Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004492.1 Hibiscus syriacus cultivar Beakdansim tig00009904_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: 302411
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 2 of 2
Found at i:178000 original size:18 final size:19
Alignment explanation
Indices: 177947--178003 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
177937 ATGTTTAATG
*
177947 AAAAATATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
**
177966 ACAAAAGAATATTAATTGTT-
1 A-AAAAG-ATACCAATTGTTA
177986 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
178004 GGAAAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 10 0.32
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.32
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:184505 original size:17 final size:17
Alignment explanation
Indices: 184454--184500 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
184444 AAACCATGAG
184454 TGCATCGATGCAT-AGTATA
1 TGCATCGATGCATCA--A-A
184473 TGCATCGATGCATCAAA
1 TGCATCGATGCATCAAA
184490 TGCATTCGATG
1 TGCA-TCGATG
184501 TTCAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.19
18 7 0.27
19 13 0.50
20 1 0.04
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (17 bp):
TGCATCGATGCATCAAA
Found at i:186251 original size:15 final size:14
Alignment explanation
Indices: 186233--186262 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
186223 TCATTATTTG
186233 TATATATTTTATTAT
1 TATATATTTT-TTAT
186248 TATATATTTTTTAT
1 TATATATTTTTTAT
186262 T
1 T
186263 TTTATGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATATATTTTTTAT
Found at i:186259 original size:17 final size:17
Alignment explanation
Indices: 186233--186267 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
186223 TCATTATTTG
186233 TATATATTTTATTATTA
1 TATATATTTTATTATTA
* *
186250 TATATTTTTTATTTTTA
1 TATATATTTTATTATTA
186267 T
1 T
186268 GGTTATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATATTTTATTATTA
Found at i:188909 original size:18 final size:18
Alignment explanation
Indices: 188886--188925 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
188876 CAGTTAAGGT
188886 TCCTGGAAACTTTGAGGA
1 TCCTGGAAACTTTGAGGA
188904 TCCTGGAAACTTTGAGGA
1 TCCTGGAAACTTTGAGGA
188922 TCCT
1 TCCT
188926 TTAGAACAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (18 bp):
TCCTGGAAACTTTGAGGA
Found at i:191572 original size:43 final size:43
Alignment explanation
Indices: 191524--191606 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
191514 ATGAAGGGGC
*
191524 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCATACCAACA
*
191567 CATCCACGATTTTAACTCCACGACGGAGGATATCATACCA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCATACCA
191607 TTCGGGGCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCATACCAACA
Found at i:191844 original size:110 final size:110
Alignment explanation
Indices: 191644--191846 Score: 311
Period size: 110 Copynumber: 1.8 Consensus size: 110
191634 GCTTCCCAAT
*
191644 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
* *
191709 CGACGAAGGGGCGGCTGATTATCAACAAATAACTTTTCAATTTCA
66 CGACGAAGGGACGGCTGACTATCAACAAATAACTTTTCAATTTCA
* *
191754 TTCAGAGTCAATTTCAACTTCATAGTGAAGGATATTAGACTCAAGACAGA-ACAAGCTCAACTTC
1 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTAGACTCAAGACA-ACACAAGCTCAACTTC
* *
191818 AC-AGCGAAGGGATGGCTGACTGTCAACAA
65 ACGA-CGAAGGGACGGCTGACTATCAACAA
191847 GCAATTTCCC
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
109 1 0.01
110 82 0.98
111 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
CGACGAAGGGACGGCTGACTATCAACAAATAACTTTTCAATTTCA
Found at i:192375 original size:36 final size:36
Alignment explanation
Indices: 192335--192406 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
192325 ATTTGAAATG
* *
192335 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
* *
192371 AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
192407 TAAACTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (36 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
Found at i:192461 original size:29 final size:29
Alignment explanation
Indices: 192389--192468 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
192379 CTCCCTTGAG
192389 ACAGTTTCTCTTGAAACATAAACTTTGAAA
1 ACAGTTTCTCTTGAAACA-AAACTTTGAAA
* * *
192419 ACAGATTCCCTTGAAACAAAACCTTTGAAT
1 ACAGTTTCTCTTGAAACAAAA-CTTTGAAA
*
192449 A-TGTTTCTCTTGAAACAAAA
1 ACAGTTTCTCTTGAAACAAAA
192469 TTTTTTCTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 19 0.44
30 24 0.56
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (29 bp):
ACAGTTTCTCTTGAAACAAAACTTTGAAA
Found at i:192470 original size:96 final size:96
Alignment explanation
Indices: 192275--192500 Score: 269
Period size: 96 Copynumber: 2.4 Consensus size: 96
192265 ACTTGTAATG
* * ***
192275 AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTGAAATGAATTT
1 AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACAATTCAAATGAAACA
***
192340 TGTCTCTCTTGAGATAGTTTCCCTTGAAACA
66 AAACTCTCTTGAGATAGTTTCCCTTGAAACA
* ***
192371 AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACAGATTCCCTTGAAAC
1 AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA-ATTCAAATGAAAC
*
192436 AAAAC-CT-TTGA-ATATGTTTCTCTTGAAACAA
65 AAAACTCTCTTGAGATA-GTTTCCCTTGAAAC-A
* *
192467 AATTTTTTCTCCCTGGAGACAATTTCTCTTGAAA
1 AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAA
192501 AAGAAAACCT
Statistics
Matches: 112, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
94 3 0.03
95 17 0.15
96 85 0.76
97 7 0.06
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.38
Consensus pattern (96 bp):
AATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACAATTCAAATGAAACA
AAACTCTCTTGAGATAGTTTCCCTTGAAACA
Found at i:192527 original size:31 final size:31
Alignment explanation
Indices: 192489--192568 Score: 81
Period size: 37 Copynumber: 2.4 Consensus size: 31
192479 CTGGAGACAA
*
192489 TTTCTCTTGAAAAAGAAAACCTTTGAAGTCT-
1 TTTCTCTTGAAAAAGAAAACCTTTGAAAT-TG
192520 TTTCTCTTGGAACACAAAAAGAAAACCTTTGAAATTG
1 TTTCTCTT-G-----AAAAAGAAAACCTTTGAAATTG
192557 TTTCTCTTGAAA
1 TTTCTCTTGAAA
192569 CAAAAAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
31 11 0.27
32 1 0.02
36 2 0.05
37 27 0.66
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (31 bp):
TTTCTCTTGAAAAAGAAAACCTTTGAAATTG
Found at i:192548 original size:37 final size:35
Alignment explanation
Indices: 192498--192579 Score: 112
Period size: 37 Copynumber: 2.3 Consensus size: 35
192488 ATTTCTCTTG
*
192498 AAAAAGAAAACCTTTGAAGTCT-TTTCTCTTGGAACAC
1 AAAAAGAAAACCTTTGAAAT-TGTTTCTCTT-GAA-AC
192535 AAAAAGAAAACCTTTGAAATTGTTTCTCTTGAAAC
1 AAAAAGAAAACCTTTGAAATTGTTTCTCTTGAAAC
*
192570 AAAAAAAAAA
1 AAAAAGAAAA
192580 TAAAACCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 11 0.26
36 4 0.10
37 27 0.64
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.27
Consensus pattern (35 bp):
AAAAAGAAAACCTTTGAAATTGTTTCTCTTGAAAC
Found at i:192592 original size:40 final size:40
Alignment explanation
Indices: 192535--192610 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
192525 CTTGGAACAC
*
192535 AAAAAGAAAACCTTTGAA-ATTGTTTCTCTTGAAACAAAAA
1 AAAAAGAAAACCATTGAACA-TGTTTCTCTTGAAACAAAAA
*
192575 AAAAATAAAACCATTGAACATGTTTCTCTTGAAACA
1 AAAAAGAAAACCATTGAACATGTTTCTCTTGAAACA
192611 CCAAAGCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (40 bp):
AAAAAGAAAACCATTGAACATGTTTCTCTTGAAACAAAAA
Found at i:203634 original size:64 final size:62
Alignment explanation
Indices: 203498--203635 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 62
203488 GCACTAAGAG
* * * **
203498 TGCATCGATGCATAAAATGCATTCGATGTTTTGAAATAGCATGAGTGCATCGATGCATTGTCTG
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAACCATGAGTGCATCGATGCA-T-TCAA
* * *
203562 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATTGATGCA-TCAAA
