Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000186.1 Hibiscus syriacus cultivar Beakdansim tig00000329_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: 3152351
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 17
Found at i:515850 original size:117 final size:107
Alignment explanation
Indices: 515651--516056 Score: 464
Period size: 117 Copynumber: 3.7 Consensus size: 107
515641 ATGCAAGGTT
* * *
515651 GAACGAGTTCTTCTCATTATGAACTTCTTTTTCCTCGTTA-GATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAA---CTTTCTCCT--TTAGGACGAGTTCTTCTCATTATGAACT
* * *
515715 CTTCACTGGAAATGTTGATTCACCTCCTTCTGTGATGAAATCGAACCAAGG
61 CTTCACTGGAAATATTGATTCACCTCTTTCTGTGATGAAATTG-A--AA-G
*
515766 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATT-GGATGAGTTCTTCTCATTATGAA
1 --GAACAAGTTCTTCTCATTATGAAC-T-TTC-TCCT--TTAGGACGAGTTCTTCTCATTATGAA
* * * *
515830 CT-TTCCACTGAAAATATTGATCCACCTCTTTATGTGATGGAACTTGAAAG
59 CTCTT-CACTGGAAATATTGATTCACCTCTTTCTGTGAT-GAAATTGAAAG
515880 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTT--
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCA
* * * *
515943 CTGGAAATATTGGTTCACATCTTTCTGTGGTGAATTTGAAAG
66 CTGGAAATATTGATTCACCTCTTTCTGTGATGAAATTGAAAG
515985 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTC-CATTATGAACTCTTCA
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCA
*
516049 TTGGAAAT
66 CTGGAAAT
516057 GTCGATCCCT
Statistics
Matches: 260, Mismatches: 19, Indels: 31
0.84 0.06 0.10
Matches are distributed among these distances:
104 14 0.05
105 58 0.22
106 32 0.12
107 2 0.01
108 24 0.09
109 6 0.02
110 3 0.01
111 1 0.00
112 24 0.09
114 2 0.01
115 3 0.01
116 4 0.02
117 82 0.32
118 5 0.02
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (107 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCA
CTGGAAATATTGATTCACCTCTTTCTGTGATGAAATTGAAAG
Found at i:516534 original size:36 final size:36
Alignment explanation
Indices: 516492--516603 Score: 107
Period size: 36 Copynumber: 3.1 Consensus size: 36
516482 AGGAAAATTG
*
516492 TCTCAAGCAAGACGAAGTAGGTTTTAAGAAAAACCA
1 TCTCAAGCAAGACAAAGTAGGTTTTAAGAAAAACCA
** * * ** * * **
516528 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
1 TCTCAAGCAAGACAAAGTAGGTTT-TAAGAAAAACCA
*
516565 TCTCAAGCCAGACAAAGTAGGTTTTAAGAAAAACCA
1 TCTCAAGCAAGACAAAGTAGGTTTTAAGAAAAACCA
516601 TCT
1 TCT
516604 GAAGTGAGAT
Statistics
Matches: 54, Mismatches: 21, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
36 28 0.52
37 26 0.48
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (36 bp):
TCTCAAGCAAGACAAAGTAGGTTTTAAGAAAAACCA
Found at i:516558 original size:73 final size:73
Alignment explanation
Indices: 516455--516701 Score: 314
Period size: 73 Copynumber: 3.4 Consensus size: 73
516445 AGAGAAGCAC
* *
516455 TCTCAAGTGAGATAAATTTTGTTCCGAAGGAAAATTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
516520 AAAAACCA
66 AAAAACCA
* * *
516528 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGCCAGACAAAGTAGGTTTTAAG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
516593 AAAAACCA
66 AAAAACCA
* ** * * * ** * *
516601 TCTGAAGTGAGATTCATTTTATTTCAAGGGAAAGTTGTCTCAAGTGAGACGAACTTGGTTTTAAG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
*
516666 AAAACCCA
66 AAAAACCA
* * *
516674 TCTCAAGGGAGACAAAACTTTGTTTCAA
1 TCTCAAGTGAGA-TAAATTTTGTTTCAA
516702 GAGAAACTGT
Statistics
Matches: 148, Mismatches: 25, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
73 138 0.93
74 10 0.07
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (73 bp):
TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
AAAAACCA
Found at i:516744 original size:28 final size:29
Alignment explanation
Indices: 516687--516744 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
516677 CAAGGGAGAC
*
516687 AAAACTTTGTTTCAAGAGAAACTGTATCA
1 AAAACTTTGTTTCAAGAGAAACTATATCA
*
516716 AAAAC-TTGTTTCAAGAGAAACTATCTCA
1 AAAACTTTGTTTCAAGAGAAACTATATCA
516744 A
1 A
516745 GGGAGACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (29 bp):
AAAACTTTGTTTCAAGAGAAACTATATCA
Found at i:516762 original size:36 final size:36
Alignment explanation
Indices: 516716--516900 Score: 289
Period size: 36 Copynumber: 5.1 Consensus size: 36
516706 AACTGTATCA
* * *
516716 AAAACTTGTTTCAAGAGAAACTATCTCAAGGGAGAC
1 AAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
*
516752 AAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGAT
1 AAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
*
516788 AAAATTTGTTTCAAGGGAAACTATCTTAAGAGAGAC
1 AAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
* *
516824 AAAATTTGTTTCGAGGGAAACTGTCTCAAGAGAGAC
1 AAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
* *
516860 AAAATTTGTTTCAAGGGAAACTATCTCAAGCGAGAT
1 AAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
516896 AAAAT
1 AAAAT
516901 CTTCTGTTTC
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 136 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
AAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
Found at i:516936 original size:40 final size:40
Alignment explanation
Indices: 516891--517181 Score: 468
Period size: 40 Copynumber: 7.4 Consensus size: 40
516881 TATCTCAAGC
* * *
516891 GAGATAAAATCTTCTGTTTCAAGAAAAAATAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
516931 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATATTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
516971 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
517011 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
517051 GAGATAAAATCTTCTGTTTC------AAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
517085 GAGATAAAATATTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
517125 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
517165 GAGATAAAATCTTCTGT
1 GAGATAAAATCTTCTGT
517182 ATTAAATGAG
Statistics
Matches: 232, Mismatches: 13, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
34 32 0.14
40 200 0.86
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:517130 original size:114 final size:115
Alignment explanation
Indices: 516891--517181 Score: 458
Period size: 114 Copynumber: 2.5 Consensus size: 115
516881 TATCTCAAGC
* * *
516891 GAGATAAAATCTTCTGTTTCAAGAAAAAATAATCTTGAGCGAGATAAAATCTTCTGTTTCAAGGA
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTC-----
* *
516956 AAAACAATATTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
61 AAAACAATATTGAGTGAGATAAAATATTCTGTTTCAAGGAAAAACAATCTTGAAT
* *
517011 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTGTTTC-AAAC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAAAC
*
517075 AATCTTGAGTGAGATAAAATATTCTGTTTCAAGGAAAAACAATCTTGAAT
66 AATATTGAGTGAGATAAAATATTCTGTTTCAAGGAAAAACAATCTTGAAT
517125 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGT
517182 ATTAAATGAG
Statistics
Matches: 161, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
114 106 0.66
120 55 0.34
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (115 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAAAC
AATATTGAGTGAGATAAAATATTCTGTTTCAAGGAAAAACAATCTTGAAT
Found at i:526787 original size:3 final size:3
Alignment explanation
Indices: 526779--526828 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
526769 GTAATAAGAT
*
526779 TAA TAA TAA TAA TAA TAA T-A TAGA TAA TAA -AA TAC TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
526822 TTAA TAA
1 -TAA TAA
526829 CATTTTTTCG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 6 0.15
3 28 0.70
4 6 0.15
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:526826 original size:20 final size:21
Alignment explanation
Indices: 526781--526828 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
526771 AATAAGATTA
526781 ATAATAATAATAATAATATAG
1 ATAATAATAATAATAATATAG
*
526802 ATAATAA-AATACTAATATA-
1 ATAATAATAATAATAATATAG
526821 ATTAATAA
1 A-TAATAA
526829 CATTTTTTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 17 0.68
21 7 0.28
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAATAATAATAATAATATAG
Found at i:532301 original size:21 final size:20
Alignment explanation
Indices: 532275--532313 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
532265 GAATTAAAAG
*
532275 TTTTAGATTTTTTTACTTTTA
1 TTTTAG-TTTGTTTACTTTTA
532296 TTTTAGTTTGTTTA-TTTT
1 TTTTAGTTTGTTTACTTTT
532314 TGGATCGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (20 bp):
TTTTAGTTTGTTTACTTTTA
Found at i:539533 original size:41 final size:42
Alignment explanation
Indices: 539455--539535 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
539445 TTATTCGGGC
* * *
539455 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCAGAT
1 CATCAGTAAGTCTTTCGACCAAGATGCATAAATCATTCAGAT
* *
539497 CATCTGTAAGTCTTTTGACCAAGATG-ATAAATCATTCAG
1 CATCAGTAAGTCTTTCGACCAAGATGCATAAATCATTCAG
539536 GCAATCCATA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 12 0.35
42 22 0.65
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGACCAAGATGCATAAATCATTCAGAT
Found at i:539755 original size:232 final size:233
Alignment explanation
Indices: 539348--540519 Score: 1340
Period size: 232 Copynumber: 5.0 Consensus size: 233
539338 TTATAAGTTA
* * * *
539348 AAAAATGAGAAAATTTTCTCATTTAAATCTAAAAATTAAAATTTTTGAAAACTAAGAAAAGTTTC
1 AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTC
* * * * * *
539413 TTACCTAGTAAACTATATCTAAAATTGGTAAGTTATTCGGGCCATCAGTAAGTCTTTCGAGCATG
66 TTACCTAGTAAACTATTTCCAAAATTAGTAAGTCATTCAGACCATCAGTAAGTCTTTCGAGCATG
* * * * *
539478 ATGCTTAAATCATTCAGATCATCTGTAAGTCTTTTGACCAAGATGATAAATCATTCAGGCAATCC
131 ATGCTTAAATCATTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCAATCC
539543 ATAAGACATTCGGGCAGGATGTTTTCACATGACTCTCG
196 ATAAGACATTCGGGCAGGATGTTTTCACATGACTCTCG
* * ** *
539581 AAAAATGAGAAAAGTTTCTCATTTAAATCGGAAAATTGAATTTTTTTTAAAGTAAGGAAAGTTTC
1 AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTC
* *
539646 TTACCTAGTAAACTATTTCCAAAATTAAT-AGTCCCTT-AGACCATCAGTAAGTCTTTCGAGCAT
66 TTACCTAGTAAACTATTTCCAAAATTAGTAAGT-CATTCAGACCATCAGTAAGTCTTTCGAGCAT
* * *
539709 GATGCTTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCGTTAAGGCAATC
130 GATGCTTAAATCATTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCAATC
* * * ** * *
539774 CATAAGACATTCGAGCATGATGTTTTTACATGTTTATCA
195 CATAAGACATTCGGGCAGGATGTTTTCACATGACTCTCG
* * * *
539813 AAAAATGAGAAATGTTTCTCATTTAAATTTGAAAATTGAAATTTTTGAGAAGTAAGGAAAGTTTC
1 AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTC
* *
539878 TTACCTAGTAAACTATTTCCAAAATTAGTAAGTTCA-TCAGACCATCAATAAGTCTTTCGAGCTT
66 TTACCTAGTAAACTATTTCCAAAATTAGTAAG-TCATTCAGACCATCAGTAAGTCTTTCGAGCAT
* *
539942 GATGTTTAAATCCTTC-GGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCAATC
130 GATGCTTAAATCATTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCAATC
* ** *
540006 CATATGA-ACTTTAGGCAGGATGTTTTCACATGTCTCT-G
195 CATAAGACA-TTCGGGCAGGATGTTTTCACATGACTCTCG
* * *
540044 AAAAATGAGAAACA-TTTCTTATTTAAATTTGAAAATTGAAATTTTTGAAAAATAGAGAAAAGTT
