Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008785.1 Hibiscus syriacus cultivar Beakdansim tig00111917_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: 1341157
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:421637 original size:44 final size:42
Alignment explanation
Indices: 421505--421651 Score: 126
Period size: 43 Copynumber: 3.5 Consensus size: 42
421495 AACGTAAGGG
* *
421505 CCTCAATTATAAAGTTAAAAA----ATTGAAT-TAAATTAGGCG
1 CCTCAATTATAAAG-TAAAAAGGGGATTGAATAAAAATTAGG-A
421544 CCTCAATTATAAATGTAAAAAGGGGATTGAA-AAAAATTAGAGA
1 CCTCAATTATAAA-GTAAAAAGGGGATTGAATAAAAATTAG-GA
** * *
421587 TTTCAATTATAAAGATAAAATGTGTGATTGAATAAAAATTAGGA
1 CCTCAATTATAAAG-TAAAAAG-GGGATTGAATAAAAATTAGGA
*
421631 CCTCAATTGTAAAGGTAAAAA
1 CCTCAATTATAAA-GTAAAAA
421652 AATAAGATTT
Statistics
Matches: 87, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
39 19 0.22
40 1 0.01
42 1 0.01
43 30 0.34
44 26 0.30
45 10 0.11
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (42 bp):
CCTCAATTATAAAGTAAAAAGGGGATTGAATAAAAATTAGGA
Found at i:421695 original size:29 final size:29
Alignment explanation
Indices: 421662--421726 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
421652 AATAAGATTT
*
421662 AAAAAATTAGAGGCCTAGTTATAAAAATG
1 AAAAAATTAGAGGCCTAATTATAAAAATG
* * * *
421691 AAAAAGTTGGGGGCCTAATTATAAAGATG
1 AAAAAATTAGAGGCCTAATTATAAAAATG
421720 AAAAAAT
1 AAAAAAT
421727 GGGGGCCCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (29 bp):
AAAAAATTAGAGGCCTAATTATAAAAATG
Found at i:421732 original size:28 final size:29
Alignment explanation
Indices: 421673--421733 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
421663 AAAAATTAGA
* *
421673 GGCCTAGTTATAAAAATGAAAAAGTTGGG
1 GGCCTAATTATAAAAATGAAAAAGATGGG
*
421702 GGCCTAATTATAAAGATGAAAAA-ATGGG
1 GGCCTAATTATAAAAATGAAAAAGATGGG
421730 GGCC
1 GGCC
421734 CAAAGCAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (29 bp):
GGCCTAATTATAAAAATGAAAAAGATGGG
Found at i:421989 original size:60 final size:60
Alignment explanation
Indices: 421925--422037 Score: 181
Period size: 60 Copynumber: 1.9 Consensus size: 60
421915 GTCAGGTGAC
* **
421925 CATTTTGTAACTTTTAATAGTTGAAGGACTTAACAAAATAACATTCTATAGTCAAAAGAT
1 CATTTTGTAACTTTTAATAGTCGAAAAACTTAACAAAATAACATTCTATAGTCAAAAGAT
* *
421985 CATTTTGTAACTTTTAATAGTCGAAAAACTTAATAAAATAATATTCTATAGTC
1 CATTTTGTAACTTTTAATAGTCGAAAAACTTAACAAAATAACATTCTATAGTC
422038 GAGGGACCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCGAAAAACTTAACAAAATAACATTCTATAGTCAAAAGAT
Found at i:422049 original size:60 final size:59
Alignment explanation
Indices: 421912--422058 Score: 179
Period size: 60 Copynumber: 2.4 Consensus size: 59
421902 AACATAATGA
* **
421912 ATAGTCAGGTGACCATTTTGTAACTTTTAATAGTTGAAGGACTTAACAAAATAACATTCT
1 ATAGTCAGG-GACCATTTTGTAACTTTTAATAGTCGAAAAACTTAACAAAATAACATTCT
** * * *
421972 ATAGTCAAAAGATCATTTTGTAACTTTTAATAGTCGAAAAACTTAATAAAATAATATTCT
1 ATAGTC-AGGGACCATTTTGTAACTTTTAATAGTCGAAAAACTTAACAAAATAACATTCT
422032 ATAGTCGAGGGACCA-TTTGTATACTTT
1 ATAGTC-AGGGACCATTTTGTA-ACTTT
422059 ACCCTTAAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
59 6 0.08
60 66 0.90
61 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (59 bp):
ATAGTCAGGGACCATTTTGTAACTTTTAATAGTCGAAAAACTTAACAAAATAACATTCT
Found at i:423770 original size:261 final size:259
Alignment explanation
Indices: 423259--423875 Score: 821
Period size: 256 Copynumber: 2.4 Consensus size: 259
423249 GAGACCCGAT
*
423259 CCGACCAAAATAAAGTTT----C-ACCTGACCTGAATATATGAATTAGAAACCCGACCCGACCCG
1 CCGACCAAAATAAAGTTTCACCCGACCCGACCTGAATATATGAATTAGAAACCCGACCCGACCCG
423319 AAATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAAATATATATATA
66 AAATAAT--AAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAAATATATATATA
* *
423384 GAGAGAGAGGTATTATTGTAATTATTCCTAAATATATAAGGTAGAATTATATATTTTTTGAGTCA
129 GAGAGAGAGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA-TTATT--GT--
423449 GGTCAGGTCGGGTATTTTTCACCCTAAACCCGAACCCGAACCAACCCGAATATCACACTTAAAAA
189 -GTCAGGTCGGGTATTTTTCACCCTAAACCCGAACCCGAACCAACCCGAATATCACACTT-AAAA
423514 AACCGACTCGAC
252 AA---ACT-GAC
*
423526 CCGACCAAAATAAAGTTTCACCCGACCCGACCTGAATATATGAATTAGAAATCCGATCAGATCCG
1 CCGACCAAAATAAAGTTTCACCCGACCCGACCTGAATATATGAATTAGAAA-CC---C-GACCCG
423591 ACCCGAAATAATAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATT-GAAAAA-AT-TAT
61 ACCCGAAATAATAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAAATATATAT
**
423653 ATTTAGAG-G-GGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA-TATT-T-T
126 ATAGAGAGAGAGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTGTGT
* * * * *
423713 CAGGTCGGGTATTTTTC-CTCCTAAACCCGAACTCGACCCGATCTGAATATCACACTTAAAAAAA
191 CAGGTCGGGTATTTTTCAC-CCTAAACCCGAACCCGAACCAACCCGAATATCACACTTAAAAAAA
423777 CTGAC
255 CTGAC
* * * *
423782 CTGACCAAAATAAAGTTTCACCGGACTCGACCTGAATATATGAATTAGAAACCCGACCCGACCCA
1 CCGACCAAAATAAAGTTTCACCCGACCCGACCTGAATATATGAATTAGAAACCCGACCCGACCCG
*
423847 AAATAATAAAAAAATATTTTTATTCAATA
66 AAATAATAAAAAATTATTTTTATTCAATA
423876 TATGAATAAG
Statistics
Matches: 322, Mismatches: 17, Indels: 38
0.85 0.05 0.10
Matches are distributed among these distances:
251 37 0.11
252 1 0.00
255 2 0.01
256 51 0.16
257 3 0.01
260 7 0.02
261 51 0.16
265 1 0.00
267 18 0.06
268 3 0.01
270 44 0.14
271 2 0.01
272 35 0.11
273 4 0.01
274 6 0.02
275 39 0.12
276 1 0.00
277 17 0.05
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.28
Consensus pattern (259 bp):
CCGACCAAAATAAAGTTTCACCCGACCCGACCTGAATATATGAATTAGAAACCCGACCCGACCCG
AAATAATAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAAATATATATATAGA
GAGAGAGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTGTGTCAGGT
CGGGTATTTTTCACCCTAAACCCGAACCCGAACCAACCCGAATATCACACTTAAAAAAACTGAC
Found at i:429422 original size:25 final size:25
Alignment explanation
Indices: 429389--429453 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
429379 ATATGTACAT
*
429389 ATAATAATAAATAA-AAA-AAACAAG
1 ATAAAAATAAATAATAAATAAA-AAG
429413 AATAAAAATAAA-AATAAATAAAAAG
1 -ATAAAAATAAATAATAAATAAAAAG
429438 ATAAAAA-AAAT-ATAAA
1 ATAAAAATAAATAATAAA
429454 GGAAATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
23 8 0.22
24 9 0.25
25 16 0.44
26 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (25 bp):
ATAAAAATAAATAATAAATAAAAAG
Found at i:429432 original size:16 final size:16
Alignment explanation
Indices: 429389--429521 Score: 63
Period size: 16 Copynumber: 7.8 Consensus size: 16
429379 ATATGTACAT
*
429389 ATAATAATAAATAAAA
1 ATAAAAATAAATAAAA
*
429405 A-AAACAA-GAATAAAA
1 ATAAA-AATAAATAAAA
429420 ATAAAAATAAATAAAAA
1 ATAAAAATAAAT-AAAA
*
429437 GATAAAAAAAATATAAAGGAA
1 -ATAAAAATAA-AT-AA--AA
* *
429458 ATAAAAGTAAAATAAAG
1 ATAAAAAT-AAATAAAA
*
429475 ATAACGAAATAAAGAAAA
1 ATAA--AAATAAATAAAA
* * *
429493 AGACAAATAAAGAAAA
1 ATAAAAATAAATAAAA
* *
429509 AGATAAATAAATA
1 ATAAAAATAAATA
429522 TTAAAAAAAC
Statistics
Matches: 92, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
15 12 0.13
16 32 0.35
17 9 0.10
18 17 0.18
19 10 0.11
20 8 0.09
21 4 0.04
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.15
Consensus pattern (16 bp):
ATAAAAATAAATAAAA
Found at i:429596 original size:2 final size:2
Alignment explanation
Indices: 429591--429670 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
429581 AAAAGGGACC
429591 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
429633 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
429671 TTAATAAAAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:429714 original size:2 final size:2
Alignment explanation
Indices: 429707--429737 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
429697 TAAAAGAATA
429707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
429738 AATACTAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:430042 original size:2 final size:2
Alignment explanation
Indices: 430037--430061 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
430027 AACCAAATAA
430037 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
430062 ATTAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:431989 original size:120 final size:123
Alignment explanation
Indices: 431745--432035 Score: 390
Period size: 120 Copynumber: 2.4 Consensus size: 123
431735 TCATTCGCTA
* * *
431745 TGAAGTTGAGCTTTGAATTGAATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGATGGATGT
1 TGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTA-AGATGGATGT
* * *
431810 TGCTTGTGGGCACGATATCCTCCGTCGTGAAGTTGAAATCGTTGATGACCAATTCGTTG
65 TGCTTATGGGCACGATATCCTCCATCGTGAAGTTGAAATCGTGGATGACCAATTCGTTG
* * * *
431869 TGAAGTTGAGCCTTAAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA-GT-A-TTGTATGTT
1 TGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAGATGGATGTT
* * * ** *
431931 GCTTATGGGCACGATATCCTTCATCGTGAAGTTGAAATTGTGGATGGCCCCTTTGTTG
66 GCTTATGGGCACGATATCCTCCATCGTGAAGTTGAAATCGTGGATGACCAATTCGTTG
* *
431989 TGAAGTTGAGCCATGAATTAGATATCCTTCGTCGTGAAGTTGAAATC
1 TGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
432036 GTGGATGGCC
Statistics
Matches: 148, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
120 100 0.68
121 1 0.01
123 1 0.01
124 46 0.31
