Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397284.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_115.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1289616
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.30
Warning! 135248 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:45105 original size:19 final size:19
Alignment explanation
Indices: 45083--45122 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
45073 TTGTTTTTTC
45083 TTTTAATTTATATATATAT
1 TTTTAATTTATATATATAT
* * *
45102 TTTTTATTTATTTATTTAT
1 TTTTAATTTATATATATAT
45121 TT
1 TT
45123 CATTTCTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTAATTTATATATATAT
Found at i:61011 original size:38 final size:37
Alignment explanation
Indices: 60948--61052 Score: 122
Period size: 38 Copynumber: 2.8 Consensus size: 37
60938 AGGTTACTGA
*
60948 TACGTAACCTCATTCTAAATGAAGAGTTTTTTTAAAGT
1 TACGTAACCTCATTCTAGATGAAGAGTTTTTTT-AAGT
* * * *
60986 TACAG-AACCTTATTCTAGATAAAGAGTAATTTTTATGT
1 TAC-GTAACCTCATTCTAGATGAAGAGT-TTTTTTAAGT
*
61024 TACGTGACCTCATTCTAGATGAAGAGTTT
1 TACGTAACCTCATTCTAGATGAAGAGTTT
61053 AAAGTTACNN
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
37 2 0.04
38 47 0.85
39 6 0.11
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (37 bp):
TACGTAACCTCATTCTAGATGAAGAGTTTTTTTAAGT
Found at i:61528 original size:14 final size:14
Alignment explanation
Indices: 61490--61530 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
61480 AAAAAATAAA
*
61490 AAATATGAAAATAT
1 AAATATGAAAAGAT
61504 AAA-A-G-AAAGAT
1 AAATATGAAAAGAT
61515 AAATATGAAAAGAT
1 AAATATGAAAAGAT
61529 AA
1 AA
61531 GGATATGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 8 0.35
12 2 0.09
13 2 0.09
14 11 0.48
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (14 bp):
AAATATGAAAAGAT
Found at i:68948 original size:38 final size:38
Alignment explanation
Indices: 68900--68999 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 38
68890 ACAGCTACGC
*
68900 AACCTCATTCTAAATGAAGAGTTTTTTTAAAGTTACA-G
1 AACCTCATTCTAGATGAAGAGTTTTTTT-AAGTTACACG
* * * * *
68938 AACCTTATTCTAGATGAAAAGTAATTTTTATGTTGCACG
1 AACCTCATTCTAGATGAAGAGT-TTTTTTAAGTTACACG
68977 -ACCTCATTCTAGATGAAGAGTTT
1 AACCTCATTCTAGATGAAGAGTTT
69000 AAAGTTACGT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
37 1 0.02
38 44 0.86
39 6 0.12
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (38 bp):
AACCTCATTCTAGATGAAGAGTTTTTTTAAGTTACACG
Found at i:69457 original size:9 final size:9
Alignment explanation
Indices: 69427--69464 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
69417 ATTGAATTTT
69427 AAAAATATA
1 AAAAATATA
*
69436 AAAAAAATA
1 AAAAATATA
69445 AAAAATAT-
1 AAAAATATA
*
69453 GAAAATATA
1 AAAAATATA
69462 AAA
1 AAA
69465 GAGGGATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (9 bp):
AAAAATATA
Found at i:72998 original size:6 final size:6
Alignment explanation
Indices: 72943--72998 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
72933 TCAATATCCC
* * *
72943 AAAAAT -AAAAT -AAAAT -AAGAT AAAAAT CAAAAT CAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
72988 AAAAAT AAAAA
1 AAAAAT AAAAA
72999 AGAAACTCAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
5 14 0.31
6 31 0.69
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:74180 original size:21 final size:19
Alignment explanation
Indices: 74147--74189 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
74137 ACATTTGCCC
*
74147 AGAAAGAAAAGGAAAATAA
1 AGAAAGAAAAGGAAAAGAA
74166 AGAAAGGATAAAGGAAAAGAA
1 AGAAA-GA-AAAGGAAAAGAA
74187 AGA
1 AGA
74190 GAGTGGGAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 2 0.10
21 14 0.67
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.05
Consensus pattern (19 bp):
AGAAAGAAAAGGAAAAGAA
Found at i:74804 original size:17 final size:18
Alignment explanation
Indices: 74784--74821 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
74774 TTTATCTCTC
74784 TTTTATATTTT-CATATT
1 TTTTATATTTTACATATT
* *
74801 TTTTATTTTTTAGATATT
1 TTTTATATTTTACATATT
74819 TTT
1 TTT
74822 AAAATTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTATATTTTACATATT
Found at i:75224 original size:73 final size:73
Alignment explanation
Indices: 75077--75237 Score: 177
Period size: 73 Copynumber: 2.2 Consensus size: 73
75067 TTAAAAGGAC
*
75077 TAAACTCCTCATCTATAATATGACTACTATAAAAAGGAATAAGCTCCTATTCTAAAACAAGGCTA
1 TAAACTTCTCATCTATAATATGACTACTATAAAAAGGAATAAGCTCCTATTCTAAAACAAGGCTA
* *
75142 CGTACCTT
66 CATAACTT
* ** **
75150 TAAACTTCTCATCT-TAAT-TGAGGCTACTATAAAAAGGAATAATCTCCTCATT-TGGAATGAGG
1 TAAACTTCTCATCTATAATATGA--CTACTATAAAAAGGAATAAGCTCCT-ATTCTAAAACAAGG
*
75212 TTACATAACTT
63 CTACATAACTT
75223 TAAAC-TCTTCATCTA
1 TAAACTTC-TCATCTA
75238 GAATGAGGTC
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
71 3 0.04
72 6 0.08
73 62 0.84
74 3 0.04
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (73 bp):
TAAACTTCTCATCTATAATATGACTACTATAAAAAGGAATAAGCTCCTATTCTAAAACAAGGCTA
CATAACTT
Found at i:75306 original size:38 final size:37
Alignment explanation
Indices: 75224--75328 Score: 108
Period size: 38 Copynumber: 2.8 Consensus size: 37
75214 ACATAACTTT
75224 AAACTCTTCATCTAGAATGAGG-TCGCGTAACATAAA
1 AAACTCTTCATCTAGAATGAGGTTCGCGTAACATAAA
* * *
75260 AATTACTCTTCATCTAGAATAAGGTTC-TGTAACTTTTAAA
1 AA--ACTCTTCATCTAGAATGAGGTTCGCGTAAC--ATAAA
* *
75300 AAACTCTTTATTTAGAATGAGGTT-GCGTA
1 AAACTCTTCATCTAGAATGAGGTTCGCGTA
75329 TCTATAACCT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
36 2 0.04
38 46 0.82
39 2 0.04
40 6 0.11
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (37 bp):
AAACTCTTCATCTAGAATGAGGTTCGCGTAACATAAA
Found at i:75402 original size:34 final size:34
Alignment explanation
Indices: 75337--75402 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
75327 TATCTATAAC
* * ** *
75337 CTCCTTATCTGGAATGAGGCTATGTAGCTTTAAA
1 CTCCTCATCTGGAATGACGCTACATAACTTTAAA
*
75371 CTCCTCATCTTGAATGACGCTACATAACTTTA
1 CTCCTCATCTGGAATGACGCTACATAACTTTA
75403 GAAAGACTCC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (34 bp):
CTCCTCATCTGGAATGACGCTACATAACTTTAAA
Found at i:80680 original size:9 final size:9
Alignment explanation
Indices: 80666--80690 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
80656 GATCTAAAAA
80666 AAAAACCCC
1 AAAAACCCC
80675 AAAAACCCC
1 AAAAACCCC
80684 AAAAACC
1 AAAAACC
80691 AAAACCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAACCCC
Found at i:81682 original size:16 final size:17
Alignment explanation
Indices: 81641--81682 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
81631 CAATTGTGAT
81641 AGAAAAAAA-AAGAGAA
1 AGAAAAAAAGAAGAGAA
*
81657 AGAAAGAAAGAAG-GAA
1 AGAAAAAAAGAAGAGAA
81673 AGAAAAAAAG
1 AGAAAAAAAG
81683 GAAAGGTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAGAAGAGAA
Found at i:84586 original size:4 final size:4
Alignment explanation
Indices: 84579--84613 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
84569 AAAAAAAAAG
*
84579 AGAA AGAA AGAA AGAA GGAA AGAA AGAA AGGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A-GAA AG
84614 GNNNNNNNNN
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:84599 original size:16 final size:17
Alignment explanation
Indices: 84567--84608 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
84557 CAATTTTGAT
*
84567 AGAAA-AAAAAAGAGAA
1 AGAAAGAAAGAAGAGAA
84583 AGAAAGAAAGAAG-GAA
1 AGAAAGAAAGAAGAGAA
84599 AGAAAGAAAG
1 AGAAAGAAAG
84609 GAAAGGNNNN
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAGAAGAGAA
Found at i:85083 original size:9 final size:9
Alignment explanation
Indices: 85056--85093 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
85046 TTTATCTCTC
85056 TTTTATA-T
1 TTTTATATT
*
85064 TTTCATATT
1 TTTTATATT
*
85073 TTTTATTTT
1 TTTTATATT
85082 TTTTATATT
1 TTTTATATT
85091 TTT
1 TTT
85094 AAAATTCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTATATT
Found at i:93274 original size:15 final size:15
Alignment explanation
Indices: 93254--93284 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
93244 TTGTGGTGAT
93254 TAATTTATTAAATAA
1 TAATTTATTAAATAA
93269 TAATTTATTAAATAA
1 TAATTTATTAAATAA
93284 T
1 T
93285 CAAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATTTATTAAATAA
Found at i:93621 original size:15 final size:15
Alignment explanation
Indices: 93597--93627 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
93587 TATATTTCTG
*
93597 ATTATTTAATAAATT
1 ATTATCTAATAAATT
93612 ATTATCTAATAAATT
1 ATTATCTAATAAATT
93627 A
1 A
93628 ATCACCACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATCTAATAAATT
Found at i:101304 original size:15 final size:15
Alignment explanation
Indices: 101284--101314 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
101274 TTGTGGTGGT
*
101284 TAGTTTATTAGATAA
1 TAGTTTATTAAATAA
101299 TAGTTTATTAAATAA
1 TAGTTTATTAAATAA
101314 T
1 T
101315 CAGAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
TAGTTTATTAAATAA
Found at i:103663 original size:11 final size:12
Alignment explanation
Indices: 103644--103673 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
103634 TCAACTAAAT
103644 AAATGATTTTTA
1 AAATGATTTTTA
103656 AAAT-ATTTTTA
1 AAATGATTTTTA
103667 AAATGAT
1 AAATGAT
103674 GAGATTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
AAATGATTTTTA
Found at i:106987 original size:13 final size:13
Alignment explanation
Indices: 106969--106993 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
106959 GTCATGTCTA
106969 AACTTTAATTTTG
1 AACTTTAATTTTG
106982 AACTTTAATTTT
1 AACTTTAATTTT
106994 TGTTATATTT
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:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
AACTTTAATTTTG
Found at i:107566 original size:5 final size:6
Alignment explanation
Indices: 107549--107576 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
107539 AGATAAGCAA
107549 TCTTTT TCTTTT TCTTTT TCTTTT TCTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT
107577 GTGTTTTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TCTTTT
Found at i:125991 original size:18 final size:18
Alignment explanation
Indices: 125964--126016 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
125954 ACGTATTTAA
*
125964 ATACAATTAAACACGATT
1 ATACCATTAAACACGATT
** *
125982 ATACGTTTAAACA-GATA
1 ATACCATTAAACACGATT
125999 ATACCATT-AACACGATT
1 ATACCATTAAACACGATT
126016 A
1 A
126017 ATTAAACGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 4 0.14
17 13 0.46
18 11 0.39
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (18 bp):
ATACCATTAAACACGATT
Found at i:129430 original size:17 final size:18
Alignment explanation
Indices: 129385--129430 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
129375 TACGTGTTTA
*
129385 AATACGATTAAACATGAT
1 AATACGATTAAACATAAT
* *
129403 TATACGTTTAAACA-AAT
1 AATACGATTAAACATAAT
129420 AATACGATTAA
1 AATACGATTAA
129431 CACGATTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (18 bp):
AATACGATTAAACATAAT
Found at i:135047 original size:251 final size:249
Alignment explanation
Indices: 134541--135116 Score: 719
Period size: 251 Copynumber: 2.3 Consensus size: 249
134531 AAATTTTAAT
* ** * * * **
134541 TTTAATGAAAAATAAATATTTAAATTTATATTCTCAAAATAAAATTATTTGATGATATATAAATT
1 TTTAGTGAAAAATAAATATTTAAATTTATATTCTTGAAATAAAAGTGTTTAACAATATATAAATT
* *
134606 TTAAATTTTAAATAAAATAATAATAATAAAAATAATTATAGTTCAAAATTGACATAAATAAGTTT
66 TTAAATTTTAAATAAAATAATAATAATAAAAATAATTATAGTTCAAAAATGACATAAATAAGCTT
* *
134671 TGACGTAAAACTATAAAAATTGACGTAAAAATTTATAAAAGTGAAATAACTAAATTTTAAATCTT
131 TAACGTAAAACTATAAAAATTGACGTAAAAACTTATAAAAGTGAAATAACTAAATTTTAAATCTT
* * * * * * *
134736 GACGTAAATGTATGAACGTTAACATCACAAGTCAATTAAGTAAAACACTATAAT
