Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009071.1 Hibiscus syriacus cultivar Beakdansim tig00112501_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: 822590
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:163472 original size:23 final size:23
Alignment explanation
Indices: 163406--163490 Score: 89
Period size: 23 Copynumber: 3.5 Consensus size: 23
163396 ATAATTTATT
*
163406 CATAAACGAATACAAATGAACGAA
1 CATAAACGAATAC-AATAAACGAA
* * * *
163430 CATAATAAATGAACATAATAAATGAA
1 C---ATAAACGAATACAATAAACGAA
163456 CATAAACGAATACAATAAACGAA
1 CATAAACGAATACAATAAACGAA
163479 CATAAACGAATA
1 CATAAACGAATA
163491 ACACAAACAC
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
23 30 0.61
24 1 0.02
26 9 0.18
27 9 0.18
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.16
Consensus pattern (23 bp):
CATAAACGAATACAATAAACGAA
Found at i:163473 original size:13 final size:13
Alignment explanation
Indices: 163407--163490 Score: 54
Period size: 13 Copynumber: 6.8 Consensus size: 13
163397 TAATTTATTC
163407 ATAAACGAATACAA
1 ATAAACGAATAC-A
* * *
163421 ATGAACGAACATA
1 ATAAACGAATACA
* * *
163434 ATAAATGAACATA
1 ATAAACGAATACA
*
163447 ATAAATG-A-AC-
1 ATAAACGAATACA
163457 ATAAACGAATACA
1 ATAAACGAATACA
163470 ATAAACG-A-AC-
1 ATAAACGAATACA
163480 ATAAACGAATA
1 ATAAACGAATA
163491 ACACAAACAC
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
10 13 0.22
11 5 0.09
12 5 0.09
13 26 0.45
14 9 0.16
ACGTcount: A:0.61, C:0.13, G:0.10, T:0.17
Consensus pattern (13 bp):
ATAAACGAATACA
Found at i:163498 original size:23 final size:23
Alignment explanation
Indices: 163453--163498 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
163443 CATAATAAAT
*
163453 GAACATAAACGAATACAATAAAC
1 GAACATAAACGAATACAACAAAC
163476 GAACATAAACGAATA-ACACAAAC
1 GAACATAAACGAATACA-ACAAAC
163499 ACAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.61, C:0.20, G:0.09, T:0.11
Consensus pattern (23 bp):
GAACATAAACGAATACAACAAAC
Found at i:169252 original size:21 final size:22
Alignment explanation
Indices: 169206--169254 Score: 50
Period size: 21 Copynumber: 2.3 Consensus size: 22
169196 GTTAGATAGA
169206 AAAAATA-AAAAAAATA-AAAAT
1 AAAAATATAAAAAAA-ATAAAAT
* *
169227 GAAAATATAAAAAAAAT-ATAT
1 AAAAATATAAAAAAAATAAAAT
169248 AAAAATA
1 AAAAATA
169255 ATGGTACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (22 bp):
AAAAATATAAAAAAAATAAAAT
Found at i:169965 original size:21 final size:19
Alignment explanation
Indices: 169939--169979 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
169929 TACAAGTCTC
169939 GACCTTTACCCTTTTTCCGGT
1 GACCTTT-CCC-TTTTCCGGT
*
169960 GACCTTTCGCTTTTCCGGT
1 GACCTTTCCCTTTTCCGGT
169979 G
1 G
169980 GTTTGCTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 2 0.11
21 7 0.37
ACGTcount: A:0.07, C:0.32, G:0.20, T:0.41
Consensus pattern (19 bp):
GACCTTTCCCTTTTCCGGT
Found at i:170686 original size:39 final size:38
Alignment explanation
Indices: 170638--170912 Score: 177
Period size: 37 Copynumber: 7.2 Consensus size: 38
170628 AATAATAATA
*
170638 ATATGATATAT-ATATTTC-AAAATGATTTTTAAACTAT
1 ATATTATATATAAT-TTTCAAAAATGATTTTTAAACTAT
*
170675 ATATTATATATAAGTTTTCAAAAATGTTTTTTAAAACTAT
1 ATATTATATATAA-TTTTCAAAAATGATTTTT-AAACTAT
* * *
170715 ATAATATATA-AATGTTTTCAAAAACG-TTTTCAAA--ACT
1 ATATTATATATAA--TTTTCAAAAATGATTTTTAAACTA-T
170752 ATATTATATATAAGTTTTCAAAAACAT-ATTTTTAAAACTAT
1 ATATTATATATAA-TTTTC-AAAA-ATGATTTTT-AAACTAT
* *
170793 ATAATATATA-AACGTTTTCAAAAAT-ATTTTCAAAACTAT
1 ATATTATATATAA--TTTTCAAAAATGATTTT-TAAACTAT
* * **
170832 ATA--ATATATAGGTTTTCAAAAATGCTTTCAAAAACTAT
1 ATATTATATATA-ATTTTCAAAAATGATTT-TTAAACTAT
*
170870 ATA-T-TATAT-ATTTT-AAAAAT-ATTTTCAAAACTAT
1 ATATTATATATAATTTTCAAAAATGATTTT-TAAACTAT
*
170904 ATAGTATAT
1 ATATTATAT
170913 GTTTTCAAAA
Statistics
Matches: 199, Mismatches: 16, Indels: 47
0.76 0.06 0.18
Matches are distributed among these distances:
34 14 0.07
35 7 0.04
36 8 0.04
37 42 0.21
38 34 0.17
39 40 0.20
40 37 0.19
41 16 0.08
42 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (38 bp):
ATATTATATATAATTTTCAAAAATGATTTTTAAACTAT
Found at i:170799 original size:78 final size:77
Alignment explanation
Indices: 170674--170923 Score: 300
Period size: 78 Copynumber: 3.3 Consensus size: 77
170664 TTTTAAACTA
** *
170674 TATATTATATATAAGTTTTCAAAAATGTTTTTTAAAACTATATAATATATAAATGTTTTCAAAAA
1 TATATTATATATAAGTTTTCAAAAACATTTTTTAAAACTATATAATATATAAACGTTTTCAAAAA
*
170739 CGTTTTCAAAAC
66 CATTTTCAAAAC
170751 TATATTATATATAAGTTTTCAAAAACATATTTTTAAAACTATATAATATATAAACGTTTTCAAAA
1 TATATTATATATAAGTTTTCAAAAACAT-TTTTTAAAACTATATAATATATAAACGTTTTCAAAA
*
170816 ATATTTTCAAAAC
65 ACATTTTCAAAAC
* * *** ** *
170829 TATATAATATATAGGTTTTCAAAAATGCTTTCAAAAACTATAT-AT-TATATA--TTTT-AAAAA
1 TATATTATATATAAGTTTTCAAAAACATTTTTTAAAACTATATAATATATAAACGTTTTCAAAAA
*
170889 TATTTTCAAAAC
