Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008324.1 Hibiscus syriacus cultivar Beakdansim tig00111028_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: 430640
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 2 of 3
Found at i:190308 original size:27 final size:25
Alignment explanation
Indices: 190261--190312 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
190251 TTTTTCTTCA
*
190261 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTGTTCTCTTTTT
190286 ATTTTCTCTTTGCTTTGTTCTCTTTTT
1 ATTTTC-CTTTG-TTTGTTCTCTTTTT
190313 GTTCTGATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 6 0.25
26 5 0.21
27 13 0.54
ACGTcount: A:0.04, C:0.17, G:0.06, T:0.73
Consensus pattern (25 bp):
ATTTTCCTTTGTTTGTTCTCTTTTT
Found at i:193572 original size:17 final size:16
Alignment explanation
Indices: 193547--193591 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
193537 TATTAATGGA
193547 GTAAAAAATAAAAAAG
1 GTAAAAAATAAAAAAG
*
193563 GTAAAGAAATTAAAAAG
1 GTAAA-AAATAAAAAAG
*
193580 GAATAAAAATAA
1 GTA-AAAAATAA
193592 TGTGTACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 5 0.21
17 17 0.71
18 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (16 bp):
GTAAAAAATAAAAAAG
Found at i:193699 original size:36 final size:36
Alignment explanation
Indices: 193617--193711 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 36
193607 TAGTATTTAC
*
193617 TAAAACAAATAAAAATAATAAATATATAATACTAAG
1 TAAAACAAATAAAAATAATAAATACATAATACTAAG
* *
193653 TAAAACAAATAAAAATAA-AGATATACATGATATTAAG
1 TAAAACAAATAAAAATAATA-A-ATACATAATACTAAG
* *
193690 -AAAAAAAATAGAAAAAAATAAA
1 TAAAACAAATA-AAAATAATAAA
193712 ATAAAGTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
35 1 0.02
36 29 0.58
37 19 0.38
38 1 0.02
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.21
Consensus pattern (36 bp):
TAAAACAAATAAAAATAATAAATACATAATACTAAG
Found at i:193876 original size:2 final size:2
Alignment explanation
Indices: 193869--193929 Score: 51
Period size: 2 Copynumber: 32.5 Consensus size: 2
193859 ACATACATAC
* *
193869 AT AT AT AT AT AT AT AT AT AT AT A- AT GAT AT A- AG AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
*
193910 A- AT AT AA AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
193930 AATAAAAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
1 5 0.10
2 41 0.85
3 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (2 bp):
AT
Found at i:193888 original size:14 final size:14
Alignment explanation
Indices: 193869--193929 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 14
193859 ACATACATAC
193869 ATATATATATATAT
1 ATATATATATATAT
193883 ATATATATA-ATGAT
1 ATATATATATAT-AT
* *
193897 ATA-AGATATACAT
1 ATATATATATATAT
*
193910 A-ATATAAATA-AT
1 ATATATATATATAT
193922 ATA-ATATA
1 ATATATATA
193930 AATAAAAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
12 8 0.21
13 15 0.39
14 15 0.39
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:193923 original size:25 final size:27
Alignment explanation
Indices: 193875--193925 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
193865 ATACATATAT
* *
193875 ATATATATATATATATAATGATATAAG
1 ATATACATATATATATAATAATATAAG
193902 ATATACATA-ATATA-AATAATATAA
1 ATATACATATATATATAATAATATAA
193926 TATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 5 0.23
27 8 0.36
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATACATATATATATAATAATATAAG
Found at i:193930 original size:14 final size:14
Alignment explanation
Indices: 193908--193934 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
193898 TAAGATATAC
193908 ATAATATAAATAAT
1 ATAATATAAATAAT
193922 ATAATATAAATAA
1 ATAATATAAATAA
193935 AAAAGGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATATAAATAAT
Found at i:193967 original size:21 final size:20
Alignment explanation
Indices: 193928--193967 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
193918 TAATATAATA
**
193928 TAAATAAAAAAGGAATATAG
1 TAAATAAAAAAAAAATATAG
193948 TAAATAAATAAAAAAATATA
1 TAAATAAA-AAAAAAATATA
193968 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (20 bp):
TAAATAAAAAAAAAATATAG
Found at i:202412 original size:20 final size:20
Alignment explanation
Indices: 202389--202461 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
202379 GAATTTGAGA
202389 ATTCGCGTTGCGATTTACCT
1 ATTCGCGTTGCGATTTACCT
* * * *
202409 ATTCGCATTGAGAATTACAT
1 ATTCGCGTTGCGATTTACCT
** * *
202429 ATTATCGTTGCAATTTAACT
1 ATTCGCGTTGCGATTTACCT
202449 ATTCGCGTTGCGA
1 ATTCGCGTTGCGA
202462 ATTTGGAAAA
Statistics
Matches: 38, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACCT
Found at i:202512 original size:57 final size:57
Alignment explanation
Indices: 202443--202576 Score: 268
Period size: 57 Copynumber: 2.4 Consensus size: 57
202433 TCGTTGCAAT
202443 TTAACTATTCGCGTTGCGAATTTGGAAAATCGCAACGTTAATTACCTATATAGGTAA
1 TTAACTATTCGCGTTGCGAATTTGGAAAATCGCAACGTTAATTACCTATATAGGTAA
202500 TTAACTATTCGCGTTGCGAATTTGGAAAATCGCAACGTTAATTACCTATATAGGTAA
1 TTAACTATTCGCGTTGCGAATTTGGAAAATCGCAACGTTAATTACCTATATAGGTAA
202557 TTAACTATTCGCGTTGCGAA
1 TTAACTATTCGCGTTGCGAA
202577 AATGAAATTC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 77 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (57 bp):
TTAACTATTCGCGTTGCGAATTTGGAAAATCGCAACGTTAATTACCTATATAGGTAA
Found at i:203007 original size:20 final size:20
Alignment explanation
Indices: 202982--203053 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
202972 GAAGAATTCG
202982 CGTTGCGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
* **
203002 CGTTGCGATTTACCTATTCG
1 CGTTGCGATTTACATATTAT
* * *
203022 CATTGAGAATTACATATTAT
1 CGTTGCGATTTACATATTAT
203042 CGTTGCGATTTA
1 CGTTGCGATTTA
203054 ACTATTCACG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Found at i:203065 original size:20 final size:20
Alignment explanation
Indices: 202977--203069 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
202967 AATTCGAAGA
*
202977 ATTCGCGTTGCGATTTACAT
1 ATTCACGTTGCGATTTACAT
*
202997 ATT-ATCGTTGCGATTTACCT
1 ATTCA-CGTTGCGATTTACAT
* * * *
203017 ATTCGCATTGAGAATTACAT
1 ATTCACGTTGCGATTTACAT
203037 ATT-ATCGTTGCGATTTA-ACT
1 ATTCA-CGTTGCGATTTACA-T
203057 ATTCACGTTGCGA
1 ATTCACGTTGCGA
203070 ATTTGGAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
19 1 0.02
20 55 0.96
21 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (20 bp):
ATTCACGTTGCGATTTACAT
Found at i:203072 original size:40 final size:40
Alignment explanation
Indices: 202977--203072 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
202967 AATTCGAAGA
* *
202977 ATTCGCGTTGCGATTTACATATTATCGTTGCGATTTACCT
1 ATTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACT
* *
203017 ATTCGCATTGAGAATTACATATTATCGTTGCGATTTAACT
1 ATTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACT
*
203057 ATTCACGTTGCGAATT
1 ATTCGCGTTGCGAATT
203073 TGGAAAATCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.41
Consensus pattern (40 bp):
ATTCGCGTTGCGAATTACATATTATCGTTGCGATTTAACT
Found at i:203313 original size:19 final size:19
Alignment explanation
Indices: 203267--203320 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
203257 AATTTGGAGA
203267 ATTCGCGTTGCGATTTACT
1 ATTCGCGTTGCGATTTACT
**
203286 ATTATCGTTGCGATTTGACT
1 ATTCGCGTTGCGATTT-ACT
*
203306 -TTCGCGTTACGATTT
1 ATTCGCGTTGCGATTT
203321 TGGAACTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 26 0.90
20 3 0.10
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (19 bp):
ATTCGCGTTGCGATTTACT
Found at i:207358 original size:15 final size:15
Alignment explanation
Indices: 207338--207369 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
207328 GGAGGTTAAG
207338 GAAGATGAAAAGGGA
1 GAAGATGAAAAGGGA
207353 GAAGATGAAAAGGGA
1 GAAGATGAAAAGGGA
207368 GA
1 GA
207370 TACCTGAGAA
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:0.53, C:0.00, G:0.41, T:0.06
Consensus pattern (15 bp):
GAAGATGAAAAGGGA
Found at i:210473 original size:2 final size:2
Alignment explanation
Indices: 210466--210549 Score: 51
Period size: 2 Copynumber: 42.0 Consensus size: 2
210456 GGAAAGAAAC
** * ** **
210466 AG AG AG AG AG AG TT AG AG AG AG AG AG AG TG TC AG AG AG TT AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* ** * * *
210508 AG AG AG AG AG AG TG TC AG AG AG GG AG TG GG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
210550 GGCCTCAGGC
Statistics
Matches: 61, Mismatches: 21, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.39, C:0.02, G:0.48, T:0.11
Consensus pattern (2 bp):
AG
Found at i:210505 original size:26 final size:26
Alignment explanation
Indices: 210472--210529 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
210462 AAACAGAGAG
210472 AGAGAGTTAGAGAGAGAGAGAGTGTC
1 AGAGAGTTAGAGAGAGAGAGAGTGTC
210498 AGAGAGTTAGAGAGAGAGAGAGTGTC
1 AGAGAGTTAGAGAGAGAGAGAGTGTC
210524 AGAGAG
1 AGAGAG
210530 GGAGTGGGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.43, T:0.14
Consensus pattern (26 bp):
AGAGAGTTAGAGAGAGAGAGAGTGTC
Found at i:210527 original size:14 final size:14
Alignment explanation
Indices: 210484--210547 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 14
210474 AGAGTTAGAG
210484 AGAGAGAGAGTGTC
1 AGAGAGAGAGTGTC
** *
210498 AGAGAGTTAGAG--
1 AGAGAGAGAGTGTC
210510 AGAGAGAGAGTGTC
1 AGAGAGAGAGTGTC
* **
210524 AGAGAGGGAGTGGG
1 AGAGAGAGAGTGTC
210538 AGAGAGAGAG
1 AGAGAGAGAG
210548 AGGGCCTCAG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
12 9 0.24
14 29 0.76
ACGTcount: A:0.38, C:0.03, G:0.48, T:0.11
Consensus pattern (14 bp):
AGAGAGAGAGTGTC
Found at i:210529 original size:18 final size:16
Alignment explanation
Indices: 210466--210513 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 16
210456 GGAAAGAAAC
210466 AGAGAGAGAGAGTTAG
1 AGAGAGAGAGAGTTAG
210482 AGAGAGAGAGAGTGTCAG
1 AGAGAGAGAGAGT-T-AG
210500 AGAGTTAGAGAGAG
1 AGAG--AGAGAGAG
210514 AGAGAGTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 13 0.46
17 1 0.04
18 6 0.21
20 8 0.29
ACGTcount: A:0.42, C:0.02, G:0.44, T:0.12
Consensus pattern (16 bp):
AGAGAGAGAGAGTTAG
Found at i:210540 original size:26 final size:26
Alignment explanation
Indices: 210480--210545 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
210470 AGAGAGAGTT
**
210480 AGAGAGAGAGAGAGTGTCAGAGAGTT
1 AGAGAGAGAGAGAGTGTCAGAGAGGG
210506 AGAGAGAGAGAGAGTGTCAGAGAGGG
1 AGAGAGAGAGAGAGTGTCAGAGAGGG
* *
210532 AGTGGGAGAGAGAG
1 AGAGAGAGAGAGAG
210546 AGAGGGCCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.38, C:0.03, G:0.48, T:0.11
Consensus pattern (26 bp):
AGAGAGAGAGAGAGTGTCAGAGAGGG
Found at i:220689 original size:80 final size:80
Alignment explanation
Indices: 220581--220734 Score: 227
Period size: 80 Copynumber: 1.9 Consensus size: 80
220571 CAGTCCTACG
* * *** * *
220581 AACTCAAAATAAACAGCAATGAGAACAACGGTCCTATTATTTACAGAATCTGCCACTAACTTTCA
1 AACTCAAAATAAACAGCAATAAGAACAACGATCCTATTATTTACAGAATCCAACACCAACTTCCA
220646 TCAAACAGTTGTAAA
66 TCAAACAGTTGTAAA
* *
220661 AACTCATAATAAACAGCAATAAGCACAACGATCCTATTATTTACAGAATCCAACACCAACTTCCA
1 AACTCAAAATAAACAGCAATAAGAACAACGATCCTATTATTTACAGAATCCAACACCAACTTCCA
220726 TCAAACAGT
66 TCAAACAGT
220735 GGTATGAACT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.23
Consensus pattern (80 bp):
AACTCAAAATAAACAGCAATAAGAACAACGATCCTATTATTTACAGAATCCAACACCAACTTCCA