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (123 bp):
TGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAGATGGATGTT
GCTTATGGGCACGATATCCTCCATCGTGAAGTTGAAATCGTGGATGACCAATTCGTTG
Found at i:432049 original size:66 final size:66
Alignment explanation
Indices: 431943--432235 Score: 263
Period size: 66 Copynumber: 4.4 Consensus size: 66
431933 TTATGGGCAC
* * *
431943 GATATCCTTCATCGTGAAGTTGAAATTGTGGATGGCCCCTTTGTTGTGAAGTTGAGCCATGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCATGAATT
*
432008 A
66 G
* * *
432009 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCATTGTGAAGTTGATCCTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCATGAATT
432074 G
66 G
* ** *** * ** * *
432075 GATATTCTTCGTCGTGAAGTTGAAATC--CAAT--CTAAATAT-GAATGTTGTTGGTGGGCACGA
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGC-CCCT-TCG-TTG-TGAAGTTGAGC-C-A
* *
432135 TAACATTC
60 TGA-ATTG
* * * *
432143 GATAACATTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCATGAATT
432208 G
66 G
*
432209 GATATCCTTCGTCATGAAGTTGAAATC
1 GATATCCTTCGTCGTGAAGTTGAAATC
432236 CAAGTATTGT
Statistics
Matches: 173, Mismatches: 42, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 5 0.03
65 6 0.03
66 113 0.65
67 4 0.02
68 28 0.16
69 7 0.04
70 5 0.03
71 2 0.01
72 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (66 bp):
GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCATGAATT
G
Found at i:432076 original size:186 final size:193
Alignment explanation
Indices: 431823--432235 Score: 527
Period size: 186 Copynumber: 2.1 Consensus size: 193
431813 TTGTGGGCAC
* * *
431823 GATATCCTCCGTCGTGAAGTTGAAATCGTTGATGACCAATTCGTTGTGAAGTTGAGCCTTAAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCAATTCATTGTGAAGTTGAGCCTTAAATT
* *
431888 GGATATCCTTCGTCGTGAAGTTGAAATCCAA-GT-AT-TGTATGTTGCTT-ATGGGCACGAT-A-
66 GGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAATATGAATGTTG-TTGATGGGCACGATAAT
* * *
431947 TC-C-TTCATCGTGAAGTTGAAATTGTGGATGGCCCCTTTGTTGTGAAGTTGAGCCATGAATTA
130 TCACATTCATCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCATGAATTA
* ** * *
432009 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCATTGTGAAGTTGATCCTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCAATTCATTGTGAAGTTGAGCCTTAAATT
* *
432074 GGATATTCTTCGTCGTGAAGTTGAAATCCAATCTAAATATGAATGTTGTTGGTGGGCACGATAAC
66 GGATATCCTTCGTCGTGAAGTTGAAATCCAATCT-AATATGAATGTTGTTGATGGGCACGAT-A-
* *
432139 ATTCGATAACATTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTG
128 ATTC----ACATTCATCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCATG
*
432204 AATTG
189 AATTA
*
432209 GATATCCTTCGTCATGAAGTTGAAATC
1 GATATCCTTCGTCGTGAAGTTGAAATC
432236 CAAGTATTGT
Statistics
Matches: 193, Mismatches: 19, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
186 87 0.45
187 1 0.01
189 4 0.02
190 18 0.09
193 1 0.01
194 2 0.01
199 1 0.01
200 79 0.41
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (193 bp):
GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCAATTCATTGTGAAGTTGAGCCTTAAATT
GGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAATATGAATGTTGTTGATGGGCACGATAATT
CACATTCATCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCATGAATTA
Found at i:432417 original size:64 final size:64
Alignment explanation
Indices: 432316--432551 Score: 341
Period size: 64 Copynumber: 3.7 Consensus size: 64
432306 TTGTGTCGTT
* * * *
432316 TTGAGTCCAATATCATTCGCTGTGAAATTGAAATTGACTCTGAATAAAACTGGAAAGTTGTTTG
1 TTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAGTTGTTTG
* * *
432380 TTGAGTCCAATAACCTTCGAC-GTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTATTTG
1 TTGAGTCCAATATCCTTCG-CTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAGTTGTTTG
*
432444 TTGAGTCCAATATTCTTCAG-TGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAGTTGTTTG
1 TTGAGTCCAATATCCTTC-GCTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAGTTGTTTG
* * *
432508 TTGAGTCTAATATCCTTTGCTATGAAGTTGAAATTGACTCTAAA
1 TTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAA
432552 AGCTGCAAAA
Statistics
Matches: 153, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
63 1 0.01
64 150 0.98
65 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (64 bp):
TTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAAAGTTGTTTG
Found at i:435098 original size:21 final size:21
Alignment explanation
Indices: 435074--435114 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
435064 TCATTTTGAC
*
435074 CATTTTCATCTAGTCTTCCAA
1 CATTTTCATCTACTCTTCCAA
* *
435095 CATTTTGATCTTCTCTTCCA
1 CATTTTCATCTACTCTTCCA
435115 TCTTCTTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.29, G:0.05, T:0.46
Consensus pattern (21 bp):
CATTTTCATCTACTCTTCCAA
Found at i:437218 original size:4 final size:4
Alignment explanation
Indices: 437209--437259 Score: 61
Period size: 4 Copynumber: 12.5 Consensus size: 4
437199 ATGTGCATAT
437209 AATA AATA AATA AA-A ACA-A GAATAA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA A-ATA -AAT-A AATA AATA AATA AATA AATA AATA
437258 AA
1 AA
437260 AATATAAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 2 0.05
4 36 0.84
5 4 0.09
6 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:437266 original size:12 final size:11
Alignment explanation
Indices: 437207--437272 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 11
437197 ATATGTGCAT
*
437207 ATAATAAATAA
1 ATAAAAAATAA
437218 ATAAAAACA-AGA
1 ATAAAAA-ATA-A
437230 ATAAAATAAATAA
1 AT-AAA-AAATAA
437243 ATAAATAAATAA
1 ATAAA-AAATAA
437255 ATAAAAATATAA
1 ATAAAAA-ATAA
*
437267 AGAAAA
1 ATAAAA
437273 TAAAAGTAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
11 9 0.19
12 28 0.60
13 7 0.15
14 3 0.06
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.20
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:437266 original size:16 final size:17
Alignment explanation
Indices: 437214--437267 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 17
437204 CATATAATAA
*
437214 ATAAATAAAAACAAGAAT
1 ATAAATAAATA-AAGAAT
*
437232 A-AAATAAATAAATAA-
1 ATAAATAAATAAAGAAT
437247 ATAAATAAATAAA-AAT
1 ATAAATAAATAAAGAAT
437263 ATAAA
1 ATAAA
437268 GAAAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 3 0.09
16 20 0.62
17 8 0.25
18 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (17 bp):
ATAAATAAATAAAGAAT
Found at i:437267 original size:33 final size:33
Alignment explanation
Indices: 437209--437276 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
437199 ATGTGCATAT
437209 AATAAATAAATAAAAACAAGAATAAA-ATAAATA
1 AATAAATAAATAAAAACAAGAATAAAGA-AAATA
437242 AATAAATAAATAAATAA-AA-ATATAAAGAAAATA
1 AATAAATAAATAAA-AACAAGA-ATAAAGAAAATA
437275 AA
1 AA
437277 AGTAAGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
32 1 0.03
33 28 0.88
34 3 0.09
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (33 bp):
AATAAATAAATAAAAACAAGAATAAAGAAAATA
Found at i:437286 original size:20 final size:18
Alignment explanation
Indices: 437212--437307 Score: 57
Period size: 17 Copynumber: 5.7 Consensus size: 18
437202 TGCATATAAT
* *
437212 AAATAAATAAAA-ACAAG
1 AAATAAAGAAAATAAAAG
*
437229 -AATAAA-ATAAAT-AAAT
1 AAATAAAGA-AAATAAAAG
*
437245 AAATAAA-TAAATAAAA-
1 AAATAAAGAAAATAAAAG
*
437261 ATATAAAGAAAATAAAAG
1 AAATAAAGAAAATAAAAG
437279 TAAGATAAAG---ATAAAAG
1 -AA-ATAAAGAAAATAAAAG
437296 AAATAAAGAAAA
1 AAATAAAGAAAA
437308 AGACAAATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 21
0.70 0.07 0.24
Matches are distributed among these distances:
15 7 0.11
16 23 0.37
17 24 0.39
18 1 0.02
19 1 0.02
20 6 0.10
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (18 bp):
AAATAAAGAAAATAAAAG
Found at i:437305 original size:8 final size:8
Alignment explanation
Indices: 437237--437306 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 8
437227 AGAATAAAAT
*
437237 AAATAAAT
1 AAATAAAG
*
437245 AAATAAAT
1 AAATAAAG
437253 AAATAAA-
1 AAATAAAG
437260 AATATAAAG
1 AA-ATAAAG
437269 AAAATAAAAG
1 -AAAT-AAAG
437279 TAAGATAAAG
1 -AA-ATAAAG
*
437289 ATA-AAAG
1 AAATAAAG
437296 AAATAAAG
1 AAATAAAG
437304 AAA
1 AAA
437307 AAGACAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
7 8 0.15
8 28 0.53
9 3 0.06
10 12 0.23
11 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (8 bp):
AAATAAAG
Found at i:437310 original size:14 final size:15
Alignment explanation
Indices: 437272--437310 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
437262 TATAAAGAAA
437272 ATAAAAGTAAGATAAAG
1 ATAAAAG-AA-ATAAAG
437289 ATAAAAGAAATAAAG
1 ATAAAAGAAATAAAG
437304 A-AAAAGA
1 ATAAAAGA
437311 CAAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.27
15 7 0.32
16 2 0.09
17 7 0.32
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (15 bp):
ATAAAAGAAATAAAG
Found at i:437827 original size:14 final size:16
Alignment explanation
Indices: 437791--437827 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
437781 TATTAATGTA
437791 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
437808 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
437823 T-AATA
1 TGAATA
437828 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:438493 original size:130 final size:130
Alignment explanation
