Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006189.1 Hibiscus syriacus cultivar Beakdansim tig00014728_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: 980383
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 4 of 7
Found at i:208871 original size:14 final size:14
Alignment explanation
Indices: 208852--208882 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
208842 TTTTATTTTA
208852 TATTATATTATTAT
1 TATTATATTATTAT
208866 TATTATATTATTAT
1 TATTATATTATTAT
208880 TAT
1 TAT
208883 AATTTCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:210164 original size:21 final size:21
Alignment explanation
Indices: 210140--210179 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
210130 GTAATTTTAA
*
210140 TATTTGATA-TTATTATAAAAT
1 TATTT-ATACTTATAATAAAAT
210161 TATTTATACTTATAATAAA
1 TATTTATACTTATAATAAA
210180 TAATATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (21 bp):
TATTTATACTTATAATAAAAT
Found at i:211711 original size:5 final size:5
Alignment explanation
Indices: 211701--211742 Score: 57
Period size: 5 Copynumber: 7.8 Consensus size: 5
211691 CGTCTGAATT
211701 TTATA TTATA TTATA TTATTA TTATTA TTATTA TTATA TTAT
1 TTATA TTATA TTATA TTA-TA TTA-TA TTA-TA TTATA TTAT
211743 TATAATTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 19 0.53
6 17 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:211722 original size:3 final size:3
Alignment explanation
Indices: 211704--211745 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
211694 CTGAATTTTA
211704 TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
211746 AATTTCTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:211827 original size:23 final size:24
Alignment explanation
Indices: 211801--211845 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
211791 TACAACCAAG
*
211801 GCCCA-GTTACAACAAAACCCGGA
1 GCCCATGTAACAACAAAACCCGGA
*
211824 GCCCATGTAACAACCAAACCCG
1 GCCCATGTAACAACAAAACCCG
211846 AGGAGGCCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.38, C:0.38, G:0.16, T:0.09
Consensus pattern (24 bp):
GCCCATGTAACAACAAAACCCGGA
Found at i:216345 original size:18 final size:18
Alignment explanation
Indices: 216324--216366 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
216314 GTTGTTTTTA
*
216324 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
* *
216342 AAATAAAATAAAATAATT
1 AAATAAAAGAAAAGAATT
216360 AAATAAA
1 AAATAAA
216367 TAAATTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:216937 original size:76 final size:73
Alignment explanation
Indices: 216723--216949 Score: 237
Period size: 76 Copynumber: 3.1 Consensus size: 73
216713 TAAAACATCT
* * * *
216723 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATAC--GTAAAAAAATAATATTTAAA
1 TAAAACCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACAAATAAAAATATAATATTTAAA
*
216786 ATAATATTC
65 ATAATATCC
* * * *
216795 TAAATCCTAATTAAAATACTAAAACCTATCTAACCTAAAATACCTAAA-ACAAAGATAAAATA-T
1 TAAAACCTAATTAAAATACTAAAA-CTATTTAAACTAAAATA-C-AAATA-AAA-ATATAATATT
*
216858 AAAAATAATATCC
61 TAAAATAATATCC
* *
216871 TAAAACTTAATTAAAATACTAAAACTTATTTAAACTAAAATACAAATATAAAATATAATGTTTAA
1 TAAAACCTAATTAAAATACTAAAAC-TATTTAAACTAAAATACAAATA-AAAATATAATATTTAA
*
216936 AATATTATCC
64 AATAATATCC
216946 TAAA
1 TAAA
216950 CTTGAGTTTA
Statistics
Matches: 128, Mismatches: 17, Indels: 17
0.79 0.10 0.10
Matches are distributed among these distances:
71 5 0.04
72 33 0.26
73 1 0.01
74 9 0.07
75 23 0.18
76 51 0.40
77 6 0.05
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.30
Consensus pattern (73 bp):
TAAAACCTAATTAAAATACTAAAACTATTTAAACTAAAATACAAATAAAAATATAATATTTAAAA
TAATATCC
Found at i:218841 original size:20 final size:20
Alignment explanation
Indices: 218816--218863 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
218806 GTTCAAAGAA
*
218816 AAAATAAAATAAA-ATTAATT
1 AAAATAAAATAAATA-GAATT
218836 AAAATAAAATAAATAGAATT
1 AAAATAAAATAAATAGAATT
218856 AAAATAAA
1 AAAATAAA
218864 TTTTTCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAATAAAATAAATAGAATT
Found at i:218884 original size:5 final size:5
Alignment explanation
Indices: 218816--218863 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
218806 GTTCAAAGAA
* * *
218816 AAAAT AAAAT AAAAT TAATT AAAAT AAAAT -AAAT AGAATT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAA
218864 TTTTTCTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
4 4 0.11
5 27 0.77
6 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (5 bp):
AAAAT
Found at i:218915 original size:21 final size:22
Alignment explanation
Indices: 218873--218938 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
218863 ATTTTTCTAA
*
218873 AAAATAAAATAAAAAAACGAAAT
1 AAAATAAAA-AATAAAACGAAAT
* *
218896 -AAATCAAAAATAAAATGAAAT
1 AAAATAAAAAATAAAACGAAAT
*
218917 AAAATAAAAAATAGAACGAAAT
1 AAAATAAAAAATAAAACGAAAT
218939 GGATTGCCGC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 11 0.31
22 25 0.69
ACGTcount: A:0.74, C:0.05, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAATAAAAAATAAAACGAAAT
Found at i:223421 original size:18 final size:18
Alignment explanation
Indices: 223400--223442 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
223390 GTTGTTTTTA
*
223400 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
* *
223418 AAATAAAATAAAATAATT
1 AAATAAAAGAAAAGAATT
223436 AAATAAA
1 AAATAAA
223443 TAAATTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:224115 original size:71 final size:70
Alignment explanation
Indices: 224035--224260 Score: 247
Period size: 76 Copynumber: 3.1 Consensus size: 70
224025 TAAAACATAT
*
224035 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAAAATAATATTTAAAATA
1 TAAATCCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAAAAAATAATATTTAAAATA
*
224100 ATATTC
65 ATATCC
* * *
224106 TAAATCCTAATTAAAATACTAAAACATATTTAATCTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAAC-TATTTAAACTAAAATACCT--AA-AAA-ATAATAT-TTA
224171 AAATAATATCC
60 AAATAATATCC
* * *
224182 TACAA-CTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATATTTA
1 TA-AATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATAC----CTAAAAAATAATATTTA
*
224246 AAATATTATCC
60 AAATAATATCC
224257 TAAA
1 TAAA
224261 CTTTAGTTTA
Statistics
Matches: 131, Mismatches: 12, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
70 6 0.05
71 36 0.27
73 2 0.02
74 5 0.04
75 20 0.15
76 54 0.41
77 5 0.04
78 2 0.02
80 1 0.01
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (70 bp):
TAAATCCTAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAAAAATAATATTTAAAATAA
TATCC
Found at i:228187 original size:22 final size:23
Alignment explanation
Indices: 228151--228193 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
228141 AAAAAAAATA
* *
228151 CATGACAAATCAATGTTACCATG
1 CATGACAAATAAATGTAACCATG
228174 CATGA-AAATAAATGTAACCA
1 CATGACAAATAAATGTAACCA
228194 ACTATGCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.23
Consensus pattern (23 bp):
CATGACAAATAAATGTAACCATG
Found at i:228500 original size:24 final size:24
Alignment explanation
Indices: 228473--228518 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
228463 ATTTATCAAC
* *
228473 TCATTTATAAGCTCGTTTACTGAT
1 TCATTTATAAACTCATTTACTGAT
228497 TCATTTATAAACTCATTTACTG
1 TCATTTATAAACTCATTTACTG
228519 GGTTCTCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (24 bp):
TCATTTATAAACTCATTTACTGAT
Found at i:229472 original size:31 final size:31
Alignment explanation
Indices: 229434--229500 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
229424 CAGCTTAGGA
** *
229434 ACCTAAAAATATAACGTCGGAAACATTAGAC
1 ACCTAAAAATATAACGGAGAAAACATTAGAC
* *
229465 ACCTAAAAGTATAACGGAGAAAACGTTAGAC
1 ACCTAAAAATATAACGGAGAAAACATTAGAC
229496 ACCTA
1 ACCTA
229501 TTTTTAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.18
Consensus pattern (31 bp):
ACCTAAAAATATAACGGAGAAAACATTAGAC
Found at i:237479 original size:13 final size:13
Alignment explanation
Indices: 237461--237488 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
237451 ATTATTTAAT
237461 AGAGCTACTTGGG
1 AGAGCTACTTGGG
237474 AGAGCTACTTGGG
1 AGAGCTACTTGGG
237487 AG
1 AG
237489 CCTTTTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.39, T:0.21
Consensus pattern (13 bp):
AGAGCTACTTGGG
Found at i:241259 original size:30 final size:29
Alignment explanation
Indices: 241225--241284 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
241215 GATTATCACT
*
241225 TTTTAAAAAAAATCCTAAATTTTTCTAAAA
1 TTTTAAAAAAAATCAT-AATTTTTCTAAAA
* *
241255 TTTTAAAAAAACTCATAATTTTTTTAAAA
1 TTTTAAAAAAAATCATAATTTTTCTAAAA
241284 T
1 T
241285 ATCATAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.43
Consensus pattern (29 bp):
TTTTAAAAAAAATCATAATTTTTCTAAAA
Found at i:241262 original size:29 final size:30
Alignment explanation
Indices: 241225--241284 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
241215 GATTATCACT
*
241225 TTTTAAAAAAAA-TCCTAAATTTTTCTAAAA
1 TTTTAAAAAAAACTCAT-AATTTTTCTAAAA
*
241255 TTTT-AAAAAAACTCATAATTTTTTTAAAA
1 TTTTAAAAAAAACTCATAATTTTTCTAAAA
241284 T
1 T
241285 ATCATAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.43
Consensus pattern (30 bp):
TTTTAAAAAAAACTCATAATTTTTCTAAAA
Found at i:242541 original size:53 final size:53
Alignment explanation
Indices: 242460--242575 Score: 205
Period size: 53 Copynumber: 2.2 Consensus size: 53
242450 ATAAGAATAG
242460 TATCGATACTATAAGGGTAAATTAAAGGAAAAACGCTTGAATCAGATGAACAA
1 TATCGATACTATAAGGGTAAATTAAAGGAAAAACGCTTGAATCAGATGAACAA
* * *
242513 TATCGATACTATAAGGGTAAATTGAAGGAAAAACGTTTGAATCGGATGAACAA
1 TATCGATACTATAAGGGTAAATTAAAGGAAAAACGCTTGAATCAGATGAACAA
242566 TATCGATACT
1 TATCGATACT
242576 GATTGAAGCA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 60 1.00
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (53 bp):
TATCGATACTATAAGGGTAAATTAAAGGAAAAACGCTTGAATCAGATGAACAA
Found at i:262349 original size:12 final size:12
Alignment explanation
Indices: 262332--262357 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
262322 AAAAAATATA
262332 TATTTAATTATT
1 TATTTAATTATT
262344 TATTTAATTATT
1 TATTTAATTATT
262356 TA
1 TA
262358 ATTCTTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTTAATTATT
Found at i:264466 original size:13 final size:13
Alignment explanation
Indices: 264448--264472 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
264438 TAGTTTTGAA
264448 AAGTAAAAGATAC
1 AAGTAAAAGATAC
264461 AAGTAAAAGATA
1 AAGTAAAAGATA
264473 TTCCAAAAAC
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:0.64, C:0.04, G:0.16, T:0.16
Consensus pattern (13 bp):
AAGTAAAAGATAC
Found at i:265954 original size:46 final size:46
