Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007749.1 Hibiscus syriacus cultivar Beakdansim tig00110015_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: 1787532
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:187350 original size:17 final size:17
Alignment explanation
Indices: 187325--187358 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
187315 CTTTATCCAA
*
187325 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
187342 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
187359 TATCTCATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:187369 original size:22 final size:21
Alignment explanation
Indices: 187326--187367 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
187316 TTTATCCAAA
*
187326 TTTATTTATTTTATTTATTTG
1 TTTATTTATTTTATTCATTTG
187347 TTTATTTAATTTTATCTCATT
1 TTTATTT-ATTTTAT-TCATT
187368 GTAATTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTATTTATTTTATTCATTTG
Found at i:187443 original size:15 final size:15
Alignment explanation
Indices: 187423--187461 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
187413 TTTTTAATTC
187423 ATTATTTATTATTTT
1 ATTATTTATTATTTT
187438 ATTATTT-TTATTTT
1 ATTATTTATTATTTT
*
187452 TTTAATTTAT
1 ATT-ATTTAT
187462 AATTATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 9 0.43
15 11 0.52
16 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTATTTATTATTTT
Found at i:187448 original size:14 final size:14
Alignment explanation
Indices: 187411--187451 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
187401 TCTTTATTAC
* *
187411 TATTTTTAATTCAT
1 TATTTTTATTTTAT
187425 TATTTATTATTTTAT
1 TATTT-TTATTTTAT
187440 TATTTTTATTTT
1 TATTTTTATTTT
187452 TTTAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTTATTTTAT
Found at i:187474 original size:22 final size:21
Alignment explanation
Indices: 187424--187477 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
187414 TTTTAATTCA
* * *
187424 TTATTTATTATTTTATTATTT
1 TTATTTTTTAATTTATAATTT
187445 TTATTTTTTTAATTTATAATTAT
1 TTA-TTTTTTAATTTATAATT-T
187468 TTATTTTTTA
1 TTATTTTTTA
187478 CACCTTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 21 0.75
23 4 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATTTTTTAATTTATAATTT
Found at i:190923 original size:41 final size:41
Alignment explanation
Indices: 190693--190920 Score: 316
Period size: 41 Copynumber: 5.5 Consensus size: 41
190683 GGTTCATCCA
* *
190693 TAGTTGCGTTTTT-TAACAAACGCCGCTAAAGACTCGTAATT
1 TAGTGGCGTTTTTAT-ACAAACGCCGCTAAAGACTCGTACTT
*
190734 TAGTGGCGTTTTTATACAAAAGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * *
190775 TAGTGGCATTTTTATACAGACGCCGCTAAAGACTCATACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* *
190816 TAGTGGCATTTTTATACAGACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* *
190857 TAGTGGTGGTTTTTCA-ACAAACGTCGCTAAAGACTCGTACTT
1 TAGTGG-CGTTTTT-ATACAAACGCCGCTAAAGACTCGTACTT
*
190899 TAATGGCGTTTTTATACAAACG
1 TAGTGGCGTTTTTATACAAACG
190921 TCGTCGTTTT
Statistics
Matches: 169, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
40 1 0.01
41 132 0.78
42 35 0.21
43 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
Found at i:192887 original size:24 final size:23
Alignment explanation
Indices: 192855--192936 Score: 116
Period size: 24 Copynumber: 3.6 Consensus size: 23
192845 GCATTGGTAG
192855 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTTAAAGAA
192879 TGCATCGATGCACTGGTTAAAGAA
1 TGCATCGATGCACT-GTTAAAGAA
*
192903 TGCATCGATGCACT-CT--AGAA
1 TGCATCGATGCACTGTTAAAGAA
192923 TGCATCGATGCACT
1 TGCATCGATGCACT
192937 TCAAAGGGAA
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
20 18 0.32
22 1 0.02
23 1 0.02
24 36 0.64
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCACTGTTAAAGAA
Found at i:195208 original size:19 final size:19
Alignment explanation
Indices: 195184--195225 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
195174 GACTCGTATT
195184 CGGGTCGGGTACGGGTTGG
1 CGGGTCGGGTACGGGTTGG
195203 CGGGTCGGGTACGGGTTGG
1 CGGGTCGGGTACGGGTTGG
195222 -GGGT
1 CGGGT
195226 GTTACAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.05, C:0.14, G:0.60, T:0.21
Consensus pattern (19 bp):
CGGGTCGGGTACGGGTTGG
Found at i:197377 original size:5 final size:5
Alignment explanation
Indices: 197367--197392 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
197357 TTAAGGTTTC
197367 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
197393 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:197844 original size:32 final size:32
Alignment explanation
Indices: 197803--198004 Score: 318
Period size: 32 Copynumber: 6.4 Consensus size: 32
197793 CCAAGAGTCG
*
197803 AGGATTACCTATGTCTTTCGGGACATATGGAC
1 AGGATTACCTATGTCTTTCGAGACATATGGAC
*
197835 AGGATTACCTATGTCTTTCGGGACATATGGAC
1 AGGATTACCTATGTCTTTCGAGACATATGGAC
* *
197867 AGGATTACATATGTCTTTCGAGAAATATGGAC
1 AGGATTACCTATGTCTTTCGAGACATATGGAC
*
197899 AAGATTACCTATGTCTTTCGAGACATATGGAC
1 AGGATTACCTATGTCTTTCGAGACATATGGAC
* *
197931 AGGATTACCTATGTCTTTAGAGACATATGGAA
1 AGGATTACCTATGTCTTTCGAGACATATGGAC
*
197963 AGGATTACCTATGTCTTTCGGGACATATGGAC
1 AGGATTACCTATGTCTTTCGAGACATATGGAC
197995 A-G-TTACCTAT
1 AGGATTACCTAT
198005 ATTCTTAGGA
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
30 8 0.05
31 1 0.01
32 149 0.94
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (32 bp):
AGGATTACCTATGTCTTTCGAGACATATGGAC
Found at i:198714 original size:22 final size:22
Alignment explanation
Indices: 198662--198721 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
198652 TAGCATTCGG
*
198662 TACTGTTCACGTTACTGTTCAT
1 TACTGTTCACGGTACTGTTCAT
* * *
198684 CA-TCATTCATGGTACTGTTCAT
1 TACT-GTTCACGGTACTGTTCAT
198706 TACTGTTCACGGTACT
1 TACTGTTCACGGTACT
198722 ATTTATACCG
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (22 bp):
TACTGTTCACGGTACTGTTCAT
Found at i:199971 original size:42 final size:43
Alignment explanation
Indices: 199864--199988 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 43
199854 TAGCGGAATT
* * *
199864 TACAAACGTCGCTATAGATCTGACCTTTTGCGGCGTTTTTAGA
1 TACAAACGCCGCTATAGATCTAACCTTTTGCGGCATTTTTAGA
* *
199907 TACAAACGCAGCTATAAATCTAACCTTTTGCGGCATTTGTTCA-A
1 TACAAACGCCGCTATAGATCTAACCTTTTGCGGCATTT-TT-AGA
* * *
199951 -A-AAATGCCGCTATAGATCTAACATTTTGCGTCATTTTT
1 TACAAACGCCGCTATAGATCTAACCTTTTGCGGCATTTTT
199989 GGGCCGCTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 2 0.03
42 30 0.43
43 34 0.49
44 3 0.04
45 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (43 bp):
TACAAACGCCGCTATAGATCTAACCTTTTGCGGCATTTTTAGA
Found at i:200083 original size:43 final size:43
Alignment explanation
Indices: 199991--200088 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 43
199981 TCATTTTTGG
* *
199991 GCCGCTATATATATCGACCTTTTGCGGCGTTTGTACCAAAAAC
1 GCCGCTATAGATATCGACCTTTTACGGCGTTTGTACCAAAAAC
* * ** * *
200034 GTCGCTAGAGATATCGATTTTTTACGGCGTTTGTTCCAAAAAT
1 GCCGCTATAGATATCGACCTTTTACGGCGTTTGTACCAAAAAC
200077 GCCGCTATAGAT
1 GCCGCTATAGAT
200089 CTTGACCTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (43 bp):
GCCGCTATAGATATCGACCTTTTACGGCGTTTGTACCAAAAAC
Found at i:200993 original size:45 final size:45
Alignment explanation
Indices: 200914--201101 Score: 315
Period size: 45 Copynumber: 4.2 Consensus size: 45
200904 AATTTCTTAT
*
200914 CAATATATTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTAC
200960 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
*
201005 CAATATACTTACCATTTATCCCATAAGCTCGTAAGATTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* * *
201050 CAATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTAATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
201094 CAATATAC
1 CAATATAC
201102 CATAAACCAT
Statistics
Matches: 136, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
44 35 0.26
45 85 0.62
46 16 0.12
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (45 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
Found at i:201124 original size:13 final size:13
Alignment explanation
Indices: 201106--201133 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
201096 ATATACCATA
201106 AACCATAGACAAT
1 AACCATAGACAAT
201119 AACCATAGACAAT
1 AACCATAGACAAT
201132 AA
1 AA
201134 ACAATAGCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.21, G:0.07, T:0.14
Consensus pattern (13 bp):
AACCATAGACAAT
Found at i:201125 original size:20 final size:21
Alignment explanation
Indices: 201094--201139 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
201084 CTAATTTTAC
* *
201094 CAATATACCATAAACCATAGA
1 CAATATACCATAAACAATAAA
*
201115 CAATA-ACCATAGACAATAAA
1 CAATATACCATAAACAATAAA
201135 CAATA
1 CAATA
201140 GCCCAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.57, C:0.22, G:0.04, T:0.17
Consensus pattern (21 bp):
CAATATACCATAAACAATAAA
Found at i:201325 original size:59 final size:58
Alignment explanation
Indices: 201203--201331 Score: 154
Period size: 59 Copynumber: 2.2 Consensus size: 58
201193 CGTAGTGCAA
* * * **
201203 TCCCGAGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCATGTCCACCATATACACTAGGTATCCTTAAGTA-AG
