TATGAGGGT
1 ATCGATTCCCTAAAGGAGGGA
40934 ATCGATTCCCT
1 ATCGATTCCCT
40945 TTGCCAAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
19 2 0.04
20 13 0.29
21 10 0.22
23 15 0.33
24 5 0.11
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (21 bp):
ATCGATTCCCTAAAGGAGGGA
Found at i:46762 original size:20 final size:19
Alignment explanation
Indices: 46703--46751 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
46693 TTGAACAGTG
46703 GGGGGGAATCGATACCCCT
1 GGGGGGAATCGATACCCCT
46722 GGGGGGAATCGATACCCCT
1 GGGGGGAATCGATACCCCT
46741 GGGGGGAATCG
1 GGGGGGAATCG
46752 GTTACCTCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.43, T:0.14
Consensus pattern (19 bp):
GGGGGGAATCGATACCCCT
Found at i:50175 original size:22 final size:21
Alignment explanation
Indices: 50133--50172 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
50123 GAGTTTATTT
*
50133 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
50154 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
50173 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:50336 original size:15 final size:15
Alignment explanation
Indices: 50316--50352 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
50306 TTCTTGTTCC
50316 TCTTCATTGGAACTT
1 TCTTCATTGGAACTT
50331 TCTTCATTGGAACTT
1 TCTTCATTGGAACTT
50346 TCTTCAT
1 TCTTCAT
50353 CGCTCCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (15 bp):
TCTTCATTGGAACTT
Found at i:55753 original size:23 final size:21
Alignment explanation
Indices: 55727--55788 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 21
55717 GGAATTATTA
55727 TGTCTTTATGACATGTTTATCTC
1 TGTCTTT-TGACA-GTTTATCTC
*
55750 TGTCTTTGTGACACGTTTATCTT
1 TGTCTTT-TGACA-GTTTATCTC
55773 TGTCTTTTGACAGTTT
1 TGTCTTTTGACAGTTT
55789 TCGATTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 4 0.11
22 5 0.14
23 27 0.75
ACGTcount: A:0.15, C:0.16, G:0.16, T:0.53
Consensus pattern (21 bp):
TGTCTTTTGACAGTTTATCTC
Found at i:57545 original size:20 final size:20
Alignment explanation
Indices: 57520--57560 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
57510 GTGCTGCCTT
57520 TCTGAAAGACTATCACCCTC
1 TCTGAAAGACTATCACCCTC
57540 TCTGAAAGACTATCACCCTC
1 TCTGAAAGACTATCACCCTC
57560 T
1 T
57561 ACAAGTATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.34, G:0.10, T:0.27
Consensus pattern (20 bp):
TCTGAAAGACTATCACCCTC
Found at i:59107 original size:13 final size:14
Alignment explanation
Indices: 59089--59123 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
59079 ACCACTGAGT
59089 TTGACTTTGACT-A
1 TTGACTTTGACTCA
59102 TTGACTTTGACTCA
1 TTGACTTTGACTCA
59116 TTGACTTT
1 TTGACTTT
59124 TTCTGAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (14 bp):
TTGACTTTGACTCA
Found at i:59874 original size:23 final size:23
Alignment explanation
Indices: 59847--59906 Score: 106
Period size: 22 Copynumber: 2.7 Consensus size: 23
59837 ATTAAAACCT
59847 TATTTTTTATTAAATAAAAGTAA
1 TATTTTTTATTAAATAAAAGTAA
59870 TA-TTTTTATTAAATAAAAGTAA
1 TATTTTTTATTAAATAAAAGTAA
59892 TATTTTTTA-TAAATA
1 TATTTTTTATTAAATA
59907 TATTATTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
22 28 0.78
23 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (23 bp):
TATTTTTTATTAAATAAAAGTAA
Found at i:62127 original size:2 final size:2
Alignment explanation
Indices: 62122--62159 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
62112 TTTTTCTTGC
62122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62160 AAAATAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76436 original size:17 final size:18
Alignment explanation
Indices: 76416--76449 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
76406 CCGTGACTTC
76416 CATCA-ATTAGAAATAGG
1 CATCATATTAGAAATAGG
*
76433 CATCATTTTAGAAATAG
1 CATCATATTAGAAATAG
76450 AAAGAATGAG
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:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (18 bp):
CATCATATTAGAAATAGG
Found at i:77645 original size:28 final size:28
Alignment explanation
Indices: 77606--77663 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
77596 ATTTTATGTT
* *
77606 AGGGGTGAACTTGAACTT-TGAAATTTC
1 AGGGGTGAACTTAAACTTATAAAATTTC
77633 AGGGGATGAACTTAAACTTATAAAATTTC
1 AGGGG-TGAACTTAAACTTATAAAATTTC
77662 AG
1 AG
77664 AGAATGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 5 0.19
28 12 0.44
29 10 0.37
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (28 bp):
AGGGGTGAACTTAAACTTATAAAATTTC
Found at i:77670 original size:29 final size:28
Alignment explanation
Indices: 77611--77671 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
77601 ATGTTAGGGG
* * * *
77611 TGAACTTGAACTTTGAAATTTCAGGGGA
1 TGAACTTAAACTTTAAAATTTCAGAGAA
77639 TGAACTTAAACTTATAAAATTTCAGAGAA
1 TGAACTTAAACTT-TAAAATTTCAGAGAA
77668 TGAA
1 TGAA
77672 AATAGATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (28 bp):
TGAACTTAAACTTTAAAATTTCAGAGAA
Found at i:79007 original size:17 final size:17
Alignment explanation
Indices: 78985--79043 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
78975 TCGGGACGGG
78985 TCGGTTCGAGTTGTTTT
1 TCGGTTCGAGTTGTTTT
*
79002 TCGGTTCGGGTTGCTTTT
1 TCGGTTCGAGTTG-TTTT
* *
79020 T-GGTTCGGGTTG-CTT
1 TCGGTTCGAGTTGTTTT
79035 TCGGTTCGA
1 TCGGTTCGA
79044 ATTATTTTCG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.08
16 6 0.16
17 23 0.62
18 5 0.14
ACGTcount: A:0.03, C:0.15, G:0.34, T:0.47
Consensus pattern (17 bp):
TCGGTTCGAGTTGTTTT
Found at i:83791 original size:22 final size:21
Alignment explanation
Indices: 83752--83804 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
83742 TAACACCTAG
*
83752 TAATTTT--AAAAAATTTATA
1 TAATTTTAAAAAAAAATTATA
83771 TAAATTTTAAAAAAAAATTATA
1 T-AATTTTAAAAAAAAATTATA
*
83793 TATTTTTAAAAA
1 TAATTTTAAAAA
83805 GGAAAAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 6 0.21
21 10 0.34
22 12 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATTTTAAAAAAAAATTATA
Found at i:85026 original size:18 final size:17
Alignment explanation
Indices: 84997--85031 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
84987 AATAGTCTTC
*
84997 TTAAAAAAATTATTTTA
1 TTAAAAAAATTAATTTA
85014 TTAAAAAATATTAATTTA
1 TTAAAAAA-ATTAATTTA
85032 GTAATAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAAAAAATTAATTTA
Found at i:85340 original size:16 final size:15
Alignment explanation
Indices: 85319--85352 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
85309 AAATTTCAGT
85319 GAGCTTAATGAGCAAC
1 GAGCTTAATGAGC-AC
85335 GAGCTTAATGAGCAC
1 GAGCTTAATGAGCAC
85350 GAG
1 GAG
85353 TCGAGCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (15 bp):
GAGCTTAATGAGCAC
Found at i:85359 original size:27 final size:28
Alignment explanation
Indices: 85328--85387 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 28
85318 TGAGCTTAAT
*