Alignment explanation
Indices: 265877--266050 Score: 226
Period size: 46 Copynumber: 3.8 Consensus size: 46
265867 AATATAACAT
* * * * *
265877 TTTTATCAATCTAGTTATCATTT-ATCCCATAAGCTCGTAAGCTTA
1 TTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTA
*
265922 TTTTACCAACATACTTACCATTTAATTCCATAAGCTCGTAAGCTTA
1 TTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTA
* *
265968 TTTTACCAATATAATTACCATTTAATTCCATAATCTCGTAAGCTTA
1 TTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTA
*
266014 TATTT-CCAATATACTTACCATTAAAATTTCCATAAGC
1 T-TTTACCAATATACTTACCATT-TAA-TTCCATAAGC
266051 CATATACCAT
Statistics
Matches: 113, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
45 18 0.16
46 81 0.72
47 5 0.04
48 9 0.08
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (46 bp):
TTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTA
Found at i:266265 original size:59 final size:59
Alignment explanation
Indices: 266140--266271 Score: 165
Period size: 59 Copynumber: 2.2 Consensus size: 59
266130 CACTGTAATG
* * * **
266140 CAATCCCGAATATGACTCATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTA
1 CAATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTA
* * * *
266199 CAGTCCCGAATATGACACATAAGGTTGTGCCCACCATATACACTAGGTATCCTTTAGTG
1 CAATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTA
* *
266258 TAATCCCGACTATG
1 CAATCCCGAATATG
266272 CAGCCTGCTG
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (59 bp):
CAATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTA
Found at i:266547 original size:96 final size:96
Alignment explanation
Indices: 266383--266622 Score: 426
Period size: 96 Copynumber: 2.5 Consensus size: 96
266373 TATCAATACC
* * * * *
266383 ATTTAACAATGGGCAGTTCATACCCGAAAACATTCATGGTAAAATATTATGCATTATCAATGTCA
1 ATTTAACATTGGGAAATTCATACCCAAAAACATTCATGGTAAAATATCATGCATTATCAATGTCA
266448 TGTCAATTTATAAAAATGACATAATATCATA
66 TGTCAATTTATAAAAATGACATAATATCATA
266479 ATTTAACATTGGGAAATTCATACCCAAAAACATTCATGGTAAAATATCATGCATTATCAATGTCA
1 ATTTAACATTGGGAAATTCATACCCAAAAACATTCATGGTAAAATATCATGCATTATCAATGTCA
*
266544 TGTCAATTTATAAAAATGCCATAATATCATA
66 TGTCAATTTATAAAAATGACATAATATCATA
266575 ATTTAACATTGGGAAATTCATACCCAAAAACATTCATGGTAAAATATC
1 ATTTAACATTGGGAAATTCATACCCAAAAACATTCATGGTAAAATATC
266623 TTGCTGATAA
Statistics
Matches: 138, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 138 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (96 bp):
ATTTAACATTGGGAAATTCATACCCAAAAACATTCATGGTAAAATATCATGCATTATCAATGTCA
TGTCAATTTATAAAAATGACATAATATCATA
Found at i:270974 original size:21 final size:20
Alignment explanation
Indices: 270946--270985 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
270936 ATGAATCGGA
270946 TGAACAATATCGATACTGAC
1 TGAACAATATCGATACTGAC
270966 TGAAGCAATATCGATACTGA
1 TGAA-CAATATCGATACTGA
270986 TGTGGAGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (20 bp):
TGAACAATATCGATACTGAC
Found at i:271776 original size:24 final size:24
Alignment explanation
Indices: 271725--271776 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
271715 GGGAGAAATC
* * *
271725 TATGTGGCACTTCGGTACATATTC
1 TATGCGGCACTTCGGTACAAATTA
* *
271749 TATGCGGCACTTTGGTGCAAATTA
1 TATGCGGCACTTCGGTACAAATTA
271773 TATG
1 TATG
271777 AGCAGTGGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (24 bp):
TATGCGGCACTTCGGTACAAATTA
Found at i:275602 original size:6 final size:6
Alignment explanation
Indices: 275586--275672 Score: 78
Period size: 6 Copynumber: 15.3 Consensus size: 6
275576 TCTCTCATTT
* * * *
275586 TTTTCTC TTTTTC -TTTTC -TTTTC TTTTTC TATATA TTTTTC ATTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
275633 TTTTTC TTTTT- TTATTC --TTTC TTTTT- TTTTTC TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
275673 CTTTTCTATT
Statistics
Matches: 65, Mismatches: 10, Indels: 11
0.76 0.12 0.13
Matches are distributed among these distances:
4 3 0.05
5 19 0.29
6 39 0.60
7 4 0.06
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:275693 original size:35 final size:34
Alignment explanation
Indices: 275593--275696 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 34
275583 TTTTTTTCTC
* * *
275593 TTTTTCTTTTCTTTTCTTTTT-CTATATATTTTTC
1 TTTTTCTTTT-TCTTCTTTTTATTATATATTTTTT
* *
275627 ATTTTCTTTTTCTT-TTTTTATTCT-T-TCTTTTT
1 TTTTTCTTTTTCTTCTTTTTATTATATAT-TTTTT
275659 TTTTTCTTTTTCTTCTTTTCTATTATATATTTTTT
1 TTTTTCTTTTTCTTCTTTT-TATTATATATTTTTT
275694 TTT
1 TTT
275697 CTTATGCCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
31 1 0.02
32 23 0.40
33 9 0.16
34 14 0.25
35 9 0.16
36 1 0.02
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (34 bp):
TTTTTCTTTTTCTTCTTTTTATTATATATTTTTT
Found at i:279887 original size:7 final size:6
Alignment explanation
Indices: 279877--279956 Score: 64
Period size: 6 Copynumber: 14.2 Consensus size: 6
279867 TCTCTCATTT
* * *
279877 TTTTATC TTTTTC -TTTTC -TTTT- TTTTTC TATAT- TTTTTC ATTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* *
279922 TTTTTC TTTTT- TTATTC TTTTT- TTATTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T
279957 GCTTTTCTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
5 24 0.41
6 30 0.52
7 4 0.07
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:279896 original size:11 final size:10
Alignment explanation
Indices: 279874--279954 Score: 90
Period size: 11 Copynumber: 7.5 Consensus size: 10
279864 TCATCTCTCA
*
279874 TTTTTTTATC
1 TTTTTTTTTC
279884 TTTTTCTTTTC
1 TTTTT-TTTTC
279895 TTTTTTTTTC
1 TTTTTTTTTC
*
279905 TATATTTTTTC
1 T-TTTTTTTTC
279916 ATTTTCTTTTTC
1 -TTTT-TTTTTC
279928 TTTTTTTATTC
1 TTTTTTT-TTC
279939 TTTTTTTATTC
1 TTTTTTT-TTC
279950 TTTTT
1 TTTTT
279955 CTGCTTTTCT
Statistics
Matches: 63, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
10 14 0.22
11 42 0.67
12 7 0.11
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:279913 original size:34 final size:32
Alignment explanation
Indices: 279874--279956 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 32
279864 TCATCTCTCA
279874 TTTTTTTATCTTTTTCTTTTCTTTTTTT-TTC
1 TTTTTTTATCTTTTTCTTTTCTTTTTTTATTC
*
279905 TATATTTTT-TCATTTTCTTTTTCTTTTTTTATTC
1 T-T-TTTTTATCTTTTTC-TTTTCTTTTTTTATTC
279939 TTTTTTTATTCTTTTTCT
1 TTTTTTTA-TCTTTTTCT
279957 GCTTTTCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
31 1 0.02
32 13 0.30
33 19 0.43
34 11 0.25
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (32 bp):
TTTTTTTATCTTTTTCTTTTCTTTTTTTATTC
Found at i:279914 original size:27 final size:27
Alignment explanation
Indices: 279874--279956 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 27
279864 TCATCTCTCA
*
279874 TTTTTTTATCTTTTTCTTTTCTTTTT-
1 TTTTTATATCTTTTTCTTTTCTTTTTC
279900 TTTTCTATAT-TTTTTCATTTTCTTTTTC
1 TTTT-TATATCTTTTTC-TTTTCTTTTTC
*
279928 TTTTTTTATTCTTTTT-TTATTCTTTTTC
1 TTTTTATA-TCTTTTTCTT-TTCTTTTTC
279956 T
1 T
279957 GCTTTTCTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
26 10 0.20
27 19 0.39
28 15 0.31
29 5 0.10
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTTTATATCTTTTTCTTTTCTTTTTC
Found at i:280050 original size:21 final size:20
Alignment explanation
Indices: 280014--280052 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
280004 CACGACTAAG
280014 AAAATCAACTTCTGATAGCC
1 AAAATCAACTTCTGATAGCC
280034 AAAACTCACACTT-TGATAG
1 AAAA-TCA-ACTTCTGATAG
280053 TTTAGCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAATCAACTTCTGATAGCC
Found at i:282856 original size:46 final size:46
Alignment explanation
Indices: 282779--282952 Score: 235
Period size: 46 Copynumber: 3.8 Consensus size: 46
282769 AATATAACAT
* * * *
282779 TTTTATCAATCTACTTATCATTT-ATCCCATAAGCTCGTAAGCTTA
1 TTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTA
* *
282824 TTTTACCAACATACGTACCATTTAATTCCATAAGCTCGTAAGCTTA
1 TTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTA
*
282870 TTTTACCAATATAATTACCATTTAATTCCATAAGCTCGTAAGCTTA
1 TTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTA
*
282916 TATTT-CCAATATACTTACCATTAAAATTTCCATAAGC
1 T-TTTACCAATATACTTACCATT-TAA-TTCCATAAGC
282953 CATATACCAT
Statistics
Matches: 114, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
45 18 0.16
46 81 0.71
47 5 0.04
48 10 0.09
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (46 bp):
TTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTA
Found at i:283449 original size:96 final size:96
Alignment explanation
Indices: 283301--283524 Score: 432
Period size: 96 Copynumber: 2.3 Consensus size: 96
283291 CAATGAGCAG
283301 TTCATA-CCAGAAAACATTCATGGTAAAATATCATGCATTATCAATGTCATGTCAATTTATAAAA
1 TTCATACCCA-AAAACATTCATGGTAAAATATCATGCATTATCAATGTCATGTCAATTTATAAAA
283365 ATGACATAATATCATAATTTAACATTGGGAAA
65 ATGACATAATATCATAATTTAACATTGGGAAA
283397 TTCATACCCAAAAACATTCATGGTAAAATATCATGCATTATCAATGTCATGTCAATTTATAAAAA
1 TTCATACCCAAAAACATTCATGGTAAAATATCATGCATTATCAATGTCATGTCAATTTATAAAAA
283462 TGACATAATATCATAATTTAACATTGGGAAA
66 TGACATAATATCATAATTTAACATTGGGAAA
283493 TTCATACCCAAAAACATTCATGGTAAAATATC
1 TTCATACCCAAAAACATTCATGGTAAAATATC
283525 TTGCTGATAA
Statistics
Matches: 127, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
96 124 0.98
97 3 0.02
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (96 bp):
TTCATACCCAAAAACATTCATGGTAAAATATCATGCATTATCAATGTCATGTCAATTTATAAAAA
TGACATAATATCATAATTTAACATTGGGAAA
Found at i:289468 original size:13 final size:13
Alignment explanation
Indices: 289450--289498 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
289440 CTTAGCATAT
*
289450 TTAAAAATAAAAC
1 TTAAAAAGAAAAC
289463 TT-AAAAGAAAA-
1 TTAAAAAGAAAAC
*
289474 -GAAAAATGAAAAC
1 TTAAAAA-GAAAAC
289487 TTAAAAAGAAAA
1 TTAAAAAGAAAA
289499 GAAATAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
11 4 0.14
12 13 0.45
13 7 0.24
14 5 0.17
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.16
Consensus pattern (13 bp):
TTAAAAAGAAAAC
Found at i:289485 original size:24 final size:24
Alignment explanation
Indices: 289452--289502 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 24
289442 TAGCATATTT
289452 AAAAATAAAACTT-AAAAGAAAAG
1 AAAAATAAAACTTAAAAAGAAAAG
289475 AAAAATGAAAACTTAAAAAGAAAAG
1 AAAAAT-AAAACTTAAAAAGAAAAG
289500 AAA
1 AAA
289503 TAACTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 6 0.23
24 7 0.27
25 13 0.50
ACGTcount: A:0.75, C:0.04, G:0.10, T:0.12
Consensus pattern (24 bp):
AAAAATAAAACTTAAAAAGAAAAG
Found at i:301522 original size:46 final size:45
Alignment explanation
Indices: 301391--301515 Score: 182
Period size: 46 Copynumber: 2.8 Consensus size: 45
301381 GTAAGTTTAC
* * *
301391 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGATA
301435 AAATAAGCTTACGAGCTTAT-GAATTTAAATGGTAAGTATTTTGATA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATTTTGATA
*
301481 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
301516 AGATTTTATA
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
43 3 0.04
44 20 0.27
45 12 0.16
46 36 0.49
47 2 0.03
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGATA
Found at i:302695 original size:19 final size:19
Alignment explanation
Indices: 302671--302744 Score: 87
Period size: 19 Copynumber: 3.8 Consensus size: 19
302661 GAATACAATA
* *
302671 AGTGCATCGATGCGTAGGT
1 AGTGCATCGATGCATAGGC
302690 AGTGCATCGATGCATAGGC
1 AGTGCATCGATGCATAGGC
*
302709 AGTGCATCGATGCACTATAG-
1 AGTGCATCGATGCA-TA-GGC
*
302729 AATGCATCGATGCATA
1 AGTGCATCGATGCATA
302745 AGGGCAATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 33 0.67
20 15 0.31
21 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCATAGGC
Found at i:303136 original size:59 final size:59
Alignment explanation
Indices: 303064--303806 Score: 1018
Period size: 59 Copynumber: 12.6 Consensus size: 59
303054 ATTACCAAAT
*
303064 GGCACTATA-TGTGCAAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCATATAG
1 GGCACTA-AGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCATATAG
* *
303123 GGCACTAAGTGTGCTAAAATGTTAAGGAAATAATACTAAGTGTATGGATTTCTATAT-G
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCATATAG
* * * * *
303181 GAGCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAA-TATATGTATTTCCATATAG
1 G-GCACTAAGTGTGCTAAAATGTTAAGGAAATCATACT-AAGTGTATGGATTTCCATATAG
* *
303241 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCTAGAT-G
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCATATAG
* * * * *
303299 GAGCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAA-TATATGTATTTCCATATAG
1 G-GCACTAAGTGTGCTAAAATGTTAAGGAAATCATACT-AAGTGTATGGATTTCCATATAG
* *
303359 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCTAGAT-G
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCATATAG
* * * * *
303417 GAGCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAA-TATATGTATTTCCATATAG
1 G-GCACTAAGTGTGCTAAAATGTTAAGGAAATCATACT-AAGTGTATGGATTTCCATATAG
* * *
303477 GGCACTAAGTGTGCTAAAATATTAAGGAAATCATACTAAGTGTATGGATTTCTAGAT-G
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCATATAG
* * * * *
303535 GAGCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAA-TATATGTATTTCCATATAG
1 G-GCACTAAGTGTGCTAAAATGTTAAGGAAATCATACT-AAGTGTATGGATTTCCATATAG
*
303595 GGCACTAAGTGTGCTAAAATGTTAATGAAATCATACTAAGTGTATGGATTTCCATATAG
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCATATAG
*
303654 GGCACTAAGTGTGCTAAAATGTTAAGGAAGTCATACTAAGTGTATGGATTTCCATATAG
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCATATAG
*
303713 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCACATAG
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCATATAG
* **
303772 AGCACTAAGTGTGCTAAAATGAGAAGGAAATCATA
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATA
303807 TTAAATATAT
Statistics
Matches: 600, Mismatches: 67, Indels: 34
0.86 0.10 0.05
Matches are distributed among these distances:
58 17 0.03
59 567 0.94
60 16 0.03
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (59 bp):
GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCATATAG
Found at i:303253 original size:118 final size:118
Alignment explanation
Indices: 303065--303866 Score: 1231
Period size: 118 Copynumber: 6.8 Consensus size: 118
303055 TTACCAAATG
* * * * * *
303065 GCACTATA-TGTGCAAAAATGTTAAGGAAATCATACT-AAGTGTATGGATTTCCATATAGGGCAC
1 GCACTA-AGTGTGCTAAAATGTGAAGGAAAACATATTGAA-TATATGTATTTCCATATAGGGCAC
* *
303128 TAAGTGTGCTAAAATGTTAAGGAAATAATACTAAGTGTATGGATTTCTATATGGA
64 TAAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCTAGATGGA
303183 GCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATGTATTTCCATATAGGGCACTA
1 GCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATGTATTTCCATATAGGGCACTA
303248 AGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCTAGATGGA
66 AGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCTAGATGGA
303301 GCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATGTATTTCCATATAGGGCACTA
1 GCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATGTATTTCCATATAGGGCACTA
303366 AGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCTAGATGGA
66 AGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCTAGATGGA
303419 GCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATGTATTTCCATATAGGGCACTA
1 GCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATGTATTTCCATATAGGGCACTA
*
303484 AGTGTGCTAAAATATTAAGGAAATCATACTAAGTGTATGGATTTCTAGATGGA
66 AGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCTAGATGGA
303537 GCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATGTATTTCCATATAGGGCACTA
1 GCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATGTATTTCCATATAGGGCACTA
* * *
303602 AGTGTGCTAAAATGTTAATGAAATCATACTAAGTGTATGGATTTCCATATAGG-
66 AGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCTAGAT-GGA
* ** * * *
303655 GCACTAAGTGTGCTAAAATGTTAAGGAAGTCATACT-AAGTGTATGGATTTCCATATAGGGCACT
1 GCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAA-TATATGTATTTCCATATAGGGCACT
* * *
303719 AAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCACATAGA
65 AAGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCTAGATGGA
* * * * *
303773 GCACTAAGTGTGCTAAAATGAGAAGGAAATCATATTAAATATATGATATCTCAAATATA--GCAC
1 GCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATG-TATTTC-CATATAGGGCAC
* * *
303836 TAAGAGTGCTAATAT-TATAAGGAAATTATAC
64 TAAGTGTGCTAAAATGT-TAAGGAAATCATAC
303867 CATGATATGA
Statistics
Matches: 642, Mismatches: 33, Indels: 18
0.93 0.05 0.03
Matches are distributed among these distances:
117 5 0.01
118 622 0.97
119 10 0.02
120 5 0.01
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (118 bp):
GCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATGTATTTCCATATAGGGCACTA
AGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCTAGATGGA
Found at i:303995 original size:44 final size:44
Alignment explanation
Indices: 303942--304911 Score: 1047
Period size: 44 Copynumber: 21.9 Consensus size: 44
303932 TTAGTGAGGC
*
303942 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGG
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-GA
303987 AA-AATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
*
304030 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGG
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-GA
304075 AA-AATGATAAGTATATT-GTAAAATAAGCTTACGAGCTTATGA
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
*
304117 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
* * *
304161 AATAATGGTAATTATATTGGTAAAATAAGCTTACAAGCTTATAGA
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-GA
* * * *
304206 AA-AATGGTAAGTAGATT-GTGAAATAAGCTTACGAACTTATGA
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
* * * *
304248 AATAATAATATGTATATAGGAAAAATAAGCTTACGAGCTTATGGAA
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-G-A
* * *
304294 AAGAAATGGTAAGTATAAT-GTAAAATAAGCTTACGAGCTTATGA
1 AA-TAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
* * * *
304338 AATAATAATATGTATATAGGTAAAATAAGCTTACGAGCATATGAAA
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATG--A
* * * *
304384 AAGAAATGGTAAGTATAAT-GTGAAATAAGCTTACGAGCTTATGA
1 AA-TAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
* * * *
304428 AATAATAATATGTATATAGGAAAAATAAGCTTACGAGCTTATGGAA
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-G-A
* * *
304474 AAGAAATGGTAAGTATAAT-GTAAAATAAGCTTACGAGCTTATGA
1 AA-TAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
* * *
304518 AATAATAATATGTATATAGGTAAAATAAGCTTACGAGCTTATGAAA
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATG--A
* * * *
304564 AAGAAATGGTAAGTATAAT-GTGAAATAAGCTTACGAGCTTATGA
1 AA-TAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
* * * *
304608 AATAATAATATGTATATAGGAAAAATAAGCTTACGAGCTTATGGAA
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-G-A
* * * *
304654 AAGAAATGGTAAGTATAAT-GTAAAATAAGCTTACGAGCTTATGG
1 AA-TAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
* * * * * *
304698 AATAATAATATGTATATAGGTGAAATAAGTTTACGAGCATATAGA
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-GA
* * *
304743 AA-AATGGTAAGTAGAAT-GTAAAATAAGCTTACGAGCTTAT--
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
* * *
304783 AATAAAGTGGTAAGTAGAAT-GTAAAATAAGCTTACGAGCTTAT--
1 AAT-AA-TGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
* *
304826 AATATATGGTAAGTATATTGGCAAAATAAGCTTACGAGCTTATGA
1 AATA-ATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
* * *
304871 AATAATAATAAGTATATTAGCAAAATAAGCTTACGAGCTTA
1 AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTA
304912 ATGGATAAAT
Statistics
Matches: 778, Mismatches: 112, Indels: 71
0.81 0.12 0.07
Matches are distributed among these distances:
40 2 0.00
42 21 0.03
43 203 0.26
44 355 0.46
45 21 0.03
46 126 0.16
47 50 0.06
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (44 bp):
AATAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
Found at i:304335 original size:90 final size:90
Alignment explanation
Indices: 303945--304916 Score: 1218
Period size: 90 Copynumber: 10.9 Consensus size: 90
303935 GTGAGGCAAT
* * * * * *
303945 AATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGAA-AATGATAAGTATATTGGTAA
1 AATGGTAAGTATAAT-GTAAAATAAGCTTACGAGCTTAT-GAAATAATAATATGTATATAGGTAA
*
304009 AATAAGCTTACGAGCTTAT-G-AAA-T
64 AATAAGCTTACGAGCTTATGGAAAAGA
* * * * * *
304033 AATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGAA-AATGATAAGTATAT-TGTAA
1 AATGGTAAGTATAAT-GTAAAATAAGCTTACGAGCTTAT-GAAATAATAATATGTATATAGGTAA
*
304096 AATAAGCTTACGAGCTTAT-G-AAA-T
64 AATAAGCTTACGAGCTTATGGAAAAGA
* * * ** *
304120 AATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATGGTAAT-TATATTGGTAA
1 AATGGTAAGTATAAT-GTAAAATAAGCTTACGAGCTTATGAAATAATAAT-ATGTATATAGGTAA
* *
304184 AATAAGCTTACAAGCTTAT--AGAA-A
64 AATAAGCTTACGAGCTTATGGAAAAGA
* * * * *
304208 AATGGTAAGTAGATTGTGAAATAAGCTTACGAACTTATGAAATAATAATATGTATATAGGAAAAA
1 AATGGTAAGTATAATGTAAAATAAGCTTACGAGCTTATGAAATAATAATATGTATATAGGTAAAA
304273 TAAGCTTACGAGCTTATGGAAAAGA
66 TAAGCTTACGAGCTTATGGAAAAGA
304298 AATGGTAAGTATAATGTAAAATAAGCTTACGAGCTTATGAAATAATAATATGTATATAGGTAAAA
1 AATGGTAAGTATAATGTAAAATAAGCTTACGAGCTTATGAAATAATAATATGTATATAGGTAAAA
* *
304363 TAAGCTTACGAGCATATGAAAAAGA
66 TAAGCTTACGAGCTTATGGAAAAGA
* *
304388 AATGGTAAGTATAATGTGAAATAAGCTTACGAGCTTATGAAATAATAATATGTATATAGGAAAAA
1 AATGGTAAGTATAATGTAAAATAAGCTTACGAGCTTATGAAATAATAATATGTATATAGGTAAAA
304453 TAAGCTTACGAGCTTATGGAAAAGA
66 TAAGCTTACGAGCTTATGGAAAAGA
