Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008310.1 Hibiscus syriacus cultivar Beakdansim tig00111000_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3887810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 15
Found at i:256997 original size:108 final size:108
Alignment explanation
Indices: 256861--257407 Score: 824
Period size: 108 Copynumber: 5.1 Consensus size: 108
256851 ATTATGTGGG
** *
256861 TTGCACACAGAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACTTTGCACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
*
256926 GTGCCGAAACGGTTATTCATCAACATATGATGAATTCTGTACT
66 GTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
256969 TTGCACACTTAGTGCCGAAACGGTTATTCATCAA-ATATGATGAATTCCGTACTTTGCACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
257033 GTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
66 GTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* * *
257076 TTGCACACTTAGTGCCAAAATGGTTATTCATCAACATATGATGAATTCCGTTCTTTGCACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
* *
257141 GTGCCAAAACGGTTATTCATCAACATACGATGAATTCCGTACT
66 GTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* ** *
257184 TTGCACACTTAGTTCCGAAACGGTTATTCATCAACATATGACAAATTTCGTACTTTGCACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
*
257249 GTGCCGAAATGGTTATTCATCAACATATGATGAATTCCGTACT
66 GTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* * * * * *
257292 TTGCACACTTAATGTCGAAATGGTTATTCAT-AATATATGAT-AATTCCATATTTTG------TA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
* *
257349 GTGCCAAAACGGTTATTCATCACCATATGATGAATTCCGTACT
66 GTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
*
257392 TTACACACTTAGTGCC
1 TTGCACACTTAGTGCC
257408 TATTTGGTAA
Statistics
Matches: 404, Mismatches: 34, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
100 55 0.14
106 11 0.03
107 111 0.27
108 227 0.56
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (108 bp):
TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
GTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
Found at i:257252 original size:162 final size:161
Alignment explanation
Indices: 256861--257407 Score: 831
Period size: 162 Copynumber: 3.4 Consensus size: 161
256851 ATTATGTGGG
** *
256861 TTGCACACAGAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTACTTTGCACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
* *
256926 GTGCCGAAACGGTTATTCATCAACATATGATGAATTCTGTACTTTGCACACTTAGTGCCGAAACG
66 GTGCCGAAATGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACG
256991 GTTATTCATCAAATATGATGAATTCCGTACT
131 GTTATTCATCAAATATGATGAATTCCGTACT
257022 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
* * *
257087 GTGCCAAAATGGTTATTCATCAACATATGATGAATTCCGTTCTTTGCACACTTAGTGCCAAAACG
66 GTGCCGAAATGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACG
*
257152 GTTATTCATCAACATACGATGAATTCCGTACT
131 GTTATTCATCAA-ATATGATGAATTCCGTACT
* ** *
257184 TTGCACACTTAGTTCCGAAACGGTTATTCATCAACATATGACAAATTTCGTACTTTGCACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
* * *
257249 GTGCCGAAATGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAATGTCGAAATG
66 GTGCCGAAATGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACG
* *
257314 GTTATTCAT-AATATATGAT-AATTCCATATT
131 GTTATTCATCAA-ATATGATGAATTCCGTACT
* * *
257344 TTG------TAGTGCCAAAACGGTTATTCATCACCATATGATGAATTCCGTACTTTACACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
257403 GTGCC
66 GTGCC
257408 TATTTGGTAA
Statistics
Matches: 355, Mismatches: 30, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
154 54 0.15
160 12 0.03
161 142 0.40
162 147 0.41
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (161 bp):
TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
GTGCCGAAATGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACG
GTTATTCATCAAATATGATGAATTCCGTACT
Found at i:262327 original size:24 final size:26
Alignment explanation
Indices: 262300--262355 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 26
262290 AAATAATTTT
262300 TTATTACATAT-TATATTTAA-TAAA
1 TTATTACATATATATATTTAACTAAA
* *
262324 TTA-TATATATATATTTTTAACTAAA
1 TTATTACATATATATATTTAACTAAA
262349 TATATTA
1 T-TATTA
262356 TTTTAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 6 0.23
24 11 0.42
25 5 0.19
26 2 0.08
27 2 0.08
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (26 bp):
TTATTACATATATATATTTAACTAAA
Found at i:262351 original size:18 final size:17
Alignment explanation
Indices: 262328--262369 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 17
262318 AATAAATTAT
262328 ATATATATATTTTTAACTAA
1 ATATAT-TA-TTTTAA-TAA
262348 ATATATTATTTTAATAA
1 ATATATTATTTTAATAA
262365 ATATA
1 ATATA
262370 AATGTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 6 0.27
19 2 0.09
20 6 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATTATTTTAATAA
Found at i:262422 original size:18 final size:17
Alignment explanation
Indices: 262399--262438 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
262389 ATGTATCTAT
262399 TTATTTATTATTATTTAA
1 TTATTTATT-TTATTTAA
*
262417 TTATTTTATTTTATTTAC
1 TTA-TTTATTTTATTTAA
262435 TTAT
1 TTAT
262439 CTCTGTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 13 0.65
19 6 0.30
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTTATTTTATTTAA
Found at i:264673 original size:48 final size:48
Alignment explanation
Indices: 264608--264703 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
264598 GTATGAAATG
* *
264608 ATGAACGACTTTCTTTAAATATCCCTCATAAAAAGAGGAAATATGTAT
1 ATGAACGACTTTATTTAAATATCCCTCATAAAAAGAGAAAATATGTAT
264656 ATGAACGACTTTATTTAAATATCCCTCATAAAAAGAGAAAATATGTAT
1 ATGAACGACTTTATTTAAATATCCCTCATAAAAAGAGAAAATATGTAT
264704 CCCTTGTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (48 bp):
ATGAACGACTTTATTTAAATATCCCTCATAAAAAGAGAAAATATGTAT
Found at i:264955 original size:11 final size:11
Alignment explanation
Indices: 264935--265004 Score: 54
Period size: 11 Copynumber: 6.2 Consensus size: 11
264925 TCAACACAAA
*
264935 AAAGAGAAAAG
1 AAAGAAAAAAG
264946 AAAGAAAAAAAG
1 AAAG-AAAAAAG
*
264958 CAAAAGAAAGAA-
1 --AAAGAAAAAAG
*
264970 AAACAAAAAAG
1 AAAGAAAAAAG
264981 CAAA-AAAAAAG
1 -AAAGAAAAAAG
*
264992 AAAGAATAAAG
1 AAAGAAAAAAG
265003 AA
1 AA
265005 TAAAGGAGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
10 11 0.23
11 19 0.40
12 9 0.19
13 5 0.10
14 4 0.08
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.01
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:264955 original size:18 final size:18
Alignment explanation
Indices: 264932--265019 Score: 71
Period size: 18 Copynumber: 4.9 Consensus size: 18
264922 AAGTCAACAC
264932 AAAAAAGAGAAAAGAAAG
1 AAAAAAGAGAAAAGAAAG
264950 AAAAAA-AGCAAAAGAAAG
1 AAAAAAGAG-AAAAGAAAG
264968 AAAAACA-A-AAAAGCAAA-
1 AAAAA-AGAGAAAAG-AAAG
*
264985 AAAAAAGA-AAGAATAAAG
1 AAAAAAGAGAA-AAGAAAG
*
265003 AATAAAG-GAGAAAGAAA
1 AAAAAAGAGA-AAAGAAA
265020 ACATATCAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 16
0.76 0.04 0.21
Matches are distributed among these distances:
16 1 0.02
17 18 0.31
18 37 0.63
19 3 0.05
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAAAGAGAAAAGAAAG
Found at i:264965 original size:14 final size:15
Alignment explanation
Indices: 264946--264997 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
264936 AAGAGAAAAG
*
264946 AAAGAAA-AAAAGCA
1 AAAGAAAGAAAAACA
264960 AAAGAAAGAAAAAC-
1 AAAGAAAGAAAAACA
264974 AAA-AAAGCAAAAA-A
1 AAAGAAAG-AAAAACA
264988 AAAGAAAGAA
1 AAAGAAAGAA
264998 TAAAGAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 4 0.12
14 20 0.61
15 9 0.27
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAACA
Found at i:264977 original size:23 final size:23
Alignment explanation
Indices: 264941--264994 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
264931 CAAAAAAGAG
*
264941 AAAAGAAAGAAAAAAAGC-AAAA
1 AAAAGAAAAAAAAAAAGCAAAAA
*
264963 GAAAGAAAAACAAAAAAGCAAAAA
1 AAAAGAAAAA-AAAAAAGCAAAAA
264987 AAAAGAAA
1 AAAAGAAA
264995 GAATAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 8 0.30
23 8 0.30
24 11 0.41
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (23 bp):
AAAAGAAAAAAAAAAAGCAAAAA
Found at i:266006 original size:25 final size:25
Alignment explanation
Indices: 265932--266008 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
265922 AAAAAAAAAC
* * *
265932 TTCATCAAACATTTTTCAAGATTAT
1 TTCATAAAACATTTTTCAAAATTCT
* *
265957 TTCATTAAACATTTTTCAAATTTCT
1 TTCATAAAACATTTTTCAAAATTCT
265982 TTCATAAAACA-TTTTCAAAACTTCT
1 TTCATAAAACATTTTTCAAAA-TTCT
266007 TT
1 TT
266009 ATCGAACTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 8 0.18
25 37 0.82
ACGTcount: A:0.35, C:0.17, G:0.01, T:0.47
Consensus pattern (25 bp):
TTCATAAAACATTTTTCAAAATTCT
Found at i:268150 original size:18 final size:18
Alignment explanation
Indices: 268127--268161 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
268117 AAACCCGGTC
268127 CAGGCCC-AGACAACCCAG
1 CAGGCCCAAGA-AACCCAG
268145 CAGGCCCAAGAAACCCA
1 CAGGCCCAAGAAACCCA
268162 AAATTCAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.37, C:0.43, G:0.20, T:0.00
Consensus pattern (18 bp):
CAGGCCCAAGAAACCCAG
Found at i:269472 original size:22 final size:20
Alignment explanation
Indices: 269433--269492 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
269423 CTTTTATAAT
*
269433 TTTA-TTATTTAATCTTTTAA
1 TTTATTTATTTAATATTTT-A
*
269453 TTTATTATATTTATTATTTTA
1 TTTATT-TATTTAATATTTTA
*
269474 TTTCTTTATTTACATATTT
1 TTTATTTATTTA-ATATTT
269493 GTCAATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 10 0.30
21 12 0.36
22 11 0.33
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATTTATTTAATATTTTA
Found at i:275933 original size:40 final size:40
Alignment explanation
Indices: 275824--275933 Score: 102
Period size: 39 Copynumber: 2.8 Consensus size: 40
275814 TTACAACTTG
* * * *
275824 AAATGTTGGGGCATTTTGGAGG-CTTGTACCAGTATGAAAT
1 AAATGTTGGGGCATGTTGAAGGTC-TGTATCAGCATGAAAT
* * *
275864 -AATGTT-GGGCACTGTTGAA-ATATTATATCAGCATGAAAT
1 AAATGTTGGGGCA-TGTTGAAGGT-CTGTATCAGCATGAAAT
275903 AAATGTTGGGGCATGTTGAAGGTCTGTATCA
1 AAATGTTGGGGCATGTTGAAGGTCTGTATCA
275934 TGTTGGAGTG
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
38 5 0.09
39 24 0.44
40 19 0.35
41 6 0.11
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (40 bp):