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAAACCATGAGTGCATCGATGCATTC-AA
203625 TGCATTCGATG
1 TGCA-TCGATG
203636 TTCAATTAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
62 2 0.03
63 4 0.06
64 38 0.60
65 19 0.30
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (62 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAACCATGAGTGCATCGATGCATTCAA
Found at i:203676 original size:20 final size:20
Alignment explanation
Indices: 203648--203686 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
203638 CAATTAATTC
*
203648 ATTGGTGCATCGGTGCATGG
1 ATTGATGCATCGGTGCATGG
203668 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGGTGCATG
203687 ACCTTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.36, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGGTGCATGG
Found at i:206259 original size:21 final size:20
Alignment explanation
Indices: 206215--206273 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
206205 TTTGGTACAG
* **
206215 AGGGAATCGATACCCCCTTGA
1 AGGGAACCGATACCCCC-ACA
*
206236 AGGGGAACCGATTCCCCCACA
1 A-GGGAACCGATACCCCCACA
*
206257 AGGGAATCGATACCCCC
1 AGGGAACCGATACCCCC
206274 TGAGGGTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 14 0.45
21 3 0.10
22 14 0.45
ACGTcount: A:0.29, C:0.34, G:0.24, T:0.14
Consensus pattern (20 bp):
AGGGAACCGATACCCCCACA
Found at i:206267 original size:20 final size:21
Alignment explanation
Indices: 206210--206274 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
206200 TCAGTTTTGG
206210 TACAGAGGGAATCGATACCCCC
1 TACA-AGGGAATCGATACCCCC
** * *
206232 TTGAAGGGGAACCGATTCCCCC
1 TACAA-GGGAATCGATACCCCC
206254 -ACAAGGGAATCGATACCCCC
1 TACAAGGGAATCGATACCCCC
206274 T
1 T
206275 GAGGGTTCTG
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
20 14 0.42
21 3 0.09
22 16 0.48
ACGTcount: A:0.29, C:0.32, G:0.23, T:0.15
Consensus pattern (21 bp):
TACAAGGGAATCGATACCCCC
Found at i:208380 original size:2 final size:2
Alignment explanation
Indices: 208373--208408 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
208363 CAGCTTAAGT
208373 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
208409 ATCAATTGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:210031 original size:19 final size:19
Alignment explanation
Indices: 209987--210040 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 19
209977 CCGTTGCAGC
*
209987 CAGGGTGTATCGATACACT
1 CAGGGTGTATGGATACACT
210006 -A--GTGTATGGATACACT
1 CAGGGTGTATGGATACACT
210022 CAGGGTGTATCGG-TACACT
1 CAGGGTGTAT-GGATACACT
210041 ATTTGCATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
16 14 0.47
17 1 0.03
18 1 0.03
19 12 0.40
20 2 0.07
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (19 bp):
CAGGGTGTATGGATACACT
Found at i:210095 original size:21 final size:20
Alignment explanation
Indices: 210069--210138 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 20
210059 AGCAGTCATA
*
210069 GGTGTATGGATACACCTGCAG
1 GGTGTATCGATACA-CTGCAG
210090 GGTGTATCGATACAC--CA-
1 GGTGTATCGATACACTGCAG
* *
210107 -GTGTCTGGATACACTGCAG
1 GGTGTATCGATACACTGCAG
210126 GGTGTATCGATAC
1 GGTGTATCGATAC
210139 CCTTTGATAC
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
16 12 0.30
18 4 0.10
20 11 0.28
21 13 0.32
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (20 bp):
GGTGTATCGATACACTGCAG
Found at i:215146 original size:20 final size:20
Alignment explanation
Indices: 215123--215169 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
215113 CCACGTGAAT
215123 AATATCGGTATAGTTCATAC
1 AATATCGGTATAGTTCATAC
* *
215143 AATATCGGTATTGTTTATAC
1 AATATCGGTATAGTTCATAC
215163 AATATCG
1 AATATCG
215170 ATACTGTACG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (20 bp):
AATATCGGTATAGTTCATAC
Found at i:215886 original size:30 final size:30
Alignment explanation
Indices: 215850--215909 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
215840 CCTGGGCTGG
215850 CTGTTTTGACTTTGTTCTTTCTGTAGTTGT
1 CTGTTTTGACTTTGTTCTTTCTGTAGTTGT
215880 CTGTTTTGACTTTGTTCTTTCTGTAGTTGT
1 CTGTTTTGACTTTGTTCTTTCTGTAGTTGT
215910 TCTTTCGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.07, C:0.13, G:0.20, T:0.60
Consensus pattern (30 bp):
CTGTTTTGACTTTGTTCTTTCTGTAGTTGT
Found at i:215909 original size:15 final size:15
Alignment explanation
Indices: 215861--215915 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
215851 TGTTTTGACT
215861 TTGTTCTTTCTGTAG
1 TTGTTCTTTCTGTAG
* *
215876 TTG-TCTGTTTTG-ACT
1 TTGTTCT-TTCTGTA-G
215891 TTGTTCTTTCTGTAG
1 TTGTTCTTTCTGTAG
215906 TTGTTCTTTC
1 TTGTTCTTTC
215916 GAAGAGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 4 0.12
15 24 0.75
16 4 0.12
ACGTcount: A:0.05, C:0.15, G:0.18, T:0.62
Consensus pattern (15 bp):
TTGTTCTTTCTGTAG
Found at i:228829 original size:2 final size:2
Alignment explanation
Indices: 228824--228858 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
228814 ATGTATATGT
228824 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
228859 ATACTCGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:229999 original size:51 final size:51
Alignment explanation
Indices: 229923--230020 Score: 196
Period size: 51 Copynumber: 1.9 Consensus size: 51
229913 TTGCAGATCT
229923 TGCTTTCAGACATGTTGATATTGTTAATGGCCTGAAATAAATTTACCTACG
1 TGCTTTCAGACATGTTGATATTGTTAATGGCCTGAAATAAATTTACCTACG
229974 TGCTTTCAGACATGTTGATATTGTTAATGGCCTGAAATAAATTTACC
1 TGCTTTCAGACATGTTGATATTGTTAATGGCCTGAAATAAATTTACC
230021 CACTTCTCGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (51 bp):
TGCTTTCAGACATGTTGATATTGTTAATGGCCTGAAATAAATTTACCTACG
Found at i:230322 original size:13 final size:13
Alignment explanation
Indices: 230304--230334 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
230294 GATCGGATTT
230304 TTTTAACCGGTTA
1 TTTTAACCGGTTA
*
230317 TTTTAACCGGTTT
1 TTTTAACCGGTTA
230330 TTTTA
1 TTTTA
230335 TCGGATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (13 bp):
TTTTAACCGGTTA
Found at i:231434 original size:21 final size:21
Alignment explanation
Indices: 231410--231451 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
231400 AGTTTATTTT
231410 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
231431 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
231452 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:231499 original size:33 final size:33
Alignment explanation
Indices: 231446--231544 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
231436 TTTGTTTCAA
231446 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
231478 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
231511 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
231544 T
1 T
231545 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:231857 original size:15 final size:17
Alignment explanation
Indices: 231831--231862 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
231821 TTCTATGGGA
231831 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
231847 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
231863 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:235397 original size:29 final size:28
Alignment explanation
Indices: 235348--235502 Score: 116
Period size: 29 Copynumber: 5.4 Consensus size: 28
235338 ATTTATCATA
* *
235348 AAAG-ACAAAACTATTTTTAAATTAAATT
1 AAAGTACAAAACT-TTTATAAATTAAAAT
*
235376 AAAGTACAAAACTTTTAATAAATTATAAT
1 AAAGTACAAAACTTTT-ATAAATTAAAAT
*** *
235405 AAAGTACATATTTTTTTATAAATCAAAAT
1 AAAGTACA-AAACTTTTATAAATTAAAAT
* * *
235434 AAAGTACAATACAATTTATAAATTACAATT
1 AAAGTACAAAAC-TTTTATAAATTA-AAAT
*** *
235464 AAA-TACAACTTTTTTAAAAATTAAAAT
1 AAAGTACAAAACTTTTATAAATTAAAAT
*
235491 AAAATACAAAAC
1 AAAGTACAAAAC
235503 AATTTACAAA
Statistics
Matches: 99, Mismatches: 22, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
27 6 0.06
28 24 0.24
29 58 0.59
30 11 0.11
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAGTACAAAACTTTTATAAATTAAAAT