1 AAAAATGAGAAA-AGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTA-AGAAAAGTT
* * * *
540108 TCTTACTTAGTAAACCATTTCCAAAATTGGTAAGTATTTCGGGCCATCGGTAAGTATTTCGGGCT
64 TCTTACCTAGTAAACTATTTCCAAAATTAGTAAG----T-----CAT---TCAG-A---C---C-
* * * *
540173 ATCGGTAAGTATTTCAAGCATGATGCTTAAATCATTCAGGTCATCTGTAAGTCTTACGAGCAAGA
109 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCAGGTCATCTGTAAGTCTTTCGAGCAAGA
* * * * *
540238 TGATAAGTTCTTCGGGCCATCCATACGACCTTCGGGCAGGATGTTTTCACAT-ATCTCTCG
174 TGATAAGTCCTTCAGGCAATCCATAAGACATTCGGGCAGGATGTTTTCACATGA-CTCTCG
* *
540298 AAAAATGAGAAAAGTTTCCCATTTAAATCTGAAAACTGAAATTTTTGAAAAGTAAGAAAAGTTTC
1 AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTC
* * * *
540363 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCTTTCAGGCCATCAGTAAGTCTTTCAAGCATG
66 TTACCTAGTAAACTATTTCCAAAATTAGTAAGTCATTCAGACCATCAGTAAGTCTTTCGAGCATG
** * *
540428 ATTATTAAAT-ACTGT-GGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGAGTC-A
131 ATGCTTAAATCA-T-TCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTC-AGGCAA
* * * *
540490 TCTATAAGACCTTTGGGCAAGATGTTTTCA
193 TCCATAAGACATTCGGGCAGGATGTTTTCA
540520 TATGGTATAT
Statistics
Matches: 801, Mismatches: 103, Indels: 70
0.82 0.11 0.07
Matches are distributed among these distances:
231 50 0.06
232 317 0.40
233 218 0.27
234 5 0.01
235 2 0.00
237 1 0.00
240 2 0.00
241 3 0.00
244 5 0.01
245 1 0.00
248 1 0.00
249 1 0.00
251 1 0.00
252 30 0.04
253 116 0.14
254 48 0.06
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (233 bp):
AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTC
TTACCTAGTAAACTATTTCCAAAATTAGTAAGTCATTCAGACCATCAGTAAGTCTTTCGAGCATG
ATGCTTAAATCATTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCAATCC
ATAAGACATTCGGGCAGGATGTTTTCACATGACTCTCG
Found at i:540159 original size:20 final size:20
Alignment explanation
Indices: 540136--540187 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
540126 TTCCAAAATT
540136 GGTAAGTATTTCGGGCCATC
1 GGTAAGTATTTCGGGCCATC
*
540156 GGTAAGTATTTCGGGCTATC
1 GGTAAGTATTTCGGGCCATC
540176 GGTAAGTATTTC
1 GGTAAGTATTTC
540188 AAGCATGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (20 bp):
GGTAAGTATTTCGGGCCATC
Found at i:540408 original size:253 final size:252
Alignment explanation
Indices: 539926--540420 Score: 724
Period size: 253 Copynumber: 2.0 Consensus size: 252
539916 AGACCATCAA
* * * * * *
539926 TAAGTCTTTCGAGCTTGATGTTTAAATCCTTCGGTCATCTGTAAGTCTTTCGAGCAAGATGATAA
1 TAAGTATTTCAAGCATGATGCTTAAATCATTCGGTCATCTGTAAGTCTTACGAGCAAGATGATAA
* * *
539991 GTCCTTCAGGCAATCCATATGAACTTTAGGCAGGATGTTTTCACATGTCTCTGAAAAATGAGAAA
66 GTCCTTCAGGCAATCCATACGAACTTCAGGCAGGATGTTTTCACATATCTCTGAAAAATGAGAAA
** * * *
540056 CATTTCTTATTTAAATTTGAAAATTGAAATTTTTGAAAAATAGAGAAAAGTTTCTTACTTAGTAA
131 CATTTCCCATTTAAATCTGAAAACTGAAATTTTTGAAAAATAGAGAAAAGTTTCTTACCTAGTAA
* *
540121 ACCATTTCCAAAATTGGTAAGTATTTCGGGCCATCGGTAAGTATTTCGGGCTATCGG
196 ACCATTTCCAAAATTGGTAAGTATTTCAGGCCATCAGTAAGTATTTCGGGCTATCGG
540178 TAAGTATTTCAAGCATGATGCTTAAATCATTCAGGTCATCTGTAAGTCTTACGAGCAAGATGATA
1 TAAGTATTTCAAGCATGATGCTTAAATCATTC-GGTCATCTGTAAGTCTTACGAGCAAGATGATA
* * * * *
540243 AGTTCTTCGGGCCATCCATACGACCTTCGGGCAGGATGTTTTCACATATCTCTCGAAAAATGAGA
65 AGTCCTTCAGGCAATCCATACGAACTTCAGGCAGGATGTTTTCACATATCTCT-GAAAAATGAGA
*
540308 AA-AGTTTCCCATTTAAATCTGAAAACTGAAATTTTTGAAAAGTA-AGAAAAGTTTCTTACCTAG
129 AACA-TTTCCCATTTAAATCTGAAAACTGAAATTTTTGAAAAATAGAGAAAAGTTTCTTACCTAG
* * *
540371 TAAACTATTTCCAAAATTGGTAAGTCTTTCAGGCCATCAGTAAGTCTTTC
193 TAAACCATTTCCAAAATTGGTAAGTATTTCAGGCCATCAGTAAGTATTTC
540421 AAGCATGATT
Statistics
Matches: 215, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
252 27 0.13
253 140 0.65
254 48 0.22
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (252 bp):
TAAGTATTTCAAGCATGATGCTTAAATCATTCGGTCATCTGTAAGTCTTACGAGCAAGATGATAA
GTCCTTCAGGCAATCCATACGAACTTCAGGCAGGATGTTTTCACATATCTCTGAAAAATGAGAAA
CATTTCCCATTTAAATCTGAAAACTGAAATTTTTGAAAAATAGAGAAAAGTTTCTTACCTAGTAA
ACCATTTCCAAAATTGGTAAGTATTTCAGGCCATCAGTAAGTATTTCGGGCTATCGG
Found at i:541065 original size:20 final size:20
Alignment explanation
Indices: 541016--541067 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
541006 CACGAAATCT
* *
541016 ACGGCAGCAACACCAAATTC
1 ACGGCAGCAGCAACAAATTC
*
541036 ACGGTAGCAGCAACAAATTC
1 ACGGCAGCAGCAACAAATTC
541056 ACGGCAGCAGCA
1 ACGGCAGCAGCA
541068 GCCCTAACAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.31, G:0.21, T:0.10
Consensus pattern (20 bp):
ACGGCAGCAGCAACAAATTC
Found at i:545072 original size:25 final size:25
Alignment explanation
Indices: 545038--545096 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
545028 TTACTCTTTT
545038 TTATTT-TATATTATATTTACCTCA
1 TTATTTATATATTATATTTACCTCA
545062 TTATTTATATATTATATTTACCTCA
1 TTATTTATATATTATATTTACCTCA
545087 TTATTTATAT
1 TTATTTATAT
545097 CCTCTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 6 0.18
25 28 0.82
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATTTATATATTATATTTACCTCA
Found at i:549428 original size:24 final size:24
Alignment explanation
Indices: 549401--549455 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
549391 TCCGGCAGCT
*
549401 TCCCTTTTGACAATAGTGTCTTCA
1 TCCCTTTTGACAAAAGTGTCTTCA
549425 TCCCTTTTGACAAAAGTGTCTTCA
1 TCCCTTTTGACAAAAGTGTCTTCA
549449 TCCCTTT
1 TCCCTTT
549456 CTCGCTCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.27, G:0.11, T:0.42
Consensus pattern (24 bp):
TCCCTTTTGACAAAAGTGTCTTCA
Found at i:550841 original size:16 final size:16
Alignment explanation
Indices: 550820--550855 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
550810 AAATTTGTAT
550820 TATTTACGAAATTTAC
1 TATTTACGAAATTTAC
550836 TATTTACGAAATTTAC
1 TATTTACGAAATTTAC
550852 TATT
1 TATT
550856 CATGTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (16 bp):
TATTTACGAAATTTAC
Found at i:551470 original size:39 final size:39
Alignment explanation
Indices: 551413--551490 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
551403 AAGTATTCAG
* *
551413 AATAAAGTTCGTGGATTGAATTGCATTACTTGGTTTATC
1 AATAAAGTTCGTGAATTGAATTACATTACTTGGTTTATC
*
551452 AATAAAGTTTGTGAATTGAATTACATTACTTGGTTTATC
1 AATAAAGTTCGTGAATTGAATTACATTACTTGGTTTATC
551491 TTACAGTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (39 bp):
AATAAAGTTCGTGAATTGAATTACATTACTTGGTTTATC
Found at i:555938 original size:16 final size:16
Alignment explanation
Indices: 555917--555949 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
555907 CGAATTTGTA
555917 CAACTCA-TAAACTACT
1 CAACTCATTAAAC-ACT
555933 CAACTCATTAAACACT
1 CAACTCATTAAACACT
555949 C
1 C
555950 CTAATTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.24
Consensus pattern (16 bp):
CAACTCATTAAACACT
Found at i:564575 original size:36 final size:36
Alignment explanation
Indices: 564504--564623 Score: 147
Period size: 35 Copynumber: 3.3 Consensus size: 36
564494 ATTCCATTAT
* *
564504 TATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
564540 TATTTTTCAAAGAAATATTTACCAAACTTTGAAAAC
1 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
* *
564576 CA-TTTTCAAAAAAACATTTACCAAACTTTGAAAA-
1 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
564610 TCATTTTCTCAAAG
1 T-ATTTT-TCAAAG
564624 TTAGTTGCCA
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
35 31 0.43
36 17 0.24
37 24 0.33
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.33
Consensus pattern (36 bp):
TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:564622 original size:72 final size:69
Alignment explanation
Indices: 564507--564644 Score: 179
Period size: 72 Copynumber: 2.0 Consensus size: 69
564497 CCATTATTAT
* *
564507 TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAAATATTTACCAAACTTTGA
1 TTTTCAAAAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG--ATAGTTACCAAACTTTGA
564572 AAACCA
64 AAACCA
* * * *
564578 TTTTCAAAAAAACATTTACCAAACTTTGAAAATC-ATTTTCTCAAAGTTAGTTGCCAAACTTTGA
1 TTTTC-AAAAAACATCTACCAAACTTTGAAAAACTATTTT-TCAAAGATAGTTACCAAACTTTGA
564642 AAA
64 AAA
564645 TTAACAATAC
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
70 18 0.31
71 10 0.17
72 31 0.53
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (69 bp):
TTTTCAAAAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGATAGTTACCAAACTTTGAAA
ACCA
Found at i:564635 original size:35 final size:35
Alignment explanation
Indices: 564522--564645 Score: 133
Period size: 35 Copynumber: 3.5 Consensus size: 35
564512 AACAAACATC
*
564522 TACCAAACTTTGAAAAACTATTTT-TCAAAGAAATATT
1 TACCAAACTTTGAAAATC-ATTTTCTCAAAG--ATATT
* ** * *
564559 TACCAAACTTTGAAAACCATTTTCAAAAAAACATT
1 TACCAAACTTTGAAAATCATTTTCTCAAAGATATT
* *
564594 TACCAAACTTTGAAAATCATTTTCTCAAAGTTAGT
1 TACCAAACTTTGAAAATCATTTTCTCAAAGATATT
*
564629 TGCCAAACTTTGAAAAT
1 TACCAAACTTTGAAAAT
564646 TAACAATACT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
35 48 0.66
36 5 0.07
37 20 0.27
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (35 bp):
TACCAAACTTTGAAAATCATTTTCTCAAAGATATT
Found at i:567632 original size:15 final size:15
Alignment explanation
Indices: 567612--567643 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
567602 AAAATCTTTC
*
567612 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
567627 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
567642 TT
1 TT
567644 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:568417 original size:16 final size:17
Alignment explanation
Indices: 568389--568421 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
568379 ATCGCCGACA
568389 AAATTTCACTATTCACG
1 AAATTTCACTATTCACG
568406 AAATTT-ACTATTCACG
1 AAATTTCACTATTCACG
568422 TGAATAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (17 bp):
AAATTTCACTATTCACG
Found at i:568888 original size:37 final size:36
Alignment explanation
Indices: 568829--568947 Score: 145
Period size: 34 Copynumber: 3.3 Consensus size: 36
568819 ATCCCATTAT
* *
568829 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
568864 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
* * *
568901 CA--TTTAAAAAAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
568935 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
568948 TTGGTTGCCA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
34 31 0.44
35 1 0.01
36 8 0.11
37 31 0.44
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:573632 original size:41 final size:41
Alignment explanation
Indices: 573519--573633 Score: 153
Period size: 41 Copynumber: 2.8 Consensus size: 41
573509 ATGTACTCTA
* * * *
573519 TTGCGGTGTTTGTTTATAAACGCCACTAAAGAATGATTCTT
1 TTGCGGCGTTTGTTTAGAAACGCCACTAAAGTAGGATTCTT
573560 TTGCGGCGTTTGTTTAGAAACGCCACTAAAGTAGGATT-TT
1 TTGCGGCGTTTGTTTAGAAACGCCACTAAAGTAGGATTCTT
*
573600 GTTGCGGCGTTTGTTTTA-AAATGCCACTAAAGTA
1 -TTGCGGCGTTTG-TTTAGAAACGCCACTAAAGTA
573634 CTTATATATT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.03
41 61 0.91
42 4 0.06
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (41 bp):