AAATGTTGGGGCATGTTGAAGGTCTGTATCAGCATGAAAT
Found at i:277591 original size:167 final size:168
Alignment explanation
Indices: 277306--277610 Score: 454
Period size: 167 Copynumber: 1.8 Consensus size: 168
277296 TAAGTTGTTT
* *
277306 TGAAAATGAGAAATCAATTCACAATGTTTCTCATTTAATCTATTTTCAGAAAAGGAAATTTTTAA
1 TGAAAATGAGAAAGCAATTCACAATGTTTCTCATTTAA-CTATTTTAAGAAAAGGAAATTTTTAA
* * * *
277371 AAAGTAAGAAAGTGATTCTAAAGTTTCTTACCTAGTAAACTATTTCTCAAAGATGATAAGTCCTT
65 AAAGTAAGAAAGCGATTCGAAAGTTTCTTACCCAGTAAACTATTTCCCAAAGATGATAAGTCCTT
277436 CGGGTCATCCGTAAGACCTCCAGGTAGGATGTTTTCACA
130 CGGGTCATCCGTAAGACCTCCAGGTAGGATGTTTTCACA
* * * * *
277475 TGAAAATGAGAAAGCGATTACCCAA-GTTTCTCATTTAA-TGTTTTAAGAAAATGAAATTTTTGA
1 TGAAAATGAGAAAGCAATT-CACAATGTTTCTCATTTAACTATTTTAAGAAAAGGAAATTTTTAA
*
277538 AAAGTAA-AAAGCGATTTCGAAAGTTTCTTACCCAGTAAACTATTTCCCAAAGATGATAAGTTCT
65 AAAGTAAGAAAGCGA-TTCGAAAGTTTCTTACCCAGTAAACTATTTCCCAAAGATGATAAGTCCT
277602 TCGGGTCAT
129 TCGGGTCAT
277611 TAGTAAGTCT
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
166 6 0.05
167 82 0.67
169 30 0.25
170 4 0.03
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (168 bp):
TGAAAATGAGAAAGCAATTCACAATGTTTCTCATTTAACTATTTTAAGAAAAGGAAATTTTTAAA
AAGTAAGAAAGCGATTCGAAAGTTTCTTACCCAGTAAACTATTTCCCAAAGATGATAAGTCCTTC
GGGTCATCCGTAAGACCTCCAGGTAGGATGTTTTCACA
Found at i:277887 original size:3 final size:3
Alignment explanation
Indices: 277879--277921 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
277869 TCCCATTTCT
277879 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
277922 AAATAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:281101 original size:30 final size:28
Alignment explanation
Indices: 281038--281111 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 28
281028 ATCAAGGGAG
281038 TTCAAAG--AAAAAAAAGAAGAAAAAAT
1 TTCAAAGAAAAAAAAAAGAAGAAAAAAT
***
281064 CAGAAAGAAAAAAAAAAGAAGAAAGAGAAT
1 TTCAAAGAAAAAAAAAAGAAGAAA-A-AAT
*
281094 TTCAAAGAAAAACAAAAG
1 TTCAAAGAAAAAAAAAAG
281112 CCAAGGAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
26 4 0.11
28 15 0.41
29 1 0.03
30 17 0.46
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.08
Consensus pattern (28 bp):
TTCAAAGAAAAAAAAAAGAAGAAAAAAT
Found at i:281104 original size:28 final size:26
Alignment explanation
Indices: 281038--281105 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
281028 ATCAAGGGAG
281038 TTCAAAGAAAAAAAAGAAGAAAAAAT
1 TTCAAAGAAAAAAAAGAAGAAAAAAT
***
281064 CAGAAAGAAAAAAAAAAGAAGAAAGAGAAT
1 TTCAAAG--AAAAAAAAGAAGAAA-A-AAT
281094 TTCAAAGAAAAA
1 TTCAAAGAAAAA
281106 CAAAAGCCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
26 4 0.12
28 20 0.62
29 1 0.03
30 7 0.22
ACGTcount: A:0.72, C:0.04, G:0.15, T:0.09
Consensus pattern (26 bp):
TTCAAAGAAAAAAAAGAAGAAAAAAT
Found at i:287294 original size:2 final size:2
Alignment explanation
Indices: 287287--287322 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
287277 TAAATGTGAA
287287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
287323 GATTATCGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:287652 original size:21 final size:24
Alignment explanation
Indices: 287596--287662 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 24
287586 TACTTTAGTA
287596 ATATTTATATATT-TTAAATATAT
1 ATATTTATATATTATTAAATATAT
287619 ATATATATATATATTATTAAATAT-T
1 ATAT-T-TATATATTATTAAATATAT
287644 -T-TTTATATATTATTTAAAT
1 ATATTTATATATTA-TTAAAT
287663 CTACATAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
21 9 0.22
22 7 0.17
23 5 0.12
24 2 0.05
25 9 0.22
26 8 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTTATATATTATTAAATATAT
Found at i:295839 original size:180 final size:178
Alignment explanation
Indices: 295341--295827 Score: 493
Period size: 181 Copynumber: 2.7 Consensus size: 178
295331 AAATTGAATG
* * * * *
295341 CATATAGTGACAACTTTTGTAACTAAAAGTTTTAGTAACTATGAC-AAAAAATTGTCACAACAAA
1 CATATAGTGACAAATTTTGTAACTATAAG-TTTAATAATTATTACAAAAAAATTGTCACAACAAA
* * * * * *
295405 TAATGAGATTTAGATTTGTTGTGACAAATTTTGTTTGTAATTATATATTTTAATTATAGTGACAA
65 TAATGAGATTCAG-TTTTTTGTGAAAAATTATATTTGTAGTTATATATTTTAATTATAGTGACAA
295470 A-ATATATAGTCACAAATGATTATCTCCAATTTTTGGTAAAAAAACAAAAT
129 ATATAT-TAGTCACAAATGATTATCTCCAATTTTTGGTAAAAAAACAAAAT
* * ** * * *
295520 TATATAATGACATGTTTTGTAACTATAAGCTATAATTATTGTTACAAAAAAAATTGTCACAACAA
1 CATATAGTGACAAATTTTGTAACTATAAG-TTTAATAATTATTAC-AAAAAAATTGTCACAACAA
* * * * * *
295585 ATAATGAGATTCAAGTTTTTAGTAAAAAATAATATTTTTCGTTATATGTTTTAATTATAGTGACA
64 ATAATGAGATTC-AGTTTTTTGTGAAAAATTATATTTGTAGTTATATATTTTAATTATAGTGACA
* *** *
295650 AAGTATATTA-TCACAAA-GATT-TCCTTCCATATTTTT-TTGCGCAAAA-AAAGT
128 AA-TATATTAGTCACAAATGATTAT-C-TCCA-ATTTTTGGT-AAAAAAACAAAAT
*
295701 CATATAGTGACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAAATTGTCACAAAAAA
1 CATATAGTGACAAATTTTGTAACTATAAGT-TTAATAATTATTACAAAAAAATTGTCACAACAAA
* * * * *
295766 TAATTATATTCACGTTTTTTGTGAAAAATTATATTTGTAGTTGTAAATTTTAACTATAGTGA
65 TAATGAGATTCA-GTTTTTTGTGAAAAATTATATTTGTAGTTATATATTTTAATTATAGTGA
295828 TAGTATATAT
Statistics
Matches: 249, Mismatches: 48, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
179 35 0.14
180 74 0.30
181 122 0.49
182 14 0.06
183 4 0.02
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (178 bp):
CATATAGTGACAAATTTTGTAACTATAAGTTTAATAATTATTACAAAAAAATTGTCACAACAAAT
AATGAGATTCAGTTTTTTGTGAAAAATTATATTTGTAGTTATATATTTTAATTATAGTGACAAAT
ATATTAGTCACAAATGATTATCTCCAATTTTTGGTAAAAAAACAAAAT
Found at i:297942 original size:2 final size:2
Alignment explanation
Indices: 297928--297988 Score: 85
Period size: 2 Copynumber: 32.0 Consensus size: 2
297918 ATATGCATTC
297928 TA TA TA T- TCA TA TA TA -A TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
297968 -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
297989 ATTAGTAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.07
2 49 0.91
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:297947 original size:13 final size:13
Alignment explanation
Indices: 297937--297988 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
297927 CTATATATTC
297937 ATATATAATATAT
1 ATATATAATATAT
297950 ATATAT--TATAT
1 ATATATAATATAT
297961 ATATATAATATAT
1 ATATATAATATAT
297974 ATATAT-ATATAT
1 ATATATAATATAT
297986 ATA
1 ATA
297989 ATTAGTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.30
12 9 0.24
13 17 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATAATATAT
Found at i:301028 original size:61 final size:62
Alignment explanation
Indices: 300959--301086 Score: 213
Period size: 62 Copynumber: 2.1 Consensus size: 62
300949 TTTAAAGGAG
*
300959 GAAAATGCACTT-AAAGTGACTCTGAATATGGTACTGGAGACCCAAATACTGAACGTAAAGT
1 GAAAATGCACTTAAAAGTGACTCAGAATATGGTACTGGAGACCCAAATACTGAACGTAAAGT
* * *
301020 GAAAATGCAGTTAAAAGTGACTCAGATTATGGTACTGGAGACCCAAATTCTGAACGTAAAGT
1 GAAAATGCACTTAAAAGTGACTCAGAATATGGTACTGGAGACCCAAATACTGAACGTAAAGT
301082 GAAAA
1 GAAAA
301087 ATTACATCCA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
61 11 0.18
62 51 0.82
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.23
Consensus pattern (62 bp):
GAAAATGCACTTAAAAGTGACTCAGAATATGGTACTGGAGACCCAAATACTGAACGTAAAGT
Found at i:301692 original size:22 final size:22
Alignment explanation
Indices: 301667--301711 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
301657 TATAGGTTTA
* *
301667 AAATTTAAAATATACAAAAAAT
1 AAATATAAAAAATACAAAAAAT
*
301689 AAATATAAAAAATACTAAAAAT
1 AAATATAAAAAATACAAAAAAT
301711 A
1 A
301712 GAAACTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATATAAAAAATACAAAAAAT
Found at i:302742 original size:3 final size:3
Alignment explanation
Indices: 302734--302775 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
302724 CTATGCTTTA
* *
302734 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
302776 TTCTTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:306637 original size:22 final size:23
Alignment explanation
Indices: 306586--306637 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
306576 ATAAGATATT
*
306586 AAAATATATTTTTAGTTATCATAA
1 AAAAT-TATTTTTAGTTATAATAA
**
306610 CCAATTA-TTTTAGTTATAATAA
1 AAAATTATTTTTAGTTATAATAA
306632 AAAATT
1 AAAATT
306638 TAAATAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
22 18 0.78
23 2 0.09
24 3 0.13
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (23 bp):
AAAATTATTTTTAGTTATAATAA
Found at i:307235 original size:33 final size:32
Alignment explanation
Indices: 307144--307276 Score: 126
Period size: 33 Copynumber: 4.1 Consensus size: 32
307134 GTCCCAATAT
* * *
307144 TTTATCAAAATGAAAAATTGTGACAAAT-TTA
1 TTTATCATAATAAAAAATTGTAACAAATATTA
* * *
307175 TTTAATCAAAATAACAAATTATAACAAATATTAA
1 TTT-ATCATAATAAAAAATTGTAACAAATATT-A
* * *
307209 TTTATCATTATAAAAAATTGTGACAAATAATA
1 TTTATCATAATAAAAAATTGTAACAAATATTA
* *
307241 TTCTTTCATAATAACAAATTGTAACAAA-ATTA
1 TT-TATCATAATAAAAAATTGTAACAAATATTA
307273 TTTA
1 TTTA
307277 GTCACAGTAA
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
31 4 0.05
32 29 0.35
33 45 0.55
34 4 0.05
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (32 bp):
TTTATCATAATAAAAAATTGTAACAAATATTA
Found at i:307288 original size:65 final size:65
Alignment explanation
Indices: 307156--307289 Score: 159
Period size: 65 Copynumber: 2.1 Consensus size: 65
307146 TATCAAAATG
* *
307156 AAAAATTGTGACAAATTTATTTAATCAAAATAACAAATTATAACAAATATTAATTTATCATTATA
1 AAAAATTGTGACAAATATATTTAATCAAAATAACAAATTATAACAAATATTAATTTATCATCATA
* * *
307221 AAAAATTGTGACAAATAATATTCT-TTCATAATAACAAATTGTAACAAA-ATT-ATTTAGTCA-C
1 AAAAATTGTGACAAAT-ATATT-TAATCAAAATAACAAATTATAACAAATATTAATTTA-TCATC
307282 AGTA
63 A-TA
307286 AAAA
1 AAAA
307290 GTTATAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
64 6 0.10
65 28 0.47
66 25 0.42
67 1 0.02
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.34
Consensus pattern (65 bp):
AAAAATTGTGACAAATATATTTAATCAAAATAACAAATTATAACAAATATTAATTTATCATCATA
Found at i:310663 original size:17 final size:18
Alignment explanation
Indices: 310643--310681 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
310633 ATACTAGAAT
310643 ATAAAAATATA-ATTATA
1 ATAAAAATATATATTATA
*
310660 ATAAAAATATATTTTATA
1 ATAAAAATATATATTATA
310678 ATAA
1 ATAA
310682 CCCACTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAAATATATATTATA
Found at i:316819 original size:16 final size:16