TCAAACAGTTGTAAA
Found at i:222857 original size:27 final size:27
Alignment explanation
Indices: 222816--222879 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
222806 GAATCATCCA
* *
222816 CCACCACCGCCAATAGACACCCTTCCT
1 CCACCACCGCCAATAAAAACCCTTCCT
* *
222843 CCACCTCCGCGAATAAAAACCCTTCCT
1 CCACCACCGCCAATAAAAACCCTTCCT
*
222870 CCACAACCGC
1 CCACCACCGC
222880 AGACCCTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.28, C:0.50, G:0.08, T:0.14
Consensus pattern (27 bp):
CCACCACCGCCAATAAAAACCCTTCCT
Found at i:248977 original size:21 final size:21
Alignment explanation
Indices: 248935--248977 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
248925 ATTTGATCAT
*
248935 ACAAGTCATAAGTGATATCCA
1 ACAAGTCATAAGTGATACCCA
*
248956 ACAAGTCATTA-TGACTACCCA
1 ACAAGTCATAAGTGA-TACCCA
248977 A
1 A
248978 GTTAAATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (21 bp):
ACAAGTCATAAGTGATACCCA
Found at i:251103 original size:33 final size:34
Alignment explanation
Indices: 251039--251104 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
251029 AAAATATTTA
*
251039 TATATTTTCTTTAAAAAAATTGAATTCATAAAAT
1 TATATTTTCTTTAAAAAAATTGAAATCATAAAAT
* *
251073 TATATTTT-TTTTACAAAATTGAAAAT-ATAAAA
1 TATATTTTCTTTAAAAAAATTG-AAATCATAAAA
251105 AGGTTTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (34 bp):
TATATTTTCTTTAAAAAAATTGAAATCATAAAAT
Found at i:256261 original size:20 final size:20
Alignment explanation
Indices: 256236--256279 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
256226 GTTTTAAAAG
*
256236 TTTTAAAC-ACTTTAAAAATA
1 TTTTAAACAAC-TCAAAAATA
*
256256 TTTTAACCAACTCAAAAATA
1 TTTTAAACAACTCAAAAATA
256276 TTTT
1 TTTT
256280 TAAATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTTAAACAACTCAAAAATA
Found at i:258409 original size:13 final size:12
Alignment explanation
Indices: 258384--258422 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
258374 TTCATTTTCA
258384 CCTATTCTCTCT
1 CCTATTCTCTCT
258396 CCTATTCATCTCT
1 CCTATTC-TCTCT
*
258409 CCTTTTCTCT-T
1 CCTATTCTCTCT
258420 CCT
1 CCT
258423 CACCCTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 4 0.16
12 10 0.40
13 11 0.44
ACGTcount: A:0.08, C:0.41, G:0.00, T:0.51
Consensus pattern (12 bp):
CCTATTCTCTCT
Found at i:258756 original size:2 final size:2
Alignment explanation
Indices: 258749--258783 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
258739 TTGTCTTTAT
258749 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
258784 TACAAGTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:280886 original size:15 final size:15
Alignment explanation
Indices: 280866--280897 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
280856 CTTTTTAAGA
280866 TTTAGAATTTAGGAC
1 TTTAGAATTTAGGAC
*
280881 TTTAGATTTTAGGAC
1 TTTAGAATTTAGGAC
280896 TT
1 TT
280898 AATATTCAAA
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:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (15 bp):
TTTAGAATTTAGGAC
Found at i:285656 original size:24 final size:25
Alignment explanation
Indices: 285608--285656 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
285598 GACAGTTTCA
* *
285608 AATTCTACGTTCTTTTTTTTTATAAG
1 AATTCTACG-TCTTCTTTTTAATAAG
285634 AATTCTACG-CTTCTTTTTAATAA
1 AATTCTACGTCTTCTTTTTAATAA
285657 TTTTTGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
26 9 0.43
ACGTcount: A:0.27, C:0.14, G:0.06, T:0.53
Consensus pattern (25 bp):
AATTCTACGTCTTCTTTTTAATAAG
Found at i:303115 original size:21 final size:21
Alignment explanation
Indices: 303091--303154 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
303081 GCAAATTCGC
303091 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
303112 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
303132 TTTTCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
303153 GT
1 GT
303155 CTACAGTTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:308802 original size:23 final size:23
Alignment explanation
Indices: 308774--308838 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
308764 TGTTTATATG
*
308774 TTTAGTGTTTACGAACATGTTCA
1 TTTAGTATTTACGAACATGTTCA
*
308797 TTTAGTATTTGCGAACATGTTCA
1 TTTAGTATTTACGAACATGTTCA
* * *
308820 TTTAATATTCATGAACATG
1 TTTAGTATTTACGAACATG
308839 CTCACTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (23 bp):
TTTAGTATTTACGAACATGTTCA
Found at i:310608 original size:12 final size:12
Alignment explanation
Indices: 310576--310615 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
310566 TGCGGGAAAA
310576 TTAAAATC-A-T
1 TTAAAATCTATT
310586 TT-AAATCTATT
1 TTAAAATCTATT
*
310597 TTAAAATTTATT
1 TTAAAATCTATT
310609 TTAAAAT
1 TTAAAAT
310616 ATAGATTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 3 0.12
12 15 0.58
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAAAATCTATT
Found at i:310627 original size:22 final size:22
Alignment explanation
Indices: 310602--310791 Score: 249
Period size: 22 Copynumber: 8.6 Consensus size: 22
310592 CTATTTTAAA
310602 ATTTATTTTAAAATAT-AGATTG
1 ATTTATTTTAAAATATGA-ATTG
310624 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGAATTG
***
310646 ATTTATTTTAAAATATAGAAAAA
1 ATTTATTTTAAAATAT-GAATTG
*
310669 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGAATTG
**
310691 ATTTATTTTAAAATATGAA-AA
1 ATTTATTTTAAAATATGAATTG
* *
310712 ATTTTATTTTAAAATAAGCATTG
1 A-TTTATTTTAAAATATGAATTG
*
310735 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGAATTG
310757 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGAATTG
*
310779 ATTTACTTTAAAA
1 ATTTATTTTAAAA
310792 AAATTATTAT
Statistics
Matches: 146, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.01
22 124 0.85
23 21 0.14
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.47
Consensus pattern (22 bp):
ATTTATTTTAAAATATGAATTG
Found at i:310671 original size:67 final size:66
Alignment explanation
Indices: 310599--310791 Score: 289
Period size: 67 Copynumber: 2.9 Consensus size: 66
310589 AATCTATTTT
*
310599 AAAATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATAG
1 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATA-AG
310664 AA
65 AA
**
310666 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAA-AAATTTTATTTTAAAATAAG
1 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTGA-TTTATTTTAAAATAAG
*
310730 CA
65 AA
*** *
310732 TTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTGATTTACTTTAAAA
1 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAA
310792 AAATTATTAT
Statistics
Matches: 114, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
66 56 0.49
67 58 0.51
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (66 bp):
AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATAAGA
A
Found at i:310872 original size:31 final size:31
Alignment explanation
Indices: 310814--310873 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
310804 TAGTTGTATG
*
310814 AATTATTTAAATTTCAGTATTATAAAACTAA
1 AATTATTTAAATTTCAGTATTACAAAACTAA
*
310845 AATTATTTAAATTTCAGTATTGCAAAACT
1 AATTATTTAAATTTCAGTATTACAAAACT
310874 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTACAAAACTAA
Found at i:313670 original size:60 final size:59
Alignment explanation
Indices: 313588--313736 Score: 183
Period size: 60 Copynumber: 2.5 Consensus size: 59
313578 TATCATGTGT
* * *
313588 TTCT-AAACTATGATCTCTATTCTAAATTAGTCCTTAATCTTTTGAATATTTTAATTTCA
1 TTCTCAAACTATGATCT-TATTCTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCA
* * *
313647 TTCTCAAACTATCATTCTTATTCTAAATTAGTTCTTAAACTTTTGAACATTTCAATTTTA
1 TTCTCAAACTATGA-TCTTATTCTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCA
* * *
313707 TCCTCAAACTATGACCCTCATTCTAAATTA
1 TTCTCAAACTATGA-TCTTATTCTAAATTA
313737 ACCTCCAAAC
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
59 4 0.05
60 70 0.91
61 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.46
Consensus pattern (59 bp):
TTCTCAAACTATGATCTTATTCTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCA
Found at i:320669 original size:60 final size:60
Alignment explanation
Indices: 320597--320730 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
320587 AAATTGGAAG
* *
320597 ATTCAAAAGTTTAGGGACCAATTTAGAAAGAGTGTCACAATTTAACGATGAAATTAAAAT
1 ATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCACAATTTAACGATGAAATTAAAAT
* * * * * * * * * *
320657 GTTCAAATGTTTAATGACTAATTTTGAATGAGAGTCATATTTTGAGGATGAAATTAAAAT
1 ATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCACAATTTAACGATGAAATTAAAAT
320717 ATTCAAAAGTTTAA
1 ATTCAAAAGTTTAA
320731 AAACCAAATT
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (60 bp):
ATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCACAATTTAACGATGAAATTAAAAT
Found at i:321368 original size:2 final size:2
Alignment explanation
Indices: 321361--321403 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
321351 ACTAAAACTT
321361 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
321403 T
1 T
321404 TATTAGCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:322962 original size:29 final size:28
Alignment explanation
Indices: 322917--322971 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
322907 GATGATGTCC
**
322917 TTTTTAGACAATTGAAGTATTTAATTCA
1 TTTTTAGACAAAAGAAGTATTTAATTCA
322945 TTTTTAGTACAAAAGAAGTATTTAATT
1 TTTTTAG-ACAAAAGAAGTATTTAATT
322972 TAGGCTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45
Consensus pattern (28 bp):
TTTTTAGACAAAAGAAGTATTTAATTCA
Found at i:326067 original size:2 final size:2
Alignment explanation
Indices: 326060--326095 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
326050 ATTATCATTC
326060 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 A
326096 GTTGAATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:326292 original size:42 final size:41
Alignment explanation
Indices: 326234--326316 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 41
326224 GATTATCGGA
* * * * *
326234 CCAAATTAATTTAATAATTTTGATTTAGTGATATAATAATG
1 CCAAATTAATGTAATAATTGTAAGTTACTGATATAATAATG
326275 CCAAATTTAATGTAATAATTGTAAGTTACTGATATAATAATG
1 CCAAA-TTAATGTAATAATTGTAAGTTACTGATATAATAATG
326317 GCATTTTGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 5 0.14
42 31 0.86
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (41 bp):
CCAAATTAATGTAATAATTGTAAGTTACTGATATAATAATG
Found at i:332021 original size:40 final size:40
Alignment explanation
Indices: 331966--332045 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
331956 GCAATCCACC
331966 ATACAGTCTGTTGTTCCTTTCTCTCCATATGACATACACA
1 ATACAGTCTGTTGTTCCTTTCTCTCCATATGACATACACA
332006 ATACAGTCTGTTGTTCCTTTCTCTCCATATGACATACACA
1 ATACAGTCTGTTGTTCCTTTCTCTCCATATGACATACACA
332046 TAGTTTGTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.38
Consensus pattern (40 bp):
ATACAGTCTGTTGTTCCTTTCTCTCCATATGACATACACA
Found at i:336875 original size:16 final size:16
Alignment explanation
Indices: 336836--336867 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
336826 AAAATAAAGG
336836 TAAAA-TTTTATTAGA
1 TAAAATTTTTATTAGA
336851 TAAAATTTTTATTAGA
1 TAAAATTTTTATTAGA
336867 T
1 T
336868 TCTATTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
TAAAATTTTTATTAGA
Found at i:338241 original size:23 final size:23
Alignment explanation
Indices: 338194--338241 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