85328 GAGCAACGAG-CTTAATGAGCACGAGTC
1 GAGCAACAAGTCTTAATGAGCACGAGTC
*
85355 GAGCAACAAGTTTTTTAATGAGCACGAGTC
1 GAGCAACAAG--TCTTAATGAGCACGAGTC
85385 GAG
1 GAG
85388 AAAAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 9 0.32
30 19 0.68
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.20
Consensus pattern (28 bp):
GAGCAACAAGTCTTAATGAGCACGAGTC
Found at i:85396 original size:26 final size:29
Alignment explanation
Indices: 85339--85398 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
85329 AGCAACGAGC
*
85339 TTAATGAGCACGAGTCGAGCAACAAGTTTT
1 TTAATGAGCACGAGTCGAGCAACAAG-ATT
85369 TTAATGAGCACGAGTCGAG-AA-AA-ATT
1 TTAATGAGCACGAGTCGAGCAACAAGATT
85395 TTAA
1 TTAA
85399 CTAGCTTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 6 0.21
28 2 0.07
29 2 0.07
30 19 0.66
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (29 bp):
TTAATGAGCACGAGTCGAGCAACAAGATT
Found at i:101070 original size:3 final size:3
Alignment explanation
Indices: 101064--101105 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
101054 TTTACTCATT
* *
101064 TTA TTA TTA TTA TTA TTA TTA TAA TAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
101106 AAAAATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:106531 original size:15 final size:15
Alignment explanation
Indices: 106511--106542 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
106501 ATCAATACCT
106511 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
106526 TTTTGCATACATTCA
1 TTTTGCATACATGCA
106541 TT
1 TT
106543 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:113880 original size:6 final size:6
Alignment explanation
Indices: 113869--113921 Score: 67
Period size: 6 Copynumber: 9.2 Consensus size: 6
113859 ATGCTTGAAG
*
113869 AGAAAA AG-AAA AGAAAA A-AAAG AGAAAA AGAAAA A-AAAA GAGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA -AGAAAA
113915 AGAAAA A
1 AGAAAA A
113922 AAGGGGTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 13 0.32
6 24 0.59
7 4 0.10
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:113905 original size:18 final size:18
Alignment explanation
Indices: 113877--113923 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
113867 AGAGAAAAAG
113877 AAAAG-AAAAAAAAGAGA
1 AAAAGAAAAAAAAAGAGA
113894 AAAAGAAAAAAAAAGAGA
1 AAAAGAAAAAAAAAGAGA
113912 AAAAGAAAAAAA
1 AAAAGAAAAAAA
113924 GGGGTCAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAAAAGAGA
Found at i:115162 original size:83 final size:83
Alignment explanation
Indices: 115057--115369 Score: 545
Period size: 83 Copynumber: 3.8 Consensus size: 83
115047 AAACATTAGC
*
115057 TTGAAAGATGAATGTGCCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
115122 TAAAACCAATCATTGAAT
66 TAAAACCAATCATTGAAT
* *
115140 TTAAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGG
1 TTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
115205 TAAAACCAATCATTGAAT
66 TAAAACCAATCATTGAAT
*
115223 TTGAAAGATAAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
* *
115288 TAAAACCAGTTATTGAAT
66 TAAAACCAATCATTGAAT
* * *
115306 TTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 TTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
115370 ATATGAAACC
Statistics
Matches: 218, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 218 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
TTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
TAAAACCAATCATTGAAT
Found at i:116409 original size:113 final size:113
Alignment explanation
Indices: 116246--116883 Score: 966
Period size: 113 Copynumber: 5.7 Consensus size: 113
116236 AGTGTCAGTT
*
116246 AAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
116311 CAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAAA
66 CAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAAA
116359 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
116424 CAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAAA
66 CAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAAA
*
116472 AAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
*
116537 CAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGA
66 CAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAAA
*
116585 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
* * *
116650 CAATCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTCT-CCAGAAA
66 CAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTT-TGCCAGAAA
* * * * * *
116698 AAATTCATAATGAGAAGAACTCATCTGAAGAAGGAATAATAAGTTCATAATAAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
* * * * * * * *
116763 CAA-TTTTTCGCTCGAATTCATCA-TTCGATAGATCAACTTT-TCATAAGA
66 CAACCTTTT-GCTCAAATCCATCACTT-GATGGATTAGCTTTGCCAGAA-A
* * *
116811 GAGTTCATAATGAGAAGAACTCATCTGAAG-A--AAGAAGAAGTTCATAATGAGAAGAGTTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
*
116873 CGACCTTTTGC
66 CAACCTTTTGC
116884 ATAACCCTAT
Statistics
Matches: 488, Mismatches: 32, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
110 30 0.06
111 4 0.01
112 12 0.02
113 441 0.90
114 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (113 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
CAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAAA
Found at i:117035 original size:117 final size:119
Alignment explanation
Indices: 116810--117035 Score: 276
Period size: 117 Copynumber: 1.9 Consensus size: 119
116800 TTTTCATAAG
* * * * *
116810 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCG
1 AGAGTTCACAATGAGAAGAACTCATCT--AGAAAGAAGAAGTTCATAATAAGAAGAGCTTATTCA
* * * * * * *
116875 ACCTTTTGCATAACCCTATCATAAAAGGAGATATATCATCATCAACATTTCCAGAA
64 ACCTTTTGAATAACCCTATCACAAAAGAAAAGAGATCAACATCAACATTTCCAGAA
116931 AGAGTTCACAATGAGAAGAACTCATCT-G-AAGAAGAAGTTCATAATAAGAAGAGCTTATTCAAC
1 AGAGTTCACAATGAGAAGAACTCATCTAGAAAGAAGAAGTTCATAATAAGAAGAGCTTATTCAAC
* * * *
116994 CTTTTGAATGACTCTATCACAGAAGAAAAGAGGTCAACATCA
66 CTTTTGAATAACCCTATCACAAAAGAAAAGAGATCAACATCA
117036 TCCCCAGTGG
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
117 62 0.70
118 1 0.01
121 26 0.29
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (119 bp):
AGAGTTCACAATGAGAAGAACTCATCTAGAAAGAAGAAGTTCATAATAAGAAGAGCTTATTCAAC
CTTTTGAATAACCCTATCACAAAAGAAAAGAGATCAACATCAACATTTCCAGAA
Found at i:117233 original size:3 final size:3
Alignment explanation
Indices: 117227--117259 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
117217 TTTACTCATT
117227 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
117260 AAAAATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:120352 original size:17 final size:17
Alignment explanation
Indices: 120330--120364 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
120320 AATATAAGTG
120330 TCTGATACGAGTATGTA
1 TCTGATACGAGTATGTA
*
120347 TCTGATACGGGTATGTA
1 TCTGATACGAGTATGTA
120364 T
1 T