Found at i:235514 original size:29 final size:29
Alignment explanation
Indices: 235345--235528 Score: 113
Period size: 29 Copynumber: 6.4 Consensus size: 29
235335 AAAATTTATC
* * *
235345 ATAAAAGACAAAACTATTTTTAAATTAAA
1 ATAAAATACAAAACAATTTATAAATTAAA
* * * *
235374 TTAAAGTACAAAAC-TTTTAATAAATTATA
1 ATAAAATACAAAACAATTT-ATAAATTAAA
* * **** *
235403 ATAAAGTACATATTTTTTTATAAATCAAA
1 ATAAAATACAAAACAATTTATAAATTAAA
* * *
235432 ATAAAGTACAATACAATTTATAAATTACA
1 ATAAAATACAAAACAATTTATAAATTAAA
* ** *
235461 ATTAAATAC--AACTTTTTTAAAAATTAAA
1 ATAAAATACAAAAC-AATTTATAAATTAAA
* **
235489 ATAAAATACAAAACAATTTACAAATTATT
1 ATAAAATACAAAACAATTTATAAATTAAA
235518 ATAAAATACAA
1 ATAAAATACAA
235529 TAAAAGGACA
Statistics
Matches: 117, Mismatches: 33, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
27 2 0.02
28 22 0.19
29 86 0.74
30 7 0.06
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.34
Consensus pattern (29 bp):
ATAAAATACAAAACAATTTATAAATTAAA
Found at i:235525 original size:57 final size:57
Alignment explanation
Indices: 235366--235528 Score: 193
Period size: 57 Copynumber: 2.8 Consensus size: 57
235356 AACTATTTTT
* * * * *
235366 AAATTAAATTAAAGTACAAAAC-TTTTAATAAATTATAATAAAGTACATATTTTTTTAT
1 AAATTAAAATAAAGTACAAAACAATTT-ATAAATTATAATAAAATACA-ACTTTTTTAA
* * * *
235424 AAATCAAAATAAAGTACAATACAATTTATAAATTACAATTAAATACAACTTTTTTAA
1 AAATTAAAATAAAGTACAAAACAATTTATAAATTATAATAAAATACAACTTTTTTAA
* * *
235481 AAATTAAAATAAAATACAAAACAATTTACAAATTATTATAAAATACAA
1 AAATTAAAATAAAGTACAAAACAATTTATAAATTATAATAAAATACAA
235529 TAAAAGGACA
Statistics
Matches: 88, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
57 49 0.56
58 36 0.41
59 3 0.03
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (57 bp):
AAATTAAAATAAAGTACAAAACAATTTATAAATTATAATAAAATACAACTTTTTTAA
Found at i:237784 original size:25 final size:26
Alignment explanation
Indices: 237730--237787 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
237720 AAATTACTGG
* **
237730 TTTAATTCAAACTCCAATTTTTATTC
1 TTTAATTCAAACTCCAAATTGGATTC
237756 TTTAATT-AAACTCCATAATTGGATT-
1 TTTAATTCAAACTCCA-AATTGGATTC
237781 TTTAATT
1 TTTAATT
237788 TGATCAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.50
Consensus pattern (26 bp):
TTTAATTCAAACTCCAAATTGGATTC
Found at i:243575 original size:21 final size:21
Alignment explanation
Indices: 243551--243593 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
243541 TAGTTTATCA
243551 TTACGATGCTGACGTGACAGT
1 TTACGATGCTGACGTGACAGT
243572 TTACGATGCTGACGTGACAGT
1 TTACGATGCTGACGTGACAGT
243593 T
1 T
243594 ATGGTGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (21 bp):
TTACGATGCTGACGTGACAGT
Found at i:245354 original size:17 final size:17
Alignment explanation
Indices: 245340--245373 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
245330 ACATATAATA
245340 TAAATTTATATATAAAT
1 TAAATTTATATATAAAT
*
245357 TATATTTATATTATAAA
1 TAAATTTATA-TATAAA
245374 CTATATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTTATATATAAAT
Found at i:245359 original size:11 final size:11
Alignment explanation
Indices: 245337--245410 Score: 51
Period size: 11 Copynumber: 6.2 Consensus size: 11
245327 TATACATATA
245337 ATATAAATTTAT
1 ATATAAA-TTAT
245349 ATATAAATTAT
1 ATATAAATTAT
* *
245360 ATTTATATTAT
1 ATATAAATTAT
245371 AAACTATATAATTAT
1 --A-TATA-AATTAT
*
245386 -TATAAGTTATAT
1 ATATAA-AT-TAT
245398 ATATAAATTAT
1 ATATAAATTAT
245409 AT
1 AT
245411 TTATGTGAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
10 1 0.02
11 23 0.47
12 11 0.22
13 6 0.12
14 3 0.06
15 5 0.10
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (11 bp):
ATATAAATTAT
Found at i:245373 original size:18 final size:18
Alignment explanation
Indices: 245343--245402 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
245333 TATAATATAA
245343 ATTTATA-TATAAATTAT
1 ATTTATATTATAAATTAT
*
245360 ATTTATATTATAAACTAT
1 ATTTATATTATAAATTAT
* *
245378 A-TAATTATTATAAGTTAT
1 ATTTA-TATTATAAATTAT
*
245396 ATATATA
1 ATTTATA
245403 AATTATATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 9 0.26
18 24 0.71
19 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTTATATTATAAATTAT
Found at i:245436 original size:13 final size:13
Alignment explanation
Indices: 245393--245440 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
245383 TATTATAAGT
*
245393 TATATATATAAAT
1 TATATATATAAAC
* *
245406 TATATTTATGTGAAC
1 TATA--TATATAAAC
245421 TATATATATAAAC
1 TATATATATAAAC
245434 TATATAT
1 TATATAT
245441 GTATAAAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 18 0.64
15 10 0.36
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:245439 original size:15 final size:15
Alignment explanation
Indices: 245346--245452 Score: 60
Period size: 15 Copynumber: 7.0 Consensus size: 15
245336 AATATAAATT
*
245346 TATATATAAATTATA
1 TATATATAAACTATA
245361 TTTATATTATAAACTATA
1 --TATA-TATAAACTATA
*
245379 TA-ATTATTATAAGT-TA
1 TATA-TA-TA-AACTATA
*
245395 TATATATAAATTATA
1 TATATATAAACTATA
* * *
245410 TTTATGTGAAC--TA
1 TATATATAAACTATA
245423 TATATATAAACTATA
1 TATATATAAACTATA
* *
245438 TATGTATAAAGTATA
1 TATATATAAACTATA
245453 AAAGTATATA
Statistics
Matches: 71, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
13 10 0.14
14 3 0.04
15 30 0.42
16 10 0.14
17 8 0.11
18 10 0.14
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.46
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:245815 original size:2 final size:2
Alignment explanation
Indices: 245808--245963 Score: 91
Period size: 2 Copynumber: 81.0 Consensus size: 2
245798 TATAATTTTC
* *
245808 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA AA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
245851 TA TA TG TA TA -A AA TA TA TA -A AA TA TA TA GTT TA TA AA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
245891 TA -A TT TA TA T- TA -A TA TA GTA TA TA TA TA TG TA TG TA TA -A
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
245930 CTA -A TA TA -A GTA -A TA TA TA AA T- TA TA TA TA TA TA
1 -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
245964 GAAACGTTAT
Statistics
Matches: 118, Mismatches: 20, Indels: 32
0.69 0.12 0.19
Matches are distributed among these distances:
1 11 0.09
2 101 0.86
3 6 0.05
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:246228 original size:35 final size:36
Alignment explanation
Indices: 246158--246231 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
246148 ACAATAGTTA
* *
246158 ATATATGTAACCTATAGTATATGTATACATGTAAACT
1 ATATATGTAACCTATAGTACATGTATA-ATATAAACT
* *
246195 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACCTATAGTACATGTATAATATAAACT
246230 AT
1 AT
246232 GTATAGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 9 0.27
37 24 0.73
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (36 bp):
ATATATGTAACCTATAGTACATGTATAATATAAACT
Found at i:246391 original size:21 final size:20
Alignment explanation
Indices: 246342--246455 Score: 82
Period size: 21 Copynumber: 5.8 Consensus size: 20
246332 AAAACCCTAA
*
246342 AATCTTAAACCCTAAA-CA-
1 AATCATAAACCCTAAATCAT
246360 ATATGCATAAACCCTAAATCAT
1 A-AT-CATAAACCCTAAATCAT
*
246382 AGATCATAAA-CCT---T-AA
1 A-ATCATAAACCCTAAATCAT
*
246398 AAT-ATAAACCCTAAACCAT
1 AATCATAAACCCTAAATCAT
*
246417 GAATCATAAAACCTAAATCAT
1 -AATCATAAACCCTAAATCAT
*
246438 AAACTATAAACCCTAAAT
1 AATC-ATAAACCCTAAAT
246456 ACTATGCATA
Statistics
Matches: 75, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
14 5 0.07
15 5 0.07
16 2 0.03
17 1 0.01
18 1 0.01
19 3 0.04
20 21 0.28
21 34 0.45
22 3 0.04
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.24
Consensus pattern (20 bp):
AATCATAAACCCTAAATCAT
Found at i:246440 original size:35 final size:36
Alignment explanation
Indices: 246365--246441 Score: 99
Period size: 35 Copynumber: 2.2 Consensus size: 36
246355 AAACAATATG
*
