Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold202
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: 2706578
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 16
Found at i:193012 original size:19 final size:20
Alignment explanation
Indices: 192975--193012 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
192965 TCCCGTAGCC
192975 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
192995 ATGTATCGATAC-ATTCAT
1 ATGTATCGATACAATTCAT
193013 TTGAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:193063 original size:13 final size:13
Alignment explanation
Indices: 193045--193072 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
193035 CCGTTACAAG
193045 CAATGTATCGATA
1 CAATGTATCGATA
193058 CAATGTATCGATA
1 CAATGTATCGATA
193071 CA
1 CA
193073 TTGTCCTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:193148 original size:20 final size:20
Alignment explanation
Indices: 193122--193176 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
193112 CTGCCAATCT
*
193122 CATGTATCGATACAATTG-T
1 CATGTATCGATACAATTGAG
193141 CTATGTATCGATACAA-TGAG
1 C-ATGTATCGATACAATTGAG
193161 CATGTATCGATACAAT
1 CATGTATCGATACAAT
193177 GTATCGATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:193180 original size:13 final size:13
Alignment explanation
Indices: 193162--193188 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
193152 TACAATGAGC
193162 ATGTATCGATACA
1 ATGTATCGATACA
193175 ATGTATCGATACA
1 ATGTATCGATACA
193188 A
1 A
193189 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:193940 original size:38 final size:37
Alignment explanation
Indices: 193886--193960 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 37
193876 GTTTGTTCAC
* * * *
193886 CACCATTTAACTAATAAACTCAAATTTAAGTAAAAGAT
1 CACCACTTAACCAATAAACTCAAA-CTAAATAAAAGAT
193924 CACCACTTAACCAATAAACTCAAACTAAATAAAAGAT
1 CACCACTTAACCAATAAACTCAAACTAAATAAAAGAT
193961 AACAAGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 11 0.33
38 22 0.67
ACGTcount: A:0.52, C:0.20, G:0.04, T:0.24
Consensus pattern (37 bp):
CACCACTTAACCAATAAACTCAAACTAAATAAAAGAT
Found at i:194353 original size:14 final size:14
Alignment explanation
Indices: 194334--194362 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
194324 TATTCTCAAA
194334 TATTATCATGAAGG
1 TATTATCATGAAGG
194348 TATTATCATGAAGG
1 TATTATCATGAAGG
194362 T
1 T
194363 GTAGTTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (14 bp):
TATTATCATGAAGG
Found at i:194720 original size:45 final size:45
Alignment explanation
Indices: 194671--194797 Score: 191
Period size: 45 Copynumber: 2.8 Consensus size: 45
194661 TTGTTTAGTT
* *
194671 AGGATTATTAATTACTACTAGGACTGTGATTAGGATTGTCCTATC
1 AGGATTATTGATTACTATTAGGACTGTGATTAGGATTGTCCTATC
* * * *
194716 AGGATTATTGATTACTATTAGGACTGTGATTAGGCTTGTGCTGTT
1 AGGATTATTGATTACTATTAGGACTGTGATTAGGATTGTCCTATC
*
194761 AGGATTATTGATTACTATTAGGACTATGATTAGGATT
1 AGGATTATTGATTACTATTAGGACTGTGATTAGGATT
194798 ATCTTTGTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (45 bp):
AGGATTATTGATTACTATTAGGACTGTGATTAGGATTGTCCTATC
Found at i:195468 original size:28 final size:28
Alignment explanation
Indices: 195436--195503 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
195426 CTCCTTGTTA
195436 ATTTCTCTTCTTTTAATAATTCTTACTG
1 ATTTCTCTTCTTTTAATAATTCTTACTG
** * **
195464 ATTTCAT-TTCCCTTAATATTTCTTGTTG
1 ATTTC-TCTTCTTTTAATAATTCTTACTG
*
195492 ATTTCACTTCTT
1 ATTTCTCTTCTT
195504 CGGTCTTTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.19, C:0.19, G:0.04, T:0.57
Consensus pattern (28 bp):
ATTTCTCTTCTTTTAATAATTCTTACTG
Found at i:199760 original size:20 final size:20
Alignment explanation
Indices: 199652--199770 Score: 82
Period size: 20 Copynumber: 6.0 Consensus size: 20
199642 CGACAAAAAC
* *
199652 AGTAAATGTATTGATATATA
1 AGTAAATGTATCGATACATA
* *
199672 AGTGAATGTATCGATACATG
1 AGTAAATGTATCGATACATA
** * *
199692 CCTAAAATGTATTGATACAAA
1 AGT-AAATGTATCGATACATA
* * *
199713 ACT-ACTTTA-C-ATACTATCA
1 AGTAAATGTATCGATAC-AT-A
*
199732 AGGAAATGTATCGATACATA
1 AGTAAATGTATCGATACATA
199752 AGTAAATGTATCGATACAT
1 AGTAAATGTATCGATACAT
199771 TTTTACAATT
Statistics
Matches: 73, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
17 4 0.05
18 1 0.01
19 6 0.08
20 40 0.55
21 18 0.25
22 4 0.05
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (20 bp):
AGTAAATGTATCGATACATA
Found at i:199797 original size:14 final size:14
Alignment explanation
Indices: 199774--199805 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
199764 GATACATTTT
*
199774 TACAATTGTATCGA
1 TACAAATGTATCGA
199788 TACAAATGTATCGA
1 TACAAATGTATCGA
199802 TACA
1 TACA
199806 TTATGGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (14 bp):
TACAAATGTATCGA
Found at i:199861 original size:32 final size:32
Alignment explanation
Indices: 199757--199861 Score: 74
Period size: 32 Copynumber: 3.2 Consensus size: 32
199747 ACATAAGTAA
199757 ATGTATCGATACATTTTTACAATTGTATCGATAC
1 ATGTATCGATACATTTTT-CAA-TGTATCGATAC
** * *
199791 AAATGTATCGATACATTATGGGTT-TTTG-ACCCA-A-
1 --ATGTATCGATACATT-T---TTCAATGTATCGATAC
199825 ATGTATCGATACATTTTTCAATGTATCGATAC
1 ATGTATCGATACATTTTTCAATGTATCGATAC
199857 ATGTA
1 ATGTA
199862 GGCAATTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
28 2 0.04
29 2 0.04
30 3 0.06
31 2 0.04
32 20 0.38
35 1 0.02
36 18 0.34
37 3 0.06
40 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (32 bp):
ATGTATCGATACATTTTTCAATGTATCGATAC
Found at i:214835 original size:18 final size:19
Alignment explanation
Indices: 214814--214865 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
214804 CATCCTCCGC
214814 CAAAAAAAAACAAAAA-AA
1 CAAAAAAAAACAAAAATAA
*
214832 CAAAAATAAACAAAAATAA
1 CAAAAAAAAACAAAAATAA
* *
214851 -GAAAAACAACAAAAA
1 CAAAAAAAAACAAAAA
214866 GGGTCCGGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 27 0.93
19 2 0.07
ACGTcount: A:0.83, C:0.12, G:0.02, T:0.04
Consensus pattern (19 bp):
CAAAAAAAAACAAAAATAA
Found at i:214856 original size:10 final size:10
Alignment explanation
Indices: 214814--214850 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
214804 CATCCTCCGC
*
214814 CAAAAAAAAA
1 CAAAAATAAA
214824 C-AAAA-AAA
1 CAAAAATAAA
214832 CAAAAATAAA
1 CAAAAATAAA
214842 CAAAAATAA
1 CAAAAATAA
214851 GAAAAACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 4 0.16
9 8 0.32
10 13 0.52
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.05
Consensus pattern (10 bp):
CAAAAATAAA
Found at i:214865 original size:10 final size:9
Alignment explanation
Indices: 214816--214865 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
214806 TCCTCCGCCA
214816 AAAAAAAAC
1 AAAAAAAAC
214825 -AAAAAAAC
1 AAAAAAAAC
214833 AAAAATAAAC
1 AAAAA-AAAC
* *
214843 AAAAATAAG
1 AAAAAAAAC
*
214852 AAAAACAAC
1 AAAAAAAAC
214861 AAAAA
1 AAAAA
214866 GGGTCCGGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
8 8 0.23
9 18 0.51
10 9 0.26
ACGTcount: A:0.84, C:0.10, G:0.02, T:0.04
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:215932 original size:37 final size:37
Alignment explanation
Indices: 215891--215973 Score: 148
Period size: 37 Copynumber: 2.2 Consensus size: 37
215881 CCACAATCAT
215891 GCATTTGTGACATTCATAACATTTCATTTTGCATGAC
1 GCATTTGTGACATTCATAACATTTCATTTTGCATGAC
* *
215928 GCATTTATGACATTCATAACATTTCATTTTGCATGAT
1 GCATTTGTGACATTCATAACATTTCATTTTGCATGAC
215965 GCATTTGTG
1 GCATTTGTG
215974 CTTCATCTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (37 bp):
GCATTTGTGACATTCATAACATTTCATTTTGCATGAC
Found at i:216379 original size:29 final size:29
Alignment explanation
Indices: 216339--216834 Score: 636
Period size: 29 Copynumber: 17.3 Consensus size: 29
216329 CTCACCTTCC
216339 AAAGCCCACAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
216368 AAAGCCCACAAGTCAGTGGCACTCTTTTC-
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCA
216397 AAAGCCCACAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
216426 AAAGCCCACAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
*
216455 AAAGCCCACAAGCCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
216484 AAAGCCCACAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
* *
216513 AAAACCCACAAGTCAGTGGCACCCTTTTC-
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCA
*
216542 AAAGCCCACAAGTCAGTGGCACCCTTTTC-
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCA
216571 AAAGCCCACAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
* * * **
216600 AAAGCCCATAAGTTAGTGACA-CCCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
*
216628 AAAGCCCACAAGTCAATGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
* *
216657 AAAGCCCACAAGTCGGTGGCACCCTTTTC-
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCA
* * *
216686 AAAGCCCACAAGTCAGTGACAAC-CTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
* *
216714 GAAGCCCACAAGTTAGTGGCATC-TTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
* * * *
216742 AAAGCCCATAAGTTAGTGGCACCTTTT-T
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
* *
216770 AAAGCCCACAAGTCAGTGGCAAC-ATTC-
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
* * * *
216797 AAAGCCCATAAGGCAGTGGCAACCTTT-A
1 AAAGCCCACAAGTCAGTGGCATCTTTTCA
216825 AAAGCCCACA
1 AAAGCCCACA
216835 TAAGTTGGTG
Statistics
Matches: 415, Mismatches: 41, Indels: 23
0.87 0.09 0.05
Matches are distributed among these distances:
27 26 0.06
28 110 0.27
29 260 0.63
30 19 0.05
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTCA
Found at i:216916 original size:43 final size:43
Alignment explanation
Indices: 216854--216941 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
216844 GGCATCTTCT
* *
216854 TTTAAGTCCAATATCGCTGGCTTTGAATCAACATATTGGCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAACACATTGGCACC
* * * * *
216897 TTTAAGTCTAATGTTGCTGGCCTTGAATTAGCACATTGGCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAACACATTGGCACC
216940 TT
1 TT
216942 CACCTTTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (43 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAACACATTGGCACC
Found at i:216965 original size:49 final size:49
Alignment explanation
Indices: 216893--217039 Score: 170
Period size: 49 Copynumber: 3.0 Consensus size: 49
216883 AACATATTGG
* * *
216893 CACCTTTAAGTCTAATGTTGCTGGCCTTGAATTAGCACATTGGCACCTT
1 CACCTTTAAATCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTT
*
216942 CACCTTTAAATCCAATGTTGCTGGCCTTGAATCAGTACATTGGCACCTT
1 CACCTTTAAATCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTT
* ** * ** * *
216991 CATCTTTAAGCCCAATATCACTGGTCC-TAAATCAGCATATTGGCACCTT