TTGCGGCGTTTGTTTAGAAACGCCACTAAAGTAGGATTCTT
Found at i:574334 original size:65 final size:63
Alignment explanation
Indices: 574183--574334 Score: 243
Period size: 65 Copynumber: 2.4 Consensus size: 63
574173 AAACATCACG
*
574183 ATAAACAACATA-TTGCGGCGTTTATTATTAATCTATTGCGGCTTTTTTGCATAAACGCCACT
1 ATAAACAATATATTTGCGGCGTTTATTATTAATCTATTGCGGCTTTTTTGCATAAACGCCACT
* *
574245 ATAAACAATACTATTTGTGACGTTTATTATTAATCTATTGCGGCATTTTTTGCATAAACGCCACT
1 ATAAACAATA-TATTTGCGGCGTTTATTATTAATCTATTGCGGC-TTTTTTGCATAAACGCCACT
574310 ATAAACAATATTATTTGCGGCGTTT
1 ATAAACAATA-TATTTGCGGCGTTT
574335 GTTTTATAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
62 9 0.11
63 2 0.02
64 28 0.35
65 42 0.52
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (63 bp):
ATAAACAATATATTTGCGGCGTTTATTATTAATCTATTGCGGCTTTTTTGCATAAACGCCACT
Found at i:574455 original size:41 final size:40
Alignment explanation
Indices: 574327--574550 Score: 136
Period size: 41 Copynumber: 5.4 Consensus size: 40
574317 ATATTATTTG
* * **
574327 CGGCGTTTGTTTTATAAACGCCGCTAAATTTCTTCTCTA-TA
1 CGGCGTTTG--TTAAAAACGCCGCTAAATTACCACTCTATTA
* * * * *
574368 GCGGCGTTTGTTAAACAAATGCCACTATAAATA--ACACTATCA
1 -CGGCGTTTGTT-AA-AAACGCCGCTA-AATTACCACTCTATTA
*
574410 CGGCGTTTGTGTAAAAACGCCGCTAAATTACCACTCTATTG
1 CGGCGTTTGT-TAAAAACGCCGCTAAATTACCACTCTATTA
** * *
574451 CGGCGTTTGTTAAAAAAAAACCACTATAA--ACGTA-TCTATTA
1 CGGCGTTTGTT--AAAAACGCCGCTA-AATTAC-CACTCTATTA
* *
574492 CGGCGTTTTTGCTATAAACGCCGCTAAATTACCACTCTATTA
1 CGGCG--TTTGTTAAAAACGCCGCTAAATTACCACTCTATTA
574534 CGGCGTTTGTTTAAAAA
1 CGGCGTTTG-TTAAAAA
574551 ACACCGTTAA
Statistics
Matches: 138, Mismatches: 27, Indels: 35
0.69 0.14 0.17
Matches are distributed among these distances:
39 4 0.03
40 18 0.13
41 61 0.44
42 45 0.33
43 10 0.07
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (40 bp):
CGGCGTTTGTTAAAAACGCCGCTAAATTACCACTCTATTA
Found at i:574541 original size:83 final size:81
Alignment explanation
Indices: 574305--574551 Score: 266
Period size: 82 Copynumber: 3.0 Consensus size: 81
574295 TGCATAAACG
* * * **
574305 CCACTATAAACAATAT-TATTTGCGGCGTTTGTTTTATAAACGCCGCTAAATTTCTTCTCTA-TA
1 CCACTATAAAC--TATCTA-TTACGGCGTTT-TTGTATAAACGCCGCTAAATTACCACTCTATTA
* **
574368 GCGGCGTTTGTTAAACAAATG
62 -CGGCGTTTGTTAAAAAAAAA
* * * * *
574389 CCACTATAAA-TAACACTATCACGGCGTTTGTGTAAAAACGCCGCTAAATTACCACTCTATTGCG
1 CCACTATAAACT-A-TCTATTACGGCGTTTTTGTATAAACGCCGCTAAATTACCACTCTATTACG
574453 GCGTTTGTTAAAAAAAAA
64 GCGTTTGTTAAAAAAAAA
574471 CCACTATAAACGTATCTATTACGGCGTTTTTGCTATAAACGCCGCTAAATTACCACTCTATTACG
1 CCACTATAAAC-TATCTATTACGGCGTTTTTG-TATAAACGCCGCTAAATTACCACTCTATTACG
*
574536 GCGTTTGTTTAAAAAA
64 GCGTTTGTTAAAAAAA
574552 CACCGTTAAA
Statistics
Matches: 137, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
81 1 0.01
82 67 0.49
83 56 0.41
84 13 0.09
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (81 bp):
CCACTATAAACTATCTATTACGGCGTTTTTGTATAAACGCCGCTAAATTACCACTCTATTACGGC
GTTTGTTAAAAAAAAA
Found at i:592048 original size:31 final size:31
Alignment explanation
Indices: 592012--592070 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
592002 TTTAAAACCG
592012 TAAAATAATTTATAGA-TAAAATACAAATTCA
1 TAAAATAATTTATAGATTAAAATA-AAATTCA
* *
592043 TAAAATCATTTATATATTAAAATAAAAT
1 TAAAATAATTTATAGATTAAAATAAAAT
592071 CCACTAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (31 bp):
TAAAATAATTTATAGATTAAAATAAAATTCA
Found at i:602138 original size:31 final size:31
Alignment explanation
Indices: 602102--602175 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
602092 GGGGCCTGAT
**
602102 AGCCTACCCAAGAAAGTTCTCGGGGCCACAG
1 AGCCTACCCAAGAAAAATCTCGGGGCCACAG
* *
602133 GGCCTACCCAAGAAAAATCTCGGGGCCATAG
1 AGCCTACCCAAGAAAAATCTCGGGGCCACAG
*
602164 AGCTTACCCAAG
1 AGCCTACCCAAG
602176 GGTCGCCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (31 bp):
AGCCTACCCAAGAAAAATCTCGGGGCCACAG
Found at i:602298 original size:31 final size:31
Alignment explanation
Indices: 602193--602299 Score: 92
Period size: 31 Copynumber: 3.3 Consensus size: 31
602183 TTAGGTCCAT
* *
602193 AAGGAATTACCAGTCGGTGTTGAACCTATAC
1 AAGGAATTACCAGTCGATGCTGAACCTATAC
* * *
602224 AAGAAATTACCAG-C-AGTGACTGAACCTGCCAGAG
1 AAGGAATTACCAGTCGA-TG-CTGAACCT---ATAC
*
602258 ATAGGAATTACCAGTCGATGCTGAACATATAC
1 A-AGGAATTACCAGTCGATGCTGAACCTATAC
602290 AAGGAATTAC
1 AAGGAATTAC
602300 TAGTAGCGAC
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
30 3 0.05
31 28 0.47
32 3 0.05
34 3 0.05
35 18 0.31
36 3 0.05
37 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (31 bp):
AAGGAATTACCAGTCGATGCTGAACCTATAC
Found at i:602311 original size:66 final size:65
Alignment explanation
Indices: 602194--602322 Score: 186
Period size: 66 Copynumber: 2.0 Consensus size: 65
602184 TAGGTCCATA
* * * *
602194 AGGAATTACCAGTCGGTGTTGAACCTATACAAGAAATTACCAGCAGTGACTGAACCTGCCAGAGA
1 AGGAATTACCAGTCGATGCTGAACATATACAAGAAATTACCAGCAGCGACTGAACCT-CCAGAGA
602259 T
65 T
* * *
602260 AGGAATTACCAGTCGATGCTGAACATATACAAGGAATTACTAGTAGCGACTGAACCTCCAGAG
1 AGGAATTACCAGTCGATGCTGAACATATACAAGAAATTACCAGCAGCGACTGAACCTCCAGAG
602323 TTTTCATACC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
65 6 0.11
66 50 0.89
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (65 bp):
AGGAATTACCAGTCGATGCTGAACATATACAAGAAATTACCAGCAGCGACTGAACCTCCAGAGAT
Found at i:603421 original size:21 final size:21
Alignment explanation
Indices: 603397--603459 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
603387 GCGTAGAATT
603397 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
603418 TGTCCCGAAAGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
603439 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
603460 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.14
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:604320 original size:24 final size:20
Alignment explanation
Indices: 604267--604324 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
604257 TTCCCATTGA
*
604267 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
604287 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
604310 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
604325 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:606968 original size:27 final size:23
Alignment explanation
Indices: 606906--606971 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 23
606896 CAGTCAGACC
606906 AGTCAAC-AGTTTGACTTGGTCAA
1 AGTCAACGAG-TTGACTTGGTCAA
*
606929 AGTCAACGAGTTGACTTGGTGAA
1 AGTCAACGAGTTGACTTGGTCAA
606952 ATGACTCAATCGAGTTGACT
1 A-G--TCAA-CGAGTTGACT
606972 CATTGATTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 20 0.54
24 3 0.08
26 4 0.11
27 10 0.27
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (23 bp):
AGTCAACGAGTTGACTTGGTCAA
Found at i:610559 original size:36 final size:36
Alignment explanation
Indices: 610519--610593 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
610509 CCATTCCACG
610519 TGGCAAGAGGAGATTGTTAATGCTATTGGAAGAACC
1 TGGCAAGAGGAGATTGTTAATGCTATTGGAAGAACC
* *
610555 TGGCAAGAGGATATTGTTGATGCTATTGGAAGAACC
1 TGGCAAGAGGAGATTGTTAATGCTATTGGAAGAACC
610591 TGG
1 TGG
610594 TGTTGGATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.31, C:0.11, G:0.32, T:0.27
Consensus pattern (36 bp):
TGGCAAGAGGAGATTGTTAATGCTATTGGAAGAACC
Found at i:613551 original size:443 final size:443
Alignment explanation
Indices: 612725--613600 Score: 1707
Period size: 443 Copynumber: 2.0 Consensus size: 443
612715 AATGATCAAT
612725 AAAACCACAACCCGTACCGATTAATCCAACGTTTCTTCCATTAACACAAAGAAGAGTTACAAAAA
1 AAAACCACAACCCGTACCGATTAATCCAACGTTTCTTCCATTAACACAAAGAAGAGTTACAAAAA
612790 ACTACAAGAGACTCATAAAATATGAACAGACTCTATCTCATTATGCAGCTGGTAAGCATCCGATG
66 ACTACAAGAGACTCATAAAATATGAACAGACTCTATCTCATTATGCAGCTGGTAAGCATCCGATG
*
612855 ACATACTCCCAGATCCGCATTTGGCATCATCCATATACTGGCTCACAAACACATAGATTGCATAA
131 ACATACTCCCAGATCCGCATTTGGCATCATCCATATACTGGCCCACAAACACATAGATTGCATAA
612920 ACAAAGAATTACCATAGCCAGTTCACATTTCCCTCATAAGATCATGACAACAATTTAACAATGCT
196 ACAAAGAATTACCATAGCCAGTTCACATTTCCCTCATAAGATCATGACAACAATTTAACAATGCT
*
612985 CCATATCCTAGGCAATTTTCCAGACCACATTATCATCAATCCTAGCTTATAGCTTAGACAGGTCA
261 CCATATCCTAGGCAATTTTCCAGACCACATTATCATCAATCCTAGCTTATAGCTTAAACAGGTCA
613050 CCTGAAATTATTATTGAAGTCCTTCCCTAGTGTCCATAATCTATAAACATCAATAATGAGCAACT
326 CCTGAAATTATTATTGAAGTCCTTCCCTAGTGTCCATAATCTATAAACATCAATAATGAGCAACT
*
613115 CCAATAATAGGTTGAAACACTAGCCATTAGATCAAAACCAAGAAGAGTTACAA
391 CCAACAATAGGTTGAAACACTAGCCATTAGATCAAAACCAAGAAGAGTTACAA
613168 AAAACCACAACCCGTACCGATTAATCCAACGTTTCTTCCATTAACACAAAGAAGAGTTACAAAAA
1 AAAACCACAACCCGTACCGATTAATCCAACGTTTCTTCCATTAACACAAAGAAGAGTTACAAAAA
613233 ACTACAAGAGACTCATAAAATATGAACAGACTCTATCTCATTATGCAGCTGGTAAGCATCCGATG
66 ACTACAAGAGACTCATAAAATATGAACAGACTCTATCTCATTATGCAGCTGGTAAGCATCCGATG
613298 ACATACTCCCAGATCCGCATTTGGCATCATCCATATACTGGCCCACAAACACATAGATTGCATAA
131 ACATACTCCCAGATCCGCATTTGGCATCATCCATATACTGGCCCACAAACACATAGATTGCATAA
*
613363 TCAAAGAATTACCATAGCCAGTTCACATTTCCCTCATAAGATCATGACAACAATTTAACAATGCT
196 ACAAAGAATTACCATAGCCAGTTCACATTTCCCTCATAAGATCATGACAACAATTTAACAATGCT
*
613428 CCATATCCTAGGCAATTTTCCAGACCACATTATCATCAATCCTAGCTTATAGCTTAAACAGTTCA
261 CCATATCCTAGGCAATTTTCCAGACCACATTATCATCAATCCTAGCTTATAGCTTAAACAGGTCA
613493 CCTGAAATTATTATTGAAGTCCTTCCCTAGTGTCCATAATCTATAAACATCAATAATGAGCAACT
326 CCTGAAATTATTATTGAAGTCCTTCCCTAGTGTCCATAATCTATAAACATCAATAATGAGCAACT
613558 CCAACAATAGGTTGAAACACTAGCCATTAGATCAAAACCAAGA
391 CCAACAATAGGTTGAAACACTAGCCATTAGATCAAAACCAAGA
613601 CTGGCCCCAA
Statistics
Matches: 428, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
443 428 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (443 bp):
AAAACCACAACCCGTACCGATTAATCCAACGTTTCTTCCATTAACACAAAGAAGAGTTACAAAAA
ACTACAAGAGACTCATAAAATATGAACAGACTCTATCTCATTATGCAGCTGGTAAGCATCCGATG
ACATACTCCCAGATCCGCATTTGGCATCATCCATATACTGGCCCACAAACACATAGATTGCATAA
ACAAAGAATTACCATAGCCAGTTCACATTTCCCTCATAAGATCATGACAACAATTTAACAATGCT
CCATATCCTAGGCAATTTTCCAGACCACATTATCATCAATCCTAGCTTATAGCTTAAACAGGTCA
CCTGAAATTATTATTGAAGTCCTTCCCTAGTGTCCATAATCTATAAACATCAATAATGAGCAACT
CCAACAATAGGTTGAAACACTAGCCATTAGATCAAAACCAAGAAGAGTTACAA
Found at i:615480 original size:14 final size:15
Alignment explanation
Indices: 615431--615478 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
615421 AAATATTAAA
*
615431 TTTTGATTTGAAATT
1 TTTTAATTTGAAATT
615446 TTTTAATTTGAAATT
1 TTTTAATTTGAAATT
*
615461 TTTTAATTTAAAATT
1 TTTTAATTTGAAATT
615476 TTT
1 TTT
615479 AAGTTTCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTTAATTTGAAATT
Found at i:615709 original size:17 final size:17
Alignment explanation
Indices: 615687--615721 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
615677 GATACGTTAA
615687 AAATTCAAATCAAATTT
1 AAATTCAAATCAAATTT
*
615704 AAATTCAAATTAAATTT
1 AAATTCAAATCAAATTT
615721 A
1 A
615722 TTAAATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTCAAATCAAATTT
Found at i:615737 original size:22 final size:22
Alignment explanation