196 AACGTAAACGTATGAAAGTTAACATAACAAGTCAATTAAGTAAAAAAATATAAC
* * *
134790 TTTAGTGAAAAATAAACATTTATATTTATATTCTTGAATTAAAAGTGTTTAACAATATATAAATT
1 TTTAGTGAAAAATAAATATTTAAATTTATATTCTTGAAATAAAAGTGTTTAACAATATATAAATT
* * *
134855 TTAAGTTTTAAATAAAGAATAATAA-AGATCAAAATAATTATAGTTCAAAAATGATATAGAA-AA
66 TTAAATTTTAAAT-AA-AATAATAATA-ATAAAAATAATTATAGTTCAAAAATGACATA-AATAA
* * * *
134918 GCTTTAACGTTAAACTATGAGAATTGACGTAAAAACTTA-AAAGGT-AGAATAACTAAATTTTAA
127 GCTTTAACGTAAAACTATAAAAATTGACGTAAAAACTTATAAAAGTGA-AATAACTAAATTTTAA
* * * *
134981 ATCTTAACGTAAGCGTGTGAAAGTTAACGTAACAAGTCAATTAAGTTAAAAAAATCTAAC
191 ATCTTAACGTAAACGTATGAAAGTTAACATAACAAGTCAATTAAG-TAAAAAAATATAAC
* ** * *
135041 TTTAGTGAAAAAAAAATATTTAAATTTATATTCTTGAGCTAAAAGTGTTTAACTATATACAAATT
1 TTTAGTGAAAAATAAATATTTAAATTTATATTCTTGAAATAAAAGTGTTTAACAATATATAAATT
*
135106 TTAATTTTTAA
66 TTAAATTTTAA
135117 GTTTTGACGT
Statistics
Matches: 280, Mismatches: 41, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
249 67 0.24
250 62 0.22
251 149 0.53
252 2 0.01
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (249 bp):
TTTAGTGAAAAATAAATATTTAAATTTATATTCTTGAAATAAAAGTGTTTAACAATATATAAATT
TTAAATTTTAAATAAAATAATAATAATAAAAATAATTATAGTTCAAAAATGACATAAATAAGCTT
TAACGTAAAACTATAAAAATTGACGTAAAAACTTATAAAAGTGAAATAACTAAATTTTAAATCTT
AACGTAAACGTATGAAAGTTAACATAACAAGTCAATTAAGTAAAAAAATATAAC
Found at i:135169 original size:21 final size:21
Alignment explanation
Indices: 135127--135169 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
135117 GTTTTGACGT
* *
135127 AAAACTGTAACAATTGACATA
1 AAAACTGTAACAAATGAAATA
135148 AAAACT-TAACAAGATGAAATA
1 AAAACTGTAACAA-ATGAAATA
135169 A
1 A
135170 TTAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.21
Consensus pattern (21 bp):
AAAACTGTAACAAATGAAATA
Found at i:135456 original size:448 final size:449
Alignment explanation
Indices: 134664--135563 Score: 1169
Period size: 447 Copynumber: 2.0 Consensus size: 449
134654 TTGACATAAA
* *
134664 TAAGTTTTGACGTAAAACTATAAAAATTGACGTAAAAATTTATAAAAGTGAAATAACTAAATTTT
1 TAAGTTTTGACGTAAAACTATAAAAATTGACATAAAAACTTATAAAAGTGAAATAACTAAATTTT
* * *
134729 AAATCTTGACGTAAATGTATGAACGTTAACATCACAAGTCAATTAAGTAAAACACTATAATTTTA
66 AAATCTTAACGTAAATGTATGAACGTTAACATAACAAGTCAATTAAGTAAAACAATATAATTTTA
* * * * * *
134794 GTGAAAAATAAACATTTATATTTATATTCTTGAATTAAAAGTGTTTAACAATATATAAATTTTAA
131 CTGAAAAATAAACATTTATATTTATATTCATCAACTAAAAGTATGTAACAATATATAAATTTTAA
* * *
134859 GTTTTAAATAAAGAATAATAAAGATCAAAATAATTATAGTTCAAAAATGATATAGAAAAGCTTTA
196 GTTTTAAATAAAGAACAATAAAGATAAAAATAATTATAGTTCAAAAATGACATAGAAAAGCTTTA
* * * *
134924 ACGTTAAACTATGAGAATTGACGTAAAAACTTAAAAGGTAGAATAACTAAATTTTAAATCTTAAC
261 ACGTAAAACTATAAGAATTCACGTAAAAACTTAAAAAGTAGAATAACTAAATTTTAAATCTTAAC
* * *
134989 GTAAGCGTGTGAAAGTTAACGTAACAAGTCAATTAAGTTAAAAAAATCTAACTTT-AGTGAAA-A
326 GTAAACCTGTGAAAGTTAACGTAACAAATCAATTAAG-TAAAAAAATCTAA-TTTAAGT-AAACA
* * *
135052 AAAAATATTTAAATTTATATTCTTGA-GCTAAAAG-TGTTTAAC-TATATACAAATTTTAATTTT
388 AAAAATATTTAAATTTATATT-TTCACACT-AAAGTTATTTAACGT-TATACAAATTTTAATTTT
* * * *
135114 TAAGTTTTGACGTAAAACTGTAACAATTGACATAAAAACTTA-ACAAGATGAAATAATTAAATTT
1 TAAGTTTTGACGTAAAACTATAAAAATTGACATAAAAACTTATAAAAG-TGAAATAACTAAATTT
* * * * *
135178 TAAATCTTAACTTAAATGTGTGAGA-GTTAACGTAACAAGTTAATTAAGTAAAA-AATCTAATTT
65 TAAATCTTAACGTAAATGTATGA-ACGTTAACATAACAAGTCAATTAAGTAAAACAATATAATTT
*
135241 TACTG-AAAATAAGCATTTATATTTATATT-ATCAAGCTAAAAGTATGTAACAATATATAAATTT
129 TACTGAAAAATAAACATTTATATTTATATTCATCAA-CTAAAAGTATGTAACAATATATAAATTT
* * * * *
135304 TAATTTTTAAATAAA-AACAAT-AAGAATAAAAATAATTATAGTTTAAGATTGACATAGATAAG-
193 TAAGTTTTAAATAAAGAACAATAAAG-ATAAAAATAATTATAGTTCAAAAATGACATAGAAAAGC
* * * * *
135366 TCTTAACGTAAAATTGTAAGAATTCATGTTAAAACTTATAAAAGTGGAATAACTAAATTTTAAAT
257 T-TTAACGTAAAACTATAAGAATTCACGTAAAAACTTA-AAAAGTAGAATAACTAAATTTTAAAT
* * *
135431 TTTAATGTAAACCTGTGAGAGTTAACGTAACAAATCAATTAAGTAAAAAAATCTAATTTAAGTAA
320 CTTAACGTAAACCTGTGAAAGTTAACGTAACAAATCAATTAAGTAAAAAAATCTAATTTAAGTAA
*
135496 ACAATAAATATTTAAATTTATATTTTCACACTAAAGTTATTTAACGTTATACAAATTTTAATTTT
385 ACAAAAAATATTTAAATTTATATTTTCACACTAAAGTTATTTAACGTTATACAAATTTTAATTTT
135561 TAA
1 TAA
135564 ATAAAAAATA
Statistics
Matches: 391, Mismatches: 48, Indels: 25
0.84 0.10 0.05
Matches are distributed among these distances:
446 17 0.04
447 135 0.35
448 124 0.32
449 16 0.04
450 98 0.25
451 1 0.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (449 bp):
TAAGTTTTGACGTAAAACTATAAAAATTGACATAAAAACTTATAAAAGTGAAATAACTAAATTTT
AAATCTTAACGTAAATGTATGAACGTTAACATAACAAGTCAATTAAGTAAAACAATATAATTTTA
CTGAAAAATAAACATTTATATTTATATTCATCAACTAAAAGTATGTAACAATATATAAATTTTAA
GTTTTAAATAAAGAACAATAAAGATAAAAATAATTATAGTTCAAAAATGACATAGAAAAGCTTTA
ACGTAAAACTATAAGAATTCACGTAAAAACTTAAAAAGTAGAATAACTAAATTTTAAATCTTAAC
GTAAACCTGTGAAAGTTAACGTAACAAATCAATTAAGTAAAAAAATCTAATTTAAGTAAACAAAA
AATATTTAAATTTATATTTTCACACTAAAGTTATTTAACGTTATACAAATTTTAATTTT
Found at i:136045 original size:250 final size:250
Alignment explanation
Indices: 135114--136156 Score: 1081
Period size: 250 Copynumber: 4.2 Consensus size: 250
135104 TTTTAATTTT
* * * * * * *
135114 TAAGTTTTGACGTAAAACTGTAACAATTGACATAAAAACTTA-ACAAGATGAAATAATTAAATTT
1 TAAGTCTTAACGTAAAATTGTAAGAATTGACGTAAAAACTTATATAAGATGAAATAACTAAATTT
*
135178 TAAATCTTAACT-TAAATGTGTGAGAGTTAACGTAACAAGTTAATTAAGT-AAAAAATCTAATTT
66 TAAATCTTAA-TGTAAATGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAATCTAATTT
* * * * * *
135241 TACT-GAAAATAAGCATTTATATTTATATTATC-AAGCTAAAAGTATGTAACAATATATAAATTT
130 TAATAAAAAATAAGTATTTATATTTATATTATCGAA-CTAAAAGTATTTAACGATATACAAATTT
* *
135304 TAATTTTTAAATAAAAACAATAAGAATAAAAATAATTATAGTTTAAGATTGACATAGA
194 TAATTTTTAAATAAAAATAATAA-AATAAAAATAATTATAGTTTAAAATTGACATAGA
* * * * *
135362 TAAGTCTTAACGTAAAATTGTAAGAATTCATGTTAAAACTTATAAAAG-TGGAATAACTAAATTT
1 TAAGTCTTAACGTAAAATTGTAAGAATTGACGTAAAAACTTATATAAGATGAAATAACTAAATTT
* ** *
135426 TAAATTTTAATGTAAACCTGTGAGAGTTAACGTAACAAATCAATTAAGTAAAAAAATCTAA-TTT
66 TAAATCTTAATGTAAATGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAATCTAATTTT
* * * * *
135490 AAGTAAACAATAAATATTTAAATTTATATTTTC-ACACT-AAAGTTATTTAACGTTATACAAATT
131 AA-TAAAAAATAAGTATTTATATTTATATTATCGA-ACTAAAAG-TATTTAACGATATACAAATT
********* *
135553 TTAATTTTTAAATAAAAAATAATANNNNNNNNNNTAATTATAGTTTAAAATAGACATAGA
193 TTAATTTTTAAAT-AAAAATAATA-AAATAAAAATAATTATAGTTTAAAATTGACATAGA
* * * * * *
135613 AAAATCTTAACGTAAAATTATAAGAATTAATGTAAAAACTTATA-AAGATGAAATAATTAAATTT
1 TAAGTCTTAACGTAAAATTGTAAGAATTGACGTAAAAACTTATATAAGATGAAATAACTAAATTT
** * *
135677 TAAATCTTAACATAAATGTATGAGAGTTAAC--AACAAGTCAATTAAGTAAAAAAATTTAATTTT
66 TAAATCTTAATGTAAATGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAATCTAATTTT
* ********** * * * *
135740 ATTAAAAAATNNNNNNNNNNATTTATATTCTTGAAATAAAAGTATTTAACGATATATAACA-TTT
131 AATAAAAAATAAGTATTTATATTTATATTATCGAACTAAAAGTATTTAACGATATACAA-ATTTT
* *
135804 AATTTTTAAATAAAATTAATAAATATAAAAATAATTATAGTTTAAAATTGATATAGA
195 AATTTTTAAATAAAAATAATAAA-ATAAAAATAATTATAGTTTAAAATTGACATAGA
* * * * *
135861 TAAGCCTTAACGTAAAACTGTAAGAATTGACATAAAAAATTATATAAG-TGGAATAACTAAATTT
1 TAAGTCTTAACGTAAAATTGTAAGAATTGACGTAAAAACTTATATAAGATGAAATAACTAAATTT
* * * * * * *
135925 TAAATCTTAATGTAAATATGTGAGAATTAACGTAATAAGTTAATTAAGTAAGAAAGTATAATTTT
66 TAAATCTTAATGTAAATGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAATCTAATTTT
* *
135990 AATAAAAAATAAGTATTTATATTTATATTATCGAGCTAAAAGTATCTAACGATATACAAATTTTA
131 AATAAAAAATAAGTATTTATATTTATATTATCGAACTAAAAGTATTTAACGATATACAAATTTTA
** * * * *
136055 ATTTTTAAATAAAAATAATGAGGATTAAAATAATTATAGTATAAAATTGATATAAA
196 ATTTTTAAATAAAAATAAT-AAAATAAAAATAATTATAGTTTAAAATTGACATAGA
* *
136111 TAAGTCTTAACGTAAAATTGTAAGAACTGACGTAAAAA-TTTTATAA
1 TAAGTCTTAACGTAAAATTGTAAGAATTGACGTAAAAACTTATATAA
136157 AAATAGAATC
Statistics
Matches: 643, Mismatches: 132, Indels: 39
0.79 0.16 0.05
Matches are distributed among these distances:
247 1 0.00
248 202 0.31
249 105 0.16
250 222 0.35
251 113 0.18
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.35
Consensus pattern (250 bp):
TAAGTCTTAACGTAAAATTGTAAGAATTGACGTAAAAACTTATATAAGATGAAATAACTAAATTT
TAAATCTTAATGTAAATGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAATCTAATTTT
AATAAAAAATAAGTATTTATATTTATATTATCGAACTAAAAGTATTTAACGATATACAAATTTTA
ATTTTTAAATAAAAATAATAAAATAAAAATAATTATAGTTTAAAATTGACATAGA
Found at i:136157 original size:499 final size:499
Alignment explanation
Indices: 135114--136157 Score: 1237
Period size: 499 Copynumber: 2.1 Consensus size: 499
135104 TTTTAATTTT
* * * * *
135114 TAAGTTTTGACGTAAAACTGTAACAATTGACATAAAAACTTA-ACAAGATGAAATAATTAAATTT
1 TAAGTCTTAACGTAAAATTGTAAGAATTGACGTAAAAACTTATA-AAGATGAAATAATTAAATTT
* * *
135178 TAAATCTTAACTTAAATGTGTGAGAGTTAACGTAACAAGTTAATTAAGTAAAAAATCTAATTTTA
65 TAAATCTTAACATAAATGTATGAGAGTTAACG-AACAAGTCAATTAAGTAAAAAATCTAATTTTA
* *
135243 CTGAAAATAAGCATTTATATTTATATTATCAAGCTAAAAGTATGTAACAATATATAAATTTTAAT
129 CTAAAAATAAGCATTTATATTTATATTATCAAGATAAAAGTATGTAACAATATATAAATTTTAAT
* *
135308 TTTTAAATAAAAACAATAAGAATAAAAATAATTATAGTTTAAGATTGACATAGATAAGTCTTAAC
194 TTTTAAATAAAAACAATAAGAATAAAAATAATTATAGTTTAAAATTGACATAGATAAGCCTTAAC
* ** * * *
135373 GTAAAATTGTAAGAATTCATGTTAAAACTTATAAAAGTGGAATAACTAAATTTTAAATTTTAATG
259 GTAAAACTGTAAGAATTCACATAAAAAATTATAAAAGTGGAATAACTAAATTTTAAATCTTAATG
* * * *
135438 TAAACCTGTGAGAGTTAACGTAACAAATCAATTAAGTAAAAAAATCTAATTTAAGTAAACAATAA
324 TAAACATGTGAGAATTAACGTAACAAATCAATTAAGTAAAAAAATATAATTTAAGTAAAAAATAA
* * *
135503 ATATTTAAATTTATATTTTCACACTAAAGTTATTTAACGTTATACAAATTTTAATTTTTAAATAA
389 ATATTTAAATTTATATTATCACACTAAAGTTATCTAACGATATACAAATTTTAATTTTTAAATAA
********** *
135568 AAAATAATANNNNNNNNNNTAATTATAGTTTAAAATAGACATAGAA
454 AAAATAATAAGGATTAAAATAATTATAGTATAAAATAGACATAGAA
* * * *
135614 -AAATCTTAACGTAAAATTATAAGAATTAATGTAAAAACTTATAAAGATGAAATAATTAAATTTT
1 TAAGTCTTAACGTAAAATTGTAAGAATTGACGTAAAAACTTATAAAGATGAAATAATTAAATTTT
* *
135678 AAATCTTAACATAAATGTATGAGAGTTAAC-AACAAGTCAATTAAGTAAAAAAATTTAATTTTAT
66 AAATCTTAACATAAATGTATGAGAGTTAACGAACAAGTCAATTAAGT-AAAAAATCTAATTTTAC
********** * * * *
135742 TAAAAAATNNNNNNNNNNATTTATATTCTTGAA-ATAAAAGTATTTAACGATATATAACA-TTTA
130 T-AAAAATAAGCATTTATATTTATATT-ATCAAGATAAAAGTATGTAACAATATATAA-ATTTTA
** *
135805 ATTTTTAAATAAAATTAATAA-ATATAAAAATAATTATAGTTTAAAATTGATATAGATAAGCCTT
192 ATTTTTAAATAAAAACAATAAGA-ATAAAAATAATTATAGTTTAAAATTGACATAGATAAGCCTT
* *
135869 AACGTAAAACTGTAAGAATTGACATAAAAAATTATATAAGTGGAATAACTAAATTTTAAATCTTA
256 AACGTAAAACTGTAAGAATTCACATAAAAAATTATAAAAGTGGAATAACTAAATTTTAAATCTTA
* * * * * *
135934 ATGTAAATATGTGAGAATTAACGTAATAAGTTAATTAAGTAAGAAAGTATAATTTTAA-TAAAAA
321 ATGTAAACATGTGAGAATTAACGTAACAAATCAATTAAGTAAAAAAATATAA-TTTAAGTAAAAA
* * *
135998 ATAAGTATTTATATTTATATTATCGA-GCTAAAAG-TATCTAACGATATACAAATTTTAATTTTT
385 ATAAATATTTAAATTTATATTATC-ACACT-AAAGTTATCTAACGATATACAAATTTTAATTTTT
* * *
136061 AAAT-AAAAATAATGAGGATTAAAATAATTATAGTATAAAATTGATATA-AA
448 AAATAAAAAATAATAAGGATTAAAATAATTATAGTATAAAATAGACATAGAA
* *
136111 TAAGTCTTAACGTAAAATTGTAAGAACTGACGTAAAAATTTTATAAA
1 TAAGTCTTAACGTAAAATTGTAAGAATTGACGTAAAAA-CTTATAAA
136158 AATAGAATCA
Statistics
Matches: 454, Mismatches: 79, Indels: 23
0.82 0.14 0.04
Matches are distributed among these distances:
497 17 0.04
498 79 0.17
499 343 0.76
500 15 0.03
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.34
Consensus pattern (499 bp):
TAAGTCTTAACGTAAAATTGTAAGAATTGACGTAAAAACTTATAAAGATGAAATAATTAAATTTT
AAATCTTAACATAAATGTATGAGAGTTAACGAACAAGTCAATTAAGTAAAAAATCTAATTTTACT
AAAAATAAGCATTTATATTTATATTATCAAGATAAAAGTATGTAACAATATATAAATTTTAATTT
TTAAATAAAAACAATAAGAATAAAAATAATTATAGTTTAAAATTGACATAGATAAGCCTTAACGT
AAAACTGTAAGAATTCACATAAAAAATTATAAAAGTGGAATAACTAAATTTTAAATCTTAATGTA
AACATGTGAGAATTAACGTAACAAATCAATTAAGTAAAAAAATATAATTTAAGTAAAAAATAAAT