66 CATTTTCAAAAC
170901 TATA-TAGTATAT--GTTTTCAAAAA
1 TATATTA-TATATAAGTTTTCAAAAA
170924 TGTTTTCAAA
Statistics
Matches: 157, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
70 11 0.07
71 1 0.01
72 26 0.17
73 4 0.03
75 5 0.03
76 2 0.01
77 39 0.25
78 69 0.44
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (77 bp):
TATATTATATATAAGTTTTCAAAAACATTTTTTAAAACTATATAATATATAAACGTTTTCAAAAA
CATTTTCAAAAC
Found at i:170928 original size:12 final size:12
Alignment explanation
Indices: 170911--170935 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
170901 TATATAGTAT
170911 ATGTTTTCAAAA
1 ATGTTTTCAAAA
170923 ATGTTTTCAAAA
1 ATGTTTTCAAAA
170935 A
1 A
170936 AACTATATAT
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:171073 original size:2 final size:2
Alignment explanation
Indices: 171062--171094 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
171052 ACTATATAAC
*
171062 AT AT AG 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 A
171095 AAATAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:175192 original size:2 final size:2
Alignment explanation
Indices: 175185--175227 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
175175 TATTAAAAAG
* *
175185 TA TA TA TA TA TA TA TA AA TA TA TA TA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
175227 T
1 T
175228 TAAAATCTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:179946 original size:60 final size:60
Alignment explanation
Indices: 179853--179990 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 60
179843 GTACACACGT
** * *
179853 ATAGTTTGGGACAAAATTGTAATGTTCCAAAAGTTTGGGGACCT-ATTTAGAATGA-AGGTC
1 ATAGTTTGGGATGAAATTGAAATGTTCCAAAAGTTTGAGGA-CTAATTTAGAATGATA-GTC
*
179913 ATAGTTTGGGGATGAAATTGAAATGTT-CAAAAGTTTGAGGACTAATTTAGAATTATAGTC
1 ATAGTTT-GGGATGAAATTGAAATGTTCCAAAAGTTTGAGGACTAATTTAGAATGATAGTC
179973 ATAGTTTAGGGATGAAAT
1 ATAGTTT-GGGATGAAAT
179991 GGGAACACTT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
59 2 0.03
60 50 0.72
61 17 0.25
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.33
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGAAATGTTCCAAAAGTTTGAGGACTAATTTAGAATGATAGTC
Found at i:180005 original size:60 final size:60
Alignment explanation
Indices: 179880--180035 Score: 151
Period size: 60 Copynumber: 2.6 Consensus size: 60
179870 TGTAATGTTC
* * * *
179880 CAAAAGTTTGGGGACCTATTTAGAATGAAGGTCATAGTTTGGGGATGAAATTGAAATGTT
1 CAAAAGTTTGAGGACCTATTTAGAATGAAGGTCATAGTTTAGGGATGAAATGGAAATCTT
*
179940 CAAAAGTTTGAGGA-CTAATTTAGAATTATA-GTCATAGTTTAGGGATGAAATGGGAACA-CTT
1 CAAAAGTTTGAGGACCT-ATTTAGAATGA-AGGTCATAGTTTAGGGATGAAAT-GGAA-ATCTT
* * * *
180001 -AAAAGTTT-AGGGACCAATTAAAAATGAGGGTCATA
1 CAAAAGTTTGA-GGACCTATTTAGAATGAAGGTCATA
180036 CTTTGAGGAC
Statistics
Matches: 79, Mismatches: 10, Indels: 14
0.77 0.10 0.14
Matches are distributed among these distances:
59 3 0.04
60 68 0.86
61 7 0.09
62 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (60 bp):
CAAAAGTTTGAGGACCTATTTAGAATGAAGGTCATAGTTTAGGGATGAAATGGAAATCTT
Found at i:186168 original size:2 final size:2
Alignment explanation
Indices: 186161--186203 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
186151 ACTATAACCA
186161 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
186203 A
1 A
186204 AGAAACTAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:201262 original size:11 final size:11
Alignment explanation
Indices: 201246--201302 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
201236 ATTAAATAGA
201246 AATATATAAAT
1 AATATATAAAT
*
201257 AATATAAAAAT
1 AATATATAAAT
*
201268 AATATAAAAAT
1 AATATATAAAT
*
201279 AATA-ATAATT
1 AATATATAAAT
201289 AATAATATTAAAT
1 AAT-ATA-TAAAT
201302 A
1 A
201303 TTAATTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 7 0.18
11 26 0.67
12 1 0.03
13 5 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATATATAAAT
Found at i:201271 original size:14 final size:11
Alignment explanation
Indices: 201246--201296 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
201236 ATTAAATAGA
*
201246 AATATATAAAT
1 AATATAAAAAT
201257 AATATAAAAAT
1 AATATAAAAAT
201268 AATATAAAAAT
1 AATATAAAAAT
*
201279 AATAATAATTAAT
1 AAT-ATAA-AAAT
201292 AATAT
1 AATAT
201297 TAAATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
11 24 0.67
12 6 0.17
13 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:201272 original size:22 final size:24
Alignment explanation
Indices: 201246--201323 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 24
201236 ATTAAATAGA
201246 AATATATAAATAAT-ATAA-AAAT
1 AATATATAAATAATAATAATAAAT
* *
201268 AATATAAAAATAATAATAATTAAT
1 AATATATAAATAATAATAATAAAT
* *
201292 AATAT-TAAATATTAAT-TTAAAT
1 AATATATAAATAATAATAATAAAT
*
201314 ATTA-ATAAAT
1 AATATATAAAT
201324 TCTACATAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
22 25 0.54
23 13 0.28