*
201262 TCCCGAATATGACACATAAGGTCATG-CCTACCATATACACTAGGTATCCTTTAATGT-AT
1 TCCCGAATATGACACATAAGGTCATGTCC-ACCATATACACTAGGTATCC-TTAA-GTAAG
201321 TCCCGAATATG
1 TCCCGAATATG
201332 CAACATGCTG
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
58 2 0.03
59 53 0.87
60 4 0.07
61 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (58 bp):
TCCCGAATATGACACATAAGGTCATGTCCACCATATACACTAGGTATCCTTAAGTAAG
Found at i:207589 original size:30 final size:29
Alignment explanation
Indices: 207551--207608 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
207541 AGAATTTACA
* *
207551 TGAACTACGTGATTAAATGTATATGTGAC
1 TGAACTACGAGATTAAATGAATATGTGAC
* *
207580 TGAAGCTACGAGTTTATATGAATATGTGA
1 TGAA-CTACGAGATTAAATGAATATGTGA
207609 TATGTTTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (29 bp):
TGAACTACGAGATTAAATGAATATGTGAC
Found at i:207863 original size:23 final size:23
Alignment explanation
Indices: 207829--207903 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
207819 CATTTTATAT
* *
207829 GGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
207852 GGTACTTCGGTGTAATTCTATGC
1 GGCACTTCGGTGCAATTCTACGC
* *
207875 GGCACTTCGGTGCAATTCTATGT
1 GGCACTTCGGTGCAATTCTACGC
207898 GGCACT
1 GGCACT
207904 AGTGCATTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.17, C:0.24, G:0.27, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:208126 original size:2 final size:2
Alignment explanation
Indices: 208114--208158 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
208104 ATATGCATGC
208114 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
208157 AT
1 AT
208159 GTTTGGATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:209739 original size:20 final size:20
Alignment explanation
Indices: 209714--209753 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
209704 TGTGTGAACA
*
209714 ATAGCAGTATCGGTACCCCT
1 ATAGCAGTATCGATACCCCT
209734 ATAGCAGTATCGATACCCCT
1 ATAGCAGTATCGATACCCCT
209754 TTTACATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (20 bp):
ATAGCAGTATCGATACCCCT
Found at i:209815 original size:20 final size:20
Alignment explanation
Indices: 209790--209858 Score: 129
Period size: 20 Copynumber: 3.5 Consensus size: 20
209780 TACTATTCAT
209790 TACTGTTCACACAGTATCGA
1 TACTGTTCACACAGTATCGA
209810 TACTGTTCACACAGTATCGA
1 TACTGTTCACACAGTATCGA
209830 TACTGTTCACACAGTATCGA
1 TACTGTTCACACAGTATCGA
*
209850 TATTGTTCA
1 TACTGTTCA
209859 TTACTGTTCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.33
Consensus pattern (20 bp):
TACTGTTCACACAGTATCGA
Found at i:210127 original size:18 final size:18
Alignment explanation
Indices: 210085--210141 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
210075 ATGTTTAATG
*
210085 AAAAAAATACCAATTGTT
1 AAAAAGATACCAATTGTT
*
210103 AACAAAAGGATATCAATTGTT
1 -A-AAAA-GATACCAATTGTT
210124 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
210142 GGAAAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 12 0.36
19 5 0.15
20 5 0.15
21 11 0.33
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:213299 original size:20 final size:20
Alignment explanation
Indices: 213274--213319 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
213264 TGTTCATTAT
* *
213274 TGTTCACACAGTATCGGTAA
1 TGTTCACACAATATCGATAA
*
213294 TGTTCACACAATATCGATAT
1 TGTTCACACAATATCGATAA
213314 TGTTCA
1 TGTTCA
213320 TTACTGTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (20 bp):
TGTTCACACAATATCGATAA
Found at i:217025 original size:22 final size:22
Alignment explanation
Indices: 216998--217039 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
216988 ATGATTTATG
*
216998 TTTAAAATATAGGATTTAAAGT
1 TTTAAAATATAAGATTTAAAGT
* *
217020 TTTAAATTTTAAGATTTAAA
1 TTTAAAATATAAGATTTAAA
217040 TAGGTACGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (22 bp):
TTTAAAATATAAGATTTAAAGT
Found at i:217374 original size:18 final size:18
Alignment explanation
Indices: 217351--217387 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
217341 ATACATCTTT
217351 GAGAGCTCAAAATCAAAA
1 GAGAGCTCAAAATCAAAA
217369 GAGAGCTCAAAATCAAAA
1 GAGAGCTCAAAATCAAAA
217387 G
1 G
217388 TTTGACTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.16, G:0.19, T:0.11
Consensus pattern (18 bp):
GAGAGCTCAAAATCAAAA
Found at i:220488 original size:31 final size:31
Alignment explanation
Indices: 220405--220489 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
220395 ATACGATTAC
* * *
220405 ATAATACATATTATGTATCAAAAGTAATGAT
1 ATAATACATATCACGTATCAAAAGTAATCAT
* * * * *
220436 ATAATATATGTCACATCTCAAAAGTTATCAT
1 ATAATACATATCACGTATCAAAAGTAATCAT
* *
220467 GTGATACATATCACGTATCAAAA
1 ATAATACATATCACGTATCAAAA
220490 TATTGACTCC
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (31 bp):
ATAATACATATCACGTATCAAAAGTAATCAT
Found at i:222362 original size:21 final size:21
Alignment explanation
Indices: 222319--222363 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
222309 TATCGTATTA
* **
222319 CGATTTTCCAAATTCGCGTTG
1 CGATTTTCCAAATTAGCAATG
*
222340 CGATTTTCCTAATTAGCAATG
1 CGATTTTCCAAATTAGCAATG
222361 CGA
1 CGA
222364 ATACGTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (21 bp):
CGATTTTCCAAATTAGCAATG
Found at i:222380 original size:20 final size:20
Alignment explanation
Indices: 222355--222405 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
222345 TTCCTAATTA
222355 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
*
222375 GCAATGCGAATGCGTAAATC
1 GCAATGCGAATACGTAAATC
*
222395 GCAACGCGAAT
1 GCAATGCGAAT
222406 CTGACTATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.18
Consensus pattern (20 bp):
GCAATGCGAATACGTAAATC
Found at i:222415 original size:20 final size:20
Alignment explanation
Indices: 222392--222434 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
222382 GAATGCGTAA
*
222392 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGAATCTGACT
* *
222412 ATCGCAATGAGATTCTGACT
1 ATCGCAACGAGAATCTGACT
222432 ATC
1 ATC
222435 ACAATACTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGAGAATCTGACT
Found at i:223493 original size:24 final size:24
Alignment explanation
Indices: 223436--223495 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
223426 TAGTCAGTAT
223436 TCGAAATTTGATCTTAGTAAATAC
1 TCGAAATTTGATCTTAGTAAATAC
* * * * *
223460 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTAGTAAATAC
*
223484 TCGAATTTTGAT
1 TCGAAATTTGAT
223496 TTTTCAGAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTAGTAAATAC
Found at i:225768 original size:20 final size:20
Alignment explanation
Indices: 225726--225819 Score: 118
Period size: 20 Copynumber: 4.7 Consensus size: 20
225716 GACATTCATT
**
225726 TGACTATCGTTACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
**
225746 TGACTATCGCAAAACGGAAA
1 TGACTATCGCAACGCGGAAA
225766 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
* *
225786 TGACTATCACAACGCAGAAA
1 TGACTATCGCAACGCGGAAA
225806 TGACTATCGCAACG
1 TGACTATCGCAACG
225820 AGAGAATCGC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 61 0.95
21 3 0.05
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:225830 original size:14 final size:14
Alignment explanation
Indices: 225811--225864 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
225801 AGAAATGACT
225811 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
225825 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
225844 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
225858 ATCGCAA
1 ATCGCAA
225865 TGCAAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:225839 original size:33 final size:34
Alignment explanation
Indices: 225799--225886 Score: 142
Period size: 33 Copynumber: 2.6 Consensus size: 34
225789 CTATCACAAC
**
225799 GCAGAAATGACTATCGCAACGAGAGAATCGCAAT
1 GCAGAAATGAAAATCGCAACGAGAGAATCGCAAT
225833 GC-GAAATGAAAATCGCAACGAGAGAATCGCAAT
1 GCAGAAATGAAAATCGCAACGAGAGAATCGCAAT
*
225866 GCAAAAATGAAAATCGCAACG
1 GCAGAAATGAAAATCGCAACG
225887 CGAAATTAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
33 31 0.62
34 19 0.38
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (34 bp):
GCAGAAATGAAAATCGCAACGAGAGAATCGCAAT
Found at i:227563 original size:42 final size:42
Alignment explanation
Indices: 227508--227598 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
227498 CCTCTTCAAC
*
227508 GATGACAGTGGCCTCTTAAACGATAGGAGG-GGACTCTTGAGG
1 GATGACAGGGGCCTCTTAAACGATA-GAGGAGGACTCTTGAGG
* * * * **
227550 GATGATAGGGGCCTCTTGAATGATAGAGGAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTAAACGATAGAGGAGGACTCTTGAGG
227592 GATGACA
1 GATGACA
227599 AGTGAGTCGG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 4 0.10
42 36 0.90
ACGTcount: A:0.27, C:0.16, G:0.34, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTAAACGATAGAGGAGGACTCTTGAGG
Found at i:227574 original size:18 final size:20
Alignment explanation
Indices: 227551--227590 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
227541 CTCTTGAGGG
227551 ATGAT-AGG-GGCCTCTTGA
1 ATGATAAGGAGGCCTCTTGA
227569 ATGATAGAGGAGGCCTCTTGA
1 ATGATA-AGGAGGCCTCTTGA
227590 A
1 A