ATTTAAATTTATATTATCACACTAAAGTTATCTAACGATATACAAATTTTAATTTTTAAATAAAA
AATAATAAGGATTAAAATAATTATAGTATAAAATAGACATAGAA
Found at i:137964 original size:259 final size:259
Alignment explanation
Indices: 137397--138167 Score: 1409
Period size: 259 Copynumber: 3.0 Consensus size: 259
137387 TTACTTAATT
* *
137397 GAATCTATCCTTTAGAATGAAATCATAAACTTTACTTAAGTTCATTGAGAAAGATAAGTTGTAAT
1 GAATCTATCCTTTCGAATGAAATCATAGACTTTACTTAAGTTCATTGAGAAAGATAAGTTGTAAT
137462 CTATGAAATAAAATTGGTTTTGGGAGTTCAATTATACGCAAAGGAAGTATTAGCATCCTTGTAAA
66 CTATGAAATAAAATTGGTTTTGGGAGTTCAATTATACGCAAAGGAAGTATTAGCATCCTTGTAAA
137527 TCTAGGTCAAAAAATGGTACCAATTGATCATGTGTTAT-ATACTTTAACCTTGACAAATATTTAT
131 TCTAGGTCAAAAAATGGTACCAATTGATCATGTGTTATAATACTTTAACCTTGACAAATATTTAT
137591 AGATTTCATATTTAGTTTTATTTCCTTATTACCATTTACTCTTTTTAGCAAGGATGTCATAAAC
196 AGATTTCATATTTAGTTTTATTTCCTTATTACCATTTACTCTTTTTAGCAAGGATGTCATAAAC
137655 GAATCTATCCTTTCGAATGAAATCATAGACTTTACTTAAGTTCATTGAGAAAGATAAGTTGTAAT
1 GAATCTATCCTTTCGAATGAAATCATAGACTTTACTTAAGTTCATTGAGAAAGATAAGTTGTAAT
137720 CTATGAAATAAAATTGGTTTTGGGAGTTCAATTATACGCAAAGGAAGTATTAGCATCCTTGTAAA
66 CTATGAAATAAAATTGGTTTTGGGAGTTCAATTATACGCAAAGGAAGTATTAGCATCCTTGTAAA
137785 TCTAGGTCAAAAAATGGTACCAATTGATCATGTGTTATAATACTTTAACCTTGACAAATATTTAT
131 TCTAGGTCAAAAAATGGTACCAATTGATCATGTGTTATAATACTTTAACCTTGACAAATATTTAT
137850 AGATTTCATATTTAGTTTTATTTCCTTATTACCATTTACTCTTTTTAGCAAGGATGTCATAAAC
196 AGATTTCATATTTAGTTTTATTTCCTTATTACCATTTACTCTTTTTAGCAAGGATGTCATAAAC
137914 GAATCTATCCTTTCGAATGAAATCATAGACTTTACTTAAGTTCATTGAGAAAGATAAGTTGTAAT
1 GAATCTATCCTTTCGAATGAAATCATAGACTTTACTTAAGTTCATTGAGAAAGATAAGTTGTAAT
* * * * * *
137979 CTATGAAATAAAATTGGTTCTGGAAGTACGATTATACGCAAAGAAAGGATTAGCATCCTTGTAAA
66 CTATGAAATAAAATTGGTTTTGGGAGTTCAATTATACGCAAAGGAAGTATTAGCATCCTTGTAAA
* * *
138044 TCTAGGTCAAAAAACGGTACCAATTGATCATGTTTTATAATACTTTACCCTTGACAAATATTTAT
131 TCTAGGTCAAAAAATGGTACCAATTGATCATGTGTTATAATACTTTAACCTTGACAAATATTTAT
* * *
138109 AGATTTCATATTTAGTTTTATTTCCTTATTACCATTTACTCCTTGTAGCCAGGATGTCA
196 AGATTTCATATTTAGTTTTATTTCCTTATTACCATTTACTCTTTTTAGCAAGGATGTCA
138168 AAATTGTCTC
Statistics
Matches: 498, Mismatches: 14, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
258 166 0.33
259 332 0.67
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (259 bp):
GAATCTATCCTTTCGAATGAAATCATAGACTTTACTTAAGTTCATTGAGAAAGATAAGTTGTAAT
CTATGAAATAAAATTGGTTTTGGGAGTTCAATTATACGCAAAGGAAGTATTAGCATCCTTGTAAA
TCTAGGTCAAAAAATGGTACCAATTGATCATGTGTTATAATACTTTAACCTTGACAAATATTTAT
AGATTTCATATTTAGTTTTATTTCCTTATTACCATTTACTCTTTTTAGCAAGGATGTCATAAAC
Found at i:153673 original size:35 final size:36
Alignment explanation
Indices: 153615--153690 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 36
153605 CTTATTTTAA
*
153615 TTGTTTTGCATTGAAGTAGCACTTCACTTGCTCTAG
1 TTGTTTTGCATTGAAATAGCACTTCACTTGCTCTAG
* * *
153651 TTGTTTTGTA-TGAAATAGCACTTCACTTGTTTTAG
1 TTGTTTTGCATTGAAATAGCACTTCACTTGCTCTAG
153686 TTGTT
1 TTGTT
153691 CTCTATACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 27 0.75
36 9 0.25
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.47
Consensus pattern (36 bp):
TTGTTTTGCATTGAAATAGCACTTCACTTGCTCTAG
Found at i:158844 original size:43 final size:43
Alignment explanation
Indices: 158792--159016 Score: 197
Period size: 43 Copynumber: 5.3 Consensus size: 43
158782 TGTTTAAAAT
* * *
158792 TTTTTAAGTTACATAACCTCATTTCACATGAGGAGTTTATTAA
1 TTTTTAAGTTACATAACCTCATTTCAGATGAGGAGCTTATTCA
** * * *
158835 TTTTTAAGTTACATAGTCTCATTTAAGATGAAGAGCCTATTCA
1 TTTTTAAGTTACATAACCTCATTTCAGATGAGGAGCTTATTCA
* *
158878 -TTTTAAGTTACGTAACCTCATTCCAGATGAGGAGCTTATTCA
1 TTTTTAAGTTACATAACCTCATTTCAGATGAGGAGCTTATTCA
* * * * * * *
158920 TTTTAAAGTTACATAGCTTCATTCCAAATAAGGAACTTATTTC-
1 TTTTTAAGTTACATAACCTCATTTCAGATGAGGAGCTTA-TTCA
* * * *
158963 TTTTTAAAGCTAC-TAACCCCA-TTCTATATGAAGAGCTTATTCA
1 TTTTT-AAGTTACATAACCTCATTTC-AGATGAGGAGCTTATTCA
*
159006 TTTTAAAGTTA
1 TTTTTAAGTTA
159017 TGCAGCCTTA
Statistics
Matches: 143, Mismatches: 34, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
42 45 0.31
43 89 0.62
44 9 0.06
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (43 bp):
TTTTTAAGTTACATAACCTCATTTCAGATGAGGAGCTTATTCA
Found at i:158942 original size:85 final size:85
Alignment explanation
Indices: 158793--159016 Score: 240
Period size: 85 Copynumber: 2.6 Consensus size: 85
158783 GTTTAAAATT
* * * *
158793 TTTTAAGTTACATAACCTCATTTCACATGAGGAGTTTATTAATTTTTAAGTTACATAGTCTCATT
1 TTTTAAGTTAC-TAACCTCATTCCACATGAGGAGCTTATTCATTTTAAAGTTACATAGTCTCATT
* *
158858 -TAAGATGAA-GAGCCTA-TTCA
65 CCAA-AT-AAGGAACCTATTTCA
*
158878 TTTTAAGTTACGTAACCTCATTCCAGATGAGGAGCTTATTCATTTTAAAGTTACATAG-CTTCAT
1 TTTTAAGTTAC-TAACCTCATTCCACATGAGGAGCTTATTCATTTTAAAGTTACATAGTC-TCAT
* *
158942 TCCAAATAAGGAACTTATTTCT
64 TCCAAATAAGGAACCTATTTCA
* * * * *
158964 TTTTAAAGCTACTAACCCCATTCTATATGAAGAGCTTATTCATTTTAAAGTTA
1 TTTT-AAGTTACTAACCTCATTCCACATGAGGAGCTTATTCATTTTAAAGTTA
159017 TGCAGCCTTA
Statistics
Matches: 119, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
84 3 0.03
85 64 0.54
86 46 0.39
87 6 0.05
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (85 bp):
TTTTAAGTTACTAACCTCATTCCACATGAGGAGCTTATTCATTTTAAAGTTACATAGTCTCATTC
CAAATAAGGAACCTATTTCA
Found at i:159037 original size:86 final size:86
Alignment explanation
Indices: 158890--159057 Score: 207
Period size: 86 Copynumber: 2.0 Consensus size: 86
158880 TTAAGTTACG
* * *
158890 TAACCTCATTCCAGATGAGGAGCTTATTCATTTTAAAGTTACATAGCTTCATTCCAAATAAGGAA
1 TAACCCCATTCCAGATGAAGAGCTTATTCATTTTAAAGTTACACAGCTTCATTCCAAATAAGGAA
158955 -CTTATTTCTTTTTAAAGCTAC
66 CCTT-TTTCTTTTTAAAGCTAC
* * ** * *
158976 TAACCCCATTCTATATGAAGAGCTTATTCATTTTAAAGTTATGCAGCCTT-ATT-TAAGATAAGT
1 TAACCCCATTCCAGATGAAGAGCTTATTCATTTTAAAGTTACACAG-CTTCATTCCAA-ATAAGG
159039 AACCTTTTTCTTTTTAAAG
64 AACCTTTTTCTTTTTAAAG
159058 TGATGTAATC
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
85 2 0.03
86 62 0.89
87 6 0.09
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (86 bp):
TAACCCCATTCCAGATGAAGAGCTTATTCATTTTAAAGTTACACAGCTTCATTCCAAATAAGGAA
CCTTTTTCTTTTTAAAGCTAC
Found at i:159589 original size:21 final size:22
Alignment explanation
Indices: 159565--159606 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
159555 GCACACATAG
159565 ATAGAGAG-AAAAATTAGGTAC
1 ATAGAGAGAAAAAATTAGGTAC
159586 ATAGAGAGAAAAAATTAGGTA
1 ATAGAGAGAAAAAATTAGGTA
159607 GAGAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (22 bp):
ATAGAGAGAAAAAATTAGGTAC
Found at i:159619 original size:22 final size:22
Alignment explanation
Indices: 159594--159635 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
159584 ACATAGAGAG
*
159594 AAAAAAT-TAGGTAGAGAAAAC
1 AAAAAATATAGGGAGAGAAAAC
159615 AAAAAATATAGGGAGAGAAAA
1 AAAAAATATAGGGAGAGAAAA
159636 GAATTAGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.64, C:0.02, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAAATATAGGGAGAGAAAAC
Found at i:170134 original size:20 final size:20
Alignment explanation
Indices: 170109--170148 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
170099 CTTGAAAAAA
170109 AAATTAGTTTAAGATAATAC
1 AAATTAGTTTAAGATAATAC
170129 AAATTAGTTTAAGATAATAC
1 AAATTAGTTTAAGATAATAC
170149 CTACCTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
AAATTAGTTTAAGATAATAC
Found at i:170173 original size:76 final size:76
Alignment explanation
Indices: 170072--170226 Score: 310
Period size: 76 Copynumber: 2.0 Consensus size: 76
170062 AGTCTTCAGT
170072 CCTACCTTTGTATTATCTTTTTTTTTGCTTGAAAAAAAAATTAGTTTAAGATAATACAAATTAGT
1 CCTACCTTTGTATTATCTTTTTTTTTGCTTGAAAAAAAAATTAGTTTAAGATAATACAAATTAGT
170137 TTAAGATAATA
66 TTAAGATAATA
170148 CCTACCTTTGTATTATCTTTTTTTTTGCTTGAAAAAAAAATTAGTTTAAGATAATACAAATTAGT
1 CCTACCTTTGTATTATCTTTTTTTTTGCTTGAAAAAAAAATTAGTTTAAGATAATACAAATTAGT
170213 TTAAGATAATA
66 TTAAGATAATA
170224 CCT
1 CCT
170227 TTGTATTATC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.43
Consensus pattern (76 bp):
CCTACCTTTGTATTATCTTTTTTTTTGCTTGAAAAAAAAATTAGTTTAAGATAATACAAATTAGT
TTAAGATAATA
Found at i:170210 original size:20 final size:20
Alignment explanation
Indices: 170185--170224 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
170175 CTTGAAAAAA
170185 AAATTAGTTTAAGATAATAC
1 AAATTAGTTTAAGATAATAC
170205 AAATTAGTTTAAGATAATAC
1 AAATTAGTTTAAGATAATAC
170225 CTTTGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
AAATTAGTTTAAGATAATAC
Found at i:172989 original size:19 final size:19
Alignment explanation
Indices: 172953--172991 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
172943 AAAATCTTAT
*
172953 TTAAATATGATTATTTAAA
1 TTAAATATGATTACTTAAA
172972 TTAAGATATGATT-CTTAAA
1 TTAA-ATATGATTACTTAAA
172991 T
1 T
172992 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (19 bp):
TTAAATATGATTACTTAAA
Found at i:177450 original size:24 final size:24
Alignment explanation
Indices: 177409--177463 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
177399 CTGAATTTTT
*
177409 AATATT-AAATAGCTTCATTCTAG
1 AATATTCAAATAGCTTCATTCTAA
*
177432 AATATTCAAATAAGC-TCATTTTAA
1 AATATTCAAAT-AGCTTCATTCTAA
177456 AATATTCA
1 AATATTCA
177464 GTGCGACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.21
24 19 0.68
25 3 0.11
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (24 bp):
AATATTCAAATAGCTTCATTCTAA
Found at i:182110 original size:15 final size:15
Alignment explanation
Indices: 182087--182117 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
182077 TTACATGAGC
182087 ACAAAAATAATAATA
1 ACAAAAATAATAATA
*
182102 ACAATAATAATAATA
1 ACAAAAATAATAATA
182117 A
1 A
182118 AACTTTAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (15 bp):
ACAAAAATAATAATA
Found at i:184109 original size:30 final size:30
Alignment explanation
Indices: 184075--184131 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
184065 TAATCAAACT
184075 TTTATAGTTTTAGTTTGAGTCAAATAAATC
1 TTTATAGTTTTAGTTTGAGTCAAATAAATC
* *
184105 TTTATATTTTTATTTTGAGTCAAATAA
1 TTTATAGTTTTAGTTTGAGTCAAATAA
184132 GTTATTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (30 bp):
TTTATAGTTTTAGTTTGAGTCAAATAAATC
Found at i:185580 original size:23 final size:23
Alignment explanation
Indices: 185550--185606 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
185540 GTTTAGAGTT
* *
185550 TGTGACACATCATGGAGGGAATA
1 TGTGACACATCAGGGAGAGAATA
* *
185573 TGTGACAC-TGTAGGGTGAGAATA
1 TGTGACACAT-CAGGGAGAGAATA
185596 TGTGACACATC
1 TGTGACACATC
185607 TATGACACGC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
22 1 0.04
23 25 0.93
24 1 0.04
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.25
Consensus pattern (23 bp):
TGTGACACATCAGGGAGAGAATA
Found at i:185660 original size:23 final size:23
Alignment explanation
Indices: 185629--185675 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
185619 AGATTTAGAG
*
185629 TTTACGACACGCCATTGAGGGAA
1 TTTACGACACGCCATGGAGGGAA
* *
185652 TTTATGACATGCCATGGAGGGAA
1 TTTACGACACGCCATGGAGGGAA
185675 T
1 T
185676 CTTAGAGAAT
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:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (23 bp):
TTTACGACACGCCATGGAGGGAA
Found at i:186383 original size:31 final size:31
Alignment explanation
Indices: 186346--186509 Score: 238
Period size: 31 Copynumber: 5.3 Consensus size: 31
186336 CTAGCATGTG
186346 ACAACATTTTACTTGATATGCATGGCGTGTA
1 ACAACATTTTACTTGATATGCATGGCGTGTA
* * *
186377 ACAACATCTTACGTGATATGCATGGCATGTA
1 ACAACATTTTACTTGATATGCATGGCGTGTA
* *
186408 ACAATATTTTACGTGATATGCATGGCGTGTA
1 ACAACATTTTACTTGATATGCATGGCGTGTA
* * *
186439 ACAATATTTTACTTTATATGCATGGCGTGCA
1 ACAACATTTTACTTGATATGCATGGCGTGTA
* *
186470 ACAATATTTTACTTGATACGCATGGCGTGTA