120365 ATTTTTTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (17 bp):
TCTGATACGAGTATGTA
Found at i:123026 original size:23 final size:23
Alignment explanation
Indices: 123000--123044 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
122990 CACCACAGCT
123000 CATATAATTACACCGAAGTGCCA
1 CATATAATTACACCGAAGTGCCA
* *
123023 CATATAATTGCACCGGAGTGCC
1 CATATAATTACACCGAAGTGCC
123045 GCGTAGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (23 bp):
CATATAATTACACCGAAGTGCCA
Found at i:123054 original size:23 final size:23
Alignment explanation
Indices: 123000--123068 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
122990 CACCACAGCT
* *
123000 CATATAATTACACCGAAGTGCCA
1 CATAGAATTGCACCGAAGTGCCA
* * *
123023 CATATAATTGCACCGGAGTGCCG
1 CATAGAATTGCACCGAAGTGCCA
* * *
123046 CGTAGAATTGCACTGTAGTGCCA
1 CATAGAATTGCACCGAAGTGCCA
123069 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (23 bp):
CATAGAATTGCACCGAAGTGCCA
Found at i:123255 original size:103 final size:103
Alignment explanation
Indices: 123084--123301 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
123074 TAATGTCCAT
* *
123084 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
123149 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
123187 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
123252 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
123290 AAGGACCACATA
1 AAGGACCACATA
123302 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:128776 original size:23 final size:23
Alignment explanation
Indices: 128750--128827 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
128740 CACCACAGCT
128750 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
128773 CATATAATTGCACC-AGAGTGCCG
1 CATATAATTGCACCGA-AGTGCCA
* * *
128796 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
128819 TATAATAAT
1 CAT-ATAAT
128828 GTCCATAAGG
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.02
23 39 0.89
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:128997 original size:103 final size:103
Alignment explanation
Indices: 128837--129051 Score: 394
Period size: 103 Copynumber: 2.1 Consensus size: 103
128827 TGTCCATAAG
* *
128837 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
*
128902 TTCACACATGTTCCAAAGAATATATATATGTCCCGAAT
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
*
128940 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
129005 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
129043 GACCACATA
1 GACCACATA
129052 GACCCTCGAC
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
Found at i:131845 original size:21 final size:22
Alignment explanation
Indices: 131819--131868 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
131809 ATAATTATAC
131819 AAATAATA-TTTAAATGATA-TT
1 AAATAATATTTTAAAT-ATATTT
131840 AAATAATATTTTAAATATATTT
1 AAATAATATTTTAAATATATTT
131862 AAA-AATA
1 AAATAATA
131869 AATAGTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATAATATTTTAAATATATTT
Found at i:131862 original size:10 final size:11
Alignment explanation
Indices: 131819--131868 Score: 61
Period size: 10 Copynumber: 4.7 Consensus size: 11
131809 ATAATTATAC
131819 AAATAATATTT
1 AAATAATATTT
*
131830 AAATGATA-TT
1 AAATAATATTT
131840 AAATAATATTTT
1 AAATAATA-TTT
131852 AAAT-ATATTT
1 AAATAATATTT
131862 AAA-AATA
1 AAATAATA
131869 AATAGTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
10 18 0.53
11 10 0.29
12 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
AAATAATATTT
Found at i:131871 original size:28 final size:28
Alignment explanation
Indices: 131839--131898 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
131829 TAAATGATAT
* *
131839 TAAATAATATTTTAAATATATTTAAAAA
1 TAAATAATATTTTAAAGAAATTTAAAAA
* *
131867 TAAATAGTATTTTTAAGAAATTTAAAAA
1 TAAATAATATTTTAAAGAAATTTAAAAA
131895 TAAA
1 TAAA
131899 CAGTAAAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (28 bp):
TAAATAATATTTTAAAGAAATTTAAAAA
Found at i:135775 original size:9 final size:9
Alignment explanation
Indices: 135761--135785 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
135751 CTATCGATTA
135761 TTAAAATTT
1 TTAAAATTT
135770 TTAAAATTT
1 TTAAAATTT
135779 TTAAAAT
1 TTAAAAT
135786 GATCTCTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTAAAATTT
Found at i:138460 original size:31 final size:29
Alignment explanation
Indices: 138425--138486 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 29
138415 TTTATGTCCC
*
138425 TATTTTGACCAAAAATATAAATTTAAATACT
1 TATTTCGACCAAAAA-AT-AATTTAAATACT
* * *
138456 TATTTCGACTAAAAAATACTTTAGATACT
1 TATTTCGACCAAAAAATAATTTAAATACT
138485 TA
1 TA
138487 AATGAGAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 12 0.44
30 2 0.07
31 13 0.48
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (29 bp):
TATTTCGACCAAAAAATAATTTAAATACT
Found at i:143596 original size:17 final size:17
Alignment explanation
Indices: 143562--143613 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
143552 ACCGGACAAA
* *
143562 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
143579 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
143596 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
143611 TTT
1 TTT
143614 CTACTGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:144225 original size:23 final size:23
Alignment explanation
Indices: 144201--144250 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
144191 AAATAGTGTT
*
144201 AATATAAT-AATAATAACATGATTA
1 AATAAAATAAATAA-AA-ATGATTA
144225 AATAAAATAAATAAAAATGATTA
1 AATAAAATAAATAAAAATGATTA
144248 AAT
1 AAT
144251 TTTACGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
24 9 0.38
25 5 0.21
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
AATAAAATAAATAAAAATGATTA
Found at i:150557 original size:20 final size:20
Alignment explanation
Indices: 150529--150570 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
150519 CAGAATAAAT
150529 GAAGCTTGAAATCGAGTTCA
1 GAAGCTTGAAATCGAGTTCA
*
150549 GAAGGTTGAAATCGAGTTCA
1 GAAGCTTGAAATCGAGTTCA
150569 GA
1 GA
150571 GGGTCGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.24
Consensus pattern (20 bp):
GAAGCTTGAAATCGAGTTCA
Found at i:158755 original size:2 final size:2
Alignment explanation
Indices: 158736--158770 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
158726 AAAAGGTAAA
* *
158736 AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
158771 CAAATGTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:158916 original size:5 final size:5
Alignment explanation
Indices: 158906--158939 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
158896 AAAAGAAAGA
158906 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
158940 CGAAAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:159194 original size:28 final size:28
Alignment explanation