227591 CGATGACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
20 3 0.16
21 11 0.58
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.25
Consensus pattern (20 bp):
ATGATAAGGAGGCCTCTTGA
Found at i:228243 original size:22 final size:20
Alignment explanation
Indices: 228081--228265 Score: 175
Period size: 20 Copynumber: 9.4 Consensus size: 20
228071 GAAACTTAAA
*
228081 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
228101 ATCACAACACGGAAATGACT
1 ATCGCAACGCGAAAATGACT
*
228121 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
*
228141 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
** **
228161 ATCGCAATACGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* **
228181 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* *
228201 ATCACAA--CG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
228215 ATCGCAATGCGCGAAAATGACT
1 ATCGCAA--CGCGAAAATGACT
228237 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
228257 ATCGCAACG
1 ATCGCAACG
228266 AGAGAATCGC
Statistics
Matches: 140, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
14 6 0.04
16 2 0.01
17 1 0.01
18 4 0.03
19 2 0.01
20 118 0.84
22 7 0.05
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:228249 original size:56 final size:56
Alignment explanation
Indices: 228113--228281 Score: 180
Period size: 56 Copynumber: 2.9 Consensus size: 56
228103 CACAACACGG
* * * *
228113 AAATGACTATCGCAACGCGGAAATGACTATCGCAATGCGAAAATGACTATCGCAAT--ACGA
1 AAATGACTATCGCAACGCGAAAATGACTATCACAA--CG-AGA-GA--ATCGCAATGCGCGA
** * **
228173 ATTTGACTATCGCAATGCGAATTTGACTATCACAACGAGAGAATCGCAATGCGCGA
1 AAATGACTATCGCAACGCGAAAATGACTATCACAACGAGAGAATCGCAATGCGCGA
*
228229 AAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCG
1 AAATGACTATCGCAACGCGAAAATGACTATCACAACGAGAGAATCGCAATGCG
228282 ATTTTCATTT
Statistics
Matches: 92, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
54 8 0.09
56 52 0.57
57 2 0.02
58 2 0.02
60 28 0.30
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (56 bp):
AAATGACTATCGCAACGCGAAAATGACTATCACAACGAGAGAATCGCAATGCGCGA
Found at i:228362 original size:20 final size:20
Alignment explanation
Indices: 228313--228447 Score: 90
Period size: 20 Copynumber: 6.3 Consensus size: 20
228303 TCTTTCGTTA
** *
228313 CGATAGTCAAATTCGCATTA
1 CGATAGTCATTTTCGCATTG
* *
228333 CGATGGTCATTTTCTCATTG
1 CGATAGTCATTTTCGCATTG
* *
228353 CGATAGTCATTTTTGCGTTG
1 CGATAGTCATTTTCGCATTG
* * *
228373 CGATTTTGTTGTTGCGATTTTCTCGTTG
1 CGA-----TAG-T-C-ATTTTCGCATTG
* *
228401 CGATAGTCATTTTCGCGTTA
1 CGATAGTCATTTTCGCATTG
228421 CGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
228441 CGATAGT
1 CGATAGT
228448 AAACTATTCT
Statistics
Matches: 90, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
20 69 0.77
21 1 0.01
22 1 0.01
23 2 0.02
25 2 0.02
26 1 0.01
27 1 0.01
28 13 0.14
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (20 bp):
CGATAGTCATTTTCGCATTG
Found at i:228386 original size:14 final size:14
Alignment explanation
Indices: 228368--228404 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
228358 GTCATTTTTG
*
228368 CGTTGCGATTTTGT
1 CGTTGCGATTTTCT
*
228382 TGTTGCGATTTTCT
1 CGTTGCGATTTTCT
228396 CGTTGCGAT
1 CGTTGCGAT
228405 AGTCATTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.08, C:0.16, G:0.27, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTCT
Found at i:228840 original size:6 final size:6
Alignment explanation
Indices: 228829--228858 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
228819 AACTCATCCC
228829 GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG
1 GTGGAG GTGGAG GTGGAG GTGGAG GTGGAG
228859 AATAGGGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.67, T:0.17
Consensus pattern (6 bp):
GTGGAG
Found at i:228900 original size:18 final size:18
Alignment explanation
Indices: 228874--228914 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
228864 GGAGATAAAC
*
228874 GTCGTGGCATCTTTGCCA
1 GTCGCGGCATCTTTGCCA
*
228892 GTCGCGGCATCTTTGCCG
1 GTCGCGGCATCTTTGCCA
228910 GTCGC
1 GTCGC
228915 CTATCATGAG
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:0.07, C:0.32, G:0.32, T:0.29
Consensus pattern (18 bp):
GTCGCGGCATCTTTGCCA
Found at i:230376 original size:20 final size:20
Alignment explanation
Indices: 230356--230536 Score: 169
Period size: 20 Copynumber: 9.4 Consensus size: 20
230346 GAAACTTAAA
**
230356 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
*
230376 ATCACAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
*
230396 ATCGTAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
*
230416 ATCGCAACACGGAAATGACT
1 ATCGCAACACGAAAATGACT
* **
230436 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
* *
230456 ATCGC-A-ATG-CAA-GA--
1 ATCGCAACACGAAAATGACT
* **
230470 ATCGCAACGCG-AAATGAAA
1 ATCGCAACACGAAAATGACT
230489 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
230509 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
230529 ATCGCAAC
1 ATCGCAAC
230537 GCAAGAATCG
Statistics
Matches: 130, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
14 5 0.04
15 1 0.01
16 5 0.04
17 2 0.02
18 1 0.01
19 11 0.08
20 105 0.81
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.17
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:230479 original size:34 final size:34
Alignment explanation
Indices: 230436--230552 Score: 128
Period size: 34 Copynumber: 3.3 Consensus size: 34
230426 GGAAATGACT
*
230436 ATCGCAACGCGAATTTGACTATCGCAATGCAAGA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
* ** *
230470 ATCGCAACGCGAA-ATGAAAATCGCAACACGAAAATGA
1 ATCGCAACGCGAATTTGACTATCGC-A-ACG-CAA-GA
230507 CTATCGCAACGCGAATTTGACTATCGCAACGCAAGA
1 --ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
230543 ATCGCAACGC
1 ATCGCAACGC
230553 AAAATGAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
33 8 0.12
34 24 0.36
35 2 0.03
36 4 0.06
37 4 0.06
38 3 0.04
39 14 0.21
40 8 0.12
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
Found at i:230527 original size:73 final size:73
Alignment explanation
Indices: 230407--230569 Score: 281
Period size: 73 Copynumber: 2.2 Consensus size: 73
230397 TCGTAACACG
** * *
230407 AAAATGACTATCGCAACACGGAAATGACTATCGCAACGCGAATTTGACTATCGCAATGCAAGAAT
1 AAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGCAAGAAT
230472 CGCAACGC
66 CGCAACGC
*
230480 GAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGCAAGAAT
1 AAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGCAAGAAT
230545 CGCAACGC
66 CGCAACGC
230553 AAAATGAAAATCGCAAC
1 AAAATGAAAATCGCAAC
230570 GACAGAATCG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 84 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (73 bp):
AAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGCAAGAAT
CGCAACGC
Found at i:230537 original size:20 final size:19
Alignment explanation
Indices: 230356--230570 Score: 144
Period size: 20 Copynumber: 11.5 Consensus size: 19
230346 GAAACTTAAA
* **
230356 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCG-AAATGACT
* *
230376 ATCACAACACGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
230396 ATCGTAACACGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
230416 ATCGCAACACGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
230436 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
*
230456 ATCGCAATGC--AA-GA--
1 ATCGCAACGCGAAATGACT
**
230470 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
*
230489 ATCGCAACACGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
230509 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
230529 ATCGCAACGC--AA-GA--
1 ATCGCAACGCGAAATGACT
* **
230543 ATCGCAACGCAAAATGAAA
1 ATCGCAACGCGAAATGACT
230562 ATCGCAACG
1 ATCGCAACG
230571 ACAGAATCGC
Statistics
Matches: 164, Mismatches: 17, Indels: 29
0.78 0.08 0.14
Matches are distributed among these distances:
14 19 0.12
16 8 0.05
17 4 0.02
18 2 0.01
19 24 0.15
20 106 0.65
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:230935 original size:22 final size:22
Alignment explanation
Indices: 230901--230962 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
230891 TGACCGTGAA
*
230901 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGAGAC
*
230923 TGATATCGTCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGAGAC
230945 TGATTTCGTCGGAGATGG
1 TGATTTCGTCGGAGATGG
230963 GGACGGATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.23, C:0.15, G:0.37, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGAGAC
Found at i:231188 original size:20 final size:20
Alignment explanation
Indices: 231165--231297 Score: 212
Period size: 20 Copynumber: 6.7 Consensus size: 20
231155 CGATAGTCAG
*
231165 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGC
231185 ATTCGCATTGCGATTTACGC
1 ATTCGCATTGCGATTTACGC
231205 ATTCGCATTGCGATTTACGC
1 ATTCGCATTGCGATTTACGC
231225 ATTCGCATTGCGATTTACGC
1 ATTCGCATTGCGATTTACGC
* *
231245 ATTCGCATTGCGATTTAAGT
1 ATTCGCATTGCGATTTACGC
* *
231265 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGC
*
231285 ATTCGCTTTGCGA
1 ATTCGCATTGCGA
231298 ATTAGGAAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 106 1.00