Indices: 615702--615760 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
615692 CAAATCAAAT
*
615702 TTAAATTC-AA-ATTAAATTTA
1 TTAAATTCTAATATTAAATCTA
615722 TTAAATTCTAATATTAAATCTA
1 TTAAATTCTAATATTAAATCTA
*
615744 TTTAATT-TAAATATTAA
1 TTAAATTCT-AATATTAA
615761 TTGAATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.24
21 3 0.09
22 23 0.68
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAATTCTAATATTAAATCTA
Found at i:616871 original size:229 final size:228
Alignment explanation
Indices: 616466--616952 Score: 866
Period size: 229 Copynumber: 2.1 Consensus size: 228
616456 GTAAATTATC
* * *
616466 TATCCTTTTTATAAAAGTGTCCATATTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATATTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
616531 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
616596 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
*
616661 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTTAAAAAAAGTATA
* * *
616694 TATCATTTTTATAAAAGTGTCTATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATATTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
616759 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
* *
616824 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
616889 GAAACATAAATTACATAACTTTAAAAAAAGTATA
195 GAAACATAAATTACATAACTTTAAAAAAAGTATA
616923 TATCATTTTTATAAAAGTGTCCATATTTAT
1 TATCATTTTTATAAAAGTGTCCATATTTAT
616953 AAAAGTAGGT
Statistics
Matches: 245, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
228 34 0.14
229 211 0.86
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATATTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAAGTATA
Found at i:617310 original size:160 final size:159
Alignment explanation
Indices: 617074--617408 Score: 444
Period size: 160 Copynumber: 2.1 Consensus size: 159
617064 CGGTATAGAA
* * * * *
617074 ATGATAAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATAGGATCGACAC
1 ATGATAAAACCGGTAAAACGCTACCGGATACATTAAAAGTGTCGATACTTTAATAGAATCGACAC
* * * *
617139 TTCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTT-TAAAAAATGTA
66 TTCGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAAAAAAAATATA
617203 TCGATCCAAAACGATATACCAGGT-AAAAAT
131 TCGATCCAAAACGATA-A-CAGGTAAAAAAT
* *
617233 ATGATAAAACCGGTAAAACGGTTACCGGATATA-TAAAAGTGTCGATAC-TTATATAAGAATCGA
1 ATGATAAAACCGGTAAAAC-GCTACCGGATACATTAAAAGTGTCGATACTTTA-AT-AGAATCGA
* ** *
617296 CACTTTGTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTAAAAAAAAA
63 CACTTCGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTT-AAAAAAAA
*
617361 TATATCGATCCACAACGATAACAGGTAAAAAAT
127 TATATCGATCCAAAACGATAACAGGTAAAAAAT
617394 ATGATAAAACCGGTA
1 ATGATAAAACCGGTA
617409 TCAAATGAAA
Statistics
Matches: 154, Mismatches: 16, Indels: 10
0.86 0.09 0.06
Matches are distributed among these distances:
158 3 0.02
159 32 0.21
160 73 0.47
161 22 0.14
162 24 0.16
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (159 bp):
ATGATAAAACCGGTAAAACGCTACCGGATACATTAAAAGTGTCGATACTTTAATAGAATCGACAC
TTCGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAAAAAAAATATA
TCGATCCAAAACGATAACAGGTAAAAAAT
Found at i:618589 original size:39 final size:40
Alignment explanation
Indices: 618503--618589 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 40
618493 TCCGATGCTC
*
618503 ATCAAAATTCAAAGCTCATATGGTGCCAAGCAAAAAGGAA
1 ATCAAAATTCAAAGCTCATATGATGCCAAGCAAAAAGGAA
*
618543 ATCAAAATTCAAATCTCATATGATGCCAAGC-AAAAGGAA
1 ATCAAAATTCAAAGCTCATATGATGCCAAGCAAAAAGGAA
618582 ATCAAAAT
1 ATCAAAAT
618590 CTACAACTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 16 0.36
40 29 0.64
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (40 bp):
ATCAAAATTCAAAGCTCATATGATGCCAAGCAAAAAGGAA
Found at i:619029 original size:23 final size:23
Alignment explanation
Indices: 618998--619070 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
618988 ATAGGTAAAC
*
618998 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
619021 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
619044 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
619067 ATAT
1 ATAT
619071 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:623291 original size:15 final size:15
Alignment explanation
Indices: 623271--623300 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
623261 CTTTCTCATA
623271 GTTATTGTTGGAATT
1 GTTATTGTTGGAATT
*
623286 GTTATTGTTGTAATT
1 GTTATTGTTGGAATT
623301 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGGAATT
Found at i:624166 original size:19 final size:19
Alignment explanation
Indices: 624123--624167 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
624113 ACTTGGACGG
624123 CTCGGTCAATAGGCTTACGA
1 CTCGGTCAATAGGCTTAC-A
*
624143 CTCGGTCAACTTGGCTTA-A
1 CTCGGTCAA-TAGGCTTACA
624162 CTCGGT
1 CTCGGT
624168 GAGTCAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 9 0.39
21 7 0.30
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (19 bp):
CTCGGTCAATAGGCTTACA
Found at i:624428 original size:44 final size:44
Alignment explanation
Indices: 624374--624459 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
624364 ACTCTCACTC
624374 AAACAAGATACTACAACTCACTCTTTCTAAGACTTTGCTTCTCA
1 AAACAAGATACTACAACTCACTCTTTCTAAGACTTTGCTTCTCA
624418 AAACAAGATACTACAACTCACTCTTTCTAAGACTTTGCTTCT
1 AAACAAGATACTACAACTCACTCTTTCTAAGACTTTGCTTCT
624460 TCACTCACTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.33
Consensus pattern (44 bp):
AAACAAGATACTACAACTCACTCTTTCTAAGACTTTGCTTCTCA
Found at i:637727 original size:23 final size:23
Alignment explanation
Indices: 637697--637779 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
637687 TTAGTACAAA
637697 GGGAATCGATACCCCCCTTGATG
1 GGGAATCGATACCCCCCTTGATG
* *
637720 GGGAATCGATTCCCCCCTTTGA-A
1 GGGAATCGATACCCCCC-TTGATG
* * *
637743 GGGAACCGAT-TCCCCCATG-TAG
1 GGGAATCGATACCCCCCTTGAT-G
637765 GGGAATCGATACCCC
1 GGGAATCGATACCCC
637780 TGGGGTTCTG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
21 2 0.04
22 14 0.29
23 28 0.58
24 4 0.08
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.20
Consensus pattern (23 bp):
GGGAATCGATACCCCCCTTGATG
Found at i:639105 original size:18 final size:18
Alignment explanation
Indices: 639084--639124 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
639074 AGAACAACAC
* *
639084 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACAACCA
639102 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
639120 GAGGA
1 GAGGA
639125 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.32, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Found at i:646841 original size:23 final size:24
Alignment explanation
Indices: 646811--646857 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
646801 TATACATATA
646811 ATAATAAATGCA-TTCATGAAAAT
1 ATAATAAATGCATTTCATGAAAAT
646834 ATAATAAATGCATTTCATGAAAAT
1 ATAATAAATGCATTTCATGAAAAT
646858 GGTATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.32
Consensus pattern (24 bp):
ATAATAAATGCATTTCATGAAAAT
Found at i:646974 original size:17 final size:18
Alignment explanation
Indices: 646943--646978 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
646933 TTAATACCAT
646943 ATGATTTGTTTTTTAACA
1 ATGATTTGTTTTTTAACA
646961 ATGATTTG-TTTTTAACA
1 ATGATTTGTTTTTTAACA
646978 A
1 A
646979 AAGAAATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (18 bp):
ATGATTTGTTTTTTAACA
Found at i:647834 original size:29 final size:24
Alignment explanation
Indices: 647775--647825 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
647765 ATATACATAT
647775 AATATAATAAATGCATTTCATGAA
1 AATATAATAAATGCATTTCATGAA
647799 AATATAATAAATGCATTTCATGAA
1 AATATAATAAATGCATTTCATGAA
647823 AAT
1 AAT
647826 GGTATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (24 bp):
AATATAATAAATGCATTTCATGAA
Found at i:647937 original size:19 final size:19
Alignment explanation
Indices: 647913--647949 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
647903 ATTAATACCA
647913 TATGATTTGTTTTTTAACT
1 TATGATTTGTTTTTTAACT
647932 TATGATTTGTTTTTTAAC
1 TATGATTTGTTTTTTAAC
647950 AAAAGAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.05, G:0.11, T:0.62
Consensus pattern (19 bp):
TATGATTTGTTTTTTAACT
Found at i:651665 original size:25 final size:25
Alignment explanation
Indices: 651636--651712 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 25
651626 ATTGAACCTT
*
651636 ACCCTAAACCACTTTAACCTACACA
1 ACCCTAAACCACTTTAACCTACAAA
** * *
651661 ACCCTTGACCACTCTAACCTTAAAAA
1 ACCCTAAACCACTTTAACC-TACAAA
*
651687 ACCCTAAACAACTTTAACCTACAAA
1 ACCCTAAACCACTTTAACCTACAAA
651712 A
1 A
651713 TCATTCACCA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
25 22 0.54
26 19 0.46
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.21
Consensus pattern (25 bp):
ACCCTAAACCACTTTAACCTACAAA
Found at i:651712 original size:26 final size:26
Alignment explanation
Indices: 651636--651712 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
651626 ATTGAACCTT
*
651636 ACCCTAAACCACTTTAACCTAC-ACA
1 ACCCTAAACCACTTTAACCTACAAAA
** *
651661 ACCCTTGACCACTCTAACCTTA-AAAA
1 ACCCTAAACCACTTTAACC-TACAAAA
*
651687 ACCCTAAACAACTTTAACCTACAAAA
1 ACCCTAAACCACTTTAACCTACAAAA
651713 TCATTCACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
25 18 0.44
26 23 0.56
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.21
Consensus pattern (26 bp):
ACCCTAAACCACTTTAACCTACAAAA
Found at i:651725 original size:25 final size:25
Alignment explanation
Indices: 651636--651726 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
651626 ATTGAACCTT
* *
651636 ACCCTAAACCACTTTAACCTACACA
1 ACCCTTAACCACTTTAACCTACAAA
* * *
651661 ACCCTTGACCACTCTAACCTTAAAAA
1 ACCCTTAACCACTTTAACC-TACAAA
* *
651687 ACCCTAAACAACTTTAACCTACAAA
1 ACCCTTAACCACTTTAACCTACAAA
* * *
651712 ATCATTCACCACTTT
1 ACCCTTAACCACTTT
651727 CATCTTAAGG
Statistics
Matches: 50, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
25 31 0.62
26 19 0.38
ACGTcount: A:0.40, C:0.35, G:0.01, T:0.24
Consensus pattern (25 bp):
ACCCTTAACCACTTTAACCTACAAA
Found at i:652318 original size:29 final size:30
Alignment explanation
Indices: 652272--652333 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
652262 CCCTTAAAAA
*
652272 TTTTAATTTAATATATATATTTTTTATATTT
1 TTTTAAATTAATATATATA-TTTTTATATTT
*
652303 TTTTAAATTAA-A-ATATATTTTTGTATTT
1 TTTTAAATTAATATATATATTTTTATATTT
652331 TTT
1 TTT
652334 GTATTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 13 0.45
29 5 0.17
30 1 0.03
31 10 0.34
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (30 bp):
TTTTAAATTAATATATATATTTTTATATTT
Found at i:656539 original size:16 final size:16
Alignment explanation
Indices: 656518--656548 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
656508 AAAAATAAAT
*
656518 AAAAATAATTTATTAA
1 AAAAATAAATTATTAA
656534 AAAAATAAATTATTA
1 AAAAATAAATTATTA
656549 TTTATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAATAAATTATTAA
Found at i:656856 original size:21 final size:21
