Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012415.1 Kokia drynarioides strain JFW-HI SEQ_127419, 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: 235286
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:2942 original size:32 final size:28
Alignment explanation
Indices: 2883--2943 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 28
2873 TTTAGGGTTG
*
2883 GTTGGATGGTGATTGGTGGTTGCGGCAA
1 GTTGGATGGTGATTGGTGGTTGAGGCAA
*
2911 GTTGTGATGGTGGTGTGGTGTGTGTGAGGCAA
1 GTTG-GATGGTGAT-TGGTG-GT-TGAGGCAA
2943 G
1 G
2944 GACGCATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.15
29 8 0.30
30 5 0.19
31 2 0.07
32 8 0.30
ACGTcount: A:0.13, C:0.05, G:0.49, T:0.33
Consensus pattern (28 bp):
GTTGGATGGTGATTGGTGGTTGAGGCAA
Found at i:6233 original size:29 final size:29
Alignment explanation
Indices: 6200--6295 Score: 104
Period size: 29 Copynumber: 3.3 Consensus size: 29
6190 CAATCATGCC
*
6200 ACAAATACAATCACGTCACATATACAGTT
1 ACAAATACAATCACGTCACAAATACAGTT
* * * *
6229 ACAAATACAGTCATGCCACAAATACAGTC
1 ACAAATACAATCACGTCACAAATACAGTT
* * *
6258 ACAGATA-AATTCACGTCATAGATACAGTT
1 ACAAATACAA-TCACGTCACAAATACAGTT
6287 ACAAATACA
1 ACAAATACA
6296 GTTATATCAC
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
28 1 0.02
29 50 0.96
30 1 0.02
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.22
Consensus pattern (29 bp):
ACAAATACAATCACGTCACAAATACAGTT
Found at i:6255 original size:17 final size:17
Alignment explanation
Indices: 6187--6258 Score: 64
Period size: 17 Copynumber: 4.5 Consensus size: 17
6177 ACAGTTACAG
*
6187 ATACAATCATGCCACAA
1 ATACAGTCATGCCACAA
* * * *
6204 ATACAATCACGTCACAT
1 ATACAGTCATGCCACAA
6221 ATACAGT--T---ACAA
1 ATACAGTCATGCCACAA
6233 ATACAGTCATGCCACAA
1 ATACAGTCATGCCACAA
6250 ATACAGTCA
1 ATACAGTCA
6259 CAGATAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
12 10 0.23
14 1 0.02
17 33 0.75
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.21
Consensus pattern (17 bp):
ATACAGTCATGCCACAA
Found at i:6309 original size:29 final size:29
Alignment explanation
Indices: 6200--6317 Score: 103
Period size: 29 Copynumber: 4.1 Consensus size: 29
6190 CAATCATGCC
* * * *
6200 ACAAATACAATCACGTCACATATACAGTT
1 ACAAATACAGTTATGTCACAGATACAGTT
* * * *
6229 ACAAATACAGTCATGCCACAAATACAGTC
1 ACAAATACAGTTATGTCACAGATACAGTT
* * * *
6258 ACAGATA-AATTCACGTCATAGATACAGTT
1 ACAAATACAGTT-ATGTCACAGATACAGTT
*
6287 ACAAATACAGTTATATCACAGATACAGTT
1 ACAAATACAGTTATGTCACAGATACAGTT
6316 AC
1 AC
6318 GGATGCAAAC
Statistics
Matches: 69, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
28 2 0.03
29 64 0.93
30 3 0.04
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (29 bp):
ACAAATACAGTTATGTCACAGATACAGTT
Found at i:9720 original size:17 final size:17
Alignment explanation
Indices: 9698--9739 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
9688 TAGAAATAAT
* *
9698 ATAGATACAGTCATGCC
1 ATAGATACAATCACGCC
*
9715 ATAGATACAATCACGTC
1 ATAGATACAATCACGCC
9732 ATAGATAC
1 ATAGATAC
9740 GTTATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (17 bp):
ATAGATACAATCACGCC
Found at i:9827 original size:17 final size:17
Alignment explanation
Indices: 9786--9832 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
9776 ATATAGTCAC
9786 GTCATAGATACAGTTA-
1 GTCATAGATACAGTTAT
9802 --CA-A-ATACAGTTAT
1 GTCATAGATACAGTTAT
9815 GTCATAGATACAGTTAT
1 GTCATAGATACAGTTAT
9832 G
1 G
9833 GATGCAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
12 9 0.35
13 1 0.04
14 2 0.08
15 2 0.08
16 1 0.04
17 11 0.42
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (17 bp):
GTCATAGATACAGTTAT
Found at i:9828 original size:29 final size:29
Alignment explanation
Indices: 9719--9830 Score: 109
Period size: 29 Copynumber: 3.9 Consensus size: 29
9709 CATGCCATAG
* * *
9719 ATACAATCACGTCATAGATAC-GTTATAA
1 ATACAGTCATGTCATAGATACAGTTACAA
* * * * * *
9747 ATACAGTCATGCCAAAAATATAGTCACAG
1 ATACAGTCATGTCATAGATACAGTTACAA
* *
9776 ATATAGTCACGTCATAGATACAGTTACAA
1 ATACAGTCATGTCATAGATACAGTTACAA
*
9805 ATACAGTTATGTCATAGATACAGTTA
1 ATACAGTCATGTCATAGATACAGTTA
9831 TGGATGCAGA
Statistics
Matches: 63, Mismatches: 20, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
28 15 0.24
29 48 0.76
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (29 bp):
ATACAGTCATGTCATAGATACAGTTACAA
Found at i:20370 original size:15 final size:16
Alignment explanation
Indices: 20350--20388 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
20340 TATAGCAATA
20350 TTTCTCTTTTT-T-TAT
1 TTTCTCTTTTTCTCT-T
20365 TTTCTCTTTTTCTCTT
1 TTTCTCTTTTTCTCTT
20381 TTTCTCTT
1 TTTCTCTT
20389 ATTCAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.50
16 10 0.45
17 1 0.05
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTCTTTTTCTCTT
Found at i:20375 original size:8 final size:8
Alignment explanation
Indices: 20350--20388 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
20340 TATAGCAATA
20350 TTTCTCTT
1 TTTCTCTT
20358 TTT-T-TAT
1 TTTCTCT-T
20365 TTTCTCTT
1 TTTCTCTT
20373 TTTCTCTT
1 TTTCTCTT
20381 TTTCTCTT
1 TTTCTCTT
20389 ATTCAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 1 0.04
7 5 0.18
8 21 0.75
9 1 0.04
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTCTCTT
Found at i:22455 original size:195 final size:192
Alignment explanation
Indices: 22025--22469 Score: 454
Period size: 194 Copynumber: 2.3 Consensus size: 192
22015 TACCAGTACT
* *
22025 CGATGCTGCTCACACAAG-TTATCGAGGACTCGCAACATATGCGGTACCCT-GACTATCGATACG
1 CGATGCTGCTCACACAAGCTT-TCGAGGACTCGCAACATATGCGGTA-CCTAG-CCATCGATACA
* * * * * * *
22088 GTGTCTGTCTGTACTATAAGTTGTTCCCTAACGATGCTGCAACATGAGTTGTCGAGAGTATGCGT
63 GTATCTG-CTGCACTATAAGCTGTTCCCTAACGATGCTGCAACACGAGCTGTCGAGAATATGCCT
** *
22153 AAAGCATAATCCCAACCATCGTAGGGCCGATAATCCATTTAGGATCCATATCTCTTTCTCGGGTC
127 AAAGCATAATCCCAACCATCGTAGGGCCGATAATCCATTTAGGATCCATATCTCTTTCTCGACTA
22218 A
192 A
* * * *
22219 TGATGATGCTCACACAAGCTGTCGAGGACTCACAACATATGCGGTACCATAGCCATCGATACAGT
1 CGATGCTGCTCACACAAGCTTTCGAGGACTCGCAACATATGCGGTACC-TAGCCATCGATACAGT
* * *
22284 ATCTG-TGCA-TATAA-CTGTTCCCTAACGATGTTGCTCACACGAGCTGTCGAGAATATGCACTT
65 ATCTGCTGCACTATAAGCTGTTCCCTAACGATGCTGC-AACACGAGCTGTCGAGAATATGC-CTA
* * * * * * *
22346 ATGCATAAATCTCAGCCATCGTAGGGCCTG-TAATCCATTCTTGGATTCTTTTCTCATTTC-CTG
128 AAGCAT-AATCCCAACCATCGTAGGGCC-GATAATCCATT-TAGGATCCATATCTC-TTTCTC-G
22409 ACTAA
188 ACTAA
* * * *
22414 CGATGCTACTCACACGAGCTTTCAAGGACTCGCAACATATGCGATACCTCAGCCAT
1 CGATGCTGCTCACACAAGCTTTCGAGGACTCGCAACATATGCGGTACCT-AGCCAT
22470 TACGTCGGTT
Statistics
Matches: 206, Mismatches: 34, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
190 18 0.09
191 24 0.12
192 9 0.04
193 30 0.15
194 70 0.34
195 55 0.27
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (192 bp):
CGATGCTGCTCACACAAGCTTTCGAGGACTCGCAACATATGCGGTACCTAGCCATCGATACAGTA
TCTGCTGCACTATAAGCTGTTCCCTAACGATGCTGCAACACGAGCTGTCGAGAATATGCCTAAAG
CATAATCCCAACCATCGTAGGGCCGATAATCCATTTAGGATCCATATCTCTTTCTCGACTAA
Found at i:40778 original size:18 final size:17
Alignment explanation
Indices: 40730--40788 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
40720 TATTTTTAAA
*
40730 AAAATTAATTTTATGGTTT
1 AAAATTAATTTT-TGG-GT
*
40749 GAAA-TAATTTTTGGGT
1 AAAATTAATTTTTGGGT
40765 AAAATTAATATTTTGGGT
1 AAAATTAAT-TTTTGGGT
*
40783 TAAATT
1 AAAATT
40789 GTAATATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.12
17 7 0.21
18 20 0.59
19 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.47
Consensus pattern (17 bp):
AAAATTAATTTTTGGGT
Found at i:54829 original size:80 final size:79
Alignment explanation
Indices: 54692--54848 Score: 260
Period size: 80 Copynumber: 2.0 Consensus size: 79
54682 TACAAGCACT
* * * *
54692 AATTTCATTTTAACTCTTGTAGGGAAGCTAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGT
1 AATTTCATTTTAACTCTTGTAAGGAAGCCAATGAGTCATGTCTCTTCATTAGAATCTGATGTAGC
54757 TAAAAAGGCATGGC
66 TAAAAAGGCATGGC
54771 AATTTCATTTTTAACTCTTGTAAGGAAGCCAATGAGTCATGTCTCTTCATTAGAATCTGATGTAG
1 AATTTCA-TTTTAACTCTTGTAAGGAAGCCAATGAGTCATGTCTCTTCATTAGAATCTGATGTAG
*
54836 CTAAAATGGCATG
65 CTAAAAAGGCATG
54849 ACATTTCTCC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
79 7 0.10
80 65 0.90
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (79 bp):
AATTTCATTTTAACTCTTGTAAGGAAGCCAATGAGTCATGTCTCTTCATTAGAATCTGATGTAGC
TAAAAAGGCATGGC
Found at i:58412 original size:80 final size:80
Alignment explanation
Indices: 58270--58420 Score: 284
Period size: 80 Copynumber: 1.9 Consensus size: 80
58260 ACTAATTTAA
*
58270 TTTTAACTCTTGTAGGGAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGTTGAAAAG
1 TTTTAACTCTTGTAGGGAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTGAAAAG
58335 GCATGGAAATTTTGT
66 GCATGGAAATTTTGT
*
58350 TTTTAACTCTTGTAGGGAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATTTAGCTGAAAAG
1 TTTTAACTCTTGTAGGGAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTGAAAAG
58415 GCATGG
66 GCATGG
58421 CATTTCTCCT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (80 bp):
TTTTAACTCTTGTAGGGAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTGAAAAG
GCATGGAAATTTTGT
Found at i:58988 original size:48 final size:48
Alignment explanation
Indices: 58863--58989 Score: 182
Period size: 48 Copynumber: 2.6 Consensus size: 48
58853 CATTTAATAG
* * * *
58863 AGATGCATTTAACAAACAAAACATTTAATAATGTAGATTACTAAACAA
1 AGATGCATTTAACAAACAAAACACTTAATGATATAGATCACTAAACAA
** **
58911 AGATGCATTTAACAAATGAAACACTTAATGATATAGATCGTTAAACAA
1 AGATGCATTTAACAAACAAAACACTTAATGATATAGATCACTAAACAA
58959 AGATGCATTTAACAAACAAAACACTTAATGA
1 AGATGCATTTAACAAACAAAACACTTAATGA
58990 AGCATAATTA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.26
Consensus pattern (48 bp):
AGATGCATTTAACAAACAAAACACTTAATGATATAGATCACTAAACAA
Found at i:75289 original size:10 final size:11
Alignment explanation
Indices: 75267--75310 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
75257 TGGCAATGTA
75267 TTTCT-TTTCT
1 TTTCTCTTTCT
75277 TTTCTCTTT-T
1 TTTCTCTTTCT
75287 TTTCTTCTTTCT
1 TTTC-TCTTTCT
75299 TTT-TCTTT-T
1 TTTCTCTTTCT
75308 TTT
1 TTT
75311 TTTGTGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 4 0.13
10 15 0.48
11 8 0.26
12 4 0.13
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTCTCTTTCT
Found at i:75311 original size:10 final size:10
Alignment explanation
Indices: 75267--75312 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 10
75257 TGGCAATGTA
75267 TTTCTTTTCTT
1 TTTCTTTT-TT
75278 TTCTCTTTTTT
1 TT-TCTTTTTT
*
75289 TCTTCTTTCTT
1 T-TTCTTTTTT
75300 TTTCTTTTTT
1 TTTCTTTTTT
75310 TTT
1 TTT
75313 TGTGATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 11 0.35
11 13 0.42
12 7 0.23
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:79906 original size:23 final size:23
Alignment explanation
Indices: 79880--79924 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
79870 AAGCAATTAC
79880 AACATCATGTTATAAACAATCAT
1 AACATCATGTTATAAACAATCAT
79903 AACATCATGTTATAAACAATCA
1 AACATCATGTTATAAACAATCA
79925 ATTAAATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (23 bp):
AACATCATGTTATAAACAATCAT
Found at i:80322 original size:28 final size:28
Alignment explanation
Indices: 80281--80372 Score: 87
Period size: 36 Copynumber: 3.0 Consensus size: 28
80271 GATATCCGAT
*
80281 TTACTCCCTTTTGACCCAAAGGTCATGC
1 TTACTCCCTTTTGACCAAAAGGTCATGC
80309 TTACT-CCTTATTGACCAAAAGGTCATAAAGCTC
1 TTACTCCCTT-TTGACCAAAAGGTCAT---G--C
80342 TTTTTACTCCCTTTTGACCAAAAGGTCATGC
1 ---TTACTCCCTTTTGACCAAAAGGTCATGC
80373 CTGTTACTAG
Statistics
Matches: 53, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
27 4 0.08
28 20 0.38
31 2 0.04
33 2 0.04
36 21 0.40
37 4 0.08
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (28 bp):
TTACTCCCTTTTGACCAAAAGGTCATGC
Found at i:80326 original size:27 final size:29
Alignment explanation
Indices: 80281--80334 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
80271 GATATCCGAT
80281 TTACTCCCTTTTGACCC-AAAGGTCATGC
1 TTACTCCCTTTTGACCCAAAAGGTCATGC
80309 TTACT-CCTTATTGA-CCAAAAGGTCAT
1 TTACTCCCTT-TTGACCCAAAAGGTCAT
80335 AAAGCTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (29 bp):
TTACTCCCTTTTGACCCAAAAGGTCATGC
Found at i:90045 original size:23 final size:24
Alignment explanation
Indices: 90018--90067 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
90008 AGAAATAATC
*
90018 TTTCAGTTAAA-TCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
*
90041 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
90065 TTT
1 TTT
90068 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:90076 original size:24 final size:24
Alignment explanation
Indices: 90029--90079 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
90019 TTCAGTTAAA
*
90029 TCTGTTTAATTGTTTCAATTAAAC
1 TCTGTTTAATTGTTTCAATCAAAC
* * *
90053 TCTGTTTATTTGTTTGAGTCAAAC
1 TCTGTTTAATTGTTTCAATCAAAC
90077 TCT
1 TCT
90080 TATTAGTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (24 bp):
TCTGTTTAATTGTTTCAATCAAAC
Found at i:96489 original size:26 final size:25
Alignment explanation
Indices: 96452--96500 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
96442 ATACATACAT
*
96452 CTTCCAAAACCTTGTCCAAACTTTC
1 CTTCCAAAACCTCGTCCAAACTTTC
* *
96477 CTTCGAAATACCTCGTGCAAACTT
1 CTTCCAAA-ACCTCGTCCAAACTT
96501 CACGTGTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.29, C:0.33, G:0.08, T:0.31
Consensus pattern (25 bp):
CTTCCAAAACCTCGTCCAAACTTTC
Found at i:96923 original size:19 final size:20
Alignment explanation
Indices: 96881--96923 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
96871 TTGGACTAAC
96881 AAACTATTCAAAGGAAACAT
1 AAACTATTCAAAGGAAACAT
*
96901 AAACTTTTCAGAA-GAAA-AT
1 AAACTATTCA-AAGGAAACAT
96920 AAAC
1 AAAC
96924 CTACTAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 13 0.62
21 2 0.10
ACGTcount: A:0.56, C:0.14, G:0.09, T:0.21
Consensus pattern (20 bp):
AAACTATTCAAAGGAAACAT
Found at i:112277 original size:25 final size:23
Alignment explanation
Indices: 112249--112294 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
112239 GTTGGATCCA
112249 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
112274 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
112295 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:113323 original size:16 final size:16
Alignment explanation
Indices: 113298--113329 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
113288 CTCAAACACA
113298 CTTTTATCTTTTTTTT
1 CTTTTATCTTTTTTTT
*
113314 CTTTTTTCTTTTTTTT
1 CTTTTATCTTTTTTTT
113330 TTCTAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (16 bp):
CTTTTATCTTTTTTTT
Found at i:114253 original size:5 final size:5
Alignment explanation
Indices: 114243--114295 Score: 61
Period size: 5 Copynumber: 9.8 Consensus size: 5
114233 AGTGCATAAT
*
114243 TAAAA TAAAA TTAAAAA TAAAA TAAGA TAAAA TAAAA TAAAA TTGAAAA
1 TAAAA TAAAA -T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA -T-AAAA
114292 TAAA
1 TAAA
114296 TATACTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 30 0.71
6 4 0.10
7 8 0.19
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:114273 original size:27 final size:27
Alignment explanation
Indices: 114243--114294 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
114233 AGTGCATAAT
114243 TAAAATAAAATTAAAAAT-AAAATAAGA
1 TAAAATAAAA-TAAAAATGAAAATAAGA
*
114270 TAAAATAAAATAAAATTGAAAATAA
1 TAAAATAAAATAAAAATGAAAATAA
114295 ATATACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (27 bp):
TAAAATAAAATAAAAATGAAAATAAGA
Found at i:114358 original size:19 final size:19
Alignment explanation
Indices: 114304--114358 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
114294 AATATACTAT
* *
114304 TTTTTTTTTGAACTTTTCAA
1 TTTTTTTTTCAA-TTTTTAA
*
114324 -TTTTTTTTCAA--ATTAA
1 TTTTTTTTTCAATTTTTAA
114340 TTTTTTTTTCAATTTTTAA
1 TTTTTTTTTCAATTTTTAA
114359 AAAAAAAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
16 3 0.11
17 11 0.39
19 14 0.50
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTTTTTCAATTTTTAA
Found at i:119859 original size:14 final size:13
Alignment explanation
Indices: 119839--119888 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 13
119829 ATAAAAGGGA
119839 AAAAAATTAAATT
1 AAAAAATTAAATT
119852 AGAAAAATTAAATT
1 A-AAAAATTAAATT
119866 -AAAAATGTAAATAAT
1 AAAAAAT-TAAAT--T
119881 AAAAAATT
1 AAAAAATT
119889 GCTAAAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.19
13 6 0.19
14 12 0.38
15 2 0.06
16 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (13 bp):
AAAAAATTAAATT
Found at i:120979 original size:25 final size:23
Alignment explanation
Indices: 120951--120996 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
120941 GTTGGATCCA
120951 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
120976 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
120997 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:121083 original size:13 final size:13
Alignment explanation
Indices: 121062--121095 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
121052 ACAATATAAT
121062 AATAATAATCCTA
1 AATAATAATCCTA
*
121075 AATATTAATCCTA
1 AATAATAATCCTA
*
121088 AAAAATAA
1 AATAATAA
121096 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:121533 original size:42 final size:42
Alignment explanation
Indices: 121463--121550 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
121453 ATTGGCAATC
* * * *
121463 ACTACCATAAAAAATTCTCGTGACTTTTCCACATTCTTCGTT
1 ACTACCATAAAAAATTCCCATAACTTTTCCACATTCTTCATT
*
121505 ACTACCATAAAAAATTCCCATAATTTTTCCACATTCTTCATT
1 ACTACCATAAAAAATTCCCATAACTTTTCCACATTCTTCATT
121547 ACTA
1 ACTA
121551 TCGCCCTTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (42 bp):
ACTACCATAAAAAATTCCCATAACTTTTCCACATTCTTCATT
Found at i:123194 original size:2 final size:2
Alignment explanation
Indices: 123187--123217 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
123177 GGAATAAACC
123187 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
123218 TGGTGAAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:127047 original size:20 final size:21