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGC
Found at i:231321 original size:21 final size:21
Alignment explanation
Indices: 231295--231334 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
231285 ATTCGCTTTG
231295 CGAATTAGGAAAACCGCAACA
1 CGAATTAGGAAAACCGCAACA
* *
231316 CGAATTTGGAAAATCGCAA
1 CGAATTAGGAAAACCGCAA
231335 TGCAATAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (21 bp):
CGAATTAGGAAAACCGCAACA
Found at i:233074 original size:14 final size:14
Alignment explanation
Indices: 233054--233087 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
233044 CGGTAGTATG
233054 CATTTTAATTTATT
1 CATTTTAATTTATT
*
233068 TATTTTAATTTATT
1 CATTTTAATTTATT
233082 CATTTT
1 CATTTT
233088 TAAGTAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (14 bp):
CATTTTAATTTATT
Found at i:234042 original size:27 final size:27
Alignment explanation
Indices: 234012--234076 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
234002 ATAATTGAAT
234012 GTAAAATTAAAGTTTATATTATAATTA
1 GTAAAATTAAAGTTTATATTATAATTA
234039 GTAAAATTAAAGTTTATATTATAATTA
1 GTAAAATTAAAGTTTATATTATAATTA
234066 GTAAAATTAAA
1 GTAAAATTAAA
234077 AATTCAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42
Consensus pattern (27 bp):
GTAAAATTAAAGTTTATATTATAATTA
Found at i:234089 original size:27 final size:27
Alignment explanation
Indices: 234012--234089 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
234002 ATAATTGAAT
* * *
234012 GTAAAATTAAAGTTTATATTATAATTA
1 GTAAAATTAAAATTCATATAATAATTA
* * *
234039 GTAAAATTAAAGTTTATATTATAATTA
1 GTAAAATTAAAATTCATATAATAATTA
234066 GTAAAATTAAAAATTCA-ATAATAA
1 GTAAAATT-AAAATTCATATAATAA
234090 AAACAATGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 41 0.87
28 6 0.13
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (27 bp):
GTAAAATTAAAATTCATATAATAATTA
Found at i:235696 original size:84 final size:82
Alignment explanation
Indices: 235586--235784 Score: 281
Period size: 82 Copynumber: 2.4 Consensus size: 82
235576 TTGATACATT
* * * *
235586 ACTGAAAAGTTCCTGAAGATGATAATGCACCACTATTTTACCCGTTTTTTAAAAAAAGTTGTTTA
1 ACTGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTTTCT--AAAAAGTTGTTTA
235651 AATTATACATTGAATGACC
64 AATTATACATTGAATGACC
* * * **
235670 TCTGAAAAGTTGCAGAAGATGGTAATGCACCACTATTTCACCTGTTTTCTAAAACTTTGTTTAAA
1 ACTGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTTTCTAAAAAGTTGTTTAAA
235735 TTATACATTGAATGACC
66 TTATACATTGAATGACC
* *
235752 AATGAAAAGTTGTAGAAGATGATAATGCACCAC
1 ACTGAAAAGTTGCAGAAGATGATAATGCACCAC
235785 CATTATTTGG
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 59 0.58
84 43 0.42
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (82 bp):
ACTGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCCGTTTTCTAAAAAGTTGTTTAAA
TTATACATTGAATGACC
Found at i:239849 original size:20 final size:20
Alignment explanation
Indices: 239824--239872 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
239814 CGATTTTCCG
239824 AATTCGCAACACAGAAGCCA
1 AATTCGCAACACAGAAGCCA
* * *
239844 AATTCGAAACACATAAGTCA
1 AATTCGCAACACAGAAGCCA
239864 AATTCGCAA
1 AATTCGCAA
239873 AACGCGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.16
Consensus pattern (20 bp):
AATTCGCAACACAGAAGCCA
Found at i:240046 original size:22 final size:22
Alignment explanation
Indices: 240021--240074 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
240011 CACTCTCTAC
*
240021 GACGACATCCATCCCCATCTCT
1 GACGAAATCCATCCCCATCTCT
* * *
240043 GACGAAATCCATTCTCATCTCC
1 GACGAAATCCATCCCCATCTCT
*
240065 GGCGAAATCC
1 GACGAAATCC
240075 GTCTATCTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.22
Consensus pattern (22 bp):
GACGAAATCCATCCCCATCTCT
Found at i:240084 original size:20 final size:22
Alignment explanation
Indices: 240036--240084 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
240026 CATCCATCCC
* * *
240036 CATCTCTGACGAAATCCATTCT
1 CATCTCCGGCGAAATCCAGTCT
240058 CATCTCCGGCGAAATCC-GTCT
1 CATCTCCGGCGAAATCCAGTCT
240079 -ATCTCC
1 CATCTCC
240085 ATCTCTCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.25
21 3 0.12
22 15 0.62
ACGTcount: A:0.22, C:0.37, G:0.12, T:0.29
Consensus pattern (22 bp):
CATCTCCGGCGAAATCCAGTCT
Found at i:242625 original size:21 final size:21
Alignment explanation
Indices: 242599--242664 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
242589 GCCCGATTCA
242599 CCTATCATCGTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
*
242620 CCTATCATCCTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
* *
242641 CCTGTCATCGTTCAAGAGGTC
1 CCTATCATCGTTCAAGAGGCC
242662 CCT
1 CCT
242665 CCCACTGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.26
Consensus pattern (21 bp):
CCTATCATCGTTCAAGAGGCC
Found at i:244096 original size:64 final size:64
Alignment explanation
Indices: 244016--244183 Score: 273
Period size: 64 Copynumber: 2.6 Consensus size: 64
244006 GGGGTACACT
* *
244016 TTTTTTTCTTCTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
* * ***
244080 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
244144 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
244184 GTTTTAAATT
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 97 1.00
ACGTcount: A:0.27, C:0.03, G:0.16, T:0.54
Consensus pattern (64 bp):
TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:244559 original size:18 final size:18
Alignment explanation
Indices: 244536--244571 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
244526 AAGCCGGTTG
*
244536 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
244554 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
244572 CCTTTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:246869 original size:24 final size:24
Alignment explanation
Indices: 246802--246869 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
246792 CTGAAACATC
* * *
246802 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCTGAGTACTGACCAAG
* *
246826 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAGTCTGAGTACTGACCAAG
* * *
246850 ATCAAATTTTGATTACTGAC
1 ATCAAAGTCTGAGTACTGAC
246870 TAGTACTCAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (24 bp):
ATCAAAGTCTGAGTACTGACCAAG
Found at i:247002 original size:12 final size:12
Alignment explanation
Indices: 246981--247014 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
246971 GGTTGTGGGT
*
246981 TTTGAGATTGTG
1 TTTGATATTGTG
246993 TTTGATATTGTG
1 TTTGATATTGTG
*
247005 TTTGGTATTG
1 TTTGATATTG
247015 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:247646 original size:15 final size:16
Alignment explanation
Indices: 247610--247647 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
247600 GAAATCATTG
*
247610 AAAATTATATAGAAAT
1 AAAATTATATAGAAAA
*
247626 AAAATTATGTA-AAAA
1 AAAATTATATAGAAAA
247641 AAAATTA
1 AAAATTA
247648 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATTATATAGAAAA
Found at i:247828 original size:20 final size:20
Alignment explanation
Indices: 247784--247891 Score: 84
Period size: 20 Copynumber: 5.5 Consensus size: 20
247774 CAAAACATTT
*
247784 GTGTTGCGAAACT-AAAA-C
1 GTGTTGCGAAATTCAAAATC
*
247802 CTGTTGCGAAATT-AAAATTC
1 GTGTTGCGAAATTCAAAA-TC
247822 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATTC-AAAATC
* *
247842 GAGTTGCGAAA-ACAAAATTC
1 GTGTTGCGAAATTCAAAA-TC
*
247862 GCGTTGCG-AATTCAGAAATC
1 GTGTTGCGAAATTCA-AAATC
*
247882 GAGTTGCGAA
1 GTGTTGCGAA
247892 TTTGAAATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
18 15 0.21
19 10 0.14
20 38 0.52
21 10 0.14
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (20 bp):
GTGTTGCGAAATTCAAAATC
Found at i:247900 original size:40 final size:39
Alignment explanation
Indices: 247804--247971 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 39
247794 ACTAAAACCT
* *
247804 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAATTGAAATTCGCGTTGCGAATTCG-AAATCGA
***
247844 GTTGCGAAAACAAAATTCGCGTTGCGAATTCAGAAATCGA
1 GTTGCGAAATTGAAATTCGCGTTGCGAATTC-GAAATCGA
* * * *
247884 GTTGCGAATTTGAAATTTAGTGTTGCGAATTTGGAAA-CTGA
1 GTTGCGAAATTGAAA-TTCGCGTTGCGAA-TTCGAAATC-GA
* * * * *
247925 GTTACGAAATTGGAGTTCGCGTTGCGAATTCGAGATCGT
1 GTTGCGAAATTGAAATTCGCGTTGCGAATTCGAAATCGA
247964 GTTGCGAA
1 GTTGCGAA
247972 TTTGTTGGTC
Statistics
Matches: 103, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
39 13 0.13
40 59 0.57
41 29 0.28
42 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (39 bp):
GTTGCGAAATTGAAATTCGCGTTGCGAATTCGAAATCGA
Found at i:247933 original size:81 final size:80
Alignment explanation
Indices: 247804--247975 Score: 195
Period size: 81 Copynumber: 2.1 Consensus size: 80
247794 ACTAAAACCT
* * *
247804 GTTGCGAAATT-AAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAACAAAATTCGCGTTG
1 GTTGCGAATTTGAAAATTAGTGTTGCGAATTCGAAAATCGAGTTACGAAAACAAAATTCGCGTTG
247868 CGAATTCAGAAATCGA
66 CGAATTC-GAAATCGA
* * * **** *
247884 GTTGCGAATTTGAAATTTAGTGTTGCGAATTTGGAAA-CTGAGTTACGAAATTGGAGTTCGCGTT
1 GTTGCGAATTTGAAAATTAGTGTTGCGAATTCGAAAATC-GAGTTACGAAAACAAAATTCGCGTT
* *
247948 GCGAATTCGAGATCGT
65 GCGAATTCGAAATCGA
247964 GTTGCGAATTTG