304478 AATGGTAAGTATAATGTAAAATAAGCTTACGAGCTTATGAAATAATAATATGTATATAGGTAAAA
1 AATGGTAAGTATAATGTAAAATAAGCTTACGAGCTTATGAAATAATAATATGTATATAGGTAAAA
*
304543 TAAGCTTACGAGCTTATGAAAAAGA
66 TAAGCTTACGAGCTTATGGAAAAGA
* *
304568 AATGGTAAGTATAATGTGAAATAAGCTTACGAGCTTATGAAATAATAATATGTATATAGGAAAAA
1 AATGGTAAGTATAATGTAAAATAAGCTTACGAGCTTATGAAATAATAATATGTATATAGGTAAAA
304633 TAAGCTTACGAGCTTATGGAAAAGA
66 TAAGCTTACGAGCTTATGGAAAAGA
* *
304658 AATGGTAAGTATAATGTAAAATAAGCTTACGAGCTTATGGAATAATAATATGTATATAGGTGAAA
1 AATGGTAAGTATAATGTAAAATAAGCTTACGAGCTTATGAAATAATAATATGTATATAGGTAAAA
* * *
304723 TAAGTTTACGAGCATAT--AGAA-A
66 TAAGCTTACGAGCTTATGGAAAAGA
* ** * * *
304745 AATGGTAAGTAGAATGTAAAATAAGCTTACGAGCTTAT--AATAAAGTGGTAAGTAGA-ATGTAA
1 AATGGTAAGTATAATGTAAAATAAGCTTACGAGCTTATGAAAT-AA-TAATATGTATATAGGTAA
*
304807 AATAAGCTTACGAGCTTAT----AATA
64 AATAAGCTTACGAGCTTATGGAAAAGA
* * * * *
304830 TATGGTAAGTATATTGGCAAAATAAGCTTACGAGCTTATGAAATAATAATAAGTATATTA-GCAA
1 AATGGTAAGTATAAT-GTAAAATAAGCTTACGAGCTTATGAAATAATAATATGTATA-TAGGTAA
304894 AATAAGCTTACGAGCTTAATGGA
64 AATAAGCTTACGAGCTT-ATGGA
304917 TAAATGGTAA
Statistics
Matches: 805, Mismatches: 59, Indels: 37
0.89 0.07 0.04
Matches are distributed among these distances:
84 2 0.00
85 16 0.02
86 59 0.07
87 200 0.25
88 105 0.13
89 3 0.00
90 420 0.52
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (90 bp):
AATGGTAAGTATAATGTAAAATAAGCTTACGAGCTTATGAAATAATAATATGTATATAGGTAAAA
TAAGCTTACGAGCTTATGGAAAAGA
Found at i:304655 original size:23 final size:23
Alignment explanation
Indices: 304629--304705 Score: 54
Period size: 23 Copynumber: 3.3 Consensus size: 23
304619 GTATATAGGA
304629 AAAATAAGCTTACGAGCTTATGG
1 AAAATAAGCTTACGAGCTTATGG
* * *
304652 AAAAGAAATG-GTA--AG-TATAATGT
1 AAAA-TAA-GCTTACGAGCT-T-ATGG
304675 AAAATAAGCTTACGAGCTTATGG
1 AAAATAAGCTTACGAGCTTATGG
304698 AATAATAA
1 AA-AATAA
304706 TATGTATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 17
0.63 0.10 0.27
Matches are distributed among these distances:
21 2 0.05
22 7 0.18
23 16 0.41
24 12 0.31
25 2 0.05
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (23 bp):
AAAATAAGCTTACGAGCTTATGG
Found at i:305429 original size:29 final size:29
Alignment explanation
Indices: 305372--305430 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
305362 TGTTAACTGT
** * *
305372 TCACTGTTCACGGTACTGTTAACTGTTCA
1 TCACTGTTCACGACACTATTAACTATTCA
*
305401 TCACTGTTCACGACACTATTCACTATTCA
1 TCACTGTTCACGACACTATTAACTATTCA
305430 T
1 T
305431 AAAAAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (29 bp):
TCACTGTTCACGACACTATTAACTATTCA
Found at i:309320 original size:23 final size:22
Alignment explanation
Indices: 309294--309338 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
309284 TTTGTTCATG
309294 AAAGGAATCAGCAAAATAATAAA
1 AAAGGAATCA-CAAAATAATAAA
* *
309317 AAAGGACTTACAAAATAATAAA
1 AAAGGAATCACAAAATAATAAA
309339 CTCCCGAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.16
Consensus pattern (22 bp):
AAAGGAATCACAAAATAATAAA
Found at i:327153 original size:59 final size:57
Alignment explanation
Indices: 327078--327692 Score: 528
Period size: 59 Copynumber: 10.4 Consensus size: 57
327068 AAAAAAATGT
327078 TAAGGAAATCATACTAAGTGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAAAGG
1 TAAGGAAATCATACTAA-TGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAAAGG
* *
327136 ATAAGGGAATCATACTAAGTGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAAATGT
1 -TAAGGAAATCATACTAA-TGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAAA-GG
* * * *
327196 TAAGGAAATCATATTGAATATATGTATTTCCATATAGG-GCATTATA-TGTGCTAAAATGG
1 TAAGGAAATCATACT-AATGTATGGATTTCCATAT-GGAGCACTA-AGTGTGCTAAAA-GG
* * *
327255 TAAGGGAATCATACTAAGTGTATGGATTTCCATATGGAGTACTAAGTGTGCTAAAATGT
1 TAAGGAAATCATACTAA-TGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAAA-GG
* * * *
327314 TAAGGAAATCATATTGAATATATGTATTTCCATATAGG-GCATTATA-TGTGCTAAAATGG
1 TAAGGAAATCATACT-AATGTATGGATTTCCATAT-GGAGCACTA-AGTGTGCTAAAA-GG
* * *
327373 TAAGGGAATCATACTAAGTGTATGGATTTTCATATGGAGCACTAAGTGTGCTAAAATGT
1 TAAGGAAATCATACTAA-TGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAAA-GG
* * * *
327432 TAAGGAAATCATATTGAATATATGTATTTCCATATAGG-GCATTATA-TGTGCTAAAATGG
1 TAAGGAAATCATACT-AATGTATGGATTTCCATAT-GGAGCACTA-AGTGTGCTAAAA-GG
* * * ** * * *
327491 TAAGGGAATCATACAAATTGTATGGATTTTCATATTAAGCACTAAGGGTGCTATAACGA
1 TAAGGAAATCATACTAA-TGTATGGATTTCCATATGGAGCACTAAGTGTGCTA-AAAGG
* * * ** * * *
327550 TAATGAAATCATACTAATAGTATGGATTTTCAGATAAAGCACTAAGGGTGCTACAACGA
1 TAAGGAAATCATACTAAT-GTATGGATTTCCATATGGAGCACTAAGTGTGCTA-AAAGG
* * *
327609 TAATGAAATCATACTAATGGTATGGATTTTCATATAGG-GCACTTTA-TGTGCTAAAAATGG
1 TAAGGAAATCATACTAAT-GTATGGATTTCCATAT-GGAGCAC-TAAGTGTGCT-AAAA-GG
*
327669 TAA-AAGAATCATACTAATGGTATG
1 TAAGGA-AATCATACTAAT-GTATG
327693 AATTCTTGAA
Statistics
Matches: 467, Mismatches: 63, Indels: 51
0.80 0.11 0.09
Matches are distributed among these distances:
58 14 0.03
59 410 0.88
60 43 0.09
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (57 bp):
TAAGGAAATCATACTAATGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAAAGG
Found at i:327484 original size:236 final size:236
Alignment explanation
Indices: 327071--327664 Score: 817
Period size: 236 Copynumber: 2.5 Consensus size: 236
327061 ATGTGCAAAA
*
327071 AAAATGTTAAGGAAATCATACTAAGTGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAAAGG
1 AAAATGTTAAGGAAATCATACTAAGTATATGGATTTCCATATGGAGCACTAAGTGTGCTAAAAGG
327136 ATAAGGGAATCATACTAAGTGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAAATGTTAAGG
66 ATAAGGGAATCATACTAAGTGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAAATGTTAAGG
327201 AAATCATATTGAATATATGTATTTCCATATAGGGCATTATATGTGCTAAAATGGTAAGGGAATCA
131 AAATCATATTGAATATATGTATTTCCATATAGGGCATTATATGTGCTAAAATGGTAAGGGAATCA
* * * *
327266 TACTAAGTGTATGGATTTCCATATGGAGTACTAAGTGTGCT
196 TACAAAGTGTATGGATTTCCATATGAAGCACTAAGGGTGCT
* * *
327307 AAAATGTTAAGGAAATCATATTGAA-TATATGTATTTCCATATAGG-GCATTATA-TGTGCTAAA
1 AAAATGTTAAGGAAATCATACT-AAGTATATGGATTTCCATAT-GGAGCACTA-AGTGTGCTAAA
*
327369 ATGG-TAAGGGAATCATACTAAGTGTATGGATTTTCATATGGAGCACTAAGTGTGCTAAAATGTT
63 A-GGATAAGGGAATCATACTAAGTGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAAATGTT
327433 AAGGAAATCATATTGAATATATGTATTTCCATATAGGGCATTATATGTGCTAAAATGGTAAGGGA
127 AAGGAAATCATATTGAATATATGTATTTCCATATAGGGCATTATATGTGCTAAAATGGTAAGGGA
* * *
327498 ATCATACAAATTGTATGGATTTTCATATTAAGCACTAAGGGTGCT
192 ATCATACAAAGTGTATGGATTTCCATATGAAGCACTAAGGGTGCT
* * * * * * ** * * *
327543 ATAACGATAATGAAATCATACTAA-TAGTATGGATTTTCAGATAAAGCACTAAGGGTGCTACAAC
1 AAAATGTTAAGGAAATCATACTAAGTA-TATGGATTTCCATATGGAGCACTAAGTGTGCTAAAAG
* * * *
327607 GATAATGAAATCATACTAA-TGGTATGGATTTTCATATAGG-GCACTTTA-TGTGCTAAAA
65 GATAAGGGAATCATACTAAGT-GTATGGATTTCCATAT-GGAGCAC-TAAGTGTGCTAAAA
327665 ATGGTAAAAG
Statistics
Matches: 318, Mismatches: 29, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
235 7 0.02
236 300 0.94
237 11 0.03
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (236 bp):
AAAATGTTAAGGAAATCATACTAAGTATATGGATTTCCATATGGAGCACTAAGTGTGCTAAAAGG
ATAAGGGAATCATACTAAGTGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAAATGTTAAGG
AAATCATATTGAATATATGTATTTCCATATAGGGCATTATATGTGCTAAAATGGTAAGGGAATCA
TACAAAGTGTATGGATTTCCATATGAAGCACTAAGGGTGCT
Found at i:327651 original size:118 final size:118
Alignment explanation
Indices: 327071--327562 Score: 776
Period size: 118 Copynumber: 4.2 Consensus size: 118
327061 ATGTGCAAAA
* * * *
327071 AAAATGTTAAGGAAATCATACT-AAGTGTATGGATTTCCATAT-GGAGCACTA-AGTGTGCTAAA
1 AAAATGTTAAGGAAATCATATTGAA-TATATGTATTTCCATATAGG-GCATTATA-TGTGCTAAA
*
327133 A-GGATAAGGGAATCATACTAAGTGTATGGATTTCCATATGGAGCACTAAGTGTGCT
63 ATGG-TAAGGGAATCATACTAAGTGTATGGATTTTCATATGGAGCACTAAGTGTGCT
327189 AAAATGTTAAGGAAATCATATTGAATATATGTATTTCCATATAGGGCATTATATGTGCTAAAATG
1 AAAATGTTAAGGAAATCATATTGAATATATGTATTTCCATATAGGGCATTATATGTGCTAAAATG
* *
327254 GTAAGGGAATCATACTAAGTGTATGGATTTCCATATGGAGTACTAAGTGTGCT
66 GTAAGGGAATCATACTAAGTGTATGGATTTTCATATGGAGCACTAAGTGTGCT
327307 AAAATGTTAAGGAAATCATATTGAATATATGTATTTCCATATAGGGCATTATATGTGCTAAAATG
1 AAAATGTTAAGGAAATCATATTGAATATATGTATTTCCATATAGGGCATTATATGTGCTAAAATG
327372 GTAAGGGAATCATACTAAGTGTATGGATTTTCATATGGAGCACTAAGTGTGCT
66 GTAAGGGAATCATACTAAGTGTATGGATTTTCATATGGAGCACTAAGTGTGCT
327425 AAAATGTTAAGGAAATCATATTGAATATATGTATTTCCATATAGGGCATTATATGTGCTAAAATG
1 AAAATGTTAAGGAAATCATATTGAATATATGTATTTCCATATAGGGCATTATATGTGCTAAAATG
* * ** *
327490 GTAAGGGAATCATACAAATTGTATGGATTTTCATATTAAGCACTAAGGGTGCT
66 GTAAGGGAATCATACTAAGTGTATGGATTTTCATATGGAGCACTAAGTGTGCT
* * * *
327543 ATAACGATAATGAAATCATA
1 AAAATGTTAAGGAAATCATA
327563 CTAATAGTAT
Statistics
Matches: 354, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
118 347 0.98
119 7 0.02
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (118 bp):
AAAATGTTAAGGAAATCATATTGAATATATGTATTTCCATATAGGGCATTATATGTGCTAAAATG
GTAAGGGAATCATACTAAGTGTATGGATTTTCATATGGAGCACTAAGTGTGCT
Found at i:327946 original size:44 final size:44
Alignment explanation
Indices: 327878--328106 Score: 433
Period size: 44 Copynumber: 5.2 Consensus size: 44
327868 CAGTGATGCA
327878 AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAG
1 AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAG
*
327922 AATAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTTATAG
1 AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAG
327966 AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAG
1 AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAG
328010 AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-G
1 AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAG
328053 AAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAG
1 -AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAG
328098 AATAATGGT
1 AATAATGGT
328107 CTAAAAATTG
Statistics
Matches: 181, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
43 1 0.01
44 179 0.99
45 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (44 bp):
AATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAG
Found at i:327970 original size:21 final size:21
Alignment explanation
Indices: 327901--328014 Score: 61
Period size: 21 Copynumber: 5.2 Consensus size: 21
327891 ATATTGGTAA
327901 AATAAGCTTACGAGCTTATAG
1 AATAAGCTTACGAGCTTATAG
* * ** *
327922 AATAATG-GTAAGTATATTGATAA
1 AATAA-GCTTACG-AGCTT-ATAG
327945 AATAAGCTTACGAGCTTATAG
1 AATAAGCTTACGAGCTTATAG
* * ** * *
327966 AATAATG-GTAAGTATATTGGTAA
1 AATAA-GCTTACG-AGCTT-ATAG
327989 AATAAGCTTACGAGCTTATAG
1 AATAAGCTTACGAGCTTATAG
328010 AATAA
1 AATAA
328015 TGGTAAGTAT
Statistics
Matches: 63, Mismatches: 22, Indels: 16
0.62 0.22 0.16