24 8 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AATATATAAATAATAATAATAAAT
Found at i:201313 original size:12 final size:13
Alignment explanation
Indices: 201291--201320 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
201281 TAATAATTAA
201291 TAATATTAAATAT
1 TAATATTAAATAT
201304 TAAT-TTAAATAT
1 TAATATTAAATAT
201316 TAATA
1 TAATA
201321 AATTCTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATATTAAATAT
Found at i:202830 original size:31 final size:31
Alignment explanation
Indices: 202770--202831 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
202760 CAACGGGGAC
* * * *
202770 CATATTGCAAACGGAGTAAGTGTTGGAGGAT
1 CATATTGCAAACAGACTAAATGTTAGAGGAT
*
202801 CATATTGCAAATAGACTAAATGTTAGAGGAT
1 CATATTGCAAACAGACTAAATGTTAGAGGAT
202832 TGTATTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.27
Consensus pattern (31 bp):
CATATTGCAAACAGACTAAATGTTAGAGGAT
Found at i:204665 original size:31 final size:31
Alignment explanation
Indices: 204627--204688 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
204617 CAGTTACGTC
*
204627 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
204658 GGGGACCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
204689 AGAGACTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:205309 original size:16 final size:16
Alignment explanation
Indices: 205281--205322 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
205271 CATAAAATTA
205281 TAAATGATT-AATATAT
1 TAAAT-ATTAAATATAT
205297 TAAATATTAAATATAT
1 TAAATATTAAATATAT
* *
205313 AAAAAATTAA
1 TAAATATTAA
205323 CTACTCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 3 0.13
16 20 0.87
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAATATTAAATATAT
Found at i:205315 original size:15 final size:16
Alignment explanation
Indices: 205275--205315 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
205265 TCATCTCATA
205275 AAAT-TATAAATGATT
1 AAATATATAAATGATT
205290 -AATATATTAAAT-ATT
1 AAATATA-TAAATGATT
205305 AAATATATAAA
1 AAATATATAAA
205316 AAATTAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.13
15 9 0.39
16 11 0.48
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AAATATATAAATGATT
Found at i:211714 original size:22 final size:22
Alignment explanation
Indices: 211696--211752 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
211686 GTACAAAGCA
*
211696 TGTACGTACATAGTTCAAAGAT
1 TGTACATACATAGTTCAAAGAT
211718 TGTACATACATAGTTCAAAGAT
1 TGTACATACATAGTTCAAAGAT
211740 TGTACATACATAG
1 TGTACATACATAG
211753 AAACTCGACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (22 bp):
TGTACATACATAGTTCAAAGAT
Found at i:212947 original size:36 final size:35
Alignment explanation
Indices: 212907--213127 Score: 192
Period size: 36 Copynumber: 5.9 Consensus size: 35
212897 AAATGTTTTT
* * *
212907 AAAATATATGTACTATATAGTTTCAAAAACATTTCG
1 AAAATATATATAATATATAGTTTAAAAAACATTT-G
* *
212943 AAAATATATATAGTATATAGTTTTTAAAAAAAATTTG
1 AAAATATATATAATATATAG--TTTAAAAAACATTTG
* **
212980 AAAATATATATAATGTATAGTTTTTGAAAATGCATTTG
1 AAAATATATATAATATATAG--TTT-AAAAAACATTTG
** *
213018 AAAATATATATAATATATAGTTTTGAAATCATTTTG
1 AAAATATATATAATATATAGTTTAAAAAACA-TTTG
213054 AAAATATATATAATATATAGTTTTTAAAAAAAAACATTTTTG
1 AAAATATATATAATATATAG--TTT---AAAAAACA--TTTG
*
213096 AAAA-ATTATATAATATATAGTTTTAAAAACAT
1 AAAATA-TATATAATATATAGTTTAAAAAACAT
213128 ATTTTGGAAT
Statistics
Matches: 156, Mismatches: 18, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
35 5 0.03
36 45 0.29
37 31 0.20
38 43 0.28
40 3 0.02
41 6 0.04
42 23 0.15
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (35 bp):
AAAATATATATAATATATAGTTTAAAAAACATTTG
Found at i:212973 original size:38 final size:36
Alignment explanation
Indices: 212907--213225 Score: 226
Period size: 38 Copynumber: 8.6 Consensus size: 36
212897 AAATGTTTTT
* * *
212907 AAAATATATGTACTATATAG-TTTCAAAAACATTTCG
1 AAAATATATATAATATATAGTTTTAAAAAACATTT-G
* *
212943 AAAATATATATAGTATATAGTTTTTAAAAAAAATTTG
1 AAAATATATATAATATATAG-TTTTAAAAAACATTTG
* **
212980 AAAATATATATAATGTATAGTTTTTGAAAATGCATTTG
1 AAAATATATATAATATATAG-TTTT-AAAAAACATTTG
* *
213018 AAAATATATATAATATATAGTTTT-GAAATCATTTTG
1 AAAATATATATAATATATAGTTTTAAAAAACA-TTTG
213054 AAAATATATATAATATATAGTTTTTAAAAAAAAACATTTTTG
1 AAAATATATATAATATATAG-TTTT---AAAAAACA--TTTG
*
213096 AAAA-ATTATATAATATATAGTTTTAAAAACATATTTTG
1 AAAATA-TATATAATATATAGTTTTAAAAA-ACA-TTTG
* * ** **
213134 -GAATCT-TAT-ATA-ATA-TTCTTAAATCATTTTTG
1 AAAATATATATAATATATAGTT-TTAAAAAACATTTG
* *
213166 AAAA-CTATATAATATATAGTTTTAAAAAAATATTTTTG
1 AAAATATATATAATATATAGTTTT-AAAAAACA--TTTG
*
213204 -AAATATATATATTATATAGTTT
1 AAAATATATATAATATATAGTTT
213226 ATATTATATT
Statistics
Matches: 233, Mismatches: 27, Indels: 44
0.77 0.09 0.14
Matches are distributed among these distances:
32 6 0.03
33 9 0.04
34 11 0.05
35 12 0.05
36 52 0.22
37 38 0.16