Alignment explanation
Indices: 316800--316852 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
316790 CCATAACCCC
316800 TATCACACATATATCA
1 TATCACACATATATCA
** * *
316816 TATCATGCACACATCA
1 TATCACACATATATCA
316832 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
316850 TAT
1 TAT
316853 ATCACATACA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:317051 original size:23 final size:23
Alignment explanation
Indices: 317025--317083 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
317015 CACCACAGCT
*
317025 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
317048 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
317071 CGTAGAATTGCAC
1 CGTAGAATTGCAC
317084 TGTAGTTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:317305 original size:103 final size:102
Alignment explanation
Indices: 317109--317315 Score: 344
Period size: 101 Copynumber: 2.0 Consensus size: 102
317099 TAATGTCCAT
* * *
317109 AAGGACCATATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTA-GTGTCTCACCA
317174 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
65 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
*
317212 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTA-TGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGTGTCTCACCAG
* *
317276 ACTTCACACATGTTCCAAAGAATACATATATGCCCCG
66 ACTTCACACATGTTCCAAAGAATATATATATGTCCCG
317313 AAG
1 AAG
317316 AACCGCGTAG
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
101 49 0.50
103 49 0.50
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGTGTCTCACCAG
ACTTCACACATGTTCCAAAGAATATATATATGTCCCG
Found at i:320964 original size:16 final size:16
Alignment explanation
Indices: 320945--320997 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
320935 CCATAACCCC
320945 TATCACACATATATCA
1 TATCACACATATATCA
** * *
320961 TATCATGCACACATCA
1 TATCACACATATATCA
320977 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
320995 TAT
1 TAT
320998 ATCACATACA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:321212 original size:23 final size:23
Alignment explanation
Indices: 321170--321238 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
321160 CACCACAGCT
* *
321170 CGTATAATTGCATCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
321193 CGTGGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
321216 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
321239 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:321424 original size:103 final size:103
Alignment explanation
Indices: 321254--321466 Score: 363
Period size: 103 Copynumber: 2.1 Consensus size: 103
321244 TAATGTCCAT
* * *
321254 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTGAACA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCAACA
*
321319 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
321357 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCAACA
321422 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
321460 AAAGACC
1 AAGGACC
321467 GCGTAGACCC
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCAACA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:327728 original size:15 final size:15
Alignment explanation
Indices: 327708--327740 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
327698 TTTCACCATG
327708 ATTTTTATTATCATT
1 ATTTTTATTATCATT
*
327723 ATTTTTATTATTATT
1 ATTTTTATTATCATT
327738 ATT
1 ATT
327741 AACAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTTATTATCATT
Found at i:329250 original size:37 final size:37
Alignment explanation
Indices: 329209--329280 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
329199 AATTTTAGAA
* *
329209 TATTTATA-TTTATTTTGTATGCTTGTTAA-TTATTTCT
1 TATTTACATTTTATTTTG-ATGCGT-TTAATTTATTTCT
329246 TATTTACATTTTATTTTGATGCGTTTAATTTATTT
1 TATTTACATTTTATTTTGATGCGTTTAATTTATTT
329281 TTCTAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 4 0.13
37 18 0.58
38 9 0.29
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.64
Consensus pattern (37 bp):
TATTTACATTTTATTTTGATGCGTTTAATTTATTTCT
Found at i:338385 original size:21 final size:22
Alignment explanation
Indices: 338361--338404 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
338351 TTAAATTTTA
*
338361 ATTTA-TTTTAATTTAGCCACT
1 ATTTATTTTTAATTTAGCAACT
*
338382 ATTTATTTTTGATTTAGCAACT
1 ATTTATTTTTAATTTAGCAACT
338404 A
1 A
338405 ACTTTTAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (22 bp):
ATTTATTTTTAATTTAGCAACT
Found at i:342738 original size:20 final size:20
Alignment explanation
Indices: 342660--342740 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 20
342650 CCAGAACCCA
* *
342660 GGGGGTATCGATTCCCT-GT
1 GGGGGAATCGATTCCCTCAT
* *
342679 GGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCC-TC-AT
**
342703 GGGGGAATCGGCTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
342723 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
342741 TGCACCAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
20 27 0.56
21 5 0.10
22 4 0.08
23 12 0.25
ACGTcount: A:0.15, C:0.26, G:0.35, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:349840 original size:30 final size:30
Alignment explanation
Indices: 349799--349856 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
349789 AACCATTTAA
*
349799 ACTAACTCGA-TTATTTTTGTCTGGTTTCT
1 ACTAACTCGATTTATTTTTATCTGGTTTCT
*
349828 ACTAACATCGATTTCTTTTTATCTGGTTT
1 ACTAAC-TCGATTTATTTTTATCTGGTTT
349857 TGTTGCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.24
30 4 0.16
31 15 0.60
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (30 bp):
ACTAACTCGATTTATTTTTATCTGGTTTCT
Found at i:351841 original size:19 final size:20
Alignment explanation
Indices: 351812--351887 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
351802 GAATGCTCGA
351812 ATGGTACCGATACCCCCCAT
1 ATGGTACCGATACCCCCCAT
*
351832 A-GGTATCGATA-CCCCCAT
1 ATGGTACCGATACCCCCCAT
* * *
351850 GCAATGGTATCGATACCCCTCAG
1 ---ATGGTACCGATACCCCCCAT
351873 ATGGTACCGATACCC
1 ATGGTACCGATACCC
351888 TAAGGCATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
18 7 0.15
19 9 0.19
20 15 0.32
21 1 0.02
22 10 0.21
23 5 0.11
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.21
Consensus pattern (20 bp):
ATGGTACCGATACCCCCCAT
Found at i:351878 original size:20 final size:19
Alignment explanation
Indices: 351812--351887 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 19
351802 GAATGCTCGA
*
351812 ATGGTACCGATACCCCC-C
1 ATGGTACCGATACCCCCAG
*
351830 ATAGGTATCGATACCCCCATG
1 AT-GGTACCGATACCCCCA-G
*
351851 CAATGGTATCGATACCCCTCAG
1 --ATGGTACCGATACCCC-CAG
351873 ATGGTACCGATACCC
1 ATGGTACCGATACCC
351888 TAAGGCATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
18 2 0.04
19 14 0.29
20 14 0.29
22 15 0.31
23 4 0.08
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.21
Consensus pattern (19 bp):
ATGGTACCGATACCCCCAG
Found at i:353784 original size:21 final size:21
Alignment explanation
Indices: 353755--353794 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
353745 TGAAAATTGT
353755 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
*
353776 TTTTGAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
353795 AAACAATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:357611 original size:23 final size:22
Alignment explanation
Indices: 357541--357618 Score: 86
Period size: 23 Copynumber: 3.5 Consensus size: 22
357531 CCTAAGACAT
*
357541 GTATCGATACCCCTTTAAATAG
1 GTATCGATACCTCTTTAAATAG
*
357563 GTATCGATACCT-TGCTACAATAG
1 GTATCGATACCTCT-TTA-AATAG
* *
357586 GTATCGATACCATCTTTGAATGG
1 GTATCGATACC-TCTTTAAATAG
357609 GTATCGATAC
1 GTATCGATAC
357619 TCCTCTGATG
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.02
22 13 0.28
23 30 0.64
24 2 0.04
25 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (22 bp):
GTATCGATACCTCTTTAAATAG
Found at i:361961 original size:19 final size:19
Alignment explanation
Indices: 361937--361982 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
361927 AAAGTACCAC
361937 ATATATATTCCAAAGGATT
1 ATATATATTCCAAAGGATT
*
361956 ATATATGTTCCAAAGGATT
1 ATATATATTCCAAAGGATT
*
361975 ACATATAT
1 ATATATAT
361983 GTCCCAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
ATATATATTCCAAAGGATT
Found at i:361961 original size:21 final size:19
Alignment explanation
Indices: 361936--361991 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
361926 CAAAGTACCA
*
361936 CATATATATTCCAAAGGAT
1 CATATATGTTCCAAAGGAT
*
361955 TATATATGTTCCAAAGGATT
1 CATATATGTTCCAAAGGA-T
*
361975 ACATATATGTCCCAAAG
1 -CATATATGTTCCAAAG
361992 AACCACGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.52
20 1 0.03
21 14 0.45
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (19 bp):
CATATATGTTCCAAAGGAT
Found at i:369824 original size:39 final size:39
Alignment explanation
Indices: 369777--370107 Score: 484
Period size: 39 Copynumber: 8.5 Consensus size: 39
369767 GAGGGATCAA
*
369777 TATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* * * *
369816 TGTATCGCTTGAGATAGTTTCACTCGATACAGAATATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* * *
369855 TATCTCGCTTGAGACAGTTTCACTCGAAACATAATATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* * *
369894 TATCTCGCTTAATATAGTTTCATTCGAAACAGAAGATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
*
369933 TATCTCGCTTGAGATAGTTTCACTCGAAGCAGAAGATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
*
369972 TATCTCGCTTGAGATAGTTTCACTCAAAACAGAAGATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* * *
370011 TATCTCGCTTAAGATAGTTTCATTCGAAAAAGAAGATTT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
*
370050 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAA-AATT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
* *
370088 TATCTCACTTGAGATTGTTT
1 TATCTCGCTTGAGATAGTTT
370108 TTCTTAAAAC
Statistics
Matches: 260, Mismatches: 32, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
38 21 0.08
39 239 0.92
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (39 bp):
TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
Found at i:370218 original size:59 final size:59
Alignment explanation
Indices: 370123--370297 Score: 305
Period size: 59 Copynumber: 3.0 Consensus size: 59
370113 AAAACAAACT
* *
370123 ACGCCCCACCAGAGGGGTTAACAGTTCCTTTGCTCGATTCACAACACTTCGAATTAGCA