Matches are distributed among these distances:
21 26 0.41
22 16 0.25
23 21 0.33
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (21 bp):
AATAAGCTTACGAGCTTATAG
Found at i:331681 original size:13 final size:13
Alignment explanation
Indices: 331659--331696 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
331649 AGGGAAGAAG
331659 AAAG-AAGAAAGA
1 AAAGAAAGAAAGA
331671 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
*
331684 AAAGAGAGAAAGA
1 AAAGAAAGAAAGA
331697 GACTGACGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:332445 original size:14 final size:14
Alignment explanation
Indices: 332426--332461 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
332416 TTTTTATTTA
*
332426 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
332440 TTTAATTTCATTAC
1 TTTAATTTCAGTAC
332454 TTTAATTT
1 TTTAATTT
332462 TCTATCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:332925 original size:2 final size:2
Alignment explanation
Indices: 332918--332955 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
332908 CAGATTTTGA
332918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
332956 GAAAACCTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:342892 original size:117 final size:116
Alignment explanation
Indices: 342686--342984 Score: 458
Period size: 117 Copynumber: 2.6 Consensus size: 116
342676 TTTTAACAGA
* *
342686 CTCAAATCTATCACAGAAGGAGGTGGATCATCGTTTCCAATAGAGAGA-TCATAATGAGAAGAAC
1 CTCAAATCCATCACAGAAGGAGGTGGATCATCATTTCCAAT-G-GAGATTCATAATGAGAAGAAC
*
342750 TCATCCAAAGAAGGAAGAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTG
64 TCATCCAAAGAAGGAAGAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTG
* * *
342803 CTCAAATCCATCACAGAAGGAGGTTGAGCATCACTTCCAATGGAGTATTCATAATGAGAAGAACT
1 CTCAAATCCATCACAGAAGGAGGTGGATCATCATTTCCAATGGAG-ATTCATAATGAGAAGAACT
*
342868 CATCCAAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTTTTCAACATTTG
65 CATCCAAAGAAGGAAG-AGAAGTTCATAATGAGAAGAACTTGTTCAACATTTG
* *
342920 CTCAAATCCATCACAGAATGAGGTGGATCATCATTTCCAATGGAGAGTTGATAATGAGAAGAACT
1 CTCAAATCCATCACAGAAGGAGGTGGATCATCATTTCCAATGGAGA-TTCATAATGAGAAGAACT
342985 TGTAATTCAG
Statistics
Matches: 166, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
115 3 0.02
116 5 0.03
117 158 0.95
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (116 bp):
CTCAAATCCATCACAGAAGGAGGTGGATCATCATTTCCAATGGAGATTCATAATGAGAAGAACTC
ATCCAAAGAAGGAAGAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTG
Found at i:343550 original size:29 final size:29
Alignment explanation
Indices: 343516--343581 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
343506 GGCAGTTCGA
343516 GTCGTGCGTCGGGTCCCCGGGAGTTTATC
1 GTCGTGCGTCGGGTCCCCGGGAGTTTATC
*
343545 GTCGTGCGTCGGGTCCCCGGGAGTTTATT
1 GTCGTGCGTCGGGTCCCCGGGAGTTTATC
343574 GTCGTGCG
1 GTCGTGCG
343582 GTTGTTGCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.06, C:0.26, G:0.39, T:0.29
Consensus pattern (29 bp):
GTCGTGCGTCGGGTCCCCGGGAGTTTATC
Found at i:343974 original size:17 final size:17
Alignment explanation
Indices: 343948--343981 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
343938 AAAATTTTAA
343948 TTATTAGTTTACTAACT
1 TTATTAGTTTACTAACT
* *
343965 TTATTGGTTTATTAACT
1 TTATTAGTTTACTAACT
343982 ACTAATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (17 bp):
TTATTAGTTTACTAACT
Found at i:346182 original size:2 final size:2
Alignment explanation
Indices: 346175--346204 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
346165 GAAAGATGGG
346175 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
346205 TTGAAAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:348786 original size:20 final size:21
Alignment explanation
Indices: 348761--348799 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
348751 AACAAGGAAA
*
348761 AGATAATTCCTAAA-ATAAAG
1 AGATAAATCCTAAAGATAAAG
348781 AGATAAATCCTAAAGATAA
1 AGATAAATCCTAAAGATAA
348800 TTCATAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (21 bp):
AGATAAATCCTAAAGATAAAG
Found at i:358332 original size:32 final size:31
Alignment explanation
Indices: 358260--358345 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
358250 CTAATGTGAC
* * **
358260 TCTTAGGTAGGCTCTGCGACCCTGTGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** *
358291 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
* *
358323 TCTTAGGTAGGCCCCGTGGCCCT
1 TCTTAGGTAGGCCCTGCGGCCCT
358346 GAAACTTCCT
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 22 0.51
32 21 0.49
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:360290 original size:7 final size:7
Alignment explanation
Indices: 360278--360302 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
360268 AAGAGAGGAA
360278 AAAAAAT
1 AAAAAAT
360285 AAAAAAT
1 AAAAAAT
360292 AAAAAAT
1 AAAAAAT
360299 AAAA
1 AAAA
360303 TAAAATAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:364380 original size:21 final size:21
Alignment explanation
Indices: 364356--364400 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
364346 TGTTTGGAAT
*
364356 TTTTCCTGGGATGCAACCAGC
1 TTTTCCTGGGATGCAACCAAC
*
364377 TTTTCCTGGGATGTAACCAAC
1 TTTTCCTGGGATGCAACCAAC
364398 TTT
1 TTT
364401 ACTTGTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (21 bp):
TTTTCCTGGGATGCAACCAAC
Found at i:367307 original size:19 final size:20
Alignment explanation
Indices: 367283--367326 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
367273 CCGGTTTTCA
* *
367283 ACCGGTTTTGACT-GGTTTG
1 ACCGGTTTCGAATCGGTTTG
367302 ACCGG-TTCGAATCGGTTTG
1 ACCGGTTTCGAATCGGTTTG
367321 ACCGGT
1 ACCGGT
367327 CTGAACCGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.14, C:0.20, G:0.32, T:0.34
Consensus pattern (20 bp):
ACCGGTTTCGAATCGGTTTG
Found at i:367336 original size:19 final size:19
Alignment explanation
Indices: 367296--367342 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
367286 GGTTTTGACT
*
367296 GGTTTGACCGGTTCGAATC
1 GGTTTGACCGGTTCGAACC
367315 GGTTTGACCGG-TCTGAACC
1 GGTTTGACCGGTTC-GAACC
*
367334 GGTCTGACC
1 GGTTTGACC
367343 CGACCCGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 2 0.08
19 23 0.92
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.28
Consensus pattern (19 bp):
GGTTTGACCGGTTCGAACC
Found at i:367358 original size:14 final size:14
Alignment explanation
Indices: 367339--367365 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
367329 GAACCGGTCT
367339 GACCCGACCCGATC
1 GACCCGACCCGATC
367353 GACCCGACCCGAT
1 GACCCGACCCGAT
367366 TGTTGACCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.48, G:0.22, T:0.07
Consensus pattern (14 bp):
GACCCGACCCGATC
Found at i:367380 original size:22 final size:22
Alignment explanation
Indices: 367352--367395 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
367342 CCGACCCGAT
**
367352 CGACCCGACCCGATTGTTGACC
1 CGACCCGACCCGACCGTTGACC
367374 CGACCCGACCCGACCGTTGACC
1 CGACCCGACCCGACCGTTGACC
367396 GTTGACCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (22 bp):
CGACCCGACCCGACCGTTGACC
Found at i:374705 original size:22 final size:22
Alignment explanation
Indices: 374677--374724 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
374667 GACCCGACCC
* *
374677 GACCCGATCCGACCCGATTGTT
1 GACCCGACCCGACCCGATCGTT
374699 GACCCGACCCGACCCGATCGTT
1 GACCCGACCCGACCCGATCGTT
374721 GACC
1 GACC
374725 GTTGACCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.42, G:0.23, T:0.17
Consensus pattern (22 bp):
GACCCGACCCGACCCGATCGTT
Found at i:379561 original size:29 final size:29
Alignment explanation
Indices: 379528--379712 Score: 316
Period size: 29 Copynumber: 6.4 Consensus size: 29
379518 ATAAATTTAT
* *
379528 TTACGAAAATAACACCCTTTTAAAATTAA
1 TTACGAAAATAGCACCCTTTTAAAAATAA
379557 TTACGAAAATAGCACCCTTTTAAAAATAA
1 TTACGAAAATAGCACCCTTTTAAAAATAA
* *
379586 TTACGAAAACATCACCCTTTTAAAAATAA
1 TTACGAAAATAGCACCCTTTTAAAAATAA
379615 TTACGAAAATAGCACCCTTTTAAAAATAA
1 TTACGAAAATAGCACCCTTTTAAAAATAA
*
379644 TTACAAAAATAGCACCCTTTTAAAAATAA
1 TTACGAAAATAGCACCCTTTTAAAAATAA
379673 TTACGAAAATAGCACCCTTTTAAAAATAA
1 TTACGAAAATAGCACCCTTTTAAAAATAA
*
379702 TTACAAAAATA
1 TTACGAAAATA
379713 TCACTGAACA
Statistics
Matches: 147, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 147 1.00
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.28
Consensus pattern (29 bp):
TTACGAAAATAGCACCCTTTTAAAAATAA
Found at i:379642 original size:17 final size:17
Alignment explanation
Indices: 379620--379671 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
379610 AATAATTACG
379620 AAAATAGCACCCTTTTA
1 AAAATAGCACCCTTTTA
**
379637 AAAATA--A---TTACA
1 AAAATAGCACCCTTTTA
379649 AAAATAGCACCCTTTTA
1 AAAATAGCACCCTTTTA
379666 AAAATA
1 AAAATA
379672 ATTACGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 10
0.65 0.10 0.25
Matches are distributed among these distances:
12 9 0.35
14 1 0.04
15 1 0.04
17 15 0.58
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.27
Consensus pattern (17 bp):
AAAATAGCACCCTTTTA
Found at i:379789 original size:58 final size:58
Alignment explanation
Indices: 379687--379797 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
379677 GAAAATAGCA
* *
379687 CCCTTTTAAAAATAATTACAAAAATATCACTGAACAGAATTTAATTACCTATTAGGCG
1 CCCTTTTAAAAATAATTACAAAAACATCACTGAACAGAAATTAATTACCTATTAGGCG
* * *
379745 CCCTTTTAAAAATATTTACAGAATAACATCA-T-AACCGAAATTAATTACGTATT
1 CCCTTTTAAAAATAATTACA-AA-AACATCACTGAACAGAAATTAATTACCTATT
379798 TATCACTCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 37 0.80
59 3 0.07
60 6 0.13
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.32
Consensus pattern (58 bp):
CCCTTTTAAAAATAATTACAAAAACATCACTGAACAGAAATTAATTACCTATTAGGCG
Found at i:387029 original size:29 final size:29
Alignment explanation
Indices: 386998--387269 Score: 447
Period size: 29 Copynumber: 9.4 Consensus size: 29
386988 TTTATTTATG
* * *
386998 AAAATAGCACCATTTTAAAATTAATTACG
1 AAAATAGCACCCTTTTAAAAATAATTACA
387027 AAAATAGCACCCTTTTAAAAATAATTACA
1 AAAATAGCACCCTTTTAAAAATAATTACA
*
387056 AAAATAGCACCCTTTTAAAATTAATTACA
1 AAAATAGCACCCTTTTAAAAATAATTACA
387085 AAAATAGCACCCTTTTTAAAAATAATTACA
1 AAAATAGCACCC-TTTTAAAAATAATTACA
*
387115 AAAATAGCA-CCTTTTAAAAATAATTACG
1 AAAATAGCACCCTTTTAAAAATAATTACA
*
387143 AAAATAGCACCCTTTTAAAAATAATTACG
1 AAAATAGCACCCTTTTAAAAATAATTACA
*
387172 AAAATAGCACCCTTTTAAAAATAATTACG
1 AAAATAGCACCCTTTTAAAAATAATTACA
387201 AAAATAGCACCCTTTTAAAAATAATTACA
1 AAAATAGCACCCTTTTAAAAATAATTACA
*
387230 AAAATAGCACTCTTTTAAAAATAATTACA
1 AAAATAGCACCCTTTTAAAAATAATTACA
*
387259 AAAATATCACC
1 AAAATAGCACC
387270 GAACATAATT
Statistics
Matches: 231, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
28 25 0.11