1 ACAACATTTTACTTGATATGCATGGCGTGTA
186501 ACAACATTT
1 ACAACATTT
186510 ATTTCTTTCT
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 120 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (31 bp):
ACAACATTTTACTTGATATGCATGGCGTGTA
Found at i:190369 original size:96 final size:96
Alignment explanation
Indices: 190057--190428 Score: 360
Period size: 96 Copynumber: 3.9 Consensus size: 96
190047 GCGTGTCACC
* * * *
190057 CCATAAAT-CAGCTTTCACTCAACATGTCATGCCCTAAATATGGTACCATTCAATGTGTCACGCC
1 CCATAAATCCA-CTTTCACTCAACGTGTCATGCCCTAAATCTGGTACCACTCAACGTGTCACGCC
* * * * *
190121 ATATATCTACTATTACTACTCAATGTGTCA-C
65 ATATATCTGCTACTACTACTCAGTGTGTGATG
* ** * * * *
190152 CCTAGAAATCTGCTTTCACTCAGCGTGTCTTGCCTTAAATCTGGTACCACTCAACGTCTCACGCC
1 CC-ATAAATCCACTTTCACTCAACGTGTCATGCCCTAAATCTGGTACCACTCAACGTGTCACGCC
** *
190217 ATATAGT-TG---CTACTACTCAGCATGCGATG
65 ATATA-TCTGCTACTACTACTCAGTGTGTGATG
* * ** ** * * *
190246 CCATAAATCTACTTTCACTTAGTGTGTCATGCCCTCTATCTAGTACCACTCAGCATGTCACGCCA
1 CCATAAATCCACTTTCACTCAACGTGTCATGCCCTAAATCTGGTACCACTCAACGTGTCACGCCA
*
190311 TATATTTGCTACTACTACTCAGTGTGTGATG
66 TATATCTGCTACTACTACTCAGTGTGTGATG
** * * *
190342 CCATAAATCCACTTTCACTCAACGTGTCATGCCCTCTATCTGGTATCACTCACCGTGTCACACCA
1 CCATAAATCCACTTTCACTCAACGTGTCATGCCCTAAATCTGGTACCACTCAACGTGTCACGCCA
*
190407 TAAATCTGCTACTACTACTCAG
66 TATATCTGCTACTACTACTCAG
190429 CATGTCATGC
Statistics
Matches: 224, Mismatches: 45, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
92 1 0.00
93 69 0.31
94 2 0.01
95 2 0.01
96 149 0.67
97 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (96 bp):
CCATAAATCCACTTTCACTCAACGTGTCATGCCCTAAATCTGGTACCACTCAACGTGTCACGCCA
TATATCTGCTACTACTACTCAGTGTGTGATG
Found at i:190391 original size:31 final size:31
Alignment explanation
Indices: 190356--190458 Score: 98
Period size: 31 Copynumber: 3.2 Consensus size: 31
190346 AAATCCACTT
190356 TCACTCAACGTGTCATGCCCTCTATCTGGTA
1 TCACTCAACGTGTCATGCCCTCTATCTGGTA
* ** * ** *
190387 TCACTCACCGTGTCACACCATAAATCTGCTA
1 TCACTCAACGTGTCATGCCCTCTATCTGGTA
* *
190418 CTACTACTCAGCATGTCATGCCCTCTATCTGGTA
1 -T-C-ACTCAACGTGTCATGCCCTCTATCTGGTA
190452 TCACTCA
1 TCACTCA
190459 CAAGATGTCA
Statistics
Matches: 54, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
31 29 0.54
32 2 0.04
33 2 0.04
34 21 0.39
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.30
Consensus pattern (31 bp):
TCACTCAACGTGTCATGCCCTCTATCTGGTA
Found at i:190439 original size:96 final size:96
Alignment explanation
Indices: 190011--190439 Score: 356
Period size: 96 Copynumber: 4.5 Consensus size: 96
190001 ACATGCTACT
* * * * **
190011 ACTCAGCGTGTAACACCATAAATCTGC--C-ACGACTCAGCGTGTCACCCCATAAAT-CAGCTTT
1 ACTCAACGTGTCACGCCATAAATCTGCTACTACTACTCAGCGTGTCATGCCATAAATCCA-CTTT
* *
190072 CACTCAACATGTCATGCCCTAAATATGGTACC
65 CACTCAACGTGTCATGCCCTAAATCTGGTACC
* * * * * ** * * **
190104 ATTCAATGTGTCACGCCATATATCTACTATTACTACTCAATGTGTCA-CCCTAGAAATCTGCTTT
1 ACTCAACGTGTCACGCCATAAATCTGCTACTACTACTCAGCGTGTCATGCC-ATAAATCCACTTT
* * *
190168 CACTCAGCGTGTCTTGCCTTAAATCTGGTACC
65 CACTCAACGTGTCATGCCCTAAATCTGGTACC
* * * *
190200 ACTCAACGTCTCACGCCATATAGT-TG---CTACTACTCAGCATG-CGATGCCATAAATCTACTT
1 ACTCAACGTGTCACGCCATA-AATCTGCTACTACTACTCAGCGTGTC-ATGCCATAAATCCACTT
* ** ** *
190260 TCACTTAGTGTGTCATGCCCTCTATCTAGTACC
64 TCACTCAACGTGTCATGCCCTAAATCTGGTACC
* * * * * *
190293 ACTCAGCATGTCACGCCATATATTTGCTACTACTACTCAGTGTGTGATGCCATAAATCCACTTTC
1 ACTCAACGTGTCACGCCATAAATCTGCTACTACTACTCAGCGTGTCATGCCATAAATCCACTTTC
** *
190358 ACTCAACGTGTCATGCCCTCTATCTGGTATC
66 ACTCAACGTGTCATGCCCTAAATCTGGTACC
* * *
190389 ACTCACCGTGTCACACCATAAATCTGCTACTACTACTCAGCATGTCATGCC
1 ACTCAACGTGTCACGCCATAAATCTGCTACTACTACTCAGCGTGTCATGCC
190440 CTCTATCTGG
Statistics
Matches: 262, Mismatches: 61, Indels: 23
0.76 0.18 0.07
Matches are distributed among these distances:
92 2 0.01
93 87 0.33
94 2 0.01
95 3 0.01
96 167 0.64
97 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (96 bp):
ACTCAACGTGTCACGCCATAAATCTGCTACTACTACTCAGCGTGTCATGCCATAAATCCACTTTC
ACTCAACGTGTCATGCCCTAAATCTGGTACC
Found at i:191237 original size:24 final size:24
Alignment explanation
Indices: 191205--191257 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
191195 CCAGTAATAG
* *
191205 CTTCACTTGGTGTAACAACAGCAA
1 CTTCACTTGATGCAACAACAGCAA
* *
191229 CTTCACTTGATGCACCAATAGCAA
1 CTTCACTTGATGCAACAACAGCAA
191253 CTTCA
1 CTTCA
191258 GTCGTTCCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.26
Consensus pattern (24 bp):
CTTCACTTGATGCAACAACAGCAA
Found at i:194005 original size:21 final size:21
Alignment explanation
Indices: 193963--194008 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
193953 TATCAAAATA
* *
193963 ATCTTCATTTAAGCCTTCTTC
1 ATCTTCATTTAAACATTCTTC
* *
193984 ATCTTCATTTAAATATTTTTC
1 ATCTTCATTTAAACATTCTTC
194005 ATCT
1 ATCT
194009 CCAACATCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.02, T:0.52
Consensus pattern (21 bp):
ATCTTCATTTAAACATTCTTC
Found at i:199238 original size:26 final size:23
Alignment explanation
Indices: 199209--199261 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
199199 CGTGTTCTAA
*
199209 ATTTCTCAATCATATTGTTACACATC
1 ATTTCTCAAT--TA-TGTTACACACC
*
199235 ATTTTTCAATTATGTTACACACC
1 ATTTCTCAATTATGTTACACACC
199258 ATTT
1 ATTT
199262 TTTAAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.56
24 2 0.08
26 9 0.36
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (23 bp):
ATTTCTCAATTATGTTACACACC
Found at i:199254 original size:23 final size:23
Alignment explanation
Indices: 199224--199277 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
199214 TCAATCATAT
* **
199224 TGTTACACATCATTTTTCAATTA
1 TGTTACACACCATTTTTCAAAAA
*
199247 TGTTACACACCATTTTTTAAAAA
1 TGTTACACACCATTTTTCAAAAA
199270 TGTTACAC
1 TGTTACAC
199278 GTTATGTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.43
Consensus pattern (23 bp):
TGTTACACACCATTTTTCAAAAA
Found at i:199345 original size:44 final size:44
Alignment explanation
Indices: 199262--199387 Score: 162
Period size: 44 Copynumber: 2.8 Consensus size: 44
199252 CACACCATTT
* * * *
199262 TTTAAAAATGTTACACGTTATGTTCAAAAAATGATACATGTCATG
1 TTTAAAAATGTTACACG-TAAGTTCAAAAATTGTTACATGCCATG
* * *
199307 TTTAAAAATGTTACATGCAAGTTCAAAAATTGTTACATGCCCTG
1 TTTAAAAATGTTACACGTAAGTTCAAAAATTGTTACATGCCATG
* *
199351 TTCAAAAATGTTACACGTAAGTTTAAAAATTGTTACA
1 TTTAAAAATGTTACACGTAAGTTCAAAAATTGTTACA
199388 CACAAGTTCA
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
44 54 0.77
45 16 0.23
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (44 bp):
TTTAAAAATGTTACACGTAAGTTCAAAAATTGTTACATGCCATG
Found at i:199418 original size:22 final size:22
Alignment explanation
Indices: 199265--199432 Score: 135
Period size: 22 Copynumber: 7.6 Consensus size: 22
199255 ACCATTTTTT
*
199265 AAAAATGTTACACGTTATGTTC
1 AAAAATGTTACACGTCATGTTC
* * *
199287 AAAAAATGATACATGTCATGTTT
1 -AAAAATGTTACACGTCATGTTC
* *
199310 AAAAATGTTACATG-CAAGTTC
1 AAAAATGTTACACGTCATGTTC
* * *
199331 AAAAATTGTTACATGCCCTGTTC
1 AAAAA-TGTTACACGTCATGTTC
* *
199354 AAAAATGTTACACGT-AAGTTT
1 AAAAATGTTACACGTCATGTTC
* *
199375 AAAAATTGTTACAC-ACAAGTTC
1 AAAAA-TGTTACACGTCATGTTC
* *
199397 AAAATTGTTACACGTTATGTTC
1 AAAAATGTTACACGTCATGTTC
*
199419 ACAACATGTTACAC
1 A-AAAATGTTACAC
199433 ACCATGTGCT
Statistics
Matches: 117, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
21 26 0.22
22 53 0.45
23 38 0.32
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (22 bp):
AAAAATGTTACACGTCATGTTC
Found at i:199428 original size:66 final size:66
Alignment explanation
Indices: 199265--199432 Score: 198
Period size: 66 Copynumber: 2.5 Consensus size: 66
199255 ACCATTTTTT
* * * **
199265 AAAAA-TGTTACACGTTATGTTCAAAAAATGATACATGTCATGTTTAAAAATGTTACATGCAAGT
1 AAAAATTGTTACACGTTATGTTC-AAAAATGTTACACGTCAAGTTTAAAAATGTTACACACAAGT
199329 TC
65 TC
* ***
199331 AAAAATTGTTACATGCCCTGTTCAAAAATGTTACACGT-AAGTTTAAAAATTGTTACACACAAGT
1 AAAAATTGTTACACGTTATGTTCAAAAATGTTACACGTCAAGTTTAAAAA-TGTTACACACAAGT
199395 TC
65 TC
*
199397 -AAAATTGTTACACGTTATGTTCACAACATGTTACAC
1 AAAAATTGTTACACGTTATGTTCA-AAAATGTTACAC
199433 ACCATGTGCT
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
65 29 0.34
66 43 0.51
67 13 0.15
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (66 bp):
AAAAATTGTTACACGTTATGTTCAAAAATGTTACACGTCAAGTTTAAAAATGTTACACACAAGTT
C
Found at i:200235 original size:14 final size:13
Alignment explanation
Indices: 200151--200236 Score: 52
Period size: 14 Copynumber: 6.4 Consensus size: 13
200141 AGTTGAAGGT
*
200151 AAAAGAAAAAAGA
1 AAAATAAAAAAGA
200164 AAAGA-AAAAGAAGA
1 AAA-ATAAAA-AAGA
*
200178 AAAAGTAAGGAAAG-
1 AAAA-TAA-AAAAGA
200192 -AAATAAAAATAGA
1 AAAATAAAAA-AGA
* * *
200205 AAAATGAAAAGGG
1 AAAATAAAAAAGA
200218 AAAATAAACAAAGA
1 AAAATAAA-AAAGA
200232 AAAAT
1 AAAAT
200237 TGGAAGATGA
Statistics
Matches: 56, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
11 2 0.04
12 5 0.09
13 19 0.34
14 24 0.43
15 5 0.09
16 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.07
Consensus pattern (13 bp):
AAAATAAAAAAGA
Found at i:200966 original size:27 final size:27
Alignment explanation
Indices: 200907--200994 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
200897 TAGAGACTAA
*
200907 GTTACACGCCATGTT--AAAAAATGTT
1 GTTACACACCATGTTCAAAAAAATGTT
*
200932 GTTATTACATACCATGTTCAAAAAAATGTT
1 G---TTACACACCATGTTCAAAAAAATGTT
* * *
200962 GTTACACACTATGTTGAAAAAAA-ATT
1 GTTACACACCATGTTCAAAAAAATGTT
200988 GTTACAC
1 GTTACAC
200995 GTTGTTTAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
25 1 0.02
26 9 0.17
27 19 0.37
28 12 0.23
30 11 0.21
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (27 bp):
GTTACACACCATGTTCAAAAAAATGTT
Found at i:201727 original size:27 final size:27
Alignment explanation
Indices: 201697--201777 Score: 153
Period size: 27 Copynumber: 3.0 Consensus size: 27
201687 TACTATACGC
201697 CAAAACTTCCTTCTTCATACTGATGTT
1 CAAAACTTCCTTCTTCATACTGATGTT
201724 CAAAACTTCCTTCTTCATACTGATGTT
1 CAAAACTTCCTTCTTCATACTGATGTT
*
201751 CAAAACTTCCTTCTTCATATTGATGTT
1 CAAAACTTCCTTCTTCATACTGATGTT
201778 ACACGCCAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.42
Consensus pattern (27 bp):
CAAAACTTCCTTCTTCATACTGATGTT
Found at i:211321 original size:61 final size:61
Alignment explanation
Indices: 211251--211370 Score: 147
Period size: 61 Copynumber: 1.9 Consensus size: 61
211241 CATACTCCCC
*
211251 AAAAAGTTCAAAA-CTTTCCAACTAAGCA-GAACTGAAAATCCTTA-TAACACATACCCTCTTA
1 AAAAAGTTCAAAATC-TTCCAACAAAG-ATGAACT-AAAATCCTTATTAACACATACCCTCTTA
* *
211312 AAAAAGTTCACAATCTTCCAACAAAGATGAACTAAAGTCCTTATTTTAACACATACCCT
1 AAAAAGTTCAAAATCTTCCAACAAAGATGAACTAAAATCCTTA--TTAACACATACCCT
211371 AGAGAAGAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
60 10 0.20
61 27 0.53
62 1 0.02
63 13 0.25
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (61 bp):
AAAAAGTTCAAAATCTTCCAACAAAGATGAACTAAAATCCTTATTAACACATACCCTCTTA
Found at i:213028 original size:53 final size:53
Alignment explanation
Indices: 212942--213047 Score: 160
Period size: 53 Copynumber: 2.0 Consensus size: 53
212932 AGTTAAAGAA
*
212942 AGTGTAAATCTTTATATATCTAGTCTTATTCTAATACACAATAGATGTGAGAT
1 AGTGTAAATCTTTATATATCTAGTCTTACTCTAATACACAATAGATGTGAGAT
* * *
212995 AGTGTAAATCTTTATATATTTAGT-TTCACTCTAATACATAATATATGTGAGAT
1 AGTGTAAATCTTTATATATCTAGTCTT-ACTCTAATACACAATAGATGTGAGAT
213048 TTATAGCATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 2 0.04
53 46 0.96
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (53 bp):
AGTGTAAATCTTTATATATCTAGTCTTACTCTAATACACAATAGATGTGAGAT
Found at i:213560 original size:15 final size:15
Alignment explanation
Indices: 213537--213566 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