Indices: 159144--159197 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
159134 ATATATGTAA
* *
159144 AATAAAAAATGATATATACAAAAATATG
1 AATAAAAAATAAAATATACAAAAATATG
159172 AATAACAAAATAAAATATA-AAAAATA
1 AATAA-AAAATAAAATATACAAAAATA
159198 ATAACAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (28 bp):
AATAAAAAATAAAATATACAAAAATATG
Found at i:167103 original size:15 final size:15
Alignment explanation
Indices: 167083--167112 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
167073 ATAACAACAA
*
167083 TTACATATGTAAAAT
1 TTACATATGCAAAAT
167098 TTACATATGCAAAAT
1 TTACATATGCAAAAT
167113 GTATATGCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (15 bp):
TTACATATGCAAAAT
Found at i:170137 original size:44 final size:44
Alignment explanation
Indices: 170088--170185 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 44
170078 TAAAGAGGAG
170088 AGAAAAGATTGTACATTTGAAGAAGATGGTTCTGGGAAGATTAT
1 AGAAAAGATTGTACATTTGAAGAAGATGGTTCTGGGAAGATTAT
*
170132 AGAAAAGATTGTACCTTTGAAGAAGATGGTTCTGGGAAGATTAT
1 AGAAAAGATTGTACATTTGAAGAAGATGGTTCTGGGAAGATTAT
* *
170176 GGAAAGGATT
1 AGAAAAGATT
170186 AGGGTTGGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.38, C:0.05, G:0.29, T:0.29
Consensus pattern (44 bp):
AGAAAAGATTGTACATTTGAAGAAGATGGTTCTGGGAAGATTAT
Found at i:173598 original size:21 final size:21
Alignment explanation
Indices: 173574--173615 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
173564 TCGAATGATA
173574 GACAATGAAGATCGGAGGATG
1 GACAATGAAGATCGGAGGATG
173595 GACAATGAAGATCGGAGGATG
1 GACAATGAAGATCGGAGGATG
173616 AAGAAATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.38, T:0.14
Consensus pattern (21 bp):
GACAATGAAGATCGGAGGATG
Found at i:176362 original size:21 final size:21
Alignment explanation
Indices: 176336--176395 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
176326 ACAGGGGTAT
176336 CGATACCCTGCTACAGTATAC
1 CGATACCCTGCTACAGTATAC
*
176357 CGATACCCTGCTACAGTGTAC
1 CGATACCCTGCTACAGTATAC
176378 CGATACCCTGCTACAGTA
1 CGATACCCTGCTACAGTA
176396 ATTTCGACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (21 bp):
CGATACCCTGCTACAGTATAC
Found at i:177131 original size:22 final size:22
Alignment explanation
Indices: 177103--177163 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
177093 GGCATGTGAA
177103 ATTTGTCCCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
* *
177125 ATTTGTCCCGAAAGACCTTTGT
1 ATTTGTCCCGAAGGACCTATGT
*
177147 ATATGTCCCGAAGGACC
1 ATTTGTCCCGAAGGACC
177164 GCGTAGACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:177388 original size:59 final size:59
Alignment explanation
Indices: 177271--177389 Score: 132
Period size: 59 Copynumber: 2.0 Consensus size: 59
177261 ACTTATTCAT
* * * *
177271 ATCATTTATCTTATAAACAAATATCTCTTCTTTTCTATCACGTATCACAAGTACGTGTA
1 ATCATTGATCTTATAAACAAATATCTCTTCTCTTCTATCACATACCACAAGTACGTGTA
* * * * * *
177330 ATCATTGATCTTATAATCACATGT-TCCTTCTCTTCTGTCACATACCACATGTATGTGTA
1 ATCATTGATCTTATAAACAAATATCT-CTTCTCTTCTATCACATACCACAAGTACGTGTA
177389 A
1 A
177390 ACATATACCT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
58 1 0.02
59 48 0.98
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (59 bp):
ATCATTGATCTTATAAACAAATATCTCTTCTCTTCTATCACATACCACAAGTACGTGTA
Found at i:177546 original size:2 final size:2
Alignment explanation
Indices: 177539--177586 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
177529 TCTTATTCAC
177539 AT AT AT AT -T CAT 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
177581 AT AT AT
1 AT AT AT
177587 CACATAACAC
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.95
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:178541 original size:30 final size:29
Alignment explanation
Indices: 178506--178577 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
178496 CAACCATTTA
178506 CAACTTTTCTAAAATTAT-GAATTGATCCCC
1 CAACTTTTCTAAAATTATAGAA-TGAT-CCC
* *
178536 CAACTTTTCAAAAATTATAGAATGGTCCC
1 CAACTTTTCTAAAATTATAGAATGATCCC
*
178565 CAAATTTTCTAAA
1 CAACTTTTCTAAA
178578 GCTTGTAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 14 0.38
30 20 0.54
31 3 0.08
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.35
Consensus pattern (29 bp):
CAACTTTTCTAAAATTATAGAATGATCCC
Found at i:190103 original size:57 final size:60
Alignment explanation
Indices: 189942--190126 Score: 200
Period size: 60 Copynumber: 3.1 Consensus size: 60
189932 TTTGGATGAA
* * * * * * *
189942 TTTGGGGATGAAATTGGAAGA-TCTAAAAGTTTAGGGACCAATTTAGAATGAGATTCATAA
1 TTTGAGGATGAAATTGAAATATTC-AAAAGTTGAAGGACTAATTTAGAATGAGATTCATAG
*
190002 TTTGAGGATGAAATTGAAATGTTCAAAAGTTGAAGGACTAATTTAGAATGAGATTCATAG
1 TTTGAGGATGAAATTGAAATATTCAAAAGTTGAAGGACTAATTTAGAATGAGATTCATAG
* * * **
190062 TTTGATGATGAAATT-ATAATATT-TAAAG-T-AAGGACTAATTTAAAATGAGGGTCATAG
1 TTTGAGGATGAAATTGA-AATATTCAAAAGTTGAAGGACTAATTTAGAATGAGATTCATAG
190119 TTTGAGGA
1 TTTGAGGA
190127 CATATGATGC
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
57 32 0.30
58 1 0.01
59 5 0.05
60 68 0.63
61 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.32
Consensus pattern (60 bp):
TTTGAGGATGAAATTGAAATATTCAAAAGTTGAAGGACTAATTTAGAATGAGATTCATAG
Found at i:190291 original size:2 final size:2
Alignment explanation
Indices: 190284--190325 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
190274 TATTTAACCT
190284 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
190325 T
1 T
190326 GAACGAATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:191376 original size:33 final size:33
Alignment explanation
Indices: 191339--191405 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
191329 CTTTGTTGGC
191339 GATTCCCTCGCATAGCTCATTATGATGGCCTCG
1 GATTCCCTCGCATAGCTCATTATGATGGCCTCG
*
191372 GATTCCCTCGCATAGCTCATTCTGATGGCCTCG
1 GATTCCCTCGCATAGCTCATTATGATGGCCTCG
191405 G
1 G
191406 TCGGATGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.30
Consensus pattern (33 bp):
GATTCCCTCGCATAGCTCATTATGATGGCCTCG
Found at i:202936 original size:25 final size:22
Alignment explanation
Indices: 202888--202937 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 22
202878 TTTTAGTGAC
*
202888 TATTTTATAATATCATAATTAT
1 TATTTTATAATATCATAAATAT
202910 TATTTTATAATAGTCCGATAAATAT
1 TATTTTATAATA-T-C-ATAAATAT
202935 TAT
1 TAT
202938 GATCATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 12 0.50
23 1 0.04
24 1 0.04
25 10 0.42
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (22 bp):
TATTTTATAATATCATAAATAT
Found at i:203642 original size:16 final size:16
Alignment explanation
Indices: 203607--203647 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
203597 GTTTACTTCA
*
203607 GAATGATT-AAACGTT
1 GAATGATTCAAACGCT
*
203622 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
203638 GAATGATTCA
1 GAATGATTCA
203648 GAGACTCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:204050 original size:18 final size:19