1 GTTGCGAATTTG
247976 TTGGTCATTT
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 29 0.38
81 48 0.62
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (80 bp):
GTTGCGAATTTGAAAATTAGTGTTGCGAATTCGAAAATCGAGTTACGAAAACAAAATTCGCGTTG
CGAATTCGAAATCGA
Found at i:249497 original size:9 final size:8
Alignment explanation
Indices: 249483--249599 Score: 69
Period size: 9 Copynumber: 13.6 Consensus size: 8
249473 GGTTTATATT
249483 ATATAATTA
1 ATATAA-TA
249492 ATATAA-A
1 ATATAATA
*
249499 ATATTATA
1 ATATAATA
249507 TATATAATTA
1 -ATATAA-TA
*
249517 ATATAAAAA
1 ATAT-AATA
249526 ATATAA-A
1 ATATAATA
*
249533 ATATTATA
1 ATATAATA
249541 TATATAATTA
1 -ATATAA-TA
249551 ATATAA-A
1 ATATAATA
*
249558 ATATATAAA
1 ATATA-ATA
*
249567 ATATTATA
1 ATATAATA
249575 TATATATATA
1 -ATATA-ATA
249585 TATATAATA
1 -ATATAATA
249594 TATATA
1 -ATATA
249600 TATGATCGGG
Statistics
Matches: 89, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
7 18 0.20
8 7 0.08
9 49 0.55
10 15 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATAATA
Found at i:249512 original size:25 final size:25
Alignment explanation
Indices: 249476--249602 Score: 105
Period size: 23 Copynumber: 5.4 Consensus size: 25
249466 GTTTTAGGGT
249476 TTATATTATATAATTAATATAAAATA
1 TTATA-TATATAATTAATATAAAATA
249502 TTATATATATAATTAATATAAAA-A
1 TTATATATATAATTAATATAAAATA
* * *
249526 ATATA-AAAT-ATT-ATAT-ATATAA
1 TTATATATATAATTAATATAAAAT-A
*
249548 TTA-ATATA-AAAT-ATATAAAATA
1 TTATATATATAATTAATATAAAATA
*
249570 TTATATATAT-A-TATATATATAATA
1 TTATATATATAATTA-ATATAAAATA
249594 -TATATATAT
1 TTATATATAT
249603 GATCGGGACG
Statistics
Matches: 84, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
20 2 0.02
21 5 0.06
22 19 0.23
23 21 0.25
24 14 0.17
25 18 0.21
26 5 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TTATATATATAATTAATATAAAATA
Found at i:249521 original size:34 final size:33
Alignment explanation
Indices: 249491--249580 Score: 162
Period size: 34 Copynumber: 2.7 Consensus size: 33
249481 TTATATAATT
249491 AATATAAAATATTATATATATAATTAATATAAAA
1 AATATAAAATATTATATATATAATTAATAT-AAA
249525 AATATAAAATATTATATATATAATTAATATAAA
1 AATATAAAATATTATATATATAATTAATATAAA
249558 ATATATAAAATATTATATATATA
1 A-ATATAAAATATTATATATATA
249581 TATATATATA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
33 4 0.07
34 51 0.93
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (33 bp):
AATATAAAATATTATATATATAATTAATATAAA
Found at i:249542 original size:2 final size:2
Alignment explanation
Indices: 249533--249602 Score: 66
Period size: 2 Copynumber: 39.0 Consensus size: 2
249523 AAAATATAAA
* *
249533 AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
249569 AT -T AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
249603 GATCGGGACG
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
1 8 0.14
2 50 0.86
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:251367 original size:2 final size:2
Alignment explanation
Indices: 251360--251413 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
251350 ATGTGAATAA
251360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
251402 AT AT AT AT AT AT
1 AT AT AT AT AT AT
251414 TTTTAAATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:251693 original size:17 final size:16
Alignment explanation
Indices: 251671--251722 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
251661 AAAATTTAAA
251671 AATTCAAATATATATTT
1 AATTCAAATATATA-TT
*
251688 AATTCATAAT-TCTATT
1 AATTCA-AATATATATT
*
251704 ATTTCAAATATAT-TT
1 AATTCAAATATATATT
251719 AATT
1 AATT
251723 TTACAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 8 0.28
16 9 0.31
17 9 0.31
18 3 0.10
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTCAAATATATATT
Found at i:252952 original size:43 final size:47
Alignment explanation
Indices: 252866--252955 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 47
252856 CTTTTTTTCC
252866 TTTTTTGTTCTGGTTGTTGGTTGTTGTTCGTATCTCTCCCTGTCTCT
1 TTTTTTGTTCTGGTTGTTGGTTGTTGTTCGTATCTCTCCCTGTCTCT
* *
252913 TTTTTTTTTCT-GTT-TTGTTTGTTG-TCGT-TCTCTCCCTGTCTCT
1 TTTTTTGTTCTGGTTGTTGGTTGTTGTTCGTATCTCTCCCTGTCTCT
252956 GACCGGTGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 15 0.37
44 4 0.10
45 9 0.22
46 3 0.07
47 10 0.24
ACGTcount: A:0.01, C:0.20, G:0.18, T:0.61
Consensus pattern (47 bp):
TTTTTTGTTCTGGTTGTTGGTTGTTGTTCGTATCTCTCCCTGTCTCT
Found at i:253368 original size:3 final size:3
Alignment explanation
Indices: 253362--253424 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
253352 AATAATTATT
* *
253362 TAA TAA TAA T-A TAC TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
253407 -ATT TAA TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA TAA
253425 ATTTAAATGA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 44 0.88
4 3 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:253370 original size:14 final size:13
Alignment explanation
Indices: 253351--253420 Score: 78
Period size: 14 Copynumber: 5.6 Consensus size: 13
253341 TTTGGGCTTG
253351 TAATAATTATTTAA
1 TAATAA-TATTTAA
*
253365 TAATAATATACTAA
1 TAATAATAT-TTAA
253379 TAATAATATTTAA
1 TAATAATATTTAA
253392 TAAT-A-A--TAA
1 TAATAATATTTAA
253401 TAATAA-ATTTAA
1 TAATAATATTTAA
253413 TAATAATA
1 TAATAATA
253421 ATAAATTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
9 7 0.14
10 2 0.04
11 1 0.02
12 10 0.20
13 11 0.22
14 18 0.37
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATAATATTTAA
Found at i:253391 original size:27 final size:25
Alignment explanation
Indices: 253351--253424 Score: 93
Period size: 24 Copynumber: 3.0 Consensus size: 25
253341 TTTGGGCTTG
253351 TAATAATTATTTAATAATAATATACTAA
1 TAATAA-TATTTAATAATAATA-A-TAA
253379 TAATAATA-TT--TAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
253401 TAATAA-ATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
253425 ATTTAAATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
21 1 0.02
22 11 0.26
23 1 0.02
24 20 0.47
26 2 0.05
27 2 0.05
28 6 0.14
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (25 bp):
TAATAATATTTAATAATAATAATAA
Found at i:253393 original size:21 final size:19
Alignment explanation
Indices: 253368--253430 Score: 83
Period size: 18 Copynumber: 3.2 Consensus size: 19
253358 TATTTAATAA
253368 TAATATACTAATAATAATATT
1 TAATATA-TAATAATAA-ATT
253389 TAATAATAATAATAATAAATT
1 TAAT-AT-ATAATAATAAATT
253410 TAATA-ATAATAATAAATT
1 TAATATATAATAATAAATT
253428 TAA
1 TAA
253431 ATGAAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
18 16 0.40
20 1 0.03
21 11 0.28
22 11 0.28
23 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATATATAATAATAAATT
Found at i:253416 original size:31 final size:27
Alignment explanation
Indices: 253351--253406 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
253341 TTTGGGCTTG
*
253351 TAATAATTATTTAATAATAATATACTAA
1 TAATAA-TATTTAATAATAATATAATAA
253379 TAATAATATTTAATAATAATAATAATAA
1 TAATAATATTTAATAATAAT-ATAATAA
253407 ATTTAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
TAATAATATTTAATAATAATATAATAA
Found at i:254448 original size:76 final size:76
Alignment explanation
Indices: 253555--254421 Score: 1627
Period size: 76 Copynumber: 11.5 Consensus size: 76
253545 GATGGAAATG
* * *
253555 TTTGAAAACATCATGCACTGAAGGGTTTACAGATGACCCGAAGGTTTTCGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT-GAAAACATCAAAAAGC
253620 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* *
253632 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
253697 CCCGAAGGCTT
66 CCCGAAGGCTT
253708 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
253773 CCCGAAGGC-T
66 CCCGAAGGCTT
253783 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
253847 CCCGAAGGC-T
66 CCCGAAGGCTT
253857 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
253922 CCCGAAGGCTT
66 CCCGAAGGCTT
253933 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
253997 CCCGAAGGC-T
66 CCCGAAGGCTT
*
254007 TTTGGAAACATCATGCACTGAAGGGCTTATAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
254072 CCCGAAGGCTT
66 CCCGAAGGCTT
254083 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
254148 CCCGAAGGCTT
66 CCCGAAGGCTT
254159 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
254224 CCCGAAGGCTT
66 CCCGAAGGCTT
254235 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
254300 CCCGAAGGCTT
66 CCCGAAGGCTT
254311 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
254376 CCCGAAGGCTT
66 CCCGAAGGCTT
*
254387 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATG
254422 TGGGAAATAG
Statistics
Matches: 776, Mismatches: 10, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
74 131 0.17
75 106 0.14
76 496 0.64
77 43 0.06
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:256769 original size:45 final size:45
Alignment explanation
Indices: 256705--256794 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
256695 AAGTGTGTTC
*
256705 AACATTACTTCTTGTTGAGATGAGCCTCCAAAAATACTCAAATAT
1 AACATTACTTCTTGTTGAGATGAGCCCCCAAAAATACTCAAATAT
256750 AACATTACTTCTTGTTGAGATGAGCCCCCAAAAATACTCAAATAT
1 AACATTACTTCTTGTTGAGATGAGCCCCCAAAAATACTCAAATAT