Indices: 438289--438536 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
438279 AATTTTCTTC
* *
438289 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
438354 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
438419 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
438484 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
438537 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:438982 original size:35 final size:35
Alignment explanation
Indices: 438932--439007 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
438922 AATTGAATTT
* *
438932 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
438967 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
439002 AATTGA
1 AATTGA
439008 GGACTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:439356 original size:14 final size:14
Alignment explanation
Indices: 439327--439363 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
439317 TATGATGTTT
439327 AATAA-AATAAGTA
1 AATAATAATAAGTA
439340 AATAATAATAA-TAA
1 AATAATAATAAGT-A
439354 AATAATAATA
1 AATAATAATA
439364 GATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
AATAATAATAAGTA
Found at i:439449 original size:9 final size:9
Alignment explanation
Indices: 439435--439468 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
439425 AAAATTAGAG
439435 AAAATAAAT
1 AAAATAAAT
439444 AAAATAAAT
1 AAAATAAAT
*
439453 AAAATAAGT
1 AAAATAAAT
439462 AAAATAA
1 AAAATAA
439469 CAAAGAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAAATAAAT
Found at i:440604 original size:21 final size:22
Alignment explanation
Indices: 440565--440605 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
440555 AAAAAAACTA
440565 ACCGATTTGGGTACTCCATTGG
1 ACCGATTTGGGTACTCCATTGG
*
440587 ACCGGTTTGGGT-CTCCATT
1 ACCGATTTGGGTACTCCATT
440606 CGGGTGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (22 bp):
ACCGATTTGGGTACTCCATTGG
Found at i:449923 original size:16 final size:16
Alignment explanation
Indices: 449898--449937 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
449888 AGTAATTGTT
*
449898 TTATTGAATCTTCCTA
1 TTATTAAATCTTCCTA
**
449914 TTATTAAATCTTTTTA
1 TTATTAAATCTTCCTA
449930 TTATTAAA
1 TTATTAAA
449938 AATTATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (16 bp):
TTATTAAATCTTCCTA
Found at i:449971 original size:18 final size:19
Alignment explanation
Indices: 449939--449974 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
449929 ATTATTAAAA
449939 ATTATAAAATAATTATTTG
1 ATTATAAAATAATTATTTG
449958 ATTATAAAAT-ATTATTT
1 ATTATAAAATAATTATTT
449975 TATTTAATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
ATTATAAAATAATTATTTG
Found at i:460430 original size:44 final size:43
Alignment explanation
Indices: 460381--460507 Score: 107
Period size: 44 Copynumber: 3.2 Consensus size: 43
460371 TTAAATATTA
*
460381 TATTTTATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATATTTATTTTAGGTATTTTAGTTTAAATA-GTTTTAG
*
460425 TATTTTA-ATTAAGTTTTAGG-A---TA--TT--AT--TTTTA-
1 TATTTTATATTTA-TTTTAGGTATTTTAGTTTAAATAGTTTTAG
* *
460457 TATTTTATTTTTGTTTTAGGTATTTTAGTTTAAATAGATTTTAG
1 TATTTTATATTTATTTTAGGTATTTTAGTTTAAATAG-TTTTAG
460501 TATTTTA
1 TATTTTA
460508 ATTAAGTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 28
0.66 0.05 0.29
Matches are distributed among these distances:
32 14 0.22
33 8 0.12
36 4 0.06
38 4 0.06
40 4 0.06
43 9 0.14
44 21 0.33
ACGTcount: A:0.27, C:0.01, G:0.12, T:0.61
Consensus pattern (43 bp):
TATTTTATATTTATTTTAGGTATTTTAGTTTAAATAGTTTTAG
Found at i:460473 original size:32 final size:32
Alignment explanation
Indices: 460419--460480 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
460409 TTTAAATAGG
460419 TTTTAGTATTTTAATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTTAATTAAGTTTTAGG-TATTAT
* **
460452 TTTTA-TATTTTATTTTTGTTTTAGGTATT
1 TTTTAGTATTTTAATTAAGTTTTAGGTATT
460481 TTAGTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 4 0.15
32 17 0.65
33 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (32 bp):
TTTTAGTATTTTAATTAAGTTTTAGGTATTAT
Found at i:460485 original size:76 final size:76
Alignment explanation
Indices: 460378--460587 Score: 350
Period size: 76 Copynumber: 2.8 Consensus size: 76
460368 ATTTTAAATA
*
460378 TTATATTTTATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
*
460443 GGATATTATTT
66 AGATATTATTT
* *
460454 TTATATTTTATTTTTGTTTTAGGTATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
460519 AGATATTATTT
66 AGATATTATTT
* *
460530 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAATTA-GTTTTAAGTGTTTTAATTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTA
460588 GAATTTAAGA
Statistics
Matches: 125, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
75 4 0.03
76 121 0.97
ACGTcount: A:0.27, C:0.01, G:0.11, T:0.60
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
AGATATTATTT
Found at i:461304 original size:15 final size:15
Alignment explanation
Indices: 461284--461336 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
461274 TTTTTAATTC
461284 ATTATTTATTATTTT
1 ATTATTTATTATTTT
* *
461299 ATTATTTTTTCTTTT
1 ATTATTTATTATTTT
*
461314 TTTATAATTATTTATTTT
1 ATTAT--TTA-TTATTTT
461332 ATTAT
1 ATTAT
461337 ATTTTTTCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 17 0.59
17 2 0.07
18 10 0.34
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTATTTATTATTTT
Found at i:461318 original size:18 final size:18
Alignment explanation
Indices: 461295--461344 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
461285 TTATTTATTA
461295 TTTTATTATTTTTTCTTT
1 TTTTATTATTTTTTCTTT
* * *
461313 TTTTATAATTATTTATTT
1 TTTTATTATTTTTTCTTT
*
461331 TATTA-TATTTTTTC
1 TTTTATTATTTTTTC
461345 AACTTTATCT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTATTTTTTCTTT
Found at i:473607 original size:17 final size:16
Alignment explanation
Indices: 473581--473614 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
473571 TTTCACTAAT
*
473581 AGAGGAAATATTACAA
1 AGAGGAAATAATACAA
473597 AGAGAGAAATAATACAA
1 AGAG-GAAATAATACAA
473614 A
1 A
473615 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AGAGGAAATAATACAA
Found at i:476494 original size:25 final size:25
Alignment explanation
Indices: 476459--476508 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
476449 TTACCGTATA
* *
476459 AATTTTACCATTGTATATTTTTTAT
1 AATTTTACCATTATATATATTTTAT
*
476484 AATTTTTCCATTATATATATTTTAT
1 AATTTTACCATTATATATATTTTAT
476509 TCATTGAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (25 bp):
AATTTTACCATTATATATATTTTAT
Found at i:479002 original size:47 final size:46
Alignment explanation
Indices: 478910--479034 Score: 159
Period size: 47 Copynumber: 2.8 Consensus size: 46
478900 GTAAGTATGC
* * *
478910 AAATAATCTTACTAGCTTAT-GAA-T-AATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGATA
* *
478953 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA-TTAAATGGTAAGTATATTGATA
*
479000 AAATAAGCTTACGAGCTTATGGTA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAG
479035 AGATTTTATA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 18 0.25
44 3 0.04
45 11 0.15
46 1 0.01
47 39 0.54
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGATA
Found at i:481685 original size:17 final size:17
Alignment explanation
Indices: 481665--481751 Score: 76
Period size: 17 Copynumber: 5.2 Consensus size: 17
481655 ATATTATAAG
481665 AAAAAAAAAGAA-ACAGA
1 AAAAAAAAAGAAGA-AGA
*
481682 AAAAGAAAAGAAGAA-A
1 AAAAAAAAAGAAGAAGA
481698 AAAAAGAAAATGAAGAAGA
1 AAAAA-AAAA-GAAGAAGA
* *
481717 AAAAAAATA-AATAA-A
1 AAAAAAAAAGAAGAAGA
*
481732 AAAAGAAAAG-AGAAGA
1 AAAAAAAAAGAAGAAGA
481748 AAAA
1 AAAA
481752 GTGAAAAATG
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
15 11 0.19
16 14 0.25
17 16 0.28
18 10 0.18
19 6 0.11
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAGAAGAAGA
Found at i:481686 original size:12 final size:11
Alignment explanation
Indices: 481662--481752 Score: 75
Period size: 12 Copynumber: 8.3 Consensus size: 11
481652 AATATATTAT
481662 AAGAAAA-AAA
1 AAGAAAAGAAA
481672 AAGAAACAGAAA
1 AAGAAA-AGAAA
481684 AAGAAAAGAAGA
1 AAGAAAAGAA-A
*
481696 AAAAAAAGAAA
1 AAGAAAAGAAA
*
481707 ATGAAGAAGAAA
1 AAGAA-AAGAAA
481719 AA-AAATA-AATA
1 AAGAAA-AGAA-A
481730 AA-AAAAG-AA
1 AAGAAAAGAAA
*
481739 AAGAGAAGAAA
1 AAGAAAAGAAA
481750 AAG
1 AAG
481753 TGAAAAATGA
Statistics
Matches: 67, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
9 3 0.04
10 15 0.22
11 23 0.34
12 26 0.39
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.03
Consensus pattern (11 bp):
AAGAAAAGAAA
Found at i:481735 original size:50 final size:53
Alignment explanation
Indices: 481666--481780 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 53
481656 TATTATAAGA
* *
481666 AAAAAAAAGAAACAGAAAAAGAAAAGAAGAA-AAAAA-AG-AAAATGA-AGAAG
1 AAAAAAAATAAACAAAAAAAGAAAAG-AGAAGAAAAAGAGAAAAATGAGAGAAG
* * *
481716 AAAAAAAATAAATAAAAAAAGAAAAGAGAAGAAAAAGTGAAAAATGAGAGACG
1 AAAAAAAATAAACAAAAAAAGAAAAGAGAAGAAAAAGAGAAAAATGAGAGAAG
481769 AGAAAAAAATAA
1 A-AAAAAAATAA
481781 TATTTCACTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
49 4 0.07
50 28 0.51
51 1 0.02
52 7 0.13
53 5 0.09
54 10 0.18
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (53 bp):