38 70 0.30
39 2 0.01
41 10 0.04
42 23 0.10
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (36 bp):
AAAATATATATAATATATAGTTTTAAAAAACATTTG
Found at i:213038 original size:111 final size:110
Alignment explanation
Indices: 212885--213086 Score: 305
Period size: 111 Copynumber: 1.8 Consensus size: 110
212875 AGCAATATAA
* * * *
212885 TATAATTTTTGAAAATGTTTTTAAAATATATGTACTATATAGTTTCAAAAACATTTCGAAAATAT
1 TATAATTTTTGAAAATGATTTGAAAATATATATAATATATAGTTTCAAAAACATTTCGAAAATAT
*
212950 ATATAGTATATAGTTTTTAAAAAAAATTTGAAAATATATATAATG
66 ATATAATATATAGTTTTTAAAAAAAATTTGAAAATATATATAATG
* ** * *
212995 TATAGTTTTTGAAAATGCATTTGAAAATATATATAATATATAGTTTTGAAATCATTTTGAAAATA
1 TATAATTTTTGAAAATG-ATTTGAAAATATATATAATATATAGTTTCAAAAACATTTCGAAAATA
213060 TATATAATATATAGTTTTTAAAAAAAA
65 TATATAATATATAGTTTTTAAAAAAAA
213087 ACATTTTTGA
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
110 16 0.20
111 65 0.80
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (110 bp):
TATAATTTTTGAAAATGATTTGAAAATATATATAATATATAGTTTCAAAAACATTTCGAAAATAT
ATATAATATATAGTTTTTAAAAAAAATTTGAAAATATATATAATG
Found at i:213145 original size:111 final size:110
Alignment explanation
Indices: 212908--213225 Score: 316
Period size: 111 Copynumber: 2.9 Consensus size: 110
212898 AATGTTTTTA
* * * * * *
212908 AAATATATGTACTATATAGTTTCAAAAACATTTCGAAAATATATATAGTATATAGTTTTTAAAAA
1 AAATATATATAATATATAGTTT-TAAATCATTTTGAAAATATATATAATATATAGTTTTTAAAAA
* **
212973 AAA--TTTG-AAAATATATATAATGTATAGTTTTTGAAAATGCATTTG
65 AAATTTTTGAAAAAT-TATATAATATATAGTTTTAAAAAAT-CATTTG
213018 AAAATATATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGTTTTTAAAA
1 -AAATATATATAATATATAGTTTT-AAATCATTTTGAAAATATATATAATATATAGTTTTT--AA
213083 AAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACAT-ATTTTG
62 AAAAA-ATTTTTGAAAAATTATATAATATATAGTTTTAAAAA-ATCA-TTTG
* * *
213134 GAATCT-TAT-ATA-ATA-TTCTTAAATCATTTTTGAAAA-CTATATAATATATAG-TTTTAAAA
1 AAATATATATAATATATAGTT-TTAAATCA-TTTTGAAAATATATATAATATATAGTTTTTAAAA
* *
213193 AAATATTTTTGAAATA-TATATATTATATAGTTT
64 AAA-ATTTTTGAAAAATTATATAATATATAGTTT
213226 ATATTATATT
Statistics
Matches: 181, Mismatches: 15, Indels: 26
0.82 0.07 0.12
Matches are distributed among these distances:
107 16 0.09
108 18 0.10
110 4 0.02
111 75 0.41
112 14 0.08
113 10 0.06
114 4 0.02
115 5 0.03
116 28 0.15
117 7 0.04
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (110 bp):
AAATATATATAATATATAGTTTTAAATCATTTTGAAAATATATATAATATATAGTTTTTAAAAAA
AATTTTTGAAAAATTATATAATATATAGTTTTAAAAAATCATTTG
Found at i:213279 original size:10 final size:10
Alignment explanation
Indices: 213264--213305 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
213254 TTATTATTAT
*
213264 TTTCATTTCA
1 TTTCATTTAA
*
213274 TTTCATTTTA
1 TTTCATTTAA
213284 -TTCATTTAA
1 TTTCATTTAA
*
213293 TTTAATTTAA
1 TTTCATTTAA
213303 TTT
1 TTT
213306 AATTGTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTCATTTAA
Found at i:216389 original size:19 final size:19
Alignment explanation
Indices: 216355--216399 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
216345 ATTTAGACAT
216355 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
216373 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
216392 TTTGCATT
1 TTTGCATT
216400 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:220031 original size:165 final size:165
Alignment explanation
Indices: 219759--220464 Score: 844
Period size: 165 Copynumber: 4.2 Consensus size: 165
219749 TCTTAAACAA
* *
219759 ATCATTTGCGGCATAACTTAAGTCGAGAAGGGTTATCCGCCAACCAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACT
* * * *
219824 ACGCTCAGCTCAAGGCACATCATTTACAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAATA
66 ACGCTCAGCTCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAAGA
219889 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
131 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* *
219924 ATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCCAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACT
* *
219989 ACGCTCAGCTCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG-CAAAAGA
66 ACGCTCAGCTCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAAGA
220053 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
131 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * * * * * *
220088 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTTGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACT
* * * * *
220152 ACACTCAGCTTCGAGGGCACATCATTTGTAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACC
66 ACGCTCAGC-TC-AAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC-A--
** * * * * *
220217 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCAT
126 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * * * *
220256 GTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAAAACCTTTGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC-CAAAGACCTTTGAGTTCGAC
* *
220321 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAAACC
65 TACGCTCAGCT-CAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGC---CA
*** * * * * *
220386 AAAGACCTTTGAGTTCGACTACGCTCATC-TCCAAGGCAC
126 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * *
220425 ATTATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTGC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC
220465 TAAAGACCTT
Statistics
Matches: 471, Mismatches: 58, Indels: 20
0.86 0.11 0.04
Matches are distributed among these distances:
163 27 0.06
164 78 0.17
165 157 0.33
166 1 0.00
167 1 0.00
168 41 0.09
169 140 0.30
170 25 0.05
172 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (165 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACT
ACGCTCAGCTCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAAGA
CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
Found at i:220159 original size:84 final size:83
Alignment explanation
Indices: 219759--220483 Score: 806
Period size: 84 Copynumber: 8.7 Consensus size: 83
219749 TCTTAAACAA
* * *
219759 ATCATTTGCGGCATAACTTAAGTCGAGAAGGGTTATCCGCCAACCAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACT
219824 ACGCTCAGCT-CAAGGCAC
65 ACGCTCAGCTCCAAGGCAC
* * * * * * ** *
219842 ATCATTTACAGTATAGCTTAAGTCGAGAAGGGCTATCTGC--CAAAATACCCCCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTA
* * *
219905 CACTCAGCTTCGAGGGCAC
66 CGCTCAGC-TCCAAGGCAC
* * *
219924 ATCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCCAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACT
219989 ACGCTCAGCT-CAAGGCAC
65 ACGCTCAGCTCCAAGGCAC
* * * ** *
220007 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGC-A--AAAGACCCCCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTA
* * *
220069 CACTCAGCTTCGAGGGCAC
66 CGCTCAGC-TCCAAGGCAC
* * * * * *
220088 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTTGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACT
* * *
220152 ACACTCAGCTTCGAGGGCAC
65 ACGCTCAGC-TCCAAGGCAC
* *
220172 ATCATTTGTAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACT
*
220237 ACGCTCAGCTCCAAGGCAT
65 ACGCTCAGCTCCAAGGCAC
* * * * * * *
220256 GTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAAAACCTTTGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAAC-CAAAGACCTTCGAGTTCGAC
220321 TACGCTCAGCTCCAAGGCAC
64 TACGCTCAGCTCCAAGGCAC
*
220341 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAAACCAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC-AACCAAAGACCTTCGAGTTCGACT
*
220406 ACGCTCATCTCCAAGGCAC
65 ACGCTCAGCTCCAAGGCAC
* * * * *
220425 ATTATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTG---CTAAAGACCTTCGAGTTCGA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGA
220484 TTATATTCAA
Statistics
Matches: 543, Mismatches: 86, Indels: 29
0.83 0.13 0.04
Matches are distributed among these distances:
79 23 0.04
80 43 0.08
81 40 0.07
82 44 0.08
83 75 0.14
84 192 0.35
85 126 0.23
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (83 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCAC
Found at i:220203 original size:248 final size:248
Alignment explanation
Indices: 219759--220483 Score: 883
Period size: 248 Copynumber: 2.9 Consensus size: 248
219749 TCTTAAACAA
* *
219759 ATCATTTGCGGCATAACTTAAGTCGAGAAGGGTTATCCGCCAACCAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA--AAAGACCTTTGAGTTCGACT
* * * * *
219824 ACGCTCAGCTCAAGGCACATCATTTACAGTATAGCTTAAGTCGAGAAGGGCTATCTGC-CAAAAT
64 ACGCTCAGCTCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAG
** *
219888 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAATCGAGAA
129 ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
* *
219953 GGGTTATCTGCCAACCCAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCAC
194 GGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * * *** *
220007 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG-C-AAAAGACCCCCGAGTTCGATTAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAAAGACCTTTGAGTTCGACTAC
* * * * *
220070 ACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAA
66 GCTCAGC-TC-AAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG-CACCAAA
* * *
220135 GACCTTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTGTAGCATAACTTAAGTCAAGA
128 GACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGA
*
220200 AGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAT
193 AGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * * * *
220256 GTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAAAACCTTTGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C--CAAAAAGACCTTTGAGTTCGAC
*
220321 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAAACC
63 TACGCTCAGCT-CAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGC--ACC
* * * * * * * * *
220386 AAAGACCTTTGAGTTCGACTACGCTCATC-TCCAAGGCACATTATTTGCAACATAGCTTAAGTCG
125 AAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCG
* *
220450 AGAAGGGCTATCTG----CTAAAGACCTTCGAGTTCGA
190 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
220484 TTATATTCAA
Statistics
Matches: 404, Mismatches: 60, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
244 24 0.06
245 2 0.00
246 40 0.10
247 2 0.00
248 141 0.35
249 58 0.14
252 1 0.00
253 84 0.21
254 52 0.13
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (248 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAAAGACCTTTGAGTTCGACTAC
GCTCAGCTCAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCAAAGAC
CTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
Found at i:221167 original size:38 final size:37
Alignment explanation
Indices: 221101--221281 Score: 179
Period size: 38 Copynumber: 4.8 Consensus size: 37
221091 AAATGTTTTT
* * *
221101 AAAATATATGTACTATATAG--TTTCAAAAACATTTCG
1 AAAATATATATAATATATAGTTTTTTAAAAACATTT-G
* *
221137 AAAATATATATAGTATATAGTTTTTTAAAAAAATTTG
1 AAAATATATATAATATATAGTTTTTTAAAAACATTTG
* * * *
221174 AAAACATATATAATGTATAGTTTTTGAAAATGCATTTG
1 AAAATATATATAATATATAGTTTTTTAAAA-ACATTTG
* * *
221212 AAAATATATATAATAATATA-TAGTTTTGAAATCATTTTG
1 AAAATATATATAAT-ATATAGT-TTTTTAAAAACA-TTTG
*
221251 AAAATATATATAATATATAGTTTTTAAAAAA
1 AAAATATATATAATATATAGTTTTTTAAAAA
221282 AAAACATTTT
Statistics
Matches: 118, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
36 18 0.15
37 27 0.23
38 44 0.37
39 29 0.25
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (37 bp):
AAAATATATATAATATATAGTTTTTTAAAAACATTTG
Found at i:221260 original size:41 final size:40
Alignment explanation
Indices: 221073--221280 Score: 146
Period size: 37 Copynumber: 5.6 Consensus size: 40
221063 TTTTATAGCA
**
221073 ATATAATATA-A-TTTTTGAAAATG--TTTTTAAA-ATAT
1 ATATAATATATAGTTTTTGAAAATGCATTTGAAAATATAT
* * * *
221108 ATGTACTATATAG--TTTCAAAA-ACATTTCG-AAA-ATAT
1 ATATAATATATAGTTTTTGAAAATGCATTT-GAAAATATAT
* * ** *
221144 ATATAGTATATAGTTTTTTAAAA-AAATTTG-AAA-ACAT
1 ATATAATATATAGTTTTTGAAAATGCATTTGAAAATATAT
*
221181 ATATAATGTATAGTTTTTGAAAATGCATTTGAAAATATAT
1 ATATAATATATAGTTTTTGAAAATGCATTTGAAAATATAT
221221 ATAATAATATATAG-TTTTG-AAAT-CATTTTG-AAA-ATAT
1 AT-ATAATATATAGTTTTTGAAAATGCA-TTTGAAAATATAT
*
221258 ATATAATATATAGTTTTTAAAAA
1 ATATAATATATAGTTTTTGAAAA
221281 AAAAACATTT
Statistics
Matches: 141, Mismatches: 18, Indels: 25
0.77 0.10 0.14
Matches are distributed among these distances:
35 15 0.11
36 33 0.23
37 37 0.26
38 25 0.18
39 11 0.08
40 10 0.07
41 10 0.07
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (40 bp):
ATATAATATATAGTTTTTGAAAATGCATTTGAAAATATAT
Found at i:221322 original size:38 final size:38
Alignment explanation
Indices: 221101--221456 Score: 163
Period size: 37 Copynumber: 9.6 Consensus size: 38
221091 AAATGTTTTT
* * * *
221101 AAAATATATGTACTATATAGTTTCAAAAACA-TTTCG-
1 AAAATATATATAATATATAGTTTTAAAAACATTTTTGA
* *
221137 AAAATATATATAGTATATAGTTTTTTAAAAA-A-ATTTG-
1 AAAATATATATAATATATAG--TTTTAAAAACATTTTTGA
* * *
221174 AAAACATATATAATGTATAGTTTTTGAAAATGCA--TTTGA
1 AAAATATATATAATATATAG-TTTT-AAAA-ACATTTTTGA
* *
221213 AAATATATATAATAATATATAGTTTTGAAATCA-TTTTG-
1 AAA-ATATAT-ATAATATATAGTTTTAAAAACATTTTTGA
221251 AAAATATATATAATATATAGTTTTTAAAAAAAAAACATTTTTGA
1 AAAATATATATAATATATAG-TTTT-----AAAAACATTTTTGA
*
221295 AAAAT-TATATAATATTTAGTTTTAAAAACATATTTTG-
1 AAAATATATATAATATATAGTTTTAAAAACAT-TTTTGA
* * *
221332 -GAATCT-TAT-ATA-ATA-TTCTT-AAATCATTTTTG-
1 AAAATATATATAATATATAGTT-TTAAAAACATTTTTGA
* **
221364 AAAA-CTATATAATATATAGTTTT-GGAA-ATTTTT--
1 AAAATATATATAATATATAGTTTTAAAAACATTTTTGA
* * *
221397 -TAAGA-ATATAATATATAGTTTTAAAAAAAATATTTTTG-
1 AAAATATATATAATATATAGTTTT---AAAAACATTTTTGA
*
221435 -AAATATATATATTATATAGTTT
1 AAAATATATATAATATATAGTTT
221457 ATATTATATT
Statistics
Matches: 257, Mismatches: 30, Indels: 63
0.73 0.09 0.18
Matches are distributed among these distances:
32 26 0.10
33 13 0.05
34 13 0.05
35 9 0.04
36 44 0.17
37 50 0.19
38 25 0.10
39 26 0.10
40 9 0.04
41 10 0.04
42 9 0.04
43 18 0.07
44 5 0.02
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.43
Consensus pattern (38 bp):
AAAATATATATAATATATAGTTTTAAAAACATTTTTGA
Found at i:221471 original size:3 final size:3
Alignment explanation
Indices: 221458--221498 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
221448 ATATAGTTTA
* *
221458 TAT TA- TAT TAT TAT TAG TA- TGT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
221499 TTCATTTCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
2 3 0.09
3 30 0.91
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:226222 original size:20 final size:20
Alignment explanation
Indices: 226183--226223 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