Alignment explanation
Indices: 204015--204055 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
204005 AAGTTTTAAA
204015 AAATTATATAATGATATT-T
1 AAATTATATAAT-ATATTAT
204034 AAATATATATAAT-TATTAT
1 AAAT-TATATAATATATTAT
204053 AAA
1 AAA
204056 AGAGTCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AAATTATATAATATATTAT
Found at i:204422 original size:14 final size:13
Alignment explanation
Indices: 204384--204426 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
204374 GACACATTAA
204384 ATTTT-AATAATT
1 ATTTTAAATAATT
* *
204396 ATATAAAATAATT
1 ATTTTAAATAATT
204409 ATTTTAAATGAATT
1 ATTTTAAAT-AATT
204423 ATTT
1 ATTT
204427 GTTTATTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 3 0.12
13 14 0.56
14 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
ATTTTAAATAATT
Found at i:205606 original size:60 final size:59
Alignment explanation
Indices: 205508--205649 Score: 137
Period size: 60 Copynumber: 2.4 Consensus size: 59
205498 CGTATGCACT
* * * * *
205508 TAAAGTATGACTTTTATTTTAAATTGATCCTCAAACTTTT-ATATGTTTCAATTTTATTCCC
1 TAAATTATGACTATCATTCTAAATTGATCCTCAAACTTTTAATAAG--TCAATTTTA-TCCC
*
205569 -AAATTATGACTATCATTCTAAATT-AGTCCTTAAACTTTTGAATAAGTCAATTTTATCCC
1 TAAATTATGACTATCATTCTAAATTGA-TCCTCAAACTTTT-AATAAGTCAATTTTATCCC
* * *
205628 TAAATTACGACTCTCTTTCTAA
1 TAAATTATGACTATCATTCTAA
205650 CCTGGTCCCC
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
59 5 0.07
60 59 0.87
62 4 0.06
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.44
Consensus pattern (59 bp):
TAAATTATGACTATCATTCTAAATTGATCCTCAAACTTTTAATAAGTCAATTTTATCCC
Found at i:207033 original size:119 final size:119
Alignment explanation
Indices: 206822--207194 Score: 701
Period size: 119 Copynumber: 3.1 Consensus size: 119
206812 CCTCATTATC
* * *
206822 AAAACAAAAATTATATCAACGGATTTGTTTAATCGATAAGTAGTTTGATATCGCTTAAGCATGTC
1 AAAACAAAAATTATATCAACGGGTTTGTTCAATCGGTAAGTAGTTTGATATCGCTTAAGCATGTC
206887 TCAAGTTTAAGTTATTGTGAATTATGAAACCAAAACCATGTGTACTTACGAAAA
66 TCAAGTTTAAGTTATTGTGAATTATGAAACCAAAACCATGTGTACTTACGAAAA
206941 AAAACAAAAATTATATCAACGGGTTTGTTCAATCGGTAAGTAGTTTGATATCGCTTAAGCATGTC
1 AAAACAAAAATTATATCAACGGGTTTGTTCAATCGGTAAGTAGTTTGATATCGCTTAAGCATGTC
207006 TCAAGTTTAAGTTATTGTGAATTATGAAACCAAAACCATGTGTACTTACGAAAA
66 TCAAGTTTAAGTTATTGTGAATTATGAAACCAAAACCATGTGTACTTACGAAAA
207060 AAAACAAAAATTATATCAACGGGTTTGTTCAATCGGTAAGTAGTTTGATATCGCTTAAGCATGTC
1 AAAACAAAAATTATATCAACGGGTTTGTTCAATCGGTAAGTAGTTTGATATCGCTTAAGCATGTC
207125 TCAAGTTTAAGTTATTGTGAATTATGAAACCAAAACCATGTGTACTTACGGGAAAA
66 TCAAGTTTAAGTTATTGTGAATTATGAAACCAAAACCATGTGTACTTAC--GAAAA
207181 AAAACAAAAATTAT
1 AAAACAAAAATTAT
207195 CTATCTACTG
Statistics
Matches: 249, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
119 230 0.92
121 19 0.08
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (119 bp):
AAAACAAAAATTATATCAACGGGTTTGTTCAATCGGTAAGTAGTTTGATATCGCTTAAGCATGTC
TCAAGTTTAAGTTATTGTGAATTATGAAACCAAAACCATGTGTACTTACGAAAA
Found at i:213412 original size:22 final size:22
Alignment explanation
Indices: 213355--213413 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
213345 ACGCGATTCT
*
213355 GACTATCGCATTACGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
213377 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
213398 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
213414 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:213445 original size:20 final size:20
Alignment explanation
Indices: 213398--213481 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
213388 GCGATTTTCC
* *
213398 GACTATCGCAATGCGAATAT
1 GACTATCGCAACGCGATTAT
* *
213418 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAACGCGATTAT
* *
213438 GACTATCGCAACGAGATTCT
1 GACTATCGCAACGCGATTAT
*
213458 GACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGATTAT
213478 GACT
1 GACT
213482 GACGCAACAC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.02
20 53 0.96
21 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (20 bp):
GACTATCGCAACGCGATTAT
Found at i:213489 original size:20 final size:20
Alignment explanation
Indices: 213422--213481 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
213412 GAATATGTAA
* *
213422 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
213442 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
213462 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
213482 GACGCAACAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:214361 original size:24 final size:24
Alignment explanation
Indices: 214310--214363 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
214300 GTATTCGAAA
*
214310 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
214334 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
214358 TTTGAT
1 TTTGAT
214364 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:216955 original size:140 final size:140
Alignment explanation
Indices: 216703--216972 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
216693 AAACGTTGTA
216703 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
216768 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACCCGAATTTGACTAT
216833 TATGTGTATT
131 TATGTGTATT
*
216843 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
216908 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACCCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACCCGAATTTGACTAT
216973 CGCAACTCAA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACCCGAATTTGACTAT
TATGTGTATT
Found at i:216968 original size:20 final size:20
Alignment explanation
Indices: 216943--217227 Score: 299
Period size: 20 Copynumber: 14.8 Consensus size: 20
216933 TTACACATTC
* *
216943 ATTTGAATATCGCAACCCGA
1 ATTTGACTATCGCAACGCGA
*
216963 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
216982 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
216997 AATTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
217017 ATATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
217037 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
217057 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
217077 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
217097 ATTTGATTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
217117 ATTTGACTATCGCAA--CG-
1 ATTTGACTATCGCAACGCGA
**
217134 A--T-AAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
217151 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
217171 ATTTGAGTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
217191 ATTTGATTATCGCAAAGGGT
1 ATTTGACTATCGCAACGCGA
217211 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
217228 AGAAAATCAC
Statistics
Matches: 223, Mismatches: 28, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
14 17 0.08
15 4 0.02
16 2 0.01
17 2 0.01
19 6 0.03
20 192 0.86