213527 AGAACCTCCC
*
213537 AAATGTTTTGGAGGG
1 AAATCTTTTGGAGGG
213552 AAATCTTTTGGAGGG
1 AAATCTTTTGGAGGG
213567 GGGAATACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.37, T:0.33
Consensus pattern (15 bp):
AAATCTTTTGGAGGG
Found at i:213948 original size:37 final size:36
Alignment explanation
Indices: 213898--214010 Score: 156
Period size: 37 Copynumber: 3.1 Consensus size: 36
213888 AGTTGGTATA
*
213898 AGAGCCATTGCGATCCAAGTGCTCGACGAAATTCCGC
1 AGAGCCATTGCGATCCAGGTGCTCGACGAAATTCC-C
*
213935 AGAGCCATTGCGATCCAGGTGCTCGACGAAATTCCT
1 AGAGCCATTGCGATCCAGGTGCTCGACGAAATTCCC
* *
213971 AGAG-CAGTTTGCGATCCAGGTGTTCGACAAAATTCCC
1 AGAGCCA--TTGCGATCCAGGTGCTCGACGAAATTCCC
214008 AGA
1 AGA
214011 CCAAAGGGAA
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
35 2 0.03
36 4 0.06
37 63 0.91
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.21
Consensus pattern (36 bp):
AGAGCCATTGCGATCCAGGTGCTCGACGAAATTCCC
Found at i:222564 original size:39 final size:39
Alignment explanation
Indices: 222515--222594 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
222505 AATAGATTAA
222515 TAAGTAAACAACATA-CAAAACT-TTTAAATTTATCTATTT
1 TAAGTAAACAACATAGC-AAA-TGTTTAAATTTATCTATTT
* ** *
222554 TAAGTTAACAAGGTAGCTAATGTTTAAATTTATCTATTT
1 TAAGTAAACAACATAGCAAATGTTTAAATTTATCTATTT
222593 TA
1 TA
222595 TTTTAAATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 1 0.03
39 33 0.94
40 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (39 bp):
TAAGTAAACAACATAGCAAATGTTTAAATTTATCTATTT
Found at i:222617 original size:22 final size:20
Alignment explanation
Indices: 222576--222626 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
222566 GTAGCTAATG
222576 TTTAAATTTATCTATTTTAT
1 TTTAAATTTATCTATTTTAT
*
222596 TTTAAATGTTATTTAATTTTAT
1 TTTAAAT-TTATCT-ATTTTAT
*
222618 TTTTAATTT
1 TTTAAATTT
222627 TAAAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 7 0.26
21 7 0.26
22 13 0.48
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTAAATTTATCTATTTTAT
Found at i:223060 original size:246 final size:246
Alignment explanation
Indices: 222808--223271 Score: 586
Period size: 247 Copynumber: 1.9 Consensus size: 246
222798 ACATCAAGGT
* * *
222808 TTTTCAATTGTAAATTTTTATCATAATT-TTTTGTA-C-T-ATTATTTATTT-A-T-AGATTAAA
1 TTTTCAATTGTAAATTTTAACCATAATTATTTT-TATCTTAATTATTT-TTTAATTAAAATTAAA
* *
222866 ATTTA-TCATCTGTTAAATACCTTAAACT-TGAGAATATAAATTTAAATTTTTATTTTTTATTAA
64 ATTTATTCATC-GTTAAATA-CTTAAA-TATGAGAATATAAATTTAAA-TATT-TTTTCT-TTAA
* * *
222929 AATTATATTTCTTTTACTTAATTGATTTATTACATTAATTCTCACATATTTATGTTAAAATTTTA
123 AATTAAATTT-TTTTACTTAATTGACTTATTACATTAACTCTCACATATTTATGTTAAAATTTTA
222994 AATTTACTTATTCAACTTTTATAAATTTTTATGTCAATTCTTACAATTTTATGTGAAGAC
187 AATTTACTTATTCAACTTTTATAAATTTTTATGTCAATTCTTACAATTTTATGTGAAGAC
* *
223054 TTTTCAATTGTAACTTTTAACCATGATTATTTTTATCTTAATTATTTTTTAATTTAAAATTAAAA
1 TTTTCAATTGTAAATTTTAACCATAATTATTTTTATCTTAATTATTTTTTAA-TTAAAATTAAAA
* * *
223119 TTTATTTATCGTTAAATACTTTAATATGAGAGTATAAATTTAAATATTTTTTCTTTAAAATTAAA
65 TTTATTCATCGTTAAATACTTAAATATGAGAATATAAATTTAAATATTTTTTCTTTAAAATTAAA
* *** * *
223184 TTTTTTTACTTAATTGACTTGTTGTGTTAACTCTCACATATTTATGTTAAAATTTTAATTTTTCT
130 TTTTTTTACTTAATTGACTTATTACATTAACTCTCACATATTTATGTTAAAATTTTAAATTTACT
* *
223249 TATTCCACTTTTATAAGTTTTTA
195 TATTCAACTTTTATAAATTTTTA
223272 CTTTAATTTT
Statistics
Matches: 187, Mismatches: 21, Indels: 19
0.82 0.09 0.08
Matches are distributed among these distances:
246 26 0.14
247 80 0.43
248 17 0.09
249 13 0.07
250 4 0.02
251 23 0.12
252 20 0.11
253 4 0.02
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (246 bp):
TTTTCAATTGTAAATTTTAACCATAATTATTTTTATCTTAATTATTTTTTAATTAAAATTAAAAT
TTATTCATCGTTAAATACTTAAATATGAGAATATAAATTTAAATATTTTTTCTTTAAAATTAAAT
TTTTTTACTTAATTGACTTATTACATTAACTCTCACATATTTATGTTAAAATTTTAAATTTACTT
ATTCAACTTTTATAAATTTTTATGTCAATTCTTACAATTTTATGTGAAGAC
Found at i:223226 original size:247 final size:251
Alignment explanation
Indices: 222860--223320 Score: 612
Period size: 247 Copynumber: 1.8 Consensus size: 251
222850 TTATTTATAG
* *
222860 ATTAAAATTTATCATCTGTTAAATACCTTAAACTTGAGAATATAAATTTAAATTTTTATTTTTTA
1 ATTAAAATTTATCATCTGTTAAATACCTTAAAC-TGAGAATATAAATTTAAATTATTATTTTCTA
* * *
222925 TTAAAATTATATTTCTTTTACTTAATTGATTTATTACATTAATTCTCACATATTTATGTTAAAAT
65 TTAAAATTAAATTTCTTTTACTTAATTGACTTATTACATTAACTCTCACATATTTATGTTAAAAT
* ** * *
222990 TTTAAATTTACTTATTCAACTTTTATAAATTTTTA-TGTCAATTCTTACAATTTTATGTGAAGAC
130 TTTAAATTTACTTATTCAACTTTTATAAATTTTTACT-TCAATTCTTACAACTTTACCTCAAAAC
**
223054 TTTTCAATTGTAACTTTTAACCATGATTATTTTTATCTTAATTATTTTTTAATTTAAA
194 TTTTCAATACTAACTTTTAACCATGATTATTTTTATCTTAATTATTTTTTAATTTAAA
* * *
223112 ATTAAAATTTATTTATC-GTTAAATACTTTAATA-TGAGAGTATAAATTTAAA-TATT-TTTTCT
1 ATTAAAATTTA-TCATCTGTTAAATACCTTAA-ACTGAGAATATAAATTTAAATTATTATTTTCT
* ***
223173 -TTAAAATTAAATTT-TTTTACTTAATTGACTTGTTGTGTTAACTCTCACATATTTATGTTAAAA
64 ATTAAAATTAAATTTCTTTTACTTAATTGACTTATTACATTAACTCTCACATATTTATGTTAAAA
* * * * * *
223236 TTTTAATTTTTCTTATTCCACTTTTATAAGTTTTTACTTTAATTTTTACAACTTTACCTCAAAAC
129 TTTTAAATTTACTTATTCAACTTTTATAAATTTTTACTTCAATTCTTACAACTTTACCTCAAAAC
223301 TTTTCAATACTAACTTTTAA
194 TTTTCAATACTAACTTTTAA
223321 AAAAATTAGA
Statistics
Matches: 181, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
247 113 0.62
248 14 0.08
249 5 0.03
250 3 0.02
251 17 0.09
252 24 0.13
253 5 0.03
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (251 bp):
ATTAAAATTTATCATCTGTTAAATACCTTAAACTGAGAATATAAATTTAAATTATTATTTTCTAT
TAAAATTAAATTTCTTTTACTTAATTGACTTATTACATTAACTCTCACATATTTATGTTAAAATT
TTAAATTTACTTATTCAACTTTTATAAATTTTTACTTCAATTCTTACAACTTTACCTCAAAACTT
TTCAATACTAACTTTTAACCATGATTATTTTTATCTTAATTATTTTTTAATTTAAA
Found at i:223523 original size:296 final size:293
Alignment explanation
Indices: 223079--223616 Score: 714
Period size: 296 Copynumber: 1.8 Consensus size: 293
223069 TTTAACCATG
* * *
223079 ATTATTTTTATCTTAATTATTTTTTAATTTAAAATTAAAATTTATTTATCGTTAAATACTTTAAT
1 ATTATTTTTATCTTAATTATTCTTTAATTTAAAATTAAAATTTATATATCATTAAATACTTTAAT
* * *
223144 ATGAGAGTATAAATTTAAATATTTTTTCTTTAAAATTAAATTTTTTTACTTAATTGACTTGTTGT
66 ATGAAAATATAAATTTAAATATTTTTTCTTTAAAATTAAATTTTTTTACTTAATTGACTTGTTAT
** *
223209 GTTAACTCTCACATATTTATGTTAAAATTTT-AATTTTTCTTATTCCACTTTTATA-AGTTTTTA
131 AATAACTCTCACATATTTATGTTAAAATTTTCAA-TTTGCTTATTCCACTTTTATATA-TTTTTA
* *
223272 CTTTAATT-TTTACAACTTTACCTCAAAACTTTTCAATACTAACTTTTAAAAAAATTAGATTAAG
194 CGTCAATTCTTT-CAACTTTACCTCAAAACTTTTCAATACTAACTTTTAAAAAAATTAGATTAAG
223336 GGTTTTCAACGGCAACTTTAAATTACATGAACTATA
258 GGTTTTCAACGGCAACTTTAAATTACATGAACTATA
*
223372 ATTATTTTT-TCCTT-ATTATTCTTTATTTTAAAATTAAAATTTATATATCATTAAATACTTTTA
1 ATTATTTTTAT-CTTAATTATTCTTTAATTTAAAATTAAAATTTATATATCATTAAATAC-TTTA
*
223435 ACT-TGAAAATATAAATTTAAATGTTTGTTT-TTTATTAAAGTT-AATTTTTTTAACTTAATTGA
64 A-TATGAAAATATAAATTTAAATATTT-TTTCTTTA--AAA-TTAAATTTTTTT-ACTTAATTGA
* ** * *
223497 CTTGTTATAATAACTCTTACATATTTATGTTAGGATTTTCAATTTGCTTGTTCTACTTTTATATA
123 CTTGTTATAATAACTCTCACATATTTATGTTAAAATTTTCAATTTGCTTATTCCACTTTTATATA
** * * *
223562 TTTTTACGTCAATTCTTTCAACTTTATGTTAAGACTTTTCAATAGTAACTTTTAA
188 TTTTTACGTCAATTCTTTCAACTTTACCTCAAAACTTTTCAATACTAACTTTTAA
223617 CTAGATTTAT
Statistics
Matches: 211, Mismatches: 23, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
292 41 0.19
293 41 0.19
294 4 0.02
295 12 0.06
296 107 0.51
297 6 0.03
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.51
Consensus pattern (293 bp):
ATTATTTTTATCTTAATTATTCTTTAATTTAAAATTAAAATTTATATATCATTAAATACTTTAAT
ATGAAAATATAAATTTAAATATTTTTTCTTTAAAATTAAATTTTTTTACTTAATTGACTTGTTAT
AATAACTCTCACATATTTATGTTAAAATTTTCAATTTGCTTATTCCACTTTTATATATTTTTACG
TCAATTCTTTCAACTTTACCTCAAAACTTTTCAATACTAACTTTTAAAAAAATTAGATTAAGGGT
TTTCAACGGCAACTTTAAATTACATGAACTATA
Found at i:223966 original size:18 final size:18
Alignment explanation
Indices: 223940--223981 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
223930 GAAAAATATA
*
223940 AATTTAAATAATTTTTTT
1 AATTAAAATAATTTTTTT
223958 AATTAAAATAATTTTTTT
1 AATTAAAATAATTTTTTT
*
223976 ATTTAA
1 AATTAA
223982 TTCACTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTAAAATAATTTTTTT
Found at i:225063 original size:21 final size:19
Alignment explanation
Indices: 225025--225064 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
225015 ATAAATGAGC
*
225025 TTTGTTTTTTATGGTTGTT
1 TTTGTTTTTTATGATTGTT
225044 TTTGTTATTATTATGATTGTT
1 TTTGTT-TT-TTATGATTGTT
225065 AGGAAGCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.12, C:0.00, G:0.17, T:0.70
Consensus pattern (19 bp):
TTTGTTTTTTATGATTGTT
Found at i:225449 original size:29 final size:29
Alignment explanation
Indices: 225402--225459 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
225392 GGTGAGAGTT
**
225402 GGGATCTTCTTTTTGGAAGAGATTTGAAG
1 GGGATCTTCTTTTCAGAAGAGATTTGAAG
225431 GGGATCTTCTTTTCAGAAGAGATTTGAAG
1 GGGATCTTCTTTTCAGAAGAGATTTGAAG
225460 CTATGAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.36
Consensus pattern (29 bp):
GGGATCTTCTTTTCAGAAGAGATTTGAAG
Found at i:236793 original size:6 final size:5
Alignment explanation
Indices: 236759--236792 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
236749 TATTAATGTA
236759 TTATT ATTATT ATTATT TTATT TTATT TTATT TT
1 TTATT -TTATT -TTATT TTATT TTATT TTATT TT
236793 TTGAGATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 17 0.61
6 11 0.39
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:240961 original size:6 final size:6
Alignment explanation
Indices: 240944--240974 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
240934 GGTAGTGATG
*
240944 TGTTCT TCTTCT TGTTCT TGTTCT TGTTCT T
1 TGTTCT TGTTCT TGTTCT TGTTCT TGTTCT T
240975 CTTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.19, G:0.13, T:0.68
Consensus pattern (6 bp):
TGTTCT
Found at i:240961 original size:12 final size:12
Alignment explanation
Indices: 240944--240977 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
240934 GGTAGTGATG
240944 TGTTCTTCTTCT
1 TGTTCTTCTTCT
*
240956 TGTTCTTGTTCT
1 TGTTCTTCTTCT
240968 TGTTCTTCTT
1 TGTTCTTCTT
240978 ATTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.12, T:0.68
Consensus pattern (12 bp):
TGTTCTTCTTCT
Found at i:250424 original size:59 final size:59
Alignment explanation
Indices: 250332--250465 Score: 268
Period size: 59 Copynumber: 2.3 Consensus size: 59
250322 AATTCCTCTG
250332 AAACAAAGAAAAAAAACCAACCGCCAACTGTTCACACAAAGCCAAAGTGCAAAATCAAA
1 AAACAAAGAAAAAAAACCAACCGCCAACTGTTCACACAAAGCCAAAGTGCAAAATCAAA
250391 AAACAAAGAAAAAAAACCAACCGCCAACTGTTCACACAAAGCCAAAGTGCAAAATCAAA
1 AAACAAAGAAAAAAAACCAACCGCCAACTGTTCACACAAAGCCAAAGTGCAAAATCAAA
250450 AAACAAAGAAAAAAAA
1 AAACAAAGAAAAAAAA
250466 ATGCAATACT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 75 1.00
ACGTcount: A:0.60, C:0.23, G:0.10, T:0.07
Consensus pattern (59 bp):
AAACAAAGAAAAAAAACCAACCGCCAACTGTTCACACAAAGCCAAAGTGCAAAATCAAA
Found at i:251192 original size:78 final size:77
Alignment explanation
Indices: 251050--251199 Score: 178
Period size: 78 Copynumber: 1.9 Consensus size: 77
251040 CCCTCCATCC
* *
251050 ATCTCCAAAAGCTGAAATTCAAGTTGCCAATTGTTTACAAAATGCATCAAATAAAGTGCTTTCTT
1 ATCTCCAAAAGCTGAAATTCAACTTGCCAATTCTTTACAAAATGCATCAAATAAAGTGCTTTCTT
*
251115 CAATGCTAAAAG
66 AAATGCTAAAAG
* * * * * *
251127 ATCTCCATAAGGCTGAAATTCAACTTGCCATTTCTTCTTCAAGAT-CATCAATTAAATTGAC-TT
1 ATCTCCA-AAAGCTGAAATTCAACTTGCCAATTCTT-TACAAAATGCATCAAATAAAGTG-CTTT
251190 CTTAAATGCT
63 CTTAAATGCT
251200 GATAGAAGAC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
77 7 0.11
78 47 0.77
79 7 0.11
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.33
Consensus pattern (77 bp):