Alignment explanation
Indices: 127013--127068 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
127003 ATTTAAAATT
*
127013 AAAT-TAATTATTTTTATTTA
1 AAATCTAAATATTTTTATTTA
127033 AAATCTAAATATTTTTATTTA
1 AAATCTAAATATTTTTATTTA
127054 AAATCTAAATATTTT
1 AAATCTAAATATTTT
127069 AACACATGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 4 0.12
21 30 0.88
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATCTAAATATTTTTATTTA
Found at i:129073 original size:20 final size:20
Alignment explanation
Indices: 129050--129148 Score: 59
Period size: 19 Copynumber: 5.2 Consensus size: 20
129040 TATATAAGTT
129050 TAAAAATTATTAAAATATTA
1 TAAAAATTATTAAAATATTA
*
129070 TAAAAATT-TTGAAAAT-TAA
1 TAAAAATTATT-AAAATATTA
* * * *
129089 AAAAAACTA-TAGAAAAACTA
1 TAAAAATTATTA-AAATATTA
** *
129109 TAAATTTTATT-AAATATCA
1 TAAAAATTATTAAAATATTA
129128 T-AAAATT-TTAAAAT-TTA
1 TAAAAATTATTAAAATATTA
129145 TAAA
1 TAAA
129149 TACTATTAAG
Statistics
Matches: 56, Mismatches: 16, Indels: 16
0.64 0.18 0.18
Matches are distributed among these distances:
17 5 0.09
18 11 0.20
19 20 0.36
20 19 0.34
21 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAAATTATTAAAATATTA
Found at i:129977 original size:48 final size:48
Alignment explanation
Indices: 129923--130067 Score: 193
Period size: 48 Copynumber: 3.0 Consensus size: 48
129913 TTGATTTCAC
129923 TTTTCGACGAAGGGTTCAATTAATTTTCTAATTTTTTTAATATTTAAG
1 TTTTCGACGAAGGGTTCAATTAATTTTCTAATTTTTTTAATATTTAAG
* * * *
129971 TTTTCGACG-AGGGATTCGATTAATTTTTTATTTTTTTTAATATTTAAA
1 TTTTCGACGAAGGG-TTCAATTAATTTTCTAATTTTTTTAATATTTAAG
* * * **
130019 TTTTTGACGAGGGGCTCAATTAATTTTCTTGTTTTTTTAATATTTAAG
1 TTTTCGACGAAGGGTTCAATTAATTTTCTAATTTTTTTAATATTTAAG
130067 T
1 T
130068 ATTTAAAATA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
47 4 0.05
48 76 0.92
49 3 0.04
ACGTcount: A:0.26, C:0.08, G:0.14, T:0.52
Consensus pattern (48 bp):
TTTTCGACGAAGGGTTCAATTAATTTTCTAATTTTTTTAATATTTAAG
Found at i:130923 original size:20 final size:24
Alignment explanation
Indices: 130898--130953 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 24
130888 TGTACGATAA
130898 ATAAATTAATTT-TTT-T-AAA-G
1 ATAAATTAATTTATTTATGAAATG
*
130918 ATAAA-TACTTTATTTATGAAATG
1 ATAAATTAATTTATTTATGAAATG
130941 ATAAATTAATTTA
1 ATAAATTAATTTA
130954 ATAGTCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 5 0.17
20 8 0.28
21 1 0.03
22 3 0.10
23 6 0.21
24 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (24 bp):
ATAAATTAATTTATTTATGAAATG
Found at i:137692 original size:36 final size:36
Alignment explanation
Indices: 137652--137776 Score: 187
Period size: 36 Copynumber: 3.5 Consensus size: 36
137642 TGATGATTGT
* * *
137652 TGTGAAAGTAAATATGTGGGTTTGTTATTCATACCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
*
137688 TGTGACAGTAAATGTGTGGGTATGTTATTCATGCCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
*
137724 TGAGACAGTAAATATGTGGGTATGTTATTCATGCCA
1 TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
* *
137760 TGTGATAGTGAATATGT
1 TGTGACAGTAAATATGT
137777 TGTGCTCATG
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 80 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.37
Consensus pattern (36 bp):
TGTGACAGTAAATATGTGGGTATGTTATTCATGCCA
Found at i:138128 original size:68 final size:68
Alignment explanation
Indices: 138019--138158 Score: 199
Period size: 68 Copynumber: 2.1 Consensus size: 68
138009 GGGAAATAAG
* * * * * * * *
138019 GAGAGTGTTAGCTTTATGCTTCGCTTTTGGGATATGTTCGACTCTATGAGTTATATTTGGTGTGT
1 GAGAGTGTTAGCTATATGCTTCACTTATGGAACATGTTCGACTCTAAGAGTCATATTTAGTGTGT
138084 TTA
66 TTA
138087 GAGAGTGTTAGCTATATGCTTCACTTATGGAACATGTTCGACTCTAAGAGTCATATTTAGTGTGT
1 GAGAGTGTTAGCTATATGCTTCACTTATGGAACATGTTCGACTCTAAGAGTCATATTTAGTGTGT
*
138152 TTG
66 TTA
138155 GAGA
1 GAGA
138159 TTCGCGTATC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (68 bp):
GAGAGTGTTAGCTATATGCTTCACTTATGGAACATGTTCGACTCTAAGAGTCATATTTAGTGTGT
TTA
Found at i:138276 original size:20 final size:20
Alignment explanation
Indices: 138250--138298 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
138240 ATGTGATTAA
138250 ATATGATTATGTGTGAC-TAT
1 ATATGATTATGTGTG-CTTAT
* *
138270 ATGTGATTATTTGTGCTTAT
1 ATATGATTATGTGTGCTTAT
138290 ATATGATTA
1 ATATGATTA
138299 ACATATGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (20 bp):
ATATGATTATGTGTGCTTAT
Found at i:138284 original size:10 final size:10
Alignment explanation
Indices: 138240--138298 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 10
138230 TTGTGACTAA
*
138240 ATGTGATTAA
1 ATGTGATTAT
*
138250 ATATGATTAT
1 ATGTGATTAT
* *
138260 GTGTGACTAT
1 ATGTGATTAT
138270 ATGTGATTAT
1 ATGTGATTAT
* *
138280 TTGTGCTTAT
1 ATGTGATTAT
*
138290 ATATGATTA
1 ATGTGATTA
138299 ACATATGACA
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (10 bp):
ATGTGATTAT
Found at i:138663 original size:23 final size:23
Alignment explanation
Indices: 138312--138656 Score: 413
Period size: 23 Copynumber: 15.0 Consensus size: 23
138302 TATGACAAAT
138312 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* ** *
138335 TGCTTAAATTTTAATACGATTTA
1 TGCTTAAATATTAATGTGATTTG
* * * * *
138358 TGCTTAGATGTTAGTATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
138381 TGCTTAAA-AGTTAATGTGATTTA
1 TGCTTAAATA-TTAATGTGATTTG
*
138404 TGCTTAAATATTAATGTAATTTG
1 TGCTTAAATATTAATGTGATTTG
*
138427 TGCTTAAATAATAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
138450 TGCTCAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
138473 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
** * * *
138496 TAATAAAATATTATTGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
138519 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
138542 TACTTAAATATTAATGTTATTTG
1 TGCTTAAATATTAATGTGATTTG
138565 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
138588 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
* * *
138611 TGATTAAATATTAATGTGACTTA
1 TGCTTAAATATTAATGTGATTTG
** *
138634 TTATTAAACATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
138657 CGATTAATGT
Statistics
Matches: 276, Mismatches: 44, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
23 275 1.00
24 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:145041 original size:29 final size:28
Alignment explanation
Indices: 145009--145322 Score: 113
Period size: 29 Copynumber: 10.8 Consensus size: 28
144999 TTAAAAAAAA
145009 TCGAGGTCAAAAATGGAATTTTGGGAAGT
1 TCGAGGT-AAAAATGGAATTTTGGGAAGT
* * *
145038 TCGAGGGT-AAATTGGTATTTTTTTGGTGAAAT
1 TCGA-GGTAAAAATGG-A--ATTTTGG-GAAGT
* *
145070 T-GAGGTCAAAAATGGAATTTTAGAAAGT
1 TCGAGGT-AAAAATGGAATTTTGGGAAGT
* * * *
145098 TCG-GGATGAAATTGTAATTTTTGGTGAA-A
1 TCGAGG-TAAAAATGGAA-TTTTGG-GAAGT
*
145127 TCGAGGTCAAAAATGGAATTTTTGGAAGT
1 TCGAGGT-AAAAATGGAATTTTGGGAAGT
* * * *
145156 TCAAGGGTAAAAATGTAATTTTTGAAAGT
1 TCGA-GGTAAAAATGGAATTTTGGGAAGT
* *** *
145185 T-TATGGT-AAAATGGTAATTTTTTATTAAAT
1 TCGA-GGTAAAAATGG-AA--TTTTGGGAAGT
* *
145215 T-AAGGTCAAAAATGGAATTTTGGAAAGTT
1 TCGAGGT-AAAAATGGAATTTTGGGAAG-T
* * * *
145244 TAGGGGTAAAAATGTAATTTTTGGTGAA-A
1 TCGAGGTAAAAATGGAA-TTTTGG-GAAGT
* *
145273 TCGAGGTTAAAATGGAATTTTGGAAAGTT
1 TCGAGGTAAAAATGGAATTTTGGGAAG-T
** *
145302 TAAAGGTAAAAATGTAATTTT
1 TCGAGGTAAAAATGGAATTTT
145323 TGAAAGTTTA
Statistics
Matches: 210, Mismatches: 49, Indels: 52
0.68 0.16 0.17
Matches are distributed among these distances:
27 8 0.04
28 40 0.19
29 93 0.44
30 40 0.19
31 18 0.09
32 11 0.05
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (28 bp):
TCGAGGTAAAAATGGAATTTTGGGAAGT
Found at i:145077 original size:60 final size:58
Alignment explanation
Indices: 145006--145179 Score: 233
Period size: 58 Copynumber: 2.9 Consensus size: 58
144996 GATTTAAAAA
* *
145006 AAATCGAGGTCAAAAATGGAATTTTGGGAAGTTCGAGGGTAAATTGGTATTTTTTTGGTG
1 AAATCGAGGTCAAAAATGGAATTTTAGGAAGTTCGAGGGTAAATT-GTA-ATTTTTGGTG
* * *
145066 AAATTGAGGTCAAAAATGGAATTTTAGAAAGTTCG-GGATGAAATTGTAATTTTTGGTG
1 AAATCGAGGTCAAAAATGGAATTTTAGGAAGTTCGAGGGT-AAATTGTAATTTTTGGTG
* * *
145124 AAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTTG
1 AAATCGAGGTCAAAAATGGAATTTTAGGAAGTTCGAGGGT-AAATTGTAATTTTTG
145180 AAAGTTTATG
Statistics
Matches: 100, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
58 40 0.40
59 23 0.23
60 37 0.37
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (58 bp):
AAATCGAGGTCAAAAATGGAATTTTAGGAAGTTCGAGGGTAAATTGTAATTTTTGGTG
Found at i:145183 original size:87 final size:87
Alignment explanation
Indices: 145077--145266 Score: 231
Period size: 87 Copynumber: 2.2 Consensus size: 87
145067 AATTGAGGTC
* * * * * * *
145077 AAAAATGGAATTTTAGAAAG-TTCGGGATGAAATTGTAATTTTTGGTGAAATCGAGGTCAAAAAT
1 AAAAATGTAATTTTTGAAAGTTTAGGG-TAAAATGGTAATTTTTGATGAAATCAAGGTCAAAAAT
145141 GGAATTTTTGG-AAGTTCAAGGGT
65 GGAA-TTTTGGAAAGTTCAAGGGT
* * * *
145164 AAAAATGTAATTTTTGAAAGTTTATGGTAAAATGGTAATTTTTTATTAAATTAAGGTCAAAAATG
1 AAAAATGTAATTTTTGAAAGTTTAGGGTAAAATGGTAATTTTTGATGAAATCAAGGTCAAAAATG
* *
145229 GAATTTTGGAAAGTTTAGGGGT