AAAAAAAATAAACAAAAAAAGAAAAGAGAAGAAAAAGAGAAAAATGAGAGAAG
Found at i:481737 original size:21 final size:19
Alignment explanation
Indices: 481665--481740 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 19
481655 ATATTATAAG
*
481665 AAAAAAAAAGAAACAGAAAA
1 AAAAAAAAAGAAA-AAAAAA
* *
481685 AGAAAAGAAGAAAAAAAAGA
1 AAAAAAAAAGAAAAAAAA-A
* *
481705 AAATGAAGAAGAAAAAAAATA
1 AAA-AAAAAAGAAAAAAAA-A
481726 AATAAAAAAAGAAAA
1 AA-AAAAAAAGAAAA
481741 GAGAAGAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
19 4 0.09
20 14 0.31
21 26 0.58
22 1 0.02
ACGTcount: A:0.82, C:0.01, G:0.13, T:0.04
Consensus pattern (19 bp):
AAAAAAAAAGAAAAAAAAA
Found at i:481742 original size:29 final size:29
Alignment explanation
Indices: 481666--481752 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 29
481656 TATTATAAGA
*
481666 AAAAAAAAGAAACAGAA-AAAGAAAAGAAG
1 AAAAAAAAGAAA-AGAAGAAAAAAAAGAAG
* *
481695 AAAAAAAAGAAAATGAAGAAGAAAAAAAATAA
1 AAAAAAAAGAAAA-GAAGAA-AAAAAAGA-AG
*
481727 ATAAAAAAAGAAAAG-AGAAGAAAAAG
1 A-AAAAAAAGAAAAGAAGAAAAAAAAG
481753 TGAAAAATGA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.02
29 15 0.31
30 7 0.15
31 10 0.21
32 3 0.06
33 12 0.25
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.03
Consensus pattern (29 bp):
AAAAAAAAGAAAAGAAGAAAAAAAAGAAG
Found at i:485921 original size:90 final size:89
Alignment explanation
Indices: 485766--485942 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
485756 CCTAACACAC
485766 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
*
485831 TTTAATTAATTAAAATTTAATAAT
66 TTTAATTAATTAAAATTAAATAAT
** * *
485855 CCTTTTATATTCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATAT
*
485920 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTAAAATTAAATA
485943 TTATGGATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 32 0.40
90 49 0.60
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
TTTAATTAATTAAAATTAAATAAT
Found at i:492799 original size:20 final size:21
Alignment explanation
Indices: 492774--492843 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 21
492764 TATTATTTTA
492774 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* *
492794 AATTAATTGAAAT-TAAATATT
1 AATTAATTAAAATATATAT-TT
*
492815 AGGGATT-ATTAAAACATATATTT
1 A---ATTAATTAAAATATATATTT
492838 AATTAA
1 AATTAA
492844 CTCTAGATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
20 15 0.38
21 8 0.21
23 9 0.23
24 7 0.18
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:494119 original size:47 final size:46
Alignment explanation
Indices: 494027--494151 Score: 168
Period size: 47 Copynumber: 2.8 Consensus size: 46
494017 GTAAGTATGC
* *
494027 AAATAAGATTACGAGCTTAT-GAA-T-AATGGAAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGATA
* *
494070 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA-TTAAATGGTAAGTATATTGATA
*
494117 AAATAAGCTTACGAGCTTATGGTA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAG
494152 AGATTTTATA
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
43 19 0.26
44 3 0.04
45 11 0.15
46 1 0.01
47 39 0.53
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGATA
Found at i:503841 original size:20 final size:20
Alignment explanation
Indices: 503818--503858 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
503808 ACCATGAACA
*
503818 ATGCTACAGTTCATCGATGC
1 ATGCTACAGTGCATCGATGC
503838 ATGCTACAGTGCATCGATGC
1 ATGCTACAGTGCATCGATGC
503858 A
1 A
503859 CTGAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (20 bp):
ATGCTACAGTGCATCGATGC
Found at i:503906 original size:21 final size:21
Alignment explanation
Indices: 503880--503921 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
503870 AAGCAAAATT
503880 GTGCATCGATGCACTGCTACA
1 GTGCATCGATGCACTGCTACA
503901 GTGCATCGATGCACTGCTACA
1 GTGCATCGATGCACTGCTACA
503922 ATAACTTTCG
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:0.29, G:0.24, T:0.24
Consensus pattern (21 bp):
GTGCATCGATGCACTGCTACA
Found at i:504610 original size:31 final size:31
Alignment explanation
Indices: 504575--504714 Score: 199
Period size: 31 Copynumber: 4.5 Consensus size: 31
504565 CATAGATTAT
* * * *
504575 GAAGAACCTAGGTAATCAGTCTATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATATCCC
504606 GAAGAACATAGGTAAACAGTCCATATATCCC
1 GAAGAACATAGGTAAACAGTCCATATATCCC
* * *
504637 AAAGAACAAAGGTAAACAGTCCATATATCTC
1 GAAGAACATAGGTAAACAGTCCATATATCCC
*
504668 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATATCCC
*
504699 GAAGAACACAGGTAAA
1 GAAGAACATAGGTAAA
504715 TCCTCGACCC
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 97 1.00
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATATCCC
Found at i:509299 original size:20 final size:20
Alignment explanation
Indices: 509276--509315 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
509266 TGAACAGTAT
509276 CGTGAACAGTGCTACAGTGC
1 CGTGAACAGTGCTACAGTGC
*
509296 CGTGAACCGTGCTACAGTGC
1 CGTGAACAGTGCTACAGTGC
509316 ATCGATGCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.20
Consensus pattern (20 bp):
CGTGAACAGTGCTACAGTGC
Found at i:510044 original size:31 final size:31
Alignment explanation
Indices: 510001--510110 Score: 157
Period size: 31 Copynumber: 3.5 Consensus size: 31
509991 CAAAGATTCT
* *
510001 GAAGAACCTAGGTAATCAGTCCATATATCCC
1 GAAGAACATAGGTAAACAGTCCATATATCCC
* *
510032 GAAAAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATATCCC
* *
510063 GAAGAACGTAGGTAAACAGTTCATATATCCC
1 GAAGAACATAGGTAAACAGTCCATATATCCC
*
510094 GAAGAACACAGGTAAAC
1 GAAGAACATAGGTAAAC
510111 CCTCGACCCT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATATCCC
Found at i:512878 original size:21 final size:21
Alignment explanation
Indices: 512852--512892 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
512842 TTCAATTAAG
*
512852 AATCAAGGAGCTTTACTTCAT
1 AATCAAGGAGCCTTACTTCAT
*
512873 AATCAAGGCGCCTTACTTCA
1 AATCAAGGAGCCTTACTTCA
512893 AAGCCATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (21 bp):
AATCAAGGAGCCTTACTTCAT
Found at i:525867 original size:80 final size:80
Alignment explanation
Indices: 525686--526187 Score: 602
Period size: 80 Copynumber: 6.3 Consensus size: 80
525676 ATAGTTCAAA
* * *
525686 TCCATCACATAATA-AGTTGGATCAGA-ATTTCCAAGAGAAGAAGTTCTTAATGAGAAGAAC-TA
1 TCCATCACAGAA-AGAGTTGGATCA-ATATTCCCAAGAGAAGAAGTTCATAATGAGAAGAACTTA
525748 GTTCAATC-TTGCTCGAT
64 -TTCAATCTTTGCTCGAT
* * * * * * *
525765 TCCATCAAAGAAAGATTTGGATCAACATTCCAAAGAGAAGAAATTCATAATGAGAAGAAATTTTT
1 TCCATCACAGAAAGAGTTGGATCAATATTCCCAAGAGAAGAAGTTCATAATGAGAAGAACTTATT
*
525830 CAATATTTGCTCGAT
66 CAATCTTTGCTCGAT
* * * *
525845 TTCATCACAGAAAGAGTTGGATCAATATTCCTAAGAGAAGAAGTTCATAATGAGAATAACTTGTT
1 TCCATCACAGAAAGAGTTGGATCAATATTCCCAAGAGAAGAAGTTCATAATGAGAAGAACTTATT
*
525910 CAATCTTTGTTCGAT
66 CAATCTTTGCTCGAT
* * * * *
525925 TCCATCATAGAAGGAGTTGGATCAGTATTCCCAAGAGAATAAGTTCATAATGAGGAGAACTTATT
1 TCCATCACAGAAAGAGTTGGATCAATATTCCCAAGAGAAGAAGTTCATAATGAGAAGAACTTATT
525990 CAATCTTTGCTCGAT
66 CAATCTTTGCTCGAT
* * * * *
526005 TCCATCATAGAAGGAGTTAGATCAGTATTCCCAAGAGAAGAAGTTCATAATGAGAAGAACATATT
1 TCCATCACAGAAAGAGTTGGATCAATATTCCCAAGAGAAGAAGTTCATAATGAGAAGAACTTATT
526070 CAATCTTTGCTCGAT
66 CAATCTTTGCTCGAT
** * * *
526085 TCCATCACAG-AAGAGTTGGATCAGCATTCCCAATAGAAGAAGTTCATAATGAGAAAAACTTGTT
1 TCCATCACAGAAAGAGTTGGATCAATATTCCCAAGAGAAGAAGTTCATAATGAGAAGAACTTATT
* ** *
526149 CAACCCCTACTCGA-
66 CAATCTTTGCTCGAT
* *
526163 TCCATCCCAGAAGGAGTTGGATCAA
1 TCCATCACAGAAAGAGTTGGATCAA
526188 CACTTTCGGA
Statistics
Matches: 368, Mismatches: 50, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
78 11 0.03
79 123 0.33
80 234 0.64
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (80 bp):
TCCATCACAGAAAGAGTTGGATCAATATTCCCAAGAGAAGAAGTTCATAATGAGAAGAACTTATT
CAATCTTTGCTCGAT
Found at i:526125 original size:239 final size:238
Alignment explanation
Indices: 525685--526186 Score: 668
Period size: 239 Copynumber: 2.1 Consensus size: 238
525675 GATAGTTCAA
* ** * *
525685 ATCCATCACATAATAAGTTGGATCAGAATTTCCAAGAGAAGAAGTTCTTAATGAGAAGAACTAGT
1 ATCCATCACAGAAGGAGTTGGATCAGAATTCCCAAGAGAAGAAGTTCATAATGAGAAGAACTAGT
* *
525750 TCAATCTTGCTCGATTCCATCAAAGAAAGATTTGGATCAACATTCCAAAGAGAAGAAATTCATAA
66 TCAATCTTGCTCGATTCCATCAAAGAAAGAGTTAGATCAACATTCCAAAGAGAAGAAATTCATAA
* * * *
525815 TGAGAAGAAATTTTTCAATATTTGCTCGATTTCATCACAGAAAGAGTTGGATCAATATTCCTAAG
131 TGAGAAGAAATTATTCAATATTTGCTCGATTCCATCACAGAAAGAGTTGGATCAACATTCCCAAG
* * ** **
525880 AGAAGAAGTTCATAATGAGAATAACTTGTTCAATCTTTGTTCG
196 AGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCCCTACTCG
* * * *
525923 ATTCCATCATAGAAGGAGTTGGATCAGTATTCCCAAGAGAATAAGTTCATAATGAGGAGAACTTA
1 A-TCCATCACAGAAGGAGTTGGATCAGAATTCCCAAGAGAAGAAGTTCATAATGAGAAGAAC-TA
* * ** * *
525988 -TTCAATCTTTGCTCGATTCCATCATAGAAGGAGTTAGATCAGTATTCCCAAGAGAAGAAGTTCA
64 GTTCAATC-TTGCTCGATTCCATCAAAGAAAGAGTTAGATCAACATTCCAAAGAGAAGAAATTCA
* *
526052 TAATGAGAAGAACA-TATTCAATCTTTGCTCGATTCCATCACAG-AAGAGTTGGATCAGCATTCC
128 TAATGAGAAGAA-ATTATTCAATATTTGCTCGATTCCATCACAGAAAGAGTTGGATCAACATTCC
*
526115 CAATAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCCCTACTCG
192 CAAGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCCCTACTCG
*
526162 ATCCATCCCAGAAGGAGTTGGATCA