ATCTCCAAAAGCTGAAATTCAACTTGCCAATTCTTTACAAAATGCATCAAATAAAGTGCTTTCTT
AAATGCTAAAAG
Found at i:254505 original size:17 final size:18
Alignment explanation
Indices: 254471--254508 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
254461 TTAAAATCAT
254471 ATTTTAAAAAATTATTAA
1 ATTTTAAAAAATTATTAA
*
254489 ATTTTAATAAA-TATTAA
1 ATTTTAAAAAATTATTAA
254506 ATT
1 ATT
254509 AATTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTAAAAAATTATTAA
Found at i:262713 original size:15 final size:18
Alignment explanation
Indices: 262676--262713 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
262666 TTTGACGAAT
262676 TTTTTCTTCTTGTTTCTG
1 TTTTTCTTCTTGTTTCTG
262694 TTTTTCTTCTT-TTT-TG
1 TTTTTCTTCTTGTTTCTG
262710 TTTT
1 TTTT
262714 AATCCTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 3 0.15
18 11 0.55
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (18 bp):
TTTTTCTTCTTGTTTCTG
Found at i:268990 original size:2 final size:2
Alignment explanation
Indices: 268983--269022 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
268973 TTTGTTTATT
* * *
268983 TC TC TC TC TC TC TC TC TT TT TC TC TC TC AC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
269023 ATATTGTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:269006 original size:20 final size:20
Alignment explanation
Indices: 268981--269019 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
268971 GATTTGTTTA
*
268981 TTTCTCTCTCTCTCTCTCTT
1 TTTCTCTCTCACTCTCTCTT
269001 TTTCTCTCTCACTCTCTCT
1 TTTCTCTCTCACTCTCTCT
269020 CTCATATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTCTCTCTCACTCTCTCTT
Found at i:277973 original size:120 final size:120
Alignment explanation
Indices: 277780--278138 Score: 538
Period size: 120 Copynumber: 3.0 Consensus size: 120
277770 TCCTGGTGAC
* * * *
277780 GAATCATCGGAGTTTGGTCTTTCACTTGCAAAACTTCCATCATTTGATGAACCGTTGGAGTTGCT
1 GAATCATCGGAGTTTGCTCTTCCACTTGCAAAACTTCCATCATTTGATGAACCGTTAGAGTTACT
*
277845 TTGGATTTGATTAGACGAATGATGGTCATGAGAGTTTTCTCCAACTATGTTTGAT
66 TTGGATTTGATTAGACGAATGATGGTCATGAGAGTTTTCTCCAACTACGTTTGAT
* * *
277900 GAATCATCGGAGTTTGTTCTTCCACTTACAAAACTTCCATCATTTGATGAACCATTAGAGTTACT
1 GAATCATCGGAGTTTGCTCTTCCACTTGCAAAACTTCCATCATTTGATGAACCGTTAGAGTTACT
* * * *
277965 TTGGATTTGGTTTGACGAATGATGATCATGAGAGTTTTCTCCAACTCCGTTTGAT
66 TTGGATTTGATTAGACGAATGATGGTCATGAGAGTTTTCTCCAACTACGTTTGAT
* * * *
278020 GAATCATCGGAATTTGCTCTTCCACGTGCAAAACCTCCAACATTTGATGAACCGTTAGAGTTACT
1 GAATCATCGGAGTTTGCTCTTCCACTTGCAAAACTTCCATCATTTGATGAACCGTTAGAGTTACT
* * * *
278085 TCGGATTTGATTAGATGAATGATGGTCATGAGAGTTTTCTCCAGCTCCGTTTGA
66 TTGGATTTGATTAGACGAATGATGGTCATGAGAGTTTTCTCCAACTACGTTTGA
278139 CGAACCATTG
Statistics
Matches: 215, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
120 215 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (120 bp):
GAATCATCGGAGTTTGCTCTTCCACTTGCAAAACTTCCATCATTTGATGAACCGTTAGAGTTACT
TTGGATTTGATTAGACGAATGATGGTCATGAGAGTTTTCTCCAACTACGTTTGAT
Found at i:281201 original size:33 final size:33
Alignment explanation
Indices: 281138--281201 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
281128 AGTTTCAACC
*
281138 TTTTCTCACATTGCACCCTGTAATTTGTTTTTT
1 TTTTCTCACATTGCACCCTGTAATTAGTTTTTT
*
281171 TTTTCTCA-ATTGGCA-CCTGTTATTAAGTTTT
1 TTTTCTCACATT-GCACCCTGTAATT-AGTTTT
281202 GTTCCCACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (33 bp):
TTTTCTCACATTGCACCCTGTAATTAGTTTTTT
Found at i:284126 original size:15 final size:16
Alignment explanation
Indices: 284106--284135 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
284096 AATATTAGTA
284106 TATAAAT-TACTTTGC
1 TATAAATCTACTTTGC
284121 TATAAATCTACTTTG
1 TATAAATCTACTTTG
284136 ACTTAAAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (16 bp):
TATAAATCTACTTTGC
Found at i:285689 original size:34 final size:34
Alignment explanation
Indices: 285651--285715 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
285641 TGGCTCTTGC
* * *
285651 GAAAAGGCAAATTTTAAGTTGTGCTTACTCCTGT
1 GAAAAAGCAAATTGTAAGTTATGCTTACTCCTGT
**
285685 GAAAAAGCAAATTGTGGGTTATGCTTACTCC
1 GAAAAAGCAAATTGTAAGTTATGCTTACTCC
285716 CATTATAAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (34 bp):
GAAAAAGCAAATTGTAAGTTATGCTTACTCCTGT
Found at i:290888 original size:237 final size:231
Alignment explanation
Indices: 290301--290895 Score: 721
Period size: 233 Copynumber: 2.5 Consensus size: 231
290291 GGTAATGCCT
* * * * *
290301 AAACTTGAACAA-AATATTTTATATAATTAGTTTGTAGTGAGAAACACATACAACAGGAAATCAA
1 AAACTTGAA-AAGAATATTATATGTAATTAGTTTGTAGCGAAAAACACATACAAAAGGAAATCAA
* * *
290365 CATGATAGTATAAGGTAATGTTTAAACCTGAACTTTGAGTTTGTTGTTGAAGAGAATTAGTTAAG
65 CATGATAGTATAAGGTAATGTCTAAACCTGAACTTTGAGTTTGTTGTTGAAGAGAATTGGTCAAG
* * **
290430 TCATTTAAAATAAAACCTAAATTATGATCAAAATCTATGTTATATACATCAACTAAGTTAAAAGA
130 TCATTTAAAATAAAACCTAAATCATGATCAAAACCTACATTATATACATCAACTAAGTTAAAAGA
* **
290495 GTTGTTTTAGAATCCATTCACTTTGGAAGATAGTGTC
195 GTTGTTCTAGAATCCATTCACTTCAGAAGATAGTGTC
* *
290532 AAACTTGAAATAGAATATTATATGTAATAAGTTTGTAGCGAAAAACACATATAAAAGGAAATCAA
1 AAACTTGAAA-AGAATATTATATGTAATTAGTTTGTAGCGAAAAACACATACAAAAGGAAATCAA
* * * * * *
290597 CATAATAATATTAAGGTAATGTCTAAACTTAAACTCTAAGTTTGTTGTTGAAGAGAATTGGTCAA
65 CATGATAGTA-TAAGGTAATGTCTAAACCTGAACTTTGAGTTTGTTGTTGAAGAGAATTGGTCAA
* * *
290662 GTCATTTAAAGTAAAACCTAAATCATGATCAAAACCTACATTATATATAT-ATA-TTAGTTGGGT
129 GTCATTTAAAATAAAACCTAAATCATGATCAAAACCTACATTATATACATCA-ACTAAG-T---T
* * * * * *
290725 CAAAAAGATTTGCTTCT-GGATCCATTCACTTCAGATGGTGGTGTG
189 --AAAAGAGTTG-TTCTAGAATCCATTCACTTCAGAAGATAGTGTC
* * * *
290770 AAACTTGAAAAGAATATTATATGTGATTTGTTTGTAGCAAAAAATCACATACAAAAAGAAATCAA
1 AAACTTGAAAAGAATATTATATGTAATTAGTTTGTAGCGAAAAA-CACATACAAAAGGAAATCAA
*
290835 CATGATGGTATAAGGTAATGTCTAAACCTGAACTTTGAGTTTGTTGTTGAAGAGAATTGGT
65 CATGATAGTATAAGGTAATGTCTAAACCTGAACTTTGAGTTTGTTGTTGAAGAGAATTGGT
290896 TGTGGTGTAT
Statistics
Matches: 307, Mismatches: 45, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
230 1 0.00
231 10 0.03
232 57 0.19
233 93 0.30
236 1 0.00
237 77 0.25
238 65 0.21
239 3 0.01
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (231 bp):
AAACTTGAAAAGAATATTATATGTAATTAGTTTGTAGCGAAAAACACATACAAAAGGAAATCAAC
ATGATAGTATAAGGTAATGTCTAAACCTGAACTTTGAGTTTGTTGTTGAAGAGAATTGGTCAAGT
CATTTAAAATAAAACCTAAATCATGATCAAAACCTACATTATATACATCAACTAAGTTAAAAGAG
TTGTTCTAGAATCCATTCACTTCAGAAGATAGTGTC
Found at i:296819 original size:35 final size:35
Alignment explanation
Indices: 296772--296841 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
296762 ATAAGTTCCC
296772 ATAACATATTCTTTTAAAATATTTTGCC-AAATATA
1 ATAACATATTCTTTTAAAATATTTT-CCAAAATATA
*
296807 ATAACATGTTCTTTTAAAATATTTTCCAAAATATA
1 ATAACATATTCTTTTAAAATATTTTCCAAAATATA
296842 TCCAGCAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (35 bp):
ATAACATATTCTTTTAAAATATTTTCCAAAATATA
Found at i:297466 original size:26 final size:25
Alignment explanation
Indices: 297436--297485 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
297426 AAAATGGTTC
297436 ATTTAATTCAAA-ATAAAAATAAAATT
1 ATTTAATT-AAACATAAAAA-AAAATT
*
297462 ATTTAATTAAACATAATAAAAAAT
1 ATTTAATTAAACATAAAAAAAAAT
297486 AAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (25 bp):
ATTTAATTAAACATAAAAAAAAATT
Found at i:299383 original size:2 final size:2
Alignment explanation
Indices: 299339--299366 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
299329 TTCTCTTTTG
299339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
299367 GCACACGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:302850 original size:18 final size:18
Alignment explanation
Indices: 302827--302862 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
302817 AATTTGTCAC
302827 AAATTTTG-TAAAATAAAT
1 AAATTTTGATAAAA-AAAT
302845 AAATTTTGATAAAAAAAT
1 AAATTTTGATAAAAAAAT
302863 TATGTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (18 bp):
AAATTTTGATAAAAAAAT
Found at i:339101 original size:12 final size:13
Alignment explanation
Indices: 339068--339112 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
339058 TTAGGTATTA
*
339068 TTTCT-TTTTTTT
1 TTTCTATTTTGTT
339080 CTTTCTATTTTGTT
1 -TTTCTATTTTGTT
339094 TTTC-ATTTTG-T
1 TTTCTATTTTGTT
339105 TTTCTATT
1 TTTCTATT
339113 GTTTTTTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 5 0.17
12 9 0.31
13 9 0.31
14 6 0.21
ACGTcount: A:0.07, C:0.11, G:0.04, T:0.78
Consensus pattern (13 bp):
TTTCTATTTTGTT
Found at i:349211 original size:3 final size:3
Alignment explanation
Indices: 349203--349232 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
349193 AATCATGATA
*
349203 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
349233 GTTTAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:362557 original size:12 final size:13
Alignment explanation
Indices: 362541--362586 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
362531 CACACGTCCT
362541 TTAAATTTTATT-
1 TTAAATTTTATTA
*
362553 TTAAAATTTATTA
1 TTAAATTTTATTA
362566 TT--ATTATTATTA
1 TTAAATT-TTATTA
362578 TTAAATTTT
1 TTAAATTTT
362587 GTATAAGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
11 2 0.07
12 19 0.68
13 4 0.14
14 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTAAATTTTATTA
Found at i:369296 original size:2 final size:2
Alignment explanation
Indices: 369289--369319 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
369279 NNNNNNNNNN
369289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
369320 AAATGATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:370986 original size:82 final size:82
Alignment explanation
Indices: 370849--371011 Score: 265
Period size: 82 Copynumber: 2.0 Consensus size: 82
370839 GAATAAAGAT
* * *
370849 TTTGTTAACCACTTGTTATCCATGAGAATATATCATTCTGTTAATTACAATTCTTTATTAAATTG
1 TTTGTTAACCACTTGTGAACCATGAGAATATATCATTCTGTTAATTACAATTCTTTACTAAATTG
370914 ACAGATTTTCAATATCA
66 ACAGATTTTCAATATCA
*
370931 TTTGTTAACCACTTGTGAACCATGAGAATATATCATTCTGTTAATT-CGGATTCTTTACTAAATT
1 TTTGTTAACCACTTGTGAACCATGAGAATATATCATTCTGTTAATTAC-AATTCTTTACTAAATT
*
370995 GACAGATTTTCTATATC
65 GACAGATTTTCAATATC
371012 CAATATTTAC
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
81 1 0.01
82 74 0.99
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.43
Consensus pattern (82 bp):
TTTGTTAACCACTTGTGAACCATGAGAATATATCATTCTGTTAATTACAATTCTTTACTAAATTG
ACAGATTTTCAATATCA
Found at i:385587 original size:2 final size:2
Alignment explanation
Indices: 385571--385667 Score: 148
Period size: 2 Copynumber: 49.5 Consensus size: 2
385561 TCTAAATAGA
385571 TC TC T- TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
385610 TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC GTC TC ATC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC -TC TC TC
385653 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
385668 ATACATACAT
Statistics
Matches: 89, Mismatches: 0, Indels: 12
0.88 0.00 0.12
Matches are distributed among these distances:
1 4 0.04
2 81 0.91
3 4 0.04
ACGTcount: A:0.01, C:0.49, G:0.01, T:0.48
Consensus pattern (2 bp):
TC
Found at i:385607 original size:27 final size:27
Alignment explanation
Indices: 385571--385667 Score: 162
Period size: 27 Copynumber: 3.6 Consensus size: 27
385561 TCTAAATAGA
385571 TCTCT-TCTCCTCTCTCTCTCTCTCTC
1 TCTCTCTCTCCTCTCTCTCTCTCTCTC
385597 TCTCTCTCTCCTCTCTCTCTCTCTCTC
1 TCTCTCTCTCCTCTCTCTCTCTCTCTC
385624 TCTCTCTCTCCTCTCTCGTCTCATCTCTC
1 TCTCTCTCTCCTCTCTC-TCTC-TCTCTC
385653 TCTCTCTCT-CTCTCT
1 TCTCTCTCTCCTCTCT
385668 ATACATACAT
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
26 5 0.07
27 38 0.56
28 10 0.15
29 15 0.22
ACGTcount: A:0.01, C:0.49, G:0.01, T:0.48
Consensus pattern (27 bp):
TCTCTCTCTCCTCTCTCTCTCTCTCTC