66 GAATTTTGGAAAGTTCAAGGGT
145251 AAAAATGTAATTTTTG
1 AAAAATGTAATTTTTG
145267 GTGAAATCGA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
86 6 0.07
87 78 0.89
88 4 0.05
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (87 bp):
AAAAATGTAATTTTTGAAAGTTTAGGGTAAAATGGTAATTTTTGATGAAATCAAGGTCAAAAATG
GAATTTTGGAAAGTTCAAGGGT
Found at i:145228 original size:58 final size:57
Alignment explanation
Indices: 145130--145325 Score: 200
Period size: 58 Copynumber: 3.4 Consensus size: 57
145120 GGTGAAATCG
* * * *
145130 AGGTCAAAAATGGAATTTTTG--GAAGTTCAAGGGTAAAAATGTAATTTTTGAAAGTTTA
1 AGGT-AAAAATGTAATTTTTGATGAA-ATCAA-GGTAAAAATGGAATTTTGGAAAGTTTA
* * * *
145188 TGGT-AAAATGGTAATTTTTTATTAAATTAAGGTCAAAAATGGAATTTTGGAAAGTTTA
1 AGGTAAAAAT-GTAATTTTTGATGAAATCAAGGT-AAAAATGGAATTTTGGAAAGTTTA
* * * *
145246 GGGGTAAAAATGTAATTTTTGGTGAAATCGAGGTTAAAATGGAATTTTGGAAAGTTTAA
1 -AGGTAAAAATGTAATTTTTGATGAAATCAAGGTAAAAATGGAATTTTGGAAAGTTT-A
145305 AGGTAAAAATGTAATTTTTGA
1 AGGTAAAAATGTAATTTTTGA
145326 AAGTTTAGGG
Statistics
Matches: 114, Mismatches: 17, Indels: 14
0.79 0.12 0.10
Matches are distributed among these distances:
56 5 0.04
57 11 0.10
58 69 0.61
59 24 0.21
60 5 0.04
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (57 bp):
AGGTAAAAATGTAATTTTTGATGAAATCAAGGTAAAAATGGAATTTTGGAAAGTTTA
Found at i:145327 original size:29 final size:28
Alignment explanation
Indices: 145130--145359 Score: 171
Period size: 29 Copynumber: 7.9 Consensus size: 28
145120 GGTGAAATCG
* * *
145130 AGGTCAAAAATGGAATTTTTGGAAGTTCA
1 AGGT-AAAAATGTAATTTTTGAAAGTTTA
145159 AGGGTAAAAATGTAATTTTTGAAAGTTTA
1 A-GGTAAAAATGTAATTTTTGAAAGTTTA
* * *
145188 TGGT-AAAATGGTAATTTTTTATTAA-ATTA
1 AGGTAAAAAT-GTAATTTTTGA--AAGTTTA
* *
145217 AGGTCAAAAATGGAATTTTGGAAAGTTTA
1 AGGT-AAAAATGTAATTTTTGAAAGTTTA
* **
145246 GGGGTAAAAATGTAATTTTTGGTGAAA--TCG
1 -AGGTAAAAATGTAA-TTTT--TGAAAGTTTA
* * *
145276 AGGTTAAAATGGAATTTTGGAAAGTTTAA
1 AGGTAAAAATGTAATTTTTGAAAGTTT-A
145305 AGGTAAAAATGTAATTTTTGAAAGTTTA
1 AGGTAAAAATGTAATTTTTGAAAGTTTA
* * *
145333 GGGTTAAAAATATAATTTTTAAAAGTT
1 AGG-TAAAAATGTAATTTTTGAAAGTT
145360 CGGGGGTCAG
Statistics
Matches: 158, Mismatches: 28, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
26 4 0.03
27 5 0.03
28 23 0.15
29 96 0.61
30 21 0.13
31 5 0.03
32 4 0.03
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (28 bp):
AGGTAAAAATGTAATTTTTGAAAGTTTA
Found at i:145913 original size:11 final size:9
Alignment explanation
Indices: 145891--145918 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
145881 AGTTTTGAAA
145891 CTCTCTCAT
1 CTCTCTCAT
145900 CTCTCTCAT
1 CTCTCTCAT
145909 CTCTCTCAT
1 CTCTCTCAT
145918 C
1 C
145919 CTATCTTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.46, G:0.00, T:0.43
Consensus pattern (9 bp):
CTCTCTCAT
Found at i:146473 original size:3 final size:3
Alignment explanation
Indices: 146467--146501 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
146457 TTATCACCAA
*
146467 TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
146502 AAGATACTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:147713 original size:18 final size:18
Alignment explanation
Indices: 147692--147726 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
147682 TCCCAATTGT
*
147692 TAAAAACAATAGTGAATG
1 TAAAAACAAAAGTGAATG
*
147710 TAAAAATAAAAGTGAAT
1 TAAAAACAAAAGTGAAT
147727 AAATATTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.03, G:0.14, T:0.23
Consensus pattern (18 bp):
TAAAAACAAAAGTGAATG
Found at i:149329 original size:26 final size:24
Alignment explanation
Indices: 149287--149347 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
149277 TTTAATTAGT
*
149287 ATAAAATATTAACAATTTAAAATAA
1 ATAAAAAATTAACAATTT-AAATAA
*
149312 ATAAAAAAGTTAATAATTTAAATAA
1 ATAAAAAA-TTAACAATTTAAATAA
*
149337 ATTAAAAATTA
1 ATAAAAAATTA
149348 GAAAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.09
25 20 0.62
26 9 0.28
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
ATAAAAAATTAACAATTTAAATAA
Found at i:150083 original size:28 final size:29
Alignment explanation
Indices: 150043--150100 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
150033 CTGTTGTAAA
150043 AATATTTACAAAA-AAGACAACT-AATTTT
1 AATATTTACAAAATAA-ACAACTAAATTTT
*
150071 AATATTTACAAAATTAACAACTAAATTTT
1 AATATTTACAAAATAAACAACTAAATTTT
150100 A
1 A
150101 CAAAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.34
Consensus pattern (29 bp):
AATATTTACAAAATAAACAACTAAATTTT
Found at i:156107 original size:16 final size:16
Alignment explanation
Indices: 156086--156116 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
156076 AAACTAAAAT
*
156086 AAACTAAGTTAAATTA
1 AAACTAAATTAAATTA
156102 AAACTAAATTAAATT
1 AAACTAAATTAAATT
156117 CCTATGCCCG
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:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (16 bp):
AAACTAAATTAAATTA
Found at i:157924 original size:22 final size:22
Alignment explanation
Indices: 157899--157942 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
157889 CTCCACCATA
157899 CATAGTTTCCACACCTTCTCCC
1 CATAGTTTCCACACCTTCTCCC
157921 CATAGTTTCCACACCTTCTCCC
1 CATAGTTTCCACACCTTCTCCC
157943 TTCCTCTACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.45, G:0.05, T:0.32
Consensus pattern (22 bp):
CATAGTTTCCACACCTTCTCCC
Found at i:161142 original size:20 final size:20
Alignment explanation
Indices: 161117--161177 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
161107 CAATTTGTGG
*
161117 ACAAGCCACTAGTAATGCAA
1 ACAAGCCACCAGTAATGCAA
** **
161137 ACAAGCTGCCAGTAATGTGA
1 ACAAGCCACCAGTAATGCAA
* *
161157 ACAAGCCACCAATAGTGCAA
1 ACAAGCCACCAGTAATGCAA
161177 A
1 A
161178 TAAACTGCCA
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.25, G:0.18, T:0.15
Consensus pattern (20 bp):
ACAAGCCACCAGTAATGCAA
Found at i:161162 original size:40 final size:40
Alignment explanation
Indices: 161112--161193 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
161102 CAATCCAATT
* * * * *
161112 TGTGGACAAGCCACTAGTAATGCAAACAAGCTGCCAGTAA
1 TGTGAACAAGCCACCAATAATGCAAACAAACTGCCAATAA
* *
161152 TGTGAACAAGCCACCAATAGTGCAAATAAACTGCCAATAA
1 TGTGAACAAGCCACCAATAATGCAAACAAACTGCCAATAA
161192 TG
1 TG
161194 CAGACAAGCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (40 bp):
TGTGAACAAGCCACCAATAATGCAAACAAACTGCCAATAA
Found at i:161201 original size:40 final size:39
Alignment explanation
Indices: 161116--161202 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 39
161106 CCAATTTGTG
* * * * *
161116 GACAAGCCACTAGTAATGCAAACAAGCTGCCAGTAATGT
1 GACAAGCCACCAATAATGCAAACAAACTGCCAATAATGA
* *
161155 GAACAAGCCACCAATAGTGCAAATAAACTGCCAATAATGCA
1 G-ACAAGCCACCAATAATGCAAACAAACTGCCAATAATG-A
161196 GACAAGC
1 GACAAGC
161203 TGTCAGTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.03
40 37 0.95
41 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.15
Consensus pattern (39 bp):
GACAAGCCACCAATAATGCAAACAAACTGCCAATAATGA
Found at i:161201 original size:60 final size:59
Alignment explanation
Indices: 161129--161310 Score: 202
Period size: 60 Copynumber: 3.0 Consensus size: 59
161119 AAGCCACTAG
* * *
161129 TAATGCAAACAAGCTGCCAGTAATGTGAACAAGCCACCAATAGTGCAAATAAACTGCCAA
1 TAATGCAGACAAGCTGCCAGTATTGTG-ACAAGCCACCAATAGTGCAGATAAACTGCCAA
* * ** * * * * * *
161189 TAATGCAGACAAGCTGTCAGTATTATGGACAAATCGCCAACAATGCAGATAAACTACTAG
1 TAATGCAGACAAGCTGCCAGTATTGT-GACAAGCCACCAATAGTGCAGATAAACTGCCAA
* *
161249 TAATGCAGACAAGCTGCCAGTATTGTCGACAAGCCACCAGTAGTGCAGATAAATTGCCAA
1 TAATGCAGACAAGCTGCCAGTATTGT-GACAAGCCACCAATAGTGCAGATAAACTGCCAA
161309 TA
1 TA
161311 CTTCCTCCTT
Statistics
Matches: 95, Mismatches: 26, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.20
Consensus pattern (59 bp):
TAATGCAGACAAGCTGCCAGTATTGTGACAAGCCACCAATAGTGCAGATAAACTGCCAA
Found at i:161270 original size:20 final size:20
Alignment explanation
Indices: 161127--161297 Score: 64
Period size: 20 Copynumber: 8.6 Consensus size: 20
161117 ACAAGCCACT
*
161127 AGTAATGCAAACAAGCTGCC
1 AGTAATGCAGACAAGCTGCC
* **
161147 AGTAATG-TGAACAAGCCACC
1 AGTAATGCAG-ACAAGCTGCC
* * * * *
161167 AATAGTGCAAATAAACTGCC
1 AGTAATGCAGACAAGCTGCC
* *
161187 AATAATGCAGACAAGCTGTC
1 AGTAATGCAGACAAGCTGCC
*
161207 AGTATTATG--GACAA-ATCGCC
1 AGTA--ATGCAGACAAGCT-GCC
** * * * *
161227 AACAATGCAGATAAACTACT
1 AGTAATGCAGACAAGCTGCC
161247 AGTAATGCAGACAAGCTGCC
1 AGTAATGCAGACAAGCTGCC
* **
161267 AGTATTGTC-GACAAGCCACC
1 AGTAATG-CAGACAAGCTGCC
*
161287 AGTAGTGCAGA
1 AGTAATGCAGA
161298 TAAATTGCCA
Statistics
Matches: 105, Mismatches: 36, Indels: 20
0.65 0.22 0.12
Matches are distributed among these distances:
18 3 0.03
19 2 0.02
20 95 0.90
21 2 0.02
22 3 0.03
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (20 bp):
AGTAATGCAGACAAGCTGCC
Found at i:169800 original size:50 final size:49
Alignment explanation
Indices: 169745--169855 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 49
169735 TTATGGCTCA
*
169745 TAAGAGTGATATTCTATCTTA-CTCGTAAGAACGTAATTCTGTCTTACTCG