Alignment explanation
Indices: 656817--656857 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
656807 TAAAACATAC
* *
656817 TATTCAAATTAAAATATTAAT
1 TATTAAAATTAAAAGATTAAT
*
656838 TATTAAAATTAAAGGATTAA
1 TATTAAAATTAAAAGATTAA
656858 ATCTGTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
TATTAAAATTAAAAGATTAAT
Found at i:657944 original size:3 final size:3
Alignment explanation
Indices: 657938--657994 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
657928 AATAATTATT
** *
657938 TAA TAA TAA T-A TAA TAA TAA TAA TTTT TAA TAA TAA TAA -ATT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TA-A TAA
657983 TAA TAA TAA TAA
1 TAA TAA TAA TAA
657995 AATTTAAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 3 0.07
3 39 0.89
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:657992 original size:31 final size:28
Alignment explanation
Indices: 657927--657989 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 28
657917 AATGGGTTTG
657927 TAATAATTATTTAATAATAATATAATAA
1 TAATAATTATTTAATAATAATATAATAA
657955 TAATAATT-TTTAATAATAATA-AATTTAA
1 TAATAATTATTTAATAATAATATAA--TAA
657983 TAATAAT
1 TAATAAT
657990 AATAAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 2 0.06
27 13 0.39
28 18 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TAATAATTATTTAATAATAATATAATAA
Found at i:658864 original size:76 final size:76
Alignment explanation
Indices: 658125--658837 Score: 1347
Period size: 76 Copynumber: 9.4 Consensus size: 76
658115 AAATGTTCGA
* *
658125 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
658190 AGGCTTTTTGG
66 AGGCTTTTTGG
*
658201 AAACATCATGCACTAAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
658266 AGGCTTTTTGG
66 AGGCTTTTTGG
*
658277 AAACATCATGCACTGAAGGACTTACAGATGATCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
658342 AGACTTTTTGG
66 AGGCTTTTTGG
658353 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
658418 AGGCTTTTTGG
66 AGGCTTTTTGG
658429 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
658494 AGGCTTTTTGG
66 AGGCTTTTTGG
658505 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
658570 AGGCTTTTTGG
66 AGGCTTTTTGG
*
658581 AAACATCATGCACTGAAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
658646 AGGCTTTTTGG
66 AGGCTTTTTGG
658657 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
658721 AGGCTTTTTGG
66 AGGCTTTTTGG
*
658732 AAACATCATGCACTGAAGGACTTACAGATTACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
658797 AGGCTTTTTGG
66 AGGCTTTTTGG
*
658808 AAACATCATGCACTGAAGGATTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
658838 TGGGAAATAG
Statistics
Matches: 623, Mismatches: 13, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
75 74 0.12
76 549 0.88
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:659519 original size:22 final size:22
Alignment explanation
Indices: 659493--659547 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
659483 GATAAAGATT
* *
659493 TCATCTTTGAAAAGATAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
659515 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
659537 TCATCTTTGAA
1 TCATCTTTGAA
659548 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:662168 original size:115 final size:114
Alignment explanation
Indices: 661991--662217 Score: 364
Period size: 115 Copynumber: 2.0 Consensus size: 114
661981 GATCATGCAG
* * * * *
661991 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCTTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAAATAACTCAAAGA
* *
662056 ACACTTCCAGAAGATGTTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAATCTTCTTATTTCTACTATGAGCAAA
* *
662105 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAAATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATCGG-TTCTGGGGTTCATACCAAACCAGATCAAATAACTCAAAG
662170 AACACTTCCAGAAGATGCTATTGAATCTTCTTATTTCTACTATGAGCA
65 AACACTTCCAGAAGATGCTATTGAATCTTCTTATTTCTACTATGAGCA
662218 CATGACACTT
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
114 23 0.22
115 80 0.78
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAAATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAATCTTCTTATTTCTACTATGAGCAAA
Found at i:664802 original size:2 final size:2
Alignment explanation
Indices: 664795--664824 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
664785 ACAGTAAAGG
664795 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
664825 TAAAGGATAA
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:667098 original size:21 final size:21
Alignment explanation
Indices: 667059--667098 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
667049 TGCAACATGA
*
667059 AAAATGCAAAGATGCAAAATG
1 AAAATGCAAAGATGAAAAATG
* *
667080 AAAATGCATATATGAAAAA
1 AAAATGCAAAGATGAAAAA
667099 GGTGTTACTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.07, G:0.15, T:0.17
Consensus pattern (21 bp):
AAAATGCAAAGATGAAAAATG
Found at i:670183 original size:16 final size:16
Alignment explanation
Indices: 670162--670192 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
670152 AAAAATAAAT
*
670162 AAAAATAATTTATTAA
1 AAAAATAAATTATTAA
670178 AAAAATAAATTATTA
1 AAAAATAAATTATTA
670193 TTTATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAATAAATTATTAA
Found at i:670500 original size:21 final size:21
Alignment explanation
Indices: 670461--670501 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
670451 TAAAACATAC
* *
670461 TATTCAAATTAAAATATTAAT
1 TATTAAAATTAAAAGATTAAT
*
670482 TATTAAAATTAAAGGATTAA
1 TATTAAAATTAAAAGATTAA
670502 ATCTGTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
TATTAAAATTAAAAGATTAAT
Found at i:671576 original size:11 final size:11
Alignment explanation
Indices: 671560--671623 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 11
671550 AATGGGTTTG
* *
671560 TAATAATTATT
1 TAATAATAATA
671571 TAATAATAATA
1 TAATAATAATA
671582 TAATAAT-A-A
1 TAATAATAATA
* *
671591 TAATATTTA-A
1 TAATAATAATA
*
671601 TAATAATAAATT
1 TAATAAT-AATA
671613 TAATAATAATA
1 TAATAATAATA
671624 ATAAAATTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
9 7 0.16
10 9 0.21
11 20 0.47
12 7 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATAATAATA
Found at i:671577 original size:3 final size:3
Alignment explanation
Indices: 671571--671627 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
671561 AATAATTATT
* *
671571 TAA TAA TAA T-A TAA TAA TAA TAA TATT TAA TAA TAA TAA -ATT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA
671616 TAA TAA TAA TAA
1 TAA TAA TAA TAA
671628 AATTTAAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 3 0.07
3 40 0.87
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:671626 original size:31 final size:27
Alignment explanation
Indices: 671560--671623 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 27
671550 AATGGGTTTG
671560 TAATAATTATTTAATAATAATATAATAA
1 TAATAA-TATTTAATAATAATATAATAA
671588 TAATAATATTTAATAATAATA-AATTTAA
1 TAATAATATTTAATAATAATATAA--TAA
671616 TAATAATA
1 TAATAATA
671624 ATAAAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 2 0.06
27 15 0.44
28 17 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TAATAATATTTAATAATAATATAATAA
Found at i:679902 original size:21 final size:21
Alignment explanation
Indices: 679878--679922 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
679868 CATTTTAATT
* *
679878 TATTTTTTTATTTGAAAAAAA
1 TATTTTTTAATATGAAAAAAA
679899 TATTTTTTAATATGAAAAAAA
1 TATTTTTTAATATGAAAAAAA
679920 TAT
1 TAT
679923 GCCACATGGA
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:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TATTTTTTAATATGAAAAAAA
Found at i:680700 original size:32 final size:32
Alignment explanation
Indices: 680659--680750 Score: 121
Period size: 32 Copynumber: 2.9 Consensus size: 32
680649 ATTGACACTC
* *
680659 ATGTGCATTATCTAAATGTAACACTAACTCTG
1 ATGTACATTATCTAAATGTAATACTAACTCTG
* *
680691 TTGTACATTATCTAAATGTAATACTTACTCTG
1 ATGTACATTATCTAAATGTAATACTAACTCTG
* * *
680723 ATGTGCATTATTTGAATGTAATACTAAC
1 ATGTACATTATCTAAATGTAATACTAAC
680751 ACTACTATGC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (32 bp):
ATGTACATTATCTAAATGTAATACTAACTCTG
Found at i:690713 original size:28 final size:27
Alignment explanation
Indices: 690627--690715 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 27
690617 TTTTAAAATA
* * *
690627 ATTAAAATAATATATTTTATAGTAATAT
1 ATTATAATAATATATTTTATAAT-ATTT
*
690655 ATTTATAATCAATTATTATTTT-TAA-AATT
1 A-TTATAAT-AA-TA-TATTTTATAATATTT
690684 ATTATAATAATATATTTTATAATATTTT
1 ATTATAATAATATATTTTATAATA-TTT
690712 ATTA
1 ATTA
690716 AATTTTTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
25 6 0.12
26 5 0.10
27 3 0.06
28 14 0.29
29 9 0.18
30 2 0.04
31 4 0.08
32 6 0.12
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (27 bp):
ATTATAATAATATATTTTATAATATTT
Found at i:690714 original size:15 final size:15
Alignment explanation
Indices: 690632--690707 Score: 74
Period size: 15 Copynumber: 5.3 Consensus size: 15
690622 AAATAATTAA
690632 AATAATATATTTTAT
1 AATAATATATTTTAT
*
690647 AGTAATATA-TTTAT
1 AATAATATATTTTAT
690661 AATCAATTATTATTTT-T
1 AAT-AA-TA-TATTTTAT
690678 AA-AAT-TA--TTAT
1 AATAATATATTTTAT
690689 AATAATATATTTTAT
1 AATAATATATTTTAT
690704 AATA
1 AATA
690708 TTTTATTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
10 2 0.04
11 3 0.06
12 5 0.10
13 2 0.04
14 8 0.16
15 20 0.40
16 2 0.04
17 5 0.10
18 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:692072 original size:24 final size:24
Alignment explanation
Indices: 692045--692107 Score: 108
Period size: 24 Copynumber: 2.5 Consensus size: 24
692035 TGCATCGTAA
692045 GATAAATGTCATTAGCTATGTAGG
1 GATAAATGTCATTAGCTATGTAGG
692069 GATAAATGTCATTAGCTATGTAGG
1 GATAAATGTCATTAGCTATGTAGG
692093 GATAAAATAGTCATT
1 GAT-AAAT-GTCATT
692108 TCACATTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 27 0.73
25 4 0.11
26 6 0.16
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (24 bp):
GATAAATGTCATTAGCTATGTAGG
Found at i:693276 original size:148 final size:147
Alignment explanation
Indices: 693009--693304 Score: 524
Period size: 148 Copynumber: 2.0 Consensus size: 147
692999 ACATAAAAAT
*
693009 TCATCATTTCATTATTCATTCAACAATCAAAGTATAACATAATTTATTATAGGTCATTTATACAA
1 TCATCATTTCATTATTCATTCAACAATCAAAGTATAACACAATTTATTATAGGTCATTTATACAA
693074 TAGCAAATAAAAAGAGTAAATTAGCATACACTTAATCAAGGATCCCATATTACCTCAAAATAAAA
66 TAGCAAATAAAAAGAGTAAATTAGCATACACTTAATCAAGGATCCCATATTACCTCAAAATAAAA
693139 CCAAGGTTCAAAATAAC
131 CCAAGGTTCAAAATAAC
*
693156 TCATCATTTCATTATTCATTCAA-GATCAAAGTATAACACAATTTATTATAGGTCATTTATACAA
1 TCATCATTTCATTATTCATTCAACAATCAAAGTATAACACAATTTATTATAGGTCATTTATACAA
693220 TAG-AAAGTGTAAAAAGAGTAAATTAGCATACACTTAATCAAGGATCCCATATTACCTCAAAATA
66 TAGCAAA---TAAAAAGAGTAAATTAGCATACACTTAATCAAGGATCCCATATTACCTCAAAATA
*
693284 AAACCAATGTTCAAAATAAC
128 AAACCAAGGTTCAAAATAAC
693304 T
1 T
693305 TTCCAAAAGC
Statistics
Matches: 143, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