29 181 0.78
30 25 0.11
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.29
Consensus pattern (29 bp):
AAAATAGCACCCTTTTAAAAATAATTACA
Found at i:388374 original size:59 final size:59
Alignment explanation
Indices: 388225--388367 Score: 232
Period size: 59 Copynumber: 2.4 Consensus size: 59
388215 TGTTTGCTTA
* * * **
388225 TGTGTTATGGATGAGTGTTTGAGCTCCGTGACCCCAGCTTCATTATTGATGTTGTATTG
1 TGTGTTGTAGATGAATGTTTGAGCTCCGTGACCCCAGCTTCACCATTGATGTTGTATTG
*
388284 TGTGTTGTAGATGAATGTTTGAGCTCCGTGACCCGAGCTTCACCATTGATGTTGTATTG
1 TGTGTTGTAGATGAATGTTTGAGCTCCGTGACCCCAGCTTCACCATTGATGTTGTATTG
388343 TGTGTTGTAGATGAATGTTTGAGCT
1 TGTGTTGTAGATGAATGTTTGAGCT
388368 TTGTGACTCG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 78 1.00
ACGTcount: A:0.18, C:0.14, G:0.28, T:0.40
Consensus pattern (59 bp):
TGTGTTGTAGATGAATGTTTGAGCTCCGTGACCCCAGCTTCACCATTGATGTTGTATTG
Found at i:388392 original size:59 final size:59
Alignment explanation
Indices: 388225--388404 Score: 209
Period size: 59 Copynumber: 3.0 Consensus size: 59
388215 TGTTTGCTTA
* * * * * * **
388225 TGTGTTATGGATGAGTGTTTGAGCTCCGTGACCCCAGCTTCATTATTGATGTTGTATTG
1 TGTGTTGTAGATGAATGTTTGAGCTCCGTGACCCGAACCTCACCATTGATGTTGTATTG
* *
388284 TGTGTTGTAGATGAATGTTTGAGCTCCGTGACCCGAGCTTCACCATTGATGTTGTATTG
1 TGTGTTGTAGATGAATGTTTGAGCTCCGTGACCCGAACCTCACCATTGATGTTGTATTG
** * *
388343 TGTGTTGTAGATGAATGTTTGAGCTTTGTGACTCGAACCTCATCC-TTGATTATTGTATTG
1 TGTGTTGTAGATGAATGTTTGAGCTCCGTGACCCGAACCTCA-CCATTGA-TGTTGTATTG
388403 TG
1 TG
388405 ATTTACGGAT
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
59 94 0.88
60 13 0.12
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (59 bp):
TGTGTTGTAGATGAATGTTTGAGCTCCGTGACCCGAACCTCACCATTGATGTTGTATTG
Found at i:391514 original size:54 final size:54
Alignment explanation
Indices: 391388--391797 Score: 383
Period size: 54 Copynumber: 7.7 Consensus size: 54
391378 CCTTTTGCCT
* * * *
391388 ACGGGTTCGCTCTCTCTTTCTTTAGGGAGTATGGAACTCAGAGACATCTTCT---T
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACT-AGA-AAATCTTCTGAAA
* *
391441 ACAGGTTCGCTCCCTCTTTCTATAGGGAGTATAGAACTAGAAAATCTTCTGAAA
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTAGAAAATCTTCTGAAA
* * * **
391495 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATGTTCTTCAA
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTAGAAAATCTTCTGAAA
* * * **
391549 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTGCCA
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTAGAAAATCTTCTGAAA
* * * * **
391603 ACAGGTTCGCTCCCTCTTTCTTTAAGGAGTATGGAACTCAGATAATCTTCTTCAA
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACT-AGAAAATCTTCTGAAA
* * * * * *
391658 ACGGG-TCTGCTCCTTATTCCTTCAGAGAG--TCGAAC-----AATCTTCTGAAA
1 ACGGGTTC-GCTCCCTCTTTCTTTAGGGAGTATAGAACTAGAAAATCTTCTGAAA
* * * * * *
391705 ATGGGTCCGTTCCCTCTTTCTTCATGGAGTATAGAACTCGAACAATCTTCTGAAA
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTAGAA-AATCTTCTGAAA
*
391760 ACGGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACT
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACT
391798 CGAACATGTT
Statistics
Matches: 293, Mismatches: 50, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
47 29 0.10
48 1 0.00
49 5 0.02
51 8 0.03
52 3 0.01
53 39 0.13
54 133 0.45
55 75 0.26
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (54 bp):
ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTAGAAAATCTTCTGAAA
Found at i:391585 original size:108 final size:109
Alignment explanation
Indices: 391388--391797 Score: 438
Period size: 108 Copynumber: 3.9 Consensus size: 109
391378 CCTTTTGCCT
* * *
391388 ACGGGTTCGCTCTCTCTTTCTTTAGGGAGTATGGAACTCAGAGACATCTTCTT---ACAGGTTCG
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCAGAGACATCTTCTTCAAACGGGTTCG
391450 CTCCCTCTTTCTAT-AGGGAGTATAGAACTAGAAAATCTTCTGAAA
66 CTCCCTCTTTCT-TCAGGGAGTATAGAACT-GAAAATCTTCTGAAA
*
391495 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTC-GA-ACATGTTCTTCAAACGGGTTCG
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCAGAGACATCTTCTTCAAACGGGTTCG
* **
391558 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTGCCA
66 CTCCCTCTTTCTTCAGGGAGTATAGAACT-GAAAATCTTCTGAAA
* * * *
391603 ACAGGTTCGCTCCCTCTTTCTTTAAGGAGTATGGAACTCAGATA-ATCTTCTTCAAACGGG-TCT
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCAGAGACATCTTCTTCAAACGGGTTC-
* * * * *
391666 GCTCCTTATTCCTTCAGAGAG--TCGAAC----AATCTTCTGAAA
65 GCTCCCTCTTTCTTCAGGGAGTATAGAACTGAAAATCTTCTGAAA
* * * * * **
391705 ATGGGTCCGTTCCCTCTTTCTTCATGGAGTATAGAACTC-GA-ACAATCTTCTGAAAACGGGTTC
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCAGAGAC-ATCTTCTTCAAACGGGTTC
* *
391768 GCTCCCTCTTTCTTTAAGGAGTATAGAACT
65 GCTCCCTCTTTCTTCAGGGAGTATAGAACT
391798 CGAACATGTT
Statistics
Matches: 254, Mismatches: 36, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
100 1 0.00
101 2 0.01
102 70 0.28
103 2 0.01
104 5 0.02
105 9 0.04
106 2 0.01
107 43 0.17
108 85 0.33
109 34 0.13
110 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (109 bp):
ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCAGAGACATCTTCTTCAAACGGGTTCG
CTCCCTCTTTCTTCAGGGAGTATAGAACTGAAAATCTTCTGAAA
Found at i:391743 original size:156 final size:156
Alignment explanation
Indices: 391559--391910 Score: 462
Period size: 156 Copynumber: 2.3 Consensus size: 156
391549 ACGGGTTCGC
**
391559 TCCCTCTTTCTTCAGGGAGTATAGAACTCGAAC-ATCTTCTGCCAACAGGTTCGCTCCCTCTTTC
1 TCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACAGGTTCGCTCCCTCTTTC
* ** *
391623 TTTAAGGAGTATGGAACTCAGATA-ATCTTCTTCAAACGGGTCTGCTCCTTATTCCTTCAGAGAG
66 TTTAAGGAGTATAGAACTC-GA-ACATCTTCAACAAACGGGTATGCTCCTTATTCCTTCAGAGAG
391687 TCGAACAATCTTCTGAAAATGGGTCCGT
129 TCGAACAATCTTCTGAAAATGGGTCCGT
* *
391715 TCCCTCTTTCTTCATGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTC
1 TCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACAGGTTCGCTCCCTCTTTC
* * * *
391780 TTTAAGGAGTATAGAACTCGAACATGTTCAACAATCGTGTATGCTCCTTATTCCTTCAGAGAGTT
66 TTTAAGGAGTATAGAACTCGAACATCTTCAACAAACGGGTATGCTCCTTATTCCTTCAGAGAGTC
* * *
391845 GAACAATCTTC--AACAATCGTGTCTGC
131 GAACAATCTTCTGAA-AAT-GGGTCCGT
* * *
391871 TCCCTATTCCTTCAGAGAGTATA-AGACTCGAACAATCTTC
1 TCCCTCTTTCTTCAGGGAGTATAGA-ACTCGAACAATCTTC
391911 ATCAATCGTG
Statistics
Matches: 172, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
154 2 0.01
155 5 0.03
156 119 0.69
157 46 0.27
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (156 bp):
TCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACAGGTTCGCTCCCTCTTTC
TTTAAGGAGTATAGAACTCGAACATCTTCAACAAACGGGTATGCTCCTTATTCCTTCAGAGAGTC
GAACAATCTTCTGAAAATGGGTCCGT
Found at i:391774 original size:55 final size:55
Alignment explanation
Indices: 391687--391803 Score: 189
Period size: 55 Copynumber: 2.1 Consensus size: 55
391677 CTTCAGAGAG
* * *
391687 TCGAACAATCTTCTGAAAATGGGTCCGTTCCCTCTTTCTTCATGGAGTATAGAAC
1 TCGAACAATCTTCTGAAAACGGGTCCGCTCCCTCTTTCTTCAAGGAGTATAGAAC
* *
391742 TCGAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAAC
1 TCGAACAATCTTCTGAAAACGGGTCCGCTCCCTCTTTCTTCAAGGAGTATAGAAC
391797 TCGAACA
1 TCGAACA
391804 TGTTCAACAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (55 bp):
TCGAACAATCTTCTGAAAACGGGTCCGCTCCCTCTTTCTTCAAGGAGTATAGAAC
Found at i:391872 original size:47 final size:49
Alignment explanation
Indices: 391797--391947 Score: 191
Period size: 55 Copynumber: 3.0 Consensus size: 49
391787 AGTATAGAAC
* *
391797 TCGAAC-ATGTTCAACAATCGTGTATGCTCCTTATTCCTTCAGAGAGT-
1 TCGAACAATCTTCAACAATCGTGTCTGCTCCTTATTCCTTCAGAGAGTA
*
391844 T-GAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGA
1 TCGAACAATCTTCAACAATCGTGTCTGCTCCTTATTCCTTCAGAGAG--T---A
*
391897 CTCGAACAATCTTCATCAATCGTGTCTGCTCCTTATTCCTTCAGAGAGTA
1 -TCGAACAATCTTCAACAATCGTGTCTGCTCCTTATTCCTTCAGAGAGTA
391947 T
1 T
391948 AAGACTCAAA
Statistics
Matches: 90, Mismatches: 5, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
46 4 0.04
47 38 0.42
49 2 0.02
50 1 0.01
53 1 0.01
54 1 0.01
55 43 0.48
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (49 bp):
TCGAACAATCTTCAACAATCGTGTCTGCTCCTTATTCCTTCAGAGAGTA
Found at i:391911 original size:55 final size:55
Alignment explanation
Indices: 391845--391964 Score: 213
Period size: 55 Copynumber: 2.2 Consensus size: 55
391835 TCAGAGAGTT
391845 GAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTC
1 GAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTC
* *
391900 GAACAATCTTCATCAATCGTGTCTGCTCCTTATTCCTTCAGAGAGTATAAGACTC
1 GAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTC
*
391955 AAACAATCTT
1 GAACAATCTT
391965 AATGCTTCAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (55 bp):
GAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTC
Found at i:393030 original size:8 final size:8
Alignment explanation
Indices: 393004--393056 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
392994 TGAACCCCCC
393004 TTTTATTCA
1 TTTT-TTCA
393013 TTTTTT-A
1 TTTTTTCA
393020 TTTTTTCA
1 TTTTTTCA
**
393028 -TTTAACA
1 TTTTTTCA
393035 TTTTTTTCA
1 -TTTTTTCA
393044 TTTTTTCA
1 TTTTTTCA
393052 TTTTT
1 TTTTT
393057 ATCTTCATGC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
7 12 0.32
8 16 0.43
9 9 0.24
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:402910 original size:16 final size:17
Alignment explanation
Indices: 402889--402926 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
402879 AACCTTATTC
402889 ACATGGTATCTACCC-A
1 ACATGGTATCTACCCAA
402905 ACATGGTATCTACCCAA
1 ACATGGTATCTACCCAA
402922 ACATG
1 ACATG
402927 CTTTAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (17 bp):
ACATGGTATCTACCCAA
Found at i:405639 original size:19 final size:19
Alignment explanation
Indices: 405617--405658 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
405607 TTCCATCATA
*
405617 ATTGCCTCTTCATTTTATC
1 ATTGCATCTTCATTTTATC
405636 ATTGCATCTTCATTTTATC
1 ATTGCATCTTCATTTTATC
405655 ATTG
1 ATTG
405659 AATGTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.52
Consensus pattern (19 bp):
ATTGCATCTTCATTTTATC
Found at i:407707 original size:15 final size:15
Alignment explanation
Indices: 407687--407739 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
407677 GGTCCAGTCA
*
407687 CCGAGTTAACTCGGT
1 CCGAGTCAACTCGGT
*
407702 CCGAGTCAAC-CCGT
1 CCGAGTCAACTCGGT
*
407716 TCGAGTCAACTCGGT
1 CCGAGTCAACTCGGT
407731 CCGAGTCAA
1 CCGAGTCAA
407740 TCGTTGAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.23, C:0.32, G:0.25, T:0.21
Consensus pattern (15 bp):
CCGAGTCAACTCGGT
Found at i:411488 original size:27 final size:27
Alignment explanation
Indices: 411438--411490 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
411428 AAGTAAATGA
*