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:217165 original size:94 final size:94
Alignment explanation
Indices: 217045--217276 Score: 349
Period size: 94 Copynumber: 2.5 Consensus size: 94
217035 GAATTTGTCT
*
217045 ATCGCAACGCGAATTTGTCTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGC
* *
217110 AACGGCTATTTGACTATCGCAACGATAAA
66 AAAGGCTATTTGACTATCGCAACGAGAAA
* *
217139 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGAGTATCACAACGCGAATTTGATTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGC
*
217204 AAAGGGTATTTGACTATCGCAACGAGAAA
66 AAAGGCTATTTGACTATCGCAACGAGAAA
* * * * * *
217233 ATCACAAAGCGTATTAGACTATCGCAACGCCAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
217277 GTTGCGATTT
Statistics
Matches: 124, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 8 0.06
94 116 0.94
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.25
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGC
AAAGGCTATTTGACTATCGCAACGAGAAA
Found at i:217295 original size:20 final size:20
Alignment explanation
Indices: 217270--217308 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
217260 CGCCAATTGA
*
217270 CTTTCGCGTTGCGATTTTGT
1 CTTTCGCATTGCGATTTTGT
*
217290 CTTTCGCATTGTGATTTTG
1 CTTTCGCATTGCGATTTTG
217309 AGTTTAGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.18, G:0.23, T:0.51
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGT
Found at i:217482 original size:14 final size:14
Alignment explanation
Indices: 217422--217483 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
217412 CACAAATCAG
*
217422 AATTATTTACACATC
1 AATT-TTTACAAATC
**
217437 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
217452 AACTTTTACAAATC
1 AATTTTTACAAATC
*
217466 AATTTTTATAAATC
1 AATTTTTACAAATC
217480 AATT
1 AATT
217484 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:219495 original size:18 final size:19
Alignment explanation
Indices: 219472--219558 Score: 95
Period size: 20 Copynumber: 4.5 Consensus size: 19
219462 GAAACTTAAA
*
219472 ATCGCAACACG-AATGACT
1 ATCGCAACGCGAAATGACT
219490 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
219510 TTCGCAACGCGAAAATGACG
1 ATCGCAACGCG-AAATGACT
* *
219530 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
219550 ATCGCAACG
1 ATCGCAACG
219559 AGAGAATCGT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
18 10 0.17
19 2 0.03
20 46 0.79
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:219508 original size:20 final size:20
Alignment explanation
Indices: 219483--219558 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
219473 TCGCAACACG
219483 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
219503 AATGACTTTCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
* *
219523 AATGACGATCACAACGCGAA
1 AATGACTATCGCAACGCGAA
**
219543 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
219559 AGAGAATCGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:219989 original size:17 final size:17
Alignment explanation
Indices: 219962--220001 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
219952 AATACTCAGA
219962 TTAATCTTACTGTTAATT
1 TTAA-CTTACTGTTAATT
219980 TTAACTTACTGTTAATT
1 TTAACTTACTGTTAATT
219997 TTAAC
1 TTAAC
220002 ATTATCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (17 bp):
TTAACTTACTGTTAATT
Found at i:220116 original size:16 final size:17
Alignment explanation
Indices: 220097--220133 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
220087 TAATAATTTT
220097 TTTTAAA-AATAT-ATAA
1 TTTTAAATAAT-TGATAA
220113 TTTTAAATAATTGATAA
1 TTTTAAATAATTGATAA
220130 TTTT
1 TTTT
220134 TTACTAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTTAAATAATTGATAA
Found at i:220918 original size:21 final size:21
Alignment explanation
Indices: 220893--220932 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
220883 AATTTCATAT
220893 ATTTATTTATTCTAATTATCA
1 ATTTATTTATTCTAATTATCA
220914 ATTTATTTATTCTAATTAT
1 ATTTATTTATTCTAATTAT
220933 AATCGATCAT
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:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTATTTATTCTAATTATCA
Found at i:221111 original size:2 final size:2
Alignment explanation
Indices: 221104--221147 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
221094 TAAGTTTCAA
221104 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
221146 AT
1 AT
221148 TTATTATCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:234989 original size:32 final size:31
Alignment explanation
Indices: 234932--235028 Score: 103
Period size: 32 Copynumber: 3.2 Consensus size: 31
234922 TTTTTCATTC
* *
234932 AAGTACTTAAAG--TATTTTTTAGTCAAATT
1 AAGTACTTAAAGTATATTTTTTGGTCAAAAT
234961 AAGTA-TCTAAAGTTATATTTTTTGGTCAAAAT
1 AAGTACT-TAAAG-TATATTTTTTGGTCAAAAT
* *
234993 AGGTACTTAAAGTATA-TTTTCGGTCAAAAT
1 AAGTACTTAAAGTATATTTTTTGGTCAAAAT
*
235023 AGGTAC
1 AAGTAC
235029 AAAGATATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
28 1 0.02
29 10 0.17
30 19 0.32
31 4 0.07
32 24 0.41
33 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.40
Consensus pattern (31 bp):
AAGTACTTAAAGTATATTTTTTGGTCAAAAT
Found at i:235020 original size:30 final size:30
Alignment explanation
Indices: 234934--235028 Score: 113
Period size: 30 Copynumber: 3.1 Consensus size: 30
234924 TTTCATTCAA
* * *
234934 GTACTTAAAGTAT-TTTTTAGTCAAATTAA
1 GTACTTAAAGTATATTTTTGGTCAAAATAG
234963 GTA-TCTAAAGTTATATTTTTTGGTCAAAATAG
1 GTACT-TAAAG-TATA-TTTTTGGTCAAAATAG
*
234995 GTACTTAAAGTATATTTTCGGTCAAAATAG
1 GTACTTAAAGTATATTTTTGGTCAAAATAG
235025 GTAC
1 GTAC
235029 AAAGATATTA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
28 1 0.02
29 8 0.14
30 22 0.39
31 4 0.07
32 21 0.37
33 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (30 bp):
GTACTTAAAGTATATTTTTGGTCAAAATAG
Found at i:236035 original size:59 final size:59
Alignment explanation
Indices: 235943--236057 Score: 212
Period size: 59 Copynumber: 1.9 Consensus size: 59
235933 TTTCTTGTCC
* *
235943 CCCCAGTGTCATGCTTGAATATTTAATGCCAAAGATTTTAGGACCCAAGCATATTTGGG
1 CCCCAGTGTCATGCTTGAATACTTAATGCCAAAGACTTTAGGACCCAAGCATATTTGGG
236002 CCCCAGTGTCATGCTTGAATACTTAATGCCAAAGACTTTAGGACCCAAGCATATTT
1 CCCCAGTGTCATGCTTGAATACTTAATGCCAAAGACTTTAGGACCCAAGCATATTT
236058 ATGTTATGAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (59 bp):
CCCCAGTGTCATGCTTGAATACTTAATGCCAAAGACTTTAGGACCCAAGCATATTTGGG
Found at i:236286 original size:2 final size:2
Alignment explanation
Indices: 236279--236341 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
236269 TACTTAAAAT
236279 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
236321 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
236342 CGTTTACTTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:238096 original size:2 final size:2
Alignment explanation