1 ACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCA
*
370182 ACTCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCA
1 ACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCA
* *
370241 ACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTTGATTCACAACACATCGAATCAG
1 ACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAG
370298 GGATGCCTCA
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 110 1.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (59 bp):
ACGCCCCACCAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCA
Found at i:370749 original size:224 final size:224
Alignment explanation
Indices: 370359--370798 Score: 666
Period size: 224 Copynumber: 2.0 Consensus size: 224
370349 AGAACCTACA
* * *
370359 GCTTGAAGAGCAGAGATTGAGTCAAAATGGCACTCTGTTATCTTTGCTTCATTCTCGTTTCATAG
1 GCTTGAAGAGAAGAGATTGAGTCAAAATGGCACTCTGTTATCTTTGCTTCATTCCCGTTTCACAG
* *
370424 AAATGAGCAAATAAGGGCAACTGTGAGCACCATTTTACAAACCCTCCCCAACCCAGTTTACAATA
66 AAATGAGCAAAGAAGGGCAACTGTGAGCACCATTTTACAAACCCGCCCCAACCCAGTTTACAATA
* * * * *
370489 CCCGACCCGGGGCCCAAACCGAGCCTCCTAAATCCCCCAATCAATTGCAACCAACCCAGTGACCA
131 CCCGACCCGGGGACCAAAACGAGCCTCCCAAATCCCCAAATCAATTACAACCAACCCAGTGACCA
* * *
370554 CTCAGTTGGCACCTCCCTCTGATATCTTT
196 CTCAGCTGGAACCTCCATCTGATATCTTT
* *
370583 GCTTGAAGAGAAGAGATTGAGTCAAAATGGCACTCTGTTATCTTTGCTTTATTCCCTTTTCACA-
1 GCTTGAAGAGAAGAGATTGAGTCAAAATGGCACTCTGTTATCTTTGCTTCATTCCCGTTTCACAG
* * * *
370647 ATAATGAGCAAAGAGGGGCAGCTGTGAGCACCATTTTACAAACCCGCCCTAACCTAGTTTACAAT
66 A-AATGAGCAAAGAAGGGCAACTGTGAGCACCATTTTACAAACCCGCCCCAACCCAGTTTACAAT
* * *
370712 ACCCGACCCGGGGACCAAAACGAGTCTCCCAAATCCCCAAATCAATTACAGCCGACCCAGTGACC
130 ACCCGACCCGGGGACCAAAACGAGCCTCCCAAATCCCCAAATCAATTACAACCAACCCAGTGACC
370777 ACTCAGCTGGAACCTCCATCTG
195 ACTCAGCTGGAACCTCCATCTG
370799 CCTCAACCAA
Statistics
Matches: 193, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
223 1 0.01
224 192 0.99
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (224 bp):
GCTTGAAGAGAAGAGATTGAGTCAAAATGGCACTCTGTTATCTTTGCTTCATTCCCGTTTCACAG
AAATGAGCAAAGAAGGGCAACTGTGAGCACCATTTTACAAACCCGCCCCAACCCAGTTTACAATA
CCCGACCCGGGGACCAAAACGAGCCTCCCAAATCCCCAAATCAATTACAACCAACCCAGTGACCA
CTCAGCTGGAACCTCCATCTGATATCTTT
Found at i:371956 original size:17 final size:18
Alignment explanation
Indices: 371936--371972 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
371926 TTTATTTTCA
371936 TTTTA-TATTTTATTGTT
1 TTTTATTATTTTATTGTT
*
371953 TTTTATTATTTTCTTGTT
1 TTTTATTATTTTATTGTT
371971 TT
1 TT
371973 AATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTATTATTTTATTGTT
Found at i:375443 original size:47 final size:47
Alignment explanation
Indices: 375374--375463 Score: 144
Period size: 47 Copynumber: 1.9 Consensus size: 47
375364 TGAATATTTT
* *
375374 TGATATTAACATTTCCAGTAGAAAAAAATAACATTTTAGGTAGCTCA
1 TGATATTAACATTACCAGTAGAAAAAAATAACATTTTAAGTAGCTCA
* *
375421 TGATATTAATATTACCGGTAGAAAAAAATAACATTTTAAGTAG
1 TGATATTAACATTACCAGTAGAAAAAAATAACATTTTAAGTAG
375464 TGCTCTACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (47 bp):
TGATATTAACATTACCAGTAGAAAAAAATAACATTTTAAGTAGCTCA
Found at i:375560 original size:37 final size:37
Alignment explanation
Indices: 375507--375583 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
375497 TTCCGATAAC
*
375507 GTCTTTTCTTAACTTTACTTTAAGTTGCTTTTCTTTA
1 GTCTTTTCTTAACTTTACATTAAGTTGCTTTTCTTTA
*
375544 GTCTTTTCTTAGCTTTACATTAAGTTGCTTTTCTTTA
1 GTCTTTTCTTAACTTTACATTAAGTTGCTTTTCTTTA
375581 GTC
1 GTC
375584 ATCTCCAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.16, C:0.17, G:0.10, T:0.57
Consensus pattern (37 bp):
GTCTTTTCTTAACTTTACATTAAGTTGCTTTTCTTTA
Found at i:380316 original size:23 final size:22
Alignment explanation
Indices: 380290--380358 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
380280 CACCACAGCT
* *
380290 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACC-AAGTGCCA
*
380313 CGTAGAAATGCACCATAGTGCCA
1 CGTAGAATTGCACCA-AGTGCCA
*
380336 CGTAGGATTGCACCAAAGTGCCA
1 CGTAGAATTGCACC-AAGTGCCA
380359 TATAACATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 1 0.03
23 37 0.95
24 1 0.03
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (22 bp):
CGTAGAATTGCACCAAGTGCCA
Found at i:380612 original size:23 final size:21
Alignment explanation
Indices: 380563--380614 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
380553 TCATTTTGTT
*
380563 TGTCACATATTCACATATTCA
1 TGTCACATATGCACATATTCA
* *
380584 TTTCACATATGCATATAATCTCA
1 TGTCACATATGCACAT-AT-TCA
380607 TGTCACAT
1 TGTCACAT
380615 TCTCATATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 13 0.52
22 2 0.08
23 10 0.40
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (21 bp):
TGTCACATATGCACATATTCA
Found at i:383868 original size:24 final size:24
Alignment explanation
Indices: 383841--383886 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
383831 GAACCTCCGT
*
383841 TTTGGCAAATGAGCAC-TTCTCTTA
1 TTTGACAAA-GAGCACATTCTCTTA
*
383865 TTTGACAAAGAGCTCATTCTCT
1 TTTGACAAAGAGCACATTCTCT
383887 CGCAACACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (24 bp):
TTTGACAAAGAGCACATTCTCTTA
Found at i:389223 original size:22 final size:22
Alignment explanation
Indices: 389197--389240 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
389187 CATGAGAATG
389197 TTTGTTATTCACCGATTATTGT
1 TTTGTTATTCACCGATTATTGT
389219 TTTGTTATTCACCGATTATTGT
1 TTTGTTATTCACCGATTATTGT
389241 GTAACCATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (22 bp):
TTTGTTATTCACCGATTATTGT
Found at i:394001 original size:23 final size:23
Alignment explanation
Indices: 393938--394027 Score: 98
Period size: 23 Copynumber: 4.0 Consensus size: 23
393928 CACAGCTCGT
393938 AATTTGCACCGAAGTGCCACAT-
1 AATTTGCACCGAAGTGCCACATA
*
393960 AATTAT-C-CCGAAAG-ACCACATA
1 AATT-TGCACCG-AAGTGCCACATA
*
393982 AATTTTCACCGAAGTGCCACATA
1 AATTTGCACCGAAGTGCCACATA
**
394005 GGTTTGCACCGAAGTGCCACATA
1 AATTTGCACCGAAGTGCCACATA
394028 TTTTTCCAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
21 10 0.18
22 16 0.28
23 31 0.54
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (23 bp):
AATTTGCACCGAAGTGCCACATA
Found at i:394744 original size:20 final size:20
Alignment explanation
Indices: 394694--394745 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
394684 ATCTTAAAAA
*
394694 TGGTATCGACACCATTCCAC
1 TGGTATCGATACCATTCCAC
*
394714 TGGTATTGATACCATTCCAC
1 TGGTATCGATACCATTCCAC
394734 TGGTATCGATAC
1 TGGTATCGATAC
394746 TACCAACTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (20 bp):
TGGTATCGATACCATTCCAC
Found at i:395398 original size:23 final size:22
Alignment explanation
Indices: 395371--395461 Score: 80
Period size: 23 Copynumber: 4.1 Consensus size: 22
395361 TCTGGAAAAA
*
395371 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAA-T
* * *
395394 TATGTGGTAATTCGGTGAAAATT
1 TATGTGGCACTTCGGTGCAAA-T
*
395417 TATGTGGTC-TTTCGG-G-ACAAT
1 TATGTGG-CACTTCGGTGCA-AAT
395438 TATGTGGCACTTCGGTGCAAAT
1 TATGTGGCACTTCGGTGCAAAT
395460 TA
1 TA
395462 CGAGCTGTGG
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.25
22 9 0.16
23 31 0.56
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.34
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGCAAAT
Found at i:395442 original size:21 final size:21
Alignment explanation
Indices: 395328--395452 Score: 76
Period size: 21 Copynumber: 5.8 Consensus size: 21
395318 GTCGAGGGTT
**
395328 TTATGTGGTCCTTTAGGACAA
1 TTATGTGGTCCTTCGGGACAA
* *
395349 TTATGTGGTCCTTCTGGAAAA
1 TTATGTGGTCCTTCGGGACAA
*
395370 ATATGTGG-CACTTCGGTG-CAAA
1 TTATGTGGTC-CTTCGG-GAC-AA
* ** *
395392 CCTATGTGGTAATTCGGTGAAAA
1 -TTATGTGGTCCTTCGG-GACAA
*
395415 TTTATGTGGTCTTTCGGGACAA
1 -TTATGTGGTCCTTCGGGACAA
395437 TTATGTGG-CACTTCGG
1 TTATGTGGTC-CTTCGG
395453 TGCAAATTAC
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
20 2 0.02
21 43 0.53
22 7 0.09
23 29 0.36
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.35
Consensus pattern (21 bp):
TTATGTGGTCCTTCGGGACAA
Found at i:401363 original size:2 final size:2
Alignment explanation
Indices: 401356--401386 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
401346 TGTTACAATA
401356 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
401387 TTTAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:401399 original size:19 final size:18
Alignment explanation
Indices: 401376--401463 Score: 65
Period size: 18 Copynumber: 4.7 Consensus size: 18
401366 ATATATATAT
401376 ATATATTATATTTTAAAA
1 ATATATTATATTTTAAAA
*
401394 ATTATATGTATAGTTTTTGAAA
1 A-TATAT-TATA--TTTTAAAA
**
401416 ATATATTATATTTT-TGA
1 ATATATTATATTTTAAAA
401433 ATATA-TATAGTTTTTAAAA
1 ATATATTATA--TTTTAAAA
401452 AT-TATATATATT
1 ATATAT-TATATT
401464 ATATATTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
16 4 0.07
17 6 0.11
18 13 0.23
19 8 0.14
20 12 0.21
21 5 0.09
22 8 0.14
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
ATATATTATATTTTAAAA
Found at i:401480 original size:22 final size:22
Alignment explanation
Indices: 401455--401500 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
401445 TTTAAAAATT
*
401455 ATATATATTATATATTTTTGAA
1 ATATATATTATATATTTTTAAA
401477 ATATATATTATATATTTTTAAA
1 ATATATATTATATATTTTTAAA
401499 AT
1 AT
401501 TACTTTTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
ATATATATTATATATTTTTAAA
Found at i:409526 original size:2 final size:2
Alignment explanation
Indices: 409472--409507 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
409462 TTATGGTTTT
409472 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
409508 TATTTTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:409534 original size:18 final size:19
Alignment explanation
Indices: 409498--409589 Score: 91
Period size: 21 Copynumber: 4.6 Consensus size: 19
409488 ATATATATAT
409498 ATATATATATTATTTTTGAAA
1 ATATATATA-TA-TTTTGAAA
*
409519 ACATATATA-ATTTTG-AA
1 ATATATATATATTTTGAAA
409536 ATATAATATATATTTT-AATA
1 ATAT-ATATATATTTTGAA-A
409556 TATATATATATATTATTGAAA
1 -ATATATATATATT-TTGAAA
409577 ATATATATTATAT
1 ATATATA-TATAT
409590 ATATTATTGT
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
17 5 0.08
18 10 0.16
19 7 0.11
20 17 0.28
21 20 0.33
22 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (19 bp):
ATATATATATATTTTGAAA
Found at i:409546 original size:20 final size:20