411438 TATGTTATAATGAAAAGTGAAAATTTG
1 TATGTTATAATGAAAAGTCAAAATTTG
* *
411465 TATGTTATAATGAAAGGTCTAAATTT
1 TATGTTATAATGAAAAGTCAAAATTT
411491 TGATATATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.40
Consensus pattern (27 bp):
TATGTTATAATGAAAAGTCAAAATTTG
Found at i:413118 original size:90 final size:90
Alignment explanation
Indices: 412962--413139 Score: 275
Period size: 90 Copynumber: 2.0 Consensus size: 90
412952 CCTAACACAC
* * * * *
412962 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGCGATTTTATTATTTCAAATTAATTAAATATAT
* *
413027 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* *
413052 CCTTTTATATCCAAGTTACCCTAATCATATCCGCGATTTTATTATTTCAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGCGATTTTATTATTTCAAATTAATTAAATATAT
413117 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
413140 TTCGGGATTA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGCGATTTTATTATTTCAAATTAATTAAATATAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:421653 original size:12 final size:13
Alignment explanation
Indices: 421633--421665 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
421623 ATTTGGCACG
421633 TGTTTTTTTCCCA
1 TGTTTTTTTCCCA
421646 TGTTTTTTTCCCA
1 TGTTTTTTTCCCA
421659 TGTTTTT
1 TGTTTTT
421666 AGTATGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.18, G:0.09, T:0.67
Consensus pattern (13 bp):
TGTTTTTTTCCCA
Found at i:422183 original size:18 final size:19
Alignment explanation
Indices: 422142--422183 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
422132 TATAGGTGTA
*
422142 TGCATATTAAATTAGGTGAT
1 TGCATATTAAATTA-GTAAT
422162 TGCATATTAAATTA-TAAT
1 TGCATATTAAATTAGTAAT
422180 TGCA
1 TGCA
422184 AGTGATAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.40
Consensus pattern (19 bp):
TGCATATTAAATTAGTAAT
Found at i:422259 original size:17 final size:18
Alignment explanation
Indices: 422237--422274 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
422227 AGTTTCATAT
422237 TAAATA-ATTGCATATTA
1 TAAATAGATTGCATATTA
422254 TAAATAGTATTGCATATTA
1 TAAATAG-ATTGCATATTA
422273 TA
1 TA
422275 TTAGATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (18 bp):
TAAATAGATTGCATATTA
Found at i:422283 original size:19 final size:19
Alignment explanation
Indices: 422233--422283 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
422223 ATATAGTTTC
*
422233 ATATTAAATAATTGCATATT
1 ATATTAGAT-ATTGCATATT
*
422253 ATAAATAG-TATTGCATATT
1 AT-ATTAGATATTGCATATT
422272 ATATTAGATATT
1 ATATTAGATATT
422284 AAATAATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.15
19 16 0.62
20 3 0.12
21 3 0.12
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (19 bp):
ATATTAGATATTGCATATT
Found at i:422653 original size:15 final size:14
Alignment explanation
Indices: 422628--422662 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
422618 TTGTTTCATT
*
422628 GAAATTGTTTTTCG
1 GAAAATGTTTTTCG
422642 GAAAATGTTTTTCG
1 GAAAATGTTTTTCG
*
422656 TAAAATG
1 GAAAATG
422663 AATTACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (14 bp):
GAAAATGTTTTTCG
Found at i:423061 original size:19 final size:19
Alignment explanation
Indices: 422993--423073 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
422983 TTATATATCT
422993 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
423012 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
423031 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
423051 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
423069 -TATTA
1 TTATTA
423074 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:423198 original size:32 final size:32
Alignment explanation
Indices: 423161--423230 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
423151 ATATTAGTAT
*
423161 AATATAATTGATTATTTTATTAT-AATA-TTAAA
1 AATATAA-T-ATTATATTATTATAAATATTTAAA
*
423193 AATATAATATTATATTATTATAAATATTTATA
1 AATATAATATTATATTATTATAAATATTTAAA
423225 AATATA
1 AATATA
423231 TTTTAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 12 0.35
31 5 0.15
32 17 0.50
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
AATATAATATTATATTATTATAAATATTTAAA
Found at i:423206 original size:22 final size:22
Alignment explanation
Indices: 423178--423219 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
423168 TTGATTATTT
423178 TATTATAATATTAAAAATATAA
1 TATTATAATATTAAAAATATAA
* *
423200 TATTATATTATTATAAATAT
1 TATTATAATATTAAAAATAT
423220 TTATAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTATAATATTAAAAATATAA
Found at i:423287 original size:12 final size:12
Alignment explanation
Indices: 423204--423291 Score: 53
Period size: 11 Copynumber: 7.4 Consensus size: 12
423194 ATATAATATT
423204 ATATTATTA-TAA
1 ATATT-TTATTAA
423216 ATA-TTTA-TAA
1 ATATTTTATTAA
*
423226 ATATATT-TTAA
1 ATATTTTATTAA
*
423237 ATATTTTAATAATTA
1 ATATTTT-AT--TAA
423252 ATATTTTGATTAA
1 ATATTTT-ATTAA
**
423265 A-ATGATATTAA
1 ATATTTTATTAA
423276 ATATTTTATT-A
1 ATATTTTATTAA
423287 ATATT
1 ATATT
423292 AAATTCATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
10 9 0.15
11 24 0.40
12 12 0.20
13 4 0.07
15 11 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
ATATTTTATTAA
Found at i:429396 original size:17 final size:17
Alignment explanation
Indices: 429374--429414 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
429364 GGTCAACAGT
*
429374 GGTCAACGCCGGTCAAC
1 GGTCAACGCAGGTCAAC
429391 GGTCAACGCAGGTCAAC
1 GGTCAACGCAGGTCAAC
429408 GGTCAAC
1 GGTCAAC
429415 AGTCGACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.27, C:0.32, G:0.29, T:0.12
Consensus pattern (17 bp):
GGTCAACGCAGGTCAAC
Found at i:429935 original size:13 final size:13
Alignment explanation
Indices: 429919--429947 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
429909 CGATGAACGG
429919 CGACGATTCACGA
1 CGACGATTCACGA
429932 CGACGATTCACGA
1 CGACGATTCACGA
429945 CGA
1 CGA
429948 AAGGTTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (13 bp):
CGACGATTCACGA
Found at i:430200 original size:8 final size:8
Alignment explanation
Indices: 430187--430212 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
430177 GTATGCCAAC
430187 TTTACAAT
1 TTTACAAT
430195 TTTACAAT
1 TTTACAAT
430203 TTTACAAT
1 TTTACAAT
430211 TT
1 TT
430213 AATCCTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTACAAT
Found at i:431211 original size:2 final size:2
Alignment explanation
Indices: 431204--431239 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
431194 ATCACCGAGA
*
431204 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
431240 CAATTACGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:432934 original size:2 final size:2
Alignment explanation
Indices: 432929--432981 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
432919 CACGTATTCT
432929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
432971 TA TA TA TA TA T
1 TA TA TA TA TA T
432982 GTAACTTAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:436084 original size:3 final size:3
Alignment explanation
Indices: 436010--436072 Score: 101
Period size: 3 Copynumber: 20.7 Consensus size: 3
436000 TTGAAGCCTG
436010 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA GTTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA
436059 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
436073 TCTTAATAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 53 0.93
5 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:436472 original size:134 final size:134
Alignment explanation
Indices: 436209--437498 Score: 1651
Period size: 134 Copynumber: 9.6 Consensus size: 134
436199 AAATATGATA
* * * * *
436209 AGGGATCTGTTCCGCTGT-TACT-CAGGGAATATCAAATCT-GGGGATGTTGATCCATTTCACTG
1 AGGGATCTGTTCCGCT-TCTTCTGAAGGGAATATCAGATCTGGGGGA-GTTGATCCATTCCGCTG
* * *
436271 TCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCC-TTAATCACTCAGGGAATATCAAATCTT
64 TCACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCT-GTCACTCAGGGAATATCAAATCTT
436335 GAAAGAG
128 GAAAGAG
* * * *
436342 AGAGATATGTTCCGCTTCTTCTGAAGGGAATATCAGATCTAGGGGAGTTGATCCATTCCGTTGTC
1 AGGGATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTCCGCTGTC
* * *
436407 AATCAGGGAAGATTGAATCGGGGCAGATTTGTTCCGCTGTCACTCAGGAAATATCAAATCTTGAA
66 ACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAA
436472 AGAG
131 AGAG
* * * **
436476 AGGGATGTGTTCCGCTTCTTCTGAAGGGAATATCAAATATGGGGGAGTTGATATATTCCGCTGTC
1 AGGGATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTCCGCTGTC
* * ** *
436541 ACTCAGGGAAGATTTAATCGGGGCAGACATGTTTTGTTGTCACTCAGGGAATATCAAATCTTGAA
66 ACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAA
*
436606 AAAG
131 AGAG
* * *
436610 AGGGATCTGTTCCGCTTCTTCTGAAGGAAATATCAGATCTGGGGGAGTTGATCTATTTCGCTGTC
1 AGGGATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTCCGCTGTC
* *
436675 ACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCACTTAGAGAATATCAAATCTTGAA
66 ACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAA
436740 AGAG
131 AGAG
* * * *
436744 AGGGATTTGTTCTGCTTCTTCT-AAAGGATATATCAGATCTGGGGGAGTTGATCCATTCCGTTGT
1 AGGGATCTGTTCCGCTTCTTCTGAAGGGA-ATATCAGATCTGGGGGAGTTGATCCATTCCGCTGT
* * **
436808 CACTCAGGGAATATTGAATCGGGGTAGACTTGTTCCATTGTCACTCAGGGAATAAT-AAATCTTG
65 CACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCACTCAGGGAAT-ATCAAATCTTG
436872 AAAGAG
129 AAAGAG
* * * * ** * * * *
436878 GGGGATTTTTTCCGCTTCTTCTAAATAGAATATCATATCTGGGGGAGTTTATCCATTTCACTGTC
1 AGGGATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTCCGCTGTC
* * * * *
436943 ACTCAGGGAAGATTGAATCGGGGCATACTTGTTCCGATGTTATTAAGGGAATATCAAATCTTGAA
66 ACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAA
437008 AGAG
131 AGAG
* * ** * *
437012 AGGGTTATGTTCATCTTCTTCTGAAGGGAATATCAGATATGGGGGAGTTGATCCATTCCGCTATC
1 AGGGATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTCCGCTGTC
*
437077 ACTCAGGGAAGATTGAATCGGGGCAGACTTATTCCGCTGTCACTCAGGGAATATCAAATCTTGAA
66 ACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAA
437142 AGAG
131 AGAG
* * * * * * * * *
437146 AGTGATGTGTTTCACTTCTTCTGAAGAGAATATTAGATATGGGGGAGTTGATCCATTCTGCTATC
1 AGGGATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTCCGCTGTC
** *
437211 ACGT-AAAGAATATTGAATCGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGA
66 AC-TCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGA
437275 AAGAG
130 AAGAG
* * * * * *
437280 ATGGATCTGTTCTGCTTCTTCTAAAGGGATTATCAGATATGGGGGAGTTGATCCATTCCGCTATC
1 AGGGATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTCCGCTGTC
* * * * *
437345 ACTCAGGGAAGATTGAATTGGGTCAGCCATGTT-CGACTGTCACTCAGGGAATATCAAATCTTAA
66 ACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCG-CTGTCACTCAGGGAATATCAAATCTTGA