1 CACCTTTAAATCCAATGTTGCTGG-CCTTGAATCAGCACATTGGCACCTT
217040 TATCACTCTT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 82 0.98
50 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.33
Consensus pattern (49 bp):
CACCTTTAAATCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTT
Found at i:222902 original size:21 final size:20
Alignment explanation
Indices: 222873--222911 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
222863 GGCTAGTGTG
*
222873 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
222894 GGGAGTGCCGGTCGCGAC
1 GGGACTGCCGGTCGCGAC
222912 TTCGTGGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.10, C:0.31, G:0.44, T:0.15
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:223376 original size:13 final size:13
Alignment explanation
Indices: 223358--223382 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223348 ATAATCCCCC
223358 TGTATCGATACAT
1 TGTATCGATACAT
223371 TGTATCGATACA
1 TGTATCGATACA
223383 AAGAATTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:250492 original size:13 final size:13
Alignment explanation
Indices: 250474--250499 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
250464 TTATCGAGGG
250474 GGAGAAAATCTTT
1 GGAGAAAATCTTT
250487 GGAGAAAATCTTT
1 GGAGAAAATCTTT
250500 TTAAATCGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
GGAGAAAATCTTT
Found at i:253154 original size:2 final size:2
Alignment explanation
Indices: 253149--253173 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
253139 ATTTTTTTGT
253149 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 T
253174 TAGTGATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:257277 original size:23 final size:23
Alignment explanation
Indices: 257245--257291 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
257235 GAATTTAATT
257245 AAAATACCTTGTAAAATCTAGAA
1 AAAATACCTTGTAAAATCTAGAA
* **
257268 AAAATGCCTTGTGGAATCTAGAA
1 AAAATACCTTGTAAAATCTAGAA
257291 A
1 A
257292 GACCTTTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.26
Consensus pattern (23 bp):
AAAATACCTTGTAAAATCTAGAA
Found at i:257847 original size:20 final size:20
Alignment explanation
Indices: 257807--257850 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
257797 TTAAGAGAAA
** *
257807 AGTTTAATTTGAATTAGATT
1 AGTTTAATTTGAACCAAATT
257827 AGTTTAATTTGAACCAAATT
1 AGTTTAATTTGAACCAAATT
257847 AGTT
1 AGTT
257851 CCAAACTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (20 bp):
AGTTTAATTTGAACCAAATT
Found at i:259809 original size:20 final size:20
Alignment explanation
Indices: 259781--259819 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
259771 TCAAAATCCC
*
259781 ATTTGCTTTATGAGTTTTTA
1 ATTTGCTTTATGAATTTTTA
* *
259801 ATTTTCTTTGTGAATTTTT
1 ATTTGCTTTATGAATTTTT
259820 CTCGTTGCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.05, G:0.13, T:0.64
Consensus pattern (20 bp):
ATTTGCTTTATGAATTTTTA
Found at i:259961 original size:165 final size:164
Alignment explanation
Indices: 259790--260121 Score: 379
Period size: 165 Copynumber: 2.0 Consensus size: 164
259780 CATTTGCTTT
* * *
259790 ATGAGTTTTTAATTTTCTTTGTGAATT-TTTCTCGTTGCT-AAAATAC-AAATTTTTTTGCTCTA
1 ATGAGTTATTAATTTTCTTT-TGAATTCTTT-T-GTT-CTCAAAATACAAAATTTTCTT-CTCCA
*
259852 TAAA-TTTTT-TGAAAAGATTTTTCTTGGTTTA-AAACTTTTAAAATTCATTAAATATCATCATT
61 TAAATTTTTTCTG-AAAGATTTTTATTGGTTTATAAA-TTTTAAAATTCATTAAATATCATCATT
* * * *
259914 TAATTATCATCAAATCAGTTTTGAAGAATTCCTTTTATTTC
124 TAATCACCATCAAATCAGTTTTGAAAAATTACTTTTATTTC
* * *
259955 ATGAGTTATTGATTTTCTTTTGAATTCCTTTTGTTTTCAAAATACAAAATTTTCTTCTCCGTAAA
1 ATGAGTTATTAATTTTCTTTTGAATT-CTTTTGTTCTCAAAATACAAAATTTTCTTCTCCATAAA
* * * * *
260020 TTTTTTCTGAACGATTTTTATTGTTTTATAAATTTTAAAATTTATTAAATATTATTATTTAATCA
65 TTTTTTCTGAAAGATTTTTATTGGTTTATAAATTTTAAAATTCATTAAATATCATCATTTAATCA
* * *
260085 CCATTAAATCGGTTTTGAAAAATTATTTTTATTTC
130 CCATCAAATCAGTTTTGAAAAATTACTTTTATTTC
260120 AT
1 AT
260122 CGAATTTTCA
Statistics
Matches: 141, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
163 1 0.01
164 23 0.16
165 109 0.77
166 8 0.06
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (164 bp):
ATGAGTTATTAATTTTCTTTTGAATTCTTTTGTTCTCAAAATACAAAATTTTCTTCTCCATAAAT
TTTTTCTGAAAGATTTTTATTGGTTTATAAATTTTAAAATTCATTAAATATCATCATTTAATCAC
CATCAAATCAGTTTTGAAAAATTACTTTTATTTC
Found at i:261984 original size:118 final size:118
Alignment explanation
Indices: 261776--262013 Score: 327
Period size: 118 Copynumber: 2.0 Consensus size: 118
261766 TTATCTTAAT
* * * * * **
261776 TTTTCAAGATTTTTGATATTCTTATGGTTTTCCATAGGGGTATAAATGTTTTCAAAACTTTTCGT
1 TTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAAGGATATAAAAATTTTCAAAACTTTTCGT
* * * * *
261841 TTCTTTTCCGTTCTCCATTAAGGTACGAAATGATTTTTTTTGGAAATTAAAAG
66 ATCTTTTCCGTTCTCCATTAAGGTACAAAATAAATTTTTTGGGAAATTAAAAG
261894 TTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAAGGATATAAAAATCTTT-AAAACTTTTCG
1 TTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAAGGATATAAAAAT-TTTCAAAACTTTTCG
*
261958 TATCTTTT-CGATTCTCTATTAAGGTACAAAATAAATTTTTTGGGAAATTAAAAG
65 TATCTTTTCCG-TTCTCCATTAAGGTACAAAATAAATTTTTTGGGAAATTAAAAG
262012 TT
1 TT
262014 AAATAAAAAT
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
117 2 0.02
118 100 0.95
119 3 0.03
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (118 bp):
TTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAAGGATATAAAAATTTTCAAAACTTTTCGT
ATCTTTTCCGTTCTCCATTAAGGTACAAAATAAATTTTTTGGGAAATTAAAAG
Found at i:262279 original size:141 final size:139
Alignment explanation
Indices: 261894--262279 Score: 510
Period size: 142 Copynumber: 2.7 Consensus size: 139
261884 AAATTAAAAG
** *
261894 TTTTCAAGATTTCTAATATTCCTATGGTTTTCCATAAGGATATAAAAATCTTTAAAACTTTTCGT
1 TTTTCAAGATTTCTAATATTCCTAT-GTTTTCTGTAAGG-TATAGAAATCTTTAAAACTTTTCGT
*
261959 ATCTTTTCGATTCTCTATTAAGGTACAAAATAAATTTTTTGGGAAATTAAAAGTTAAATAAAAAT
64 ATCTTTTCG-TTCTCTATTAAGGTACAAAATGAATTTTTTGGGAAATTAAAAGTTAAATAAAAAT
*
262024 TATTCTCTTAAT
128 TATTATCTTAAT
* * *
262036 TTATT-AAGATTTCTAATATTCCTATGATTTTCTGTAGGGGTATAGAAGTCTTCAAAACTTTTCG
1 TT-TTCAAGATTTCTAATATTCCTATG-TTTTCTGTA-AGGTATAGAAATCTTTAAAACTTTTCG
*
262100 TATCTTTTCGGTTCT-TCATTAAGGTACGAAATGAATTTTTT-GGAAATTAGAAA-TTAAATAAA
63 TATCTTTTC-GTTCTCT-ATTAAGGTACAAAATGAATTTTTTGGGAAATTA-AAAGTTAAATAAA
262162 AATTATTATCTTAAT
125 AATTATTATCTTAAT
* * * *
262177 TTTTCAAGATTTTTATTACTCCTATGTTTTCTGTATAGGTATAGAAATCTTTAAAACTTTTTGTA
1 TTTTCAAGATTTCTAATATTCCTATGTTTTCTGTA-AGGTATAGAAATCTTTAAAACTTTTCGTA
*
262242 TCTTTTCAGTTCTCTATTAAGATACAAAATGAGATTTT
65 TCTTTTC-GTTCTCTATTAAGGTACAAAATGA-ATTTT
262280 CTAAAGTTAT
Statistics
Matches: 215, Mismatches: 20, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
140 63 0.29
141 59 0.27
142 88 0.41
143 5 0.02
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (139 bp):
TTTTCAAGATTTCTAATATTCCTATGTTTTCTGTAAGGTATAGAAATCTTTAAAACTTTTCGTAT
CTTTTCGTTCTCTATTAAGGTACAAAATGAATTTTTTGGGAAATTAAAAGTTAAATAAAAATTAT
TATCTTAAT
Found at i:263893 original size:38 final size:38
Alignment explanation
Indices: 263850--263927 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
263840 GTGTTAACTA
*
263850 AATTTTGATTAATTTAGTTTCAACTAATATTTAATTAT
1 AATTTTGATTAATTTAGTTTCAACTAATATCTAATTAT
263888 AATTTTGATTAATTTAGTTTCAACTAATATCTAATTAT
1 AATTTTGATTAATTTAGTTTCAACTAATATCTAATTAT
263926 AA
1 AA
263928 CCCCTAGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.50
Consensus pattern (38 bp):
AATTTTGATTAATTTAGTTTCAACTAATATCTAATTAT
Found at i:264224 original size:42 final size:43
Alignment explanation
Indices: 264161--264338 Score: 218
Period size: 43 Copynumber: 4.2 Consensus size: 43
264151 AGGTGTCCCA
* * *
264161 GGTCAAAGTCAATAGGCAGACAAAAGGTAAAGAAGTTTCTTA-
1 GGTCAAAGTCGATGGGCAGACAAAAGGTAAAGAAGTCTCTTAG
* * *
264203 GGTCAAAATCGATGGGTAGACAAAGGGTAAAGAAGTCT-TCTAG
1 GGTCAAAGTCGATGGGCAGACAAAAGGTAAAGAAGTCTCT-TAG
** * *
264246 GGTCAAAGTCGACCGGTAGACAAAAGGTAAAGAAGTCTCTCAG
1 GGTCAAAGTCGATGGGCAGACAAAAGGTAAAGAAGTCTCTTAG
*
264289 GGTCAAAGTCGATGGGCAAACAAAAGGTAAAGAAGTCTCTT-G
1 GGTCAAAGTCGATGGGCAGACAAAAGGTAAAGAAGTCTCTTAG
*
264331 GGTTAAAG
1 GGTCAAAG
264339 CCAACTAGCA
Statistics
Matches: 116, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 42 0.36
43 72 0.62
44 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (43 bp):
GGTCAAAGTCGATGGGCAGACAAAAGGTAAAGAAGTCTCTTAG
Found at i:264400 original size:41 final size:41
Alignment explanation
Indices: 264178--264462 Score: 154
Period size: 43 Copynumber: 6.8 Consensus size: 41
264168 GTCAATAGGC
* * * * *
264178 AGACAAAAGGTAAAGAAGTTTCTTAGGTCAAA-ATCGATGGGT
1 AGACAAAAGGTAAAGAAGTCTCCTAGGTTAAAGCT-GA-CGGT
* * *
264220 AGACAAAGGGTAAAGAAGTCTTCTAGGGTCAAAG-TCGACCGGT
1 AGACAAAAGGTAAAGAAGTCTCCTA-GGTTAAAGCT-GA-CGGT
* * *
264263 AGACAAAAGGTAAAGAAGTCT-CTCAGGGTCAAAG-TCGATGGGC
1 AGACAAAAGGTAAAGAAGTCTCCT-A-GGTTAAAGCT-GA-CGGT
* * * **
264306 AAACAAAAGGTAAAGAAGTCTCTTGGGTTAAAGCCAAC--T
1 AGACAAAAGGTAAAGAAGTCTCCTAGGTTAAAGCTGACGGT
* *
264345 AGCAAATAAAGGTAAAGAAGTCTCCCAGGTTAAAGCTGACGGT
1 AG-ACA-AAAGGTAAAGAAGTCTCCTAGGTTAAAGCTGACGGT
* * * * *
264388 AGACAAAGGGTAAAGAA-T-TTCTTGAGTTGAAGCTGACGGGC
1 AGACAAAAGGTAAAGAAGTCTCCTAG-GTTAAAGCTGAC-GGT
* * * *
264429 AGACAAAGGGTCAAGAAGTCTCTTAGGTCAAAGC
1 AGACAAAAGGTAAAGAAGTCTCCTAGGTTAAAGC
264463 CAATGGGCCA
Statistics
Matches: 192, Mismatches: 38, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
39 4 0.02
40 14 0.07
41 57 0.30
42 40 0.21
43 76 0.40
44 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.20
Consensus pattern (41 bp):
AGACAAAAGGTAAAGAAGTCTCCTAGGTTAAAGCTGACGGT
Found at i:265257 original size:89 final size:90
Alignment explanation
Indices: 265105--265277 Score: 287
Period size: 89 Copynumber: 1.9 Consensus size: 90
265095 CAGCCTTCGT
*
265105 GATGCATCAATATCATCTAGCAATTGAAGGAAAAGGATATGACTAGGAAATGGATGGGCCACACC
1 GATGCATCAATATCATCTAGCAATTGAAGGAAAAAGATATGACTAGGAAATGGATGGGCCACACC
265170 TTTACCCTAAGGTATTTGGCTCTGG
66 TTTACCCTAAGGTATTTGGCTCTGG
* * *
265195 GATGCATCAATATCATCTCA-TAATT-AGGGAAAAAGATATGACTAGGAAATGGATGGGTCACAC
1 GATGCATCAATATCATCT-AGCAATTGAAGGAAAAAGATATGACTAGGAAATGGATGGGCCACAC
265258 CTTTACCCTAAGGTATTTGG
65 CTTTACCCTAAGGTATTTGG
265278 ATTTAATGCA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
89 55 0.71
90 22 0.28
91 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (90 bp):
GATGCATCAATATCATCTAGCAATTGAAGGAAAAAGATATGACTAGGAAATGGATGGGCCACACC
TTTACCCTAAGGTATTTGGCTCTGG
Found at i:269917 original size:20 final size:20
Alignment explanation
Indices: 269892--269967 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
269882 AAAAAGATAG
269892 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