256795 TCATATTGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (45 bp):
AACATTACTTCTTGTTGAGATGAGCCCCCAAAAATACTCAAATAT
Found at i:257986 original size:114 final size:114
Alignment explanation
Indices: 257786--258014 Score: 377
Period size: 114 Copynumber: 2.0 Consensus size: 114
257776 GATCATGCAG
* * * *
257786 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
257851 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
257900 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
257965 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
258014 T
1 T
258015 GGCACTTGCT
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:260175 original size:15 final size:14
Alignment explanation
Indices: 260155--260185 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
260145 CTTGATTCAA
260155 TTTTCCTTTTTCTTT
1 TTTTCCTTTTT-TTT
260170 TTTTCCTTTTTTTT
1 TTTTCCTTTTTTTT
260184 TT
1 TT
260186 CTTCTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTCCTTTTTTTT
Found at i:262640 original size:22 final size:22
Alignment explanation
Indices: 262606--262647 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
262596 TTAAATAAAA
262606 AAAATGAAAAATGCATAAATGGA
1 AAAATGAAAAATGCA-AAATGGA
*
262629 AAAAT-AAGAATGCAAAATG
1 AAAATGAAAAATGCAAAATG
262648 TGCAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.62, C:0.05, G:0.17, T:0.17
Consensus pattern (22 bp):
AAAATGAAAAATGCAAAATGGA
Found at i:264745 original size:17 final size:15
Alignment explanation
Indices: 264720--264763 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
264710 TTAATACCTG
*
264720 AATAAAAAAATAATA
1 AATATAAAAATAATA
264735 TTAATATAAAAATAATA
1 --AATATAAAAATAATA
264752 AATAATAAAAAT
1 AAT-ATAAAAAT
264764 TTGAAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 3 0.12
16 8 0.32
17 14 0.56
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATATAAAAATAATA
Found at i:266515 original size:40 final size:45
Alignment explanation
Indices: 266423--266520 Score: 116
Period size: 46 Copynumber: 2.3 Consensus size: 45
266413 TCTCTTTTTT
*
266423 TCCTTTTTTGTTCTGGTTGTTGGTTGCTGTTCGTATCTCTCCCTG
1 TCCTTTTTTTTTCTGGTTGTTGGTTGCTGTTCGTATCTCTCCCTG
* * *
266468 TCTCTTTTTTTTTCT-GTT-TTGTTTGTTG-TCGT-TCTCTGCCTG
1 TC-CTTTTTTTTTCTGGTTGTTGGTTGCTGTTCGTATCTCTCCCTG
266510 -CCTTTTTTTTT
1 TCCTTTTTTTTT
266521 TTTTGCAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
40 10 0.21
41 1 0.02
42 9 0.19
43 4 0.08
44 8 0.17
45 5 0.10
46 11 0.23
ACGTcount: A:0.01, C:0.20, G:0.17, T:0.61
Consensus pattern (45 bp):
TCCTTTTTTTTTCTGGTTGTTGGTTGCTGTTCGTATCTCTCCCTG
Found at i:266519 original size:42 final size:46
Alignment explanation
Indices: 266425--266522 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 46
266415 TCTTTTTTTC
* *
266425 CTTTTTTGTTCTGGTTGTTGGTTGCTGTTCGTATCTCTCCCTGTCT
1 CTTTTTTTTTCTGGTTGTTGGTTGCTGTTCGTATCTCTCCCTGCCT
* * *
266471 CTTTTTTTTTCT-GTT-TTGTTTGTTG-TCGT-TCTCTGCCTGCCT
1 CTTTTTTTTTCTGGTTGTTGGTTGCTGTTCGTATCTCTCCCTGCCT
*
266513 TTTTTTTTTT
1 CTTTTTTTTT
266523 TTGCAAGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 20 0.43
43 4 0.09
44 8 0.17
45 3 0.07
46 11 0.24
ACGTcount: A:0.01, C:0.19, G:0.17, T:0.62
Consensus pattern (46 bp):
CTTTTTTTTTCTGGTTGTTGGTTGCTGTTCGTATCTCTCCCTGCCT
Found at i:266967 original size:3 final size:3
Alignment explanation
Indices: 266961--267026 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
266951 AATAATTATT
* *
266961 TAA TAA TAA T-A TAC TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
267006 TAA -ATT TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA
267027 ATTTAAATGA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 47 0.89
4 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:266990 original size:27 final size:25
Alignment explanation
Indices: 266950--267026 Score: 120
Period size: 24 Copynumber: 3.0 Consensus size: 25
266940 TTTGGGCTTG
266950 TAATAATTATTTAATAATAATATACTAA
1 TAATAA-TATTTAATAATAATA-A-TAA
266978 TAATAATATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
267003 TAATAA-ATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
267027 ATTTAAATGA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
24 18 0.37
25 9 0.18
26 1 0.02
27 15 0.31
28 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATAATATTTAATAATAATAATAA
Found at i:268643 original size:29 final size:29
Alignment explanation
Indices: 268598--268655 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
268588 GTGTTGGCCG
*
268598 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
268627 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
268656 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:268727 original size:24 final size:23
Alignment explanation
Indices: 268695--268758 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
268685 ACACGCTGGG
* *
268695 CATCTGAGGCCATCCGACCGAGGC
1 CATCCGAGGCCATCCGAACGA-GC
268719 CATCCGAGGCCATCCGAACGAGC
1 CATCCGAGGCCATCCGAACGAGC
* * *
268742 TATGCGAGGGCATCCGA
1 CATCCGAGGCCATCCGA
268759 GGGCAACCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 16 0.46
24 19 0.54
ACGTcount: A:0.23, C:0.34, G:0.30, T:0.12
Consensus pattern (23 bp):
CATCCGAGGCCATCCGAACGAGC
Found at i:268756 original size:33 final size:33
Alignment explanation
Indices: 268713--268793 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
268703 GCCATCCGAC
* *
268713 CGAGGCCATCCGAGGCCATCCGAACGAGCTATG
1 CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
* *
268746 CGAGGGCATCCGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
*
268779 CGAGGGAATCCGAGG
1 CGAGGGCATCCGAGG
268794 AAAGCCGAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.25, C:0.28, G:0.37, T:0.10
Consensus pattern (33 bp):
CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
Found at i:268802 original size:33 final size:33
Alignment explanation
Indices: 268732--268806 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
268722 CCGAGGCCAT
* * *
268732 CCGAACGAGCTATGCGAGGGCATCCGAGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAA
268765 CCGAGCGAGCTATGCGAGGGAATCCGA-GGAAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAA
268797 GCCGAGCGAG
1 -CCGAGCGAG
268807 GGTAAGTCGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 4 0.11
33 34 0.89
ACGTcount: A:0.28, C:0.25, G:0.39, T:0.08
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAA
Found at i:268941 original size:29 final size:29
Alignment explanation
Indices: 268899--268984 Score: 163
Period size: 29 Copynumber: 3.0 Consensus size: 29
268889 GAGCAAGGGT
268899 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
268928 AGGTCGCCAGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
268957 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
268985 GGCCAACACT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.21, C:0.30, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:271025 original size:21 final size:22
Alignment explanation
Indices: 270989--271029 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
270979 TTAAAAATTA
270989 TAAAAGAAGTACCGATACTCAT
1 TAAAAGAAGTACCGATACTCAT
*
271011 TAAAAG-AGTATCGATACTC
1 TAAAAGAAGTACCGATACTC
271030 TATGTCCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (22 bp):
TAAAAGAAGTACCGATACTCAT
Found at i:274704 original size:29 final size:29
Alignment explanation
Indices: 274637--274704 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
274627 ACATGACAGA
* * *
274637 GATTTAATCCCATATAGAATTAGGACGGG
1 GATTTAATCTCATATAGAATCAGGAAGGG
*
274666 GATTTAATCTCATGTAGAATCAGGAAGGG
1 GATTTAATCTCATATAGAATCAGGAAGGG
274695 GATTTAATCT
1 GATTTAATCT
274705 AGGGGTGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (29 bp):
GATTTAATCTCATATAGAATCAGGAAGGG
Found at i:275824 original size:41 final size:41
Alignment explanation
Indices: 275767--275849 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
275757 ACTTGATCTG
275767 TATGCTTTTCATTTTGTTCATTTCATGTTTCCTTTGCTCAA
1 TATGCTTTTCATTTTGTTCATTTCATGTTTCCTTTGCTCAA
*
275808 TATGCTTTTCATTTTGTTCATTTCATGTTTCCTTTGTTCAA
1 TATGCTTTTCATTTTGTTCATTTCATGTTTCCTTTGCTCAA
275849 T
1 T
275850 CATTTTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.14, C:0.18, G:0.10, T:0.58
Consensus pattern (41 bp):
TATGCTTTTCATTTTGTTCATTTCATGTTTCCTTTGCTCAA
Found at i:275845 original size:20 final size:20
Alignment explanation
Indices: 275779--275847 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
275769 TGCTTTTCAT
275779 TTTGTTCATTTCATGTTTCC
1 TTTGTTCATTTCATGTTTCC
* * *
275799 TTTGCTCA-AT-ATGCTTTTCAT
1 TTTGTTCATTTCATG--TTTC-C
275820 TTTGTTCATTTCATGTTTCC
1 TTTGTTCATTTCATGTTTCC
275840 TTTGTTCA
1 TTTGTTCA
275848 ATCATTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 3 0.08
19 1 0.03
20 19 0.50
21 11 0.29
22 1 0.03
23 3 0.08
ACGTcount: A:0.13, C:0.19, G:0.10, T:0.58
Consensus pattern (20 bp):
TTTGTTCATTTCATGTTTCC
Found at i:278035 original size:15 final size:17
Alignment explanation
Indices: 278000--278036 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
277990 AACAAAACTG
278000 AAATATGATAAAAATAA