437409 AAGAG
130 AAGAG
* * * * *
437414 TGGGATCTGTTCTGCTTTTTCTGAAGGGAATATCAGTTCTGGGGGAGTTGATCCATTCCGCTATC
1 AGGGATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTCCGCTGTC
*
437479 ACTTAGGGAAGATTGAATCG
66 ACTCAGGGAAGATTGAATCG
437499 AGTTTGATTT
Statistics
Matches: 1008, Mismatches: 138, Indels: 21
0.86 0.12 0.02
Matches are distributed among these distances:
132 1 0.00
133 26 0.03
134 968 0.96
135 13 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (134 bp):
AGGGATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTCCGCTGTC
ACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAA
AGAG
Found at i:463960 original size:5 final size:5
Alignment explanation
Indices: 463950--464053 Score: 95
Period size: 5 Copynumber: 20.8 Consensus size: 5
463940 TGTTCATAGA
* * *
463950 AAAAT AAAAT AAAAT -AAAT CAAAAT AAAAT -AAAT AGAAT GAAAT AAAGT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
**** * *
463999 TTTCT AAAAT AAAAT AAAAT AAAACT AAAAT AAAAT AAAAT GAAAT AAAAC
1 AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT
464050 AAAA
1 AAAA
464054 ATAGAACGAA
Statistics
Matches: 79, Mismatches: 16, Indels: 8
0.77 0.16 0.08
Matches are distributed among these distances:
4 8 0.10
5 62 0.78
6 9 0.11
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:464054 original size:16 final size:15
Alignment explanation
Indices: 464004--464056 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
463994 AAAGTTTTCT
464004 AAAATAAAATAAAATA
1 AAAATAAAATAAAA-A
* *
464020 AAACTAAAATAAAAT
1 AAAATAAAATAAAAA
*
464035 AAAATGAAATAAAACA
1 AAAATAAAATAAAA-A
464051 AAAATA
1 AAAATA
464057 GAACGAAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (15 bp):
AAAATAAAATAAAAA
Found at i:464065 original size:26 final size:26
Alignment explanation
Indices: 464003--464066 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
463993 TAAAGTTTTC
* * *
464003 TAAAATAAAATAAAATAAAACTAAAA
1 TAAAACAAAATGAAATAAAACAAAAA
*
464029 TAAAATAAAATGAAATAAAACAAAAA
1 TAAAACAAAATGAAATAAAACAAAAA
* *
464055 TAGAACGAAATG
1 TAAAACAAAATG
464067 GGTTGCCTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.72, C:0.05, G:0.06, T:0.17
Consensus pattern (26 bp):
TAAAACAAAATGAAATAAAACAAAAA
Found at i:468189 original size:21 final size:21
Alignment explanation
Indices: 468159--468208 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
468149 CTTTGGAATT
* * *
468159 TTTTCCTGGGATATGACTAGC
1 TTTTCTTGGGACATAACTAGC
*
468180 TTTTCTTGGGACCTAACTAGC
1 TTTTCTTGGGACATAACTAGC
468201 TTTTCTTG
1 TTTTCTTG
468209 TGAAATTGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (21 bp):
TTTTCTTGGGACATAACTAGC
Found at i:469720 original size:16 final size:15
Alignment explanation
Indices: 469688--469728 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
469678 TTAAAAGGGA
469688 AAATAATAAAATAAT
1 AAATAATAAAATAAT
*
469703 AAATAATAATAGTAAT
1 AAATAATAA-AATAAT
469719 AAAT-ATAAAA
1 AAATAATAAAA
469729 GAGGGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 1 0.04
15 13 0.57
16 9 0.39
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
AAATAATAAAATAAT
Found at i:470717 original size:12 final size:12
Alignment explanation
Indices: 470700--470733 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
470690 CGTCTGATGT
470700 TTCATGCCCAAA
1 TTCATGCCCAAA
470712 TTCATGCCCAAA
1 TTCATGCCCAAA
470724 TTCATGCCCA
1 TTCATGCCCA
470734 CTAGTCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.35, G:0.09, T:0.26
Consensus pattern (12 bp):
TTCATGCCCAAA
Found at i:473430 original size:109 final size:111
Alignment explanation
Indices: 473276--473495 Score: 385
Period size: 109 Copynumber: 2.0 Consensus size: 111
473266 GTTTAACATA
*
473276 AACTGAAAGATAATAAAGTCCATATAATAACATTATTAAAAGATCCATAGTCAAGTATTATTATG
1 AACTGAAAGATAATAAAGTCCATATAATAACATTATTAAAAGATCCATAGTCAAGTATGATTATG
473341 GGCATGGACAATAATAA-ACGCTTAAGACTAAC-TGTTATTGATTGAT
66 GGCATGGACAATAATAATACGCTTAAG-C-AACATGTTATTGATTGAT
473387 AACTGAAAGATAAT-AAGTCCATATAATAACA-TATTAAAAGATCCATAGTCAAGTATGATTATG
1 AACTGAAAGATAATAAAGTCCATATAATAACATTATTAAAAGATCCATAGTCAAGTATGATTATG
473450 GGCATGGACAATAATAATACGCTTAAGCAACATGTTATTGATTGAT
66 GGCATGGACAATAATAATACGCTTAAGCAACATGTTATTGATTGAT
473496 GACAAGGAGT
Statistics
Matches: 106, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
108 3 0.03
109 63 0.59
110 26 0.25
111 14 0.13
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (111 bp):
AACTGAAAGATAATAAAGTCCATATAATAACATTATTAAAAGATCCATAGTCAAGTATGATTATG
GGCATGGACAATAATAATACGCTTAAGCAACATGTTATTGATTGAT
Found at i:493586 original size:16 final size:17
Alignment explanation
Indices: 493561--493594 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
493551 TAAGATAACG
*
493561 ATTAAGTAGAA-AAAAT
1 ATTAAATAGAATAAAAT
493577 ATTAAATAGAATAAAAT
1 ATTAAATAGAATAAAAT
493594 A
1 A
493595 GTAATTGCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
ATTAAATAGAATAAAAT
Found at i:495148 original size:2 final size:2
Alignment explanation
Indices: 495141--495167 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
495131 ATTAATAATA
495141 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
495168 AACACAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:510112 original size:18 final size:18
Alignment explanation
Indices: 510089--510128 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
510079 AAGTCGTGGT
510089 GGTGGTGATGGAGATGGA
1 GGTGGTGATGGAGATGGA
*
510107 GGTGGTGGTGGAGATGGA
1 GGTGGTGATGGAGATGGA
510125 GGTG
1 GGTG
510129 ATGGAGGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.60, T:0.23
Consensus pattern (18 bp):
GGTGGTGATGGAGATGGA
Found at i:510140 original size:18 final size:18
Alignment explanation
Indices: 510098--510143 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
510088 TGGTGGTGAT
* *
510098 GGAGATGGAGGTGGTGGT
1 GGAGATGGAGGTGATGGA
510116 GGAGATGGAGGTGATGGA
1 GGAGATGGAGGTGATGGA
*
510134 GGTGATGGAG
1 GGAGATGGAG
510144 ATGGAGATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.59, T:0.20
Consensus pattern (18 bp):
GGAGATGGAGGTGATGGA
Found at i:510154 original size:24 final size:24
Alignment explanation
Indices: 510086--510155 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
510076 TGCAAGTCGT
* *
510086 GGTGGTGGTGATGGAGATGGA-GGT
1 GGTGGTGGAGATGGAGAT-GATGGA
*
510110 GGTGGTGGAGATGGAGGTGATGGA
1 GGTGGTGGAGATGGAGATGATGGA
*
510134 GGTGATGGAGATGGAGATGATG
1 GGTGGTGGAGATGGAGATGATG
510156 AAGATAAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 2 0.05
24 38 0.95
ACGTcount: A:0.21, C:0.00, G:0.56, T:0.23
Consensus pattern (24 bp):
GGTGGTGGAGATGGAGATGATGGA
Found at i:510155 original size:9 final size:9
Alignment explanation
Indices: 510101--510143 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
510091 TGGTGATGGA
510101 GATGGAGGT
1 GATGGAGGT
* * *
510110 GGTGGTGGA
1 GATGGAGGT
510119 GATGGAGGT
1 GATGGAGGT
510128 GATGGAGGT
1 GATGGAGGT
510137 GATGGAG
1 GATGGAG
510144 ATGGAGATGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.58, T:0.21
Consensus pattern (9 bp):
GATGGAGGT
Found at i:513554 original size:172 final size:173
Alignment explanation
Indices: 513267--513613 Score: 687
Period size: 172 Copynumber: 2.0 Consensus size: 173
513257 ATTATCTCAC
513267 CACAACTAGCTAGATTGTAACAAACAGACTTGATTTTCATCAAGTAATCTCTCATACTCAGCTCC
1 CACAACTAGCTAGATTGTAACAAACAGACTTGATTTTCATCAAGTAATCTCTCATACTCAGCTCC
513332 CCCTTCCTCTGAGAATGAAGCATTCTCCTATAGGACATTAACCTAGAAGTAGTCTTACCACTGTA
66 CCCTTCCTCTGAGAATGAAGCATTCTCCTATAGGACATTAACCTAGAAGTAGTCTTACCACTGTA
513397 TAACCTATGTAGGGTACTCTAGATTCCAGCTGCAGTATTAAGA
131 TAACCTATGTAGGGTACTCTAGATTCCAGCTGCAGTATTAAGA
513440 CACAACTAGCTAGATTGTAACAAACAGACTTGATTTTCATCAAGTAA-CTCTCATACTCAGCTCC
1 CACAACTAGCTAGATTGTAACAAACAGACTTGATTTTCATCAAGTAATCTCTCATACTCAGCTCC
513504 CCCTTCCTCTGAGAATGAAGCATTCTCCTATAGGACATTAACCTAGAAGTAGTCTTACCACTGTA
66 CCCTTCCTCTGAGAATGAAGCATTCTCCTATAGGACATTAACCTAGAAGTAGTCTTACCACTGTA
513569 TAACCTATGTAGGGTACTCTAGATTCCAGCTGCAGTATTAAGA
131 TAACCTATGTAGGGTACTCTAGATTCCAGCTGCAGTATTAAGA
513612 CA
1 CA
513614 TATGAGATTA
Statistics
Matches: 174, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
172 127 0.73
173 47 0.27
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (173 bp):
CACAACTAGCTAGATTGTAACAAACAGACTTGATTTTCATCAAGTAATCTCTCATACTCAGCTCC
CCCTTCCTCTGAGAATGAAGCATTCTCCTATAGGACATTAACCTAGAAGTAGTCTTACCACTGTA
TAACCTATGTAGGGTACTCTAGATTCCAGCTGCAGTATTAAGA
Found at i:516234 original size:18 final size:18
Alignment explanation
Indices: 516211--516255 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
516201 AAATTTGTTT
516211 TAAAATAAAAGACAAGGA
1 TAAAATAAAAGACAAGGA
*
516229 TAAAATAAAAGATAAGGA
1 TAAAATAAAAGACAAGGA
*
516247 TGAAATAAA
1 TAAAATAAA
516256 TAAATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.67, C:0.02, G:0.16, T:0.16
Consensus pattern (18 bp):
TAAAATAAAAGACAAGGA
Found at i:518146 original size:21 final size:19
Alignment explanation
Indices: 518114--518152 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
518104 CCAGCTGTCG
518114 AAATGAGTTTTAAAAAAAC
1 AAATGAGTTTTAAAAAAAC
518133 AAATGTAGCTTTTAAAAAAA
1 AAATG-AG-TTTTAAAAAAA
518153 TATTGTCTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.28
Consensus pattern (19 bp):
AAATGAGTTTTAAAAAAAC
Found at i:520613 original size:22 final size:19
Alignment explanation
Indices: 520586--520637 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 19
520576 GAAATAAAGG
520586 AATAAAAAATAAAAATAATGAA
1 AATAAAAAATAAAAAT-A--AA
*
520608 AATAAAAAATGAAAATAAA
1 AATAAAAAATAAAAATAAA
520627 AATAAAAAATA
1 AATAAAAAATA
520638 GCTAGATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
21 1 0.04
22 15 0.54
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (19 bp):
AATAAAAAATAAAAATAAA
Found at i:520635 original size:13 final size:13
Alignment explanation
Indices: 520586--520637 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
520576 GAAATAAAGG
520586 AATAAAAAATAAA
1 AATAAAAAATAAA
520599 AATAATGAAAATAAA
1 AATAA--AAAATAAA
*
520614 AA-ATGAAAATAAA
1 AATA-AAAAATAAA
520627 AATAAAAAATA
1 AATAAAAAATA
520638 GCTAGATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 21 0.64
14 2 0.06
15 10 0.30
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:522965 original size:18 final size:18
Alignment explanation
Indices: 522942--522977 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
522932 GGGGATTTTG
* *
522942 GTAAAATGAGATTCAATA
1 GTAAAAAGAGATTAAATA
522960 GTAAAAAGAGATTAAATA
1 GTAAAAAGAGATTAAATA
522978 AATAAAGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.17, T:0.25
Consensus pattern (18 bp):
GTAAAAAGAGATTAAATA
Done.