* *
269912 AATGTATCGATACATTCATA
1 AATGTATCGATACATTGAAA
* *
269932 CATGTATCGATACAATGAAA
1 AATGTATCGATACATTGAAA
269952 AATGTATCGATACATT
1 AATGTATCGATACATT
269968 TGGGTAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:270909 original size:28 final size:28
Alignment explanation
Indices: 270799--271273 Score: 518
Period size: 28 Copynumber: 16.4 Consensus size: 28
270789 TTTTTAAAAA
* *
270799 GGTGCCACTAACTTGTGTAGGTTTTGAAGAG
1 GGTGCCACTGACTTGTG--GGCTTTGAA-AG
* *
270830 AGTTGCCACTAACTCGTGTGGGCTTTGAAAAG
1 -GGTGCCACTGACT--TGTGGGCTTTG-AAAG
* * *
270862 AGTTACCACTGGCTTGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
270891 GGTGCCACTGATTTATGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
270919 GGTGCCATTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
270947 GATGCCACTGACTTATGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
270976 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
271004 GATGCCACTAACTTGTGGGCATTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
271032 GATGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
271060 GATGCCACTGACTTGTGGGCTTTAAAAAG
1 GGTGCCACTGACTTGTGGGCTTT-GAAAG
* *
271089 AGTGCCACTGACTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
271117 GGTGCCACTGACTTGTTGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
271145 GGTGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
271174 AGTGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
271203 AGTTACCACCGACTCGTGTGGGCTTTGAAAG
1 -GGTGCCACTGACT--TGTGGGCTTTGAAAG
* * * *
271234 GGTACCACCGACTTGTGGGTTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
271262 GATGCCACTGAC
1 GGTGCCACTGAC
271274 CTTTTATTGG
Statistics
Matches: 387, Mismatches: 47, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
28 217 0.56
29 86 0.22
30 32 0.08
31 4 0.01
32 42 0.11
33 2 0.01
34 4 0.01
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:270998 original size:85 final size:85
Alignment explanation
Indices: 270799--271273 Score: 564
Period size: 85 Copynumber: 5.5 Consensus size: 85
270789 TTTTTAAAAA
* * * *
270799 GGTGCCACTAACTTGTGTAGGTTTTGAAGAGAGTTGCCACTAACTCGTGTGGGCTTTGAAAAGAG
1 GGTGCCACTGACTTGTG--GGCTTTGAA-A-AGGTGCCACTGACT--TGTGGGCTTTGAAAAG-G
* * *
270864 TTACCACTGGCTTGTGGGCTTTGAAAG
59 ATGCCACTGACTTGTGGGCTTTGAAAG
* * *
270891 GGTGCCACTGATTTATGGGCTTTGAAAAGGTGCCATTGACTTGTGGGCTTTG-AAAGGATGCCAC
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCAC
*
270955 TGACTTATGGGCTTTGAAAAG
66 TGACTTGTGGGCTTTG-AAAG
* * *
270976 AGTGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTAACTTGTGGGCATTG-AAAGGATGCCA
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCA
*
271039 CTAACTTGTGGGCTTTGAAAG
65 CTGACTTGTGGGCTTTGAAAG
* *
271060 GATGCCACTGACTTGTGGGCTTTAAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCA
1 GGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCA
*
271124 CTGACTTGTTGGCTTTGAAAG
65 CTGACTTGTGGGCTTTGAAAG
* *
271145 GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTTACC
1 GGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTGAAAAG-GATGCC
*
271210 ACCGACTCGTGTGGGCTTTGAAAG
64 ACTGACT--TGTGGGCTTTGAAAG
* * *
271234 GGTACCACCGACTTGTGGG-TTTTAAAAGGATGCCACTGAC
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGAC
271274 CTTTTATTGG
Statistics
Matches: 339, Mismatches: 34, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
84 50 0.15
85 178 0.53
86 18 0.05
87 10 0.03
88 29 0.09
89 32 0.09
90 8 0.02
92 14 0.04
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.29
Consensus pattern (85 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGGATGCCAC
TGACTTGTGGGCTTTGAAAG
Found at i:271000 original size:113 final size:115
Alignment explanation
Indices: 270795--271273 Score: 612
Period size: 113 Copynumber: 4.1 Consensus size: 115
270785 TTTTTTTTTA
* * * *
270795 AAAAGG-TGCCACTAACTTGTGTAGGTTTTGAAGAGAGTTGCCACTAACTCGTGTGGGCTTTGAA
1 AAAAGGATGCCACTGACTTGTG--GGCTTTGAA-AG-GATGCCACTGACT--TGTGGGCTTTGAA
* * *
270859 AAGAGTTACCACTGGCTTGTGGGCTTTGAAAGGGTGCCACTGATTTATGGGCTTTG
60 AAGAGTTACCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
270915 AAAAGG-TGCCATTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAAGAG-
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGT
* * * *
270978 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCATTG
66 TACCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
271028 -AAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAAGAG-
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGT
* * *
271091 TGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTTGGCTTTG
66 TACCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
271141 -AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAG
1 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAG
* * * *
271205 TTACCACCGACTCGTGTGGGCTTTGAAAGGGTACCACCGACTTGTGGG-TTTT
65 TTACCACTGACT--TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
271257 AAAAGGATGCCACTGAC
1 AAAAGGATGCCACTGAC
271274 CTTTTATTGG
Statistics
Matches: 319, Mismatches: 34, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
112 5 0.02
113 172 0.54
114 45 0.14
115 9 0.03
116 14 0.04
117 47 0.15
118 8 0.03
120 19 0.06
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (115 bp):
AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGT
TACCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:272215 original size:11 final size:10
Alignment explanation
Indices: 272199--272258 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 10
272189 CCCTTTTATG
272199 TTTTTTTGTT
1 TTTTTTTGTT
*
272209 ATTTTTTTCTT
1 -TTTTTTTGTT
272220 GGTTTTTTTGTT
1 --TTTTTTTGTT
272232 TTTTTGTT-TT
1 TTTTT-TTGTT
272242 TTTGTTTTGGTT
1 TTT-TTTT-GTT
272254 TTTTT
1 TTTTT
272259 GGGTATGAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
10 12 0.29
11 15 0.37
12 14 0.34
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:272232 original size:31 final size:30
Alignment explanation
Indices: 272192--272259 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 30
272182 TCTGGACCCC
*
272192 TTTTATGTTTTTTTGTTATTTTT-TTCTTGGT
1 TTTTTTGTTTTTTTGTT-TTTTTGTT-TTGGT
272223 TTTTTTGTTTTTTTGTTTTTTTGTTTTGGT
1 TTTTTTGTTTTTTTGTTTTTTTGTTTTGGT
272253 TTTTTTG
1 TTTTTTG
272260 GGTATGAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 17 0.49
31 18 0.51
ACGTcount: A:0.03, C:0.01, G:0.15, T:0.81
Consensus pattern (30 bp):
TTTTTTGTTTTTTTGTTTTTTTGTTTTGGT
Found at i:272249 original size:23 final size:24
Alignment explanation
Indices: 272198--272249 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
272188 CCCCTTTTAT
*
272198 GTTTTTTTGTTATTTT-TTTCTTG
1 GTTTTTTTGTTTTTTTGTTTCTTG
* *
272221 GTTTTTTTGTTTTTTTGTTTTTTT
1 GTTTTTTTGTTTTTTTGTTTCTTG
272245 GTTTT
1 GTTTT
272250 GGTTTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (24 bp):
GTTTTTTTGTTTTTTTGTTTCTTG
Found at i:272257 original size:16 final size:16
Alignment explanation
Indices: 272192--272259 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 16
272182 TCTGGACCCC
* *
272192 TTTTATGTTTTTTTGT
1 TTTTTTGTTTTGTTGT
272208 TATTTTT-TTCTTG--GT
1 T-TTTTTGTT-TTGTTGT
*
272223 TTTTTTGTTTTTTTGT
1 TTTTTTGTTTTGTTGT
272239 TTTTTTGTTTTG--GT
1 TTTTTTGTTTTGTTGT
272253 TTTTTTG
1 TTTTTTG
272260 GGTATGAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
14 16 0.37
15 5 0.12
16 16 0.37
17 6 0.14
ACGTcount: A:0.03, C:0.01, G:0.15, T:0.81
Consensus pattern (16 bp):
TTTTTTGTTTTGTTGT
Found at i:272260 original size:9 final size:8
Alignment explanation
Indices: 272192--272249 Score: 73
Period size: 8 Copynumber: 7.4 Consensus size: 8
272182 TCTGGACCCC
*
272192 TTTTATGT
1 TTTTTTGT
272200 TTTTTTGT
1 TTTTTTGT
*
272208 TATTTT-T
1 TTTTTTGT
* *
272215 TTCTTGGT
1 TTTTTTGT
272223 TTTTTTGT
1 TTTTTTGT
272231 TTTTTTGT
1 TTTTTTGT
272239 TTTTTTGT
1 TTTTTTGT
272247 TTT
1 TTT
272250 GGTTTTTTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
7 4 0.10
8 38 0.90
ACGTcount: A:0.03, C:0.02, G:0.12, T:0.83
Consensus pattern (8 bp):
TTTTTTGT
Found at i:286162 original size:20 final size:20
Alignment explanation
Indices: 286091--286165 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
286081 AAAAAGATAG
286091 AATGTATTGATACATTCATA
1 AATGTATTGATACATTCATA
*
286111 CATGT-TTCGATACATTCATA
1 AATGTATT-GATACATTCATA
* * * * *
286131 TATATATCGATACATTAAAA
1 AATGTATTGATACATTCATA
286151 AATGTATTGATACAT
1 AATGTATTGATACAT
286166 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 2 0.05
20 41 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (20 bp):
AATGTATTGATACATTCATA
Found at i:286226 original size:18 final size:18
Alignment explanation
Indices: 286203--286237 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
286193 TACATTGAAA
*
286203 AATGTATTGATACATTTC
1 AATGTATCGATACATTTC
286221 AATGTATCGATACATTT
1 AATGTATCGATACATTT
286238 GGGTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (18 bp):
AATGTATCGATACATTTC
Found at i:287160 original size:28 final size:28
Alignment explanation
Indices: 287120--287619 Score: 523
Period size: 28 Copynumber: 17.5 Consensus size: 28
287110 CACCAACTAG
*
287120 TGTGGACTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
287148 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
287176 TATGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
287204 TATGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
287233 TATGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
***
287261 TGTGGGCTTTGAAAAAATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
287289 TGTGGGCTTTGAATGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
287317 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
287346 TGTGGGCTTTGAAAGGGTGGCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
287374 TGTGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
287402 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * **
287430 TGTGGGCTTTGAAAAGAGTGCCATTGAGA
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
287459 AGTGGGCTTTGAAAAGAGTTACCACTGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* *
287489 CGTGTGGGCTTTGAAAAGAGTGCCACTAACT
1 --TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
287520 TGTGAGTTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
287548 TGTGAGCTTTGACAGGATGCCACTAACTT
1 TGTGGGCTTTGAAAGGGTGCCACTGAC-T
** * *
287577 GTGTGGGCTTTGAAAAAAGTGCCCCTAACT
1 -TGTGGGCTTTG-AAAGGGTGCCACTGACT
287607 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
287620 GAGATGAAAG
Statistics
Matches: 404, Mismatches: 59, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