Alignment explanation
Indices: 409521--409584 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
409511 TTTTGAAAAC
409521 ATATATAATTTTGAAATATA
1 ATATATAATTTTGAAATATA
409541 ATATAT-ATTTT--AATATA
1 ATATATAATTTTGAAATATA
409558 TATATATATATTATTGAAA-AT-
1 -ATATATA-ATT-TTGAAATATA
409579 ATATAT
1 ATATAT
409585 TATATATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
17 6 0.16
18 6 0.16
19 5 0.13
20 15 0.39
21 2 0.05
22 2 0.05
23 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (20 bp):
ATATATAATTTTGAAATATA
Found at i:409595 original size:25 final size:24
Alignment explanation
Indices: 409552--409598 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
409542 TATATATTTT
409552 AATATATATATATATATTATTGAA
1 AATATATATATATATATTATTGAA
409576 AATATATATTATATATATTATTG
1 AATATATA-TATATATATTATTG
409599 TTTTTGTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
AATATATATATATATATTATTGAA
Found at i:411914 original size:30 final size:30
Alignment explanation
Indices: 411874--411930 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
411864 TGTTTTGGCA
* * * *
411874 TTTTGAAATTTTATAAGTTTAAGTTCGCTC
1 TTTTAAAATTTTAAAAATTTAAATTCGCTC
411904 TTTTAAAATTTTAAAAATTTAAATTCG
1 TTTTAAAATTTTAAAAATTTAAATTCG
411931 TCCCCTAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (30 bp):
TTTTAAAATTTTAAAAATTTAAATTCGCTC
Found at i:416028 original size:156 final size:156
Alignment explanation
Indices: 415732--416043 Score: 599
Period size: 156 Copynumber: 2.0 Consensus size: 156
415722 CGTTAGGAGG
415732 ATTACCTAGCACTATTCAAAAACTCTTGGTGATGGAAGATGGTGTGGGCTAGTCCCGTGTTGCTT
1 ATTACCTAGCACTATTCAAAAACTCTTGGTGATGGAAGATGGTGTGGGCTAGTCCCGTGTTGCTT
415797 TCACTTTTCATTATTTACATGGATTCCATGTGCACGAACTATAAAGCCTGTGGAGTTGTTCAAAT
66 TCACTTTTCATTATTTACATGGATTCCATGTGCACGAACTATAAAGCCTGTGGAGTTGTTCAAAT
415862 CATGTTTCGTCA-TAAGATGGCGTCA
131 CATGTTTCGTCATTAAGATGGCGTCA
415887 ATTACCTAGCACTATTCAAAAACTCTTGGTGATGGAAGATGGTGTGGGCTAGTCCCGTGTTGCTT
1 ATTACCTAGCACTATTCAAAAACTCTTGGTGATGGAAGATGGTGTGGGCTAGTCCCGTGTTGCTT
*
415952 TTACTTTTTCATTATTTACATGGATTCCATGTGCACGAACTATAAAGCCTGTGGAGTTGTTCAAA
66 TCAC-TTTTCATTATTTACATGGATTCCATGTGCACGAACTATAAAGCCTGTGGAGTTGTTCAAA
416017 TCATGTTTCGTCATTAAGATGGCGTCA
130 TCATGTTTCGTCATTAAGATGGCGTCA
416044 TGATAGGGAA
Statistics
Matches: 154, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
155 68 0.44
156 73 0.47
157 13 0.08
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (156 bp):
ATTACCTAGCACTATTCAAAAACTCTTGGTGATGGAAGATGGTGTGGGCTAGTCCCGTGTTGCTT
TCACTTTTCATTATTTACATGGATTCCATGTGCACGAACTATAAAGCCTGTGGAGTTGTTCAAAT
CATGTTTCGTCATTAAGATGGCGTCA
Found at i:428689 original size:6 final size:6
Alignment explanation
Indices: 428673--428726 Score: 99
Period size: 6 Copynumber: 8.8 Consensus size: 6
428663 ATGTAGCTCA
428673 CACAGCT CACACT CACACT CACACT CACACT CACACT CACACT CACACT
1 CACA-CT CACACT CACACT CACACT CACACT CACACT CACACT CACACT
428722 CACAC
1 CACAC
428727 AACTCACACT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 43 0.91
7 4 0.09
ACGTcount: A:0.33, C:0.50, G:0.02, T:0.15
Consensus pattern (6 bp):
CACACT
Found at i:429442 original size:28 final size:28
Alignment explanation
Indices: 429402--429458 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
429392 ATTGTGAAAC
429402 CCGATTAACATTAAAGATAATATGGGGT
1 CCGATTAACATTAAAGATAATATGGGGT
*
429430 CCGATTAACATTAAAGGTAATATGGGGT
1 CCGATTAACATTAAAGATAATATGGGGT
429458 C
1 C
429459 GCGTATGGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (28 bp):
CCGATTAACATTAAAGATAATATGGGGT
Found at i:430186 original size:33 final size:33
Alignment explanation
Indices: 430144--430214 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
430134 ACTAGCCTCG
430144 CTTTATACCTAGCGAAAAAATCATCAACATGGC
1 CTTTATACCTAGCGAAAAAATCATCAACATGGC
430177 CTTTATACCTAGCGAAAAAATCATCAACATGGC
1 CTTTATACCTAGCGAAAAAATCATCAACATGGC
*
430210 ATTTA
1 CTTTA
430215 ACATTGAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (33 bp):
CTTTATACCTAGCGAAAAAATCATCAACATGGC
Found at i:439027 original size:26 final size:26
Alignment explanation
Indices: 438997--439059 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
438987 GGTGAAATTC
* *
438997 TTGGTCATTTGCATACTAGAGGTATT
1 TTGGTCATTTCCATACTAGAGGTAAT
*
439023 TTGGTCATTTCCATACTAGGGGTAAT
1 TTGGTCATTTCCATACTAGAGGTAAT
439049 TTGGTCATTTC
1 TTGGTCATTTC
439060 ACAGATCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.43
Consensus pattern (26 bp):
TTGGTCATTTCCATACTAGAGGTAAT
Found at i:444995 original size:26 final size:26
Alignment explanation
Indices: 444965--445027 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
444955 GGTGAAATTC
* *
444965 TTGGTCATTTGCATACTAGAGGTATT
1 TTGGTCATTTCCATACTAGAGGTAAT
*
444991 TTGGTCATTTCCATACTAGGGGTAAT
1 TTGGTCATTTCCATACTAGAGGTAAT
445017 TTGGTCATTTC
1 TTGGTCATTTC
445028 ACAGATCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.43
Consensus pattern (26 bp):
TTGGTCATTTCCATACTAGAGGTAAT
Found at i:456189 original size:26 final size:24
Alignment explanation
Indices: 456127--456189 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
456117 CATTTTCATC
456127 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
456151 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
456174 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
456190 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:456191 original size:22 final size:23
Alignment explanation
Indices: 456144--456207 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
456134 TAATTATTAA
* *
456144 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
456165 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
456188 -ATATTTTTAATATTATAATA
1 AATATTTATAATAATATAATA
456208 AAATAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 11 0.30
22 22 0.59
23 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:456206 original size:30 final size:33
Alignment explanation
Indices: 456155--456224 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
456145 ATATTTAAAA
*
456155 TATATTTATTAATATTTATAATAATATAAT-AT
1 TATATTTATTAATATTTATAATAAAATAATAAT
456187 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT-AAT
456219 TATATT
1 TATATT
456225 AGAATAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
30 14 0.40
31 6 0.17
32 15 0.43
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (33 bp):
TATATTTATTAATATTTATAATAAAATAATAAT
Found at i:456269 original size:55 final size:53
Alignment explanation
Indices: 456174--456276 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 53
456164 TAATATTTAT
*
456174 AATAATATAATATTATATTTTTAATATTATAATAAAATAATCAATTATATTAG
1 AATAATATAATATTATATTTTTAATATTATAATAAAATAATAAATTATATTAG
456227 AATAATATAAGATATTATATTTTT-AT-TT-TAATAAATATATAATAAATTAT
1 AATAATAT-A-ATATTATATTTTTAATATTATAAT-AA-A-ATAATAAATTAT
456277 TTATATATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
52 4 0.09
53 12 0.27
54 4 0.09
55 24 0.55
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (53 bp):
AATAATATAATATTATATTTTTAATATTATAATAAAATAATAAATTATATTAG
Found at i:456342 original size:23 final size:23
Alignment explanation
Indices: 456316--456360 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
456306 AACAATATTT
456316 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
456339 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
456361 ATATAACACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:456671 original size:14 final size:14
Alignment explanation
Indices: 456652--456687 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
456642 AAATGTAATT
456652 CATTTTACGGAAAA
1 CATTTTACGGAAAA
*
456666 CATTTTCCGGAAAA
1 CATTTTACGGAAAA
*
456680 CGTTTTAC
1 CATTTTAC
456688 AGAATTCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (14 bp):
CATTTTACGGAAAA
Found at i:458322 original size:6 final size:6
Alignment explanation
Indices: 458311--458341 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
458301 CCCCATGCAG
458311 CTCACA CTCACA CTCACA CTCACA CTCACA C
1 CTCACA CTCACA CTCACA CTCACA CTCACA C
458342 AGCTATGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (6 bp):
CTCACA
Found at i:459364 original size:20 final size:20
Alignment explanation
Indices: 459341--459378 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
459331 GGATCGGTCT
459341 GAACCGAGTCAACCCGACCC
1 GAACCGAGTCAACCCGACCC
* *
459361 GAACTGAGTTAACCCGAC
1 GAACCGAGTCAACCCGAC
459379 TCGTTGACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.11
Consensus pattern (20 bp):
GAACCGAGTCAACCCGACCC
Found at i:461062 original size:19 final size:19
Alignment explanation
Indices: 461019--461064 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
461009 TGTCCTGAAT
* *
461019 TTTGATATTTGTTTTGATA
1 TTTGATTTTTGTTATGATA
* *
461038 TCTGATTTTTGTTATGATC
1 TTTGATTTTTGTTATGATA
461057 TTTGATTT
1 TTTGATTT
461065 CTGCTCTGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.63
Consensus pattern (19 bp):
TTTGATTTTTGTTATGATA
Found at i:463467 original size:20 final size:20
Alignment explanation
Indices: 463442--463483 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
463432 AGACCAGTCT
*
463442 GAATCGACTCAACCCGACCC
1 GAATCGACTCAACCCGAACC
*
463462 GAATCGAGTCAACCCGAACC
1 GAATCGACTCAACCCGAACC
463482 GA
1 GA
463484 CCCGTTGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.38, G:0.19, T:0.10
Consensus pattern (20 bp):
GAATCGACTCAACCCGAACC
Found at i:465612 original size:16 final size:16
Alignment explanation
Indices: 465587--465620 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
465577 ATTTTTTGTC
465587 TTGATTCGACTTG-AA
1 TTGATTCGACTTGTAA
465602 TTGACTTCGACTTGTAA
1 TTGA-TTCGACTTGTAA
465619 TT
1 TT
465621 TCATAAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 9 0.53
17 4 0.24
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.44
Consensus pattern (16 bp):
TTGATTCGACTTGTAA
Found at i:469094 original size:28 final size:29
Alignment explanation
Indices: 468943--469114 Score: 134
Period size: 31 Copynumber: 5.6 Consensus size: 29
468933 ATGTCCTAAG
468943 TTTAAAATATATATATTTATT-TTTTATTCAA
1 TTTAAAA-ATATAT-TTTATTCTTTTATT-AA
* * *
468974 CTTATTAAATATATTTTATTTTAATTTTAACTTTAA
1 TTTA-AAAATATATTTTA--TT-CTTTT-A--TTAA
*
469010 CTTTAAAAATGTATTTTATTCTTTTATTAA
1 -TTTAAAAATATATTTTATTCTTTTATTAA