Indices: 238089--238121 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
238079 TGAAACAATG
238089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238122 TGAGGAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:238610 original size:21 final size:21
Alignment explanation
Indices: 238586--238625 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
238576 TCAACTCATT
238586 ACTCGTTAAGCTCGTTGCTCG
1 ACTCGTTAAGCTCGTTGCTCG
238607 ACTCGTTAAGCTCGTTGCT
1 ACTCGTTAAGCTCGTTGCT
238626 GGTTAAGTTC
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:0.15, C:0.28, G:0.23, T:0.35
Consensus pattern (21 bp):
ACTCGTTAAGCTCGTTGCTCG
Found at i:238649 original size:16 final size:16
Alignment explanation
Indices: 238611--238651 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
238601 TGCTCGACTC
*
238611 GTTAAGCTCGTTGCTG
1 GTTAAGTTCGTTGCTG
238627 GTTAAGTTCGTTGCTG
1 GTTAAGTTCGTTGCTG
238643 GTTAAGTTC
1 GTTAAGTTC
238652 ACTAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.41
Consensus pattern (16 bp):
GTTAAGTTCGTTGCTG
Found at i:238715 original size:43 final size:43
Alignment explanation
Indices: 238652--238738 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
238642 GGTTAAGTTC
* *
238652 ACTAAAATAACAATCAACAAATACACCAAACTAATATATTAAA
1 ACTAAAATAACAATCAACAAACACACCAAACTAACATATTAAA
* * * ** *
238695 ACTAAAGTGACAATCCACAAACACGTCAAGCTAACATATTAAA
1 ACTAAAATAACAATCAACAAACACACCAAACTAACATATTAAA
238738 A
1 A
238739 ATATTCTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.55, C:0.21, G:0.05, T:0.20
Consensus pattern (43 bp):
ACTAAAATAACAATCAACAAACACACCAAACTAACATATTAAA
Found at i:242573 original size:60 final size:59
Alignment explanation
Indices: 242509--242633 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 59
242499 CTCTAGGGTT
* *
242509 AAAGTACACAAA-CGATTATCTAACTATAGAATATTATTTTATTAAGTCCCTCAACTATTA
1 AAAGTACA-AAATAGATT-TCTAACTATAGAATATTACTTTATTAAGTCCCTCAACTATTA
* * * *
242569 AAAGTTATAAAATAGGTTTCTAATTATAGAATATTGCTTTATTAAGTCCCTCAACTATTA
1 AAAG-TACAAAATAGATTTCTAACTATAGAATATTACTTTATTAAGTCCCTCAACTATTA
242629 AAAGT
1 AAAGT
242634 TATAAATAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.02
60 50 0.88
61 6 0.11
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.37
Consensus pattern (59 bp):
AAAGTACAAAATAGATTTCTAACTATAGAATATTACTTTATTAAGTCCCTCAACTATTA
Found at i:242634 original size:60 final size:60
Alignment explanation
Indices: 242527--242639 Score: 199
Period size: 60 Copynumber: 1.9 Consensus size: 60
242517 CAAACGATTA
*
242527 TCTAACTATAGAATATTATTTTATTAAGTCCCTCAACTATTAAAAGTTATAAAATAGGTT
1 TCTAACTATAGAATATTACTTTATTAAGTCCCTCAACTATTAAAAGTTATAAAATAGGTT
* *
242587 TCTAATTATAGAATATTGCTTTATTAAGTCCCTCAACTATTAAAAGTTATAAA
1 TCTAACTATAGAATATTACTTTATTAAGTCCCTCAACTATTAAAAGTTATAAA
242640 TAGTCATCTG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (60 bp):
TCTAACTATAGAATATTACTTTATTAAGTCCCTCAACTATTAAAAGTTATAAAATAGGTT
Found at i:243607 original size:21 final size:21
Alignment explanation
Indices: 243581--243622 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
243571 TCATGAACAG
243581 TGCTACAATGCATCGATGCAT
1 TGCTACAATGCATCGATGCAT
*
243602 TGCTACAGTGCATCGATGCAT
1 TGCTACAATGCATCGATGCAT
243623 CAAAAATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (21 bp):
TGCTACAATGCATCGATGCAT
Found at i:244313 original size:31 final size:31
Alignment explanation
Indices: 244278--244461 Score: 287
Period size: 31 Copynumber: 5.9 Consensus size: 31
244268 GAAGGACCAA
* * * *
244278 TCCATAGGTTCCGAAGAACCTAGGTAATCAG
1 TCCATATGTCCCGAAGAACATAGGTAAACAG
* *
244309 TCCATATGTTCCGAAGAACATAGGTAAACAA
1 TCCATATGTCCCGAAGAACATAGGTAAACAG
*
244340 TCCATATGTCCCGAAGAAAATAGGTAAACAG
1 TCCATATGTCCCGAAGAACATAGGTAAACAG
*
244371 TCCATATGTCCCGAAGAACATAGGTAAACAA
1 TCCATATGTCCCGAAGAACATAGGTAAACAG
244402 TCCATATGTCCCGAAGAACATAGGTAAACAG
1 TCCATATGTCCCGAAGAACATAGGTAAACAG
*
244433 TCCATATGTCCCGAAGAACATAAGTAAAC
1 TCCATATGTCCCGAAGAACATAGGTAAAC
244462 CTCGACCCTT
Statistics
Matches: 142, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 142 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.21
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTAAACAG
Found at i:248148 original size:21 final size:21
Alignment explanation
Indices: 248122--248163 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
248112 CCATGAACAG
248122 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAT
248143 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAT
248164 CAAAAATTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCTACAGTGCATCGATGCAT
Found at i:249012 original size:9 final size:9
Alignment explanation
Indices: 249000--249025 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
248990 TCTCTCTTTT
249000 TCTTCTTCA
1 TCTTCTTCA
249009 TCTTCTTCA
1 TCTTCTTCA
249018 TCTTCTTC
1 TCTTCTTC
249026 TTCCTCCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.35, G:0.00, T:0.58
Consensus pattern (9 bp):
TCTTCTTCA
Found at i:252061 original size:31 final size:31
Alignment explanation
Indices: 252039--252178 Score: 226
Period size: 31 Copynumber: 4.5 Consensus size: 31
252029 ATAGGTTCTA
* * *
252039 AAGAACCTAGGTAATCAGTCCATATGTTCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
*
252070 AAGAACATAGGTAAATAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
252101 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
252132 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
* *
252163 AAGAACAAAAGTAAAC
1 AAGAACATAGGTAAAC
252179 CCTTGACCCT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 102 1.00
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.20
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCG
Found at i:254177 original size:148 final size:147
Alignment explanation
Indices: 253908--254239 Score: 472
Period size: 148 Copynumber: 2.2 Consensus size: 147
253898 GTTATGAAAC
* * * *
253908 TTTTTTTAATTAATTTAGGG-TAAGTACAAGGCAATATATGTTCAAATATAACTCTCAACCTTTC
1 TTTTTTT-ATTAATCT-GGGATAAGTACAA-ACAATATATATTCAAAGATAACTCTCAACCTTTC
* *
253972 GACATTGAACGCTCACACCCCTGATATCTATGGTGCTCGAACCATTGAACCATTGAAATAATGAT
63 GACATTGAACGCTCACACACCTGACATCTATGGTGCTCGAACCATTGAACCATTGAAATAATGAT
*
254037 ATATAATCAAAATTCAACTA
128 ACATAATCAAAATTCAACTA
254057 TTTTTTTATTAATCTGGGATAAGTACAATACAATATATATTCAAAGATAAC-CTTCAACCTTTCG
1 TTTTTTTATTAATCTGGGATAAGTACAA-ACAATATATATTCAAAGATAACTC-TCAACCTTTCG
* * * *
254121 ATATTGAACTCTCACACACTTTACATCTATGGTGCTCGAACCATTGAACCATTGAAATAATGATA
64 ACATTGAACGCTCACACACCTGACATCTATGGTGCTCGAACCATTGAACCATTGAAATAATGATA
*
254186 CATAATCAAAATTCAGCTA
129 CATAATCAAAATTCAACTA
*
254205 -TTTTTTATTAATCTGGAATAAGTACAAAGCAATAT
1 TTTTTTTATTAATCTGGGATAAGTACAAA-CAATAT
254240 CGATTAATAA
Statistics
Matches: 166, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
146 1 0.01
147 36 0.22
148 122 0.73