28 253 0.63
29 98 0.24
30 18 0.04
31 20 0.05
32 15 0.04
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:287232 original size:85 final size:86
Alignment explanation
Indices: 287120--287619 Score: 582
Period size: 85 Copynumber: 5.8 Consensus size: 86
287110 CACCAACTAG
* * * *
287120 TGTGGACTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTAACTTATGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGC
*
287183 TTTGAAAGGATGCCACTAACT
66 TTTGAAAGGATGCCACTGACT
* * *
287204 TATGGGCTTTGAAAAGAGTGCCACTGACTTATGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGC
**
287268 TTTGAAAAAATGCCACTGACT
66 TTTGAAAGGATGCCACTGACT
** *
287289 TGTGGGCTTTGAATGGA-TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGC
* * *
287353 TTTGAAAGGGTGGCATTGACT
66 TTTGAAAGGATGCCACTGACT
* * * *
287374 TGTGGGCTTTG-AAAGGGTGCCATTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGC
* * **
287437 TTTGAAAAGAGTGCCATTGAGA
66 TTTGAAAGGA-TGCCACTGACT
* *
287459 AGTGGGCTTTGAAAAGAGTTACCACTGACTCGTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTG
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTG
* * *
287524 AGTTTTGAAAGGGTGCCACTGACT
63 GGCTTTGAAAGGATGCCACTGACT
* * * * * *
287548 TGTGAGCTTTGACAGGA-TGCCACTAACTTGTGTGGGCTTTGAAAAAAGTGCCCCTAACTTGTGG
1 TGTGGGCTTTGAAAAGAGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGG
287612 GCTTTGAA
64 GCTTTGAA
287620 GAGATGAAAG
Statistics
Matches: 352, Mismatches: 54, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
84 61 0.17
85 169 0.48
86 5 0.01
87 56 0.16
88 1 0.00
89 37 0.11
90 23 0.07
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.29
Consensus pattern (86 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGC
TTTGAAAGGATGCCACTGACT
Found at i:287295 original size:113 final size:113
Alignment explanation
Indices: 287077--287619 Score: 570
Period size: 113 Copynumber: 4.7 Consensus size: 113
287067 AAAAATGGTA
* * *
287077 CCACTAACTTGTGTGGGCTTTGAAAAGAGTTACCACCAAC-TAGTGTGGACTTTGAAAGGGTGCC
1 CCACTAAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTAACTTA-TG-GG-CTTTGAAAGGATGCC
** *
287141 ACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGATG
60 ACTGACTTGTGGGCTTTGAAAAAATGCCACTAACTTGTGGGCTTTGAAAGGATG
* * *
287195 CCACTAACTTATGGGCTTTGAAAAGAGTGCCACTGACTTATGGGCTTTGAAAGGATGCCACTAAC
1 CCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTATGGGCTTTGAAAGGATGCCACTGAC
* *
287260 TTGTGGGCTTTGAAAAAATGCCACTGACTTGTGGGCTTTGAATGGATG
66 TTGTGGGCTTTGAAAAAATGCCACTAACTTGTGGGCTTTGAAAGGATG
* * * *
287308 CCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGGCATTGAC
1 CCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTATGGGCTTTGAAAGGATGCCACTGAC
*** * *
287373 TTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTTGAAAGGATG
66 TTGTGGGCTTTGAAAAAATGCCACTAACTTGTGGGCTTTGAAAGGATG
* * * ** * *
287421 CCACTGACTTGTGGGCTTTGAAAAGAGTGCCATTGA-GAAGTGGGCTTTGAAAAGAGTTACCACT
1 CCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTA-TGGGCTTTG-AAAG-GATGCCACT
* * * *
287485 GACTCGTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGAGTTTTGAAAGGGTG
63 GACT--TGTGGGCTTTGAAAA-AATGCCACTAACTTGTGGGCTTTGAAAGGATG
* * * * * ** *
287539 CCACTGACTTGTGAGCTTTGACAGGA-TGCCACTAACTTGTGTGGGCTTTGAAAAAAGTGCCCCT
1 CCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAAC-T-TATGGGCTTTGAAAGGA-TGCCACT
*
287603 AACTTGTGGGCTTTGAA
63 GACTTGTGGGCTTTGAA
287620 GAGATGAAAG
Statistics
Matches: 360, Mismatches: 54, Indels: 24
0.82 0.12 0.05
Matches are distributed among these distances:
113 205 0.57
114 6 0.02
115 18 0.05
116 32 0.09
117 22 0.06
118 68 0.19
119 9 0.03
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (113 bp):
CCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTATGGGCTTTGAAAGGATGCCACTGAC
TTGTGGGCTTTGAAAAAATGCCACTAACTTGTGGGCTTTGAAAGGATG
Found at i:288698 original size:8 final size:8
Alignment explanation
Indices: 288665--288711 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
288655 CCACTTTCTA
288665 TTTTTTTG
1 TTTTTTTG
*
288673 TTATTTT-
1 TTTTTTTG
* *
288680 TTTCTTGG
1 TTTTTTTG
288688 TTTTTTTG
1 TTTTTTTG
288696 TTTTTTTGG
1 TTTTTTT-G
288705 TTTTTTT
1 TTTTTTT
288712 TGGGTATGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
7 4 0.13
8 19 0.61
9 8 0.26
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (8 bp):
TTTTTTTG
Found at i:288704 original size:17 final size:18
Alignment explanation
Indices: 288678--288711 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
288668 TTTTGTTATT
288678 TTTTTCTTGGTTTTTTTG
1 TTTTTCTTGGTTTTTTTG
288696 TTTTT-TTGGTTTTTTT
1 TTTTTCTTGGTTTTTTT
288712 TGGGTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (18 bp):
TTTTTCTTGGTTTTTTTG
Found at i:288714 original size:10 final size:9
Alignment explanation
Indices: 288678--288711 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
288668 TTTTGTTATT
288678 TTTTTCTTGG
1 TTTTT-TTGG
288688 TTTTTTT-G
1 TTTTTTTGG
288696 TTTTTTTGG
1 TTTTTTTGG
288705 TTTTTTT
1 TTTTTTT
288712 TGGGTATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 10 0.43
10 5 0.22
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (9 bp):
TTTTTTTGG
Found at i:304612 original size:20 final size:20
Alignment explanation
Indices: 304587--304756 Score: 110
Period size: 20 Copynumber: 7.9 Consensus size: 20
304577 GAAAAAAGAC
*
304587 AGAATGCATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
304607 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
304627 TAG-ATGTATCAACACATTGA
1 -AGAATGTATCGATACATTGA
*
304647 AAAATGTATCGATACATCTGGGTAAAAAAAA
1 AGAATGTATCGATACAT-T--G--------A
304678 TAGAATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* * *
304699 AAAATATATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
304719 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
304739 AAAATGTATCGATACATT
1 AGAATGTATCGATACATT
304757 TGGGTAAAAA
Statistics
Matches: 118, Mismatches: 16, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
19 2 0.02
20 91 0.77
21 5 0.04
23 1 0.01
29 1 0.01
31 2 0.02
32 16 0.14
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:304713 original size:92 final size:92
Alignment explanation
Indices: 304537--304767 Score: 349
Period size: 92 Copynumber: 2.5 Consensus size: 92
304527 TAATTTTAAC
* * *
304537 TAGATGTATCGATACATTGAAAAATATATCGATACATCT-AG-AAAAAAGACAGAATGCATCGAT
1 TAGATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAAAACAGAATGCATCGAT
* *
304600 ACATTGAAGAATGTATCGATACATTCA
66 ACATTGAAAAATATATCGATACATTCA
* * * *
304627 TAGATGTATCAACACATTGAAAAATGTATCGATACATCTGGGTAAAAAAAATAGAATGTATCGAT
1 TAGATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAAAACAGAATGCATCGAT
304692 ACATTGAAAAATATATCGATACATTCA
66 ACATTGAAAAATATATCGATACATTCA
* *
304719 TACATGTATCGATACATTGAAAAATGTATCGATACATTTGGGTAAAAAA
1 TAGATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAA
304768 GTGACTTTTC
Statistics
Matches: 126, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
90 36 0.29
91 1 0.01
92 89 0.71
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (92 bp):
TAGATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAAAACAGAATGCATCGAT
ACATTGAAAAATATATCGATACATTCA
Found at i:310826 original size:18 final size:19
Alignment explanation
Indices: 310803--310854 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
310793 CTACCACTAT
*
310803 TTGTATCGATACATG-GCA
1 TTGTATCGATACATGAGAA
310821 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGA-GAA
310841 TTGTATCGATACAT
1 TTGTATCGATACAT
310855 TTCTTCAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 15 0.48
20 16 0.52
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:321161 original size:19 final size:18
Alignment explanation
Indices: 321136--321203 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
321126 AATTCAACGA
321136 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
321154 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
321170 --TCTATCGATACATAAG
1 TTTGTATCGATACATAAG
321186 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
321204 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
18 1 0.02
19 26 0.63
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:321176 original size:32 final size:32
Alignment explanation
Indices: 321140--321200 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
321130 CAACGATTTG
*
321140 TATCGATACATAAGTGTTGTATCGATACAATC
1 TATCGATACATAAGTATTGTATCGATACAATC
321172 TATCGATACATAAGTATTGTATCGATACA
1 TATCGATACATAAGTATTGTATCGATACA
321201 TAATTAGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (32 bp):
TATCGATACATAAGTATTGTATCGATACAATC
Found at i:324836 original size:23 final size:23
Alignment explanation
Indices: 324817--324860 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
324807 AGAAAGTCAA
*
324817 AATAATTATCAAAAACAAGTAAC
1 AATAAGTATCAAAAACAAGTAAC
324840 AATAAGTATCAAAAACAAGTA
1 AATAAGTATCAAAAACAAGTA
324861 CGACTAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.61, C:0.11, G:0.07, T:0.20
Consensus pattern (23 bp):
AATAAGTATCAAAAACAAGTAAC
Found at i:328644 original size:15 final size:17
Alignment explanation
Indices: 328626--328657 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
328616 TGTTCATCAA
328626 CTTC-TTTTGGA-GCTT
1 CTTCATTTTGGATGCTT
328641 CTTCATTTTGGATGCTT
1 CTTCATTTTGGATGCTT
328658 TCATCTAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 7 0.47
17 4 0.27
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (17 bp):
CTTCATTTTGGATGCTT
Found at i:330385 original size:19 final size:19
Alignment explanation
Indices: 330361--330414 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
330351 ATTCAACGAT
*
330361 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTA
330380 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
330399 TTGTATCGATACATAA
1 TTGTATCGATACATAA
330415 TTAGCTACTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:336280 original size:19 final size:20
Alignment explanation
Indices: 336243--336280 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
336233 TCCCGTAGCT
336243 ATGTATCGATACAATTGATA
1 ATGTATCGATACAATTGATA
336263 ATGTATCGATAC-ATTGAT
1 ATGTATCGATACAATTGAT
336281 TTGAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTGATA
Found at i:336352 original size:13 final size:13
Alignment explanation
Indices: 336336--336360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
336326 CAATTCATCA
336336 TGTATCGATACAT
1 TGTATCGATACAT
336349 TGTATCGATACA
1 TGTATCGATACA
336361 ATGTCCATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:336434 original size:20 final size:20