**
469040 TTTAAAAATATATATTTTATTAATTTA-T-A
1 TTT-AAAA-ATATATTTTATTCTTTTATTAA
469069 TTTAAATAATATATTTTATTCTTTTATTAA
1 TTTAAA-AATATATTTTATTCTTTTATTAA
*
469099 CTTAAAAATATATTTT
1 TTTAAAAATATATTTT
469115 GTTATATCTT
Statistics
Matches: 115, Mismatches: 12, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
28 19 0.17
29 19 0.17
30 19 0.17
31 24 0.21
32 5 0.04
33 4 0.03
34 6 0.05
35 1 0.01
36 13 0.11
37 5 0.04
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (29 bp):
TTTAAAAATATATTTTATTCTTTTATTAA
Found at i:469140 original size:59 final size:60
Alignment explanation
Indices: 468946--469247 Score: 225
Period size: 59 Copynumber: 4.9 Consensus size: 60
468936 TCCTAAGTTT
* * *
468946 AAAATATATATATTTATT-TTTTATTCAACTTATTAAATATATTTTATTTTAATTTTAACTTTAA
1 AAAATATATAT-TTTATTCTTTTATT-AACTTA-AAAATATA-TTT-TGTT-A--TTATC-TTAA
*
469010 CTTT
57 CTTC
* * *
469014 AAAA-ATGTATTTTATTCTTTTATTAATTTAAAAATATATATT-TTATTAAT-TTATA-TT-
1 AAAATATATATTTTATTCTTTTATTAACTTAAAAATATATTTTGTTATT-ATCTTA-ACTTC
*
469071 TAAATAATATATTTTATTCTTTTATTAACTTAAAAATATATTTTGTTA-TATCTTAACTTC
1 AAAAT-ATATATTTTATTCTTTTATTAACTTAAAAATATATTTTGTTATTATCTTAACTTC
*
469131 AAAATATATATATATATATTATTCTTTTATTAACTTAAAAGATGTA-TTTGTTA-TATCTTAACT
1 --AA-A-ATATATAT-T-TTATTCTTTTATTAACTTAAAA-ATATATTTTGTTATTATCTTAACT
469194 TC
59 TC
* * * *
469196 --AATATACA--TTATTCTTTTATTAACTTAAAGATGTATTTTATTATTATCTTAA
1 AAAATATATATTTTATTCTTTTATTAACTTAAAAATATATTTTGTTATTATCTTAA
469248 GTTTAAAAAA
Statistics
Matches: 202, Mismatches: 14, Indels: 48
0.77 0.05 0.18
Matches are distributed among these distances:
54 5 0.02
55 27 0.13
56 8 0.04
57 3 0.01
58 8 0.04
59 50 0.25
60 5 0.02
61 1 0.00
62 3 0.01
63 8 0.04
64 5 0.02
65 48 0.24
66 15 0.07
67 12 0.06
68 4 0.02
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (60 bp):
AAAATATATATTTTATTCTTTTATTAACTTAAAAATATATTTTGTTATTATCTTAACTTC
Found at i:469148 original size:28 final size:28
Alignment explanation
Indices: 469095--469149 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
469085 TATTCTTTTA
* *
469095 TTAACTTAAAAATATATTTTGTTATATC
1 TTAACTTAAAAATATATTATGATATATC
*
469123 TTAACTTCAAAATATATATAT-ATATAT
1 TTAACTTAAAAATATAT-TATGATATAT
469150 TATTCTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (28 bp):
TTAACTTAAAAATATATTATGATATATC
Found at i:469153 original size:124 final size:121
Alignment explanation
Indices: 468947--469247 Score: 299
Period size: 124 Copynumber: 2.4 Consensus size: 121
468937 CCTAAGTTTA
* * * * *
468947 AAATATATATATTTATT-TTTTATTCAACTTATTAAATATATTTTATTTTAATTTTAACTTTAAC
1 AAATATATAT-TTTATTCTTTTATT-AACTTA-AAAATATATTTTATTAT-ATCTTAACTTAAAA
* * * * *
469011 TTTAAAAATGTATTTTATTCTTTTATTAATTTAAAA-ATATATATT-TTATTAAT-TTATATTT
62 TATAAAAATATATATTATTCTTTTATTAACTTAAAAGATATAT-TTGTTA-T-ATCTTA-ACTT
*
469072 AAATAATATATTTTATTCTTTTATTAACTTAAAAATATATTTTGTTATATCTTAACTTCAAAATA
1 AAAT-ATATATTTTATTCTTTTATTAACTTAAAAATATATTTTATTATATCTTAACTT-AAAATA
* * *
469137 TATATATATATATTATTCTTTTATTAACTTAAAAGATGTATTTGTTATATCTTAACTT
64 TAAAAATATATATTATTCTTTTATTAACTTAAAAGATATATTTGTTATATCTTAACTT
* * * *
469195 CAATATACA--TTATTCTTTTATTAACTTAAAGATGTATTTTATTATTATCTTAA
1 AAATATATATTTTATTCTTTTATTAACTTAAAAATATATTTTATTA-TATCTTAA
469248 GTTTAAAAAA
Statistics
Matches: 150, Mismatches: 19, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
120 32 0.21
121 8 0.05
122 4 0.03
123 17 0.11
124 52 0.35
125 24 0.16
126 13 0.09
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (121 bp):
AAATATATATTTTATTCTTTTATTAACTTAAAAATATATTTTATTATATCTTAACTTAAAATATA
AAAATATATATTATTCTTTTATTAACTTAAAAGATATATTTGTTATATCTTAACTT
Found at i:469201 original size:55 final size:56
Alignment explanation
Indices: 469142--469247 Score: 171
Period size: 55 Copynumber: 1.9 Consensus size: 56
469132 AAATATATAT
* *
469142 ATATATATTATTCTTTTATTAACTTAAAAGATGTA-TTTGTTA-TATCTTAACTTCA
1 ATATACATTATTCTTTTATTAACTT-AAAGATGTATTTTATTATTATCTTAACTTCA
469197 ATATACATTATTCTTTTATTAACTTAAAGATGTATTTTATTATTATCTTAA
1 ATATACATTATTCTTTTATTAACTTAAAGATGTATTTTATTATTATCTTAA
469248 GTTTAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
54 9 0.19
55 30 0.64
56 8 0.17
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (56 bp):
ATATACATTATTCTTTTATTAACTTAAAGATGTATTTTATTATTATCTTAACTTCA
Found at i:469242 original size:27 final size:27
Alignment explanation
Indices: 469157--469242 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
469147 TATTATTCTT
*
469157 TTATTAACTTAAAAGATGTA-TTTGTTA
1 TTATTAACTT-AAAGATGTATTTTATTA
* * * ** *
469184 TATCTTAACTTCAATATACATTATTCTT-
1 T-TATTAACTTAAAGATGTATT-TTATTA
469212 TTATTAACTTAAAGATGTATTTTATTA
1 TTATTAACTTAAAGATGTATTTTATTA
469239 TTAT
1 TTAT
469243 CTTAAGTTTA
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
26 4 0.09
27 25 0.58
28 10 0.23
29 4 0.09
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (27 bp):
TTATTAACTTAAAGATGTATTTTATTA
Found at i:471721 original size:33 final size:32
Alignment explanation
Indices: 471667--471729 Score: 74
Period size: 33 Copynumber: 1.9 Consensus size: 32
471657 CTTAAATTTG
* *
471667 AATTAATTAAATTAATTATTAACGTTATTTTAA
1 AATTAATTAAATTAATAATTAA-ATTATTTTAA
*
471700 AATTAATTTAATTTAA-AATTAAATTATTTT
1 AATTAA-TTAAATTAATAATTAAATTATTTT
471730 TTCTCATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 7 0.27
33 11 0.42
34 8 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (32 bp):
AATTAATTAAATTAATAATTAAATTATTTTAA
Found at i:471772 original size:13 final size:13
Alignment explanation
Indices: 471756--471781 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
471746 TGACGTGATT
471756 AATTTTAAATTAA
1 AATTTTAAATTAA
471769 AATTTTAAATTAA
1 AATTTTAAATTAA
471782 CATTAAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTTAAATTAA
Found at i:474333 original size:19 final size:20
Alignment explanation
Indices: 474286--474336 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
474276 GAAACCCCTT
**
474286 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
474306 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
474325 TGAATATACATG
1 TGAAAATACATG
474337 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:481543 original size:26 final size:25
Alignment explanation
Indices: 481508--481559 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
481498 TATCAATAAC
*
481508 TAATATTTTATAAAAAAAATTAGGTT
1 TAATAATTTA-AAAAAAAATTAGGTT
* *
481534 TAATAATTTAGATAAAAATTAGGTT
1 TAATAATTTAAAAAAAAATTAGGTT
481559 T
1 T
481560 TAAATTAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (25 bp):
TAATAATTTAAAAAAAAATTAGGTT
Found at i:487396 original size:9 final size:9
Alignment explanation
Indices: 487382--487474 Score: 82
Period size: 9 Copynumber: 10.2 Consensus size: 9
487372 TTTGAAGAGG
487382 AAAAGAAAA
1 AAAAGAAAA
*
487391 AAAAGAGAA
1 AAAAGAAAA
487400 AAAAGAAAA
1 AAAAGAAAA
487409 AAAAGAGGAAA
1 AAAAGA--AAA
*
487420 AATAG-AAA
1 AAAAGAAAA
*
487428 AAAGGAAAA
1 AAAAGAAAA
*
487437 AATAGAAAA
1 AAAAGAAAA
* *
487446 AATGAGAAGA
1 AA-AAGAAAA
*
487456 AAAA-AACA
1 AAAAGAAAA
487464 AAAAGAAAA
1 AAAAGAAAA
487473 AA
1 AA
487475 GTGAAGAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
8 13 0.19
9 40 0.60
10 7 0.10
11 7 0.10
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:487405 original size:18 final size:18
Alignment explanation
Indices: 487382--487475 Score: 95
Period size: 18 Copynumber: 5.3 Consensus size: 18
487372 TTTGAAGAGG
487382 AAAAGAAAAAAAAGAGAA
1 AAAAGAAAAAAAAGAGAA
*
487400 AAAAGAAAAAAAAGAGGA
1 AAAAGAAAAAAAAGAGAA
* *
487418 AAAATAGAAAAAAG-GAA
1 AAAAGAAAAAAAAGAGAA
* *
487435 AAAATAGAAAAAATGAGAA
1 AAAAGA-AAAAAAAGAGAA
*
487454 GAAAA-AAACAAAA-AGAA
1 -AAAAGAAAAAAAAGAGAA
487471 AAAAG
1 AAAAG
487476 TGAAGAAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
16 4 0.06
17 12 0.19
18 40 0.62
19 4 0.06
20 4 0.06
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAAAAAGAGAA
Found at i:487412 original size:20 final size:20
Alignment explanation
Indices: 487387--487430 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
487377 AGAGGAAAAG
487387 AAAAAAAAGAGAAAAA-AGAA
1 AAAAAAAAG-GAAAAATAGAA
*
487407 AAAAAAGAGGAAAAATAGAA
1 AAAAAAAAGGAAAAATAGAA
487427 AAAA
1 AAAA
487431 GGAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGGAAAAATAGAA
Found at i:487420 original size:27 final size:25
Alignment explanation
Indices: 487389--487484 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 25
487379 AGGAAAAGAA
487389 AAAAAAGAGAAAAAAGAAAAAAAAG
1 AAAAAAGAGAAAAAAGAAAAAAAAG
* *
487414 AGGAAAAATAGAAAAAAGGAAAAAATAG
1 A--AAAAAGAGAAAAAA-GAAAAAAAAG
487442 AAAAAATGAGAAGAAAA-AAACAAAAAG
1 AAAAAA-GAGAA-AAAAGAAA-AAAAAG
*
487469 AAAAAAGTGAAGAAAA
1 AAAAAAGAGAA-AAAA
487485 TAAATTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.02
26 17 0.28
27 28 0.47
28 14 0.23
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (25 bp):
AAAAAAGAGAAAAAAGAAAAAAAAG
Found at i:489725 original size:91 final size:91
Alignment explanation
Indices: 489557--489820 Score: 368
Period size: 91 Copynumber: 2.9 Consensus size: 91
489547 CAATCGACAT
* ** * * * *
489557 TTTC-AATGGAAGGGTTCATAATGAGAAGAACTTGTCCGACGAGGGAGTATAAGTTAATAATGAG
1 TTTCAAATGG-AGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAG
*
489621 AAGAACTTGTTCAACCTTGGATCATCA
65 AAGAACTTGTTCAACCTTGGATCAACA
* * *
489648 TTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGA
1 TTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGA
*
489713 AGAGCTTGTTCAACCTTGGATCAACA
66 AGAACTTGTTCAACCTTGGATCAACA
* *
489739 TTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAGGAAGTTCATAATGAG
1 TTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCC-AACGAGGGAGAAGAAGTTCATAATGAG
*
489804 AAGAACTTGTTCGACCT
65 AAGAACTTGTTCAACCT
489821 ATTGCTCGAT
Statistics
Matches: 153, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
91 109 0.71
92 44 0.29
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (91 bp):
TTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTGGATCAACA
Found at i:490139 original size:135 final size:135
Alignment explanation
Indices: 489738--490149 Score: 486
Period size: 136 Copynumber: 3.0 Consensus size: 135
489728 TTGGATCAAC
* * *
489738 ATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAGGAAGTTCATAATGA
1 ATTTC-AATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAAGAAGTTCATAATGA
* * * * ** * *
489803 GAAGAACTTGTTCGACCTATTGCTCGATTCGCGACATTTCGAATCAGCAATGCCTTGCTTGAGAG
65 GAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCGAATCAACGATACCTAACTTAAGGG
*
489868 -TTCAAC
130 ATT-AAT
* *
489874 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGA-AGGAGAAGATGTTCATAATG
1 ATTT-CAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGA-GAGAAGAAGTTCATAATG
* * * * * *
489938 AGAAGAGCTTGTTCGACCTATCGCTTGATTCATGACATTTCAAATCAACGATACCTAACTTTAGG
64 AGAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCGAATCAACGATACCTAACTTAAGG
490003 GATTAAT
129 GATTAAT
* * * *
490010 ATTTCAATAGAGAGTTCATAATGAGAATAACTCATCCGACAGAGAAAGAATAAGTTCATAATGAG
1 ATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAAGAAGTTCATAATGAG
* * * * * * *
490075 AAGAACTTGTTCGACCTATTACTCGATTCACAACACTACGAATCAATGACACCTCACTTAAGGGA
66 AAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCGAATCAACGATACCTAACTTAAGGGA
*
490140 TCAAT
131 TTAAT
490145 ATTTC
1 ATTTC
490150 CAGAAGAAAC
Statistics
Matches: 233, Mismatches: 39, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
135 114 0.49
136 116 0.50
137 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (135 bp):
ATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAAGAAGTTCATAATGAG
AAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCGAATCAACGATACCTAACTTAAGGGA
TTAAT
Found at i:494196 original size:13 final size:13
Alignment explanation
Indices: 494178--494202 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
494168 GAATGTTTCA
494178 AAATTTATGAAAT
1 AAATTTATGAAAT
494191 AAATTTATGAAA
1 AAATTTATGAAA
494203 AATTGACCAA
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AAATTTATGAAAT
Found at i:497717 original size:188 final size:186
Alignment explanation
Indices: 497446--497828 Score: 518
Period size: 188 Copynumber: 2.0 Consensus size: 186
497436 CTTTTCCAAG
* * *
497446 TATATGCATCAAATTATCTATACTTTAGAAATTTAAAAAAAGTACAATAATAGCACTATAAAGTA
1 TATATGTATCAAATTATCAAAACTTTAGAAATTTAAAAAAAGTACAATAATAGCACTATAAAGTA
* * *
497511 TCGATACTTTATAAACATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACCT-G
66 TCGATACTTTATAAACATGTACCAATACATAACAATATAACAAGTAAAAA-ATGACAAAA-CTGG
*
497575 TTTCAATATGA-AAAACCGGTAAAGAACTACCAGATATGTTGAAGGTATCGATACTTT
129 TTTCAATATGACAAAACCGGTAAAGAACTACCAGATATGTTGAAGGTATCAATACTTT
* * * * *
497632 TATATGTATCATATTATCAAAACTTTAGGAATTTTAAAAGAATTACAATAATAGCGCCTATAAAG
1 TATATGTATCAAATTATCAAAACTTTA-GAAATTTAAAAAAAGTACAATAATAGC-ACTATAAAG
* *
497697 TATCGATACTTTATAAACATGTACCAATACATGACAATATAACAAGTTAAAAATGACAAAACTGG
64 TATCGATACTTTATAAACATGTACCAATACATAACAATATAACAAGTAAAAAATGACAAAACTGG
* * ** * *
497762 TTTCAGTATGACAAAATCGGTAAAGCGCTACCGGATATGTTTAAGGTATCAATACTTT
129 TTTCAATATGACAAAACCGGTAAAGAACTACCAGATATGTTGAAGGTATCAATACTTT
* *
497820 AATAAGTAT
1 TATATGTAT
497829 ATGTATCATA
Statistics
Matches: 171, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
186 25 0.15
187 44 0.26
188 102 0.60
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (186 bp):
TATATGTATCAAATTATCAAAACTTTAGAAATTTAAAAAAAGTACAATAATAGCACTATAAAGTA
TCGATACTTTATAAACATGTACCAATACATAACAATATAACAAGTAAAAAATGACAAAACTGGTT
TCAATATGACAAAACCGGTAAAGAACTACCAGATATGTTGAAGGTATCAATACTTT
Found at i:498510 original size:229 final size:230
Alignment explanation
Indices: 498153--498572 Score: 650
Period size: 229 Copynumber: 1.8 Consensus size: 230
498143 TCAAAAATAG
*
498153 GGGTTTTATGGGTTTGGGGTTTTCGAAGTAAAGAAGCATTTAAGACCGATTACAGTTAGAAAGTG
1 GGGTTTTATGGGTTTGGGGTTTTCGAAGCAAAGAAGCATTTAAGACCGATTACAGTTAGAAAGTG
* *
498218 ATATTCAAGGTAAATAATAAATATTGATACTTTTATAAAATATTATAGGTAGAAAATGATATTGT
66 ATATTCAAGGTAAATAATAAATATCGATACTTGTATAAAATATTATAGGTAGAAAATGATATTGT
* *
498283 ATGTTGTATAAATGTACGGATACTTGTAGTAGAGAGTATTCACATTCGTTTGGAGGAAACCCTAG
131 AGGTTGTATAAATGTACGGATACTTGTAGTAGAGAGTATTCACATTCGTTTGAAGGAAACCCTAG
498348 TTTTTTTTAGTATTAGTAATTGAAAATAGGGATTA
196 TTTTTTTTAGTATTAGTAATTGAAAATAGGGATTA
* * * * *
498383 GGGTTTT-TGGGTTTGGGGATTTT-GAAGCAAATAAGTATTTGAGACCGATTAGAGTTGGAAAGT
1 GGGTTTTATGGGTTTGGGG-TTTTCGAAGCAAAGAAGCATTTAAGACCGATTACAGTTAGAAAGT
*
498446 GATATT-ATAGGTAGAA-AATAAATATCGATACTTGTATACAATATTATAGGTAGAAAATGATAT
65 GATATTCA-AGGTA-AATAATAAATATCGATACTTGTATAAAATATTATAGGTAGAAAATGATAT
* ** *
498509 TGTAGGTTGTATAAATGTACTGATACTTGTAGTAGAGAGTATTCTGATTCTTTTGAAGGAAACC
128 TGTAGGTTGTATAAATGTACGGATACTTGTAGTAGAGAGTATTCACATTCGTTTGAAGGAAACC
498573 GTTTTACTAT
Statistics
Matches: 172, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
228 1 0.01
229 158 0.92
230 13 0.08
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (230 bp):
GGGTTTTATGGGTTTGGGGTTTTCGAAGCAAAGAAGCATTTAAGACCGATTACAGTTAGAAAGTG
ATATTCAAGGTAAATAATAAATATCGATACTTGTATAAAATATTATAGGTAGAAAATGATATTGT
AGGTTGTATAAATGTACGGATACTTGTAGTAGAGAGTATTCACATTCGTTTGAAGGAAACCCTAG
TTTTTTTTAGTATTAGTAATTGAAAATAGGGATTA
Found at i:500142 original size:12 final size:12
Alignment explanation
Indices: 500136--500183 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
500126 AAGGAGGAAG
500136 AGGAGGAAGAG-
1 AGGAGGAAGAGA
500147 --GAGGAAGAGA
1 AGGAGGAAGAGA
500157 AGGA-GAAGAGA
1 AGGAGGAAGAGA
*
500168 AGGAAGAAGAGA
1 AGGAGGAAGAGA
500180 AGGA
1 AGGA
500184 AGAGAAGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
9 9 0.27
11 11 0.33
12 13 0.39
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (12 bp):
AGGAGGAAGAGA
Found at i:500150 original size:18 final size:20
Alignment explanation
Indices: 500127--500174 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
500117 GTTATTGGCA
*
500127 AGGAGGAAGAGGA-G-GAAG
1 AGGAGGAAGAGAAGGAGAAG
500145 AGGAGGAAGAGAAGGAGAAG
1 AGGAGGAAGAGAAGGAGAAG
*
500165 AGAAGGAAGA
1 AGGAGGAAGA
500175 AGAGAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 12 0.46
19 1 0.04
20 13 0.50
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (20 bp):
AGGAGGAAGAGAAGGAGAAG
Found at i:500158 original size:23 final size:21
Alignment explanation
Indices: 500126--500190 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
500116 GGTTATTGGC
*
500126 AAGGAGGAAGAGGAGGAAGAG
1 AAGGAAGAAGAGGAGGAAGAG
*
500147 GAGGAAG-AGAAGGA-GAAGAG
1 AAGGAAGAAG-AGGAGGAAGAG
*
500167 AAGGAAGAAGAGAAGGAAGAG
1 AAGGAAGAAGAGGAGGAAGAG
500188 AAG
1 AAG
500191 CTAGTTCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (21 bp):
AAGGAAGAAGAGGAGGAAGAG
Found at i:500184 original size:12 final size:12
Alignment explanation
Indices: 500145--500186 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
500135 GAGGAGGAAG
*
500145 AGGAGGAAGAGA
1 AGGAAGAAGAGA
500157 AGG-AGAAGAGA
1 AGGAAGAAGAGA
500168 AGGAAGAAGAGA
1 AGGAAGAAGAGA
500180 AGGAAGA
1 AGGAAGA
500187 GAAGCTAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (12 bp):
AGGAAGAAGAGA
Found at i:500185 original size:9 final size:9
Alignment explanation
Indices: 500130--500190 Score: 60
Period size: 9 Copynumber: 7.2 Consensus size: 9
500120 ATTGGCAAGG
*
500130 AGGAAGAGG
1 AGGAAGAGA
*
500139 AGGAAGAGG
1 AGGAAGAGA
500148 AGGAAGAGA
1 AGGAAGAGA
500157 A-G--GAGA
1 AGGAAGAGA
500163 AGAGAAG-GA
1 AG-GAAGAGA
500172 A-GAAGAGA
1 AGGAAGAGA
500180 AGGAAGAGA
1 AGGAAGAGA
500189 AG
1 AG
500191 CTAGTTCAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
6 5 0.11
7 4 0.09
8 5 0.11
9 30 0.67
10 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (9 bp):
AGGAAGAGA
Found at i:501590 original size:19 final size:20
Alignment explanation
Indices: 501566--501606 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
501556 TAAGTAAACA
501566 TAAAGTG-TCGATACTTTTT
1 TAAAGTGATCGATACTTTTT
501585 TAAAGTGTATCGATACTTTTT
1 TAAAGTG-ATCGATACTTTTT
501606 T
1 T
501607 TCCAATATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.49
Consensus pattern (20 bp):
TAAAGTGATCGATACTTTTT
Found at i:501679 original size:200 final size:200
Alignment explanation
Indices: 501228--501779 Score: 677
Period size: 200 Copynumber: 2.8 Consensus size: 200
501218 CCTAAACTGG
* * * * *
501228 AAGTAAAAAGAAAGTATCGATACATGTATGAAAAGTGTCGATTCTTAAAAATTTGAAACCGGTTA
1 AAGTAGAAAGAAAGTATCGATAC-TGTATGAAAAGTATCGATTCTTAAAACTTTAAAACCGATT-
* * * * * *
501293 ACT-TAAAGTAATAGGTAAATTTACAATGTTAGCGGTAAAAAGATATTGATTT-ATGATAAAATA
64 ATTATAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATATAATGGTTTAATGACAAAATA
* * * * * *
501356 GGTTAACTTAAAGTATCGATACTTTTTGAATGTATATCGATACTTCTTTCCAGTATGCTTCCCAA
129 AGTAAACATAAAGTATCGATACTTTTTGAAAGTATATCGATACTTCTTTCCAATATGCATCCCAA
501421 ACTTAAGT
194 AC-TAAGT
501429 AAGTAGAAAGAAAGTATCGATACTAGTATGAAAAGTATCGATTCTTAAAACTTTAAAACCGATT-
1 AAGTAGAAAGAAAGTATCGATACT-GTATGAAAAGTATCGATTCTTAAAACTTTAAAACCGATTA
* * *
501493 TGTATAAAATAATATGTAAATTTACAATGTAAGCGGTAAAAATATAATGGTTTAATGAGAAAATA
65 T-TATAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATATAATGGTTTAATGACAAAATA
* * * *
501558 AGTAAACATAAAGTGTCGATACTTTTTTAAAGTGTATCGATACTTTTTTTCCAATATGCATCCCA
129 AGTAAACATAAAGTATCGATACTTTTTGAAAGTATATCGATAC-TTCTTTCCAATATGCATCCCA
*
501623 AAC-GAG-
193 AACTAAGT
* * * * *
501629 ATGTACG-TAGAAAGTATCGATACGTGTATGAGAAGTATCGATTATTAAAACTTCAAAACCGATT
1 AAGTA-GAAAGAAAGTATCGATAC-TGTATGAAAAGTATCGATTCTTAAAACTTTAAAACCGATT
* *
501693 ATTATAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATAT-ATCGGTTTAAAGACAAATT
64 ATTATAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATATAAT-GGTTTAATGACAAAAT
*
501757 ATGTAAACATAAAGTATCGATAC
128 AAGTAAACATAAAGTATCGATAC
501780 ATAGTATCGA
Statistics
Matches: 306, Mismatches: 36, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
199 2 0.01
200 132 0.43
201 105 0.34
202 46 0.15
203 21 0.07
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (200 bp):
AAGTAGAAAGAAAGTATCGATACTGTATGAAAAGTATCGATTCTTAAAACTTTAAAACCGATTAT
TATAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATATAATGGTTTAATGACAAAATAAG
TAAACATAAAGTATCGATACTTTTTGAAAGTATATCGATACTTCTTTCCAATATGCATCCCAAAC
TAAGT
Found at i:503761 original size:21 final size:22
Alignment explanation
Indices: 503735--503779 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
503725 TGCTTACTTT
503735 TATTTAT-TTATGACT-CCTGTA
1 TATTTATGTT-TGACTACCTGTA
*
503756 TATTTATGTTTGACTATCTGTA
1 TATTTATGTTTGACTACCTGTA
503778 TA
1 TA
503780 AACATGATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.53
Consensus pattern (22 bp):
TATTTATGTTTGACTACCTGTA
Found at i:505881 original size:453 final size:451
Alignment explanation