338184 ATTAACATAT
**
338194 TAGGTAACGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATAAAA
* *
338217 TAGGTAGCGTTTATATAATAAAA
1 TAGGTAACGCTTATATAATAAAA
338240 TA
1 TA
338242 TGTATTTAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (23 bp):
TAGGTAACGCTTATATAATAAAA
Found at i:338269 original size:87 final size:86
Alignment explanation
Indices: 338153--338319 Score: 262
Period size: 87 Copynumber: 1.9 Consensus size: 86
338143 CGGTTATATT
* * *
338153 ATATTATTTAACTAGAAATATTATTAAGTACATTAACATATTAGGTAACGCTTATATAATGTAAT
1 ATATTATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAAT
* *
338218 AGGTAGCGTTTATATAATAAA
66 AAGTAGCGCTTATATAATAAA
* *
338239 ATATGTATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAA
1 ATAT-TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAA
338304 TAAGTAGCGCTTATAT
65 TAAGTAGCGCTTATAT
338320 TGACCTATTT
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 4 0.05
87 69 0.95
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (86 bp):
ATATTATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAAT
AAGTAGCGCTTATATAATAAA
Found at i:338705 original size:199 final size:200
Alignment explanation
Indices: 338360--339037 Score: 605
Period size: 201 Copynumber: 3.4 Consensus size: 200
338350 TGTACCGGTA
* *
338360 ACATTACAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTTTGATCAATACTTTTT
1 ACATTACAAATTTACCTATTACATTATAATTATCGGTTTCGAT-TTTTTGTGATCGATACTTTTT
* * * * * *
338425 ATAAATGTATCGATAATATATGCGTTCACCCTTTTGGGCATTCATTCTGGA-AAAAAGTATCGAC
65 AAAAATGTATCGATACTTTATGAGTGCACCCGTTTGGGCATTCATTCTGGACAAAAA-TATCGAC
* * *
338489 ACAACA-TTAAAAAGTTTCGACACATTATGT-A-GACATATTCTCACATAAAATCGGTATAAATA
129 ACAA-ATTTAAAAAGTTTCGACACATTATATGATGACATATTCTCACATAAAACCGATATAAATA
338551 TA-TCGGTT
193 TACT-GGTT
* * * *
338559 ATATTACAAAATTACCTATTACATCATAATTAT-GAGTTTCGATGTTTTTGGGATCGATACTTTT
1 ACATTACAAATTTACCTATTACATTATAATTATCG-GTTTCGAT-TTTTTGTGATCGATACTTTT
* *
338623 TAAAAATGTATCGATACTTTATGAGTGCACCCGTCT-GGCATTCATTATGGACAAAATATATCGA
64 TAAAAATGTATCGATACTTTATGAGTGCACCCGTTTGGGCATTCATTCTGGACAAAA-ATATCGA
* * ** * * * **
338687 CACAAATTTAATAAGTTTCGATATTTTATATGATGACCTATTTTCTCATAAAACCGATATATTTA
128 CACAAATTTAAAAAGTTTCGACACATTATATGATGACATATTCTCACATAAAACCGATATAAATA
338752 TACTGGTT
193 TACTGGTT
** * *
338760 ACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGATTTTATTGTGATTGATAC-TTTT
1 ACATTACAAATTTACCTATTACATTATAATTATCGGTTTCGATTTT-TTGTGATCGATACTTTTT
* * *
338824 AATAATTGTATCGACACTTTAT-ACGTGCACCCCGTTTGGGCATTCATTCTGGACAATAAGTATC
65 AA-AAATGTATCGATACTTTATGA-GTGCA-CCCGTTTGGGCATTCATTCTGGACAA-AAATATC
* * ** * * * * * * *
338888 AACACAAA-TTACACAAGAGTCGATATA-T-TATGTTGACATGTTTTCTA-AT-TAACCGGTATA
126 GACACAAATTTA-AAAAGTTTCGACACATTATATGATGACATATTCTC-ACATAAAACCGATATA
** * *
338948 TTTATACCGGGT
189 AATATACTGGTT
*** * * *
338960 ACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCCAAGTTTTTTG-GGTCGATAC-TTT
1 ACATTACAAATTTACCTATTACATTATAATTATCGGTTT-CGA-TTTTTTGTGATCGATACTTTT
339023 TAGAAAATGTATCGA
64 TA-AAAATGTATCGA
339038 CATATATTTA
Statistics
Matches: 400, Mismatches: 60, Indels: 37
0.80 0.12 0.07
Matches are distributed among these distances:
198 16 0.04
199 118 0.29
200 89 0.22
201 120 0.30
202 16 0.04
203 39 0.10
204 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (200 bp):
ACATTACAAATTTACCTATTACATTATAATTATCGGTTTCGATTTTTTGTGATCGATACTTTTTA
AAAATGTATCGATACTTTATGAGTGCACCCGTTTGGGCATTCATTCTGGACAAAAATATCGACAC
AAATTTAAAAAGTTTCGACACATTATATGATGACATATTCTCACATAAAACCGATATAAATATAC
TGGTT
Found at i:338823 original size:201 final size:198
Alignment explanation
Indices: 338337--339037 Score: 677
Period size: 199 Copynumber: 3.5 Consensus size: 198
338327 TTTTATAAGT
* * *
338337 AAACTGGTATATTTGTACCGGTAACATTACAAATTTACCTATTACATTATAATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTACAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * * * * * * *
338402 TATTTTTTTGATCAATACTTTTTATAAATGTATCGATAATATATGCGTTCACCCTTTTGGGCATT
66 TATTTTTGTGATCGATAC-TTTTAAAAATGTATCGATACTTTATGAGTGCACCCGTTTGGGCATT
* ** *
338467 CATTCTGGA-AAAAAGTATCGACACAACATTAAAAAGTTTCGACACAT-TATG-TAGACATATTC
130 CATTCTGGACAAAAA-TATCGACACAA-ATTAAAAAGTTTCGATATTTATATGAT-GACATATTT
*
338529 TCACATA
192 TCTCATA
* ** * * * *
338536 AAATCGGTATAAATATATCGGTTATATTACAAAATTACCTATTACATCATAATTAT-GAGTTTCG
1 AAACCGGTATATTTATACCGGTTACATTACAAATTTACCTATTACATTATAATTATCG-GTTTCG
* * *
338600 ATGTTTTTGGGATCGATACTTTTTAAAAATGTATCGATACTTTATGAGTGCACCCGTCT-GGCAT
65 ATATTTTTGTGATCGATAC-TTTTAAAAATGTATCGATACTTTATGAGTGCACCCGTTTGGGCAT
* * *
338664 TCATTATGGACAAAATATATCGACACAAATTTAATAAGTTTCGATATTTTATATGATGACCTATT
129 TCATTCTGGACAAAA-ATATCGACACAAA-TTAAAAAGTTTCGATA-TTTATATGATGACATATT
338729 TTCTCATA
191 TTCTCATA
* * ** *
338737 AAACCGATATATTTATACTGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTACAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * *
338802 T-TTTATTGTGATTGATACTTTTAATAATTGTATCGACACTTTAT-ACGTGCACCCCGTTTGGGC
66 TATTT-TTGTGATCGATACTTTTAA-AAATGTATCGATACTTTATGA-GTGCA-CCCGTTTGGGC
* * * ** * * *
338865 ATTCATTCTGGACAATAAGTATCAACACAAATTACACAAGAGTCGATATAT-TATGTTGACATGT
127 ATTCATTCTGGACAA-AAATATCGACACAAATTA-AAAAGTTTCGATATTTATATGATGACATAT
*
338929 TTTCTAAT-
190 TTTCTCATA
* * *** * *
338937 TAACCGGTATATTTATACCGGGTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCCA
1 AAACCGGTATATTTATACCGGTTACATTACAAATTTACCTATTACATTATAATTATCGGTTTCGA
*
339002 -AGTTTTT-TGGGTCGATACTTTTAGAAAATGTATCGA
66 TA-TTTTTGT-GATCGATACTTTTA-AAAATGTATCGA
339038 CATATATTTA
Statistics
Matches: 415, Mismatches: 68, Indels: 37
0.80 0.13 0.07
Matches are distributed among these distances:
198 16 0.04
199 130 0.31
200 93 0.22
201 123 0.30
202 13 0.03
203 38 0.09
204 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (198 bp):
AAACCGGTATATTTATACCGGTTACATTACAAATTTACCTATTACATTATAATTATCGGTTTCGA
TATTTTTGTGATCGATACTTTTAAAAATGTATCGATACTTTATGAGTGCACCCGTTTGGGCATTC
ATTCTGGACAAAAATATCGACACAAATTAAAAAGTTTCGATATTTATATGATGACATATTTTCTC
ATA
Found at i:342731 original size:199 final size:198
Alignment explanation
Indices: 342379--343539 Score: 1182
Period size: 199 Copynumber: 5.8 Consensus size: 198
342369 TTTTGTTTAT
* * * * * * * * *
342379 AAGTATCGACACAAATCTAAAACGTGTCGATAAATTATGTTCACCTATTTTCTCACAAAACCGAT
1 AAGTATCGACACAAATTTAAAA-GTGTCGACACATTATGTACACCTATTCTCACATAAAATCGGT
* ** *
342444 ACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
65 ATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
* *
342509 GGATCGATACTTTTTATAAATGTATCGACACTTTCTGAGTTCACCCTTTTGGGCATTCATTCTGG
130 GGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTTCACCCTTTTGGGCATTCATTCTGG
342574 CAAA
195 CAAA
* * * *
342578 AAGTATCGACACATCATTTAAAAGTGTCGACAAATTATGTAGACCTATTCTGACATAAAATCGGT
1 AAGTATCGACACA-AATTTAAAAGTGTCGACACATTATGTACACCTATTCTCACATAAAATCGGT
* * *
342643 ATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTAG
65 ATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
* * * * * * *
342708 GGATCGATA-TTGTTTAAAAATGTATCGACAGTTTATGAGTGCAACATTTTTGG-ATTTTCCTTG
130 GGATCGATACTT-TTTAAAAATGTATCGACACTTTATGAGTTCACCCTTTTGGGCA--TTCATTC
* *
342771 TGAACCAA
192 TG-GCAAA
* * * * *
342779 AAGTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTA-A-AAAAACAG
1 AAGTATCGACACAAATTTAAAA-GTGTCGACACATTATGTACACCTATTCTC-ACATAAAATC-G
* * * ** *
342842 GTACATTTATA-CTGATACATT-GTAATTTACCTA-TACATTATAATTATCGGTTTCGATG-TTT
63 GTATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * *
342903 TGGGATCGATACTTTTTATAAATATATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCT
128 TGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTTCACCCTTTTGGGCATTCATTCT
342968 GGCAAA
193 GGCAAA
* * * * * * * *
342974 AAGTATTGACATACCATTCAAAAGTGTCGACACATTATGTAGAACTATTCTAACGTAAAATCGGT
1 AAGTATCGACACA-AATTTAAAAGTGTCGACACATTATGTACACCTATTCTCACATAAAATCGGT
* * * * *
343039 ATATTTATATCGG-T--ATCACAAAATTACCTATTATATTATATTTAT-GGATTTTGATGTTTTT
65 ATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATCGG-TTTCGATGTTTTT
* * * * * *
343100 GGGATCGATACTGTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGG-ATTTTCCTTG
129 GGGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTTCACCCTTTTGGGCA--TTCATTC
*
343164 TGGACCAA
192 TGG-CAAA
* * * * * * * * *
343172 AAGTATCGACA-ATAATTCTATAAGTGTCGATACATTATGTATATCTATTTTCTCAAAAAACCAG
1 AAGTATCGACACA-AATT-TAAAAGTGTCGACACATTATGTACACCTATTCTCACATAAAATCGG
* * ** * * * *
343236 TTTATTTGTACCGGTTACATTGTAAATTTAACTATTATATTATAATTATCGGTTTCGATATTTTT
64 TATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
* * * * * *
343301 GGGATCAATACTTTTTATAATTGTATCGACACTTTATGCGTTGACCCTTTTGGGCATTCATTATG
129 GGGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTTCACCCTTTTGGGCATTCATTCTG
343366 GCAAA
194 GCAAA
*
343371 AAGTATCGACACAACA-TTAACAAGTGTCGACACATTATGTAAACCTATTCTCACATAAAATCGG
1 AAGTATCGACACAA-ATTTAA-AAGTGTCGACACATTATGTACACCTATTCTCACATAAAATCGG
* * * * * *
343435 TATATTTATACCGGTTATATTACAAAATTATCTATTACATTATATTTATTGATTTCGATGTTTCT
64 TATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
* *
343500 GAGATCGATACTTTTTAAAACTGTATCGACACTTTATGAG
129 GGGATCGATACTTTTTAAAAATGTATCGACACTTTATGAG
343540 AAACTTTAAG
Statistics
Matches: 778, Mismatches: 154, Indels: 60
0.78 0.16 0.06
Matches are distributed among these distances:
193 2 0.00
194 12 0.02
195 69 0.09
196 72 0.09
197 58 0.07
198 90 0.12
199 295 0.38
200 43 0.06
201 133 0.17
202 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (198 bp):
AAGTATCGACACAAATTTAAAAGTGTCGACACATTATGTACACCTATTCTCACATAAAATCGGTA
TATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
GATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTTCACCCTTTTGGGCATTCATTCTGGC
AAA
Found at i:343280 original size:396 final size:396
Alignment explanation
Indices: 342379--343539 Score: 1685
Period size: 396 Copynumber: 2.9 Consensus size: 396
342369 TTTTGTTTAT
* *
342379 AAGTATCGACACAAATCTAAAACGTGTCGATAAATTATGTTCACCTATTTTCTCACAAAACC-GA
1 AAGTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCAAAAAACCAG-
342443 TACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
65 TACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG-TTTT
* *
342508 GGGATCGATACTTTTTATAAATGTATCGACACTTTCTGAGTTCACCCTTTTGGGCATTCATTCTG
129 GGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTG
* * * *
342573 GCAAAAAGTATCGACACATCATTTAAAAGTGTCGACAAATTATGTAGACCTATTCTGACATAAAA
194 GCAAAAAGTATCGACACAACA-TTAAAAGTGTCGACACATTATGTAGAACTATTCTAACATAAAA
* *
342638 TCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
258 TCGGTATATTTATACCGG-T-TATTACAAAATTACCTATTACATTATATTTATGGATTTCGATGT
* * *
342703 TTTAGGGATCGATATTGTTTAAAAATGTATCGACAGTTTATGAGTGCAACATTTTTGGATTTTCC
321 TTTTGGGATCGATACTGTTTAAAAATGTATCGACACTTTATGAGTGCAACATTTTTGGATTTTCC
342768 TTGTGAACCAA
386 TTGTGAACCAA
*
342779 AAGTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCT-AAAAAAACAGG
1 AAGTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCAAAAAACCA-G
* *
342843 TACATTTATA-CTGATACATTGT-AATTTACCTA-TACATTATAATTATCGGTTTCGATGTTTTG
65 TACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTG
*
342905 GGATCGATACTTTTTATAAATATATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGG
130 GGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGG
* * * *