Alignment explanation
Indices: 336408--336463 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
336398 ACTGCCAGTT
336408 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAATTGA
*
336427 TCCATGTATTGATACAA-TGA
1 T-CATGTATCGATACAATTGA
*
336447 TCACGTATCGATACAAT
1 TCATGTATCGATACAAT
336464 GTATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (20 bp):
TCATGTATCGATACAATTGA
Found at i:336469 original size:13 final size:13
Alignment explanation
Indices: 336451--336475 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
336441 CAATGATCAC
336451 GTATCGATACAAT
1 GTATCGATACAAT
336464 GTATCGATACAA
1 GTATCGATACAA
336476 AGCATAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:336935 original size:59 final size:59
Alignment explanation
Indices: 336843--336958 Score: 223
Period size: 59 Copynumber: 2.0 Consensus size: 59
336833 TTTATTTTTA
336843 AAAATATAAAAAAAATTGCATTTTTAAAAGGATATTTTGGTATAAGATTAGTCCGTATG
1 AAAATATAAAAAAAATTGCATTTTTAAAAGGATATTTTGGTATAAGATTAGTCCGTATG
*
336902 AAAATATAAAAAAAATTGCATTTTTAAAAGGATATTTTGTTATAAGATTAGTCCGTA
1 AAAATATAAAAAAAATTGCATTTTTAAAAGGATATTTTGGTATAAGATTAGTCCGTA
336959 AAACCCCTCT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (59 bp):
AAAATATAAAAAAAATTGCATTTTTAAAAGGATATTTTGGTATAAGATTAGTCCGTATG
Found at i:338616 original size:19 final size:20
Alignment explanation
Indices: 338585--338622 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
338575 GCTTTGATTG
*
338585 CTGTTGCTGCTTGTTGTTTA
1 CTGTTGCTGCTTGGTGTTTA
338605 CTGTTG-TGCTTGGTGTTT
1 CTGTTGCTGCTTGGTGTTT
338623 GTTGTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.03, C:0.13, G:0.29, T:0.55
Consensus pattern (20 bp):
CTGTTGCTGCTTGGTGTTTA
Found at i:338656 original size:25 final size:25
Alignment explanation
Indices: 338622--338681 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
338612 GCTTGGTGTT
338622 TGTTGTTGTTTTTTCTATTGCTTGC
1 TGTTGTTGTTTTTTCTATTGCTTGC
338647 TGTTGTTGTTTTTTCTATTGCTTGC
1 TGTTGTTGTTTTTTCTATTGCTTGC
338672 TGTTGTTGTT
1 TGTTGTTGTT
338682 GCTATGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.03, C:0.10, G:0.22, T:0.65
Consensus pattern (25 bp):
TGTTGTTGTTTTTTCTATTGCTTGC
Found at i:338898 original size:24 final size:25
Alignment explanation
Indices: 338867--338938 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 25
338857 TATCCGTTTC
338867 TCTTTTGCTATCGCTATTTCATTTT
1 TCTTTTGCTATCGCTATTTCATTTT
* *
338892 T-TTTTGCTA-CAGCTA-TCCGTTTT
1 TCTTTTGCTATC-GCTATTTCATTTT
*
338915 TCTTTTGCTATAGCTATTTCATTT
1 TCTTTTGCTATCGCTATTTCATTT
338939 GCTTTTTCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
23 8 0.21
24 24 0.63
25 6 0.16
ACGTcount: A:0.14, C:0.19, G:0.10, T:0.57
Consensus pattern (25 bp):
TCTTTTGCTATCGCTATTTCATTTT
Found at i:338959 original size:54 final size:52
Alignment explanation
Indices: 338857--339038 Score: 174
Period size: 52 Copynumber: 3.5 Consensus size: 52
338847 CTTGCTTTGA
* *
338857 TATCCGTTTCTCTTTTGCTATCGCTATTTCA---TTTTT-TTTTGCTACAGC
1 TATCCGTTTCTCTTTTGCTATAGCTATTTCATTTTTTTTCTTTTACTACAGC
* *
338905 TATCCGTTTTTCTTTTGCTATAGCTATTTCATTTGCTTTTTCTTTTACTGCAGC
1 TATCCGTTTCTCTTTTGCTATAGCTATTTCATTT--TTTTTCTTTTACTACAGC
* * * ** * **
338959 TATCTGTTTCTCCTTTGTTGCAGCTATTTCATTTTTTTTCTTTTACTTCAAT
1 TATCCGTTTCTCTTTTGCTATAGCTATTTCATTTTTTTTCTTTTACTACAGC
* ** *
339011 TGTCTATTTCTCCTTTGCTATAGCTATT
1 TATCCGTTTCTCTTTTGCTATAGCTATT
339039 ACTTATTTAT
Statistics
Matches: 110, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
48 29 0.26
52 38 0.35
53 5 0.05
54 38 0.35
ACGTcount: A:0.13, C:0.21, G:0.10, T:0.56
Consensus pattern (52 bp):
TATCCGTTTCTCTTTTGCTATAGCTATTTCATTTTTTTTCTTTTACTACAGC
Found at i:339310 original size:16 final size:16
Alignment explanation
Indices: 339291--339334 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
339281 TAATTCTTGA
339291 TTTTTTTATTTTAAT-
1 TTTTTTTATTTTAATC
*
339306 TTTTTTATATTATAATC
1 TTTTTT-TATTTTAATC
*
339323 ATTTTTTATTTT
1 TTTTTTTATTTT
339335 TATATTATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 6 0.25
16 13 0.54
17 5 0.21
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTTATTTTAATC
Found at i:339339 original size:24 final size:23
Alignment explanation
Indices: 339307--339356 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
339297 TATTTTAATT
*
339307 TTTTTATATTATAATCATTTTTTA
1 TTTTTATATTATAAT-ATATTTTA
*
339331 TTTTTATATTATCATATATTTTA
1 TTTTTATATTATAATATATTTTA
339354 TTT
1 TTT
339357 AATTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTTATATTATAATATATTTTA
Found at i:339357 original size:27 final size:25
Alignment explanation
Indices: 339297--339357 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 25
339287 TTGATTTTTT
*
339297 TATTTTAATT-TTTTTATATTATAA
1 TATTTTATTTATTTTTATATTATAA
339321 TCA-TTT-TTTATTTTTATATTATCATA
1 T-ATTTTATTTATTTTTATATTAT-A-A
339347 TATTTTATTTA
1 TATTTTATTTA
339358 ATTATTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
23 2 0.07
24 16 0.53
25 3 0.10
26 5 0.17
27 4 0.13
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (25 bp):
TATTTTATTTATTTTTATATTATAA
Found at i:339363 original size:23 final size:22
Alignment explanation
Indices: 339304--339363 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 22
339294 TTTTATTTTA
*
339304 ATTTT-TTTATATTATAATCATT
1 ATTTTATTTA-ATTATTATCATT
*
339326 -TTTTATTT-TTATATTATCATAT
1 ATTTTATTTAAT-TATTATCAT-T
339348 ATTTTATTTAATTATT
1 ATTTTATTTAATTATT
339364 TTATATCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
20 1 0.03
21 12 0.40
22 4 0.13
23 12 0.40
24 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTTATTTAATTATTATCATT
Found at i:339370 original size:27 final size:25
Alignment explanation
Indices: 339294--339371 Score: 61
Period size: 27 Copynumber: 2.9 Consensus size: 25
339284 TTCTTGATTT
*
339294 TTTTATTTTAATTTTTTTATATTATAA
1 TTTTA-TTTAA-TTTTTTATATCATAA
339321 TCATTT-TTT-ATTTTTATATTATCATATA
1 T--TTTATTTAATTTTT-TA-TATCATA-A
339349 TTTTATTTAATTATTTTATATCA
1 TTTTATTTAATT-TTTTATATCA
339372 AATAAACCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 16
0.71 0.02 0.27
Matches are distributed among these distances:
25 5 0.12
26 6 0.14
27 18 0.43
28 7 0.17
29 6 0.14
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTATTTAATTTTTTATATCATAA
Found at i:344150 original size:25 final size:25
Alignment explanation
Indices: 344122--344211 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
344112 TGGCAATAGT
344122 TGAAGAAACAAGCAACGACAACTGC
1 TGAAGAAACAAGCAACGACAACTGC
* * *
344147 TGAAGAAATAAGCAACGGCAGCTGC
1 TGAAGAAACAAGCAACGACAACTGC
** * ** *
344172 CAAAGAAGCAAGCAACGACATTTGA
1 TGAAGAAACAAGCAACGACAACTGC
*
344197 TGAAGAAGCAAGCAA
1 TGAAGAAACAAGCAA
344212 TGGCAAACAA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (25 bp):
TGAAGAAACAAGCAACGACAACTGC
Found at i:344433 original size:14 final size:14
Alignment explanation
Indices: 344414--344443 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
344404 AGAAAGAAAA
344414 AGAATTCTGTTTTT
1 AGAATTCTGTTTTT
344428 AGAATTCTGTTTTT
1 AGAATTCTGTTTTT
344442 AG
1 AG
344444 CAAAGTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (14 bp):
AGAATTCTGTTTTT
Found at i:350389 original size:201 final size:201
Alignment explanation
Indices: 349955--350593 Score: 867
Period size: 201 Copynumber: 3.1 Consensus size: 201
349945 TTTTAAAAAA
*
349955 GGTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACTAACTCGTGTGGGCTTTGAAAAGAG
1 GGTGCCACTGAC-T-TGTGGGCTTTG-AAAGAG-TGCCACTAACT--TGTGGGCTTTGAAAAG-G
* * * * *
350020 TTGCCACTGACTCGTGTGGGCTTTGAAAAGAGTTACCACTGGCTTGTGGGCTTTGAAAAGAGTGC
59 ATGCCACTGACT--TGTGGGCTTTGAAAAGAGTTGCCACTGACTCGTGGGCTTTGAAAGGA-TGC
* * *
350085 CACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTG-GGCTTT-AAAAG-GATGCCACTGA
121 CACTGACTTGTGGGCTTTAAAAAGGTGCCATTGACTTGTGTGGCTTTGAAAAGAG-TGCCACCGA
350147 CTTGTGGGCTTTGAAAG
185 CTTGTGGGCTTTGAAAG
* * * *
350164 GGTGCCACTGACTTGTGAGCTTTGAAAGAGTGCTACTGACTTGTGGGCTTTGAAATGG-TGCCAC
1 GGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGGATGCCAC
* *
350228 TGACTTGCGGGCTTTGAAAAGAGTTGCCACTGACTCATGGGCTTTGAAAGGATGCCACTGACTTG
66 TGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTG
* * *
350293 TGGGCTTTAAAAAGGTGCCATTGACTTGTGTGGCTTTGAAAAGAGTTGCCACCAACTCGGGGGCT
131 TGGGCTTTAAAAAGGTGCCATTGACTTGTGTGGCTTTGAAAAGAG-TGCCACCGACTTGTGGGCT
350358 TTGAAAG
195 TTGAAAG
* *
350365 GATGCCACTGACTTGTGGGCTTTGAAA-AGGTGCCACTAACTTGTGGG-TTTTAAAAGGATGCCA
1 GGTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTAACTTGTGGGCTTTGAAAAGGATGCCA
* *
350428 CTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGGGCTTTGAAAGGATGCCACTGATTT
65 CTGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTT
* * *
350493 GTGGGCTTTGAAAAGAGTTGCCATTGACTCGTGTGGGCTTTGAAAAGAGTGCCACCGACTTATGG
130 GTGGGCTTT-AAAA-AGGTGCCATTGACTTGTGT-GGCTTTGAAAAGAGTGCCACCGACTTGTGG
350558 GCTTTGAAAG
192 GCTTTGAAAG
350568 GGTGCCACTGACTTGTGGGCTTTGAA
1 GGTGCCACTGACTTGTGGGCTTTGAA
350594 GAGATGAATG
Statistics
Matches: 387, Mismatches: 35, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
198 41 0.11
199 47 0.12
200 14 0.04
201 150 0.39
202 5 0.01
203 79 0.20
204 14 0.04
205 9 0.02
206 6 0.02
207 10 0.03
208 1 0.00
209 11 0.03
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (201 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGGATGCCAC
TGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTTG
TGGGCTTTAAAAAGGTGCCATTGACTTGTGTGGCTTTGAAAAGAGTGCCACCGACTTGTGGGCTT
TGAAAG
Found at i:350591 original size:28 final size:28
Alignment explanation
Indices: 349955--350593 Score: 657
Period size: 28 Copynumber: 21.9 Consensus size: 28
349945 TTTTAAAAAA
*
349955 GGTGCCACTAACTTGTGTGGGCTTTGAAAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTG-AAAG
* *
349986 AGTTGCCACTAACTCGTGTGGGCTTTGAAAAG
1 -GGTGCCACTGACT--TGTGGGCTTTG-AAAG
*
350018 AGTTGCCACTGACTCGTGTGGGCTTTGAAAAG
1 -GGTGCCACTGACT--TGTGGGCTTTG-AAAG
* * *
350050 AGTTACCACTGGCTTGTGGGCTTTGAAAAG
1 -GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
350080 AGTGCCACTGACTTGTGGGCTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
350108 GGTGCCACTGACTTGTGGGCTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
350136 GATGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
350164 GGTGCCACTGACTTGTGAGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
350192 AGTGCTACTGACTTGTGGGCTTTGAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
350220 GGTGCCACTGACTTGCGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* **
350249 AGTTGCCACTGACTCATGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
350278 GATGCCACTGACTTGTGGGCTTTAAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
350306 GGTGCCATTGACTTGTGTGGCTTTGAAAAG
1 GGTGCCACTGACTTGTG-GGCTTTG-AAAG
* ** * *
350336 AGTTGCCACCAACTCGGGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
350365 GATGCCACTGACTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
350393 GGTGCCACTAACTTGTGGGTTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
350421 GATGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
350450 AGTTGCCACCGACTCGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
350479 GATGCCACTGATTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
350508 AGTTGCCATTGACTCGTGTGGGCTTTGAAAAG
1 -GGTGCCACTGACT--TGTGGGCTTTG-AAAG
* * *
350540 AGTGCCACCGACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
350568 GGTGCCACTGACTTGTGGGCTTTGAA
1 GGTGCCACTGACTTGTGGGCTTTGAA
350594 GAGATGAATG
Statistics
Matches: 521, Mismatches: 74, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
28 278 0.53
29 58 0.11
30 77 0.15
31 21 0.04
32 87 0.17
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:351842 original size:9 final size:9
Alignment explanation
Indices: 351828--351887 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
351818 TTGGGTTATT
351828 TTTTTTTTG
1 TTTTTTTTG
*
351837 -TTTTTTTA
1 TTTTTTTTG
*
351845 TTTTTTAT-
1 TTTTTTTTG
*
351853 TTTTTTTGG
1 TTTTTTTTG
* *
351862 TTTTTTCTA
1 TTTTTTTTG
*
351871 TTTTTTTGG
1 TTTTTTTTG
351880 TTTTTTTT
1 TTTTTTTT
351888 AGGTATGAAG
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
8 13 0.34
9 25 0.66
ACGTcount: A:0.05, C:0.02, G:0.08, T:0.85
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:351845 original size:19 final size:19
Alignment explanation
Indices: 351823--351877 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
351813 TTTTTTTGGG
351823 TTATTTTTT-TTTTGTTTTT
1 TTATTTTTTATTTT-TTTTT
*
351842 TTATTTTTTATTTTTTTTGG
1 TTATTTTTTATTTTTTTT-T
*
351862 TT-TTTTCTATTTTTTT
1 TTATTTTTTATTTTTTT
351878 GGTTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 26 0.81
20 6 0.19
ACGTcount: A:0.07, C:0.02, G:0.05, T:0.85
Consensus pattern (19 bp):
TTATTTTTTATTTTTTTTT
Found at i:351848 original size:18 final size:18
Alignment explanation
Indices: 351813--351886 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 18
351803 CCCCTTTCTG
* *
351813 TTTTTTTGGGTTATTTTTT
1 TTTTTTTTGGTT-TTTTTA
**
351832 TTTTGTTTTTTTATTTTTTA
1 TTTT-TTTTGGT-TTTTTTA
351852 TTTTTTTTGGTTTTTTCTA
1 TTTTTTTTGGTTTTTT-TA
351871 -TTTTTTTGGTTTTTTT
1 TTTTTTTTGGTTTTTTT
351887 TAGGTATGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.02
18 20 0.43
19 11 0.24
20 13 0.28
21 1 0.02
ACGTcount: A:0.05, C:0.01, G:0.11, T:0.82
Consensus pattern (18 bp):
TTTTTTTTGGTTTTTTTA
Found at i:351852 original size:26 final size:26
Alignment explanation
Indices: 351827--351876 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
351817 TTTGGGTTAT
*
351827 TTTTTTTTTGTTTTTT-TATTTTTTA
1 TTTTTTTTGGTTTTTTCTATTTTTTA
351852 TTTTTTTTGGTTTTTTCTATTTTTT
1 TTTTTTTTGGTTTTTTCTATTTTTT
351877 TGGTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.06, C:0.02, G:0.06, T:0.86
Consensus pattern (26 bp):
TTTTTTTTGGTTTTTTCTATTTTTTA
Found at i:366023 original size:51 final size:51
Alignment explanation
Indices: 365960--366075 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
365950 TTATTTTTGA
** *
365960 GGGGATACTCCAACTTTGGTTTTA-TTTCTAAAACACTAATTTTTCATAATT
1 GGGGATACTCCAACTCCGATTTTATTTTC-AAAACACTAATTTTTCATAATT
* * * *
366011 GGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCACAGTC
1 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCATAATT
*
366062 AGGGATACTCCAAC
1 GGGGATACTCCAAC
366076 CCCGTTATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 51 0.93
52 4 0.07
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCATAATT
Found at i:366024 original size:79 final size:78
Alignment explanation
Indices: 365820--366009 Score: 238
Period size: 79 Copynumber: 2.4 Consensus size: 78
365810 TAGATAAAAT
* * *
365820 GTTTTATTT-TCAAAACATCAATTGTTCATAATCGAGGATTCTCCAATCCCGTTATTTCTGAGGG
1 GTTTTATTTCT-AAAACAT-AATTTTTCATAATCGAGGATTCTCCAACCCCATTATTTCTGAGGG
365884 GATACTCCAACCCCG
64 GATACTCCAACCCCG
* * * * *
365899 ATTTTATTCCCAAAACAATAATTTTTCAGAATCGAGGATTCTCCAACCCCATTATTTTTGAGGGG
1 GTTTTATTTCTAAAAC-ATAATTTTTCATAATCGAGGATTCTCCAACCCCATTATTTCTGAGGGG
***
365964 ATACTCCAACTTTG
65 ATACTCCAACCCCG
365978 GTTTTATTTCTAAAACACTAATTTTTCATAAT
1 GTTTTATTTCTAAAACA-TAATTTTTCATAAT
366010 TGGGGATATT
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
78 1 0.01
79 90 0.97
80 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (78 bp):
GTTTTATTTCTAAAACATAATTTTTCATAATCGAGGATTCTCCAACCCCATTATTTCTGAGGGGA
TACTCCAACCCCG
Found at i:366096 original size:28 final size:27
Alignment explanation
Indices: 366062--366135 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
366052 TTTCACAGTC
366062 AGGGATACTCCAACCCCGTTATTTCATCG
1 AGGGATACTCCAACCCCGTTATTT--TCG
*
366091 A-GGATACTCTAACCCCGTTATTTTCG
1 AGGGATACTCCAACCCCGTTATTTTCG
*
366117 AGGAGATACTCCAATCCCG
1 AGG-GATACTCCAACCCCG
366136 GCTTTATTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
26 4 0.10
27 1 0.03
28 34 0.85
29 1 0.03
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (27 bp):
AGGGATACTCCAACCCCGTTATTTTCG
Found at i:366184 original size:79 final size:80
Alignment explanation
Indices: 366087--366293 Score: 212
Period size: 79 Copynumber: 2.6 Consensus size: 80
366077 CCGTTATTTC
* * * *
366087 ATCGAGGATACTCTAACCCCGTTATTTTCGAGGAGATACTCCAATCCC-GGCTTTATTTCTAAAA
1 ATCGAGGATACTCCAACCCCGTTATTTTCGAGGAGATACTCCAAGCCCTGACCTTATTTCTAAAA
* *
366151 TATTGA-TTTCTCAAA
66 CATCGATTTTC-CAAA
** *
366166 ATCGAGGATACTCCAACCCTATTATTTTTGCG-GGA-ATACTCC-AGCCCTGACCTTATTTTTAA
1 ATCGAGGATACTCCAACCCCGTTA-TTTT-CGAGGAGATACTCCAAGCCCTGACCTTATTTCTAA
*
366228 AGCATCGATTTTCCAAA
64 AACATCGATTTTCCAAA
* * *
366245 ATCG-GGAATACTCCAACTCCGTTATTTTTGAGGGGATACTCCAA-CCCTG
1 ATCGAGG-ATACTCCAACCCCGTTATTTTCGAGGAGATACTCCAAGCCCTG
366294 TTATTTTCGA
Statistics
Matches: 105, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
77 1 0.01
78 12 0.11
79 78 0.74
80 12 0.11
81 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (80 bp):
ATCGAGGATACTCCAACCCCGTTATTTTCGAGGAGATACTCCAAGCCCTGACCTTATTTCTAAAA
CATCGATTTTCCAAA
Found at i:366289 original size:28 final size:28
Alignment explanation
Indices: 366252--366318 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
366242 AAAATCGGGA
*
366252 ATACTCCAACTCC-GTTATTTTTGAGGGG
1 ATACTCCAAC-CCTGTTATTTTCGAGGGG
366280 ATACTCCAACCCTGTTATTTTCGAGGGG
1 ATACTCCAACCCTGTTATTTTCGAGGGG
*
366308 ATACTTCAACC
1 ATACTCCAACC
366319 TCGATTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 2 0.06
28 34 0.94
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (28 bp):
ATACTCCAACCCTGTTATTTTCGAGGGG
Found at i:369581 original size:14 final size:15
Alignment explanation
Indices: 369558--369595 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
369548 AAATTTTATC
369558 TTAA-TTTTTA-AAT
1 TTAATTTTTTACAAT
*
369571 TTTATTTTTTACAAT
1 TTAATTTTTTACAAT
369586 TTAATTTTTT
1 TTAATTTTTT
369596 TATTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 3 0.14
14 6 0.29
15 12 0.57
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTAATTTTTTACAAT
Found at i:370062 original size:22 final size:22
Alignment explanation
Indices: 370037--370078 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
370027 GAAAAGAAGG
* *
370037 CAATTCCTACAATGGAGAAAAA
1 CAATTACTACAATGAAGAAAAA
*
370059 CAATTACTGCAATGAAGAAA
1 CAATTACTACAATGAAGAAA
370079 GTAACGGCTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (22 bp):
CAATTACTACAATGAAGAAAAA
Found at i:370153 original size:25 final size:25
Alignment explanation
Indices: 370119--370271 Score: 153
Period size: 25 Copynumber: 6.1 Consensus size: 25
370109 CAAGACAGTA
* **
370119 AAGCAAGCAACGGTAGCAACTGAAG
1 AAGCAAGCAACGGCAGCTGCTGAAG
* *
370144 AAGCAAGCAATGGCAGCTGTTGAAG
1 AAGCAAGCAACGGCAGCTGCTGAAG
* *
370169 AAGCAAGCAACGACAGTTGCTGAAG
1 AAGCAAGCAACGGCAGCTGCTGAAG
* ** *
370194 AAGCAAGCAATGATAGCTACTGAAG
1 AAGCAAGCAACGGCAGCTGCTGAAG
* * * *
370219 AAGTAAGCAATGGCAGCAGCTAAAG
1 AAGCAAGCAACGGCAGCTGCTGAAG
* *
370244 AAGCAAGCAACGGCATCTGATGAAG
1 AAGCAAGCAACGGCAGCTGCTGAAG
370269 AAG
1 AAG
370272 GAAGTAACAG
Statistics
Matches: 103, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 103 1.00
ACGTcount: A:0.42, C:0.18, G:0.28, T:0.12
Consensus pattern (25 bp):
AAGCAAGCAACGGCAGCTGCTGAAG
Found at i:370178 original size:50 final size:50
Alignment explanation
Indices: 370119--370271 Score: 173
Period size: 50 Copynumber: 3.1 Consensus size: 50
370109 CAAGACAGTA
* * *
370119 AAGCAAGCAACGGTAGCAACTGAAGAAGCAAGCAATGGCAGCTGTTGAAG
1 AAGCAAGCAACGGCAGCAGCTGAAGAAGCAAGCAATGGCAGCTGATGAAG
* ** **
370169 AAGCAAGCAACGACAGTTGCTGAAGAAGCAAGCAATGATAGCT-ACTGAAG
1 AAGCAAGCAACGGCAGCAGCTGAAGAAGCAAGCAATGGCAGCTGA-TGAAG
* * * * *
370219 AAGTAAGCAATGGCAGCAGCTAAAGAAGCAAGCAACGGCATCTGATGAAG
1 AAGCAAGCAACGGCAGCAGCTGAAGAAGCAAGCAATGGCAGCTGATGAAG
370269 AAG
1 AAG
370272 GAAGTAACAG
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
50 82 0.99
51 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.28, T:0.12
Consensus pattern (50 bp):
AAGCAAGCAACGGCAGCAGCTGAAGAAGCAAGCAATGGCAGCTGATGAAG
Found at i:370268 original size:75 final size:75
Alignment explanation
Indices: 370119--370271 Score: 209
Period size: 75 Copynumber: 2.0 Consensus size: 75
370109 CAAGACAGTA
* * * *
370119 AAGCAAGCAACGGTAGCAACTGAAGAAGCAAGCAATGGCAGCTGTTGAAGAAGCAAGCAACGACA
1 AAGCAAGCAACGATAGCAACTGAAGAAGCAAGCAATGGCAGCAGCTAAAGAAGCAAGCAACGACA
*
370184 GTTGCTGAAG
66 GTTGATGAAG
* * * *
370194 AAGCAAGCAATGATAGCTACTGAAGAAGTAAGCAATGGCAGCAGCTAAAGAAGCAAGCAACGGCA
1 AAGCAAGCAACGATAGCAACTGAAGAAGCAAGCAATGGCAGCAGCTAAAGAAGCAAGCAACGACA
370259 -TCTGATGAAG
66 GT-TGATGAAG
370269 AAG
1 AAG
370272 GAAGTAACAG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 1 0.01
75 67 0.99
ACGTcount: A:0.42, C:0.18, G:0.28, T:0.12
Consensus pattern (75 bp):
AAGCAAGCAACGATAGCAACTGAAGAAGCAAGCAATGGCAGCAGCTAAAGAAGCAAGCAACGACA
GTTGATGAAG
Found at i:370718 original size:25 final size:25
Alignment explanation
Indices: 370688--370741 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
370678 CAGCAACACG
370688 ATAGCAACTGATGGAAGAAAAAACA
1 ATAGCAACTGATGGAAGAAAAAACA
** * *
370713 ATAGCAGTTGATGGAAGAAGAAATA
1 ATAGCAACTGATGGAAGAAAAAACA
370738 ATAG
1 ATAG
370742 AAGCATGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.07, G:0.24, T:0.17