1 TAAGAG-GATATTCTATC-TAGCTCGTAAGAACGTAATTCTGTCTGACTCG
* * * * *
169795 TAAGAGCATAATTCTGTCTAGCTCGTAAGACCGTGATTCTGTCTGGCTCG
1 TAAGAGGAT-ATTCTATCTAGCTCGTAAGAACGTAATTCTGTCTGACTCG
169845 TAAGAGCGATA
1 TAAGAG-GATA
169856 CTTTGTTTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
49 4 0.08
50 45 0.88
51 2 0.04
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (49 bp):
TAAGAGGATATTCTATCTAGCTCGTAAGAACGTAATTCTGTCTGACTCG
Found at i:169833 original size:25 final size:25
Alignment explanation
Indices: 169766--169849 Score: 107
Period size: 25 Copynumber: 3.4 Consensus size: 25
169756 TTCTATCTTA
169766 CTCGTAAGAACGTAATTCTGTCTTA-
1 CTCGTAAGAACGTAATTCTGTC-TAG
* *
169791 CTCGTAAGAGCATAATTCTGTCTAG
1 CTCGTAAGAACGTAATTCTGTCTAG
* * *
169816 CTCGTAAGACCGTGATTCTGTCTGG
1 CTCGTAAGAACGTAATTCTGTCTAG
169841 CTCGTAAGA
1 CTCGTAAGA
169850 GCGATACTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
24 2 0.04
25 50 0.96
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (25 bp):
CTCGTAAGAACGTAATTCTGTCTAG
Found at i:169866 original size:25 final size:25
Alignment explanation
Indices: 169738--169868 Score: 99
Period size: 25 Copynumber: 5.2 Consensus size: 25
169728 ATTCTGATTA
* * *
169738 TGGCTCATAAGAGTGATATTCTATC
1 TGGCTCGTAAGAGCGATATTCTGTC
** *
169763 TTACTCGTAAGAACG-TAATTCTGTC
1 TGGCTCGTAAGAGCGAT-ATTCTGTC
**
169788 TTACTCGTAAGAGC-ATAATTCTGTC
1 TGGCTCGTAAGAGCGAT-ATTCTGTC
* *
169813 TAGCTCGTAAGACCG-TGATTCTGTC
1 TGGCTCGTAAGAGCGAT-ATTCTGTC
*
169838 TGGCTCGTAAGAGCGATACTT-TGTT
1 TGGCTCGTAAGAGCGATA-TTCTGTC
169863 TGGCTC
1 TGGCTC
169869 ATTTGAGCGG
Statistics
Matches: 87, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
24 1 0.01
25 83 0.95
26 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (25 bp):
TGGCTCGTAAGAGCGATATTCTGTC
Found at i:169902 original size:26 final size:25
Alignment explanation
Indices: 169838--169902 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
169828 TGATTCTGTC
*
169838 TGGCTCGTAAGAGCGATACTTTGTT
1 TGGCTCGTTAGAGCGATACTTTGTT
* * * *
169863 TGGCTCATTTGAGCGGTA-TTTTTT
1 TGGCTCGTTAGAGCGATACTTTGTT
169887 GTGGGCTCGTTAGAGC
1 -T-GGCTCGTTAGAGC
169903 TAAATTCTAG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
24 5 0.16
25 15 0.48
26 11 0.35
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.38
Consensus pattern (25 bp):
TGGCTCGTTAGAGCGATACTTTGTT
Found at i:171805 original size:15 final size:16
Alignment explanation
Indices: 171766--171811 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
171756 ATATAATATT
171766 TATTATAAA-AATAATAA
1 TATT-TAAATAAT-ATAA
171783 TATTTAAATAATATAA
1 TATTTAAATAATATAA
171799 T-TTTAAATAATAT
1 TATTTAAATAATAT
171812 TTATTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.43
16 9 0.32
17 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTTAAATAATATAA
Found at i:172654 original size:21 final size:20
Alignment explanation
Indices: 172606--172654 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
172596 AGTAAATAGA
172606 ATAATTACTCATTTTTACTT
1 ATAATTACTCATTTTTACTT
**
172626 ATTGTTACTCATATTTTACCTT
1 ATAATTACTCAT-TTTTA-CTT
172648 A-AATTAC
1 ATAATTAC
172655 CAAGTTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 10 0.43
21 9 0.39
22 4 0.17
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (20 bp):
ATAATTACTCATTTTTACTT
Found at i:173379 original size:18 final size:18
Alignment explanation
Indices: 173358--173399 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
173348 ATTAATTACG
*
173358 TAAAATACGAAAATAACC
1 TAAAATACAAAAATAACC
173376 TAAAATACAAAAATAACC
1 TAAAATACAAAAATAACC
173394 TAAAAT
1 TAAAAT
173400 TTACAGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.64, C:0.14, G:0.02, T:0.19
Consensus pattern (18 bp):
TAAAATACAAAAATAACC
Found at i:173545 original size:17 final size:18
Alignment explanation
Indices: 173523--173564 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
173513 ATAAATAGCA
173523 TGAAAATACTAAAAA-AC-
1 TGAAAATA-TAAAAAGACT
173540 TGAAAA-ATAAAAAGACT
1 TGAAAATATAAAAAGACT
173557 TGAAAATA
1 TGAAAATA
173565 ATTTTACCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.27
16 3 0.14
17 12 0.55
18 1 0.05
ACGTcount: A:0.64, C:0.07, G:0.10, T:0.19
Consensus pattern (18 bp):
TGAAAATATAAAAAGACT
Found at i:173765 original size:109 final size:109
Alignment explanation
Indices: 173574--173833 Score: 378
Period size: 109 Copynumber: 2.4 Consensus size: 109
173564 AATTTTACCT
* * * * * * * * *
173574 TTTTTTTGTGGTTCTATATTAGATGGTGCCATCATTTCCCCAAAAGAATGTTAGACTTCTCTTTT
1 TTTTTTTGTGGTGCCATATTAAATTGTGCCACCACTTCCCCAAAAGAATATCAGACTTCTCTTCT
*
173639 CATGATTTATTATTTGTTTATTATTTATTTTTTAAAATTTTAAA
66 CATGATCTATTATTTGTTTATTATTTATTTTTTAAAATTTTAAA
*
173683 TTTTTTTGGTGGTGCCATATTAAATTGTGCCACCACTTCTCCAAAA-AATATCAGACTTCTCTTC
1 TTTTTTT-GTGGTGCCATATTAAATTGTGCCACCACTTCCCCAAAAGAATATCAGACTTCTCTTC
*
173747 TCATGATCTATTATTTGTTTATTATTTATTTTTTTAAATTTTAAAA
65 TCATGATCTATTATTTGTTTATTATTTATTTTTTAAAATTTT-AAA
*
173793 TTTTTTTGTGGTGCCATATTAAATTGCGCCACCACTTCCCC
1 TTTTTTTGTGGTGCCATATTAAATTGTGCCACCACTTCCCC
173834 TACAAATAAC
Statistics
Matches: 135, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
109 94 0.70
110 41 0.30
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (109 bp):
TTTTTTTGTGGTGCCATATTAAATTGTGCCACCACTTCCCCAAAAGAATATCAGACTTCTCTTCT
CATGATCTATTATTTGTTTATTATTTATTTTTTAAAATTTTAAA
Found at i:174304 original size:18 final size:18
Alignment explanation
Indices: 174281--174315 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
174271 GAGTCAGCTT
* *
174281 CGGCATTGTTGACGGCGG
1 CGGCATCGTTAACGGCGG
174299 CGGCATCGTTAACGGCG
1 CGGCATCGTTAACGGCG
174316 TCACAAGAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.26, G:0.40, T:0.20
Consensus pattern (18 bp):
CGGCATCGTTAACGGCGG
Found at i:175823 original size:18 final size:19
Alignment explanation
Indices: 175802--175839 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
175792 TTTTAAAAAA
*
175802 TATAA-AATTTTTAATTTT
1 TATAAGAATTTTGAATTTT
*
175820 TATAAGTATTTTGAATTTT
1 TATAAGAATTTTGAATTTT
175839 T
1 T
175840 GAAAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TATAAGAATTTTGAATTTT
Found at i:175849 original size:20 final size:19
Alignment explanation
Indices: 175808--175854 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
175798 AAAATATAAA
* *
175808 ATTTTTAATTTTTATAAGT
1 ATTTTGAATTTTTAAAAGT
*
175827 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAAGT
175847 ATTTTGAA
1 ATTTTGAA
175855 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAAGT
Found at i:176047 original size:19 final size:20
Alignment explanation
Indices: 176004--176048 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
175994 AACTCGAATT
176004 ATTT-ATTTAAATTAACTCG
1 ATTTAATTTAAATTAACTCG
* *
176023 A-ATAATTTAAA-TAATTCG
1 ATTTAATTTAAATTAACTCG
176041 ATTTAATT
1 ATTTAATT
176049 AATTTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (20 bp):
ATTTAATTTAAATTAACTCG
Found at i:176316 original size:14 final size:14
Alignment explanation
Indices: 176284--176317 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
176274 ATAGAAGAGG
176284 GTTTAGACTTTAGA
1 GTTTAGACTTTAGA
* *
176298 CTTTAGACTTTGGA
1 GTTTAGACTTTAGA
176312 GTTTAG
1 GTTTAG
176318 TATGGGACCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.44
Consensus pattern (14 bp):
GTTTAGACTTTAGA
Found at i:182805 original size:43 final size:41
Alignment explanation
Indices: 182757--183047 Score: 141
Period size: 43 Copynumber: 6.9 Consensus size: 41
182747 GCCACTAATA
*
182757 ATTGCAGATATACTGCCAGAAATATGTGGACAAGCCATCAGT
1 ATTGCAGATA-ACTACCAGAAATATGTGGACAAGCCATCAGT
* * * * *
182799 ATTTGCAG-TCAAGTTACCAGTAAGATGTGGATAAACCA-CTAGT
1 A-TTGCAGAT-AA-CTACCAGAAATATGTGGACAAGCCATC-AGT
* *
182842 ATTG-ATGATAACTTA-CAAAAATATGTGGACAAGCCATTAGT
1 ATTGCA-GATAAC-TACCAGAAATATGTGGACAAGCCATCAGT
* *
182883 CTTTGCAG-TCAAGCTACCA-ATAATATGTGGACAAGCCATTAGT
1 -ATTGCAGAT-AA-CTACCAGA-AATATGTGGACAAGCCATCAGT
* * * *
182926 ATTACAGATAAACT-GCAGAAATATGTGGGCAATCCA-CTAGT
1 ATTGCAGAT-AACTACCAGAAATATGTGGACAAGCCATC-AGT
* * * * * *
182967 ATTTGTAG-TCGATCTATCAGTAACATGTGGACAAGCCACCAGT
1 A-TTGCAGAT--AACTACCAGAAATATGTGGACAAGCCATCAGT
* * * **
183010 ACTGCAGATAAACTGCTATTAATATGTGGACAAGCCAT
1 ATTGCAGAT-AACTACCAGAAATATGTGGACAAGCCAT
183048 TAATATTACG
Statistics
Matches: 187, Mismatches: 40, Indels: 44
0.69 0.15 0.16
Matches are distributed among these distances:
41 43 0.23
42 61 0.33
43 82 0.44
44 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (41 bp):
ATTGCAGATAACTACCAGAAATATGTGGACAAGCCATCAGT
Found at i:182936 original size:84 final size:84
Alignment explanation
Indices: 182742--183054 Score: 306
Period size: 84 Copynumber: 3.7 Consensus size: 84
182732 CCAGTTTGCA
* * * * *
182742 GACAAGCCACTAATAATTGCAGATATACTGCCAGAAATATGTGGACAAGCCATCAGTATTTGCAG
1 GACAAGCCACTAGT-ATTACAGATAAACTG-CAAAAATATGTGGACAAGCCATTAGTATTTGCAG
* *
182807 TCAAGTTACCAGTAAGATGTG
64 TCAAGCTACCAGTAACATGTG
* * * * *
182828 GATAAACCACTAGTATTGA-TGAT-AACTTACAAAAATATGTGGACAAGCCATTAGTCTTTGCAG