246365 CATAAACCCTAAATCATAGATCATAAACCTTAAAAT
1 CATAAACCCTAAACCATAGATCATAAACCTTAAAAT
246401 -ATAAACCCTAAACCAT-GAATCATAAAACC-T-AAAT
1 CATAAACCCTAAACCATAG-ATCAT-AAACCTTAAAAT
246435 CATAAAC
1 CATAAAC
246442 TATAAACCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
34 5 0.14
35 27 0.73
36 5 0.14
ACGTcount: A:0.52, C:0.23, G:0.03, T:0.22
Consensus pattern (36 bp):
CATAAACCCTAAACCATAGATCATAAACCTTAAAAT
Found at i:246566 original size:20 final size:19
Alignment explanation
Indices: 246541--246633 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 19
246531 TACATGTATG
*
246541 TATAAACTATGTATACTATA
1 TATAAACTATATATA-TATA
246561 TATAAACTATATATATATA
1 TATAAACTATATATATATA
* * *
246580 -ACCTATAGTATATGTATATA
1 TA--TAAACTATATATATATA
* * * *
246600 TACAATCTATTTATATGTTA
1 TATAAACTATATATAT-ATA
246620 TATAAACTATATAT
1 TATAAACTATATAT
246634 GTAACTTATA
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
18 1 0.02
19 12 0.22
20 41 0.75
21 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (19 bp):
TATAAACTATATATATATA
Found at i:246577 original size:15 final size:16
Alignment explanation
Indices: 246552--246592 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
246542 ATAAACTATG
246552 TATACTATATATAAAC
1 TATACTATATATAAAC
*
246568 TATA-TATATATAACC
1 TATACTATATATAAAC
*
246583 TATAGTATAT
1 TATACTATAT
246593 GTATATATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (16 bp):
TATACTATATATAAAC
Found at i:246580 original size:35 final size:39
Alignment explanation
Indices: 246541--246615 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 39
246531 TACATGTATG
246541 TATAAACTAT-GTATA-CTATATATA-AA-CTATATATA
1 TATAAACTATAGTATATCTATATATACAATCTATATATA
* * *
246576 TATAACCTATAGTATATGTATATATACAATCTATTTATA
1 TATAAACTATAGTATATCTATATATACAATCTATATATA
246615 T
1 T
246616 GTTATATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 9 0.27
36 5 0.15
37 8 0.24
38 2 0.06
39 9 0.27
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (39 bp):
TATAAACTATAGTATATCTATATATACAATCTATATATA
Found at i:246597 original size:24 final size:22
Alignment explanation
Indices: 246572--246630 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
246562 ATAAACTATA
*
246572 TATATATAACCTATAGTATATG
1 TATATATAAACTATAGTATATG
*
246594 TATATATACAATCTAT-TTATATG
1 TATATATA-AA-CTATAGTATATG
246617 T-TATATAAACTATA
1 TATATATAAACTATA
246631 TATGTAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 14 0.44
23 8 0.25
24 4 0.12
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (22 bp):
TATATATAAACTATAGTATATG
Found at i:246644 original size:57 final size:55
Alignment explanation
Indices: 246505--246645 Score: 167
Period size: 57 Copynumber: 2.5 Consensus size: 55
246495 ATATGTATAC
* *
246505 ATATAAACTATACATGTAACTTATAGTACATGTATGTATAAACTATGTATACTAT
1 ATATAAACTATATATGTAACTTATAGTACATGTATATATAAACTATGTATACTAT
* * * * *
246560 ATATAAACTATATATATATAACCTATAGTATATGTATATATACAATCTATTTATA-TGTT
1 ATATAAAC--TATATATGTAACTTATAGTACATGTATATATA-AA-CTATGTATACT-AT
246619 ATATAAACTATATATGTAACTTATAGT
1 ATATAAACTATATATGTAACTTATAGT
246646 TTATAAACAA
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
55 8 0.11
57 44 0.61
58 3 0.04
59 17 0.24
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (55 bp):
ATATAAACTATATATGTAACTTATAGTACATGTATATATAAACTATGTATACTAT
Found at i:246664 original size:21 final size:20
Alignment explanation
Indices: 246639--246730 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 20
246629 TATATGTAAC
246639 TTATAGTTTATAAACAATAGT
1 TTATA-TTTATAAACAATAGT
** *
246660 TTATA-TTAGTGTACTATATATT
1 TTATATTTA-TAAAC-A-ATAGT
* *
246682 TTATACTTTATAACCTATAGT
1 TTATA-TTTATAAACAATAGT
* *
246703 ATATAATTTATAAACTATAGT
1 TTAT-ATTTATAAACAATAGT
246724 TTATATT
1 TTATATT
246731 AATGTTAATT
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.06
20 6 0.11
21 30 0.56
22 10 0.19
23 2 0.04
24 3 0.06
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (20 bp):
TTATATTTATAAACAATAGT
Found at i:246781 original size:67 final size:65
Alignment explanation
Indices: 246697--246865 Score: 191
Period size: 65 Copynumber: 2.6 Consensus size: 65
246687 CTTTATAACC
* *
246697 TATAGTATATAATTTATAAACTATAGTTTATATTAATGTTAATTATCT-TA-ACTATAATTTATA
1 TATAGTATATAATTTATAAACTATA--CTATATTAATATTAATT-T-TATAGACTATAATTTATA
246760 TTAA
62 TTAA
* *
246764 TATAGTATATAGTTTATAAACTATACTATATTAATATTAATTTTATAGACTATACTTTATATTAA
1 TATAGTATATAATTTATAAACTATACTATATTAATATTAATTTTATAGACTATAATTTATATTAA
* * * * *
246829 TATTAAT-TACAAATTGTAAACTATATTATATTAATAT
1 TA-TAGTATATAATTTATAAACTATACTATATTAATAT
246866 AAGTTAATAT
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 3 0.03
65 58 0.65
66 3 0.03
67 24 0.27
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (65 bp):
TATAGTATATAATTTATAAACTATACTATATTAATATTAATTTTATAGACTATAATTTATATTAA
Found at i:246796 original size:34 final size:32
Alignment explanation
Indices: 246756--246866 Score: 86
Period size: 34 Copynumber: 3.4 Consensus size: 32
246746 AACTATAATT
246756 TATATTAATATAGTATATAGTTTATAAACTATAC
1 TATATTAATATA-TATATA-TTTATAAACTATAC
*
246790 TATATTAATAT-TA-AT-TTTATAGACTATAC
1 TATATTAATATATATATATTTATAAACTATAC
* * * *
246819 TTTATATTAATAT-TAATTACAAATTGTAAACTATAT
1 --TATATTAATATAT-A-TA-TATTTATAAACTATAC
246855 TATATTAATATA
1 TATATTAATATA
246867 AGTTAATATT
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
29 13 0.21
31 14 0.22
32 3 0.05
34 23 0.37
36 10 0.16
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (32 bp):
TATATTAATATATATATATTTATAAACTATAC
Found at i:246808 original size:29 final size:30
Alignment explanation
Indices: 246709--246959 Score: 114
Period size: 31 Copynumber: 8.2 Consensus size: 30
246699 TAGTATATAA
* *
246709 TTTATAAACTATAGTTTATATTAATGTTAAT
1 TTTATAAACTATA-CTTATATTAATATTAAT
* * * *
246740 TATCTTAACTATAATTTATATTAATATAGTATAT
1 TTTATAAACTAT-ACTTATATTAATAT--TA-AT
246774 AGTTTATAAACTATAC-TATATTAATATTAAT
1 --TTTATAAACTATACTTATATTAATATTAAT
*
246805 TTTATAGACTATACTTTATATTAATATTAAT
1 TTTATAAACTATAC-TTATATTAATATTAAT
*
246836 TACAAATTGTAAACTATA-TTATATTAATA-TAAGT
1 T-----TTATAAACTATACTTATATTAATATTAA-T
* * * *
246870 TAATATTAA-TATTAATTAAATTAATATTAA-
1 T-TTATAAACTA-TACTTATATTAATATTAAT
* *
246900 -TTATAATA-TATAATTATTTTAATATTAA-
1 TTTATAA-ACTATACTTATATTAATATTAAT
*
246928 -TTAT-AA--ATACTT-TATTAATATAAAT
1 TTTATAAACTATACTTATATTAATATTAAT
*
246953 TATATAA
1 TTTATAA
246960 GGCGGTGGCG
Statistics
Matches: 176, Mismatches: 23, Indels: 46
0.72 0.09 0.19
Matches are distributed among these distances:
24 10 0.06
25 5 0.03
26 4 0.02
27 2 0.01
28 24 0.14
29 18 0.10
30 7 0.04
31 49 0.28
32 6 0.03
33 5 0.03
34 26 0.15
35 1 0.01
36 19 0.11
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTATAAACTATACTTATATTAATATTAAT
Found at i:246828 original size:31 final size:31
Alignment explanation
Indices: 246709--246836 Score: 134
Period size: 31 Copynumber: 4.0 Consensus size: 31
246699 TAGTATATAA
* *
246709 TTTATAAACTATAGTTTATATTAATGTTAAT
1 TTTATAAACTATACTTTATATTAATATTAAT
* * * *
246740 TATCTTAACTATAATTTATATTAATATAGTATAT
1 TTTATAAACTATACTTTATATTAATAT--TA-AT
246774 AGTTTATAAACTATAC--TATATTAATATTAAT
1 --TTTATAAACTATACTTTATATTAATATTAAT
*
246805 TTTATAGACTATACTTTATATTAATATTAAT
1 TTTATAAACTATACTTTATATTAATATTAAT
246836 T
1 T
246837 ACAAATTGTA
Statistics
Matches: 80, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
29 13 0.16
31 40 0.50
32 2 0.03
33 2 0.03
34 13 0.16
36 10 0.12
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (31 bp):
TTTATAAACTATACTTTATATTAATATTAAT
Found at i:246877 original size:21 final size:20
Alignment explanation
Indices: 246851--246902 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
246841 ATTGTAAACT
*
246851 ATATTATATTAATATAAGTTA
1 ATATTATATTAAT-TAAATTA
246872 ATATTAATATTAATTAAATTA
1 ATATT-ATATTAATTAAATTA
246893 ATATTA-ATTA
1 ATATTATATTA