1 AAATATGATAAAAATAA
*
278017 AAATA-GATAAATA-AA
1 AAATATGATAAAAATAA
278032 AAATA
1 AAATA
278037 ATTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 7 0.37
17 5 0.26
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (17 bp):
AAATATGATAAAAATAA
Found at i:284384 original size:12 final size:11
Alignment explanation
Indices: 284347--284395 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
284337 TTTATAAAAG
284347 TTTTATTTTCCT
1 TTTTATTTT-CT
*
284359 TTTAATTTTCT
1 TTTTATTTTCT
*
284370 TTTTATTTTAGT
1 TTTTATTTT-CT
*
284382 TTTTACTTTCT
1 TTTTATTTTCT
284393 TTT
1 TTT
284396 AAAAAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 14 0.45
12 17 0.55
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTTATTTTCT
Found at i:284384 original size:23 final size:23
Alignment explanation
Indices: 284347--284395 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
284337 TTTATAAAAG
* *
284347 TTTTATTTTCCTTTTAATTTTCT
1 TTTTATTTTACTTTTAACTTTCT
* *
284370 TTTTATTTTAGTTTTTACTTTCT
1 TTTTATTTTACTTTTAACTTTCT
284393 TTT
1 TTT
284396 AAAAAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTATTTTACTTTTAACTTTCT
Found at i:300495 original size:84 final size:82
Alignment explanation
Indices: 300376--300671 Score: 308
Period size: 84 Copynumber: 3.6 Consensus size: 82
300366 TACCCCGTCT
* * ** * * * *
300376 CTGTCAAGGTTTTCAGAATTAGAGGTTTTGTGGAAGTAAGCTGCAGCATACTTGTTTTCCAAACT
1 CTGTCAAGGTTTTTAGCAGCAGAGCTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACT
*
300441 CTTCATCATCTTGTCATCC
66 CTTCATC--CTTCTCATCC
*
300460 CTGTCAAGGTTTTTAGCAGCAGAGTTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACT
1 CTGTCAAGGTTTTTAGCAGCAGAGCTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACT
* *
300525 CTTCA-CCTTCTCCTCT
66 CTTCATCCTTCTCATCC
* * *
300541 TTGCCATGGTTTTTAGCAGCAGAGCTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACT
1 CTGTCAAGGTTTTTAGCAGCAGAGCTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACT
* * * *
300606 CATCATCTCCTCCTCGTCT
66 CTTCA--TCCTTCTCATCC
* * ** * *
300625 CT-TCAATGGTTTTCAGAATTAGAGGTTTTGTGAAAGTAAGCAGTAGC
1 CTGTCAA-GGTTTTTAGCAGCAGAGCTTTTGTGGAAGTAAGCAGTAGC
300672 GAAATTTTCT
Statistics
Matches: 181, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
81 72 0.40
83 3 0.02
84 106 0.59
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (82 bp):
CTGTCAAGGTTTTTAGCAGCAGAGCTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACT
CTTCATCCTTCTCATCC
Found at i:300687 original size:84 final size:83
Alignment explanation
Indices: 300310--300671 Score: 353
Period size: 81 Copynumber: 4.4 Consensus size: 83
300300 ATGGTGTTTT
* * * * ** *
300310 GAAGCAGAGGTTTTGTGAAAGTAAGCCGCAGCATACTTAT-TATTAAAACGCTTCA-CTAC-CC-
1 GAAGCAGAGGTTTTGTGGAAGTAAGCAGTAGCATACTTGTCT-TCCAAACTCTTCATCT-CTCCT
300371 CGTCTCTGTCAAGGTTTTCA
64 CGTCTCTGTCAAGGTTTTCA
** * * * **
300391 GAATTAGAGGTTTTGTGGAAGTAAGCTGCAGCATACTTGTTTTCCAAACTCTTCATCATCTTGTC
1 GAAGCAGAGGTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCATC-TCTCCTC
* * *
300456 ATCCCTGTCAAGGTTTTTA
65 GTCTCTGTCAAGGTTTTCA
* * *
300475 GCAGCAGAGTTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCACCTTCTCCTC
1 GAAGCAGAGGTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCATC-TCTCCTC
* * *
300540 -T-T-TGCCATGGTTTTTA
65 GTCTCTGTCAAGGTTTTCA
* * *
300556 GCAGCAGAGCTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCATCATCTCCTCCTC
1 GAAGCAGAGGTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCATCT-CTCCTC
300621 GTCTCT-TCAATGGTTTTCA
65 GTCTCTGTCAA-GGTTTTCA
** *
300640 GAATTAGAGGTTTTGTGAAAGTAAGCAGTAGC
1 GAAGCAGAGGTTTTGTGGAAGTAAGCAGTAGC
300672 GAAATTTTCT
Statistics
Matches: 233, Mismatches: 38, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
80 1 0.00
81 117 0.50
82 4 0.02
83 5 0.02
84 106 0.45
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (83 bp):
GAAGCAGAGGTTTTGTGGAAGTAAGCAGTAGCATACTTGTCTTCCAAACTCTTCATCTCTCCTCG
TCTCTGTCAAGGTTTTCA
Found at i:303373 original size:154 final size:154
Alignment explanation
Indices: 303002--303407 Score: 733
Period size: 154 Copynumber: 2.6 Consensus size: 154
302992 AATTTATTAA
* * *
303002 TATAATTAACTTGATGAATAAAATTTAAAATGATTCAATATCTTGATCATATCAAATAGTATCAA
1 TATAATTTATTTGATGTATAAAATTTAAAATGATTCAATATCTTGATCATATCAAATAGTATCAA
303067 TAGTGGATATCATAATAACTGATACGGTCTATAGAAAATTTCTAAAATAATTGTACATACAACGC
66 TAGTGGATATCATAATAACTGATACGGTCTA-AGAAAATTTCTAAAATAATTGTACATACAACGC
303132 AGTTTGAGTATCAAATATTTTTTTT
130 AGTTTGAGTATCAAATATTTTTTTT
303157 TATAATTTATTTGATGTATAAAATTTAAAATGATTCAATATCTTGATCATATCAAATAGTATCAA
1 TATAATTTATTTGATGTATAAAATTTAAAATGATTCAATATCTTGATCATATCAAATAGTATCAA
303222 TAGTGGATATCATAATAACTGATACGGTCTAAGAAAATTTTCTAAAATAATTGTAC-TACAACGC
66 TAGTGGATATCATAATAACTGATACGGTCTAAGAAAA-TTTCTAAAATAATTGTACATACAACGC
303286 AGTTTGAGTATCAAATATTTTTTTT
130 AGTTTGAGTATCAAATATTTTTTTT
303311 TATAATTTATTTGATGTATAAAATTTAAAATGATTCAATATCTTGATCATATCAAATAGTATCAA
1 TATAATTTATTTGATGTATAAAATTTAAAATGATTCAATATCTTGATCATATCAAATAGTATCAA
* * *
303376 TAGTCGATATCGTAATAATTGATACGGTCTAA
66 TAGTGGATATCATAATAACTGATACGGTCTAA
303408 AAGATAACAT
Statistics
Matches: 244, Mismatches: 6, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
154 133 0.55
155 111 0.45
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (154 bp):
TATAATTTATTTGATGTATAAAATTTAAAATGATTCAATATCTTGATCATATCAAATAGTATCAA
TAGTGGATATCATAATAACTGATACGGTCTAAGAAAATTTCTAAAATAATTGTACATACAACGCA
GTTTGAGTATCAAATATTTTTTTT
Found at i:310154 original size:32 final size:32
Alignment explanation
Indices: 310109--310187 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
310099 CCTAAGGTGA
* * *
310109 CCCTTGGGGAGGCTCTTAGG-CACCAAGTTACT
1 CCCTTGGGTAGGCTCTAAGGAC-CCAAGGTACT
*
310141 CTCTTGGGTAGGCTCTAAGGACCCAAGGTACT
1 CCCTTGGGTAGGCTCTAAGGACCCAAGGTACT
* *
310173 CCCTTAGGTTGGCTC
1 CCCTTGGGTAGGCTC
310188 CTACGCCTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 38 0.97
33 1 0.03
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.27
Consensus pattern (32 bp):
CCCTTGGGTAGGCTCTAAGGACCCAAGGTACT
Found at i:310686 original size:216 final size:206
Alignment explanation
Indices: 310294--310726 Score: 571
Period size: 216 Copynumber: 2.0 Consensus size: 206
310284 TGAAATAAAC
* * *
310294 TACTATTTATGGTTTTCTTTAACACACTAGACCCCCAAACTCAATCTTCTAAATTTGTCTCTATG
1 TACTATTTATGGTTTTCTTGAACACACTAGACCCCCAAACTCAATATTCTAAATCTGTCTCTATG
* **
310359 AACGTTTCATTGAATCATAATCTTTTTAACTGTTACTAGTTAGTGAAATCTCAACTCATCACTAG
66 AACGTTTCATTGAATCATAAGCTTCCTAACTGTTACTAGTTAGTGAAATCTCAACTCATCACTAG
*
310424 GACATGTCTATGCCTGGATAAATAAGAAAATTTTCACGTTGCACCATATATATGCTTGCTCTTTA
131 GACATGCCTATGCCTGGATAAATAAGAAAATTTTCACGTTGCACCATATATATGCTTGCTCTTTA
*
310489 GCATCATATGG
196 GCACCATATGG
* * *
310500 TACTATTTCTGGTTTT-TTGGAACACACTAGACCCCCAAACTCAATATTCTAACTCTGTCTCTCT
1 TACTATTTATGGTTTTCTT-GAACACACTAGACCCCCAAACTCAATATTCTAAATCTGTCTCTAT
* * *
310564 GAACGTTTCATTTGAATCGTAAGCTTCCTAATTGTTACATGAAGATTTAATTAGTAGAATCTCAA
65 GAACGTTTCA-TTGAATCATAAGCTTCCTAACTGTTAC-T--AG--TT-AGT-G-A-AATCTCAA
* * *
310629 CTCATCACTAGGACCTGCCTATGCCTGGATAACTAAGAAAATTTTCATGTTGCACCATATATATG
120 CTCATCACTAGGACATGCCTATGCCTGGATAAATAAGAAAATTTTCACGTTGCACCATATATATG
* *
310694 TTTGCTCTTTAGCACCATCTGG
185 CTTGCTCTTTAGCACCATATGG
*
310716 TAGTTATTTAT
1 TA-CTATTTAT
310727 TATTGAGATT
Statistics
Matches: 194, Mismatches: 21, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
205 2 0.01
206 65 0.34
207 22 0.11
208 1 0.01
210 2 0.01
212 2 0.01
213 2 0.01
214 1 0.01
215 1 0.01
216 90 0.46
217 6 0.03
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (206 bp):
TACTATTTATGGTTTTCTTGAACACACTAGACCCCCAAACTCAATATTCTAAATCTGTCTCTATG
AACGTTTCATTGAATCATAAGCTTCCTAACTGTTACTAGTTAGTGAAATCTCAACTCATCACTAG
GACATGCCTATGCCTGGATAAATAAGAAAATTTTCACGTTGCACCATATATATGCTTGCTCTTTA
GCACCATATGG
Found at i:314490 original size:15 final size:15
Alignment explanation
Indices: 314470--314508 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
314460 GAACTGTGGA
*
314470 AAGAAGGGTCACTTG
1 AAGAAGGATCACTTG
314485 AAGAAGGATCACTTG
1 AAGAAGGATCACTTG
314500 AAGAAGGAT
1 AAGAAGGAT
314509 TGTTGGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.31, T:0.18
Consensus pattern (15 bp):
AAGAAGGATCACTTG
Found at i:315367 original size:3 final size:3
Alignment explanation
Indices: 315359--315396 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
315349 AAATTTTTGA
315359 TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
315397 TCACCTGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:316329 original size:37 final size:37
Alignment explanation
Indices: 316274--316352 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
316264 AGGTGAAGTT
*
316274 GGTGACAATAATGAATGACTATCAATTTAATGGAGTA
1 GGTGACAATAATGAATGACTAACAATTTAATGGAGTA
* *
316311 GGTGGCAATAATGTATGACTAACAATTTAATGGAGTA
1 GGTGACAATAATGAATGACTAACAATTTAATGGAGTA
316348 GGTGA
1 GGTGA
316353 TAATGTATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (37 bp):
GGTGACAATAATGAATGACTAACAATTTAATGGAGTA
Found at i:321096 original size:46 final size:46
Alignment explanation