1 GACAAGCCACTAGTATT-ACAGATAAAC-TGCAAAAATATGTGGACAAGCCATTAGTATTTGCAG
* *
182891 TCAAGCTACCAATAATATGTG
64 TCAAGCTACCAGTAACATGTG
* * * * * *
182912 GACAAGCCATTAGTATTACAGATAAACTGCAGAAATATGTGGGCAATCCACTAGTATTTGTAGTC
1 GACAAGCCACTAGTATTACAGATAAACTGCAAAAATATGTGGACAAGCCATTAGTATTTGCAGTC
* * *
182977 GATCTATCAGTAACATGTG
66 AAGCTACCAGTAACATGTG
* * * ** *
182996 GACAAGCCACCAGTACTGCAGATAAACTGCTATTAATATGTGGACAAGCCATTAATATT
1 GACAAGCCACTAGTATTACAGATAAACTGC-AAAAATATGTGGACAAGCCATTAGTATT
183055 ACGTATAAAC
Statistics
Matches: 183, Mismatches: 39, Indels: 11
0.79 0.17 0.05
Matches are distributed among these distances:
83 1 0.01
84 139 0.76
85 32 0.17
86 11 0.06
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (84 bp):
GACAAGCCACTAGTATTACAGATAAACTGCAAAAATATGTGGACAAGCCATTAGTATTTGCAGTC
AAGCTACCAGTAACATGTG
Found at i:183846 original size:25 final size:26
Alignment explanation
Indices: 183794--183875 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 26
183784 ATAGTTTTAT
* * * *
183794 AGAGAGTTCGCCATAAAGGCCTT-AC
1 AGAGAATTCGCCACAAAGGCTTTCCC
*
183819 AGAGTATTCGCCACAAAGG-TTTCCC
1 AGAGAATTCGCCACAAAGGCTTTCCC
* *
183844 AGAGAATTCGTCACAAAGGCTTT-CT
1 AGAGAATTCGCCACAAAGGCTTTCCC
183869 AGAGAAT
1 AGAGAAT
183876 ATGTTGCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
24 2 0.04
25 42 0.89
26 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (26 bp):
AGAGAATTCGCCACAAAGGCTTTCCC
Found at i:185963 original size:10 final size:10
Alignment explanation
Indices: 185941--186016 Score: 61
Period size: 10 Copynumber: 7.6 Consensus size: 10
185931 CATATTAATC
*
185941 AATTTTCAT-
1 AATTTTTATG
185950 AATTTTTATG
1 AATTTTTATG
*
185960 AATTTTTATA
1 AATTTTTATG
185970 AATTTTTAT-
1 AATTTTTATG
*
185979 TATTTTTATTG
1 AATTTTTA-TG
185990 AA-TTTTA-G
1 AATTTTTATG
185998 TATATTTTTATG
1 -A-ATTTTTATG
186010 ATATTTT
1 A-ATTTT
186017 AAATTTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
8 1 0.02
9 16 0.29
10 25 0.45
11 13 0.23
12 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.63
Consensus pattern (10 bp):
AATTTTTATG
Found at i:185994 original size:30 final size:29
Alignment explanation
Indices: 185941--186017 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
185931 CATATTAATC
*
185941 AATTTTCATAATTTTTATGAATTTTTA-TA
1 AATTTTTATAATTTTTATGAA-TTTTAGTA
*
185970 AATTTTTATTATTTTTATTGAATTTTAGTA
1 AATTTTTATAATTTTTA-TGAATTTTAGTA
* *
186000 TATTTTTATGATATTTTA
1 AATTTTTATAAT-TTTTA
186018 AATTTTTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 20 0.49
30 16 0.39
31 5 0.12
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.62
Consensus pattern (29 bp):
AATTTTTATAATTTTTATGAATTTTAGTA
Found at i:186635 original size:28 final size:30
Alignment explanation
Indices: 186570--186638 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 30
186560 TTTAATAATT
* * *
186570 TATATTTTTATAAGTTTTAGAGAATTAAAT
1 TATAATTTTATAAGTTTTAAAGAATTAAAA
* *
186600 TAAAATTTTATAA-TTTTAAAGGA-TAAAA
1 TATAATTTTATAAGTTTTAAAGAATTAAAA
186628 TATAATTTTAT
1 TATAATTTTAT
186639 TTTTATTCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 14 0.42
29 8 0.24
30 11 0.33
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (30 bp):
TATAATTTTATAAGTTTTAAAGAATTAAAA
Found at i:187625 original size:25 final size:26
Alignment explanation
Indices: 187597--187645 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
187587 TAAAATAATA
* *
187597 AATATGTAAAAATG-TTTATTTAAAC
1 AATACGTAAAAATGATATATTTAAAC
*
187622 AATACGTGAAAATGATATATTTAA
1 AATACGTAAAAATGATATATTTAA
187646 CACTTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (26 bp):
AATACGTAAAAATGATATATTTAAAC
Found at i:195487 original size:10 final size:10
Alignment explanation
Indices: 195468--195496 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
195458 TGTACAAATA
195468 TAAT-ATTTT
1 TAATAATTTT
195477 TAATAATTTT
1 TAATAATTTT
195487 TAATAATTTT
1 TAATAATTTT
195497 ACAATTGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TAATAATTTT
Found at i:198172 original size:17 final size:18
Alignment explanation
Indices: 198150--198183 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
198140 ATAACAATTA
*
198150 TGAAGATTTTGG-ATATG
1 TGAAGATCTTGGCATATG
198167 TGAAGATCTTGGCATAT
1 TGAAGATCTTGGCATAT
198184 TCCCTGAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.38
Consensus pattern (18 bp):
TGAAGATCTTGGCATATG
Found at i:203392 original size:17 final size:17
Alignment explanation
Indices: 203362--203401 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
203352 AGGTGGAGAA
* * *
203362 CTTGTTCGTTGAGAGTT
1 CTTGTCCGTAGAGAATT
203379 CTTGTCCGTAGAGAATT
1 CTTGTCCGTAGAGAATT
203396 CTTGTC
1 CTTGTC
203402 AAGGTGGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (17 bp):
CTTGTCCGTAGAGAATT
Found at i:205363 original size:96 final size:97
Alignment explanation
Indices: 205178--205370 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 97
205168 GAATTTTGGA
* * **
205178 AAAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAAATTTTC
1 AAAGGATATTCGATCATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTC
* *
205243 AGAGTCGAAGATAAGAAAACATTGCCTCGATT
66 AAACTCGAAGATAAGAAAACATTGCCTCGATT
* * *
205275 AAAGG-TATTCGATCATTTCGATTTGAAGAAAAATTGTATCTAGTAAGTTAAGGCACAAAATTTT
1 AAAGGATATTCGATCATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCAC-AAATTTT
* * *
205339 GAAACTCGAA-ATGAA-AGAATATTGCCTCGATT
65 CAAACTCGAAGAT-AAGAAAACATTGCCTCGATT
205371 TTAAAGTTTT
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
96 61 0.74
97 21 0.26
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (97 bp):
AAAGGATATTCGATCATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTC
AAACTCGAAGATAAGAAAACATTGCCTCGATT
Found at i:205736 original size:59 final size:58
Alignment explanation
Indices: 205673--205799 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 58
205663 AAAAAAAGAG
205673 TTTTTAGACACCCAGGGGTAAAATAGTAATTTTTAGAAAAATCAGGATCAAAAACAAAA
1 TTTTTAGACACCCAGGGGTAAAATAGTAATTTTTAGAAAAATCAGGAT-AAAAACAAAA
** * * * * ***
205732 TTTTT-GAACATTCGGGGGTAAAATGGTAATTTTTAGGAAAATCGGGATAAAAATGGAA
1 TTTTTAG-ACACCCAGGGGTAAAATAGTAATTTTTAGAAAAATCAGGATAAAAACAAAA
205790 TTTTTAGACA
1 TTTTTAGACA
205800 TTCGAGTATA
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
58 16 0.28
59 41 0.72
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.30
Consensus pattern (58 bp):
TTTTTAGACACCCAGGGGTAAAATAGTAATTTTTAGAAAAATCAGGATAAAAACAAAA
Found at i:205762 original size:29 final size:29
Alignment explanation
Indices: 205730--205825 Score: 92
Period size: 29 Copynumber: 3.3 Consensus size: 29
205720 TCAAAAACAA
*
205730 AATTTTTGAACATTCGGGGGTAAAATGGT
1 AATTTTTGAACATTCGGGGATAAAATGGT
*
205759 AATTTTTAGGAA-AATC-GGGATAAAAATGG-
1 AATTTTT--GAACATTCGGGGAT-AAAATGGT
* *
205788 AATTTTT-AGACATTCGAGTATAAAATGGT
1 AATTTTTGA-ACATTCGGGGATAAAATGGT
205817 AATTTTTGA
1 AATTTTTGA
205826 GAGTTTTGGG
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 10 0.19
29 28 0.52
30 11 0.20
31 3 0.06
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (29 bp):
AATTTTTGAACATTCGGGGATAAAATGGT
Found at i:205812 original size:58 final size:59
Alignment explanation
Indices: 205691--205823 Score: 162
Period size: 58 Copynumber: 2.3 Consensus size: 59
205681 CACCCAGGGG
* * *
205691 TAAAATAGTAATTTTTAGAAAAATCAGGATCAAAAACAAAATTTTTGAACATTCGGGGG
1 TAAAATGGTAATTTTTAGAAAAATCAGGATCAAAAACAAAATTTTTGAACATTCGAGGA
* * *** *
205750 TAAAATGGTAATTTTTAGGAAAATCGGGAT-AAAAATGGAATTTTT-AGACATTCGAGTA
1 TAAAATGGTAATTTTTAGAAAAATCAGGATCAAAAACAAAATTTTTGA-ACATTCGAGGA
205808 TAAAATGGTAATTTTT
1 TAAAATGGTAATTTTT
205824 GAGAGTTTTG
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
57 1 0.02
58 36 0.56
59 27 0.42
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (59 bp):
TAAAATGGTAATTTTTAGAAAAATCAGGATCAAAAACAAAATTTTTGAACATTCGAGGA
Found at i:205902 original size:30 final size:30
Alignment explanation
Indices: 205859--206097 Score: 249
Period size: 29 Copynumber: 8.1 Consensus size: 30
205849 ATTTTTTAAT
* *
205859 GTTTGGAGG-TAAAAATATAATTTTTGGAA
1 GTTTTGAGGTTAAAAATAGAATTTTTGGAA
*
205888 GTTTCGAGGTTAAAAATAGAATTTTTGGAA
1 GTTTTGAGGTTAAAAATAGAATTTTTGGAA
*
205918 G-TTCGAGGTTAAAAAT-GTAATTTTTGGAA
1 GTTTTGAGGTTAAAAATAG-AATTTTTGGAA
* *
205947 GTTTTGGGGTCAAAAATAGAATTTTTGGAA
1 GTTTTGAGGTTAAAAATAGAATTTTTGGAA
* * * *
205977 G-TTTGGGGGTGAAAAT-GTAATTTTTGTAA
1 GTTTTGAGGTTAAAAATAG-AATTTTTGGAA
* *
206006 GTTTTGAGGTCAAAAATGGAA-TTTTGGAA
1 GTTTTGAGGTTAAAAATAGAATTTTTGGAA
* * *
206035 GTTTAG-GGGTAAAAATATAATTTTTGGAA
1 GTTTTGAGGTTAAAAATAGAATTTTTGGAA
**
206064 GTTTTGAGGTTAAAAAGGGAATTTTTGGACA
1 GTTTTGAGGTTAAAAATAGAATTTTTGGA-A
206095 GTT
1 GTT
206098 CGGGGACCTC
Statistics
Matches: 176, Mismatches: 24, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
28 12 0.07
29 83 0.47
30 75 0.43
31 6 0.03
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (30 bp):
GTTTTGAGGTTAAAAATAGAATTTTTGGAA
Found at i:205941 original size:59 final size:59