246903 TAATATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 4 0.14
20 1 0.03
21 16 0.55
22 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATTATATTAATTAAATTA
Found at i:246878 original size:6 final size:6
Alignment explanation
Indices: 246851--246928 Score: 53
Period size: 6 Copynumber: 13.3 Consensus size: 6
246841 ATTGTAAACT
*
246851 ATATT- ATATTA ATA-TA A-GTTA ATATTA ATATT- A-ATTA A-ATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
246893 ATATTA AT-TATA ATATATA ATTATTTTA ATATTA AT
1 ATATTA ATAT-TA ATAT-TA A-TA--TTA ATATTA AT
246929 TATAAATACT
Statistics
Matches: 61, Mismatches: 2, Indels: 19
0.74 0.02 0.23
Matches are distributed among these distances:
4 3 0.05
5 19 0.31
6 26 0.43
7 5 0.08
8 4 0.07
9 3 0.05
10 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:246906 original size:21 final size:22
Alignment explanation
Indices: 246870--246956 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 22
246860 TAATATAAGT
246870 TAATATTAATATTAATTA-AAT
1 TAATATTAATATTAATTATAAT
246891 TAATATTAAT-TATAATATATAAT
1 TAATATTAATAT-TAAT-TATAAT
* *
246914 T-ATTTTAATATTAATTATAAA
1 TAATATTAATATTAATTATAAT
* *
246935 TACTTTATTAATATAAATTATA
1 TA--ATATTAATATTAATTATA
246957 TAAGGCGGTG
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
20 1 0.02
21 20 0.37
22 13 0.24
23 5 0.09
24 15 0.28
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATATTAATATTAATTATAAT
Found at i:246915 original size:13 final size:12
Alignment explanation
Indices: 246856--246933 Score: 54
Period size: 15 Copynumber: 6.1 Consensus size: 12
246846 AAACTATATT
246856 ATATTAA-TATA
1 ATATTAATTATA
*
246867 A-GTTAA-TATTA
1 ATATTAATTA-TA
246878 ATATTAATTAAATTA
1 ATATTAATT--A-TA
246893 ATATTAATTATA
1 ATATTAATTATA
246905 ATATATAATTATTTTA
1 ATAT-TAATTA---TA
246921 ATATTAATTATA
1 ATATTAATTATA
246933 A
1 A
246934 ATACTTTATT
Statistics
Matches: 56, Mismatches: 2, Indels: 17
0.75 0.03 0.23
Matches are distributed among these distances:
10 6 0.11
11 4 0.07
12 13 0.23
13 8 0.14
15 19 0.34
16 6 0.11
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (12 bp):
ATATTAATTATA
Found at i:246922 original size:28 final size:27
Alignment explanation
Indices: 246876--246933 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
246866 AAGTTAATAT
246876 TAATATTAATTAAATTAATATTAATTA
1 TAATATTAATTAAATTAATATTAATTA
**
246903 TAATATATAATTATTTTAATATTAATTA
1 TAATAT-TAATTAAATTAATATTAATTA
246931 TAA
1 TAA
246934 ATACTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TAATATTAATTAAATTAATATTAATTA
Found at i:250307 original size:22 final size:24
Alignment explanation
Indices: 250264--250320 Score: 82
Period size: 22 Copynumber: 2.5 Consensus size: 24
250254 ATTAATAATG
*
250264 TTTTATCTAATTTACATTAAATAA
1 TTTTATATAATTTACATTAAATAA
*
250288 TTTTAT-TAATTT-TATTAAATAA
1 TTTTATATAATTTACATTAAATAA
250310 TTTTATATAAT
1 TTTTATATAAT
250321 AGGTCTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 15 0.48
23 10 0.32
24 6 0.19
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTATATAATTTACATTAAATAA
Found at i:250435 original size:19 final size:19
Alignment explanation
Indices: 250411--250447 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
250401 CATTATAATC
250411 TTAAAAACTTATAATTTTA
1 TTAAAAACTTATAATTTTA
*
250430 TTAAAATCTTATAATTTT
1 TTAAAAACTTATAATTTT
250448 GATCATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAAACTTATAATTTTA
Found at i:250533 original size:16 final size:16
Alignment explanation
Indices: 250514--250580 Score: 98
Period size: 16 Copynumber: 4.2 Consensus size: 16
250504 TCATTTACAT
250514 GTCAGGTTAAAAACAG
1 GTCAGGTTAAAAACAG
*
250530 GTCAGGTTAAAAATAG
1 GTCAGGTTAAAAACAG
* *
250546 GTCAGGTTCATAACAG
1 GTCAGGTTAAAAACAG
*
250562 GTCAGGTTGAAAACAG
1 GTCAGGTTAAAAACAG
250578 GTC
1 GTC
250581 GGGTAATACC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.22
Consensus pattern (16 bp):
GTCAGGTTAAAAACAG
Found at i:251029 original size:2 final size:2
Alignment explanation
Indices: 251024--251049 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
251014 GAATATATCC
251024 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
251050 GAAAAGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:254581 original size:36 final size:36
Alignment explanation
Indices: 254531--254749 Score: 357
Period size: 36 Copynumber: 6.1 Consensus size: 36
254521 AGAGGATGAA
* * * **
254531 GAACGAAAGAAAGCATCGGCACTTCTAATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
*
254567 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* *
254603 GAACGGAAGAAAGCATCGGCACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
254639 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
*
254675 GAACGGAAGGAAACATCGACACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
254711 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
254747 GAA
1 GAA
254750 TGAAAGAATG
Statistics
Matches: 174, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 174 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
Found at i:254617 original size:72 final size:72
Alignment explanation
Indices: 254531--254780 Score: 378
Period size: 72 Copynumber: 3.5 Consensus size: 72
254521 AGAGGATGAA
* ** *
254531 GAACGAAAGAAAGCATCGGCACTTCTAATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCCGAT
1 GAACGGAAGAAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGACACTTCCGAT
254596 TCAAGTC
66 TCAAGTC
254603 GAACGGAAGAAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGACACTTCCGAT
1 GAACGGAAGAAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGACACTTCCGAT
254668 TCAAGTC
66 TCAAGTC
*
254675 GAACGGAAGGAAA-CATCGACACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGACACTTCCGA
1 GAACGGAA-GAAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGACACTTCCGA
254739 TTCAAGTC
65 TTCAAGTC
* * * * * *
254747 GAATGAAAGAATGTATC-GCACTTTCGTTTCAAGT
1 GAACGGAAGAAAGCATCGGCACTTCCGATTCAAGT
254781 TTTCATCTTT
Statistics
Matches: 164, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
71 17 0.10
72 143 0.87
73 4 0.02
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (72 bp):
GAACGGAAGAAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGACACTTCCGAT
TCAAGTC
Found at i:255067 original size:19 final size:19
Alignment explanation
Indices: 255040--255104 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 19
255030 AATGTTTTTA
* *
255040 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
255059 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
255078 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
255097 TGAACAGT
1 TGAACAGT
255105 TACCCGAGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:257025 original size:23 final size:23
Alignment explanation
Indices: 256989--257034 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
256979 ACATATTATA
256989 TGGCACTACAGTGCAATTCTACG
1 TGGCACTACAGTGCAATTCTACG
* * *
257012 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACAGTGCAATTCTACG
257035 CGGTCATTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (23 bp):
TGGCACTACAGTGCAATTCTACG
Found at i:257044 original size:23 final size:23
Alignment explanation
Indices: 256990--257045 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
256980 CATATTATAT
* * *
256990 GGCACTACAGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
257013 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
257036 GGTCA-TTCGG
1 GG-CACTTCGG
257046 GACAAAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:258207 original size:21 final size:21
Alignment explanation
Indices: 258181--258223 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
258171 ATTTGAATAT
258181 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
258202 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
258223 T
1 T
258224 CTGTTCTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCC
Found at i:258542 original size:11 final size:11
Alignment explanation
Indices: 258505--258552 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
258495 GATAAAGAAG
258505 AAAGAAAGAGA
1 AAAGAAAGAGA
258516 GAAAGGAAATGAGA
1 -AAA-GAAA-GAGA
*
258530 AAATAAAGAGA
1 AAAGAAAGAGA
258541 AAAGAAA-AGA
1 AAAGAAAGAGA
258551 AA
1 AA
258553 TTTATTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 5 0.16
11 10 0.31
12 6 0.19
13 7 0.22
14 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (11 bp):
AAAGAAAGAGA
Found at i:264210 original size:13 final size:13
Alignment explanation
Indices: 264186--264220 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
264176 GGAAGAAATG
264186 TTGGTTTACTCTT
1 TTGGTTTACTCTT
* *
264199 TTTGTTTGCTCTT
1 TTGGTTTACTCTT
264212 TTGGTTTAC
1 TTGGTTTAC
264221 CCCTAGAATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.14, G:0.17, T:0.63
Consensus pattern (13 bp):
TTGGTTTACTCTT
Found at i:272269 original size:3 final size:3
Alignment explanation
Indices: 272261--272285 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
272251 ACAAATTTTC
272261 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
272286 TTGAGTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:272708 original size:22 final size:23
Alignment explanation
Indices: 272674--272757 Score: 70
Period size: 22 Copynumber: 3.7 Consensus size: 23
272664 AAAAAGAGAT
*
272674 TTTTTAATATGAGTTAAATAATA
1 TTTTTAATTTGAGTTAAATAATA
*
272697 TTTTT-ATTTGAGCTACAA-AAT-
1 TTTTTAATTTGAGTTA-AATAATA
*
272718 TTTAATTAAATTT-ATTTAAATAATA
1 TTT--TT-AATTTGAGTTAAATAATA
272743 TTTTT-ATTTGAGTTA
1 TTTTTAATTTGAGTTA
272758 CAAAATTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
21 7 0.15
22 15 0.31
23 13 0.27
24 6 0.12
25 7 0.15
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (23 bp):
TTTTTAATTTGAGTTAAATAATA
Found at i:272739 original size:46 final size:46
Alignment explanation
Indices: 272687--272775 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
272677 TTAATATGAG
272687 TTAAATAATATTTTTATTTGAGCTACAAAATTTTAATTAAATTTAT
1 TTAAATAATATTTTTATTTGAGCTACAAAATTTTAATTAAATTTAT
*
272733 TTAAATAATATTTTTATTTGAGTTACAAAATTTTAATTAAATT
1 TTAAATAATATTTTTATTTGAGCTACAAAATTTTAATTAAATT
272776 AAATTTATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (46 bp):
TTAAATAATATTTTTATTTGAGCTACAAAATTTTAATTAAATTTAT
Found at i:273415 original size:29 final size:29
Alignment explanation
Indices: 273383--273538 Score: 109
Period size: 29 Copynumber: 5.4 Consensus size: 29
273373 AAAATTTATC
* *
273383 ATAAAGAACAAAACTATTAATAAATTACA
1 ATAAAGTACAAAACTATTTATAAATTACA
* ** * *
273412 ATAAAGTACATATTTTTTTATAAATCACA
1 ATAAAGTACAAAACTATTTATAAATTACA
*
273441 ATAAAGTACAATACTATTTATAAATTACA
1 ATAAAGTACAAAACTATTTATAAATTACA
*** * * * *
273470 ATTAAA-TACAATTTTTTTTAAAAAATAAA
1 A-TAAAGTACAAAACTATTTATAAATTACA
* * *
273499 ATAAAATACAAAGCAATTTATAAATTA-A
1 ATAAAGTACAAAACTATTTATAAATTACA
*
273527 TATAAAATACAA
1 -ATAAAGTACAA
273539 TAAAAGGAAC
Statistics
Matches: 98, Mismatches: 26, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
28 5 0.05
29 89 0.91
30 4 0.04
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (29 bp):
ATAAAGTACAAAACTATTTATAAATTACA
Found at i:273502 original size:58 final size:58
Alignment explanation
Indices: 273383--273540 Score: 164
Period size: 58 Copynumber: 2.7 Consensus size: 58
273373 AAAATTTATC
* * * *
273383 ATAAAGAACAAAACTATTAATAAATTACAA-TAAAGTAC-ATATTTTTTTATAAATCACA
1 ATAAAGTAC-AAACTATTTATAAATTACAATTAAA-TACAATATTTTTTTAAAAATCAAA
273441 ATAAAGTACAATACTATTTATAAATTACAATTAAATACAAT-TTTTTTTAAAAAAT-AAA
1 ATAAAGTACAA-ACTATTTATAAATTACAATTAAATACAATATTTTTTT-AAAAATCAAA
* * *
273499 ATAAAATACAAAGCAATTTATAAATTA-ATATAAAATACAATA
1 ATAAAGTACAAA-CTATTTATAAATTACA-ATTAAATACAATA
273541 AAAGGAACAA
Statistics
Matches: 86, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
57 4 0.05
58 71 0.83
59 11 0.13
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.34
Consensus pattern (58 bp):
ATAAAGTACAAACTATTTATAAATTACAATTAAATACAATATTTTTTTAAAAATCAAA
Found at i:274918 original size:2 final size:2
Alignment explanation
Indices: 274911--274949 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
274901 CACGCGTCAA
274911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
274950 AAGTTGAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:275591 original size:21 final size:21
Alignment explanation
Indices: 275565--275641 Score: 145
Period size: 21 Copynumber: 3.7 Consensus size: 21
275555 GCGAATAAGT
275565 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
275586 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
275607 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
275628 AAATCGCAATGCGA
1 AAATCGCAACGCGA
275642 TACTGACTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.14
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:275655 original size:20 final size:20
Alignment explanation
Indices: 275630--275743 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
275620 AATTGGGAAA
*
275630 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
275650 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
275670 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
275691 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
275711 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
275731 TTCGCAACGCGAT
1 ATCGCAACGCGAT
275744 TTACATAGCA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:275692 original size:61 final size:61
Alignment explanation
Indices: 275627--275743 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
275617 GCGAATTGGG
* * * * *
275627 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
275688 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
275744 TTACATAGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:276010 original size:27 final size:26
Alignment explanation
Indices: 275954--276004 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
275944 ATCGCCGGCG
*
275954 AAATCCCTCACAACCATTCACAGTAAA
1 AAATCCCTCACAACCATT-ACAGAAAA
*
275981 AAATCCCTCACAATCATT-CAGAAA
1 AAATCCCTCACAACCATTACAGAAA
276005 TGAAAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
27 17 0.77
ACGTcount: A:0.45, C:0.31, G:0.04, T:0.20
Consensus pattern (26 bp):
AAATCCCTCACAACCATTACAGAAAA
Found at i:276363 original size:33 final size:33
Alignment explanation
Indices: 276321--276488 Score: 219
Period size: 33 Copynumber: 4.9 Consensus size: 33
276311 CAAAATCACA
* *
276321 TTGCAATTTTCATTTCGCGTTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
276354 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC---TCTCG
276392 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
276425 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
276458 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
276489 ATTATCTCGT
Statistics
Matches: 123, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
33 74 0.60
34 15 0.12
35 3 0.02
36 3 0.02
38 28 0.23
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:276378 original size:19 final size:19
Alignment explanation
Indices: 276321--276513 Score: 164
Period size: 19 Copynumber: 10.8 Consensus size: 19
276311 CAAAATCACA
*
276321 TTGCAATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
276340 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCG
276354 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
276373 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
276392 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
276411 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
276425 TTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
276444 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
276458 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* *
276478 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