145 3 0.02
146 42 0.29
147 23 0.16
148 75 0.52
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (147 bp):
TCATCATTTCATTATTCATTCAACAATCAAAGTATAACACAATTTATTATAGGTCATTTATACAA
TAGCAAATAAAAAGAGTAAATTAGCATACACTTAATCAAGGATCCCATATTACCTCAAAATAAAA
CCAAGGTTCAAAATAAC
Found at i:698547 original size:3 final size:3
Alignment explanation
Indices: 698539--698579 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
698529 ATGTACATTA
*
698539 AAT AAT AAT AAT AAT AAT AAT AAT AATT AA- AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AA
698580 AAAAGACCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:698971 original size:134 final size:134
Alignment explanation
Indices: 698721--699210 Score: 712
Period size: 134 Copynumber: 3.7 Consensus size: 134
698711 GTTTGATGGT
** * * * *
698721 GGGGATGACATTGCTCATATGTGATGAAGAATTCGTGGCCATCTTTAAGAAGGGTGATAACTCGA
1 GGGGATGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTTTAGGAAGGGTGATAACTCGG
* * * * * *
698786 TTTCTACGTGATGAGGACGACTGGTTAACT-GGGGTGACACGGTTCATACGTGATGAGGAGTTCT
65 TTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCT
698850 GGTCG
130 GGTCG
* * *
698855 GTGGATGACACGGCTCATACGTGATGAAGAGTTCTAGCCATCTTTAGGAAGGGTGATAACTTGGT
1 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGT
*
698920 TCCTACGCGATGAGGACAACTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTG
66 TCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTG
*
698985 GTTG
131 GTCG
* * *
698989 GGGGATGACACGGCTTATACGTGATGAAGAGTTCTTGTCATCTTTAGGAAGGGTGATAACTCGGT
1 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGT
* * *
699054 TCCTACGCGATGAGGATGGCTGGTTATCTAGGAGTGACACGGCTCATACGTGATGAAGAGATCTG
66 TCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTG
699119 GTCG
131 GTCG
* * *
699123 GGGGATGACACGGCTCATACATAATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGT
1 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGT
* *
699188 TCCTAAGCGATGAGGACGGCTGG
66 TCCTACGCGATGAGGACGACTGG
699211 CCATCTTTAA
Statistics
Matches: 322, Mismatches: 33, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
133 52 0.16
134 270 0.84
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (134 bp):
GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGT
TCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTG
GTCG
Found at i:699356 original size:44 final size:44
Alignment explanation
Indices: 699306--699390 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
699296 TCCAAGGAAA
*
699306 TGACTCAAAGATGGTTTTGTTTCAAGAGAAACATA-CTCAAATGT
1 TGACTCAAAAATGGTTTTGTTTCAAGAGAAACA-ACCTCAAATGT
*
699350 TGACTCAAAAATTGTTTTGTTTCAAGAGAAACAACCTCAAA
1 TGACTCAAAAATGGTTTTGTTTCAAGAGAAACAACCTCAAA
699391 GATTTTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 1 0.03
44 37 0.97
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (44 bp):
TGACTCAAAAATGGTTTTGTTTCAAGAGAAACAACCTCAAATGT
Found at i:699781 original size:30 final size:30
Alignment explanation
Indices: 699723--699782 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
699713 AGAGACAAAA
*
699723 TTTTGTTTCAACAGAAATAGAATCAAAGATC
1 TTTTGTTTCAAAAGAAATA-AATCAAAGATC
*
699754 TTTTGTTTCAAAAGGAAAT-ACTCAAAGAT
1 TTTTGTTTCAAAA-GAAATAAATCAAAGAT
699783 GATAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 9 0.35
31 12 0.46
32 5 0.19
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAATAAATCAAAGATC
Found at i:699820 original size:129 final size:133
Alignment explanation
Indices: 699572--699884 Score: 386
Period size: 131 Copynumber: 2.4 Consensus size: 133
699562 TATGAAAAAT
* * * * *
699572 TGTCTCAAGAGAGACAAAACTTTATTTCAAAAGAAAAACACTCAAAGATGGGTTTTGTTTCAAGG
1 TGTCTCAAGAGAGACAAAATTTTGTTTCAAAAGAAAAAGACTCAAAGAT-GCTTTTGTTTCAAAG
** * * *
699637 GAAACAGACTCACGGATGGTAAATGTTGTTTCCAAAGAAACAGACTCAAAGA-TTTT-TCAAAAG
65 GAAACAGACTCAAAGATGATAAATGTTGTTTACAAAGAAACAGAATCAAAGATTTTTCTCAAAAG
699700 AAAC
130 AAAC
* * *
699704 TGTCTCAAGAGAGACAAAATTTTGTTTCAACAGAAATAGAATCAAAGAT-CTTTTGTTTCAAAAG
1 TGTCTCAAGAGAGACAAAATTTTGTTTCAAAAGAAAAAGACTCAAAGATGCTTTTGTTTC-AAAG
* * *
699768 G-AA-ATACTCAAAGATGATAAATTTTGTTTACAAAGAAACAGAATCAAAGATTTTTCTCAAAAT
65 GAAACAGACTCAAAGATGATAAATGTTGTTTACAAAGAAACAGAATCAAAGATTTTTCTCAAAAG
699831 AAAC
130 AAAC
* * *
699835 TGTCTCAAGAGTGACAAAATTTTGTTT-ACAGAGAAACAGACTCAAAGATG
1 TGTCTCAAGAGAGACAAAATTTTGTTTCA-AAAGAAAAAGACTCAAAGATG
699885 GATTATGTCT
Statistics
Matches: 156, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
129 40 0.26
130 16 0.10
131 57 0.37
132 43 0.28
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (133 bp):
TGTCTCAAGAGAGACAAAATTTTGTTTCAAAAGAAAAAGACTCAAAGATGCTTTTGTTTCAAAGG
AAACAGACTCAAAGATGATAAATGTTGTTTACAAAGAAACAGAATCAAAGATTTTTCTCAAAAGA
AAC
Found at i:699870 original size:65 final size:64
Alignment explanation
Indices: 699657--699883 Score: 250
Period size: 63 Copynumber: 3.5 Consensus size: 64
699647 CACGGATGGT
* * * *
699657 AAATGTTGTTTCCAAAGAAACAGACTCAAAGA-TTTTTCAAAAGAAACTGTCTCAAGAGAGACA
1 AAATTTTGTTTACAAAGAAACAGAATCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGTGACA
* *
699720 AAATTTTGTTT-CAACAGAAATAGAATCAAAGATCTTTTGTTTCAAAAGGAAA-T-ACTCAA-AG
1 AAATTTTGTTTACAA-AGAAACAGAATCAAAGA---TTT-TTTCAAAA-GAAACTGTCTCAAGAG
*
699781 ATGA-T
60 -TGACA
*
699786 AAATTTTGTTTACAAAGAAACAGAATCAAAGATTTTTCTCAAAATAAACTGTCTCAAGAGTGACA
1 AAATTTTGTTTACAAAGAAACAGAATCAAAGATTTTT-TCAAAAGAAACTGTCTCAAGAGTGACA
* *
699851 AAATTTTGTTTACAGAGAAACAGACTCAAAGAT
1 AAATTTTGTTTACAAAGAAACAGAATCAAAGAT
699884 GGATTATGTC
Statistics
Matches: 138, Mismatches: 12, Indels: 26
0.78 0.07 0.15
Matches are distributed among these distances:
62 8 0.06
63 35 0.25
64 8 0.06
65 33 0.24
66 29 0.21
67 12 0.09
68 9 0.07
69 4 0.03
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.28
Consensus pattern (64 bp):
AAATTTTGTTTACAAAGAAACAGAATCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGTGACA
Found at i:700432 original size:104 final size:104
Alignment explanation
Indices: 700244--700548 Score: 355
Period size: 104 Copynumber: 2.9 Consensus size: 104
700234 ATTGATTTTG
* * * * * * *
700244 ACAATCTCAAGTGAAATTAATTTTGTTTCAAGTAAAACAACTTTGAAATTTGTATTCTAAGGGAA
1 ACAATCTCAAGTGAGATTAATTTTGTTTAAAGTGAAACAAATTCGAAATTTGTATTCAAAGGAAA
* * *
700309 AATGTCTCAAGTGAGACGAAATTTGTTTTGAAATAAACA
66 AATGTCTCAAGCGAGACGAAATATGTTTTGAAAGAAACA
* *
700348 ACAATCTCAAGTGAGATTAATTTTG-TTAAAGTGAAGCAAATTCAAAATTT-TCATATCAAAGGA
1 ACAATCTCAAGTGAGATTAATTTTGTTTAAAGTGAAACAAATTCGAAATTTGT-AT-TCAAAGGA
*
700411 AAAATGTCTCAAGCGCA-ACGAAATATGTTTTGAAAGAAATA
64 AAAATGTCTCAAGCG-AGACGAAATATGTTTTGAAAGAAACA
* * *
700452 ACAATATCAAGTGAGATTAATTTTGTTTAAAGTGAATCAAATTCGAAATTTGTATCTCAAAGAAA
1 ACAATCTCAAGTGAGATTAATTTTGTTTAAAGTGAAACAAATTCGAAATTTGTAT-TCAAAG-GA
* * * *
700517 AATAATGTCTCAAACAAGATGAAATTTGTTTT
64 AA-AATGTCTCAAGCGAGACGAAATATGTTTT
700549 TTAGAGAGAT
Statistics
Matches: 171, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
102 1 0.01
103 21 0.12
104 89 0.52
105 32 0.19
106 5 0.03
107 23 0.13
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (104 bp):
ACAATCTCAAGTGAGATTAATTTTGTTTAAAGTGAAACAAATTCGAAATTTGTATTCAAAGGAAA
AATGTCTCAAGCGAGACGAAATATGTTTTGAAAGAAACA
Found at i:700657 original size:35 final size:36
Alignment explanation
Indices: 700608--700681 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 36
700598 AATTTGTGGA
*
700608 AAATTTTCTCAAGCGAGATAGAA-TTTGTTTTTAGAG
1 AAATTTTCTCAAGCGAGACA-AAGTTTGTTTTTAGAG
*
700644 AAATTTT-TCAAGCGAGACAAAGTTTGTTTTTTGAG
1 AAATTTTCTCAAGCGAGACAAAGTTTGTTTTTAGAG
700679 AAA
1 AAA
700682 ACGATCTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
34 2 0.06
35 26 0.74
36 7 0.20
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (36 bp):
AAATTTTCTCAAGCGAGACAAAGTTTGTTTTTAGAG
Found at i:700792 original size:36 final size:36
Alignment explanation
Indices: 700744--700884 Score: 135
Period size: 35 Copynumber: 3.9 Consensus size: 36
700734 TATCTCAAAG
*
700744 GAAAATGTCTCAAGCGAGACGAAATTTGTTTTTCAA
1 GAAATTGTCTCAAGCGAGACGAAATTTGTTTTTCAA
* * **
700780 GAAATTGTCTCAAACGATAC-AAATTT-TTTTTTTA
1 GAAATTGTCTCAAGCGAGACGAAATTTGTTTTTCAA
* *
700814 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTCCAAAA
1 G-AAATTGTCTCAAGCGAGACGAAATTTGTTTTTC--AA
* *
700853 GAAGTTGTCT-ATAGCGAGACGACATTTTGTTT
1 GAAATTGTCTCA-AGCGAGACGA-AATTTGTTT
700885 CGAGAGAAAC
Statistics
Matches: 85, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
34 7 0.08
35 23 0.27
36 23 0.27
37 5 0.06
38 17 0.20
39 10 0.12
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (36 bp):
GAAATTGTCTCAAGCGAGACGAAATTTGTTTTTCAA
Found at i:702560 original size:18 final size:18
Alignment explanation
Indices: 702532--702610 Score: 87
Period size: 17 Copynumber: 4.6 Consensus size: 18
702522 TTGTCCTCTT
702532 TTTGTTCTTTGCTCTTTTC
1 TTTGTTCTTTGCT-TTTTC
702551 TTTGTT-TTTGCTTTTTC
1 TTTGTTCTTTGCTTTTTC
702568 TTT-TTCTTT--TTTTTC
1 TTTGTTCTTTGCTTTTTC
* *
702583 -TTGCTCTTTGTTTTTTC
1 TTTGTTCTTTGCTTTTTC
702600 TTTGCTTCTTT
1 TTTG-TTCTTT
702611 TCTCTTTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
14 2 0.04
15 11 0.21
16 2 0.04
17 17 0.33
18 9 0.17
19 11 0.21
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (18 bp):
TTTGTTCTTTGCTTTTTC
Found at i:702608 original size:25 final size:24
Alignment explanation
Indices: 702537--702623 Score: 66
Period size: 25 Copynumber: 3.5 Consensus size: 24
702527 CTCTTTTTGT
* *
702537 TCTTTGCTCTTTTCTTTGTTTTTGC
1 TCTTTG-TTTTTTCTTTGTTCTTGC
* * * *
702562 TTTTTCTTTTTCTTTTTTTTCTTGC
1 TCTTTGTTTTT-TCTTTGTTCTTGC
*
702587 TCTTTGTTTTTTCTTTGCTTCTTTTC
1 TCTTTGTTTTTTCTTTG-TTC-TTGC
*
702613 TCTTTATTTTT
1 TCTTTGTTTTT
702624 CTGTTCTCTT
Statistics
Matches: 47, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
24 8 0.17
25 26 0.55
26 13 0.28
ACGTcount: A:0.01, C:0.17, G:0.07, T:0.75
Consensus pattern (24 bp):
TCTTTGTTTTTTCTTTGTTCTTGC
Found at i:703941 original size:13 final size:14
Alignment explanation
Indices: 703911--703945 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
703901 TGCAAAGATG
703911 AAAATGCAGATACA
1 AAAATGCAGATACA
703925 AAAATGCAGATACA
1 AAAATGCAGATACA
703939 AAAATGC
1 AAAATGC
703946 TGATCCCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAATGCAGATACA
Found at i:704488 original size:31 final size:31
Alignment explanation
Indices: 704432--704491 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
704422 TGACAAAATG
*
704432 ACACAAAAAAAGAGAAGAAATAAGTTAGTGT
1 ACACAAAAAAAGAGAAGAAACAAGTTAGTGT
704463 ACACAAACAAAAGAGAA-AAACAAGTTAGT
1 ACACAAA-AAAAGAGAAGAAACAAGTTAGT
704492 ACATGTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.60, C:0.10, G:0.17, T:0.13
Consensus pattern (31 bp):
ACACAAAAAAAGAGAAGAAACAAGTTAGTGT
Found at i:704609 original size:32 final size:32
Alignment explanation
Indices: 704563--704643 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
704553 GTCATAATAT
* *
704563 CTACCCGAAAATGCTTTCAATAGACAGCAATC
1 CTACCCGGACATGCTTTCAATAGACAGCAATC