342970 CAAAAAGTATTGACATACCATTCAAAAGTGTCGACACATTATGTAGAACTATTCTAACGTAAAAT
195 CAAAAAGTATCGACACAACATT-AAAAGTGTCGACACATTATGTAGAACTATTCTAACATAAAAT
* * * *
343035 CGGTATATTTATATCGG-TATCACAAAATTACCTATTATATTATATTTATGGATTTTGATGTTTT
259 CGGTATATTTATACCGGTTATTACAAAATTACCTATTACATTATATTTATGGATTTCGATGTTTT
* * *
343099 TGGGATCGATACTGTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGGATTTTCCTTG
324 TGGGATCGATACTGTTTAAAAATGTATCGACACTTTATGAGTGCAACATTTTTGGATTTTCCTTG
*
343164 TGGACCAA
389 TGAACCAA
* *
343172 AAGTATCGACA-ATAATTCTATAA-GTGTCGATACATTATGTAT-ATCTATTTTCTCAAAAAACC
1 AAGTATCGACACA-AA-TCTAAAACGTGTCGATACATTATGT-TCACCTATTTTCTCAAAAAACC
** * * * *
343234 AGTTTATTTGTACCGGTTACATTGTAAATTTAACTATTATATTATAATTATCGGTTTCGATATTT
63 AGTACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGAT-GTT
* * * *
343299 TTGGGATCAATACTTTTTATAATTGTATCGACACTTTATGCGTTGACCCTTTTGGGCATTCATTA
127 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTC
*
343364 TGGCAAAAAGTATCGACACAACATTAACAAGTGTCGACACATTATGTA-AACCTATTCTCACATA
192 TGGCAAAAAGTATCGACACAACATTAA-AAGTGTCGACACATTATGTAGAA-CTATTCTAACATA
* *
343428 AAATCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATATTTATTGATTTCGA
255 AAATCGGTATATTTATACCGG-T-TATTACAAAATTACCTATTACATTATATTTATGGATTTCGA
* * * *
343493 TGTTTCTGAGATCGATACTTTTTAAAACTGTATCGACACTTTATGAG
318 TGTTTTTGGGATCGATACTGTTTAAAAATGTATCGACACTTTATGAG
343540 AAACTTTAAG
Statistics
Matches: 685, Mismatches: 60, Indels: 32
0.88 0.08 0.04
Matches are distributed among these distances:
392 1 0.00
393 156 0.23
394 25 0.04
395 11 0.02
396 165 0.24
397 160 0.23
398 10 0.01
399 16 0.02
400 140 0.20
401 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (396 bp):
AAGTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCAAAAAACCAGT
ACATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTGG
GATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGGC
AAAAAGTATCGACACAACATTAAAAGTGTCGACACATTATGTAGAACTATTCTAACATAAAATCG
GTATATTTATACCGGTTATTACAAAATTACCTATTACATTATATTTATGGATTTCGATGTTTTTG
GGATCGATACTGTTTAAAAATGTATCGACACTTTATGAGTGCAACATTTTTGGATTTTCCTTGTG
AACCAA
Found at i:343559 original size:15 final size:15
Alignment explanation
Indices: 343534--343576 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
343524 ATCGACACTT
343534 TATGAGAAACTTTAAG
1 TATG-GAAACTTTAAG
* *
343550 TTTGGAAACTTTATG
1 TATGGAAACTTTAAG
*
343565 TATGAAAACTTT
1 TATGGAAACTTT
343577 GTTATGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (15 bp):
TATGGAAACTTTAAG
Found at i:343861 original size:25 final size:25
Alignment explanation
Indices: 343831--343883 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
343821 GTACACAAGA
*
343831 AATTTAAACATAATAATGTTCAAAT
1 AATTTAAACATAACAATGTTCAAAT
* *
343856 AATTTATACATAACAATGTTTAAAT
1 AATTTAAACATAACAATGTTCAAAT
343881 AAT
1 AAT
343884 GTACCTACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.38
Consensus pattern (25 bp):
AATTTAAACATAACAATGTTCAAAT
Found at i:344854 original size:6 final size:6
Alignment explanation
Indices: 344847--344892 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
344837 GTTTGGATCA
* * * *
344847 TCATCA TCATCA TCATCT TCTTCT TCATCG TCATCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
344893 TGACCTCTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.20, C:0.33, G:0.02, T:0.46
Consensus pattern (6 bp):
TCATCT
Found at i:344880 original size:18 final size:18
Alignment explanation
Indices: 344847--344892 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
344837 GTTTGGATCA
*
344847 TCATCATCATCATCATCT
1 TCATCTTCATCATCATCT
* *
344865 TCTTCTTCATCGTCATCT
1 TCATCTTCATCATCATCT
344883 TCATCTTCAT
1 TCATCTTCAT
344893 TGACCTCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.33, G:0.02, T:0.46
Consensus pattern (18 bp):
TCATCTTCATCATCATCT
Found at i:346768 original size:200 final size:198
Alignment explanation
Indices: 346419--347511 Score: 1241
Period size: 200 Copynumber: 5.5 Consensus size: 198
346409 CTTATTTTCT
* * * *
346419 CATAAAACCGATATATTTATACCGGTTACATTGA-AAATTTA-C-A-T--ATTATAATTATCGG-
1 CATAAAACCGGTATATTTATACCGGTTATATT-ACAAAATTACCTATTACATTATAATTATAGGT
* * * * * * *
346477 TTCGATGTTATTGTGATCGACA-GTTTTAAAAATGTATCAACACTTTATGCGTGCA--ACTTTTG
65 TTCGATGTT-TTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTTG
* * * * *
346539 G-ATTTCCTTCTAGACAAAAAAAGTATCGACACAAATTCCACAAGTGTCGATACATGT-TGTAGA
129 GCA-TTCATTCTGGAC--AAAAAGTATCGACACAAAAT-AAAAAGTGTCGATACAT-TATGTAGA
346602 CCTATTCTCT-
189 CCTATTCT-TA
* * ** * * *
346612 CATAAAACCCAGTAT-TGTTATACCGGTTACATTGTAAATTTA-CTATTACATTATATTTATGGG
1 CATAAAA-CCGGTATAT-TTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATAGG
* *
346675 TTTCGATGTTTCTGGTATCAACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTT
64 TTTCGATGTTT-TGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTT
* * * *
346740 TGAATTCATTCTGGACAAAAAGTATCGACACAAAATAAAAAAGTATCGATATATTATGTAGACCT
128 GGCATTCATTCTGGACAAAAAGTATCGACACAAAAT-AAAAAGTGTCGATACATTATGTAGACCT
346805 ATTCTTA
192 ATTCTTA
**
346812 CATAAAAAACC--TAT-TTATATA--GGTTATATTACAAAATTACCTATTACATTATAATTATTT
1 CAT--AAAACCGGTATATT-TATACCGGTTATATTACAAAATTACCTATTACATTATAATTATAG
* * *
346872 GTTTCGATGTTTTTGGGATCAACACTTTTTATAAATGTATCGACACTTTATTCGTTTATCTTTTT
63 GTTTCGATG-TTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTT
* * *
346937 TGGCATTCATTCTGGACAAAAAGCATCGACACAAAATAAAAAATGTCGATACATTATGTATACCT
127 TGGCATTCATTCTGGACAAAAAGTATCGACACAAAATAAAAAGTGTCGATACATTATGTAGACCT
347002 ATTCTTA
192 ATTCTTA
* *
347009 CATAAAATCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATATGTT
1 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATAGGTT
* * * *
347074 TCTATGTTTTTGGGATCGACGCTTTTTTTAAATGTATCGACACTTTATTCGTTCTTCATTTTTGG
66 TCGATG-TTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTTGG
* ** *
347139 CATTCATT-TCAGACAAAAAGTATCGACACAAAATAAAAAAGTGTTAATACATTATGTAGACATA
130 CATTCATTCT-GGACAAAAAGTATCGACACAAAAT-AAAAAGTGTCGATACATTATGTAGACCTA
347203 TTCTTA
193 TTCTTA
* **
347209 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATCTG-T
1 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATAGGTT
347273 TCGATGTTTTGGGATCGACACTTTTTATAAATGTATCGACAC-TTATTCGTTCAT--TTTTTGGC
66 TCGATGTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTTGGC
* * * * *
347335 ATTCATTCTGGACAAAAAGTATTGACACAACATTAAAAAGTGTCGCTACATTATGTAAATCTATT
131 ATTCATTCTGGACAAAAAGTATCGACACAA-AATAAAAAGTGTCGATACATTATGTAGACCTATT
*
347400 CTCA
195 CTTA
* * *
347404 CATAAAATCGGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTAT-ATATATAGAT
1 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAAT-TATAGGT
* *
347468 TTCAATGTTTCTAGGATCGACACTTTTTA-AAACTGTATCGACAC
65 TTCGATGTTT-TGGGATCGACACTTTTTATAAA-TGTATCGACAC
347512 AAAATAAAAA
Statistics
Matches: 786, Mismatches: 81, Indels: 62
0.85 0.09 0.07
Matches are distributed among these distances:
193 8 0.01
194 31 0.04
195 122 0.16
196 16 0.02
197 94 0.12
198 160 0.20
199 165 0.21
200 167 0.21
201 2 0.00
202 20 0.03
203 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (198 bp):
CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATAGGTT
TCGATGTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTTGGC
ATTCATTCTGGACAAAAAGTATCGACACAAAATAAAAAGTGTCGATACATTATGTAGACCTATTC
TTA
Found at i:347108 original size:397 final size:392
Alignment explanation
Indices: 346463--347511 Score: 1287
Period size: 397 Copynumber: 2.6 Consensus size: 392
346453 AAATTTACAT
* * * * * * *
346463 ATTATAATTATCGGTTCGATGTTATTGTGATCGACA-GTTTTAAAAATGTATCAACACTTTATGC
1 ATTATAATTATCTGTTCGATGTT-TTGGGATCAACACTTTTTATAAATGTATCGACAC-TTATTC
* ** * * * *
346527 GTGCAACTTTTGG-ATTTCCTTCTAGACAAAAAAAGTATCGACACAAATTCCACAAGTGTCGATA
64 GTTCATTTTTTGGCA-TTCATTCTGGAC--AAAAAGTATCGACACAAATT-AAAAAGTGTCGATA
* * * * ** *
346591 CATGT-TGTAGACCTATTCTCT-CATAAAACCCAGTAT-TGTTATACCGGTTACATTGTAAATTT
125 CAT-TATGTAAACCTATTCT-TACATAAAA-TCGGTATAT-TTATACCGGTTATATTACAAAATT
* ** * * * *
346653 A-CTATTACATTATATTTATGGGTTTCGATGTTTCTGGTATCAACACTTTTTATAAATGTATCGA
186 ACCTATTACATTATAATTATATGTTTCAATGTTTCTGGGATCGACACTTTTTTTAAATGTATCGA
* *
346717 CACTTTATTCGTTCATCATTTTTTGAATTCA-TTCTGGACAAAAAGTATCGACACAAAATAAAAA
251 CACTTTATTCGTTCATCATTTTTGGAATTCATTTC-AGACAAAAAGTATCGACACAAAATAAAAA
* * * *
346781 AGTATCGATATATTATGTAGACCTATTCTTACATAAAAAACC-TAT-TTATATA-GGTTATATTA
315 AGTATCAATACATTATGTAGACATATTCTTACAT--AAAACCGTATATT-TATACGATTATATTA
346843 CAAAATTACCTATTAC
377 CAAAATTACCTATTAC
*
346859 ATTATAATTATTTGTTTCGATGTTTTTGGGATCAACACTTTTTATAAATGTATCGACACTTTATT
1 ATTATAATTATCTG-TTCGATG-TTTTGGGATCAACACTTTTTATAAATGTATCGACAC-TTATT
* * * *
346924 CGTTTATCTTTTTTGGCATTCATTCTGGACAAAAAGCATCGACACAAAATAAAAAATGTCGATAC
63 CGTTCA--TTTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAATTAAAAAGTGTCGATAC
*
346989 ATTATGTATACCTATTCTTACATAAAATCGGTATATTTATACCGGTTATATTACAAAATTACCTA
126 ATTATGTAAACCTATTCTTACATAAAATCGGTATATTTATACCGGTTATATTACAAAATTACCTA
* * *
347054 TTACATTATAATTATATGTTTCTATGTTTTTGGGATCGACGCTTTTTTTAAATGTATCGACACTT
191 TTACATTATAATTATATGTTTCAATGTTTCTGGGATCGACACTTTTTTTAAATGTATCGACACTT
* * * *
347119 TATTCGTTCTTCATTTTTGGCATTCATTTCAGACAAAAAGTATCGACACAAAATAAAAAAGTGTT
256 TATTCGTTCATCATTTTTGGAATTCATTTCAGACAAAAAGTATCGACACAAAATAAAAAAGTATC
347184 AATACATTATGTAGACATATTCTTACATAAAACCGGTATATTTATACCGATTATATTACAAAATT
321 AATACATTATGTAGACATATTCTTACATAAAACC-GTATATTTATA-CGATTATATTACAAAATT
347249 ACCTATTAC
384 ACCTATTAC
*
347258 ATTATAATTATCTGTTCGATGTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTATTCGT
1 ATTATAATTATCTGTTCGATGTTTTGGGATCAACACTTTTTATAAATGTATCGACACTTATTCGT
* *
347323 TCATTTTTTGGCATTCATTCTGGACAAAAAGTATTGACACAACATTAAAAAGTGTCGCTACATTA
66 TCATTTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAA-ATTAAAAAGTGTCGATACATTA
* * *
347388 TGTAAATCTATTCTCACATAAAATCGGTATATTTATACCAGTTATATTACAAAATTACCTATTAC
130 TGTAAACCTATTCTTACATAAAATCGGTATATTTATACCGGTTATATTACAAAATTACCTATTAC
* *
347453 ATTAT-A-TATATAGATTTCAATGTTTCTAGGATCGACAC-TTTTTAAAACTGTATCGACAC
195 ATTATAATTATAT-G-TTTCAATGTTTCTGGGATCGACACTTTTTTTAAA-TGTATCGACAC
347512 AAAATAAAAA
Statistics
Matches: 571, Mismatches: 62, Indels: 41
0.85 0.09 0.06
Matches are distributed among these distances:
393 5 0.01
394 47 0.08
395 122 0.21
396 50 0.09
397 233 0.41
398 59 0.10
399 38 0.07
400 16 0.03
401 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (392 bp):
ATTATAATTATCTGTTCGATGTTTTGGGATCAACACTTTTTATAAATGTATCGACACTTATTCGT
TCATTTTTTGGCATTCATTCTGGACAAAAAGTATCGACACAAATTAAAAAGTGTCGATACATTAT
GTAAACCTATTCTTACATAAAATCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACA
TTATAATTATATGTTTCAATGTTTCTGGGATCGACACTTTTTTTAAATGTATCGACACTTTATTC
GTTCATCATTTTTGGAATTCATTTCAGACAAAAAGTATCGACACAAAATAAAAAAGTATCAATAC
ATTATGTAGACATATTCTTACATAAAACCGTATATTTATACGATTATATTACAAAATTACCTATT
AC
Found at i:347119 original size:199 final size:199
Alignment explanation
Indices: 346419--347511 Score: 1238
Period size: 199 Copynumber: 5.5 Consensus size: 199
346409 CTTATTTTCT
* * * * *
346419 CATAAAACCGATATATTTATACCGGTTACATTGA-AAATTTA-C-A-T--ATTATAATTAT-CGG
1 CATAAAACCGGTATATTTATACCGGTTATATT-ACAAAATTACCTATTACATTATAATTATATGT
* * * * * * * *
346477 TTCGATGTTATTGTGATCGACA-GTTTTAAAAATGTATCAACACTTTATGCGTGCAAC--TTTTG
65 TTCGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCTTTTTTG
* * * * * *
346539 G-ATTTCCTTCTAGACAAAAAAAGTATCGACACAAATTCCACAAGTGTCGATACATGT-TGTAGA
130 GCA-TTCATTCTGGAC--AAAAAGTATCGACACAAAAT-AAAAAATGTCGATACAT-TATGTAGA
346602 CCTATTCTCT-
190 CCTATTCT-TA
* * ** * * **
346612 CATAAAACCCAGTAT-TGTTATACCGGTTACATTGTAAATTTA-CTATTACATTATATTTATGGG
1 CATAAAA-CCGGTATAT-TTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATATG
* * *
346675 TTTCGATGTTTCTGGTATCAACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTT
64 TTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATC-TTTTT
* * *
346740 T-GAATTCATTCTGGACAAAAAGTATCGACACAAAATAAAAAAGTATCGATATATTATGTAGACC
128 TGGCATTCATTCTGGACAAAAAGTATCGACACAAAATAAAAAA-TGTCGATACATTATGTAGACC
346804 TATTCTTA
192 TATTCTTA
*
346812 CATAAAAAACC--TAT-TTATATA--GGTTATATTACAAAATTACCTATTACATTATAATTATTT
1 CAT--AAAACCGGTATATT-TATACCGGTTATATTACAAAATTACCTATTACATTATAATTATAT
* *
346872 GTTTCGATGTTTTTGGGATCAACACTTTTTATAAATGTATCGACACTTTATTCGTTTATCTTTTT
63 GTTTCGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCTTTTT
* *
346937 TGGCATTCATTCTGGACAAAAAGCATCGACACAAAATAAAAAATGTCGATACATTATGTATACCT
128 TGGCATTCATTCTGGACAAAAAGTATCGACACAAAATAAAAAATGTCGATACATTATGTAGACCT
347002 ATTCTTA
193 ATTCTTA
*
347009 CATAAAATCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATATGTT
1 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATATGTT
* * * * *
347074 TCTATGTTTTTGGGATCGACGCTTTTTTTAAATGTATCGACACTTTATTCGTTCTTCATTTTTGG
66 TCGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCTTTTTTGG
* ** *
347139 CATTCATT-TCAGACAAAAAGTATCGACACAAAATAAAAAAGTGTTAATACATTATGTAGACATA
131 CATTCATTCT-GGACAAAAAGTATCGACACAAAATAAAAAA-TGTCGATACATTATGTAGACCTA
347203 TTCTTA
194 TTCTTA
* *
347209 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATCTG-T
1 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATATGTT
347273 TCGATG-TTTTGGGATCGACACTTTTTATAAATGTATCGACAC-TTATTCGTTCA--TTTTTTGG
66 TCGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCTTTTTTGG
* * * * * *
347334 CATTCATTCTGGACAAAAAGTATTGACACAACATTAAAAAGTGTCGCTACATTATGTAAATCTAT
131 CATTCATTCTGGACAAAAAGTATCGACACAA-AATAAAAAATGTCGATACATTATGTAGACCTAT
*
347399 TCTCA
195 TCTTA
* *
347404 CATAAAATCGGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTAT-A-TATATAGA
1 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATAT-G-
* * *
347467 TTTCAATGTTTCTAGGATCGACACTTTTTA-AAACTGTATCGACAC
64 TTTCGATGTTTTTGGGATCGACACTTTTTATAAA-TGTATCGACAC
347512 AAAATAAAAA
Statistics
Matches: 784, Mismatches: 81, Indels: 66
0.84 0.09 0.07
Matches are distributed among these distances:
193 12 0.02
194 31 0.04
195 113 0.14
196 18 0.02
197 96 0.12
198 161 0.21
199 172 0.22
200 159 0.20
201 2 0.00
202 15 0.02
203 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (199 bp):
CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATATGTT
TCGATGTTTTTGGGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCATCTTTTTTGG
CATTCATTCTGGACAAAAAGTATCGACACAAAATAAAAAATGTCGATACATTATGTAGACCTATT
CTTA
Found at i:347634 original size:149 final size:149
Alignment explanation
Indices: 347353--347660 Score: 390
Period size: 149 Copynumber: 2.1 Consensus size: 149
347343 TGGACAAAAA
* * * * * *
347353 GTATTGACACAACATTAAAAAGTGTCGCTACATTATGTAAATCTATTCTCACATAAAATCGGTAT
1 GTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAAATCTATTCTCACATAAAACCGATAT
347418 ATTTATACCAGTTATATTACAAAATTACCTATTACATTATATATATAGATTTCAATGTTTCTAGG
66 ATTTATACCAGTTATATTACAAAATTACCTATTACATTATATATATAGATTTCAATGTTTCTAGG
347483 ATCGACACTTTTTA-AAACT
131 ATCGACACTTTTTATAAA-T
* *
347502 GTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGA-CATATTCTCACATAAAACCGATG
1 GTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAAATC-TATTCTCACATAAAACCGATA
* * * * * * * *
347566 TATTTATATCGGTTATATTATAAAGTTACCTATTATATTATA-ATTATTTG-TTTCGATGTTTTT
65 TATTTATACCAGTTATATTACAAAATTACCTATTACATTATATA-TA-TAGATTTCAATGTTTCT
* *
347629 GGGATCGACACTTTTTATATAT
128 AGGATCGACACTTTTTATAAAT
347651 GTATCGACAC
1 GTATCGACAC
347661 TTTATTCGTT
Statistics
Matches: 137, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
148 2 0.01
149 131 0.96
150 4 0.03
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.38
Consensus pattern (149 bp):
GTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAAATCTATTCTCACATAAAACCGATAT
ATTTATACCAGTTATATTACAAAATTACCTATTACATTATATATATAGATTTCAATGTTTCTAGG
ATCGACACTTTTTATAAAT
Found at i:347792 original size:349 final size:343
Alignment explanation
Indices: 347153--347858 Score: 1058
Period size: 349 Copynumber: 2.0 Consensus size: 343
347143 CATTTCAGAC
* * *
347153 AAAAAGTATCGACACAAAATAAAAAAGTGTTAATACATTATGTAGACATATTCTTACATAAAACC
1 AAAATGTATCGACACAAAATAAAAAAGTGTCAATACATTATGTAGACATATTCTCACATAAAACC
*
347218 GGTATATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATCTGTTCGATGTTTT
66 GATATATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATCTGTTCGATGTTTT
347283 GGGATCGACACTTTTTATAAATGTATCGACACTTATTCGTTCATTTTTTGGCATTCATTCTGGAC
131 GGGATCGACACTTTTTATAAATGTATCGACACTTATTCGTTCATTTTTTGGCATTCATTCTGGAC
* * * * * *
347348 AAAAAGTATTGACACAACATTAAAAAGTGTCGCTACATTATGTAAATCTATTCTCACATAAAATC
196 AAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAAACCTATTCTCACATAAAACC
*
347413 GGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTAT-ATATAT-AGATTTCAATGT
261 GGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAAT-TATCAG-TTTCAATAT
*
347476 TTCTAGGATCGACACTTTTT
324 TTCTAGGATCGACACGTTTT
*
347496 AAAACTGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACATATTCTCACATAAAAC
1 AAAA-TGTATCGACACAAAATAAAAAAGTGTCAATACATTATGTAGACATATTCTCACATAAAAC
* * * * * * *
347561 CGATGTATTTATATCGGTTATATTATAAAGTTACCTATTATATTATAATTATTTGTTTCGATGTT
65 CGATATATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATCTG-TTCGATG-T
*
347626 TTTGGGATCGACACTTTTTATATATGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCATT
128 TTTGGGATCGACACTTTTTATAAATGTATCGACAC-TTATTCGTTCAT--TTTTTGGCATTCATT
*
347691 CTGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACAT
190 CTGGACAAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAAACCTATTCTCACAT
* *
347756 AAAACCGGTATATTTATACC-GATTATATTACAAAATTACCTTTTACATTATAATTATCTGTTTC
255 AAAACCGGTATATTTATACCAG-TTATATTACAAAATTACCTATTACATTATAATTATCAGTTTC
* * *
347820 GATATTTTTGGGATCGACACGTTTT
319 AATATTTCTAGGATCGACACGTTTT
*
347845 ATAATGTATCGACA
1 AAAATGTATCGACA
347859 TTTATAAATG
Statistics
Matches: 326, Mismatches: 28, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
343 4 0.01
344 103 0.32
345 7 0.02
346 35 0.11
347 12 0.04
348 11 0.03
349 151 0.46
350 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (343 bp):
AAAATGTATCGACACAAAATAAAAAAGTGTCAATACATTATGTAGACATATTCTCACATAAAACC
GATATATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATCTGTTCGATGTTTT
GGGATCGACACTTTTTATAAATGTATCGACACTTATTCGTTCATTTTTTGGCATTCATTCTGGAC
AAAAAGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAAACCTATTCTCACATAAAACC
GGTATATTTATACCAGTTATATTACAAAATTACCTATTACATTATAATTATCAGTTTCAATATTT
CTAGGATCGACACGTTTT
Found at i:347847 original size:200 final size:198
Alignment explanation
Indices: 347502--347863 Score: 598
Period size: 200 Copynumber: 1.8 Consensus size: 198
347492 TTTTAAAACT
*
347502 GTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACATATTCTCACATAAAACCGATGT
1 GTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACATATTCTCACATAAAACCGATAT
* * * * * * *
347567 ATTTATATCGGTTATATTATAAAGTTACCTATTATATTATAATTATTTGTTTCGATGTTTTTGGG
66 ATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATCTGTTTCGATATTTTTGGG
*
347632 ATCGACACTTTTTATATATGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGAC
131 ATCGACACGTTTTATA-ATGTATCGACA-TTTATTCGTTCATCATTTTTGGCATTCATTCTGGAC
347697 AAAAA
194 AAAAA
* *
347702 GTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
1 GTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACATATTCTCACATAAAACCGATAT
*
347767 ATTTATACCGATTATATTACAAAATTACCTTTTACATTATAATTATCTGTTTCGATATTTTTGGG
66 ATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATCTGTTTCGATATTTTTGGG
347832 ATCGACACGTTTTATAATGTATCGACATTTAT
131 ATCGACACGTTTTATAATGTATCGACATTTAT
347864 AAATGTATCG
Statistics
Matches: 150, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
198 5 0.03
199 11 0.07
200 134 0.89
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (198 bp):
GTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACATATTCTCACATAAAACCGATAT
ATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATCTGTTTCGATATTTTTGGG
ATCGACACGTTTTATAATGTATCGACATTTATTCGTTCATCATTTTTGGCATTCATTCTGGACAA
AAA
Found at i:347857 original size:20 final size:19
Alignment explanation
Indices: 347832--347877 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
347822 TATTTTTGGG
347832 ATCGACACGTTT-TATAATGT
1 ATCGACAC-TTTATA-AATGT
347852 ATCGACA-TTTATAAATGT
1 ATCGACACTTTATAAATGT
347870 ATCGACAC
1 ATCGACAC
347878 ATATGCTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 15 0.62
19 2 0.08
20 7 0.29
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (19 bp):
ATCGACACTTTATAAATGT
Found at i:347862 original size:17 final size:18
Alignment explanation
Indices: 347842--347876 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
347832 ATCGACACGT
347842 TTTAT-AATGTATCGACA
1 TTTATAAATGTATCGACA
347859 TTTATAAATGTATCGACA
1 TTTATAAATGTATCGACA
347877 CATATGCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (18 bp):
TTTATAAATGTATCGACA
Found at i:348168 original size:18 final size:19
Alignment explanation
Indices: 348128--348176 Score: 82
Period size: 18 Copynumber: 2.6 Consensus size: 19
348118 ATTACATCCA
348128 TATACAAAATTATAAATCG
1 TATACAAAATTATAAATCG
*
348147 TATACAAAATTAT-AATCT
1 TATACAAAATTATAAATCG
348165 TATACAAAATTA
1 TATACAAAATTA
348177 ACTCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (19 bp):
TATACAAAATTATAAATCG
Found at i:349673 original size:30 final size:29
Alignment explanation
Indices: 349632--349698 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
349622 CGACATTCTT
*
349632 CCTCATTTCCTC-CATCTTTCTTCTTCATC
1 CCTCTTTTCCTCTC-TCTTTCTTCTTCATC
* *
349661 CCTTCTTTTCCTCTCTCTTTTTTCTTCCTC
1 CC-TCTTTTCCTCTCTCTTTCTTCTTCATC
349691 CCTCTTTT
1 CCTCTTTT
349699 TTTTCTCCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.24
30 24 0.73
31 1 0.03
ACGTcount: A:0.04, C:0.40, G:0.00, T:0.55
Consensus pattern (29 bp):
CCTCTTTTCCTCTCTCTTTCTTCTTCATC
Found at i:349706 original size:15 final size:17
Alignment explanation
Indices: 349668--349736 Score: 90
Period size: 17 Copynumber: 4.2 Consensus size: 17
349658 ATCCCTTCTT
*
349668 TTCCTCTCTCTTTTTTC
1 TTCCTCCCTCTTTTTTC
349685 TTCCTCCCTCTTTTTT-
1 TTCCTCCCTCTTTTTTC
349701 TT-CTCCCTCTTTTCTTC
1 TTCCTCCCTCTTTT-TTC
*
349718 TTCCT-CCTCTTTATTC
1 TTCCTCCCTCTTTTTTC
349734 TTC
1 TTC
349737 ATATTGTTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
15 11 0.23
16 10 0.21
17 24 0.51
18 2 0.04
ACGTcount: A:0.01, C:0.38, G:0.00, T:0.61
Consensus pattern (17 bp):
TTCCTCCCTCTTTTTTC
Found at i:349736 original size:19 final size:18
Alignment explanation
Indices: 349663--349736 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 18
349653 TCTTCATCCC
349663 TTCTT-TTCCT-CTCTCTT
1 TTCTTCTTCCTCCTCT-TT
349680 TT-TTCTTCCTCCCTCTTT
1 TTCTTCTTCCT-CCTCTTT
*