1 ATCCATCACAGAAGGAGTTGGATCA
526187 ACACTTTCGG
Statistics
Matches: 228, Mismatches: 32, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
238 23 0.10
239 116 0.51
240 88 0.39
241 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (238 bp):
ATCCATCACAGAAGGAGTTGGATCAGAATTCCCAAGAGAAGAAGTTCATAATGAGAAGAACTAGT
TCAATCTTGCTCGATTCCATCAAAGAAAGAGTTAGATCAACATTCCAAAGAGAAGAAATTCATAA
TGAGAAGAAATTATTCAATATTTGCTCGATTCCATCACAGAAAGAGTTGGATCAACATTCCCAAG
AGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCCCTACTCG
Found at i:529078 original size:18 final size:18
Alignment explanation
Indices: 529052--529090 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
529042 TTGAAGAAGA
**
529052 ACAAGATGTGATTCCTCC
1 ACAAGATGTGAACCCTCC
*
529070 ACAATATGTGAACCCTCC
1 ACAAGATGTGAACCCTCC
529088 ACA
1 ACA
529091 TGATATGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.23
Consensus pattern (18 bp):
ACAAGATGTGAACCCTCC
Found at i:529575 original size:23 final size:23
Alignment explanation
Indices: 529549--529593 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
529539 ATGTATGTGA
* *
529549 ATATTCATCATGAATGGATATAC
1 ATATTCATAATGAATAGATATAC
*
529572 ATATTCGTAATGAATAGATATA
1 ATATTCATAATGAATAGATATA
529594 ACTCTTGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (23 bp):
ATATTCATAATGAATAGATATAC
Found at i:531127 original size:13 final size:13
Alignment explanation
Indices: 531109--531136 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
531099 TCCATCTCAT
531109 CTTTCATGGAAGA
1 CTTTCATGGAAGA
531122 CTTTCATGGAAGA
1 CTTTCATGGAAGA
531135 CT
1 CT
531137 CCCACTTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (13 bp):
CTTTCATGGAAGA
Found at i:533615 original size:16 final size:16
Alignment explanation
Indices: 533591--533622 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
533581 TATCGCATAC
*
533591 CAAATTTTACTATTCA
1 CAAAATTTACTATTCA
533607 CAAAATTTACTATTCA
1 CAAAATTTACTATTCA
533623 TATGAATAGT
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:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (16 bp):
CAAAATTTACTATTCA
Found at i:535280 original size:16 final size:15
Alignment explanation
Indices: 535239--535283 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
535229 CCCAAAAAAT
535239 TAAAAGTAAAAATAAA
1 TAAAA-TAAAAATAAA
*
535255 TAAATCTAAAACATAAA
1 TAAA-ATAAAA-ATAAA
535272 TAAAATAAAAAT
1 TAAAATAAAAAT
535284 TATTAAATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 2 0.08
16 14 0.56
17 9 0.36
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (15 bp):
TAAAATAAAAATAAA
Found at i:545722 original size:2 final size:2
Alignment explanation
Indices: 545717--545750 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
545707 AATTCCAGTT
545717 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
545751 AAATTAAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:545972 original size:29 final size:29
Alignment explanation
Indices: 545939--546001 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
545929 TAGATCCATC
*
545939 ATTAATTAA-AGGTAGAGTTAGAATCAAAT
1 ATTAATTAAGA-GTAGAGTGAGAATCAAAT
*
545968 ATTAATTAAGAGTAGAGTGAGAATGAAAT
1 ATTAATTAAGAGTAGAGTGAGAATCAAAT
545997 ATTAA
1 ATTAA
546002 AAGAGATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.19, T:0.30
Consensus pattern (29 bp):
ATTAATTAAGAGTAGAGTGAGAATCAAAT
Found at i:546114 original size:22 final size:22
Alignment explanation
Indices: 546071--546120 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
546061 GTTAAAGAGG
*
546071 ATAAAATTTAATTTAATTTAAC
1 ATAAAATTTAATTTAATATAAC
*
546093 ATAAATTTTAA-TTAATAATAAC
1 ATAAAATTTAATTTAAT-ATAAC
*
546115 TTAAAA
1 ATAAAA
546121 ATATTAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAAAATTTAATTTAATATAAC
Found at i:546246 original size:2 final size:2
Alignment explanation
Indices: 546239--546269 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
546229 CGAAAATTTA
546239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
546270 AAGATATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:546289 original size:17 final size:17
Alignment explanation
Indices: 546264--546298 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
546254 TATATATATA
*
546264 TATATAAAGATATTATC
1 TATAAAAAGATATTATC
546281 TATAAAAAGATATTATC
1 TATAAAAAGATATTATC
546298 T
1 T
546299 TGTTTTTATC
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:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (17 bp):
TATAAAAAGATATTATC
Found at i:549111 original size:29 final size:29
Alignment explanation
Indices: 549076--549157 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
549066 AAACTAAATT
*
549076 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
549105 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
549134 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
549158 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:553879 original size:29 final size:29
Alignment explanation
Indices: 553844--553925 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
553834 AAACTAAATT
*
553844 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
553873 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
553902 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
553926 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:564864 original size:22 final size:21
Alignment explanation
Indices: 564835--564877 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
564825 AACATTTGAG
564835 ATCCCTTTGA-TGTATCTCAAT
1 ATCCCTTT-ACTGTATCTCAAT
*
564856 ATCCTCTTTACTGTATTTCAAT
1 ATCC-CTTTACTGTATCTCAAT
564878 GCTCTTTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (21 bp):
ATCCCTTTACTGTATCTCAAT
Found at i:568807 original size:11 final size:11
Alignment explanation
Indices: 568791--568816 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
568781 CACTTTTTAA
568791 CCAACTTGCTG
1 CCAACTTGCTG
568802 CCAACTTGCTG
1 CCAACTTGCTG
568813 CCAA
1 CCAA
568817 TTTTCAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.23
Consensus pattern (11 bp):
CCAACTTGCTG
Found at i:569565 original size:9 final size:9
Alignment explanation
Indices: 569551--569592 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
569541 ATATCATTTC
*
569551 ATTATCCTT
1 ATTATCATT
569560 ATTATCATT
1 ATTATCATT
569569 -TTATCATT
1 ATTATCATT
*
569577 ATTAGCATT
1 ATTATCATT
569586 ATTATCA
1 ATTATCA
569593 ATCATATCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.52
Consensus pattern (9 bp):
ATTATCATT
Found at i:569578 original size:17 final size:18
Alignment explanation
Indices: 569551--569592 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
569541 ATATCATTTC
* *
569551 ATTATCCTTATTATCATT
1 ATTATCATTATTAGCATT
569569 -TTATCATTATTAGCATT
1 ATTATCATTATTAGCATT
569586 ATTATCA
1 ATTATCA
569593 ATCATATCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTATCATTATTAGCATT
Found at i:569865 original size:18 final size:17
Alignment explanation
Indices: 569837--569872 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
569827 GACGTGTAGA
*
569837 ATTTTTCCCGAATGACC
1 ATTTTTCCCGAAGGACC
569854 ATTTTGTCCCGAAGGACC
1 ATTTT-TCCCGAAGGACC
569872 A
1 A
569873 CCGTCCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (17 bp):
ATTTTTCCCGAAGGACC
Found at i:569913 original size:31 final size:31
Alignment explanation
Indices: 569875--569964 Score: 162
Period size: 31 Copynumber: 2.9 Consensus size: 31
569865 AAGGACCACC
569875 GTCCATATGTCCCAAAGGACATAGGTAAACT
1 GTCCATATGTCCCAAAGGACATAGGTAAACT
569906 GTCCATATGTCCCAAAGGACATAGGTAAACT
1 GTCCATATGTCCCAAAGGACATAGGTAAACT
* *
569937 GTACATATGTCCCGAAGGACATAGGTAA
1 GTCCATATGTCCCAAAGGACATAGGTAA
569965 CCCTCGACTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (31 bp):
GTCCATATGTCCCAAAGGACATAGGTAAACT
Found at i:570770 original size:21 final size:21
Alignment explanation
Indices: 570744--570800 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
570734 AAATTGGTAT
** *
570744 TAGGGTATCGGTACCCATTCG
1 TAGGGTATCAATACCCATTCA
570765 TAGGGTATCAATACCCATTCA
1 TAGGGTATCAATACCCATTCA
*
570786 TAGAGTATC-ATACCC
1 TAGGGTATCAATACCC
570801 CTTGCCCAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 6 0.19
21 26 0.81
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (21 bp):
TAGGGTATCAATACCCATTCA
Found at i:576534 original size:34 final size:34
Alignment explanation
Indices: 576489--576555 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
576479 AATAGGAATT
*
576489 ACAACTTCTCTC-GATCTAATAAGGAGAAAACAATA
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATA
576524 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
576556 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:576742 original size:11 final size:11
Alignment explanation
Indices: 576726--576751 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
576716 CACTTTTCAA
576726 CCAACTTGCTG
1 CCAACTTGCTG
576737 CCAACTTGCTG
1 CCAACTTGCTG
576748 CCAA
1 CCAA
576752 TTTTCAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.23
Consensus pattern (11 bp):
CCAACTTGCTG
Found at i:579015 original size:16 final size:16
Alignment explanation
Indices: 578994--579032 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