276498 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
276514 TACCAAAAGA
Statistics
Matches: 141, Mismatches: 16, Indels: 34
0.74 0.08 0.18
Matches are distributed among these distances:
14 29 0.21
16 7 0.05
17 8 0.06
19 65 0.46
20 31 0.22
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:276428 original size:14 final size:14
Alignment explanation
Indices: 276409--276464 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
276399 TTTCATTTCG
276409 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
276423 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
276442 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
276456 CGTTGCGAT
1 CGTTGCGAT
276465 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:276442 original size:71 final size:66
Alignment explanation
Indices: 276321--276488 Score: 219
Period size: 71 Copynumber: 2.5 Consensus size: 66
276311 CAAAATCACA
* **
276321 TTGCAATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATTTTCATTTCGCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCATTTCGCGTTGCGA--TTC--
276386 TTCGCG
62 -TCGCG
* *
276392 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCATTTCGCGTTGCGATTCTCGC
276457 G
66 G
**
276458 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
276489 ATTATCTCGT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
66 17 0.19
67 15 0.17
69 3 0.03
71 54 0.61
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (66 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCATTTCGCGTTGCGATTCTCGC
G
Found at i:278684 original size:42 final size:42
Alignment explanation
Indices: 278606--278769 Score: 177
Period size: 42 Copynumber: 3.9 Consensus size: 42
278596 GACTCGCCGG
* * * *
278606 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCTATCGTTCAAGAGGCCCCTA
* * * *
278648 TCATTCCTCGAGAGTCCCCTCTTA-CTGTTCACGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCTATC-GTTCAAGAGGCCCCTA
* * * *
278690 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCTATCGTTCAAGAGGCCCCTA
* * *
278732 TCATTCCTCGAGAGTCCCCTCCCACCGTTTAAGAGGCC
1 TCATTCCTCGAGAGTCCCCTCCTATCGTTCAAGAGGCC
278770 ACTGTCATCG
Statistics
Matches: 98, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
41 1 0.01
42 96 0.98
43 1 0.01
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.25
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCTATCGTTCAAGAGGCCCCTA
Found at i:278787 original size:84 final size:84
Alignment explanation
Indices: 278605--278778 Score: 303
Period size: 84 Copynumber: 2.1 Consensus size: 84
278595 CGACTCGCCG
*
278605 GTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCT
1 GTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC
* * *
278670 TACTGTTCACGAGGCCACT
66 CACCGTTCAAGAGGCCACT
278689 GTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC
1 GTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC
*
278754 CACCGTTTAAGAGGCCACT
66 CACCGTTCAAGAGGCCACT
278773 GTCATC
1 GTCATC
278779 GTTGAAGAGG
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (84 bp):
GTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC
CACCGTTCAAGAGGCCACT
Found at i:278799 original size:21 final size:20
Alignment explanation
Indices: 278748--278808 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 20
278738 CTCGAGAGTC
* *
278748 CCCTCCCACCGTTTAAGAGG
1 CCCTCCCATCGTTCAAGAGG
** *
278768 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCATCGTTCAAGAGG
*
278789 TCCCTCCCATCATTCAAGAG
1 -CCCTCCCATCGTTCAAGAG
278809 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (20 bp):
CCCTCCCATCGTTCAAGAGG
Found at i:278808 original size:84 final size:84
Alignment explanation
Indices: 278605--278808 Score: 266
Period size: 84 Copynumber: 2.4 Consensus size: 84
278595 CGACTCGCCG
* * * *
278605 GTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCT
1 GTCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC
* * *
278670 TACTGTTCACGAGGCCACT
66 CACCGTTCAAGAGGCCACT
* * *
278689 GTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC
1 GTCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC
*
278754 CACCGTTTAAGAGGCCACT
66 CACCGTTCAAGAGGCCACT
** *
278773 GTCATCGTTGAAGAGGTCC-CTCCCATCATTCAAGAG
1 GTCATCCCTCAAGA-GTCCACTCCCATCATTCAAGAG
278809 CCCGATTCAC
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 104 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.25
Consensus pattern (84 bp):
GTCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC
CACCGTTCAAGAGGCCACT
Found at i:280185 original size:14 final size:14
Alignment explanation
Indices: 280166--280201 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
280156 ATTGTTTAAT
280166 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
280180 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
280194 TGATTTGT
1 TGATTTGT
280202 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:280355 original size:33 final size:33
Alignment explanation
Indices: 280310--280390 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
280300 AAAAAGTACT
*
280310 ATCGCAATGCGAAATGAAAAT-AGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCA-CAACGAGAGA
*
280343 ATCGCAACGCGAAATGAAAATCACAATGAGAGA
1 ATCGCAACGCGAAATGAAAATCACAACGAGAGA
*
280376 ATCGCAACGTGAAAT
1 ATCGCAACGCGAAAT
280391 TAAATTCGCG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 43 0.98
34 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCACAACGAGAGA
Found at i:280441 original size:33 final size:32
Alignment explanation
Indices: 280399--280525 Score: 157
Period size: 33 Copynumber: 3.9 Consensus size: 32
280389 ATTAAATTCG
280399 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* ** **
280432 CGTTGCGATTTTCATTTCACATTGTAAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTG--CGATTCCT
*
280465 AGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
280498 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
280526 AGTAATTTTC
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
31 3 0.04
33 72 0.92
35 3 0.04
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:280491 original size:19 final size:19
Alignment explanation
Indices: 280467--280525 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
280457 AAAATTAGAG
280467 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
280486 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
280500 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
280519 TTGCGAT
1 TTGCGAT
280526 AGTAATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:282832 original size:12 final size:12
Alignment explanation
Indices: 282815--282839 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
282805 TCTTCGGGGA
282815 CTTTTTCTTCTT
1 CTTTTTCTTCTT
282827 CTTTTTCTTCTT
1 CTTTTTCTTCTT
282839 C
1 C
282840 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:283048 original size:24 final size:24
Alignment explanation
Indices: 283014--283067 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
283004 CTAAAACATC
*
283014 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
283038 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
283062 ATCAAA
1 ATCAAA
283068 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:283840 original size:20 final size:20
Alignment explanation
Indices: 283817--283862 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
283807 ATTATCTCGT
283817 TGCGAAAGTAAGT-ATCGCAA
1 TGCGAAA-TAAGTAATCGCAA
283837 TGCG-AATAAGTAAATCGCAA
1 TGCGAAATAAGT-AATCGCAA
283857 TGCGAA
1 TGCGAA
283863 TTTGGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.22
19 2 0.09
20 15 0.65
21 1 0.04
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (20 bp):
TGCGAAATAAGTAATCGCAA
Found at i:283848 original size:18 final size:19
Alignment explanation
Indices: 283825--283863 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
283815 GTTGCGAAAG