349698 TTTTTC-T-C-CCTC-TT
1 TTCTTCTTCCTCCTCTTT
349712 TTCTTCTTCCTCCTCTTT
1 TTCTTCTTCCTCCTCTTT
349730 ATTCTTC
1 -TTCTTC
349737 ATATTGTTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
14 7 0.15
15 5 0.11
16 3 0.06
17 12 0.26
18 7 0.15
19 13 0.28
ACGTcount: A:0.01, C:0.36, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCTTCTTCCTCCTCTTT
Found at i:350006 original size:20 final size:20
Alignment explanation
Indices: 349981--350020 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
349971 CATTATGCCT
349981 CTCAAGTGTATCTTCGACTC
1 CTCAAGTGTATCTTCGACTC
* *
350001 CTCAAGTTTCTCTTCGACTC
1 CTCAAGTGTATCTTCGACTC
350021 TTGATTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.33, G:0.12, T:0.38
Consensus pattern (20 bp):
CTCAAGTGTATCTTCGACTC
Found at i:350120 original size:15 final size:15
Alignment explanation
Indices: 350100--350131 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
350090 TACTCTATTT
350100 CCTCACCGTCATCCC
1 CCTCACCGTCATCCC
*
350115 CCTCACTGTCATCCC
1 CCTCACCGTCATCCC
350130 CC
1 CC
350132 AATACAACCA
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:0.12, C:0.59, G:0.06, T:0.22
Consensus pattern (15 bp):
CCTCACCGTCATCCC
Found at i:353095 original size:182 final size:181
Alignment explanation
Indices: 352337--353172 Score: 1066
Period size: 182 Copynumber: 4.7 Consensus size: 181
352327 AACACGTACT
* * * *
352337 TATTAAAGTATCGACACTTTC-ATATATC-GGTAGCGCTTTACTGGTTTTGTCTTTTCGAGATCG
1 TATTAAAGTATCGACACTTGCAATATATCTGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACCG
* * * * * * *
352400 GCTTTATCATATTTTTACATGTTATATCGTTATGGAACGATACATTTTTATTAAGTATCGACACT
66 GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
* * * *
352465 TTATAGGCGCTAAAACT-ATTTCTCTTTTAAATTCACAAAGTGACGATACTTA
131 TTATA-GCGCTAAAACTGCTTT-TCCTTTAAATTCACAATGTGTCGATACTTA
* * * *
352517 TATTAAATTATCGACACTTACAATATATCTGGTAGCGCTTTACCGGTTTTGTCTTTTCGAGATCG
1 TATTAAAGTATCGACACTTGCAATATATCTGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACCG
* * *
352582 GCTTTAT--TATTTTTACATG-T-TATCGTTCTGGATCGATACATA-TTATAAAGAATCGACACT
66 GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
352642 TTATAGCGCT-AAACTGC--TTCCTTTAAATTCACAATGTGTC--TACTTA
131 TTATAGCGCTAAAACTGCTTTTCCTTTAAATTCACAATGTGTCGATACTTA
* * * *
352688 TA-TAAAGTATCGACACTTGCAATATAT-TCGTTATCTCTTTA-CGGTTTTG--TTTTCCTGACC
1 TATTAAAGTATCGACACTTGCAATATATCT-GGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACC
* *
352748 GGTTTTGTCATATTTTTACCTGTTGTATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
65 GGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
*
352813 TTTATAGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
130 TTTATAGCGCTAAAACTGCTTTTCCTTTAAATTCACAATGTGTCGATACTTA
* * * *
352865 TATTAAAGTATCGACACTTGCAATATAT-TCAGTATCTCTTTACCGGTTTTGTCTTTTCCTGACC
1 TATTAAAGTATCGACACTTGCAATATATCT-GGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACC
*
352929 GGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAT
65 GGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
* * *
352994 TTTATAGGTGTTAAAACTGCTTTTCCTTTAAATTCACTATGTGTCGATACTTA
130 TTTATA-GCGCTAAAACTGCTTTTCCTTTAAATTCACAATGTGTCGATACTTA
* * *
353047 TATTAAAGTATCGACACGTGTAATATATCTGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACTG
1 TATTAAAGTATCGACACTTGCAATATATCTGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACCG
* * * * * *
353112 GTTTTGTCATATTTTTTCCTGTTATATTGATGTGGATC-ATACAT-TTTTTAAAGTATCGACA
66 GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACA
353173 TAAACCGACA
Statistics
Matches: 589, Mismatches: 47, Indels: 40
0.87 0.07 0.06
Matches are distributed among these distances:
167 14 0.02
169 20 0.03
170 33 0.06
171 29 0.05
172 28 0.05
173 26 0.04
174 1 0.00
175 27 0.05
176 5 0.01
177 29 0.05
178 56 0.10
179 9 0.02
180 46 0.08
181 92 0.16
182 173 0.29
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (181 bp):
TATTAAAGTATCGACACTTGCAATATATCTGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACCG
GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
TTATAGCGCTAAAACTGCTTTTCCTTTAAATTCACAATGTGTCGATACTTA
Found at i:353340 original size:54 final size:55
Alignment explanation
Indices: 353238--353348 Score: 163
Period size: 54 Copynumber: 2.0 Consensus size: 55
353228 GACTTACTAC
* * *
353238 ATTATTATTACTCACATTTTCGGTAGCGCTAAATCGAATTTATTAATATATTTTA
1 ATTATTATTACTCACATTTTCGATAGCGCTAAACCGAATTTATTAATATATTGTA
*
353293 ATTATTATTACTCACATTTT-TATAGCGCTAAACCGAA-TTATTAAATATATTGTA
1 ATTATTATTACTCACATTTTCGATAGCGCTAAACCGAATTTATT-AATATATTGTA
353347 AT
1 AT
353349 GAATCCGGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
53 5 0.10
54 26 0.51
55 20 0.39
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (55 bp):
ATTATTATTACTCACATTTTCGATAGCGCTAAACCGAATTTATTAATATATTGTA
Found at i:360787 original size:21 final size:21
Alignment explanation
Indices: 360753--360803 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
360743 ATTATGACTA
*
360753 TCGCAATGCGATTTTT-CAATT
1 TCGCAATGCAATTTTTCCAA-T
*
360774 TCGCATTGCAATTTTTCCAAT
1 TCGCAATGCAATTTTTCCAAT
360795 TCGCAATGC
1 TCGCAATGC
360804 GAATAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.39
Consensus pattern (21 bp):
TCGCAATGCAATTTTTCCAAT
Found at i:360819 original size:19 final size:21
Alignment explanation
Indices: 360795--360845 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
360785 TTTTTCCAAT
360795 TCGCAATGCGAA-TAAG-AAA
1 TCGCAATGCGAATTAAGAAAA
* **
360814 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
360835 TCGCAATGCGA
1 TCGCAATGCGA
360846 TACTGACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 11 0.42
20 2 0.08
21 13 0.50
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:360859 original size:20 final size:20
Alignment explanation
Indices: 360834--360928 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
360824 AATTGGGAAA
*
360834 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
360854 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
360875 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
360895 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
360915 TTCGCAACGAGATA
1 ATCGCAACGCGATA
360929 ATACATAATC
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 2 0.03
20 46 0.71
21 15 0.23
22 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:360864 original size:41 final size:41
Alignment explanation
Indices: 360831--360908 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
360821 GCGAATTGGG
*
360831 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
360872 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATA
360909 CTGACTTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:360942 original size:21 final size:20
Alignment explanation
Indices: 360834--360948 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
360824 AATTGGGAAA
* *
360834 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAATGACT
*
360854 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATAATGAC--T
*
360875 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* *
360895 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* *
360915 TTCGCAACGAGATAAT-ACAT
1 ATCGCAACGCGATAATGAC-T
*
360935 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
360949 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.05
20 48 0.61
21 25 0.32
22 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATAATGACT
Found at i:361143 original size:22 final size:22
Alignment explanation
Indices: 361115--361158 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
361105 CACTCTCTCA
361115 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
361137 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
361159 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:361445 original size:20 final size:20
Alignment explanation
Indices: 361420--361457 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
361410 TTATTCTCTC
361420 GTTGCGATTGTCATTTTCGT
1 GTTGCGATTGTCATTTTCGT
*
361440 GTTGCGATTTTCATTTTC
1 GTTGCGATTGTCATTTTC
361458 AAAAACTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.16, G:0.21, T:0.53
Consensus pattern (20 bp):
GTTGCGATTGTCATTTTCGT
Found at i:362778 original size:18 final size:18
Alignment explanation
Indices: 362752--362799 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
362742 TACACTTCGG
362752 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
362770 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
362788 GAGCCATCACCT
1 GAGCCATCACCT
362800 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:363182 original size:48 final size:48
Alignment explanation
Indices: 363111--363208 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
363101 CTCTAAGCAA
363111 CGAGGTAAGTTTAAGATTTTTCATATTTAACTTGATGATAAATTTACT
1 CGAGGTAAGTTTAAGATTTTTCATATTTAACTTGATGATAAATTTACT
363159 CGAGGTAAGTTTAAGATTTTTCATATTTAACTTGATGATAAATTTACT
1 CGAGGTAAGTTTAAGATTTTTCATATTTAACTTGATGATAAATTTACT
363207 CG
1 CG
363209 TAATTTCACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (48 bp):
CGAGGTAAGTTTAAGATTTTTCATATTTAACTTGATGATAAATTTACT
Found at i:363434 original size:19 final size:20
Alignment explanation
Indices: 363380--363446 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
363370 ATAGTTTATT
* *
363380 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
363400 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
363420 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
363439 TCGCAACG
1 TCGCAACG
363447 ACAAAATTGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:363464 original size:33 final size:33
Alignment explanation
Indices: 363419--363510 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
363409 GGAAATGGCT
363419 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
363452 ATTGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
363485 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
363511 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:363477 original size:19 final size:19
Alignment explanation
Indices: 363419--363515 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
363409 GGAAATGGCT
363419 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
363438 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
363452 ATTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
363471 ATCGCAA--CG--AT-AAA
1 ATCGCAATGCGAAATGAAA
*
363485 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
363504 ATCGCAATGCGA
1 ATCGCAATGCGA
363516 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 19 0.30
15 3 0.05
16 4 0.06
17 4 0.06
18 3 0.05
19 30 0.48
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:363487 original size:14 final size:14
Alignment explanation
Indices: 363435--363493 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
363425 ATGCGAAATG
*
363435 AAAATCGCAACGAC
1 AAAATCGCAACGAT
*
363449 AAAATTGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
363467 GAAAATCGCAACGAT
1 -AAAATCGCAACGAT
363482 AAAATCGCAACG
1 AAAATCGCAACG
363494 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
15 2 0.05
16 2 0.05
17 2 0.05
18 1 0.03
19 9 0.24
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:363546 original size:14 final size:14
Alignment explanation