Consensus pattern (25 bp):
ATAGCAACTGATGGAAGAAAAAACA
Found at i:370813 original size:33 final size:33
Alignment explanation
Indices: 370710--370842 Score: 88
Period size: 33 Copynumber: 3.9 Consensus size: 33
370700 GGAAGAAAAA
* * *
370710 ACAATAGCAGTTGATGGAAGAAGAAATAATAGAAGC
1 ACAATAGCACTTGATGGACG-A-AAA-AATAGCAGC
** * ** * * *
370746 ATGATAGCAATTGATGGGGGAAGAGATAGTAGC
1 ACAATAGCACTTGATGGACGAAAAAATAGCAGC
370779 ACAATAGCAGC-TGATGGACGAAAAAATAGCAGC
1 ACAATAGCA-CTTGATGGACGAAAAAATAGCAGC
* * * *
370812 ACAATGGCACTTGGTGGAGGAAAAAAAAGCA
1 ACAATAGCACTTGATGGACGAAAAAATAGCA
370843 ACAGCTGATG
Statistics
Matches: 75, Mismatches: 20, Indels: 7
0.74 0.20 0.07
Matches are distributed among these distances:
32 1 0.01
33 56 0.75
34 2 0.03
35 1 0.01
36 15 0.20
ACGTcount: A:0.44, C:0.11, G:0.29, T:0.16
Consensus pattern (33 bp):
ACAATAGCACTTGATGGACGAAAAAATAGCAGC
Found at i:371988 original size:19 final size:19
Alignment explanation
Indices: 371964--372000 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
371954 TTTGTATCGA
371964 TTCATTGTATCGATACATG
1 TTCATTGTATCGATACATG
371983 TTCATTGTATCGATACAT
1 TTCATTGTATCGATACAT
372001 TGACAATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (19 bp):
TTCATTGTATCGATACATG
Found at i:376267 original size:13 final size:13
Alignment explanation
Indices: 376249--376274 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
376239 CAATTTTTTG
376249 TGTATCGATACAT
1 TGTATCGATACAT
376262 TGTATCGATACAT
1 TGTATCGATACAT
376275 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:382713 original size:21 final size:21
Alignment explanation
Indices: 382684--382728 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
382674 AAGTTTTCAT
*
382684 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
382704 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
382726 TTT
1 TTT
382729 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:384964 original size:13 final size:13
Alignment explanation
Indices: 384946--384971 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
384936 CAACTTTTTG
384946 TGTATCGATACAT
1 TGTATCGATACAT
384959 TGTATCGATACAT
1 TGTATCGATACAT
384972 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:390196 original size:20 final size:19
Alignment explanation
Indices: 390150--390203 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
390140 ACATTATGCT
* **
390150 TTGTATTGATACATGTTCA
1 TTGTATCGATACATGGACA
*
390169 TTGAATCGATACATGGACAA
1 TTGTATCGATACATGGAC-A
390189 TTGTATCGATACATG
1 TTGTATCGATACATG
390204 AAACTGGCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGGACA
Found at i:390267 original size:13 final size:13
Alignment explanation
Indices: 390249--390278 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
390239 GATATAGGGC
390249 ACATTGTATCGAT
1 ACATTGTATCGAT
390262 ACATTGTATCGAT
1 ACATTGTATCGAT
390275 ACAT
1 ACAT
390279 GATGAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:391095 original size:13 final size:13
Alignment explanation
Indices: 391077--391101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
391067 ATATTGCATA
391077 GTATCGATACATT
1 GTATCGATACATT
391090 GTATCGATACAT
1 GTATCGATACAT
391102 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:397132 original size:8 final size:8
Alignment explanation
Indices: 397119--397144 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
397109 ATTTGATTAA
397119 ATTTTGTG
1 ATTTTGTG
397127 ATTTTGTG
1 ATTTTGTG
397135 ATTTTGTG
1 ATTTTGTG
397143 AT
1 AT
397145 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:397365 original size:13 final size:13
Alignment explanation
Indices: 397347--397371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
397337 TAGCATTCTC
397347 TGTATCGATACAT
1 TGTATCGATACAT
397360 TGTATCGATACA
1 TGTATCGATACA
397372 AAGGGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:397538 original size:20 final size:20
Alignment explanation
Indices: 397503--397544 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
397493 AAAATTTCTT
397503 ATTTTTCACTTCAAAATACATC
1 ATTTTTCAC-TCAAAAT-CATC
397525 ATTTTTCA-TCAAAATCATC
1 ATTTTTCACTCAAAATCATC
397544 A
1 A
397545 ACAAAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTTTCACTCAAAATCATC
Found at i:399850 original size:13 final size:13
Alignment explanation
Indices: 399832--399856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
399822 ATATTGCACA
399832 GTATCGATACATT
1 GTATCGATACATT
399845 GTATCGATACAT
1 GTATCGATACAT
399857 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:399974 original size:13 final size:13
Alignment explanation
Indices: 399956--400013 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
399946 TACACACAAG
399956 ATGTATCGATACA
1 ATGTATCGATACA
399969 ATGTATCGATAC-
1 ATGTATCGATACA
* *
399981 A--T-CCCA-A-A
1 ATGTATCGATACA
399989 ATGTATCGATACA
1 ATGTATCGATACA
400002 ATGTATCGATAC
1 ATGTATCGATAC
400014 GTCCCAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 2 0.06
11 2 0.06
12 2 0.06
13 25 0.71
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:399993 original size:20 final size:20
Alignment explanation
Indices: 399968--400035 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
399958 GTATCGATAC
399968 AATGTATCGATACATCCCAA
1 AATGTATCGATACATCCCAA
399988 AATGTATCGAT--A---C--
1 AATGTATCGATACATCCCAA
*
400001 AATGTATCGATACGTCCCAA
1 AATGTATCGATACATCCCAA
400021 AATGTATCGATACAT
1 AATGTATCGATACAT
400036 TGGCTTGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
13 11 0.28
15 1 0.03
18 2 0.05
20 25 0.64
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACATCCCAA
Found at i:399998 original size:33 final size:33
Alignment explanation
Indices: 399938--400034 Score: 160
Period size: 33 Copynumber: 3.0 Consensus size: 33
399928 CTTAACTGTT
* *
399938 TGTATCGATACA-CACAAGATGTATCGATACAA
1 TGTATCGATACATCCCAAAATGTATCGATACAA
399970 TGTATCGATACATCCCAAAATGTATCGATACAA
1 TGTATCGATACATCCCAAAATGTATCGATACAA
*
400003 TGTATCGATACGTCCCAAAATGTATCGATACA
1 TGTATCGATACATCCCAAAATGTATCGATACA
400035 TTGGCTTGTA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 12 0.20
33 49 0.80
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACATCCCAAAATGTATCGATACAA
Found at i:403573 original size:110 final size:112
Alignment explanation
Indices: 403370--403583 Score: 265
Period size: 110 Copynumber: 1.9 Consensus size: 112
403360 AACTTGGAAG
* * * **
403370 AACATCAAATTTGTTTGATTTTTGAAGAAATTCATAGTTTATACATTCTGATCCATTTGTGCCTA
1 AACATCAAATTTGTCTAATTTTTGAAGAAATTCATAGTTTATACATTATGATCCATTCATGCCTA
* ** *
403435 GGAAAATGGGGCACTTATCTTATGAGTTTTGAAATTTTTGAGCTAAC
66 GGAAAATGGGGCACTTACCCAATCAGTTTTGAAATTTTTGAGCTAAC
* * **
403482 AACATTAAATTTGTCTAATTTTTGAA-AAATTCATATTTTATAC-TATATGATTTA-TCATGCCT
1 AACATCAAATTTGTCTAATTTTTGAAGAAATTCATAGTTTATACAT-TATGATCCATTCATGCCT
403544 AGGAAAATGGGGCA-TGTACCCAATCAGTTTTGAAATTTTT
65 AGGAAAATGGGGCACT-TACCCAATCAGTTTTGAAATTTTT
403584 AGGCCAACCA
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
109 1 0.01
110 41 0.47
111 22 0.25
112 23 0.26
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (112 bp):
AACATCAAATTTGTCTAATTTTTGAAGAAATTCATAGTTTATACATTATGATCCATTCATGCCTA
GGAAAATGGGGCACTTACCCAATCAGTTTTGAAATTTTTGAGCTAAC
Found at i:404656 original size:92 final size:91
Alignment explanation
Indices: 404430--404766 Score: 381
Period size: 92 Copynumber: 3.7 Consensus size: 91
404420 GGAGAGGGTG
* * *
404430 CAGACCACACATTCCTAATCATATTCCTTTTATCCAACCACTAGATAGTATTGATGCTTCACAAA
1 CAGACCACACATTCCTAATCATA-TCCCTTTATCCAACCACTAGATGGTATTGATGCATCACAAA
* *
404495 GCCTGATTTCCTTGGGGC-AAG-GATG
65 GCCTGATTTCCTTGGGGCAAAGATATC
* * * *
404520 CAGACCACATATTCCTAATCATATCTTCTTTATCCAATCGCTAGATGGTATTGATGCATCACAAA
1 CAGACCACACATTCCTAATCATATC-CCTTTATCCAACCACTAGATGGTATTGATGCATCACAAA
* * * *
404585 GCCTAATTTTCTCGAGGCAAAGATATC
65 GCCTGATTTCCTTGGGGCAAAGATATC
* * *
404612 CCGGCCACACATTCCCAATCATATCCCTTTAATCCAACCACTAGATGGTATTGATGCATCACAAA
1 CAGACCACACATTCCTAATCATATCCCTTT-ATCCAACCACTAGATGGTATTGATGCATCACAAA
* * *
404677 ACCCGATTTCCTTGGGGCAAGGATATC
65 GCCTGATTTCCTTGGGGCAAAGATATC
* * * * * ** *
404704 CAAACGACTCATTCTTAATCATATCCCTTTCTTTTAGCCACTAGATGGTATTGATGCATCACA
1 CAGACCACACATTCCTAATCATATCCCTTT-ATCCAACCACTAGATGGTATTGATGCATCACA
404767 TGACCACAAA
Statistics
Matches: 204, Mismatches: 39, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
89 2 0.01
90 69 0.34
91 7 0.03
92 126 0.62
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (91 bp):
CAGACCACACATTCCTAATCATATCCCTTTATCCAACCACTAGATGGTATTGATGCATCACAAAG
CCTGATTTCCTTGGGGCAAAGATATC
Found at i:405523 original size:85 final size:85
Alignment explanation
Indices: 405382--405632 Score: 267
Period size: 85 Copynumber: 3.0 Consensus size: 85
405372 GTTCATTCTT
* * ** *
405382 GGTCAACCCATTGATCCTTTGTTTACCTATCGACTTAGTATCGGGTAAATCCTTTTATCTTTTGT
1 GGTCAACCCTTTCATCCTTTGTTTACCTATCGACTTAGTATCAAGTAAATCCTTTTATCCTTTGT
*
405447 TGAGTTATCGATTCAATCCC
66 TGACTTATCGATTCAATCCC
* * * * * * *
405467 GGTTAACTCTTTCATCCTTTGTTTACCTATTGGCTTATTCTCAAGTAAATCTTTTTATCCTTTGT
1 GGTCAACCCTTTCATCCTTTGTTTACCTATCGACTTAGTATCAAGTAAATCCTTTTATCCTTTGT
* **
405532 TGACTTATCGGTTCAATCTT
66 TGACTTATCGATTCAATCCC
* * ***
405552 GGTCAACCCTTTTATCCTTTGTTTACCTATC-AGC-TAGTCTTGGGTAAATCC-TTTATCCTTTG
1 GGTCAACCCTTTCATCCTTTGTTTACCTATCGA-CTTAGTATCAAGTAAATCCTTTTATCCTTTG
405614 TTGACTTATC-AGTTCAATC
65 TTGACTTATCGA-TTCAATC
405633 TTGGCAATTT
Statistics
Matches: 137, Mismatches: 27, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
83 28 0.20
84 12 0.09
85 97 0.71
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.45
Consensus pattern (85 bp):
GGTCAACCCTTTCATCCTTTGTTTACCTATCGACTTAGTATCAAGTAAATCCTTTTATCCTTTGT
TGACTTATCGATTCAATCCC
Found at i:405605 original size:42 final size:41
Alignment explanation
Indices: 405511--405636 Score: 128
Period size: 42 Copynumber: 3.0 Consensus size: 41
405501 TTATTCTCAA
* * * *
405511 GTAAATCTTTTTATCCTTTGTTGACTTATCGGTTCAATCTTG
1 GTAAATCCTTTTATCCTTTGTTGACCTATCAGCT-AATCTTG
* * * *
405553 GTCAACCCTTTTATCCTTTGTTTACCTATCAGCTAGTCTTGG
1 GTAAATCCTTTTATCCTTTGTTGACCTATCAGCTAATCTT-G
* *
405595 GTAAATCC-TTTATCCTTTGTTGACTTATCAGTTCAATCTTG
1 GTAAATCCTTTTATCCTTTGTTGACCTATCAGCT-AATCTTG
405636 G
1 G
405637 CAATTTTTTC
Statistics
Matches: 68, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
41 29 0.43
42 39 0.57
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46
Consensus pattern (41 bp):
GTAAATCCTTTTATCCTTTGTTGACCTATCAGCTAATCTTG
Found at i:405680 original size:83 final size:83
Alignment explanation
Indices: 405363--405752 Score: 229