578984 AGCTTAAAAT
578994 ATATATTTAATATATA
1 ATATATTTAATATATA
*
579010 ATATATTTAATATTTA
1 ATATATTTAATATATA
579026 ATA-ATTT
1 ATATATTT
579033 TGATTATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATATTTAATATATA
Found at i:583332 original size:22 final size:22
Alignment explanation
Indices: 583304--583352 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
583294 GTGTTTTTCT
583304 GCTTTCGAATA-GAAAAATAATA
1 GCTTTCGAATATG-AAAATAATA
*
583326 GCTTTCGAATATGATAATAATA
1 GCTTTCGAATATGAAAATAATA
583348 GCTTT
1 GCTTT
583353 TCAAAACGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
GCTTTCGAATATGAAAATAATA
Found at i:584564 original size:41 final size:41
Alignment explanation
Indices: 584443--584569 Score: 123
Period size: 41 Copynumber: 3.1 Consensus size: 41
584433 TTTAGAGGCA
**
584443 TTTTTATACAAACGCCACAATAGGTGTAATCTATAGTGGTG
1 TTTTTATACAAACGCTGCAATAGGTGTAATCTATAGTGGTG
* * ** * * * *
584484 TTTTAATACCAAACGCTGCAAAATAT-TTATACAAAAGTGGCG
1 TTTTTATA-CAAACGCTGCAATAGGTGTAAT-CTATAGTGGTG
584526 TTTTTATTA-AAACGCTGCAATAGGTGTAATCTATAGTGGTG
1 TTTTTA-TACAAACGCTGCAATAGGTGTAATCTATAGTGGTG
584567 TTT
1 TTT
584570 GGATAAAAAA
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
41 34 0.53
42 28 0.44
43 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35
Consensus pattern (41 bp):
TTTTTATACAAACGCTGCAATAGGTGTAATCTATAGTGGTG
Found at i:584696 original size:83 final size:83
Alignment explanation
Indices: 584420--584697 Score: 240
Period size: 83 Copynumber: 3.4 Consensus size: 83
584410 AAATGTCGCA
* * * *
584420 AAAATATTTGTACTTTAGA-GGCATTTTTATACAAACGCCACAATAGGTGTAATCTATAGTGGTG
1 AAAATATTTATACTTTA-ACAGCGTTTTTTTACAAACGCCACAATAGGTGTAATCTATAGTGGTG
* *
584484 TTTTAATACCAAACGCTGC
65 TTTTAATAACAAACGCCGC
** ** **
584503 AAAATATTTATAC-AAAAGTGGCGTTTTTATTA-AAACGCTGCAATAGGTGTAATCTATAGTGGT
1 AAAATATTTATACTTTAA-CAGCGTTTTT-TTACAAACGCCACAATAGGTGTAATCTATAGTGGT
** * * * **
584566 GTTTGGATAAAAAATGTCAT
64 GTTTTAATAACAAACGCCGC
* * * * * * *
584586 AAAATATTTAAACTTTAGCGGCGTTTTTGTACAAATGCCACAATAGGTGTAATCTATAATTGT-T
1 AAAATATTTATACTTTAACAGCGTTTTTTTACAAACGCCACAATAGGTGTAATCTATAGTGGTGT
**
584650 TTTTTTAACAAACGCCGC
66 TTTAATAACAAACGCCGC
*
584668 AAAATATTTGTACTTTAACAGCGTTTTTTT
1 AAAATATTTATACTTTAACAGCGTTTTTTT
584698 TTAAACACCG
Statistics
Matches: 150, Mismatches: 40, Indels: 11
0.75 0.20 0.05
Matches are distributed among these distances:
81 1 0.01
82 39 0.26
83 107 0.71
84 3 0.02
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (83 bp):
AAAATATTTATACTTTAACAGCGTTTTTTTACAAACGCCACAATAGGTGTAATCTATAGTGGTGT
TTTAATAACAAACGCCGC
Found at i:590893 original size:15 final size:15
Alignment explanation
Indices: 590873--590904 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
590863 CTTACATTAA
590873 ACACTTATTTGTTGT
1 ACACTTATTTGTTGT
590888 ACACTTATTTGTTGT
1 ACACTTATTTGTTGT
590903 AC
1 AC
590905 CGGAGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (15 bp):
ACACTTATTTGTTGT
Found at i:592333 original size:43 final size:42
Alignment explanation
Indices: 592281--592372 Score: 148
Period size: 43 Copynumber: 2.2 Consensus size: 42
592271 TCAAAAGCGT
592281 CGTTAAAGAACATAACTATTACGGCGTTTGTGTGAATAAACGC
1 CGTTAAAGAACATAACTATTACGGCGTTTGTGTGAA-AAACGC
* * *
592324 CGTTAAAGAACATACCTATTACGGCGTTTGTGTTAAAAACGT
1 CGTTAAAGAACATAACTATTACGGCGTTTGTGTGAAAAACGC
592366 CGTTAAA
1 CGTTAAA
592373 TATTGAAAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 12 0.26
43 34 0.74
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (42 bp):
CGTTAAAGAACATAACTATTACGGCGTTTGTGTGAAAAACGC
Found at i:592396 original size:43 final size:42
Alignment explanation
Indices: 592339--592484 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 42
592329 AAGAACATAC
* * *
592339 CTATTACGGCGTTTGTGTTAAAAACGTCGTTAAATATTGAAAA
1 CTATTGCGGTGTTTGTGTTAAAAACGTCGCTAAATATT-AAAA
* * *
592382 CTATTGCGGTGTTTGTG-AAAGAAACGCCGCTAAATATCAAAA
1 CTATTGCGGTGTTTGTGTTAA-AAACGTCGCTAAATATTAAAA
* * * * *
592424 CATATTGTGTTGTTTGT-TTAAAAAACGTCGCGAAATCTTAATAC
1 C-TATTGCGGTGTTTGTGTT-AAAAACGTCGCTAAATATTAA-AA
*
592468 CTATTGTGGTGTTTGTG
1 CTATTGCGGTGTTTGTG
592485 GAAAAATACC
Statistics
Matches: 82, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
42 7 0.09
43 71 0.87
44 4 0.05
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (42 bp):
CTATTGCGGTGTTTGTGTTAAAAACGTCGCTAAATATTAAAA
Found at i:592490 original size:43 final size:42
Alignment explanation
Indices: 592378--592582 Score: 117
Period size: 43 Copynumber: 4.8 Consensus size: 42
592368 TTAAATATTG
* *
592378 AAAA-CTATTGCGGTGTTTGTGAAAGAAACGCCGCTAAATATC
1 AAAACCTATTGTGGTGTTTGTGAAA-AAACGCCGCGAAATATC
* * * * * *
592420 AAAACATATTGTGTTGTTTGTTTAAAAAACGTCGCGAAATCTT
1 AAAACCTATTGTGGTGTTTG-TGAAAAAACGCCGCGAAATATC
* * ** *
592463 AATACCTATTGTGGTGTTTGTGGAAAAATACCGC-AAATTTTC
1 AAAACCTATTGTGGTGTTTGTGAAAAAACGCCGCGAAA-TATC
* * * * * * * *
592505 AACACCTATTGCGGCGTTTTTTGGACAAATGCCGCTAAATATC
1 AAAACCTATTGTGGTG-TTTGTGAAAAAACGCCGCGAAATATC
* * * **
592548 AAATCCTATTGCGGCGTTTGTTGTCAAAACGCCGC
1 AAAACCTATTGTGGTGTTTG-TGAAAAAACGCCGC
592583 TATATATCGT
Statistics
Matches: 125, Mismatches: 32, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
41 3 0.02
42 31 0.25
43 84 0.67
44 7 0.06
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (42 bp):
AAAACCTATTGTGGTGTTTGTGAAAAAACGCCGCGAAATATC
Found at i:592991 original size:19 final size:19
Alignment explanation
Indices: 592958--592994 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
592948 ATGACCAACA
**
592958 AAATCGCAATTCGATCTCT
1 AAATCGCAACGCGATCTCT
592977 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
592995 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:593125 original size:20 final size:20
Alignment explanation
Indices: 593078--593125 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
593068 GAATATGTAA
593078 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
593098 ATCACAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
593118 GTCGCAAC
1 ATCGCAAC
593126 ACTGAATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:593744 original size:19 final size:20
Alignment explanation
Indices: 593713--593754 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
593703 ATAGTTTCTA
*
593713 AAACTTAAAATCGCAACATG
1 AAACTTAAAATCGCAACACG
593733 AAACTT-AAATCGCAACACG
1 AAACTTAAAATCGCAACACG
593752 AAA
1 AAA
593755 ATGACTATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.52, C:0.21, G:0.10, T:0.17
Consensus pattern (20 bp):
AAACTTAAAATCGCAACACG
Found at i:593766 original size:20 final size:20
Alignment explanation
Indices: 593741--593809 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
593731 TGAAACTTAA
*
593741 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
593761 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
593781 ATCGCAACGTGAATTTGACT
1 ATCGCAACGCGAAAATGACT
593801 ATCGCAACG
1 ATCGCAACG
593810 GGATAATCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:593905 original size:20 final size:20
Alignment explanation
Indices: 593849--593888 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
593839 AACATGAAAC
593849 TAAATTCGCGTTGCGATAGT
1 TAAATTCGCGTTGCGATAGT
*
593869 TAAATTCGCATTGCGATAGT
1 TAAATTCGCGTTGCGATAGT
593889 CATTTCTGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (20 bp):
TAAATTCGCGTTGCGATAGT
Found at i:594121 original size:20 final size:21
Alignment explanation
Indices: 594082--594127 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
594072 TGAAATGGTT
594082 AATCTAAGTGAAATTATGAATA
1 AATCTAAGTGAAATTATGAA-A
*
594104 AATC-AAGTTAAA-TATGAAA
1 AATCTAAGTGAAATTATGAAA
594123 AATCT
1 AATCT
594128 TAAACTTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 5 0.23
20 6 0.27
21 7 0.32
22 4 0.18
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (21 bp):
AATCTAAGTGAAATTATGAAA
Found at i:596207 original size:19 final size:21
Alignment explanation
Indices: 596183--596246 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
596173 TCTGAGAGAT
596183 GGAGAT-AGAC-GATTTCGTC
1 GGAGATGAGACGGATTTCGTC
*
596202 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGTC
* *
596224 GGAGATGGGGACGGATGTCGTC
1 GGAGAT-GAGACGGATTTCGTC
596246 G
1 G
596247 TAGAGAGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.15
21 3 0.08
22 31 0.77
ACGTcount: A:0.20, C:0.14, G:0.44, T:0.22
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGTC
Found at i:596221 original size:22 final size:22
Alignment explanation
Indices: 596193--596246 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
596183 GGAGATAGAC
596193 GATTTCGTCGGAGATGGGGACG
1 GATTTCGTCGGAGATGGGGACG
596215 GATTTCGTCGGAGATGGGGACG
1 GATTTCGTCGGAGATGGGGACG
*
596237 GATGTCGTCG
1 GATTTCGTCG
596247 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.15, G:0.44, T:0.24
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACG
Found at i:596470 original size:21 final size:21
Alignment explanation
Indices: 596424--596518 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 21
596414 CGATAGTCAG
* *
596424 AATCGCGTTGCGA-TTTACAT
1 AATCGCATTGCGATTTTACAA
*
596444 ATTCGCATTGCGATTTTACAA