226173 GATCAAGCAG
* *
226183 CTTGTCATATAGCCTAAAAT
1 CTTGTCATAAACCCTAAAAT
*
226203 CTTGTCATAAACCCTCAAAT
1 CTTGTCATAAACCCTAAAAT
226223 C
1 C
226224 CAGCAATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (20 bp):
CTTGTCATAAACCCTAAAAT
Found at i:228795 original size:30 final size:31
Alignment explanation
Indices: 228737--228797 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
228727 AATTACCATT
** * *
228737 AACCGAACTTTTTTTCTTTAACTGTTAACCG
1 AACCGAACTTTTTTTCTGAAAATATTAACCG
228768 AACCGAACTTTTTTT-TGAAAATATTAACCG
1 AACCGAACTTTTTTTCTGAAAATATTAACCG
228798 GATCGAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (31 bp):
AACCGAACTTTTTTTCTGAAAATATTAACCG
Found at i:229288 original size:31 final size:31
Alignment explanation
Indices: 229248--229318 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
229238 CTCCGTTATG
*
229248 CTTTTAGGTGTCTAA-CATTGTT-TCGATTACA
1 CTTTTAGGTG-CCAACCATT-TTGTCGATTACA
* *
229279 CTTTAAGGTGCCAACCATTTTGTCTATTACA
1 CTTTTAGGTGCCAACCATTTTGTCGATTACA
229310 CTTTTAGGT
1 CTTTTAGGT
229319 AACTACGCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 5 0.15
31 29 0.85
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (31 bp):
CTTTTAGGTGCCAACCATTTTGTCGATTACA
Found at i:230585 original size:30 final size:30
Alignment explanation
Indices: 230549--230609 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
230539 GAGCGGAGCT
* * *
230549 ATAAAATTTATTTTTGGGTGTCAAATTTAG
1 ATAAAATTTATTTTAGGATGTCAAAATTAG
230579 ATAAAATTTATTTTAGGATGTCAAAATTAG
1 ATAAAATTTATTTTAGGATGTCAAAATTAG
230609 A
1 A
230610 AATTGTATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.43
Consensus pattern (30 bp):
ATAAAATTTATTTTAGGATGTCAAAATTAG
Found at i:246484 original size:16 final size:18
Alignment explanation
Indices: 246442--246485 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
246432 TCACGGAATG
246442 TAAGATTATCAGTGAGAA
1 TAAGATTATCAGTGAGAA
246460 TAAAAGATTATCAG-GA-AA
1 T--AAGATTATCAGTGAGAA
246478 TAAGATTA
1 TAAGATTA
246486 CTGGGAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 7 0.29
18 4 0.17
19 2 0.08
20 11 0.46
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (18 bp):
TAAGATTATCAGTGAGAA
Found at i:246701 original size:36 final size:36
Alignment explanation
Indices: 246630--246702 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
246620 GTTGGAAGAT
* *
246630 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
246666 ATTTATATAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTGAAAATCATAAA
246702 A
1 A
246703 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:250573 original size:5 final size:5
Alignment explanation
Indices: 250558--250593 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
250548 AATTTAAAAT
* *
250558 ACAAA AAAAA ATAAA ACAAA ACAAA ACAAA ACAAA A
1 ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA A
250594 ACCCAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.03
Consensus pattern (5 bp):
ACAAA
Found at i:250578 original size:15 final size:15
Alignment explanation
Indices: 250558--250634 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
250548 AATTTAAAAT
250558 ACAAAAAAAAATAAA
1 ACAAAAAAAAATAAA
* *
250573 ACAAAACAAAACAAA
1 ACAAAAAAAAATAAA
*
250588 ACAAAAACCCAAA-AAA
1 ACAAAAA--AAAATAAA
** *
250604 ATTAAAAAAATTAAA
1 ACAAAAAAAAATAAA
* *
250619 ATAAAATAAAATAAA
1 ACAAAAAAAAATAAA
250634 A
1 A
250635 ATAATATATA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
14 2 0.04
15 35 0.73
16 8 0.17
17 3 0.06
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (15 bp):
ACAAAAAAAAATAAA
Found at i:250637 original size:16 final size:15
Alignment explanation
Indices: 250600--250638 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
250590 AAAAACCCAA
*
250600 AAAAATTAAAAAAAT
1 AAAAATAAAAAAAAT
*
250615 TAAAATAAAATAAAAT
1 AAAAATAAAA-AAAAT
250631 AAAAATAA
1 AAAAATAA
250639 TATATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATAAAAAAAAT
Found at i:251740 original size:20 final size:20
Alignment explanation
Indices: 251715--251758 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
251705 AAATAAATTA
251715 ATATGTATAAATAA-TATAAT
1 ATATGT-TAAATAATTATAAT
* *
251735 ATATGTTATATAATTATAGT
1 ATATGTTAAATAATTATAAT
251755 ATAT
1 ATAT
251759 AACATAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATATGTTAAATAATTATAAT
Found at i:253286 original size:22 final size:22
Alignment explanation
Indices: 253258--253331 Score: 148
Period size: 22 Copynumber: 3.4 Consensus size: 22
253248 TTCAGTATTT
253258 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
253280 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
253302 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
253324 GTCCCGAA
1 GTCCCGAA
253332 TGACTAATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.27, C:0.32, G:0.27, T:0.14