Found at i:387409 original size:2 final size:2
Alignment explanation
Indices: 387402--387428 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
387392 AATTAATGAG
387402 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
387429 TCTACATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:398188 original size:12 final size:13
Alignment explanation
Indices: 398167--398195 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
398157 GCTCCCAAAG
398167 AAAATAAAAAATA
1 AAAATAAAAAATA
398180 AAAAT-AAAAATA
1 AAAATAAAAAATA
398192 AAAA
1 AAAA
398196 AGAAAAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:398208 original size:19 final size:19
Alignment explanation
Indices: 398166--398209 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
398156 AGCTCCCAAA
* *
398166 GAAAATAAAAAATAAAAAT
1 GAAAATAAAAAAGAAAAAG
*
398185 AAAAATAAAAAAGAAAAAG
1 GAAAATAAAAAAGAAAAAG
398204 GAAAAT
1 GAAAAT
398210 CCTTTTACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (19 bp):
GAAAATAAAAAAGAAAAAG
Found at i:398788 original size:18 final size:17
Alignment explanation
Indices: 398751--398798 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
398741 GCGATTACAC
398751 GGATGATGAAG--AAGA
1 GGATGATGAAGAAAAGA
*
398766 TGATGATGAAGAAAGAGA
1 GGATGATGAAGAAA-AGA
*
398784 GGATGATGATGAAAA
1 GGATGATGAAGAAAA
398799 TGGGGATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 10 0.37
17 2 0.07
18 15 0.56
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.17
Consensus pattern (17 bp):
GGATGATGAAGAAAAGA
Found at i:402804 original size:18 final size:16
Alignment explanation
Indices: 402781--402814 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
402771 GAAACAGCTG
402781 ATGCTTTTAGTGTTGGTT
1 ATGCTTTT-GTG-TGGTT
402799 ATGCTTTTGTGTGGTT
1 ATGCTTTTGTGTGGTT
402815 GTCTACTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.09, C:0.06, G:0.29, T:0.56
Consensus pattern (16 bp):
ATGCTTTTGTGTGGTT
Found at i:404571 original size:23 final size:22
Alignment explanation
Indices: 404543--404609 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 22
404533 TAAATTTGCC
404543 AAAGTAAACTTGGAATAATTGA
1 AAAGTAAACTTGGAATAATTGA
* * *
404565 AACAGTAAACAT--AA-ATTTGCC
1 AA-AGTAAACTTGGAATAATTG-A
404586 AAAGTAAACTTGGAATAATTGA
1 AAAGTAAACTTGGAATAATTGA
404608 AA
1 AA
404610 TAGGCTATCT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
20 12 0.35
21 4 0.12
22 6 0.18
23 12 0.35
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (22 bp):
AAAGTAAACTTGGAATAATTGA
Found at i:404585 original size:43 final size:43
Alignment explanation
Indices: 404524--404609 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
404514 CTCTCTCAGG
*
404524 CAGTAAATATAAATTTGCCAAAGTAAACTTGGAATAATTGAAA
1 CAGTAAACATAAATTTGCCAAAGTAAACTTGGAATAATTGAAA
404567 CAGTAAACATAAATTTGCCAAAGTAAACTTGGAATAATTGAAA
1 CAGTAAACATAAATTTGCCAAAGTAAACTTGGAATAATTGAAA
404610 TAGGCTATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (43 bp):
CAGTAAACATAAATTTGCCAAAGTAAACTTGGAATAATTGAAA
Found at i:404593 original size:20 final size:20
Alignment explanation
Indices: 404525--404594 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
404515 TCTCTCAGGC
*
404525 AGTAAATATAAATTTGCCAA
1 AGTAAACATAAATTTGCCAA
* * *
404545 AGTAAACTTGGAATAATTG-AAA
1 AGTAAACAT--AA-ATTTGCCAA
404567 CAGTAAACATAAATTTGCCAA
1 -AGTAAACATAAATTTGCCAA
404588 AGTAAAC
1 AGTAAAC
404595 TTGGAATAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
20 18 0.47
21 4 0.11
22 4 0.11
23 12 0.32
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (20 bp):
AGTAAACATAAATTTGCCAA
Found at i:415295 original size:2 final size:2
Alignment explanation
Indices: 415288--415314 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
415278 AATGATTTCC
415288 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
415315 TACTAAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:419732 original size:85 final size:85
Alignment explanation
Indices: 419580--419739 Score: 205
Period size: 85 Copynumber: 1.9 Consensus size: 85
419570 CTGAGATCAG
* * *
419580 ATGGTGCATTTAAGGTTTGAAAGATTTATTAGATTTTTGAGATGAAGATGGAAAATGGGTATTTT
1 ATGGTGCATTTAAGGTTTGAAAGATTTATTACATTCTTGAGATGAAGATGGAAAATGGGTATATT
*
419645 TTTGCTTTTGTTTATAAAGA
66 TTTCCTTTTGTTTATAAAGA
* * * * * * *
419665 ATGGTGTATTTAATGTTTGAATGTTTTATTACATTCTTG-GCATGAAGATGGCAGATGGTTATAT
1 ATGGTGCATTTAAGGTTTGAAAGATTTATTACATTCTTGAG-ATGAAGATGGAAAATGGGTATAT
419729 TTTTCCTTTTG
65 TTTTCCTTTTG
419740 CGTATATGAG
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
84 1 0.02
85 62 0.98
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.46
Consensus pattern (85 bp):
ATGGTGCATTTAAGGTTTGAAAGATTTATTACATTCTTGAGATGAAGATGGAAAATGGGTATATT
TTTCCTTTTGTTTATAAAGA
Found at i:423693 original size:20 final size:17
Alignment explanation
Indices: 423670--423714 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 17
423660 TAACATAATT
423670 AAAAAAGAAAGAAAAGAACA
1 AAAAAAG-AAGAAAAG--CA
423690 AAAAAATGAAGAAAAGCA
1 AAAAAA-GAAGAAAAGCA
423708 AAAAAAG
1 AAAAAAG
423715 GTTGAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 8 0.33
20 14 0.58
21 1 0.04
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAGAAAAGCA
Found at i:427441 original size:51 final size:53
Alignment explanation
Indices: 427386--427516 Score: 119
Period size: 51 Copynumber: 2.5 Consensus size: 53
427376 AAGTCACAAA
* *
427386 TTCAAACTTAGTCTTGATCACAAACTTC-ACTTG-ATCTTCGCTTCATGGGTC
1 TTCAAACTTAGTCTTGATCACAAACTTCAACTTGAATCTTCACTTCAAGGGTC
* * * * *
427437 TTCAAGA-TTAATCTTAATCACGAAC-TCAATTTGATATCTTCACTTGAAGGGTC
1 TTCAA-ACTTAGTCTTGATCACAAACTTCAACTTGA-ATCTTCACTTCAAGGGTC
*
427490 TTCACGACTT-GATCTTGATCACAAACT
1 TTCA-AACTTAG-TCTTGATCACAAACT
427517 ATTCCGAAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
50 2 0.03
51 24 0.39
52 1 0.02
53 20 0.33
54 14 0.23
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (53 bp):
TTCAAACTTAGTCTTGATCACAAACTTCAACTTGAATCTTCACTTCAAGGGTC
Found at i:432002 original size:29 final size:28
Alignment explanation
Indices: 431964--432022 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
431954 AACCATCTTC
* *
431964 AAATGTGACAAATTCAAAAATTAAATTTTA
1 AAATGTGACAAA-T-AAAAATAAAATATTA
431994 AAAT-TGACAAATAAAAATAAAATATTA
1 AAATGTGACAAATAAAAATAAAATATTA
432021 AA
1 AA
432023 GAAAAAAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 15 0.56
28 1 0.04
29 7 0.26
30 4 0.15
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (28 bp):
AAATGTGACAAATAAAAATAAAATATTA
Found at i:442149 original size:324 final size:322
Alignment explanation
Indices: 441465--442405 Score: 1375
Period size: 324 Copynumber: 2.9 Consensus size: 322
441455 ATGAATTGAT
* * * *
441465 GAAATTGATGTAACTTTATGAGTCAAGCAAGTTAAAATTTCATAAGAATTTCGCATCAAGGCTAG
1 GAAAATGATGTAACTTTACGAGTCAAGCAAGTTGAAATTTCATAAGAATTTCGTATCAAGGCTAG
* * *
441530 GCCAAAGCTAGCCAACATCATTTAAGATATTACTCTAAGTATTGCAACTTCTTTTAAGGGTTCGA
66 GCCAAAGCTGGCCAACATCATTTAAGATATTAC-CCAAGTATTGCAACTTCTTTTAA-GGTTCAA
* * * * *
441595 AATTTCTTCTAAGATATTACATCAAATTGATTCATGTTTGTTGAGTATATAGTTGGCTAT-AAGT
129 AATTTCTTCTAAGATATTACATTAAAATGACTCATGTTTGTTGAGTATTTTGTTGGCTATAAAGT
* * * * * *
441659 AATGAAAATGAAGTAATTTAGCAGGTCAAGCAAGTTGAAATTTCCCAAAGACTTCCTATCAAAAC
194 AATGAAAATGAAGTAATCTAACGGGTCAAGCAAGTTGAAATTTCACAAAAACTTCATATCAAAAC
* * * *
441724 TTGATGAGAGTTTAGTCAATGGTGCTCCCGATTGGTTGGGTAAATGGTGCCGCTATAAATTAAC
259 TTGGTGGGAGTTGAGTCAATGGTGCTCCCAATTGGTTGGGTAAATGGTGCCGCTATAAATTAAC
* * * *
441788 -AAAATTGATGTAACTTTACGGGTCAAGCAAGTTGAAATCTCACAAGAATTTCGTATCAAGGGTA
1 GAAAA-TGATGTAACTTTACGAGTCAAGCAAGTTGAAATTTCATAAGAATTTCGTATCAAGGCTA
*
441852 GGCCAAAGCTGGCCAACATCATTAAAGATATTACCACAAGTATTGCAACTTCTTTTAAGAGTTCA
65 GGCCAAAGCTGGCCAACATCATTTAAGATATTACC-CAAGTATTGCAACTTCTTTTAAG-GTTCA
*
441917 AAATTTCTTCTAAGATATTACATTAAAATGACTCATGTTTGTTGAGTATTTTGTTAGCTATAAAG
128 AAATTTCTTCTAAGATATTACATTAAAATGACTCATGTTTGTTGAGTATTTTGTTGGCTATAAAG
* * *
441982 TAATGAAAATGAAGTAACCTAACGGGTCAAACAAGTTGAAATTTTACAAAAACTGT-ATATCAAA
193 TAATGAAAATGAAGTAATCTAACGGGTCAAGCAAGTTGAAATTTCACAAAAACT-TCATATCAAA
* ** *
442046 ACTTGGTGGGAGTTGAGTCAATGGTGCTCCCAATTGGTTGGGTAAATGTTGTTGTTATAAATTAA
257 ACTTGGTGGGAGTTGAGTCAATGGTGCTCCCAATTGGTTGGGTAAATGGTGCCGCTATAAATTAA
442111 C
322 C
* *
442112 GAAAATGATGTAACTTTACGAGTCAAGCAAGTTGAAATTTCATAAGAATTTGGTATCAAGTCTAG
1 GAAAATGATGTAACTTTACGAGTCAAGCAAGTTGAAATTTCATAAGAATTTCGTATCAAGGCTAG
* **
442177 GCTAAAGCTGGCCAACATCATTTAAGATATTTTTCCAAGTATTGCAACTTCTTTTAAGGTTTCAA
66 GCCAAAGCTGGCCAACATCATTTAAGATA-TTACCCAAGTATTGCAACTTCTTTTAAGG-TTCAA
*
442242 AATTTCTTCTAAGATATTACATTAAAATGACTCATGTCTGTTGAGTATTTTGTTGGCTATAAAGT
129 AATTTCTTCTAAGATATTACATTAAAATGACTCATGTTTGTTGAGTATTTTGTTGGCTATAAAGT
* * * *
442307 AATGAAAATGAAGTAATCTAAAGGGTCAAGCAAATTGAAATTTCACTAAAACTTCATCTCAAAAC
194 AATGAAAATGAAGTAATCTAACGGGTCAAGCAAGTTGAAATTTCACAAAAACTTCATATCAAAAC
*
442372 TTGGTGGGAGTTGAGTCAATGGCGCTCCCAATTG
259 TTGGTGGGAGTTGAGTCAATGGTGCTCCCAATTG
442406 ATGTAATTTT
Statistics
Matches: 554, Mismatches: 55, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
322 5 0.01
323 166 0.30
324 375 0.68
325 8 0.01
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (322 bp):
GAAAATGATGTAACTTTACGAGTCAAGCAAGTTGAAATTTCATAAGAATTTCGTATCAAGGCTAG
GCCAAAGCTGGCCAACATCATTTAAGATATTACCCAAGTATTGCAACTTCTTTTAAGGTTCAAAA
TTTCTTCTAAGATATTACATTAAAATGACTCATGTTTGTTGAGTATTTTGTTGGCTATAAAGTAA
TGAAAATGAAGTAATCTAACGGGTCAAGCAAGTTGAAATTTCACAAAAACTTCATATCAAAACTT
GGTGGGAGTTGAGTCAATGGTGCTCCCAATTGGTTGGGTAAATGGTGCCGCTATAAATTAAC
Found at i:442633 original size:286 final size:279
Alignment explanation
Indices: 442117--442683 Score: 823
Period size: 286 Copynumber: 2.0 Consensus size: 279
442107 TTAACGAAAA
* * *
442117 TGATGTAACTTTACGAGTCAAGCAAGTTGAAATTTCATAAGAATTTGGTATCAAGTCTAGGCTAA
1 TGATGTAACTTTACGAGTCAAGCAAGTTGAAATTTCACAAGAATTTGGTATCAAGGCTAGGCCAA
** *
442182 AGCTGGCCAACATCATTTAAGATATTTTTCCAAGTATTGCAACTTCTTTTAAGGTTTCAAAATTT
66 AGCTGGCCAACATCATTTAAGATATTACTCCAAGTATTGCAACTTCTTTTAAGGGTTCAAAATTT
* * *
442247 CTTCTAAGATATTACATTAAAATGACTCATGTCTGTTGAGTATTTTGTTGGCTATAAAGTAATGA
131 CTTCTAAGATATTACATCAAAATGACTCATGTCTGTTGAGTATTTTGATGGCTATAAAGCAATGA
* *
442312 AAATGAAGTAATCTAAAGGGTCAAGCAAATTGAAATTTCACTAAAACTTCATCTCAAAACTTGGT
196 AAATGAAGTAATCTAAACGATCAAGCAAATTGAAATTTCAC-AAAA----A-CT--AAACTTGGT
442377 GGGAGTTGAGTCAATGGCGCTCCCAAT
253 GGGAGTTGAGTCAATGGCGCTCCCAAT
* * * *
442404 TGATGTAATTTTACGGGTCCAA-CAAGTTGAAATTTCACAAGAGTTTTGTATCAAGGCTAGGCCA
1 TGATGTAACTTTACGAGT-CAAGCAAGTTGAAATTTCACAAGAATTTGGTATCAAGGCTAGGCCA
442468 AAGCTGGCCAACATCATTTAAGATATTACTCCAAGTATTGCAACTT-TTTTAAGGGTTCAAAATT
65 AAGCTGGCCAACATCATTTAAGATATTACTCCAAGTATTGCAACTTCTTTTAAGGGTTCAAAATT
* * * *
442532 TTTTCTAAGATATTATATCAAAATGACTCATGTTTGTTGAGTATTTTGATGGCTGTAAAGCAATG
130 TCTTCTAAGATATTACATCAAAATGACTCATGTCTGTTGAGTATTTTGATGGCTATAAAGCAATG
* * *
442597 AAAATGAAGTAATCTAACCGATCAAGCAAGTTGAAATTTCACAAAAACTTAACTTGGTGGGAGTT
195 AAAATGAAGTAATCTAAACGATCAAGCAAATTGAAATTTCACAAAAACTAAACTTGGTGGGAGTT
* *
442662 GAGTCAATGGTGTTCCCAAT
260 GAGTCAATGGCGCTCCCAAT
442682 TG
1 TG
442684 GTTAGTTAAA
Statistics
Matches: 255, Mismatches: 24, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
278 35 0.14
280 2 0.01
281 1 0.00
285 4 0.02
286 113 0.44
287 97 0.38
288 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (279 bp):
TGATGTAACTTTACGAGTCAAGCAAGTTGAAATTTCACAAGAATTTGGTATCAAGGCTAGGCCAA
AGCTGGCCAACATCATTTAAGATATTACTCCAAGTATTGCAACTTCTTTTAAGGGTTCAAAATTT
CTTCTAAGATATTACATCAAAATGACTCATGTCTGTTGAGTATTTTGATGGCTATAAAGCAATGA
AAATGAAGTAATCTAAACGATCAAGCAAATTGAAATTTCACAAAAACTAAACTTGGTGGGAGTTG
AGTCAATGGCGCTCCCAAT
Found at i:453342 original size:30 final size:30
Alignment explanation