1 AATCGCATTGCGATTTTACAA
** * **
596465 AATCGCAACGCGAATTTGGAA
1 AATCGCATTGCGATTTTACAA
* **
596486 AATCGCAATGCGATAGT-CAA
1 AATCGCATTGCGATTTTACAA
*
596506 AATCGCGTTGCGA
1 AATCGCATTGCGA
596519 ATCTGGAAAC
Statistics
Matches: 58, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 24 0.41
21 34 0.59
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (21 bp):
AATCGCATTGCGATTTTACAA
Found at i:596519 original size:41 final size:41
Alignment explanation
Indices: 596412--596527 Score: 108
Period size: 41 Copynumber: 2.8 Consensus size: 41
596402 ATTATCGCGT
* ** * * *
596412 TGCGATAGTCAGAATCGCGTTGCG-ATTTACATATTCGCAT
1 TGCGATAGTCAAAATCGCGTTGCGAATTTGGAAAATCGCAA
** ***
596452 TGCGATTTTACAAAATCGCAACGCGAATTTGGAAAATCGCAA
1 TGCGATAGT-CAAAATCGCGTTGCGAATTTGGAAAATCGCAA
*
596494 TGCGATAGTCAAAATCGCGTTGCGAATCTGGAAA
1 TGCGATAGTCAAAATCGCGTTGCGAATTTGGAAA
596528 CTGATTTGCG
Statistics
Matches: 57, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
40 7 0.12
41 32 0.56
42 18 0.32
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (41 bp):
TGCGATAGTCAAAATCGCGTTGCGAATTTGGAAAATCGCAA
Found at i:597205 original size:19 final size:21
Alignment explanation
Indices: 597167--597207 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
597157 GTTTAGATAT
597167 GATTTAGGGATTAAAGTTTAG
1 GATTTAGGGATTAAAGTTTAG
*
597188 GATTTA-GG-TTAAATTTTAG
1 GATTTAGGGATTAAAGTTTAG
597207 G
1 G
597208 TATTAAGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 2 0.11
21 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.41
Consensus pattern (21 bp):
GATTTAGGGATTAAAGTTTAG
Found at i:597234 original size:21 final size:21
Alignment explanation
Indices: 597196--597247 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
597186 AGGATTTAGG
597196 TTAAATTTTA-GGTATTAAGAG-
1 TTAAA-TTTAGGGTATTAA-AGT
597217 TTATAATTTAGGGT-TTAAAGT
1 TTA-AATTTAGGGTATTAAAGT
597238 TTAAATTTAG
1 TTAAATTTAG
597248 TTTTGACTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 9 0.32
21 14 0.50
22 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (21 bp):
TTAAATTTAGGGTATTAAAGT
Found at i:597377 original size:29 final size:29
Alignment explanation
Indices: 597334--597392 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
597324 TGTAAAGCCT
*
597334 AGAAAGTTAGTTTCAATCCATGCAAACTTA
1 AGAAAGTTAGGTTCAATCCATGCAAA-TTA
*
597364 AGAAA-TTAGGTTCAATTCATGCAAATTA
1 AGAAAGTTAGGTTCAATCCATGCAAATTA
597392 A
1 A
597393 TTAAGGATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 4 0.15
29 18 0.67
30 5 0.19
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (29 bp):
AGAAAGTTAGGTTCAATCCATGCAAATTA
Found at i:598105 original size:18 final size:19
Alignment explanation
Indices: 598070--598106 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
598060 CACGGAATGT
598070 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
598090 AAGATTATCA-GGGAATA
1 AAGATTATCAGGGGAATA
598107 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Found at i:606122 original size:16 final size:16
Alignment explanation
Indices: 606103--606141 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
606093 TTTATGTTAG
606103 TATT-TTTTTAAATAGT
1 TATTATTTTTAAATA-T
*
606119 TATTATTTTTATATAT
1 TATTATTTTTAAATAT
606135 TATTATT
1 TATTATT
606142 AATATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TATTATTTTTAAATAT
Found at i:606182 original size:13 final size:13
Alignment explanation
Indices: 606120--606191 Score: 67
Period size: 13 Copynumber: 5.5 Consensus size: 13
606110 TTAAATAGTT
606120 ATTATT-TTTATA
1 ATTATTATTTATA
*
606132 TATTATTATTAAT-
1 -ATTATTATTTATA
*
606145 ATTATTTTTTATTA
1 ATTATTATTTA-TA
* *
606159 AATAATATTTATA
1 ATTATTATTTATA
*
606172 ATTATTATTTAGA
1 ATTATTATTTATA
606185 ATTATTA
1 ATTATTA
606192 ATTTTTTTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
12 9 0.19
13 26 0.55
14 12 0.26
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (13 bp):
ATTATTATTTATA
Found at i:606344 original size:17 final size:17
Alignment explanation
Indices: 606322--606375 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
606312 AATGTTAATA
606322 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
606339 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
606356 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
606373 TTT
1 TTT
606376 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:607913 original size:21 final size:21
Alignment explanation
Indices: 607883--607930 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
607873 GCAGGGGTAC
* *
607883 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
607904 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
607925 ATGCCA
1 ATGCCA
607931 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:607960 original size:21 final size:21
Alignment explanation
Indices: 607934--608006 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
607924 TATGCCATCT
*
607934 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
607955 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
607976 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
607997 CCGCAGGGTT
1 CCGCAGGGTT
608007 TTACCATATG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:608572 original size:29 final size:33
Alignment explanation
Indices: 608539--608603 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 33
608529 ATATTATTCG
608539 AAATTTAAAA-A-AAA-TAT-TATTCGAAATTT
1 AAATTTAAAATATAAATTATATATTCGAAATTT
608568 AAATTTAAAATATAAATTATAGTATTCGAAATTT
1 AAATTTAAAATATAAATTATA-TATTCGAAATTT
608602 AA
1 AA
608604 CATTAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 10 0.32
30 1 0.03
31 3 0.10
32 3 0.10
34 14 0.45
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (33 bp):
AAATTTAAAATATAAATTATATATTCGAAATTT
Found at i:609759 original size:116 final size:120
Alignment explanation
Indices: 609065--610083 Score: 1178
Period size: 128 Copynumber: 8.4 Consensus size: 120
609055 CTATGACAAA
609065 ATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATAT
1 ATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATAT
609130 ATCTAGTGTCCCCGAGGGACATGAGTGACAT-ATAGGGCAATGATAACATATTCTATGAC
66 ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATA---TAT--C
609189 AAAATAATGGAA-GCGCGCCCCCGGGAACGCGCCTTCATGT-AATAGTGAAATAATA--TACTGA
1 ---ATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGA
609250 TATAT-TAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATAT-TC
63 TATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATATC
*
609305 TATGACGAAATGGAAGGCGCGCCCCC-GGAATGCGCCTTCA--TGAATAGTGAAATAAT--GTAC
1 -AT-----AATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
* *
609365 TG-TATATCTAGTGT-CCCGAGGGACATGAGTGA-TTAATAGGGCAATGAGAACATATTCTATGA
60 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATA---TAT--
609427 C
120 C
* *
609428 GAAATAATGGAAGGCG-GGCCACGGGAA--CGCCTTCATGTGAATAGTGAAATAATAGGTACTGA
1 ---ATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGA
*
609490 TATATCTAGTTGTCCCCGAGGGACATGA-TGACATAAT--GGCAATGATAACATGTTCTATGAC
63 TATATCTAG-TGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACA---TATAT--C
609551 GAAATAATGGAA-GCGCGCCCCCGGG-ACGCG-CTT-ATGTGAATAGTGAAATAATA-GTACTGA
1 ---ATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGA
609611 TATATCTAGTGTCCCCGA-GGACATGAGTGACATAATAGGGCAATGATAACATAT-TC
63 TATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATATC
* **
609667 -TAATGGAAGGTGCGCCATCGGGAACGCGCCTTCATGTG-A-A-TGAAATAATAGGTACTGATAT
1 ATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATAT
*
609728 ATCTAGTTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATGTTCTATGAC
66 ATCTAG-TGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACA---TATAT--C
*
609789 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTAATGTGAATAGTGAAATAATAGGTACTGA
1 ---ATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGA
609854 TATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTATGAC
63 TATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATA---TAT--C
*
609917 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGTACTG-
1 ---ATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGA
* *
609981 -ATATCTAGTGT-CCCGAGGGATATGAGTGACATAATAGGGCAATGATAATATAT-TC
63 TATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATATC
610036 TGAAATAATGGAAGGCGCGCCCCCGGGAACGCG-CTTCATGTGAATAGT
1 ----ATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
610084 ACTCCGATTA
Statistics
Matches: 805, Mismatches: 27, Indels: 128
0.84 0.03 0.13
Matches are distributed among these distances:
112 8 0.01
113 20 0.02
114 24 0.03
115 13 0.02
116 40 0.05
117 26 0.03
118 53 0.07
119 52 0.06
120 93 0.12
121 39 0.05
122 70 0.09
123 61 0.08
124 8 0.01
125 75 0.09
126 74 0.09
127 10 0.01
128 112 0.14
129 27 0.03
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.24
Consensus pattern (120 bp):
ATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATAT
ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATATC
Found at i:623422 original size:21 final size:21
Alignment explanation
Indices: 623397--623437 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
623387 AAGGTTAAAG
*
623397 ACCTTTCGATGAAATGACTTA