Indices: 363527--363585 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
363517 TTGTGTTTCG
363527 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
363541 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
363558 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
363574 CGTTACGATTTT
1 CGTTGCGATTTT
363586 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 17 0.46
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:363559 original size:33 final size:33
Alignment explanation
Indices: 363522--363601 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
363512 GCGATTTGTG
* *
363522 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTACGATTTTCA
363555 TTTCGCATTGCGATTTTGTCGTTACGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTACGATTTTCA
363588 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
363602 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTACGATTTTCA
Found at i:363616 original size:20 final size:19
Alignment explanation
Indices: 363586--363640 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
363576 TTACGATTTT
363586 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
*
363605 CATTTCCGCATTGCGATAGT
1 CATTT-CGCATTGCGATAGC
*
363625 CATTTTCGCGTTGCGA
1 CA-TTTCGCATTGCGA
363641 AAGTAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:363651 original size:21 final size:20
Alignment explanation
Indices: 363627--363666 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
363617 GCGATAGTCA
363627 TTTTCGCGTTGCGAAAGTAAG
1 TTTT-GCGTTGCGAAAGTAAG
*
363648 TTTTGTGTTGCGAAAGTAA
1 TTTTGCGTTGCGAAAGTAA
363667 ACTATTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.38
Consensus pattern (20 bp):
TTTTGCGTTGCGAAAGTAAG
Found at i:364093 original size:21 final size:21
Alignment explanation
Indices: 364069--364135 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
364059 TCATTCCTCG
364069 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
364090 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
364111 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
364132 AGAG
1 AGAG
364136 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:364093 original size:42 final size:41
Alignment explanation
Indices: 364022--364135 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 41
364012 GCCTGTTATC
* * * * * *
364022 CCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATT
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCA-T
*
364064 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCAT
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCAT
* * *
364105 CGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
364136 CCCGATTCAC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.07
42 54 0.90
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (41 bp):
CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCAT
Found at i:365523 original size:14 final size:14
Alignment explanation
Indices: 365481--365517 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
365471 TATTGTTTAA
*
365481 TTGATTTGTAAAAG
1 TTGATTTGTAAAAT
*
365495 ATGATTTGTAAAAT
1 TTGATTTGTAAAAT
365509 TTGATTTGT
1 TTGATTTGT
365518 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAT
Found at i:365661 original size:14 final size:14
Alignment explanation
Indices: 365642--365696 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
365632 ACGAAATGAA
365642 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
365656 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
365675 AATCGCAACGAGAG
1 AATCGCAACGAGAG
365689 AATCGCAA
1 AATCGCAA
365697 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:365670 original size:33 final size:33
Alignment explanation
Indices: 365624--365736 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
365614 AAAAATGACT
*
365624 ATCGCAACACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
365657 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * * *
365690 ATCGCAATGCGAAATGAAAATCACAACAAGGGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
365723 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
365737 CTAAATTCGC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:365680 original size:19 final size:18
Alignment explanation
Indices: 365624--365716 Score: 67
Period size: 19 Copynumber: 5.4 Consensus size: 18
365614 AAAAATGACT
365624 ATCGCAACACGAAATGAAA
1 ATCGCAAC-CGAAATGAAA
*
365643 ATCGCAA-CG--A-GAGA
1 ATCGCAACCGAAATGAAA
365657 ATCGCAACGCGAAATGAAA
1 ATCGCAAC-CGAAATGAAA
*
365676 ATCGCAA-CG--A-GAGA
1 ATCGCAACCGAAATGAAA
*
365690 ATCGCAATGCGAAATGAAA
1 ATCGCAA-CCGAAATGAAA
*
365709 ATCACAAC
1 ATCGCAAC
365717 AAGGGAATCG
Statistics
Matches: 58, Mismatches: 6, Indels: 21
0.68 0.07 0.25
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 26 0.45
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (18 bp):
ATCGCAACCGAAATGAAA
Found at i:365764 original size:19 final size:18
Alignment explanation
Indices: 365742--365892 Score: 83
Period size: 19 Copynumber: 8.7 Consensus size: 18
365732 CGAAACTAAA
365742 TTCGCATTGCGATTTTCAT
1 TTCGC-TTGCGATTTTCAT
*
365761 TTCGCTTTGCGA--TTC-C
1 TTCGC-TTGCGATTTTCAT
*
365777 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
**
365794 TTCATATTGCGA--TTC-T
1 TTC-GCTTGCGATTTTCAT
*
365810 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
365827 TTCGCGTTGCGA--TTC-T
1 TTCGC-TTGCGATTTTCAT
*
365843 CTCG-TTGCGATTTTCAT
1 TTCGCTTGCGATTTTCAT
**
365860 TTCGCATTGCGATAGTCAT
1 TTCGC-TTGCGATTTTCAT
365879 TTCCGCGTTGCGAT
1 TT-CGC-TTGCGAT
365893 AGACATTAAG
Statistics
Matches: 102, Mismatches: 14, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
14 18 0.18
16 19 0.19
17 19 0.19
19 36 0.35
20 10 0.10
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (18 bp):
TTCGCTTGCGATTTTCAT
Found at i:365790 original size:33 final size:33
Alignment explanation
Indices: 365748--365872 Score: 198
Period size: 33 Copynumber: 3.8 Consensus size: 33
365738 TAAATTCGCA
*
365748 TTGCGATTTTCATTTCGCTTTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCTTTGCGATTCTCTCG
*
365781 TTGCGATTTTCATTTC-ATATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCT-TTGCGATTCTCTCG
*
365814 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCTTTGCGATTCTCTCG
*
365847 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCTTTGCGAT
365873 AGTCATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
32 1 0.01
33 84 0.99
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCTTTGCGATTCTCTCG
Found at i:365819 original size:14 final size:14
Alignment explanation
Indices: 365800--365854 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
365790 TCATTTCATA
365800 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
365814 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
365833 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
365847 TTGCGATT
1 TTGCGATT
365855 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:365891 original size:20 final size:20
Alignment explanation
Indices: 365845--365938 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
365835 GCGATTCTCT
**
365845 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
365864 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
365884 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
365903 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
365925 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
365939 AATGATTGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:368923 original size:64 final size:63
Alignment explanation
Indices: 368838--368998 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
368828 TTGTTTAAGG
* * * *
368838 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAAGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAAGATTTA
* * * *
368902 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAAGATTTA
*
368966 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
368999 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAAGATTTA
Found at i:369369 original size:22 final size:20
Alignment explanation
Indices: 369344--369383 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
369334 ATTTATATGA
*
369344 TATGTGTTATATGGCAATTATT
1 TATGTATTATA-GG-AATTATT
369366 TATGTATTATAGGAATTA
1 TATGTATTATAGGAATTA
369384 GATGAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (20 bp):
TATGTATTATAGGAATTATT
Found at i:371111 original size:12 final size:12
Alignment explanation
Indices: 371094--371118 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
371084 TCTTCGGGGA
371094 CTTTTTCTTCTT
1 CTTTTTCTTCTT
371106 CTTTTTCTTCTT
1 CTTTTTCTTCTT
371118 C
1 C
371119 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:371327 original size:24 final size:24
Alignment explanation
Indices: 371293--371346 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
371283 CTGAAACATC
*
371293 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
371317 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
371341 ATCAAA
1 ATCAAA
371347 TTTCGAATAC
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:372187 original size:41 final size:41
Alignment explanation
Indices: 372068--372199 Score: 142
Period size: 41 Copynumber: 3.2 Consensus size: 41
372058 AACTTTGAAA
* * *
372068 ATCGCATTGCGATTATGTATTATCTCGTTACGATAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGATAGTCAGT
* * * ** *
372109 ATCTCGTTGCGA--AAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGATAGTCAGT
* *
372149 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGATAGTCAGT
372190 ATCGCATTGC
1 ATCGCATTGC
372200 AATTTTCCAA
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.04
40 28 0.39
41 39 0.54
42 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGATAGTCAGT
Found at i:372194 original size:20 final size:20
Alignment explanation
Indices: 372088--372199 Score: 109
Period size: 20 Copynumber: 5.5 Consensus size: 20
372078 GATTATGTAT
* *
372088 TATCTCGTTACGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
372108 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
372128 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
372148 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
372169 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
372189 TATCGCATTGC
1 TATCGCGTTGC
372200 AATTTTCCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 59 0.76
21 14 0.18
22 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:372221 original size:41 final size:41
Alignment explanation
Indices: 372129--372223 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
372119 GAAAGTCAGA
* * * ** *
372129 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCAAAT
372170 ATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTT-CAAAT
*
372212 -TCGCATTGCGAT
1 ATCGCGTTGCGAT
372224 TTACTTATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCAAAT
Found at i:372235 original size:20 final size:20
Alignment explanation
Indices: 372210--372262 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
372200 AATTTTCCAA
372210 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
372230 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
372250 ATTCGCATTGCGA
1 ATTCGCATTGCGA
372263 ATTGGGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:372379 original size:13 final size:13