704595 CTACCCGGACATGCTTTCAATAGACAGCAATC
1 CTACCCGGACATGCTTTCAATAGACAGCAATC
704627 CTACCCGGACATGCTTT
1 CTACCCGGACATGCTTT
704644 TTACCCACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (32 bp):
CTACCCGGACATGCTTTCAATAGACAGCAATC
Found at i:714482 original size:21 final size:21
Alignment explanation
Indices: 714442--714482 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
714432 ACTCATTACT
*
714442 ACTCAATAATCATTTCTTTAA
1 ACTCAATAATCATATCTTTAA
714463 ACTCAAT-ATCATATCATTTA
1 ACTCAATAATCATATC-TTTA
714483 TATGGCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (21 bp):
ACTCAATAATCATATCTTTAA
Found at i:721636 original size:22 final size:21
Alignment explanation
Indices: 721611--721652 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
721601 TAACAAGCAA
*
721611 TAAAGAATGATATGGTAAAAAG
1 TAAAAAATGATATGG-AAAAAG
721633 TAAAAAATGATATGGAAAAA
1 TAAAAAATGATATGGAAAAA
721653 TTACGTTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (21 bp):
TAAAAAATGATATGGAAAAAG
Found at i:724225 original size:3 final size:3
Alignment explanation
Indices: 724198--724247 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
724188 TGGTGAAAGA
*
724198 AAG ATG AAG AAG ATA- AAGG AA- AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG A-AG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG
724243 AAG AA
1 AAG AA
724248 TCAATGGCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (3 bp):
AAG
Found at i:731067 original size:21 final size:23
Alignment explanation
Indices: 731043--731085 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
731033 GTCTGATAAA
*
731043 CATATAT-C-CTCCACCTGACCT
1 CATATATACTCTCCACCCGACCT
731064 CATATATACTCTCCACCCGACC
1 CATATATACTCTCCACCCGACC
731086 CTGATCAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.26, C:0.44, G:0.05, T:0.26
Consensus pattern (23 bp):
CATATATACTCTCCACCCGACCT
Found at i:732975 original size:19 final size:20
Alignment explanation
Indices: 732948--732986 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
732938 ATTTCATGAT
732948 ACAATTCATGTATCATAGAG
1 ACAATTCATGTATCATAGAG
732968 ACAA-TCATGTATCATAGAG
1 ACAATTCATGTATCATAGAG
732987 TTCATAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
ACAATTCATGTATCATAGAG
Found at i:735996 original size:33 final size:33
Alignment explanation
Indices: 735954--736020 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
735944 TACGTCATCC
*
735954 AAATTAATGGATTTTTAATTTTTAAAATGTAAA
1 AAATTAATGGAATTTTAATTTTTAAAATGTAAA
735987 AAATTAATGGAATTTTAATTTTTAAAATGTAAA
1 AAATTAATGGAATTTTAATTTTTAAAATGTAAA
736020 A
1 A
736021 TAGGTAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (33 bp):
AAATTAATGGAATTTTAATTTTTAAAATGTAAA
Found at i:736316 original size:25 final size:24
Alignment explanation
Indices: 736270--736317 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
736260 CAGGTAAAAT
* * *
736270 GAAATTTTTTGAAATTTGAAATAG
1 GAAATTTTTTAAAATATAAAATAG
736294 GAAATATTTTTAAAATATAAAATA
1 GAAAT-TTTTTAAAATATAAAATA
736318 TGATTTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (24 bp):
GAAATTTTTTAAAATATAAAATAG
Found at i:751048 original size:10 final size:10
Alignment explanation
Indices: 751033--751060 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
751023 TTATGAGATT
751033 ACTATTCATC
1 ACTATTCATC
751043 ACTATTCATC
1 ACTATTCATC
751053 ACTATTCA
1 ACTATTCA
751061 CGTGAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
ACTATTCATC
Found at i:755135 original size:16 final size:17
Alignment explanation
Indices: 755105--755139 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
755095 TGGAAGATTG
755105 TTGGAAAAGAGTCAAAA
1 TTGGAAAAGAGTCAAAA
755122 TTGGAAAA-AGTCAAAA
1 TTGGAAAAGAGTCAAAA
755138 TT
1 TT
755140 AGTGGGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (17 bp):
TTGGAAAAGAGTCAAAA
Found at i:763334 original size:17 final size:16
Alignment explanation
Indices: 763314--763362 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
763304 AAACCCAACC
*
763314 AAAATAATATATTTATT
1 AAAATAAT-TATTTAAT
*
763331 AAAAAAATTATTTAAT
1 AAAATAATTATTTAAT
763347 AAAAT-ATGTATTTAAT
1 AAAATAAT-TATTTAAT
763363 TGAAAGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 2 0.07
16 19 0.68
17 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AAAATAATTATTTAAT
Found at i:764731 original size:21 final size:21
Alignment explanation
Indices: 764673--764731 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
764663 ATTATCCAAT
*
764673 AAACTTGACAA-CCATACCAAC
1 AAACTTGA-AATCCATAACAAC
764694 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
764715 CAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
764732 TAATAAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 2 0.06
21 33 0.94
ACGTcount: A:0.49, C:0.27, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:768811 original size:41 final size:41
Alignment explanation
Indices: 768721--768933 Score: 208
Period size: 41 Copynumber: 5.3 Consensus size: 41
768711 CAATTGCGAT
* * *
768721 GTTTATTACAAAAACGCTGCT-AAGTGTATGACTA--CGG-
1 GTTTATTACAAAAACGCCGCTAAAGTGCATGACTATTGGGC
* * *
768758 GTTCATTACAAAAACGCCGTTAAAGTGCATGATTATTGGGC
1 GTTTATTACAAAAACGCCGCTAAAGTGCATGACTATTGGGC
**
768799 GTTTATTACAAAAACGCCATTAAAGTGCATGACTATTGCGGC
1 GTTTATTACAAAAACGCCGCTAAAGTGCATGACTATTG-GGC
* * * * *
768841 ATTTA-T-CGAAAACGCCACTAAAATGCATGATTATTGCGGC
1 GTTTATTACAAAAACGCCGCTAAAGTGCATGACTATTG-GGC
* *
768881 ATTTA-TAAAAAAACGCCGCT-AAGATGCATGACTATTGGGC
1 GTTTATTACAAAAACGCCGCTAAAG-TGCATGACTATTGGGC
768921 GTTTATTACAAAA
1 GTTTATTACAAAA
768934 GGGTTGCCTT
Statistics
Matches: 147, Mismatches: 21, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
37 18 0.12
38 11 0.07
40 47 0.32
41 64 0.44
42 7 0.05
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (41 bp):
GTTTATTACAAAAACGCCGCTAAAGTGCATGACTATTGGGC
Found at i:768872 original size:81 final size:80
Alignment explanation
Indices: 768768--768926 Score: 205
Period size: 81 Copynumber: 2.0 Consensus size: 80
768758 GTTCATTACA
** * * * *
768768 AAAACGCCGTTAAAGTGCATGATTATTG-GGCGTTTATTACAAAAACGCCATTAA-AGTGCATGA
1 AAAACGCCACTAAAATGCATGATTATTGCGGCATTTA-TAAAAAAACGCCACTAAGA-TGCATGA
768831 CTATTGCGGCATTTATCG
64 CTATTG-GGCATTTATCG
*
768849 AAAACGCCACTAAAATGCATGATTATTGCGGCATTTATAAAAAAACGCCGCTAAGATGCATGACT
1 AAAACGCCACTAAAATGCATGATTATTGCGGCATTTATAAAAAAACGCCACTAAGATGCATGACT
*
768914 ATTGGGCGTTTAT
66 ATTGGGCATTTAT
768927 TACAAAAGGG
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
80 8 0.12
81 52 0.76
82 8 0.12
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (80 bp):
AAAACGCCACTAAAATGCATGATTATTGCGGCATTTATAAAAAAACGCCACTAAGATGCATGACT
ATTGGGCATTTATCG
Found at i:769530 original size:75 final size:74
Alignment explanation
Indices: 769434--769720 Score: 317
Period size: 75 Copynumber: 3.9 Consensus size: 74
769424 ATTATGTTAA
* * * * **
769434 GTTTCTTTGAAGGTTTCTAATAATGTAAACAGTAAAATAAAATAGGCGCTACCTATTATATTAAA
1 GTTTGTTTAAAGGTTACTAATAATATAAACAGTAAAATAAAATAGGCGCTACCTATTACGTTAAA
* *
769499 ATACCTATTG
66 CTACCTA-CG
* * * *
769509 GTTTGTTTAAAGGTTACTAATAATATAAACGGTAAAATAAAATAAGCACTACCTATTGCGTTAAA
1 GTTTGTTTAAAGGTTACTAATAATATAAACAGTAAAATAAAATAGGCGCTACCTATTACGTTAAA
769574 CTACC-ACG
66 CTACCTACG
* * * *
769582 GTTTGTTT-AAGGCTACTAATAATATAATCGGTAAAATAAAATAGGCGTTACCTATTACGTTAAA
1 GTTTGTTTAAAGGTTACTAATAATATAAACAGTAAAATAAAATAGGCGCTACCTATTACGTTAAA
** *
769646 CTAATTACCC
66 CTACCTA-CG
* ** * * *
769656 GTTTGTTTAAAGGTTAATAATAAGGTAAACAATAAAATAAAATAGACGCTATCTATTACGTTAAA
1 GTTTGTTTAAAGGTTACTAATAATATAAACAGTAAAATAAAATAGGCGCTACCTATTACGTTAAA
769721 TAAGCACTAC
Statistics
Matches: 178, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
72 53 0.30
73 10 0.06
74 10 0.06
75 105 0.59
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.33
Consensus pattern (74 bp):
GTTTGTTTAAAGGTTACTAATAATATAAACAGTAAAATAAAATAGGCGCTACCTATTACGTTAAA
CTACCTACG
Found at i:769718 original size:147 final size:147
Alignment explanation
Indices: 769450--769720 Score: 346
Period size: 147 Copynumber: 1.8 Consensus size: 147
769440 TTGAAGGTTT
* * * ***
769450 CTAATAATGTAAACAGTAAAATAAAATAGGCGCTACCTATTATATTAAAATACCTATTGGTTTGT
1 CTAATAATATAAACAGTAAAATAAAATAGGCGCTACCTATTACATTAAAATAACTACCCGTTTGT
* * ** *
769515 TTAAAGGTTACTAATAATATAAACGGTAAAATAAAATAAGCACTACCTATTGCGTTAAACTACCA
66 TTAAAGGTTAATAATAAGATAAACAATAAAATAAAATAAGCACTACCTATTACGTTAAACTACCA
769580 CGGTTTGTTTAAGGCTA
131 CGGTTTGTTTAAGGCTA
* * * * * *
769597 CTAATAATATAATCGGTAAAATAAAATAGGCGTTACCTATTACGTTAAACTAATTACCCGTTTGT
1 CTAATAATATAAACAGTAAAATAAAATAGGCGCTACCTATTACATTAAAATAACTACCCGTTTGT
* * *
769662 TTAAAGGTTAATAATAAGGTAAACAATAAAATAAAAT-AGACGCTATCTATTACGTTAAA
66 TTAAAGGTTAATAATAAGATAAACAATAAAATAAAATAAG-CACTACCTATTACGTTAAA
769721 TAAGCACTAC
Statistics
Matches: 103, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
146 2 0.02
147 101 0.98
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (147 bp):
CTAATAATATAAACAGTAAAATAAAATAGGCGCTACCTATTACATTAAAATAACTACCCGTTTGT
TTAAAGGTTAATAATAAGATAAACAATAAAATAAAATAAGCACTACCTATTACGTTAAACTACCA
CGGTTTGTTTAAGGCTA
Found at i:769790 original size:98 final size:98
Alignment explanation
Indices: 769630--769841 Score: 300
Period size: 98 Copynumber: 2.2 Consensus size: 98
769620 AAATAGGCGT
* *
769630 TACCTATTACGTTAAACTAATTACCCGTTTGTTTAAAGGTTAATAATAAGGTAAACAATAAAATA
1 TACCTATTACGTTAAACTAACTACCCGTTTGTTTAAAGATTAATAATAAGGTAAACAATAAAATA
*
769695 AAATAGACGCTATCTATTACGTTAAATAAGCAC
66 AAATAGACGCTACCTATTACGTTAAATAAGCAC
* * * * *
769728 TACCTATTACTTTAAACTAGCTA-TCGATTTGTTTAAAGATTAATAATAATGTAAACAGTAAAAT
1 TACCTATTACGTTAAACTAACTACCCG-TTTGTTTAAAGATTAATAATAAGGTAAACAATAAAAT
** * *
769792 AAAATAGGTGCTACCTATTATGTTAAATAGGCAC
65 AAAATAGACGCTACCTATTACGTTAAATAAGCAC
769826 TACCTATTACGTTAAA
1 TACCTATTACGTTAAA
769842 TAAGCGTTAC
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
97 2 0.02
98 98 0.98
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (98 bp):
TACCTATTACGTTAAACTAACTACCCGTTTGTTTAAAGATTAATAATAAGGTAAACAATAAAATA
AAATAGACGCTACCTATTACGTTAAATAAGCAC
Found at i:769819 original size:23 final size:23
Alignment explanation
Indices: 769793--769864 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
769783 CAGTAAAATA
* *
769793 AAATAGGTGCTACCTATTATGTT
1 AAATAGGCGCTACCTATTACGTT
*
769816 AAATAGGCACTACCTATTACGTT
1 AAATAGGCGCTACCTATTACGTT
* *
769839 AAATAAGCGTTACCTATTACGTT
1 AAATAGGCGCTACCTATTACGTT
769862 AAA
1 AAA
769865 CTAGCTACTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (23 bp):
AAATAGGCGCTACCTATTACGTT
Found at i:772619 original size:39 final size:38
Alignment explanation
Indices: 772576--772717 Score: 187
Period size: 39 Copynumber: 3.7 Consensus size: 38
772566 AGGTCGAACA
772576 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTCAAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTC-AGATG
* * * *
772615 AGTTCTTCTCATTATGAACTTATTATTCTTCTTTAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTC-TCAGATG