283825 TAAGT-ATCGCAATGCGAA
1 TAAGTAATCGCAATGCGAA
283843 TAAGTAAATCGCAATGCGAA
1 TAAGT-AATCGCAATGCGAA
283863 T
1 T
283864 TTGGAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
20 14 0.74
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (19 bp):
TAAGTAATCGCAATGCGAA
Found at i:283863 original size:20 final size:21
Alignment explanation
Indices: 283830--283882 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
283820 GAAAGTAAGT
*
283830 ATCGCAATGCGAA-TAAGTAA
1 ATCGCAATGCGAATTAAGAAA
**
283850 ATCGCAATGCGAATTTGGAAA
1 ATCGCAATGCGAATTAAGAAA
283871 ATCGCAATGCGA
1 ATCGCAATGCGA
283883 TACTGACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
ATCGCAATGCGAATTAAGAAA
Found at i:283896 original size:20 final size:20
Alignment explanation
Indices: 283871--283928 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
283861 AATTTGGAAA
* *
283871 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
*
283891 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
283911 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
283929 AAATTGCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:284238 original size:20 final size:20
Alignment explanation
Indices: 284171--284224 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
284161 GAAAATGGCT
284171 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
284191 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
284211 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
284225 ATGGCTATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.09
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:284293 original size:14 final size:16
Alignment explanation
Indices: 284269--284342 Score: 57
Period size: 19 Copynumber: 4.5 Consensus size: 16
284259 TGAAAATCGC
*
284269 ATTGCGGTTTTC-TCG
1 ATTGCGATTTTCTTCG
284284 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
284301 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
284320 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
284336 -TTGCGAT
1 ATTGCGAT
284343 AGTCAGTTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
14 17 0.32
16 3 0.06
17 3 0.06
19 30 0.57
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:284306 original size:19 final size:19
Alignment explanation
Indices: 284284--284332 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
284274 GGTTTTCTCG
284284 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
284303 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
284322 TTGCGATTTTC
1 TTGCGATTTTC
284333 TCGTTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:284488 original size:14 final size:14
Alignment explanation
Indices: 284469--284505 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
284459 CATCAATTAA
284469 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
284483 ACAAATCATCTTTT
1 ACAAATCAACATTT
284497 ACAAATCAA
1 ACAAATCAA
284506 TTAAACAATC
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:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:285972 original size:21 final size:21
Alignment explanation
Indices: 285948--286012 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
285938 AACGGTGGGG
285948 GGGGACTCTTGAGGGAGGATA
1 GGGGACTCTTGAGGGAGGATA
* **
285969 GGGGCCTCTTGAACGATTGG--A
1 GGGGACTCTTGAGGGA--GGATA
*
285990 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGAGGATA
286011 GG
1 GG
286013 TGAGTCGGGC
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
19 1 0.03
21 30 0.91
23 2 0.06
ACGTcount: A:0.22, C:0.12, G:0.45, T:0.22
Consensus pattern (21 bp):
GGGGACTCTTGAGGGAGGATA
Found at i:285975 original size:42 final size:42
Alignment explanation
Indices: 285929--286012 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
285919 CGATGACAGT
* *
285929 GGCCTCTTGAACGGTGGGGGGGGACTCTTGAGGGAGGATAGG
1 GGCCTCTTGAACGATGGGAGGGGACTCTTGAGGGAGGATAGG
* *
285971 GGCCTCTTGAACGATTGGAGGGGACTCTTGAGGGATGATAGG
1 GGCCTCTTGAACGATGGGAGGGGACTCTTGAGGGAGGATAGG
286013 TGAGTCGGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.19, C:0.14, G:0.45, T:0.21
Consensus pattern (42 bp):
GGCCTCTTGAACGATGGGAGGGGACTCTTGAGGGAGGATAGG
Found at i:286398 original size:20 final size:19
Alignment explanation
Indices: 286375--286442 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
286365 GAAACTTAAA
286375 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
286395 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
286415 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
286434 ATCGCAACG
1 ATCGCAACG
286443 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:286516 original size:20 final size:20
Alignment explanation
Indices: 286464--286507 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
286454 ATGCGATTTT
*
286464 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
286483 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
286503 CATTT
1 CATTT
286508 TCGTGTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:287020 original size:18 final size:18
Alignment explanation
Indices: 286994--287038 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
286984 GTCGATCAGA
*
286994 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
287012 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
287030 TGATGGCTC
1 TGATGGCTC
287039 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:288407 original size:20 final size:20
Alignment explanation
Indices: 288359--288417 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
288349 AATAGTTTCT
** *
288359 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
288379 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
288399 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
288418 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:288939 original size:20 final size:20
Alignment explanation
Indices: 288914--288985 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
288904 ATTATGTATT
288914 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
288934 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
* *
288954 ATTGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
288974 ATCTCGTTGCGA
1 ATCGCGTTGCGA
288986 TTTTGTATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:289022 original size:20 final size:20
Alignment explanation
Indices: 288994--289047 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
288984 GATTTTGTAT
*
288994 TATCACATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
289014 TATCGCATTGCGGTAGTCAG
1 TATCGCATTGCGATAGTAAG
289034 TATCGCATTGCGAT
1 TATCGCATTGCGAT
289048 TTTCCCAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:296329 original size:29 final size:29
Alignment explanation
Indices: 296294--296375 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
296284 AAACTAAATT
* *
296294 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
296323 GCTGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
296352 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
296376 GTTAGGTGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 42 0.89
30 5 0.11
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:297685 original size:15 final size:15
Alignment explanation
Indices: 297662--297691 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
297652 ACGAGGCTGG
297662 AATTACAACAACAAC
1 AATTACAACAACAAC
*
297677 AATTCCAACAACAAC
1 AATTACAACAACAAC
297692 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:301091 original size:29 final size:29
Alignment explanation
Indices: 301056--301130 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
301046 AAACTAAATT
* *
301056 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
301085 GCTGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
301114 GATGTCATTGCTTACAT
1 GATGTCATTGCTTACAT
301131 TAATTTAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Done.