Indices: 453306--453365 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
453296 GTCTATCATT
453306 ATTCTTTTC-ACATAAGATTTTATGAGGTGA
1 ATTCTTTTCGA-ATAAGATTTTATGAGGTGA
*
453336 ATTCTTTTCGATTAAGATTTTATGAGGTGA
1 ATTCTTTTCGAATAAGATTTTATGAGGTGA
453366 GTAAAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.45
Consensus pattern (30 bp):
ATTCTTTTCGAATAAGATTTTATGAGGTGA
Found at i:466781 original size:26 final size:26
Alignment explanation
Indices: 466719--466785 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
466709 NNNNNNNNNN
*
466719 TTTTTGTATCATGTT-CATATTATTCT
1 TTTTTATATCAT-TTACATATTATTCT
* *
466745 TTGTTGA-ATCATTTACATATTTTTCT
1 TT-TTTATATCATTTACATATTATTCT
466771 TTTTTATATCATTTA
1 TTTTTATATCATTTA
466786 ACAAAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 5 0.15
26 27 0.79
27 2 0.06
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.61
Consensus pattern (26 bp):
TTTTTATATCATTTACATATTATTCT
Found at i:472350 original size:22 final size:22
Alignment explanation
Indices: 472308--472351 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
472298 AAAAAACATT
*
472308 CTTAACAGATGATAAATTATGA
1 CTTAACAGATGATAAAGTATGA
*
472330 CTTAACA-ATGTATTAAGTATGA
1 CTTAACAGATG-ATAAAGTATGA
472352 ATTCTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (22 bp):
CTTAACAGATGATAAAGTATGA
Found at i:481813 original size:187 final size:186
Alignment explanation
Indices: 481498--482621 Score: 781
Period size: 187 Copynumber: 5.9 Consensus size: 186
481488 CCTTGATACT
* * * * *
481498 AAGTTTTTGAGAAATTTTAACTTCTTTGACTCGTAAGGCTACTTCAATTTT-GTTACTTTGTAGT
1 AAGTTTTTGTGAAATTTTAACTTC-TTGACTCGTTAGGTTACTTC-ATTTTCATTACTTTATAGT
*
481562 TAACAAATATGATAGT-TATTTTGATGTAATATCTTAGAATAAATTTTGATCCCTTAAAAGAAGT
64 TAACAAATATGATAGTCT-TTTTGATGTAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGT
* * * * **********
481626 TGCATTATTAGAGCAATATCTTTAATGATATTGGCTAGCTNNNNNNNNNNCTTCATATA
128 TGCAATATTAAAGCAATATCTTTAATGATATTGGCCACCTTTTTTCCAACCTTCATATA
* *
481685 AAGTTTTTGTGAAATTTTAACTTACTTGACTCGTTAGGTTAGTTCATTTTCATTACTTTATAATT
1 AAGTTTTTGTGAAATTTTAACTT-CTTGACTCGTTAGGTTACTTCATTTTCATTACTTTATAGTT
* * *
481750 AACGAACATAATAGTCTTTTTGATGTAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGTTG
65 AACAAATATGATAGTCTTTTTGATGTAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGTTG
* * * * * * *
481815 TAATGTTAAAGTAATGTCTTTAATGATGTTGGCCACCTTTTTTCCAACCTTGATATG
130 CAATATTAAAGCAATATCTTTAATGATATTGGCCACCTTTTTTCCAACCTTCATATA
* * * ** * *
481872 AAGTTCTTGTGAACTTTCAACTTCCTTGACAAGTTAGGTTATTTCATTTTCATTATTTTATAGTT
1 AAGTTTTTGTGAAATTTTAACTT-CTTGACTCGTTAGGTTACTTCATTTTCATTACTTTATAGTT
* * * * *
481937 TACAAATATGATAGCCTTTTTGATATAATATCTTAGAAGAAATTTTGATCCTTTAAAGGAAGTTG
65 AACAAATATGATAGTCTTTTTGATGTAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGTTG
* * * * * * ** * * * *
482002 GAATGTTAGAGTC-ATGTTTTTAATGATGTTGGCCAGTTTTTTTTCAACCATGATATG
130 CAATATTAAAG-CAATATCTTTAATGATATTGGCCACCTTTTTTCCAACCTTCATATA
* * * * * *********
482059 AAGTTCTTGTGAACTTTCAACTTGCTTAAC-CTATTAGGTTACTTCATTTTCATTNNNNNNNNNN
1 AAGTTTTTGTGAAATTTTAACTT-CTTGACTC-GTTAGGTTACTTCATTTTCATT-ACTTTATAG
* * * * *
482123 CT-ACAAACATGATAGTCTTTTT-TTATAATATCTTAGAAGAAATTATGATCCCTTAAAAGAAGT
63 TTAACAAATATGATAGTCTTTTTGATGTAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGT
* * * * * * * ** * *
482186 TGGAATGTTAGAGTAATCTTTTTAATGATGCATGTTCGCCAGCC-TTTTTAAAACCTTGATATG
128 TGCAATATTAAAGCAATATCTTTAATGAT--A--TTGGCCA-CCTTTTTTCCAACCTTCATATA
* * * * * * * *** *
482249 AAGTTCTTATGAACTTTCAATTTGATTGACCCACCAGGTTACTTCATTTTCATTATTTTATAGTT
1 AAGTTTTTGTGAAATTTTAACTT-CTTGACTCGTTAGGTTACTTCATTTTCATTACTTTATAGTT
* * * *
482314 TACAAACATGATAGTTTTTTTTATGTAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGTTG
65 AACAAATATGATAGTCTTTTTGATGTAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGTTG
* * * ** * * * * * *
482379 CAATGTTAAAGTAATATCTTTGACAATGTTGGCTAGCTTTTTTCTAACCTTGATATG
130 CAATATTAAAGCAATATCTTTAATGATATTGGCCACCTTTTTTCCAACCTTCATATA
* * *
482436 AAGTTCTTT-TGAAATTTCAACTTGCTTGACTCATTTTCTTAACTCATTAGGTTACCTCATTTTC
1 AAGTT-TTTGTGAAATTTTAACTT-CTTG-------------ACTCGTTAGGTTACTTCATTTTC
* * * * *
482500 ATTACTTTATAGTCAACAAACATGATAGTCTTTTTGATGTAATACCTTAGAAGAAAGTTTGATTC
51 ATTACTTTATAGTTAACAAATATGATAGTCTTTTTGATGTAATATCTTAGAAGAAATTTTGATCC
* * * * *
482565 CTTAAAAGAAGTTGCAA-AGTTAAAGTAATATCTTTGATGATGTTAGCCAACTTTTTT
116 CTTAAAAGAAGTTGCAATA-TTAAAGCAATATCTTTAATGATATTGGCCACCTTTTTT
482622 TTAATATTGA
Statistics
Matches: 764, Mismatches: 142, Indels: 49
0.80 0.15 0.05
Matches are distributed among these distances:
186 69 0.09
187 415 0.54
188 5 0.01
189 1 0.00
190 87 0.11
191 61 0.08
200 126 0.16
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (186 bp):
AAGTTTTTGTGAAATTTTAACTTCTTGACTCGTTAGGTTACTTCATTTTCATTACTTTATAGTTA
ACAAATATGATAGTCTTTTTGATGTAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGTTGC
AATATTAAAGCAATATCTTTAATGATATTGGCCACCTTTTTTCCAACCTTCATATA
Found at i:482348 original size:377 final size:364
Alignment explanation
Indices: 481754--482462 Score: 886
Period size: 377 Copynumber: 1.9 Consensus size: 364
481744 ATAATTAACG
* * *
481754 AACATAATAGTCTTTTTGATGTAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGTTGTAAT
1 AACATAATAGTCTTTTTGATATAATATCTTAGAAGAAATTATGATCCCTTAAAAGAAGTTGGAAT
* * ** *
481819 GTTAAAGTAATGTCTTTAATGATGTTGGCCACCTTTTTTCCAACCTTGATATGAAGTTCTTGTGA
66 GTTAAAGTAATCTCTTTAATGATGTTCGCCACCTTTTTTAAAACCTTGATATGAAGTTCTTATGA
* ** * *
481884 ACTTTCAACTTCCTTGACAAGTTAGGTTATTTCATTTTCATTATTTTATAGTTTACAAATATGAT
131 ACTTTCAACTTCATTGACAAGCCAGGTTACTTCATTTTCATTATTTTATAGTTTACAAACATGAT
* * * *
481949 AGCCTTTTTGATATAATATCTTAGAAGAAATTTTGATCCTTTAAAGGAAGTTGGAATGTTAGAGT
196 AGCCTTTTTGATATAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGTTGCAATGTTAAAGT
* * * ** * *
482014 CATGTTTTTAATGATGTTGGCCAG-TTTTTTTTCAACCATGATATGAAGTTCTTGTGAACTTTCA
261 AATATCTTTAACAATGTTGGCCAGCTTTTTTCT-AACCATGATATGAAGTTCTTGTGAAATTTCA
482078 ACTTGCTTAACCTATTAGGTTACTTCATTTTCATTNNNNNNNNNNCTACA
325 ACTTGCTTAACCTATTAGGTTACTTCATTTTCATT----------CTACA
* *
482128 AACATGATAGTCTTTTT-TTATAATATCTTAGAAGAAATTATGATCCCTTAAAAGAAGTTGGAAT
1 AACATAATAGTCTTTTTGATATAATATCTTAGAAGAAATTATGATCCCTTAAAAGAAGTTGGAAT
* *
482192 GTTAGAGTAATCTTTTTAATGATGCATGTTCGCCAGCC-TTTTTAAAACCTTGATATGAAGTTCT
66 GTTAAAGTAATCTCTTT-A--ATG-ATGTTCGCCA-CCTTTTTTAAAACCTTGATATGAAGTTCT
* * *
482256 TATGAACTTTCAATTTGATTGACCCA-CCAGGTTACTTCATTTTCATTATTTTATAGTTTACAAA
126 TATGAACTTTCAACTTCATTGA-CAAGCCAGGTTACTTCATTTTCATTATTTTATAGTTTACAAA
** * *
482320 CATGATAGTTTTTTTTATGTAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGTTGCAATGT
190 CATGATAGCCTTTTTGATATAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGTTGCAATGT
* * * *
482385 TAAAGTAATATCTTTGACAATGTTGGCTAGCTTTTTTCTAACCTTGATATGAAGTTCTTTTGAAA
255 TAAAGTAATATCTTTAACAATGTTGGCCAGCTTTTTTCTAACCATGATATGAAGTTCTTGTGAAA
482450 TTTCAACTTGCTT
320 TTTCAACTTGCTT
482463 GACTCATTTT
Statistics
Matches: 289, Mismatches: 39, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
373 57 0.20
374 17 0.06
376 3 0.01
377 201 0.70
378 11 0.04
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (364 bp):
AACATAATAGTCTTTTTGATATAATATCTTAGAAGAAATTATGATCCCTTAAAAGAAGTTGGAAT
GTTAAAGTAATCTCTTTAATGATGTTCGCCACCTTTTTTAAAACCTTGATATGAAGTTCTTATGA
ACTTTCAACTTCATTGACAAGCCAGGTTACTTCATTTTCATTATTTTATAGTTTACAAACATGAT
AGCCTTTTTGATATAATATCTTAGAAGAAATTTTGATCCCTTAAAAGAAGTTGCAATGTTAAAGT
AATATCTTTAACAATGTTGGCCAGCTTTTTTCTAACCATGATATGAAGTTCTTGTGAAATTTCAA
CTTGCTTAACCTATTAGGTTACTTCATTTTCATTCTACA
Found at i:482542 original size:200 final size:203
Alignment explanation
Indices: 482284--482803 Score: 611
Period size: 200 Copynumber: 2.6 Consensus size: 203
482274 TTGACCCACC
* * * *
482284 AGGTTACTTCATTTTCATTATTTTATAGTTTACAAACATGATAGTTTTTTTTATGTAATATCTTA
1 AGGTTACTTCATTTTCATTACTTTATAGTTAACAAACATGATAGTCTTTTTGATGTAATATCTTA
* *
482349 GAAGAAATTTTGATCCCTTAAAAGAAGTTGCAATGTTAAAGTAATATCTTTGACAATGTTGGCTA
66 GAAGAAATTTTGATCCCTTAAAAGAAGTTGCAATGTTAAAGTAATATCTTTGACAATGTTAGCCA
* * * * * *
482414 GCTTTTTTCTAACCTTGATATGAAGTTCTTTTGAAATTTCAACTTGCTTGA-C-TCA-TTTTCTT
131 ACTTTTTTCTAACATTGATAAGAAATTCTTTTCAAATTTCAACTTGCTTGACCGTCACTTATCTT
*
482476 AACTCAT-T
196 -ACTAATGT
* * *
482484 AGGTTACCTCATTTTCATTACTTTATAGTCAACAAACATGATAGTCTTTTTGATGTAATACCTTA
1 AGGTTACTTCATTTTCATTACTTTATAGTTAACAAACATGATAGTCTTTTTGATGTAATATCTTA
* * * **
482549 GAAGAAAGTTTGATTCCTTAAAAGAAGTTGCAAAGTTAAAGTAATATCTTTGATGATGTTAGCCA
66 GAAGAAATTTTGATCCCTTAAAAGAAGTTGCAATGTTAAAGTAATATCTTTGACAATGTTAGCCA
* * * * *
482614 ACTTTTTTTTAATATTGATAAGAAATTCTTTTCTAATTTTAACTTGCTTGACCCCGTTAGCTTAT
131 ACTTTTTTCTAACATTGATAAGAAATTCTTTTCAAATTTCAACTTGCTTGA--CCGTCA-CTTAT
*
482679 CTTAGTAATGT
193 CTTACTAATGT
** * * * * *
482690 ACCTTACTTCAATTTCATTACTTTATAGTTAGCAAGCATGATAGTC-ATTCGATGTAATATCTTA
1 AGGTTACTTCATTTTCATTACTTTATAGTTAACAAACATGATAGTCTTTTTGATGTAATATCTTA
** * *
482754 GAAGAAATTTTGATACTTTTAAAA-AAATTGCAATGTTAGAGTAATATCTT
66 GAAGAAATTTTGAT-CCCTTAAAAGAAGTTGCAATGTTAAAGTAATATCTT
482804 AAATGATGTT
Statistics
Matches: 268, Mismatches: 44, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
200 158 0.59
203 1 0.00
204 2 0.01
205 55 0.21
206 52 0.19
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (203 bp):
AGGTTACTTCATTTTCATTACTTTATAGTTAACAAACATGATAGTCTTTTTGATGTAATATCTTA
GAAGAAATTTTGATCCCTTAAAAGAAGTTGCAATGTTAAAGTAATATCTTTGACAATGTTAGCCA
ACTTTTTTCTAACATTGATAAGAAATTCTTTTCAAATTTCAACTTGCTTGACCGTCACTTATCTT
ACTAATGT
Found at i:483414 original size:180 final size:173
Alignment explanation
Indices: 483170--483503 Score: 352
Period size: 180 Copynumber: 1.9 Consensus size: 173
483160 ATCTACTATC
* ** *
483170 TTAGAATAAATTTTGATCCTTTAAAAGAAGTTGCAATGTTGGAGTAATACCGTTAATGATGTTGG
1 TTAGAATAAATTTTGATCCCTTAAAAGAAGTTGCAATGTTAAAGTAATACCGTTAATAATGTTGG
* * * * ** *
483235 CCATCTTTTTTCTAAACTTGATATGAAGTTTTTGTGAACTTTCAAC-AC-CC-ATTAGGTTACTT
66 CAAGCTTTTTTCCAAACTTGATATGAAATTTGGGTGAAATTTCAACAACTCCTATTAGGTTACTT
483297 CATTTTCATTACTTTATAGTNNNNNNNNNNGATAGTTTTTTTTATGTAATATT
131 CATTTTCATTACTTTATAGT----------GATAGTTTTTTTTATGTAATATT
* *
483350 TTAGAATAGATTTTGATCCCTTAAAAGAAGTTGGAATGTTAAAGTAATATCC-TTAATAATGTTG
1 TTAGAATAAATTTTGATCCCTTAAAAGAAGTTGCAATGTTAAAGTAATA-CCGTTAATAATGTTG
* *
483414 GTAAGCTTTTTTCCAACCTTGATATGAAATTTGGGTGAAATTTCAACTAACTTGACCTATTAGGT
65 GCAAGCTTTTTTCCAAACTTGATATGAAATTTGGGTGAAATTTCAAC-AAC-T--CCTATTAGGT
* *
483479 TTCTTCATTTTCCTTACTTTATAGT
126 TACTTCATTTTCATTACTTTATAGT
483504 CAACAACATA
Statistics
Matches: 129, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
180 93 0.72
181 2 0.02
182 2 0.02
186 2 0.02
187 30 0.23
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.42
Consensus pattern (173 bp):
TTAGAATAAATTTTGATCCCTTAAAAGAAGTTGCAATGTTAAAGTAATACCGTTAATAATGTTGG
CAAGCTTTTTTCCAAACTTGATATGAAATTTGGGTGAAATTTCAACAACTCCTATTAGGTTACTT
CATTTTCATTACTTTATAGTGATAGTTTTTTTTATGTAATATT
Found at i:502832 original size:24 final size:24
Alignment explanation
Indices: 502804--502850 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
502794 AGATGACATC
502804 AATGGCTTGCTTACACAGATAGGA
1 AATGGCTTGCTTACACAGATAGGA
* *
502828 AATGGTTTGCTTACATAGATAGG
1 AATGGCTTGCTTACACAGATAGG
502851 GGTGAACACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (24 bp):
AATGGCTTGCTTACACAGATAGGA
Found at i:503232 original size:18 final size:18
Alignment explanation
Indices: 503211--503246 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
503201 AATTTAAAAC
*
503211 ATAATATATATAAAATAT
1 ATAATATATAAAAAATAT
503229 ATAATATATAAAAAATAT
1 ATAATATATAAAAAATAT
503247 TTGTTTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATATATAAAAAATAT
Done.