* *
772654 AGTTCTTCTAATTATGAATTTCTTCTTCCTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCC-TC-TCAGATG
772694 AGTTCTTCTCATTATGAAC-TCTTC
1 AGTTCTTCTCATTATGAACTTCTTC
772718 CACTGGGGAT
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 62 0.70
40 27 0.30
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (38 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTCTCAGATG
Found at i:773044 original size:122 final size:123
Alignment explanation
Indices: 772895--773576 Score: 713
Period size: 122 Copynumber: 5.7 Consensus size: 123
772885 AAATTAAGGC
** * *
772895 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC-TCCTTCTTCTGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
772959 TGAACATT-TCTAGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAAAGTCAAACAA
66 TGAAC-TTCTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAAAGTCAAGCAA
*
773017 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
** * * *
773082 TGAACTTTCTCTGGAAAAATTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
66 TGAAC-TTCTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAAAGTCAAGCAA
*
773141 AAGGTTGAACAGGCTCTTCTCATTATGAACTTCTTCTTCC-TC-TCAAGATGAGTTCTTCTCATT
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTC-AGATGAGTTCTTCTCATT
* * * * *
773204 ATGAACTTCTCTGGACAA-ATTAATGTTGATCTATCTCTTTCTGTGATAGAA-TCATGAAA
65 ATGAACTTCTCTGGA-AATGTTGATGTTGATCTATCTCCTTCTGTGATA-AAGTCAAGCAA
* * * *
773263 AAGATTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * ** * *
773328 TGAAC-TCTACCTGG-CA-----ATGTTGATCCA--T-C--GAGTGATGAATTCAAGCAA
66 TGAACTTCT--CTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAAAGTCAAGCAA
* * *
773376 AATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* ** ** * **
773441 TGAAC-TCTTCTGG-AA-----ATGTTGATCCA--T-C--AAGTGATGGATTTGAGCAA
66 TGAACTTC-TCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAAAGTCAAGCAA
*
773488 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
773553 TGAACTTTCTCTGGAAATGTTGAT
66 TGAAC-TTCTCTGGAAATGTTGAT
773577 CCATCAAGTG
Statistics
Matches: 494, Mismatches: 47, Indels: 41
0.85 0.08 0.07
Matches are distributed among these distances:
112 101 0.20
113 83 0.17
114 5 0.01
116 1 0.00
118 10 0.02
119 2 0.00
122 116 0.23
123 88 0.18
124 88 0.18
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTCTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAAAGTCAAGCAA
Found at i:773177 original size:246 final size:232
Alignment explanation
Indices: 772895--773589 Score: 747
Period size: 246 Copynumber: 3.0 Consensus size: 232
772885 AAATTAAGGC
* * *
772895 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTC-TCCTTCTTCTGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
772959 TGAACATTTCTAGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAAAGTCAAACAAAAGGTTG
66 TGAAC-TTTCT-GAAA--TT-ATGTTGATCTATCTCCTTCTGTGATAAA-TCAAACAAAAGGTTG
*
773024 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTT
125 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
* * *
773089 TCTCTGGAAAAATTGATGCTGATCTATCTCCTTCTGTGAT-AGAGTCATGCAA
190 TCTCTGGAAAAA-TG-T--TGATCCA--T-C--CAGTGATGA-AGTCAAGCAA
* *
773141 AAGGTTGAACAGGCTCTTCTCATTATGAACTTCTTCTTCC-TC-TCAAGATGAGTTCTTCTCATT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC-AGATGAGTTCTTCTCATT
* * *
773204 ATGAACTTCTCTGGACAAATTAATGTTGATCTATCTCTTTCTGTGATAGAATCATGA-AAAAGAT
65 ATGAACTT-TCT-G--AAATT-ATGTTGATCTATCTCCTTCTGTGATA-AATCA-AACAAAAGGT
* * *
773268 TGAACAAGTTCTTTTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAC
123 TGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
* * * *
773333 TCTAC-CTGG--CAATGTTGATCCATCGAGTGATGAATTCAAGCAA
188 T-TTCTCTGGAAAAATGTTGATCCATCCAGTGATGAAGTCAAGCAA
* *
773376 AATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *** ** ** *
773441 TGAACTCTTCTGGAA--ATGTTGATCCATCAAGTGATG-GAT---TTGAGCAAAAGGTTGAACAA
66 TGAACT-TTCTGAAATTATGTTGATCTATCTCCTTCTGTGATAAATCAAACAAAAGGTTGAACAA
*
773500 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTATGAACTTTCTCT
130 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
*
773565 GG--AAATGTTGATCCATCAAGTGATG
195 GGAAAAATGTTGATCCATCCAGTGATG
773590 GATTTGAATC
Statistics
Matches: 391, Mismatches: 44, Indels: 49
0.81 0.09 0.10
Matches are distributed among these distances:
224 2 0.01
225 94 0.24
229 3 0.01
230 15 0.04
233 2 0.01
235 51 0.13
236 30 0.08
237 4 0.01
238 1 0.00
240 6 0.02
242 1 0.00
243 2 0.01
244 2 0.01
245 4 0.01
246 163 0.42
247 8 0.02
248 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (232 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTGAAATTATGTTGATCTATCTCCTTCTGTGATAAATCAAACAAAAGGTTGAACAAG
CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAATGTTGATCCATCCAGTGATGAAGTCAAGCAA
Found at i:773515 original size:112 final size:113
Alignment explanation
Indices: 773137--773596 Score: 547
Period size: 113 Copynumber: 4.0 Consensus size: 113
773127 ATAGAGTCAT
*
773137 GCAAAAGGTTGAACAGGCTCTTCTCATTATGAACTTCTTCTTCC-TC-TCAAGATGAGTTCTTCT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAA-ATGAGTTCTTCT
* ** *
773200 CATTATGAACT-TCTCTGGACAAATTAATGTTGATCTATCTCTTTCTGTGATAGAATCATGA
65 CATTATGAACTCTCTCTGG----A--AATGTTGATCCA--TC---AAGTGAT-GAAT-TTGA
* * * * *
773261 --AAAAGATTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
* * **
773324 ATTATGAACTCTAC-CTGGCAATGTTGATCCATCGAGTGATGAATTCAA
66 ATTATGAACTCT-CTCTGGAAATGTTGATCCATCAAGTGATGAATTTGA
* *
773372 GCAAAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
*
773437 ATTATGAACTCT-TCTGGAAATGTTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTCTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGA
* *
773484 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
* *
773549 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTCTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGA
773597 ATCTTTGCTA
Statistics
Matches: 300, Mismatches: 28, Indels: 27
0.85 0.08 0.08
Matches are distributed among these distances:
111 1 0.00
112 105 0.35
113 110 0.37
116 2 0.01
118 11 0.04
122 37 0.12
123 25 0.08
124 8 0.03
125 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
ATTATGAACTCTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGA
Found at i:773545 original size:225 final size:228
Alignment explanation
Indices: 773137--773589 Score: 582
Period size: 225 Copynumber: 2.0 Consensus size: 228
773127 ATAGAGTCAT
*
773137 GCAAAAGGTTGAACAGGCTCTTCTCATTATGAACTTCTTCTTCCTCTCAAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTCAAGATGAGTTCTTCTCA
* **
773202 TTATGAACTTCTCTGGACAAATTAATGTTGATCTATCTCTTTCTGTGATAGAATCATGAAAAAGA
66 TTATGAACTTCTCTGG---AA-TAATGTTGATCCA-CTC--TAAGTGATAGAATCATGAAAAAGA
* *
773267 TTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAA
124 TTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAA
* *
773332 CTCTAC-CTGGCAATGTTGATCCATCGAGTGATGAATTCAA
189 CT-TACTCTGGAAATGTTGATCCATCAAGTGATGAATTCAA
* *
773372 GCAAAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAA-ATGAGTTCTTCT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TC-TCAAGATGAGTTCTTCT
* * *
773436 CATTATGAAC-TCTTCTGG-A-AATGTTGATCCA-TC-AAGTGAT-GGAT-TTGAGCAAAAGGTT
64 CATTATGAACTTC-TCTGGAATAATGTTGATCCACTCTAAGTGATAGAATCATGA--AAAAGATT
* *
773494 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTATGAACT
126 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACT
*
773559 TTCTCTGGAAATGTTGATCCATCAAGTGATG
191 TACTCTGGAAATGTTGATCCATCAAGTGATG
773590 GATTTGAATC
Statistics
Matches: 196, Mismatches: 16, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
223 3 0.02
224 5 0.03
225 98 0.50
228 2 0.01
230 11 0.06
232 1 0.01
235 43 0.22
236 29 0.15
237 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (228 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTCAAGATGAGTTCTTCTCA
TTATGAACTTCTCTGGAATAATGTTGATCCACTCTAAGTGATAGAATCATGAAAAAGATTGAACA
AGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTACTC
TGGAAATGTTGATCCATCAAGTGATGAATTCAA
Found at i:774111 original size:22 final size:22
Alignment explanation
Indices: 773989--774109 Score: 206
Period size: 22 Copynumber: 5.5 Consensus size: 22
773979 AATAAAGCTT
*
773989 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
774011 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
774033 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
774055 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
774077 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
774099 TCATCTTTGAA
1 TCATCTTTGAA
774110 GAATGTAGAT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 93 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:776763 original size:114 final size:114
Alignment explanation
Indices: 776554--776773 Score: 323
Period size: 114 Copynumber: 1.9 Consensus size: 114
776544 GATCATGCAG
* * * *
776554 TTCATCTTTCAATTCTAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
776619 ACACTTCTAGCAGATGTTATTAGGTCTCCTTATTTCTGCTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTGCTATGAGCAAA
* * *
776668 TTCATCTTTTAAATCTAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
776733 TCACTTCCAGAAGATGCTATTGGGTTTCCTTATTTCTGCTA
66 ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTGCTA
776774 CGAGAACGTG
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
114 93 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (114 bp):
TTCATCTTTCAAATCTAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTGCTATGAGCAAA
Found at i:778957 original size:22 final size:22
Alignment explanation
Indices: 778926--778984 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
778916 TTCTCCCCTT
*
778926 TTTTTATTTTTCTCATTT-TTCC
1 TTTTTCTTTTTCTC-TTTGTTCC
* **
778948 TTTTTCTTTTTTTCTTTGTTTT
1 TTTTTCTTTTTCTCTTTGTTCC
778970 TTTTTCTTTTT-TCTT
1 TTTTTCTTTTTCTCTT
778985 CTTTCTTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 7 0.22
22 25 0.78
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTTTCTCTTTGTTCC
Found at i:778981 original size:7 final size:7
Alignment explanation
Indices: 778925--778992 Score: 66
Period size: 7 Copynumber: 9.4 Consensus size: 7
778915 TTTCTCCCCT
*
778925 TTTTTTA
1 TTTTTTC
778932 TTTTTCTC
1 TTTTT-TC
*
778940 ATTTTTC
1 TTTTTTC
*
778947 CTTTTTC
1 TTTTTTC
778954 TTTTTTTC
1 -TTTTTTC
778962 TTTGTTT-
1 TTT-TTTC
778969 TTTTTTC
1 TTTTTTC
778976 TTTTTTC
1 TTTTTTC
*
778983 TTCTTTC
1 TTTTTTC
778990 TTT
1 TTT
778993 GCTGGATGAG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
6 3 0.06
7 34 0.67
8 14 0.27
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:781770 original size:6 final size:6
Alignment explanation
Indices: 781759--781799 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
781749 ATAATTATGA
* *
781759 AAATGT AAATGT AAATGCA AAATGT AAATGC AAATGT AAAT
1 AAATGT AAATGT AAATG-T AAATGT AAATGT AAATGT AAAT
781800 ATGTGAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.27
Consensus pattern (6 bp):
AAATGT
Done.