Alignment explanation
Indices: 205866--206099 Score: 301
Period size: 59 Copynumber: 4.0 Consensus size: 59
205856 AATGTTTGGA
* *
205866 GGTAAAAATATAATTTTTGGAAGTTTCGAGGTTAAAAATAGAATTTTTGGAAGTTCGAG
1 GGTAAAAATATAATTTTTGGAAGTTTTGAGGTCAAAAATAGAATTTTTGGAAGTTCGAG
* * * * *
205925 GTTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATAGAATTTTTGGAAGTTTGGG
1 GGTAAAAATATAATTTTTGGAAGTTTTGAGGTCAAAAATAGAATTTTTGGAAGTTCGAG
* * * * *
205984 GGTGAAAATGTAATTTTTGTAAGTTTTGAGGTCAAAAATGGAA-TTTTGGAAGTT-TAGG
1 GGTAAAAATATAATTTTTGGAAGTTTTGAGGTCAAAAATAGAATTTTTGGAAGTTCGA-G
* **
206042 GGTAAAAATATAATTTTTGGAAGTTTTGAGGTTAAAAAGGGAATTTTTGGACAGTTCG
1 GGTAAAAATATAATTTTTGGAAGTTTTGAGGTCAAAAATAGAATTTTTGGA-AGTTCG
206100 GGGACCTCTA
Statistics
Matches: 151, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
58 50 0.33
59 97 0.64
60 4 0.03
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (59 bp):
GGTAAAAATATAATTTTTGGAAGTTTTGAGGTCAAAAATAGAATTTTTGGAAGTTCGAG
Found at i:207079 original size:15 final size:15
Alignment explanation
Indices: 207015--207081 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
207005 TCTTTCTTTT
*
207015 TTATTTTTATTAATG
1 TTATTATTATTAATG
*
207030 TTATTATTAAT-ATAG
1 TTATTATTATTAAT-G
* *
207045 ATATTATTATTAATA
1 TTATTATTATTAATG
*
207060 CTATTATTATTAATG
1 TTATTATTATTAATG
207075 TTATTAT
1 TTATTAT
207082 AAATAATGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
14 2 0.05
15 38 0.90
16 2 0.05
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (15 bp):
TTATTATTATTAATG
Found at i:208453 original size:6 final size:6
Alignment explanation
Indices: 208444--208519 Score: 59
Period size: 6 Copynumber: 12.5 Consensus size: 6
208434 CAACCTCTCC
* * *
208444 TTTTCT TTTTCT TTTT-T TTCTT-T TTTGTTT TTTTCT TTTTGT TGTTCTT
1 TTTTCT TTTTCT TTTTCT TT-TTCT TTT-TCT TTTTCT TTTTCT TTTTC-T
*
208493 TTTTCT TCTTCT TTTT-T CTTTTCT TTT
1 TTTTCT TTTTCT TTTTCT -TTTTCT TTT
208520 ATTCATTGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
5 5 0.09
6 42 0.74
7 10 0.18
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:208464 original size:15 final size:15
Alignment explanation
Indices: 208444--208519 Score: 77
Period size: 15 Copynumber: 5.0 Consensus size: 15
208434 CAACCTCTCC
208444 TTTTCTTTTTCTTTT
1 TTTTCTTTTTCTTTT
208459 TTTTCTTTTT-TGTTT
1 TTTTCTTTTTCT-TTT
*
208474 TTTTCTTTTTGTTGTT
1 TTTTCTTTTTCTT-TT
*
208490 CTTTT-TTCTTCTTCTT
1 -TTTTCTTTTTCTT-TT
208506 TTTTC-TTTTCTTTT
1 TTTTCTTTTTCTTTT
208520 ATTCATTGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
14 3 0.06
15 34 0.65
16 11 0.21
17 4 0.08
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTTCTTTT
Found at i:208467 original size:7 final size:7
Alignment explanation
Indices: 208444--208514 Score: 58
Period size: 7 Copynumber: 10.3 Consensus size: 7
208434 CAACCTCTCC
208444 TTTTCTT
1 TTTTCTT
*
208451 TTTCTTTT
1 TTT-TCTT
208459 TTTTCTT
1 TTTTCTT
*
208466 TTTTGTT
1 TTTTCTT
208473 TTTT-TCT
1 TTTTCT-T
*
208480 TTTT-GT
1 TTTTCTT
*
208486 TGTTCTT
1 TTTTCTT
208493 TTTTC-T
1 TTTTCTT
*
208499 TCTTCTT
1 TTTTCTT
208506 TTTTCTT
1 TTTTCTT
208513 TT
1 TT
208515 CTTTTATTCA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
6 10 0.20
7 35 0.69
8 6 0.12
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (7 bp):
TTTTCTT
Found at i:208474 original size:13 final size:13
Alignment explanation
Indices: 208444--208519 Score: 64
Period size: 13 Copynumber: 5.7 Consensus size: 13
208434 CAACCTCTCC
*
208444 TTTTCTTTTTCTTTT
1 TTTTC-TTTT-TTGT
208459 TTTTCTTTTTTGT
1 TTTTCTTTTTTGT
*
208472 TTTTTTCTTTTTGT
1 TTTTCT-TTTTTGT
* *
208486 TGTTCTTTTTTCT
1 TTTTCTTTTTTGT
* *
208499 TCTTCTTTTTT-C
1 TTTTCTTTTTTGT
208511 TTTTCTTTT
1 TTTTCTTTT
208520 ATTCATTGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
12 8 0.15
13 24 0.46
14 15 0.29
15 5 0.10
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTTGT
Found at i:209397 original size:12 final size:12
Alignment explanation
Indices: 209372--209405 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
209362 ACCCATTTTC
*
209372 TTTTTCTCTATTT
1 TTTTTCT-TGTTT
209385 TTTTTCTTGTTT
1 TTTTTCTTGTTT
209397 TTTTTCTTG
1 TTTTTCTTG
209406 ATAACACGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTCTTGTTT
Found at i:214181 original size:29 final size:29
Alignment explanation
Indices: 214075--214300 Score: 89
Period size: 29 Copynumber: 7.7 Consensus size: 29
214065 TTGGATACCT
*
214075 GAGGGTAAAATGGTAA-TTTTGGACTAAT-
1 GAGGGTAAAATGGTAATTTTTAGAC-AATC
* **
214103 GGGGGTAAAATGGTAATTTTGGGA-AAGTTC
1 GAGGGTAAAATGGTAATTTTTAGACAA--TC
* * *
214133 GAGGTTAAAAACT-G-AGTTTTTAGACACTC
1 GAGGGT-AAAA-TGGTAATTTTTAGACAATC
* *
214162 GAGGGTAAAATGGTAATTTTTAGAAAAATT
1 GAGGGTAAAATGGTAATTTTTAG-ACAATC
* * *
214192 GA-GATCAAAAATAG-AATTTTTGGAC-ATCC
1 GAGGGT--AAAATGGTAATTTTTAGACAAT-C
*
214221 G-GGAGTAAAATGGTAATTTTTAGGAAAATC
1 GAGG-GTAAAATGGTAATTTTTA-GACAATC
* * * *
214251 G-GGATCAAAAAT-GAAAGTTTTGGA-AATTC
1 GAGGGT--AAAATGGTAATTTTTAGACAA-TC
214280 GAGGGTAAAATGGTAATTTTT
1 GAGGGTAAAATGGTAATTTTT
214301 GGGAGTTTCG
Statistics
Matches: 146, Mismatches: 29, Indels: 45
0.66 0.13 0.20
Matches are distributed among these distances:
27 3 0.02
28 35 0.24
29 47 0.32
30 41 0.28
31 19 0.13
32 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.31
Consensus pattern (29 bp):
GAGGGTAAAATGGTAATTTTTAGACAATC
Found at i:214202 original size:59 final size:57
Alignment explanation
Indices: 214105--214300 Score: 200
Period size: 59 Copynumber: 3.3 Consensus size: 57
214095 GGACTAATGG
* * * * *
214105 GGGTAAAATGGTAA-TTTTGGGAAAGTTCGAGGTTAAAAACTGAGTTTTTAGACACTCGA
1 GGGTAAAATGGTAATTTTTAGGAAAATT-GAGATCAAAAA-TGAGTTTTTGGACA-TCGA
* *
214164 GGGTAAAATGGTAATTTTTAGAAAAATTGAGATCAAAAATAGAATTTTTGGACATCCG-
1 GGGTAAAATGGTAATTTTTAGGAAAATTGAGATCAAAAAT-GAGTTTTTGGACAT-CGA
* * *
214222 GGAGTAAAATGGTAATTTTTAGGAAAATCGGGATCAAAAATGAAAG-TTTTGGAAATTCGA
1 GG-GTAAAATGGTAATTTTTAGGAAAATTGAGATCAAAAATG--AGTTTTTGGACA-TCGA
214282 GGGTAAAATGGTAATTTTT
1 GGGTAAAATGGTAATTTTT
214301 GGGAGTTTCG
Statistics
Matches: 117, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
58 5 0.04
59 98 0.84
60 14 0.12
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.31
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTTAGGAAAATTGAGATCAAAAATGAGTTTTTGGACATCGA
Found at i:214331 original size:59 final size:58
Alignment explanation
Indices: 214194--214366 Score: 156
Period size: 59 Copynumber: 2.9 Consensus size: 58
214184 GAAAAATTGA
* * * ***
214194 GATCAAAAAT-AGAATTTTTGGACATCCGGGAGTAAAATGGTAATTTTTAGGAAAATCGG
1 GATCAAAAATCA-AATTTTTGGAAATTCGGG-GTAAAATGGTAATTTTTGGGAGTTTCGG
* *
214253 GATCAAAAATGAAAGTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTGGGAGTTTCGG
1 GATCAAAAATCAAATTTTTGGAAATTCG-GGGTAAAATGGTAATTTTTGGGAGTTTCGG
* * *
214312 GGTC-AAAATCAAGATTTTT-GAAAGTTCGGATGTAAAAAT-GTAATTTTTGGAAGTT
1 GATCAAAAATCAA-ATTTTTGGAAA-TTCGG-GGT-AAAATGGTAATTTTTGGGAGTT
214367 CGAGGTAAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
58 12 0.12
59 76 0.79
60 8 0.08
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.32
Consensus pattern (58 bp):
GATCAAAAATCAAATTTTTGGAAATTCGGGGTAAAATGGTAATTTTTGGGAGTTTCGG
Found at i:214379 original size:30 final size:29
Alignment explanation
Indices: 214277--214601 Score: 265
Period size: 30 Copynumber: 11.0 Consensus size: 29
214267 GTTTTGGAAA
**
214277 TTCGAGGGT-AAAATGGTAATTTTTGGGAGT
1 TTCGA-GGTAAAAAT-GTAATTTTTGAAAGT
* * **
214307 TTCGGGGTCAAAATCAAGATTTTTGAAAG-
1 TTCGAGGTAAAAATGTA-ATTTTTGAAAGT
* *
214336 TTCGGATGTAAAAATGTAATTTTTGGAAG-
1 TTC-GAGGTAAAAATGTAATTTTTGAAAGT
214365 TTCGAGGTAAAAAAATGTAATTTTTTG-AAGT
1 TTCGAGGT--AAAAATGTAA-TTTTTGAAAGT
* *
214396 TTCGAGGTGAAAAATGGAATTTTTGGAAG-
1 TTCGAGGT-AAAAATGTAATTTTTGAAAGT
*
214425 TTC-AGGGTAAAAATGTAATTTTCGAAAGT
1 TTCGA-GGTAAAAATGTAATTTTTGAAAGT
*
214454 TTCAAGGTCAAAAAT-TGAATTTTTGAAAG-
1 TTCGAGGT-AAAAATGT-AATTTTTGAAAGT
* *
214483 TTCGTGGGTAAAAATATAATTTTCT-AAAGT
1 TTCG-AGGTAAAAATGTAATTTT-TGAAAGT
* *
214513 TTCGAGGTTAAAAATGGAATTTTTTAAAG-
1 TTCGAGG-TAAAAATGTAATTTTTGAAAGT
*
214542 TTCGAGGGTAAAAATATAATTTTTGAAAGT
1 TTCGA-GGTAAAAATGTAATTTTTGAAAGT
*
214572 TTCGAGGATAAAAATGGAATTTTTGGAAAG
1 TTCGAGG-TAAAAATGTAATTTTT-GAAAG
214602 CTCGGGGACC
Statistics
Matches: 244, Mismatches: 28, Indels: 45
0.77 0.09 0.14
Matches are distributed among these distances:
28 22 0.09
29 86 0.35
30 117 0.48
31 19 0.08
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (29 bp):
TTCGAGGTAAAAATGTAATTTTTGAAAGT
Found at i:214388 original size:59 final size:58
Alignment explanation
Indices: 214277--214599 Score: 347
Period size: 59 Copynumber: 5.5 Consensus size: 58
214267 GTTTTGGAAA
* *
214277 TTCGAGGGT-AAAATGGTAATTTTTGGGAGTTTCG-GGGTCAAAATCA-AGATTTTTGAAAG-
1 TTCGA-GGTAAAAATGG-AATTTTTGGAAG-TTCGAGGGTAAAAAT-ATA-ATTTTTGAAAGT
* * *
214336 TTCGGATGTAAAAATGTAATTTTTGGAAGTTCGA-GGTAAAAAAATGTAATTTTTTG-AAGT
1 TTC-GAGGTAAAAATGGAATTTTTGGAAGTTCGAGGGT--AAAAATATAA-TTTTTGAAAGT
* *
214396 TTCGAGGTGAAAAATGGAATTTTTGGAAGTTC-AGGGTAAAAATGTAATTTTCGAAAGT