Indices: 505283--506138 Score: 1118
Period size: 453 Copynumber: 1.9 Consensus size: 451
505273 TCATAGGTAA
* *** *
505283 AAAATTGATAAAACCGGTTTCCATAATTGCGCTATAAAGTAGCGATACACGTTTTAAATTATCGA
1 AAAATTGATAAAACCGGTTTCCATAATTGCGCTATAAAGTAGCAATACACGTCGAAAACTATCGA
* *
505348 TTCTTAAAACTTCAAAACGGATTACTTTAAGTAATAGGTAAATTTACAATGTCAATGGTAAAAAT
66 TTCTTAAAACTTCAAAACCGATTACTTTAAATAATAGGTAAATTTACAATGTCAATGGTAAAAAT
** * * *
505413 ATATTAGTTTAATGACAAAATACATTAAAATAAAGTATCGATACTTTTT-TATGTGTATCGATAC
131 ATACGAGTTTAATGACAAAATACATTAAAATAAAGTATCAACACTTTTTGTATATGTATCGATAC
* * * * *
505477 TTTTTTT-CAGTATGCTTTCCAAGCTAGATGCATGCA-TAATGTATCGATACCT-ATGAAACATG
196 TTTTTTTCCAGTATGCTTCCCAAACTAGATGCACGCACGAA-GTATCGATACCTAAT-AAA-ATA
* * *
505539 TATCGATACAAGACAATATAATAGGTTCAAAATTGATAAAAACCAGTTTTAAAATGACAAAACCG
258 TATCGATACAAGACAATATAACAGGTTCAAAATTGA-AAAAACCAGTTTCAAAATGACAAAACAG
* * * *
505604 GTAAAGAGCTA-CCGTTTACAAAAAAAATGAAACGTCTCAAAAGTATCGATATCTTACAAAAAAA
322 ATAAAAAGATATCCGTTTA-AAAAAAAATGAAACGTCTCAAAAGTATCGATATCATACAAAAAAA
* *
505668 TATTGATACTTCAGTAAGGGTAATGGTATTGATTGAATATAAATAACATAACATAACAAGTTCAA
386 TATAGACACTTCAGTAAGGGTAATGGTATTGATTGAATATAAATAACATAACATAACAAGTTCAA
505733 T
451 T
* * *
505734 AAAATTGA-AAAACTGGTTTCCATAATTGTGCCTATAAAGTATCAATACACGTACGAAAACTATC
1 AAAATTGATAAAACCGGTTTCCATAATTGCG-CTATAAAGTAGCAATACACGT-CGAAAACTATC
*
505798 GATTCTTAAAACTTCGAAACCGATTACTTTAAAATAATAGGTAAATTTACAATGT-AA-GCTGTA
64 GATTCTTAAAACTTCAAAACCGATTACTTT-AAATAATAGGTAAATTTACAATGTCAATG--GTA
** * * *
505861 AAAATATACCGA-TTTAATGACAAAATATGTTTACATAAAGTATCAACACTTTTTGTATATGTGT
126 AAAATATA-CGAGTTTAATGACAAAATACATTAAAATAAAGTATCAACACTTTTTGTATATGTAT
* *
505925 CGATACTTTTTTTCCAGTATGCTTCCCAAACTAGATTCACGTACGAAGTATCGATACCTAATAAA
190 CGATACTTTTTTTCCAGTATGCTTCCCAAACTAGATGCACGCACGAAGTATCGATACCTAATAAA
* * * * *
505990 ATATATCGATACATGACAATATAACAGGTTGAAAATTGACAAAACCGGTTTCAATATGACAAAAC
255 ATATATCGATACAAGACAATATAACAGGTTCAAAATTGAAAAAACCAGTTTCAAAATGACAAAAC
* * * * *
506055 AGATAAAAAGATATCGGTTTAAACAAAAATGAAACGTCTCGAAAGTATCGATATCATATACAAAA
320 AGATAAAAAGATATCCGTTTAAAAAAAAATGAAACGTCTCAAAAGTATCGATATCATACAAAAAA
*
506120 GTATAGACACTTCAGTAAG
385 ATATAGACACTTCAGTAAG
506139 TGTATTCAAT
Statistics
Matches: 346, Mismatches: 48, Indels: 20
0.84 0.12 0.05
Matches are distributed among these distances:
450 20 0.06
451 28 0.08
452 37 0.11
453 156 0.45
454 62 0.18
455 39 0.11
456 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (451 bp):
AAAATTGATAAAACCGGTTTCCATAATTGCGCTATAAAGTAGCAATACACGTCGAAAACTATCGA
TTCTTAAAACTTCAAAACCGATTACTTTAAATAATAGGTAAATTTACAATGTCAATGGTAAAAAT
ATACGAGTTTAATGACAAAATACATTAAAATAAAGTATCAACACTTTTTGTATATGTATCGATAC
TTTTTTTCCAGTATGCTTCCCAAACTAGATGCACGCACGAAGTATCGATACCTAATAAAATATAT
CGATACAAGACAATATAACAGGTTCAAAATTGAAAAAACCAGTTTCAAAATGACAAAACAGATAA
AAAGATATCCGTTTAAAAAAAAATGAAACGTCTCAAAAGTATCGATATCATACAAAAAAATATAG
ACACTTCAGTAAGGGTAATGGTATTGATTGAATATAAATAACATAACATAACAAGTTCAAT
Found at i:508107 original size:280 final size:276
Alignment explanation
Indices: 507612--508153 Score: 802
Period size: 280 Copynumber: 1.9 Consensus size: 276
507602 TATCAATACT
* * * *
507612 TTAATTCCACATAAAGGCTCAAACAATATGCACGTAAAATGTATCGATACATACATATATACATA
1 TTAATTCCACATAAAGGCCCAAACAATATGCACGTAAAATGTACCGACACACACATATATACATA
* *
507677 TATATATATATTCCATACTTATAATTCCAAAACCTATTACTTTTAAGTAATAGGTTAATTGACAA
66 TATATATATATTCCATACTTATAATTCCAAAACCTATTACTTTAAAGTAATAGATTAATTGACAA
* * *
507742 TGAAAATGGTTAAAGTCAATCGATATCTTGATAATATGCGTAAACAATGTACATGGTAATATGTT
131 TGAAAACGGTTAAAGTCAATCGATATCATAATAATATGCGTAAACAATGTACATGGTAATATGTT
* *
507807 GATAAAGCTTGATAACAAATCAAGTAATTAACCGGTTATGTTATCATCGG-TT-CTAAGGCTCCA
196 GATAAAGCTTGATAACAAATCAAATAATTAACCGATTATGTTATCATCGGATTCCTAAGGCTCCA
507870 TCCGCTTTAACTTTGG
261 TCCGCTTTAACTTTGG
* * *
507886 TTAATTCCGCTTAAAGGCCCAAACAATCTGCACGTAAAATGTACCGACACACACACACAGATATA
1 TTAATTCCACATAAAGGCCCAAACAATATGCACGTAAAATGTACCG----ACACACAC--ATATA
* * *
507951 TATATATATATATATATAT-CATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGATTAA
60 TACATATATATATATAT-TCCATACTTATAATTCCAAAACCTATTACTTTAAAGTAATAGATTAA
** *
508015 TTTCCAATGAAAACGGTTAAAGTCAATCGATATCATAATAATATGTGTAAACAATGTACATGGTA
124 TTGACAATGAAAACGGTTAAAGTCAATCGATATCATAATAATATGCGTAAACAATGTACATGGTA
* *
508080 ATATGTTGATAAAGCTTGATAACAAATCAAATAATTAACCGATTATGTTATCGTTGGATTCCTAA
189 ATATGTTGATAAAGCTTGATAACAAATCAAATAATTAACCGATTATGTTATCATCGGATTCCTAA
508145 GGCTCCATC
254 GGCTCCATC
508154 AGCTGAAATT
Statistics
Matches: 237, Mismatches: 22, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
274 41 0.17
278 6 0.03
280 174 0.73
281 3 0.01
282 13 0.05
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (276 bp):
TTAATTCCACATAAAGGCCCAAACAATATGCACGTAAAATGTACCGACACACACATATATACATA
TATATATATATTCCATACTTATAATTCCAAAACCTATTACTTTAAAGTAATAGATTAATTGACAA
TGAAAACGGTTAAAGTCAATCGATATCATAATAATATGCGTAAACAATGTACATGGTAATATGTT
GATAAAGCTTGATAACAAATCAAATAATTAACCGATTATGTTATCATCGGATTCCTAAGGCTCCA
TCCGCTTTAACTTTGG
Found at i:508513 original size:227 final size:227
Alignment explanation
Indices: 508111--508822 Score: 765
Period size: 227 Copynumber: 3.1 Consensus size: 227
508101 ACAAATCAAA
* ** * * *
508111 TAATTAACCGATTATGTTATCGTTGGATTCCTAAGGCTCCATCAGCTGAAATTTTGTTTAACATT
1 TAATTAACCGGTTATGTTATCGTCAGATTTCTAAGGCTCCATCAGCTGAAACTTTGTGTAACATT
* *
508176 TTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATT
66 TTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATC
* * *
508241 GTCAGATTTCCAAAGCCCTATCAACTTTAAAAATGCACTACCTATTACGTTATATAAGCGCTACC
131 GTCAGATTTCAAAAGCCCCATCAACTTTAAAAAGGCACTACCTATTACGTTATATAAGCGCTACC
*
508306 TAAAATGTTTTTATGCTTGATAATGTTTCCAG
196 TAAAATGTTATTATGCTTGATAATGTTTCCAG
* * * *
508338 TAATTAATCGGTTATGTTATCGTCAGATTTGTAAGGCTCTATCAGCTTAAACTTTG-GTAACATT
1 TAATTAACCGGTTATGTTATCGTCAGATTTCTAAGGCTCCATCAGCTGAAACTTTGTGTAACATT
508402 TTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATC
66 TTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATC
* * *
508467 GTCAGATTTGCAAAAGCCCCGTCAGCTTTAAAAAGGCGCTACCTATTACGTTATATAAGCGCTAC
131 GTCAGATTT-CAAAAGCCCCATCAACTTTAAAAAGGCACTACCTATTACGTTATATAAGCGCTAC
* *
508532 CTAATATGTTATTATGCTTGATAATGTTTCTAG
195 CTAAAATGTTATTATGCTTGATAATGTTTCCAG
* * * * * *** *
508565 TAATTAACCAGTTATGTTATCGTCAGATTTCCAAAGCCCCATCAGCTTTAAA-AAGGCGATACCT
1 TAATTAACCGGTTATGTTATCGTCAGATTTCTAAGGCTCCATCAGC-TGAAACTTTGTG-TA---
* * * * * * * *** * *
508629 ATTATTTTATATAAGCGCTACCTAGTATGTT-ATTATGCTTGATAA-TGTTTCCAGTAATTAATC
61 A-CA--TT-T-TAGGCGTTACCTAATATGTTGATAATAC-TAATAACAAATT-AAGTAATTAACC
** * *
508692 GGTTATGTTATCGTC-GAATTTCCAAAGCCCCATCAACTTTAAAAAGG-AGCTACCTATTACGTT
119 TATTTTGTTATCGTCAG-ATTTCAAAAGCCCCATCAACTTTAAAAAGGCA-CTACCTATTACGTT
* * *
508755 ATATAAACGCTACCTAATATGTTATTAAT-CTTGATAATG-TTCTAG
182 ATATAAGCGCTACCTAAAATGTTATT-ATGCTTGATAATGTTTCCAG
**
508800 TAATTAACCGAATATGTTATCGT
1 TAATTAACCGGTTATGTTATCGT
508823 GTGTATTTTT
Statistics
Matches: 414, Mismatches: 54, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
226 79 0.19
227 166 0.40
228 6 0.01
229 2 0.00
232 1 0.00
233 1 0.00
235 28 0.07
236 81 0.20
237 50 0.12
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (227 bp):
TAATTAACCGGTTATGTTATCGTCAGATTTCTAAGGCTCCATCAGCTGAAACTTTGTGTAACATT
TTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATC
GTCAGATTTCAAAAGCCCCATCAACTTTAAAAAGGCACTACCTATTACGTTATATAAGCGCTACC
TAAAATGTTATTATGCTTGATAATGTTTCCAG
Found at i:508640 original size:118 final size:118
Alignment explanation
Indices: 508444--508822 Score: 552
Period size: 118 Copynumber: 3.2 Consensus size: 118
508434 TAACAAATTA
* * *
508444 AGTAATTAACCTA-TTTTGTTATCGTCAGATTTGCAAAAGCCCCGTCAGCTTTAAAAAGGCGCTA
1 AGTAATTAACC-AGTTATGTTATCGTCAGATTT-CCAAAGCCCCATCAGCTTTAAAAAGGCGCTA
508508 CCTATTACGTTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCT
64 CCTATTACGTTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCT
*
508563 AGTAATTAACCAGTTATGTTATCGTCAGATTTCCAAAGCCCCATCAGCTTTAAAAAGGCGATACC
1 AGTAATTAACCAGTTATGTTATCGTCAGATTTCCAAAGCCCCATCAGCTTTAAAAAGGCGCTACC
** * *
508628 TATTATTTTATATAAGCGCTACCTAGTATGTTATTATGCTTGATAATGTTTCC
66 TATTACGTTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCT
* * * *
508681 AGTAATTAATCGGTTATGTTATCGTC-GAATTTCCAAAGCCCCATCAACTTTAAAAAGGAGCTAC
1 AGTAATTAACCAGTTATGTTATCGTCAG-ATTTCCAAAGCCCCATCAGCTTTAAAAAGGCGCTAC
*
508745 CTATTACGTTATATAAACGCTACCTAATATGTTATTAAT-CTTGATAATG-TTCT
65 CTATTACGTTATATAAGCGCTACCTAATATGTTATT-ATGCTTGATAATGTTTCT
*
508798 AGTAATTAACC-GAATATGTTATCGT
1 AGTAATTAACCAG-TTATGTTATCGT
508823 GTGTATTTTT
Statistics
Matches: 236, Mismatches: 20, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
116 1 0.00
117 25 0.11
118 179 0.76
119 31 0.13
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (118 bp):
AGTAATTAACCAGTTATGTTATCGTCAGATTTCCAAAGCCCCATCAGCTTTAAAAAGGCGCTACC
TATTACGTTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCT
Found at i:509703 original size:24 final size:23
Alignment explanation
Indices: 509648--509703 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
509638 ATATGCTCAC
* *
509648 CAACATGTTCTTTTAATATTCTT
1 CAACATGTTCATTTAATATTCAT
* **
509671 GAATGTGTTCATTTATATATTCAT
1 CAACATGTTCATTTA-ATATTCAT
509695 CAACATGTT
1 CAACATGTT
509704 TGTTTAGGAT
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (23 bp):
CAACATGTTCATTTAATATTCAT
Found at i:516139 original size:19 final size:18
Alignment explanation
Indices: 516117--516157 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
516107 TTTATTTATC
*
516117 ATTTATACTAATTTTTACA
1 ATTTA-ACTAATGTTTACA
*
516136 ATTTAACTGATGTTTACA
1 ATTTAACTAATGTTTACA
516154 ATTT
1 ATTT
516158 CATTGGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTAACTAATGTTTACA
Found at i:518227 original size:43 final size:43
Alignment explanation
Indices: 518179--518301 Score: 201
Period size: 43 Copynumber: 2.9 Consensus size: 43
518169 AATTCAAAAC
* * * *
518179 TAACAACCCATAAATACACCAAAGTAGCATATTAAAACTAAAG
1 TAACAATCCACAAATACACCAAACTAACATATTAAAACTAAAG
*
518222 TAACAATCCACAAATTCACCAAACTAACATATTAAAACTAAAG
1 TAACAATCCACAAATACACCAAACTAACATATTAAAACTAAAG
518265 TAACAATCCACAAATACACCAAACTAACATATTAAAA
1 TAACAATCCACAAATACACCAAACTAACATATTAAAA
518302 GCATTCTCGA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (43 bp):
TAACAATCCACAAATACACCAAACTAACATATTAAAACTAAAG
Done.