Period size: 85 Copynumber: 4.7 Consensus size: 83
405353 ATAATTAATC
* * * * * * **
405363 GACTTTTCAGTTCATTCTTGGTCAACCCATTGATCCTTTGTTTACCTATC-GACTTAGTATCGGG
1 GACTTATCAGTTCAATCTTGGTCAACCCTTTTATCATGTGTTTACCTATCAG-C-TAGCCTCGGG
*
405427 TAAATCCTTTTATCTTTTGTT
64 TAAATCC-TTTATCCTTTGTT
* ** * * * * * ** ** **
405448 GAGTTATC-GATTCAATCCCGGTTAACTCTTTCATCCTTTGTTTACCTATTGGCTTATTCTCAAG
1 GACTTATCAG-TTCAATCTTGGTCAACCCTTTTATCATGTGTTTACCTATCAGC-TAGCCTCGGG
*
405512 TAAATCTTTTTATCCTTTGTT
64 TAAATC-CTTTATCCTTTGTT
* * * * *
405533 GACTTATCGGTTCAATCTTGGTCAACCCTTTTATCCTTTGTTTACCTATCAGCTAGTCTTGGGTA
1 GACTTATCAGTTCAATCTTGGTCAACCCTTTTATCATGTGTTTACCTATCAGCTAGCCTCGGGTA
405598 AATCCTTTATCCTTTGTT
66 AATCCTTTATCCTTTGTT
** * *
405616 GACTTATCAGTTCAATCTTGG-CAA-TTTTTTCATCATGTGTTTACTTGTC-GACTTAGCCTCGG
1 GACTTATCAGTTCAATCTTGGTCAACCCTTTT-ATCATGTGTTTACCTATCAG-C-TAGCCTCGG
* *
405678 GTAAA-CCATTTTATCCTCTATT
63 GTAAATCC--TTTATCCTTTGTT
* * * * * * * *
405700 GGCTTGTCAGTTTAATC-TAGTCAA-CCTTTGTATCCTATATCTACCTATCAGCT
1 GACTTATCAGTTCAATCTTGGTCAACCCTTT-TATCATGTGTTTACCTATCAGCT
405753 TATTCTTAGG
Statistics
Matches: 241, Mismatches: 52, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
81 5 0.02
82 20 0.08
83 48 0.20
84 57 0.24
85 109 0.45
86 2 0.01
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (83 bp):
GACTTATCAGTTCAATCTTGGTCAACCCTTTTATCATGTGTTTACCTATCAGCTAGCCTCGGGTA
AATCCTTTATCCTTTGTT
Found at i:406750 original size:20 final size:20
Alignment explanation
Indices: 406725--406762 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
406715 CAAAATCCTT
*
406725 TTTTCTTTATGAGTTTTTAA
1 TTTTCTTTATGAATTTTTAA
*
406745 TTTTCTTTGTGAATTTTT
1 TTTTCTTTATGAATTTTT
406763 CGTTGCTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (20 bp):
TTTTCTTTATGAATTTTTAA
Found at i:407931 original size:11 final size:10
Alignment explanation
Indices: 407898--407949 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
407888 AAGTAGAGAA
*
407898 AAAAAGAGAG
1 AAAAAGAAAG
*
407908 TAAAAGAAAG
1 AAAAAGAAAG
407918 AAAAAGAAAGG
1 AAAAAGAAA-G
*
407929 AAAAAAGAGAG
1 -AAAAAGAAAG
407940 AAAATAGAAA
1 AAAA-AGAAA
407950 AAATAAGCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
10 20 0.59
11 6 0.18
12 8 0.24
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:408842 original size:141 final size:138
Alignment explanation
Indices: 408690--409332 Score: 731
Period size: 139 Copynumber: 4.6 Consensus size: 138
408680 TAGGATTTTT
* *
408690 ATATTCCTATGGGTATCCGTA-AGGGTATAAAAGTCTTCAAAATTTCTCGTATCTTTTCAGTTCT
1 ATATTCCTATGGTTTTCCGTAGA-GGTATAAAA-TCTTCAAAATTT-TCGTATCTTTTCAGTTCT
408754 CCATTAAGGTATGAAATGATTTTTTTAGAGATTAAAAATTAAATAAAAATTATTATCTTAATTTT
63 CCATTAAGGTATGAAATGATTTTTTTAGA-ATTAAAAATTAAATAAAAATTATTATCTTAATTTT
*
408819 TCAAGATTTTTA
127 TCAAGATTTCTA
* *
408831 ATATTCCTATGGTTTTCCGTA-ATGGGTATAAAAGTCTT-AAAACTTTTCTTATCTTTTCAGTTT
1 ATATTCCTATGGTTTTCCGTAGA--GGTATAAAA-TCTTCAAAA-TTTTCGTATCTTTTCAGTTC
* * *
408894 TTCATTAAGGTATGAAATAATTTTTTTA-AATTAAAAATTAAATAAAAATTATTATTTTAATTTT
62 TCCATTAAGGTATGAAATGATTTTTTTAGAATTAAAAATTAAATAAAAATTATTATCTTAATTTT
*
408958 TTAAGATTTCTA
127 TCAAGATTTCTA
* * * * *
408970 ATATTCCTATGGTTTTTCATAGAGGTATAACAATTTTCGAAACTTTTCGTATTTTTTCAGTTCTC
1 ATATTCCTATGGTTTTCCGTAGAGGTATAA-AATCTTC-AAAATTTTCGTATCTTTTCAGTTCTC
* * * *
409035 CATTAAGGTACGAAATGATTTTTTTATAATTAAAAA-TAAATAAAAATGATTATCTTAATTTCTC
64 CATTAAGGTATGAAATGATTTTTTTAGAATTAAAAATTAAATAAAAATTATTATCTTAATTTTTC
* *
409099 AAAATTTGTA
129 AAGATTTCTA
* * *
409109 ATATTCCTATGGTTTTCCGTAGAGGAATAGAAATCTTTAAAATTTTTCGTATCTTTT-TGATTCT
1 ATATTCCTATGGTTTTCCGTAGAGGTATA-AAATCTTCAAAA-TTTTCGTATCTTTTCAG-TTCT
* * * ** * * *
409173 CCATCAAGATATGAAATAAAATTTTTAGAAATTAGAAATTAAATAAAAAGTATTGTCTTAATTTT
63 CCATTAAGGTATGAAATGATTTTTTTAG-AATTAAAAATTAAATAAAAATTATTATCTTAATTTT
*
409238 TCAAGATTCCTA
127 TCAAGATTTCTA
* * * * * * *
409250 ATATTCTTATGGTTTTTCGTAGTGGTATAAAAATCTTTAAAACTTTTTGTATTTTTTTAGTTCTC
1 ATATTCCTATGGTTTTCCGTAGAGGTAT-AAAATCTTCAAAA-TTTTCGTATCTTTTCAGTTCTC
* *
409315 CATTAAGTTACGAAATGA
64 CATTAAGGTATGAAATGA
409333 GATTTTTGAA
Statistics
Matches: 428, Mismatches: 60, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
138 14 0.03
139 208 0.49
140 23 0.05
141 163 0.38
142 20 0.05
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (138 bp):
ATATTCCTATGGTTTTCCGTAGAGGTATAAAATCTTCAAAATTTTCGTATCTTTTCAGTTCTCCA
TTAAGGTATGAAATGATTTTTTTAGAATTAAAAATTAAATAAAAATTATTATCTTAATTTTTCAA
GATTTCTA
Found at i:409214 original size:280 final size:279
Alignment explanation
Indices: 408713--409332 Score: 813
Period size: 280 Copynumber: 2.2 Consensus size: 279
408703 TATCCGTAAG
* * * *
408713 GGTATAAAAGTCTTCAAAA-TTTCTCGTATCTTTTCAGTTCTCCATTAAGGTATGAAATGATTTT
1 GGTATAAAAATCTTTAAAACTTT-TCGTATTTTTTCAGTTCTCCATTAAGGTACGAAATGATTTT
* * * *
408777 TTTAGAGATTAAAAATTAAATAAAAATTATTATCTTAATTTTTCAAGATTTTTAATATTCCTATG
65 TTTAGAGATTAAAAATTAAATAAAAATGATTATCTTAATTTCTCAAAATTTGTAATATTCCTATG
* * * * * *
408842 GTTTTCCGTAATGGGTATAAAAGTCTTAAAACTTTTCTTATCTTTTCAGTTTTTCATTAAGGTAT
130 GTTTTCCGTAA-GGGAATAAAAGTCTTAAAACTTTTCGTATCTTTTCAGTTCTCCATCAAGATAT
** * * * *
408907 GAAATAATTTTTTTAAATTAAAAATTAAATAAAAATTATTATTTTAATTTTTTAAGATTTCTAAT
194 GAAATAATTTTTAGAAATTAAAAATTAAATAAAAAGTATTATCTTAATTTTTCAAGATTCCTAAT
408972 ATTCCTATGGTTTTTCATAGA
259 ATTCCTATGGTTTTTCATAGA
* *
408993 GGTATAACAAT-TTTCGAAACTTTTCGTATTTTTTCAGTTCTCCATTAAGGTACGAAATGATTTT
1 GGTATAAAAATCTTT-AAAACTTTTCGTATTTTTTCAGTTCTCCATTAAGGTACGAAATGATTTT
*
409057 TTTATA-ATTAAAAA-TAAATAAAAATGATTATCTTAATTTCTCAAAATTTGTAATATTCCTATG
65 TTTAGAGATTAAAAATTAAATAAAAATGATTATCTTAATTTCTCAAAATTTGTAATATTCCTATG
* *
409120 GTTTTCCGT-AGAGGAATAGAAA-TCTTTAAAATTTTTCGTATCTTTT-TGATTCTCCATCAAGA
130 GTTTTCCGTAAG-GGAATA-AAAGTC-TTAAAACTTTTCGTATCTTTTCAG-TTCTCCATCAAGA
* *
409182 TATGAAATAAAATTTTTAGAAATTAGAAATTAAATAAAAAGTATTGTCTTAATTTTTCAAGATTC
191 TATGAAAT--AATTTTTAGAAATTAAAAATTAAATAAAAAGTATTATCTTAATTTTTCAAGATTC
* * *
409247 CTAATATTCTTATGGTTTTTCGTAGT
254 CTAATATTCCTATGGTTTTTCATAGA
* * *
409273 GGTATAAAAATCTTTAAAACTTTTTGTATTTTTTTAGTTCTCCATTAAGTTACGAAATGA
1 GGTATAAAAATCTTTAAAACTTTTCGTATTTTTTCAGTTCTCCATTAAGGTACGAAATGA
409333 GATTTTTGAA
Statistics
Matches: 296, Mismatches: 35, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
276 1 0.00
277 9 0.03
278 93 0.31
279 10 0.03
280 177 0.60
281 6 0.02
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (279 bp):
GGTATAAAAATCTTTAAAACTTTTCGTATTTTTTCAGTTCTCCATTAAGGTACGAAATGATTTTT
TTAGAGATTAAAAATTAAATAAAAATGATTATCTTAATTTCTCAAAATTTGTAATATTCCTATGG
TTTTCCGTAAGGGAATAAAAGTCTTAAAACTTTTCGTATCTTTTCAGTTCTCCATCAAGATATGA
AATAATTTTTAGAAATTAAAAATTAAATAAAAAGTATTATCTTAATTTTTCAAGATTCCTAATAT
TCCTATGGTTTTTCATAGA
Found at i:412417 original size:22 final size:21
Alignment explanation
Indices: 412384--412425 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
412374 CATCTCCATG
412384 AATGTCATTCATTGTCTTCTTA
1 AATGTCATTCA-TGTCTTCTTA
*
412406 AATGTTCA-TCATGTTTTCTT
1 AATG-TCATTCATGTCTTCTT
412426 GGTCAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 8 0.44
22 7 0.39
23 3 0.17
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (21 bp):
AATGTCATTCATGTCTTCTTA
Found at i:424796 original size:19 final size:21
Alignment explanation
Indices: 424774--424821 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
424764 TAGAATAACA
424774 TAAAAAAAAC-AAAAAA-AGG
1 TAAAAAAAACAAAAAAATAGG
*
424793 TAAAAAAACCAAAAAAATAGG
1 TAAAAAAAACAAAAAAATAGG
424814 TAAAAAAA
1 TAAAAAAA
424822 TGAAAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 9 0.35
20 6 0.23
21 11 0.42
ACGTcount: A:0.77, C:0.06, G:0.08, T:0.08
Consensus pattern (21 bp):
TAAAAAAAACAAAAAAATAGG
Found at i:426396 original size:50 final size:50
Alignment explanation
Indices: 426269--426464 Score: 171
Period size: 50 Copynumber: 3.9 Consensus size: 50
426259 AAATATTTTT
* * * * * *
426269 TCTTTAAATCCGATATCGCTGGCCTTGAATCAACACATTA--ACACTTTTA
1 TCTTTAAGTCCAATATCACTAGCCTTGAATCAGCACATTAGCACAC-TTCA
** * * * *
426318 TTTTCTTTAAACCCAATGTCACTGGCCTTAAATCAGCACTTTAGCACACTTCA
1 ---TCTTTAAGTCCAATATCACTAGCCTTGAATCAGCACATTAGCACACTTCA
* * * *
426371 TCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCACATTGGCATACTTCG
1 TCTTTAAGTCCAATATCACTAGCCTTGAATCAGCACATTAGCACACTTCA
* * *
426421 TCTTTAAGTCCAATATCATTAGCCTTGAATCAGCATATTGGCAC
1 TCTTTAAGTCCAATATCACTAGCCTTGAATCAGCACATTAGCAC
426465 TTTCTATTAG
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
50 80 0.67
52 33 0.28
53 3 0.03
54 4 0.03
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.34
Consensus pattern (50 bp):
TCTTTAAGTCCAATATCACTAGCCTTGAATCAGCACATTAGCACACTTCA
Found at i:426502 original size:53 final size:50
Alignment explanation
Indices: 426342--426516 Score: 174
Period size: 50 Copynumber: 3.4 Consensus size: 50
426332 AATGTCACTG
* * * *
426342 GCCTTAAATCAGCACTTTAGCACACTTCA-TCTTTAAGTCCAATATCGCTA
1 GCCTTGAATCAGCACATTGGCATACTT-AGTCTTTAAGTCCAATATCGCTA
* **
426392 GCCTTGAATCAGCACATTGGCATACTTCGTCTTTAAGTCCAATATCATTA
1 GCCTTGAATCAGCACATTGGCATACTTAGTCTTTAAGTCCAATATCGCTA
* * * * *
426442 GCCTTGAATCAGCATATTGGCACTTTCTATTAG-CTTTAAGCCCAATGTCGCCA
1 GCCTTGAATCAGCACATTGGCA--TAC--TTAGTCTTTAAGTCCAATATCGCTA
*
426495 GCCTTGAATCAACACATTGGCA
1 GCCTTGAATCAGCACATTGGCA
426517 GTTTTCTCAT
Statistics
Matches: 103, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
50 63 0.61
52 2 0.02
53 35 0.34
54 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.31
Consensus pattern (50 bp):
GCCTTGAATCAGCACATTGGCATACTTAGTCTTTAAGTCCAATATCGCTA
Found at i:426617 original size:52 final size:52
Alignment explanation
Indices: 426561--426669 Score: 164
Period size: 52 Copynumber: 2.1 Consensus size: 52
426551 TGAGTCAACT
*
426561 TATTGGCATCTTTATCATTTTTAAGCCTAATGTCACTGGCCTTGAATTCGCA
1 TATTGGCACCTTTATCATTTTTAAGCCTAATGTCACTGGCCTTGAATTCGCA
* * * *
426613 TATTGGCACCTTTATCGTTTTTAAGTCTAATGTCGCTGGCCTTGAATTTGCA
1 TATTGGCACCTTTATCATTTTTAAGCCTAATGTCACTGGCCTTGAATTCGCA
*
426665 CATTG
1 TATTG
426670 CACTTTTCTG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.41
Consensus pattern (52 bp):
TATTGGCACCTTTATCATTTTTAAGCCTAATGTCACTGGCCTTGAATTCGCA
Found at i:429959 original size:21 final size:19
Alignment explanation
Indices: 429914--429969 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
429904 GTATCGATAT
**
429914 ATTGTATCGATACATGTTC
1 ATTGTATCGATACATGGAC
429933 ATTGTATCGATACATGGAC
1 ATTGTATCGATACATGGAC
*
429952 AAATTGTATCAATACATG
1 --ATTGTATCGATACATG
429970 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 17 0.53
21 15 0.47
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGGAC
Done.