1 ACCTTTCGATGAAAAGACTTA
* *
623418 ACCTTTTGATTAAAAGACTT
1 ACCTTTCGATGAAAAGACTT
623438 CTCCCTTTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (21 bp):
ACCTTTCGATGAAAAGACTTA
Found at i:624060 original size:166 final size:166
Alignment explanation
Indices: 623786--624118 Score: 621
Period size: 166 Copynumber: 2.0 Consensus size: 166
623776 TTGAACTATC
*
623786 ATGTCGTTAGTGTAAACGATGACATACCTTGCATATATATCTCACTGACAAGAATTTGGTTCTCA
1 ATGTCGTTAGTGTAAACGATGACATACCTTGCATAAATATCTCACTGACAAGAATTTGGTTCTCA
623851 TGGTTATGTCCATATAGTCATGGACATCTCCTGGTTCTGCAAGAGTTTAGAGAACTATGCCCCAA
66 TGGTTATGTCCATATAGTCATGGACATCTCCTGGTTCTGCAAGAGTTTAGAGAACTATGCCCCAA
623916 TAGTCTCTTTGAAGCGGTTCCACTTCACTCTCACAT
131 TAGTCTCTTTGAAGCGGTTCCACTTCACTCTCACAT
* *
623952 ATGTCGTTAGTGTAAACGATGACATACCTTGCATAAATATCTCATTGACAATAATTTGGTTCTCA
1 ATGTCGTTAGTGTAAACGATGACATACCTTGCATAAATATCTCACTGACAAGAATTTGGTTCTCA
* *
624017 TGGTTATGTCCATATAGTCGTGGACATCTCCTGGTTCTGCAAGAGTTTAGAGAACTATGCCTCAA
66 TGGTTATGTCCATATAGTCATGGACATCTCCTGGTTCTGCAAGAGTTTAGAGAACTATGCCCCAA
624082 TAGTCTCTTTGAAGCGGTTCCACTTCACTCTCACAT
131 TAGTCTCTTTGAAGCGGTTCCACTTCACTCTCACAT
624118 A
1 A
624119 GGTGACTTAT
Statistics
Matches: 162, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
166 162 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (166 bp):
ATGTCGTTAGTGTAAACGATGACATACCTTGCATAAATATCTCACTGACAAGAATTTGGTTCTCA
TGGTTATGTCCATATAGTCATGGACATCTCCTGGTTCTGCAAGAGTTTAGAGAACTATGCCCCAA
TAGTCTCTTTGAAGCGGTTCCACTTCACTCTCACAT
Found at i:627225 original size:21 final size:21
Alignment explanation
Indices: 627199--627252 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
627189 TGAGACTTCT
* *
627199 TCTTTTGATGAAAGGGCTTAA
1 TCTTTTCATGAAAGGACTTAA
* *
627220 TCTTTTCATAAAAGGATTTAA
1 TCTTTTCATGAAAGGACTTAA
627241 TCTTTTCATGAA
1 TCTTTTCATGAA
627253 GAGAATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (21 bp):
TCTTTTCATGAAAGGACTTAA
Found at i:630681 original size:30 final size:30
Alignment explanation
Indices: 630647--630718 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 30
630637 TTTAAATAGT
*
630647 TATTATATTATATT-AATATATTTATGTAAA
1 TATTAT-TTATATTAAATATATTTATATAAA
* *
630677 TATTATTTTTTATTAAAATATATTTATATAAT
1 TATTA-TTTATATT-AAATATATTTATATAAA
630709 TATTATTTAT
1 TATTATTTAT
630719 TTAGAATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 11 0.31
31 5 0.14
32 19 0.54
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
TATTATTTATATTAAATATATTTATATAAA
Found at i:630750 original size:51 final size:46
Alignment explanation
Indices: 630648--630751 Score: 106
Period size: 47 Copynumber: 2.2 Consensus size: 46
630638 TTAAATAGTT
630648 ATTATA-TTATATTAATATATTTATGTAAATATTATTTTTTATTAA
1 ATTATATTTATATTAATATATTTATGTAAATATTATTTTTTATTAA
* *
630693 AATATATTTATA-TAATTATTATTTATTTAGAATTATTAATTTTTT-TTGATA
1 ATTATATTTATATTAA-TA-TATTTATGTA-AA-TATT-ATTTTTTATT-A-A
630744 ATTATATT
1 ATTATATT
630752 GTTTTGTCTA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
45 8 0.17
46 7 0.15
47 9 0.19
48 2 0.04
49 6 0.12
50 8 0.17
51 8 0.17
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (46 bp):
ATTATATTTATATTAATATATTTATGTAAATATTATTTTTTATTAA
Found at i:632426 original size:21 final size:21
Alignment explanation
Indices: 632396--632443 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
632386 GCAGGGGTAC
* *
632396 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
632417 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
632438 ATGCCA
1 ATGCCA
632444 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:632473 original size:21 final size:21
Alignment explanation
Indices: 632447--632540 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
632437 TATGCCATCT
632447 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
632468 CCGCAGGGTTATATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
632489 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
632510 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
632531 CCGCAGGGTT
1 CCGCAGGGTT
632541 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:632480 original size:42 final size:42
Alignment explanation
Indices: 632423--632540 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
632413 TCATATGCCA
* * *
632423 AGCCCACCAGTTTATATGCC-ATCTCCGCAGGGTTACATTCCG
1 AGCCCGCCAGGTTATATGCCGAGC-CCGCAGGGTTACATTCCG
* *
632465 AGCCCG-CAGGGTTATATTCCGAGCCCGCAGGGTTACATTCCT
1 AGCCCGCCA-GGTTATATGCCGAGCCCGCAGGGTTACATTCCG
* *
632507 AGCCCGCCAGGTTACATGCCTAGCCCGCAGGGTT
1 AGCCCGCCAGGTTATATGCCGAGCCCGCAGGGTT
632541 TTATACCATA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.03
42 59 0.91
43 4 0.06
ACGTcount: A:0.19, C:0.33, G:0.25, T:0.23
Consensus pattern (42 bp):
AGCCCGCCAGGTTATATGCCGAGCCCGCAGGGTTACATTCCG
Found at i:633163 original size:34 final size:34
Alignment explanation
Indices: 633058--633164 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
633048 ATAAATGTTT
*
633058 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
633092 TAAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* * * *
633126 TTAAAATATAAATTATAGTATTTGAAATTTAACA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
633160 TTAAA
1 TTAAA
633165 TTTCAACTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:633793 original size:128 final size:128
Alignment explanation
Indices: 633516--634015 Score: 862
Period size: 128 Copynumber: 3.9 Consensus size: 128
633506 TTACCTGATT
633516 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATAATT-T
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACAT-ATTCT
* * *** *
633580 CTGAC-AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCT-GAGAAATAATAGG
65 CTGACAAAATAATGGAAGACGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
633643 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
633708 TGACAAAATAATGGAAGGCGCGCCCCCGGAAACGCGCCTTCATGTGAATAGTGAAATAATATG
66 TGACAAAATAATGGAAGACGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
633771 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
633836 TGACAAAATAATGGAAGACGCGCCCCCGGGAACGCGCCATCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGACGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
633899 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
633964 TGACAAAATAATGGAAGACGCGCCCCCGGGAACGCGCCTTCATATGAATAGT
66 TGACAAAATAATGGAAGACGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
634016 ACTCCGATTA
Statistics
Matches: 357, Mismatches: 13, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
126 3 0.01
127 66 0.18
128 288 0.81
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGACGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:634099 original size:8 final size:8
Alignment explanation
Indices: 634086--634126 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
634076 TCACAAGCTT
634086 TCAAATTC
1 TCAAATTC
634094 TCAAATTC
1 TCAAATTC
* *
634102 CCAAACTC
1 TCAAATTC
634110 T-AAATTC
1 TCAAATTC
634117 TCAAATTC
1 TCAAATTC
634125 TC
1 TC
634127 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:643400 original size:25 final size:25
Alignment explanation
Indices: 643366--643430 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
643356 TCCCCCTTAC
643366 TTTAACACTTCTCCCATTTAAAACA
1 TTTAACACTTCTCCCATTTAAAACA
643391 TTTAACACTTCTCCCATTTAAAACA
1 TTTAACACTTCTCCCATTTAAAACA
643416 TTTAACACTTCTCCC
1 TTTAACACTTCTCCC
643431 CCTTTTTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.32, C:0.31, G:0.00, T:0.37
Consensus pattern (25 bp):
TTTAACACTTCTCCCATTTAAAACA
Found at i:657114 original size:40 final size:40
Alignment explanation
Indices: 657058--657259 Score: 386
Period size: 40 Copynumber: 5.0 Consensus size: 40
657048 TGCAGGTTTA
657058 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
657098 TAATACACTTCCGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
657138 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTA
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
657178 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
657218 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
657258 TA
1 TA
657260 GCACTACGGT
Statistics
Matches: 158, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 158 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:664310 original size:40 final size:40
Alignment explanation
Indices: 664255--664336 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
664245 TGTAGGTTTA
664255 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
664295 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
664335 TA
1 TA
664337 GGACTACGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:665650 original size:24 final size:23
Alignment explanation
Indices: 665595--665660 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
665585 AGAAAGAGGT
*
665595 AATATTTTCAAAACTTTTGATTA
1 AATATTTTCAAAACTTTTAATTA
665618 AATATTTTTCAAAACTCTTCTAATT-
1 AATA-TTTTCAAAACT-TT-TAATTA
* *
665643 GATATTTTCATAACTTTT
1 AATATTTTCAAAACTTTT
665661 GAAAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.03
23 6 0.16
24 21 0.57
25 5 0.14
26 4 0.11
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (23 bp):
AATATTTTCAAAACTTTTAATTA
Done.