149 7 0.04
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (147 bp):
TTTTTTTATTAATCTGGGATAAGTACAAACAATATATATTCAAAGATAACTCTCAACCTTTCGAC
ATTGAACGCTCACACACCTGACATCTATGGTGCTCGAACCATTGAACCATTGAAATAATGATACA
TAATCAAAATTCAACTA
Found at i:255776 original size:32 final size:33
Alignment explanation
Indices: 255735--255820 Score: 124
Period size: 32 Copynumber: 2.7 Consensus size: 33
255725 AGTCCTTAAC
*
255735 ATGGTTGAGGGACTAAAATCGAACG-ATAGTTA
1 ATGGTTGAGGGACTAAAATCGAACGAATAGATA
*
255767 ATGGTTGAGGGACTAAAATCGAACGAATCGATA
1 ATGGTTGAGGGACTAAAATCGAACGAATAGATA
*
255800 AT-GTT-AGAGACTAAAATCGAA
1 ATGGTTGAGGGACTAAAATCGAA
255821 TAGATCGATA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
31 15 0.30
32 28 0.56
33 7 0.14
ACGTcount: A:0.41, C:0.10, G:0.26, T:0.23
Consensus pattern (33 bp):
ATGGTTGAGGGACTAAAATCGAACGAATAGATA
Found at i:255828 original size:31 final size:32
Alignment explanation
Indices: 255735--255831 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
255725 AGTCCTTAAC
* * *
255735 ATGGTTGAGGGACTAAAATCGAACGATAGTTA
1 ATGGTTGAGAGACTAAAATCGAACGATCGATA
*
255767 ATGGTTGAGGGACTAAAATCGAACGAATCGATA
1 ATGGTTGAGAGACTAAAATCGAACG-ATCGATA
*
255800 AT-GTT-AGAGACTAAAATCGAATAGATCGATA
1 ATGGTTGAGAGACTAAAATCGAA-CGATCGATA
255831 A
1 A
255832 CATTAGGGAC
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
31 23 0.39
32 29 0.49
33 7 0.12
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (32 bp):
ATGGTTGAGAGACTAAAATCGAACGATCGATA
Found at i:264166 original size:10 final size:10
Alignment explanation
Indices: 264142--264198 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
264132 TTATATTATT
*
264142 TTTTTATTAA
1 TTTTTATTCA
*
264152 ATTTTATTCA
1 TTTTTATTCA
* *
264162 CTTTTAATTCT
1 -TTTTTATTCA
264173 TTTTTATTGCA
1 TTTTTATT-CA
*
264184 TTTTTATTGA
1 TTTTTATTCA
264194 TTTTT
1 TTTTT
264199 TTTAAAATAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 21 0.57
11 16 0.43
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (10 bp):
TTTTTATTCA
Found at i:264197 original size:21 final size:21
Alignment explanation
Indices: 264142--264198 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
264132 TTATATTATT
*
264142 TTTTTATTAAATTTTATTCAC
1 TTTTTATTAATTTTTATTCAC
* **
264163 TTTTAATTCTTTTTTATTGCA-
1 TTTTTATTAATTTTTATT-CAC
*
264184 TTTTTATTGATTTTT
1 TTTTTATTAATTTTT
264199 TTTAAAATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTTTATTAATTTTTATTCAC
Found at i:265955 original size:21 final size:21
Alignment explanation
Indices: 265930--265973 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
265920 GAAAATATTA
* *
265930 AAAAATATTAATATTTTAGAT
1 AAAAATAATAATATTTTAAAT
265951 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
265972 AA
1 AA
265974 TTTTTTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:266786 original size:33 final size:33
Alignment explanation
Indices: 266744--266842 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
266734 CCCCCTAAAC
*
266744 CCTACAATTTAAAGCTAAGCTTATCTTTTTAAT
1 CCTACAATTTAAAGCTAAGCTTATCTTCTTAAT
*
266777 CCTACAATTTAAAGCTAACCTTATCTTCTTAGA-
1 CCTACAATTTAAAGCTAAGCTTATCTTCTTA-AT
*
266810 CCTACAATTTAAGGCTAAGCTTATCTTCTTAAT
1 CCTACAATTTAAAGCTAAGCTTATCTTCTTAAT
266843 AAAAATTATT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.02
33 58 0.97
34 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.39
Consensus pattern (33 bp):
CCTACAATTTAAAGCTAAGCTTATCTTCTTAAT
Found at i:267338 original size:60 final size:60
Alignment explanation
Indices: 267207--267349 Score: 141
Period size: 60 Copynumber: 2.4 Consensus size: 60
267197 TAATGAATAG
* * * * * *
267207 TCGGGTGACCATTTCGTAACTTTTAATAGTCAAGAGACTCAACAAATCAATACTCTATAG
1 TCGGGGGACCATTTTGTAACTTTTAACAGTCAAGAAACTCAAAAAATCAATACTCTATAC
* * *
267267 TCGGAGAACCATTTTGTAACTTTTAACAGTCGAA-AAACTTAATAAAAT-AATA-TCATATAC
1 TCGGGGGACCATTTTGTAACTTTTAACAGTC-AAGAAACTCAA-AAAATCAATACTC-TATAC
267327 TCGGGGGACCATTTGTGT-ACTTT
1 TCGGGGGACCATTT-TGTAACTTT
267350 ACCCAAAATA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
59 2 0.03
60 57 0.84
61 9 0.13
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (60 bp):
TCGGGGGACCATTTTGTAACTTTTAACAGTCAAGAAACTCAAAAAATCAATACTCTATAC
Found at i:269745 original size:2 final size:2
Alignment explanation
Indices: 269738--269763 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
269728 CAGTTCTCCA
269738 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
269764 CATTTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:278334 original size:7 final size:7
Alignment explanation
Indices: 278322--278362 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
278312 AAAAGACAGT
278322 TGAAGGA
1 TGAAGGA
278329 TGAAGGA
1 TGAAGGA
278336 TGAAGGA
1 TGAAGGA
278343 TGAAGGA
1 TGAAGGA
278350 TGAAGGA
1 TGAAGGA
278357 TGAAGG
1 TGAAGG
278363 GGATTTACCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (7 bp):
TGAAGGA
Found at i:281698 original size:31 final size:31
Alignment explanation
Indices: 281658--281718 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
281648 ATCTTTAGGC
* * *
281658 ACTAGAATATTTTTCGAATCATAGTTTAAGT
1 ACTAAAATATTTTTAGAAGCATAGTTTAAGT
*
281689 ACTAAAATATTTTTAGAGGCATAGTTTAAG
1 ACTAAAATATTTTTAGAAGCATAGTTTAAG
281719 CATTTATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (31 bp):
ACTAAAATATTTTTAGAAGCATAGTTTAAGT
Found at i:282731 original size:22 final size:24
Alignment explanation
Indices: 282686--282733 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
282676 AATGATGACT
* *
282686 AAACGTTAAGTATTATTTTTTTAA
1 AAACGTTAAGTATTATTGTATTAA
282710 AAACGTTAAGT-TT-TTGTATTAA
1 AAACGTTAAGTATTATTGTATTAA
282732 AA
1 AA
282734 CATATCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 2 0.09
24 11 0.50
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (24 bp):
AAACGTTAAGTATTATTGTATTAA
Found at i:290555 original size:28 final size:27
Alignment explanation
Indices: 290478--290555 Score: 66
Period size: 28 Copynumber: 2.7 Consensus size: 27
290468 ATTTAAGCAT
* *
290478 CTAAAATATTTTTATCAAAATAAATAC
1 CTAATATATTTTTGTCAAAATAAATAC
* * *
290505 TTAAATTTATCTTTTTGATCAAAATAGATAC
1 CT-AA--TATATTTTTG-TCAAAATAAATAC
290536 CTAATATATTTTATGTCAAA
1 CTAATATATTTT-TGTCAAA
290556 CTTGGTACCT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
27 1 0.03
28 14 0.36
29 2 0.05
30 9 0.23
31 13 0.33
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (27 bp):
CTAATATATTTTTGTCAAAATAAATAC
Found at i:292295 original size:21 final size:21
Alignment explanation
Indices: 292271--292310 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
292261 TTTTCAAAGG
292271 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
292292 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
292311 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Done.