Alignment explanation
Indices: 372361--372389 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
372351 AATGGAGATC
372361 GCGTTGCGAATTA
1 GCGTTGCGAATTA
372374 GCGTTGCGAATTA
1 GCGTTGCGAATTA
372387 GCG
1 GCG
372390 ATCGCATTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.28
Consensus pattern (13 bp):
GCGTTGCGAATTA
Found at i:374832 original size:2 final size:2
Alignment explanation
Indices: 374825--374869 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
374815 CCCGTCGGAT
374825 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
374867 TA T
1 TA T
374870 TATCAAATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:377013 original size:42 final size:42
Alignment explanation
Indices: 376951--377033 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
376941 TCTAAATTTA
*
376951 AATAAGTAATCGAAACAATATTTAAATTTTAATAACATATCG
1 AATAAATAATCGAAACAATATTTAAATTTTAATAACATATCG
* *
376993 AATAAATAATCGAAATAATATTTAACTTTTAATAACATATC
1 AATAAATAATCGAAACAATATTTAAATTTTAATAACATATC
377034 TAATTTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.35
Consensus pattern (42 bp):
AATAAATAATCGAAACAATATTTAAATTTTAATAACATATCG
Found at i:377965 original size:17 final size:18
Alignment explanation
Indices: 377919--377965 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
377909 AATGTTTGAG
377919 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
** *
377937 GGAATTAAAATCTGT-CA
1 GGAATTGGAATCTGTGAA
377954 GGAATTGGAATC
1 GGAATTGGAATC
377966 CAATTCCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:378559 original size:27 final size:28
Alignment explanation
Indices: 378497--378567 Score: 126
Period size: 28 Copynumber: 2.6 Consensus size: 28
378487 CCTAAACCCG
*
378497 AACCCGACCCGAATACCACACTTAAAAA
1 AACCCGACCCGAATATCACACTTAAAAA
378525 AACCCGACCCGAATATCACACTT-AAAA
1 AACCCGACCCGAATATCACACTTAAAAA
378552 AACCCGACCCGAATAT
1 AACCCGACCCGAATAT
378568 ATGAATTAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 20 0.48
28 22 0.52
ACGTcount: A:0.44, C:0.35, G:0.08, T:0.13
Consensus pattern (28 bp):
AACCCGACCCGAATATCACACTTAAAAA
Found at i:378865 original size:253 final size:244
Alignment explanation
Indices: 378313--378879 Score: 678
Period size: 254 Copynumber: 2.2 Consensus size: 244
378303 ATTTTTATTC
* ** * * *
378313 AATATATAAATTAGAAACCCGACCCGATACAAAATAATTATAAAATTATTTTTATTCATTAAAAA
1 AATATATGAATTAGAAACCCGACCCGACCCGAAATAA-TAAAAAATTATTTTTATTCAATAAAAA
* *
378378 CATTGACTTAATTGAAAAAAAATTATATATAGAGGAGATTTATTGTAATTATTCCTAAATATATA
65 CAGTGACTTAATTGAAAAAAAATTATATAGAGAGGAGATTTATTGTAATTATTCCTAAATATATA
* * *
378443 AGGTAAAATTATATTTTTTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCG
130 AGGTAAAATTATATATATTTTCGGGTCGG--CGGTATTTTTCACCCTAAACCCGAACCCGACCCG
**
378508 AATACCACACTTAAAAAAACCCGACCCGAATATCACACTTAAAAAACCCGACCCG
193 AATACCACACTTAAAAAAACCCGACCAAAATATCACACTT---AAACCCGACCCG
378563 AATATATGAATTAGAAATCCGATCTGACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATA
1 AATATATGAATTAGAAA-CC---C-GACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATA
* *
378628 AAAACAGTGACTTAATTGAAAAAATA-TATATAGAGAGG-GGTATTATTGTAATTATTCCTAAAT
61 AAAACAGTGACTTAATTGAAAAAAAATTATATAGAGAGGAGAT-TTATTGTAATTATTCCTAAAT
*
378691 ATATTAGGTAAAATTATATATATTTTCGGGTC-G-GGTATTTTTCACCCTAAACCAC-AACTCGA
125 ATATAAGGTAAAATTATATATATTTTCGGGTCGGCGGTATTTTTCACCCTAAACC-CGAA--C--
* ** *
378753 CCTGACCCGAATATCACACTTAAAAAACCGACCCGACCAAAATAAAGTTTCACTT-GACCCGACC
185 CC-GACCCGAATACCACACTTAAAAAA---ACCCGACCAAAAT--A-TCACACTTAAACCCGACC
378817 CG
243 CG
*
378819 AATATATGAATTAGAAACCCGACCCGACCCGAAATAATAAAAAAAATATTTTTATTCAATA
1 AATATATGAATTAGAAACCCGACCCGACCCGAAATAAT-AAAAAATTATTTTTATTCAATA
378880 TATGAATAAG
Statistics
Matches: 277, Mismatches: 21, Indels: 36
0.83 0.06 0.11
Matches are distributed among these distances:
249 21 0.08
250 17 0.06
251 21 0.08
252 25 0.09
253 63 0.23
254 69 0.25
255 16 0.06
256 27 0.10
257 11 0.04
259 1 0.00
260 6 0.02
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (244 bp):
AATATATGAATTAGAAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATAAAAAC
AGTGACTTAATTGAAAAAAAATTATATAGAGAGGAGATTTATTGTAATTATTCCTAAATATATAA
GGTAAAATTATATATATTTTCGGGTCGGCGGTATTTTTCACCCTAAACCCGAACCCGACCCGAAT
ACCACACTTAAAAAAACCCGACCAAAATATCACACTTAAACCCGACCCG
Found at i:382793 original size:29 final size:30
Alignment explanation
Indices: 382761--382817 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
382751 ATATATAATC
*
382761 TAATATTAATACATATAATTAA-TAAAAAA
1 TAATATTAATACATATAATAAAGTAAAAAA
382790 TAATATTAATACATATAATAAAGTAAAA
1 TAATATTAATACATATAATAAAGTAAAA
382818 GTAATAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (30 bp):
TAATATTAATACATATAATAAAGTAAAAAA
Found at i:383117 original size:45 final size:45
Alignment explanation
Indices: 383058--383201 Score: 120
Period size: 41 Copynumber: 3.2 Consensus size: 45
383048 ATATTATACG
* *
383058 ATAAATTATTTTAATTCAAATATACTAAGAAAAA-ATTCCTACATA
1 ATAAATAATATTAATT-AAATATACTAAGAAAAAGATTCCTACATA
* * *
383103 ATAAATAATATTAATTTAATATATTAAGAAAAAGATTCGTAC---
1 ATAAATAATATTAATTAAATATACTAAGAAAAAGATTCCTACATA
* * * * *
383145 GT-AATAATATTAATTTAATATA-TAAAGAAAAATATTCATACGTA
1 ATAAATAATATTAATTAAATATACT-AAGAAAAAGATTCCTACATA
383189 ATAATATTAATAT
1 ATAA-A-TAATAT
383202 AATATATTAA
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
40 1 0.01
41 35 0.43
42 1 0.01
44 16 0.20
45 22 0.27
46 1 0.01
47 6 0.07
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (45 bp):
ATAAATAATATTAATTAAATATACTAAGAAAAAGATTCCTACATA
Found at i:383161 original size:41 final size:41
Alignment explanation
Indices: 383106--383215 Score: 177
Period size: 41 Copynumber: 2.7 Consensus size: 41
383096 CTACATAATA
*
383106 AATAATATTAATTTAATATATTAAGAAAAAGATTCGTACGT
1 AATAATATTAATTTAATATATTAAGAAAAAGATTCATACGT
* *
383147 AATAATATTAATTTAATATATAAAGAAAAATATTCATACGT
1 AATAATATTAATTTAATATATTAAGAAAAAGATTCATACGT
*
383188 AATAATATTAATATAATATATTAA-AAAA
1 AATAATATTAATTTAATATATTAAGAAAA
383216 TCCTACATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
40 4 0.06
41 60 0.94
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (41 bp):
AATAATATTAATTTAATATATTAAGAAAAAGATTCATACGT
Found at i:388056 original size:30 final size:30
Alignment explanation
Indices: 388001--388057 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
387991 CGAGTGATAT
* *
388001 ATCATTTAAAGTGATTACATGATATGTGTC
1 ATCAATTAAAGTGATTACATAATATGTGTC
388031 ATCAATTAAAGTGA-TACTATAATATGT
1 ATCAATTAAAGTGATTAC-ATAATATGT
388058 ATAACGTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (30 bp):
ATCAATTAAAGTGATTACATAATATGTGTC
Found at i:403042 original size:60 final size:61
Alignment explanation
Indices: 402968--403090 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 61
402958 AATTAAGTTT
* * * * * *
402968 ATCCCTAAATTATGA-ATATCATTCTAAATTAGTTCTCAAAC-TTTTAAATATTTCAATTTC
1 ATCCCCAAAATATGACAT-TCATTCTAAATTAGTCCCCAAACTTTTTAAACATTCCAATTTC
* *
403028 ATCCCCAAAATATGACATTCATTCTAAATTGGTCCCCAAACTTTTTGAACATTCCAATTTC
1 ATCCCCAAAATATGACATTCATTCTAAATTAGTCCCCAAACTTTTTAAACATTCCAATTTC
403089 AT
1 AT
403091 ACCAAACTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 33 0.62
61 20 0.38
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (61 bp):
ATCCCCAAAATATGACATTCATTCTAAATTAGTCCCCAAACTTTTTAAACATTCCAATTTC
Found at i:403096 original size:60 final size:60
Alignment explanation
Indices: 402978--403106 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
402968 ATCCCTAAAT
* * * * *
402978 TATGAATATCATTCTAAATTAGTTCTCAAACTTTTAAATATTTCAATTTCATCCCCAAAA
1 TATGAATATCATTCTAAATTAGTCCCCAAACTTTTAAACATTCCAATTTCATCACCAAAA
* * *
403038 TATGACAT-TCATTCTAAATTGGTCCCCAAACTTTTTGAACATTCCAATTTCAT-ACCAAAC
1 TATGA-ATATCATTCTAAATTAGTCCCCAAAC-TTTTAAACATTCCAATTTCATCACCAAAA
*
403098 TATGCATAT
1 TATGAATAT
403107 ATGCTAATCG
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
59 2 0.04
60 35 0.61
61 20 0.35
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (60 bp):
TATGAATATCATTCTAAATTAGTCCCCAAACTTTTAAACATTCCAATTTCATCACCAAAA
Found at i:403307 original size:60 final size:60
Alignment explanation
Indices: 403209--403488 Score: 313
Period size: 60 Copynumber: 4.7 Consensus size: 60
403199 TTACATATTT
** * * *
403209 GGATGAAATTGGAATATTCAAAAGTTTGAGGACCAATTTATAAAGATGGCCATAGTTTAG
1 GGATGAAATTATAATATTCAAAAGTTTAAGGACCAATTTAGAAAGATGGTCATAGTTTAG
** * *
403269 GGATGAAATTATAAT-TTGCAAAAGTTTAAGGATTAATTTAGAATGA-GAGTCATGGTTT-G
1 GGATGAAATTATAATATT-CAAAAGTTTAAGGACCAATTTAGAAAGATG-GTCATAGTTTAG
* *
403328 ACGATGAAATTATAATATTCAAAAGTTTGAGGACCAATTTAGAAAGATGGTCATAGTTTAG
1 -GGATGAAATTATAATATTCAAAAGTTTAAGGACCAATTTAGAAAGATGGTCATAGTTTAG
* *
403389 GGATGAAATTATAAT-TTACAAAAGTTTAAGGACTAATTTAGAATGA-GAGTCAT-GATTT-G
1 GGATGAAATTATAATATT-CAAAAGTTTAAGGACCAATTTAGAAAGATG-GTCATAG-TTTAG
* *
403448 ACGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTA
1 -GGATGAAATTATAATATTCAAAAGTTTAAGGACCAATTTA
403489 CAATGAGTGT
Statistics
Matches: 187, Mismatches: 22, Indels: 22
0.81 0.10 0.10
Matches are distributed among these distances:
59 9 0.05
60 172 0.92
61 6 0.03
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (60 bp):
GGATGAAATTATAATATTCAAAAGTTTAAGGACCAATTTAGAAAGATGGTCATAGTTTAG
Found at i:403426 original size:120 final size:120
Alignment explanation
Indices: 403210--403488 Score: 486
Period size: 120 Copynumber: 2.3 Consensus size: 120
403200 TACATATTTG
* *
403210 GATGAAATTGGAATATTCAAAAGTTTGAGGACCAATTTATAAAGATGGCCATAGTTTAGGGATGA
1 GATGAAATTAGAATATTCAAAAGTTTGAGGACCAATTTAGAAAGATGGCCATAGTTTAGGGATGA
* * *
403275 AATTATAATTTGCAAAAGTTTAAGGATTAATTTAGAATGAGAGTCATGGTTTGAC
66 AATTATAATTTACAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATGATTTGAC
* *
403330 GATGAAATTATAATATTCAAAAGTTTGAGGACCAATTTAGAAAGATGGTCATAGTTTAGGGATGA
1 GATGAAATTAGAATATTCAAAAGTTTGAGGACCAATTTAGAAAGATGGCCATAGTTTAGGGATGA
403395 AATTATAATTTACAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATGATTTGAC
66 AATTATAATTTACAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATGATTTGAC
*
403450 GATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTA
1 GATGAAATTAGAATATTCAAAAGTTTGAGGACCAATTTA
403489 CAATGAGTGT
Statistics
Matches: 150, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 150 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (120 bp):
GATGAAATTAGAATATTCAAAAGTTTGAGGACCAATTTAGAAAGATGGCCATAGTTTAGGGATGA
AATTATAATTTACAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATGATTTGAC
Found at i:405827 original size:21 final size:21
Alignment explanation
Indices: 405785--405827 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
405775 TTTCTAGGCT
* *
405785 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
405806 AGGGGAGTCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
405827 A
1 A
405828 TGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:406535 original size:23 final size:23
Alignment explanation
Indices: 406504--406564 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
406494 TATTATATGC
406504 CACTACGGTGCAATTCTACGCGG
1 CACTACGGTGCAATTCTACGCGG
* *
406527 CACTCCGGTGCAATTCTACGTGG
1 CACTACGGTGCAATTCTACGCGG
*
406550 CACTAAGGTGCAATT
1 CACTACGGTGCAATT
406565 ATTTGAGCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCGG
Done.