1 TTCGAGGT-AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGAAAGT
* * * *
214454 TTCAAGGTCAAAAATTGAATTTTTGAAAGTTCGTGGGTAAAAATATAATTTTCT-AAAGT
1 TTCGAGGT-AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTT-TGAAAGT
**
214513 TTCGAGGTTAAAAATGGAATTTTTTAAAGTTCGAGGGTAAAAATATAATTTTTGAAAGT
1 TTCGAGG-TAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGAAAGT
214572 TTCGAGGATAAAAATGGAATTTTTGGAA
1 TTCGAGG-TAAAAATGGAATTTTTGGAA
214600 AGCTCGGGGA
Statistics
Matches: 227, Mismatches: 22, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
57 5 0.02
58 50 0.22
59 123 0.54
60 49 0.22
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.36
Consensus pattern (58 bp):
TTCGAGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGAAAGT
Found at i:215593 original size:15 final size:15
Alignment explanation
Indices: 215535--215595 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
215525 TTTTTTTTAT
215535 TTATTAATGTTATTA
1 TTATTAATGTTATTA
* *
215550 TTAAT-ATAGATATTA
1 TTATTAAT-GTTATTA
**
215565 TTATTAATACTATTA
1 TTATTAATGTTATTA
215580 TTATTAATGTTATTA
1 TTATTAATGTTATTA
215595 T
1 T
215596 AAATAATGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (15 bp):
TTATTAATGTTATTA
Found at i:216397 original size:6 final size:6
Alignment explanation
Indices: 216386--216469 Score: 86
Period size: 6 Copynumber: 14.7 Consensus size: 6
216376 AATTTGAAAA
* *
216386 TAAATT TAAATT T-AATT TTAATT TAAATT TAAAAT T-AATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * * *
216432 CAAATT TAAA-A TAAATC TAAATT TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
216470 AGGCGACCGG
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
5 17 0.27
6 47 0.73
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:216403 original size:23 final size:22
Alignment explanation
Indices: 216376--216454 Score: 86
Period size: 23 Copynumber: 3.5 Consensus size: 22
216366 AATCTTTTAA
* *
216376 AATTTGAAAATAAATTTAAATTT
1 AATTT-AAATTAAATTTAAAATT
*
216399 AATTTTAATTTAAATTTAAAATT
1 AA-TTTAAATTAAATTTAAAATT
*
216422 AATTTAAATTCAAATTTAAAATA
1 AATTTAAATT-AAATTTAAAATT
*
216445 AATCTAAATT
1 AATTTAAATT
216455 TAAAATAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.15
23 38 0.79
24 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (22 bp):
AATTTAAATTAAATTTAAAATT
Found at i:216408 original size:11 final size:11
Alignment explanation
Indices: 216388--216468 Score: 72
Period size: 11 Copynumber: 7.2 Consensus size: 11
216378 TTTGAAAATA
216388 AATTTAAATTT
1 AATTTAAATTT
*
216399 AATTTTAATTT
1 AATTTAAATTT
*
216410 AAATTTAAAATT
1 -AATTTAAATTT
*
216422 AATTTAAATTCA
1 AATTTAAATT-T
* *
216434 AATTTAAAATA
1 AATTTAAATTT
*
216445 AATCTAAATTT
1 AATTTAAATTT
**
216456 AAAATAAATTT
1 AATTTAAATTT
216467 AA
1 AA
216469 AAGGCGACCG
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
11 39 0.68
12 18 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:216410 original size:17 final size:17
Alignment explanation
Indices: 216388--216469 Score: 92
Period size: 17 Copynumber: 4.8 Consensus size: 17
216378 TTTGAAAATA
*
216388 AATTTAAATTTAATTTT
1 AATTTAAATTTAAATTT
*
216405 AATTTAAATTTAAAATT
1 AATTTAAATTTAAATTT
*
216422 AATTTAAATTCAAATTT
1 AATTTAAATTTAAATTT
** *
216439 AAAATAAATCTAAATTT
1 AATTTAAATTTAAATTT
**
216456 AAAATAAATTTAAA
1 AATTTAAATTTAAA
216470 AGGCGACCGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAAATTTAAATTT
Found at i:216627 original size:17 final size:17
Alignment explanation
Indices: 216605--216668 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
216595 AAATACACTC
216605 TCTCTTTTGCTTTCCAT
1 TCTCTTTTGCTTTCCAT
* *
216622 TCTCTTTGTTCTTTAATACACT
1 TCTCTTT-TGC-TT--TCCA-T
216644 CTCTCTTTTGCTTTCCAT
1 -TCTCTTTTGCTTTCCAT
216662 TCTCTTT
1 TCTCTTT
216669 GTTCTTTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
17 14 0.38
18 3 0.08
19 5 0.14
21 5 0.14
22 3 0.08
23 7 0.19
ACGTcount: A:0.09, C:0.28, G:0.05, T:0.58
Consensus pattern (17 bp):
TCTCTTTTGCTTTCCAT
Found at i:216651 original size:40 final size:40
Alignment explanation
Indices: 216596--216676 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
216586 TGATCAATAA
216596 AATACACTCTCTCTTTTGCTTTCCATTCTCTTTGTTCTTT
1 AATACACTCTCTCTTTTGCTTTCCATTCTCTTTGTTCTTT
216636 AATACACTCTCTCTTTTGCTTTCCATTCTCTTTGTTCTTT
1 AATACACTCTCTCTTTTGCTTTCCATTCTCTTTGTTCTTT
216676 A
1 A
216677 CTCTTTGTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.14, C:0.27, G:0.05, T:0.54
Consensus pattern (40 bp):
AATACACTCTCTCTTTTGCTTTCCATTCTCTTTGTTCTTT
Found at i:216682 original size:14 final size:14
Alignment explanation
Indices: 216663--216689 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
216653 GCTTTCCATT
216663 CTCTTTGTTCTTTA
1 CTCTTTGTTCTTTA
216677 CTCTTTGTTCTTT
1 CTCTTTGTTCTTT
216690 TATTTTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.22, G:0.07, T:0.67
Consensus pattern (14 bp):
CTCTTTGTTCTTTA
Found at i:219306 original size:22 final size:22
Alignment explanation
Indices: 219271--219313 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
219261 GATATTTACA
**
219271 CAAATTTATTATTCAAATTATT
1 CAAATTTAAAATTCAAATTATT
*
219293 CAAATTTAAAATTCAACTTAT
1 CAAATTTAAAATTCAAATTAT
219314 CTCGAACTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (22 bp):
CAAATTTAAAATTCAAATTATT
Found at i:223557 original size:19 final size:19
Alignment explanation
Indices: 223535--223605 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
223525 AAATTACAAA
223535 AAAAATT-AAAATAATTTT
1 AAAAATTCAAAATAATTTT
*
223553 CAAAAATTGAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
223573 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
223592 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
223606 TTCTATTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.09
19 26 0.57
20 16 0.35
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:224045 original size:21 final size:21
Alignment explanation
Indices: 224021--224061 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
224011 ACCATTTCTA
224021 AAGTTAAAA-GTCAAAACTATC
1 AAGTTAAAAGGT-AAAACTATC
224042 AAGTTAAAAGGTAAAACTAT
1 AAGTTAAAAGGTAAAACTAT
224062 GTCGTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACTATC
Found at i:224234 original size:25 final size:25
Alignment explanation
Indices: 224206--224255 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
224196 CAACATTGAG
224206 TATAAATAATAAGATTCATTAATTC
1 TATAAATAATAAGATTCATTAATTC
*
224231 TATAAATAATAAGATTCGTTAATTC
1 TATAAATAATAAGATTCATTAATTC
224256 GACTCGACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (25 bp):
TATAAATAATAAGATTCATTAATTC
Found at i:224533 original size:25 final size:25
Alignment explanation
Indices: 224491--224570 Score: 63
Period size: 24 Copynumber: 3.1 Consensus size: 25
224481 AAAATTTAAA
*
224491 TATATATATATATATTATTTTTAATTT
1 TATATAT-TTTAT-TTATTTTTAATTT
**
224518 TATATATTTTATTTA-TTAAAATTT
1 TATATATTTTATTTATTTTTAATTT
** *
224542 TATATAACCTTAATTATTTTTAATGTT
1 TATAT-ATTTTATTTATTTTTAAT-TT
224569 TA
1 TA
224571 CATCATAGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 12 0.29
25 10 0.24
26 9 0.21
27 11 0.26
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (25 bp):
TATATATTTTATTTATTTTTAATTT
Found at i:224540 original size:24 final size:21
Alignment explanation
Indices: 224497--224547 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
224487 TAAATATATA
224497 TATATATATTATTTTTAATTT
1 TATATATATTATTTTTAATTT
*
224518 TATATATTTTATTTATTAAAATTT
1 TATATATATTATTT-TT--AATTT
224542 TATATA
1 TATATA
224548 ACCTTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 13 0.50
22 2 0.08
24 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATATATATTATTTTTAATTT
Found at i:227264 original size:24 final size:24
Alignment explanation
Indices: 227237--227293 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
227227 ATATGAAAAG
* *
227237 AAATAACTAAGATTTTATGCTAAT
1 AAATAACTAAGATATTATACTAAT
* *
227261 AAATAACAAATATATTATACTAAT
1 AAATAACTAAGATATTATACTAAT
227285 AAAT-ACTAA
1 AAATAACTAA
227294 ATCTTCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAACTAAGATATTATACTAAT
Found at i:231643 original size:24 final size:24
Alignment explanation
Indices: 231615--231667 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
231605 GTATGAAAAG
* * *
231615 AAATAACTAAGATTTTATACTAAT
1 AAATAACAAACATATTATACTAAT
231639 AAATAACAAACATATTATACTAAT
1 AAATAACAAACATATTATACTAAT
231663 AAATA
1 AAATA
231668 TTAAATCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATAACAAACATATTATACTAAT
Found at i:233039 original size:19 final size:18
Alignment explanation
Indices: 233014--233059 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
233004 TATCATTAAT
* *
233014 AATTCAATTTTAATATAAA
1 AATTCAATATGAATA-AAA
*
233033 TATTCAATATGAATAAAA
1 AATTCAATATGAATAAAA
233051 AATTCAATA
1 AATTCAATA
233060 ATATAAATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (18 bp):
AATTCAATATGAATAAAA
Done.