Indices: 321046--321172 Score: 164
Period size: 46 Copynumber: 2.8 Consensus size: 46
321036 TGAAAATTTC
* *
321046 TCAATTTAATGGAGTAGGTGAAGTAGGTGGCAATAATGAATGACTA
1 TCAATTTAATGGAGTAGGTGAACTAGGTGGCAATAATGAATAACTA
* * *
321092 TCAATTTAATGGAGTAGGTGGACTATGTGGCAATAATGTATAACTA
1 TCAATTTAATGGAGTAGGTGAACTAGGTGGCAATAATGAATAACTA
* * * * *
321138 GCAATTTAATAGAGTAGGTGGACTATGTGGTAATA
1 TCAATTTAATGGAGTAGGTGAACTAGGTGGCAATA
321173 TATGGCTAGG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (46 bp):
TCAATTTAATGGAGTAGGTGAACTAGGTGGCAATAATGAATAACTA
Found at i:322450 original size:31 final size:28
Alignment explanation
Indices: 322394--322451 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
322384 CAACTAATGG
*
322394 CATGTCCATATCATAATAGATGATATGA
1 CATGTCCATATCATAAGAGATGATATGA
322422 CATGTCCATATCATAGTAGATGATGATATG
1 CATGTCCATATCATA--AGA-GATGATATG
322452 GCATATCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 15 0.58
30 2 0.08
31 9 0.35
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (28 bp):
CATGTCCATATCATAAGAGATGATATGA
Found at i:323588 original size:34 final size:34
Alignment explanation
Indices: 323550--323665 Score: 146
Period size: 34 Copynumber: 3.5 Consensus size: 34
323540 TGTAAATTTG
** *
323550 TTATTTAATAAATAAAATTTTATCGTATAAAATT
1 TTATTTAATATTTAAAATATTATCGTATAAAATT
**
323584 TTATTTTTTATTTAAAATATTATCGTATAAAATT
1 TTATTTAATATTTAAAATATTATCGTATAAAATT
* *
323618 TTATTTTATATTTAAAATATTATTGTAT-AAATT
1 TTATTTAATATTTAAAATATTATCGTATAAAATT
*
323651 TTAATTAAT-TTTAAA
1 TTATTTAATATTTAAA
323666 TTTATAAATT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
32 6 0.08
33 12 0.16
34 55 0.75
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (34 bp):
TTATTTAATATTTAAAATATTATCGTATAAAATT
Found at i:323599 original size:19 final size:19
Alignment explanation
Indices: 323577--323646 Score: 58
Period size: 19 Copynumber: 3.9 Consensus size: 19
323567 TTTTATCGTA
* *
323577 TAAAATTTTATTTTTTATT
1 TAAAATATTATTTTATATT
**
323596 TAAAATATTA--TCGTA--
1 TAAAATATTATTTTATATT
*
323611 TAAAATTTTATTTTATATT
1 TAAAATATTATTTTATATT
*
323630 TAAAATATTATTGTATA
1 TAAAATATTATTTTATA
323647 AATTTTAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
15 9 0.23
17 6 0.15
19 24 0.62
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (19 bp):
TAAAATATTATTTTATATT
Found at i:323627 original size:15 final size:15
Alignment explanation
Indices: 323561--323621 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 15
323551 TATTTAATAA
323561 ATAAAATTTTATCGT
1 ATAAAATTTTATCGT
**
323576 ATAAAATTTTATTTTTT
1 ATAAAATTTTA--TCGT
*
323593 ATTTAAAATATTATCGT
1 A--TAAAATTTTATCGT
323610 ATAAAATTTTAT
1 ATAAAATTTTAT
323622 TTTATATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
15 21 0.58
17 6 0.17
19 9 0.25
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (15 bp):
ATAAAATTTTATCGT
Found at i:326261 original size:88 final size:88
Alignment explanation
Indices: 326158--326342 Score: 370
Period size: 88 Copynumber: 2.1 Consensus size: 88
326148 AACGGGAGCG
326158 ATCAAAATAGTACACACATTTCATTAAAAAAATATTCAAACAGGAGGAATAAAAAATGGCTTATT
1 ATCAAAATAGTACACACATTTCATTAAAAAAATATTCAAACAGGAGGAATAAAAAATGGCTTATT
326223 TCAAAGCAATTGGAACAAATTTT
66 TCAAAGCAATTGGAACAAATTTT
326246 ATCAAAATAGTACACACATTTCATTAAAAAAATATTCAAACAGGAGGAATAAAAAATGGCTTATT
1 ATCAAAATAGTACACACATTTCATTAAAAAAATATTCAAACAGGAGGAATAAAAAATGGCTTATT
326311 TCAAAGCAATTGGAACAAATTTT
66 TCAAAGCAATTGGAACAAATTTT
326334 ATCAAAATA
1 ATCAAAATA
326343 ATTTCATGAA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 97 1.00
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27
Consensus pattern (88 bp):
ATCAAAATAGTACACACATTTCATTAAAAAAATATTCAAACAGGAGGAATAAAAAATGGCTTATT
TCAAAGCAATTGGAACAAATTTT
Found at i:327037 original size:21 final size:21
Alignment explanation
Indices: 327011--327059 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
327001 CCAATACGCA
327011 CTGCAACTACAGAATCTCGAG
1 CTGCAACTACAGAATCTCGAG
327032 CTGCAACTACAGAATCTCGAG
1 CTGCAACTACAGAATCTCGAG
327053 CTGCAAC
1 CTGCAAC
327060 AGCTACTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.18
Consensus pattern (21 bp):
CTGCAACTACAGAATCTCGAG
Found at i:328045 original size:3 final size:3
Alignment explanation
Indices: 328039--328179 Score: 273
Period size: 3 Copynumber: 47.0 Consensus size: 3
328029 GATGATGATG
328039 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
328087 ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
328135 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
328180 TCACCTTCCG
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
3 136 1.00
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:332150 original size:36 final size:35
Alignment explanation
Indices: 332102--332169 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
332092 CATCTTCATG
332102 AGGTATCAATACCAAAAATGATA-GTATCGATACCAT
1 AGGTATCAATACCAAAAA-G-TAGGTATCGATACCAT
* *
332138 AGGTATCGATACCAGAAAGTAGGTATCGATAC
1 AGGTATCAATACCAAAAAGTAGGTATCGATAC
332170 TTAGAAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 2 0.07
35 11 0.38
36 16 0.55
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (35 bp):
AGGTATCAATACCAAAAAGTAGGTATCGATACCAT
Found at i:338384 original size:194 final size:194
Alignment explanation
Indices: 338027--338385 Score: 450
Period size: 194 Copynumber: 1.9 Consensus size: 194
338017 GTGTTTTGCT
* * *
338027 ACAATATCTATTTCGTCACATATAAGTTGATTTTAATGCATTAATTGTGACAATATAAATTATCA
1 ACAATATCTATTTCGTCACATATAAGTTGATATTAATGCATTAATCGTGACAATATAAATCATCA
** * *
338092 ATAACGAAATCTTATTTAATTTAGTGACGTAACCAACTGTCATAGAATATAAATTATAAAGTGAT
66 ATAACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATAAATTATAAAGTGAC
* * * *
338157 GTTATGCATAAACGTCATTCATAATATTATTAGGTAGCATTTATATTATGTCACTAAAAATGTG
131 GTTATACATAAACGCCATCCATAATACTATTAGGTAGCATTTATATTATGTCACTAAAAATGTG
* * * *
338221 ACAATATCTCTTTCGTCACATATAGGTTGATATTAATGTATT-ATCCGTGACGATATAAATCATC
1 ACAATATCTATTTCGTCACATATAAGTTGATATTAATGCATTAAT-CGTGACAATATAAATCATC
* * ** ** * * *
338285 AATAATGAAATTTTACATAATTTAGTGACATAATTAGTTGTCATTGAATATTAATTATATAGTGA
65 AATAACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATAAATTATAAAGTGA
* * **
338350 CGTTATATATAAATGCCATCCATGCTACTATTAGGT
130 CGTTATACATAAACGCCATCCATAATACTATTAGGT
338386 GACGATATAC
Statistics
Matches: 136, Mismatches: 28, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
193 2 0.01
194 134 0.99
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (194 bp):
ACAATATCTATTTCGTCACATATAAGTTGATATTAATGCATTAATCGTGACAATATAAATCATCA
ATAACGAAATCTTACATAATTTAGTGACATAACCAACTGTCATAGAATATAAATTATAAAGTGAC
GTTATACATAAACGCCATCCATAATACTATTAGGTAGCATTTATATTATGTCACTAAAAATGTG
Found at i:339368 original size:14 final size:15
Alignment explanation
Indices: 339334--339371 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
339324 GAAATCATTG
339334 AAAAATTATATATAA
1 AAAAATTATATATAA
*
339349 ATAAAATTATGTA-AA
1 A-AAAATTATATATAA
339364 AAAAATTA
1 AAAAATTA
339372 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
AAAAATTATATATAA
Found at i:339556 original size:20 final size:20
Alignment explanation
Indices: 339509--339720 Score: 68
Period size: 20 Copynumber: 10.7 Consensus size: 20
339499 CAAAATATTT
* *
339509 GTGTTGCGAAAATAAAA-GC
1 GTGTTGCGAAATTAAAATTC
*
339528 -TGTTACGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
339547 GTGTTGCG-AATTCGAAAA-TC
1 GTGTTGCGAAATT--AAAATTC
* ** *
339567 GAGTTGCGAAAACAAAATTT
1 GTGTTGCGAAATTAAAATTC
* *
339587 GTGTTGCG-ATTTAGAAAATC
1 GTGTTGCGAAATTA-AAATTC
* * ** *
339607 TTGTTGTGAAAAGGAAACTT-
1 GTGTTGCG-AAATTAAAATTC
*
339627 GTGTTGCGAAA-AAGAAATTC
1 GTGTTGCGAAATTA-AAATTC
*
339647 GCGTTGCG-AATTCAGAAA-TC
1 GTGTTGCGAAATT-A-AAATTC
* *
339667 GAGTTGCGAATTTGGAAAA-TC
1 GTGTTGCGAAATT--AAAATTC
* *
339688 GTGTTGCGAATTTGGAAATT-
1 GTGTTGCGAAATT-AAAATTC
*
339708 GTGCTGCGAAATT
1 GTGTTGCGAAATT
339721 GGAGTTCGCG
Statistics
Matches: 143, Mismatches: 34, Indels: 31
0.69 0.16 0.15
Matches are distributed among these distances:
18 15 0.10
19 20 0.14
20 70 0.49
21 35 0.24
22 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:339618 original size:40 final size:40
Alignment explanation
Indices: 339540--339697 Score: 120
Period size: 40 Copynumber: 3.9 Consensus size: 40
339530 TTACGAAATT
* *
339540 AAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAAC
1 AAAATTTGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAC
* ** * *
339580 AAAATTTGTGTTGCGATTTAGAAAATCTTGTTGTGAAAAG
1 AAAATTTGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAC
* * ** * * **
339620 GAAACTTGTGTTGCGAAAAAGAAATTCGCGTTGCGAATTC
1 AAAATTTGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAC
* * * *
339660 AGAAA-TCGAGTTGCGAATTTGGAAAATCGTGTTGCGAA
1 A-AAATTTGTGTTGCGAA-TTAGAAAATCGAGTTGCGAA
339698 TTTGGAAATT
Statistics
Matches: 89, Mismatches: 27, Indels: 3
0.75 0.23 0.03
Matches are distributed among these distances:
40 71 0.80
41 18 0.20
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (40 bp):
AAAATTTGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAC
Done.