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:254922 original size:21 final size:21
Alignment explanation
Indices: 254896--254940 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
254886 GATTTCTGGG
* *
254896 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
254917 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
254938 CAA
1 CAA
254941 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:255605 original size:31 final size:31
Alignment explanation
Indices: 255567--255720 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
255557 GGGTCGAGGG
255567 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
255598 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
255629 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
255660 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
255691 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
255721 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:258710 original size:21 final size:21
Alignment explanation
Indices: 258684--258728 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
258674 GATTTCTGGG
* *
258684 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
258705 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
258726 CAA
1 CAA
258729 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:259393 original size:31 final size:31
Alignment explanation
Indices: 259355--259508 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
259345 GGGTCGAGGG
259355 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
259386 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
259417 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
259448 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
259479 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
259509 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:261205 original size:36 final size:35
Alignment explanation
Indices: 261157--261287 Score: 181
Period size: 35 Copynumber: 3.7 Consensus size: 35
261147 AAATGATGAA
*
261157 CACTTGAATCGAAAGTGTCGATGATTCCTTCCGTT
1 CACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
* * *
261192 CGACTTGAATCGAAAGTGCCGATGCTTTCTTCCATT
1 C-ACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
* * *
261228 CACTTAAATCGAAAGTGTCGATGCTTCATTTCGTT
1 CACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
*
261263 CACTTGAATCGAAGGTGTCGATGCT
1 CACTTGAATCGAAAGTGTCGATGCT
261288 CTTTTCGTTC
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
35 52 0.63
36 31 0.37
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (35 bp):
CACTTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
Found at i:267485 original size:14 final size:14
Alignment explanation
Indices: 267451--267504 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
267441 TTGTGCAATA
* *
267451 CAAATGCAAAGATG
1 CAAATGTAAATATG
267465 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
267480 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
267494 TAAATGTAAAT
1 CAAATGTAAAT
267505 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:269091 original size:18 final size:18
Alignment explanation
Indices: 269068--269117 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 18
269058 TTAATTCTTG
269068 AATATAATAAAAAAAAAT
1 AATATAATAAAAAAAAAT
269086 AATAT-AT-AAAAAAAAT
1 AATATAATAAAAAAAAAT
269102 AATAAGTAATAAAAAA
1 AAT-A-TAATAAAAAA
269118 TTTGAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 12 0.43
17 3 0.11
18 6 0.21
19 2 0.07
20 5 0.18
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (18 bp):
AATATAATAAAAAAAAAT
Found at i:269100 original size:19 final size:20
Alignment explanation
Indices: 269069--269117 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
269059 TAATTCTTGA
269069 ATATAATAAAAAAAAATAA-T
1 ATATAA-AAAAAAAAATAAGT
*
269089 ATATAAAAAAAATAATAAGT
1 ATATAAAAAAAAAAATAAGT
269109 A-ATAAAAAA
1 ATATAAAAAA
269118 TTTGAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (20 bp):
ATATAAAAAAAAAAATAAGT
Found at i:269560 original size:6 final size:7
Alignment explanation
Indices: 269540--269569 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
269530 TGTCTCTATT
269540 ATTAAAA
1 ATTAAAA
269547 ATTAAAA
1 ATTAAAA
269554 ATTAAAA
1 ATTAAAA
269561 ATTAAAA
1 ATTAAAA
269568 AT
1 AT
269570 ATATTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATTAAAA
Found at i:269950 original size:16 final size:15
Alignment explanation
Indices: 269916--269996 Score: 63
Period size: 15 Copynumber: 4.9 Consensus size: 15
269906 AATATTAGTG
269916 AATAAAAATATAAAT
1 AATAAAAATATAAAT
*
269931 AATAAAAATATGAAT
1 AATAAAAATATAAAT
*
269946 AAATAAATAAATAAAATACT
1 -AAT-AA-AAATATAA-A-T
*
269966 AATTTAAACATATAAAT
1 AA--TAAAAATATAAAT
*
269983 GATAAAAATATAAA
1 AATAAAAATATAAA
269997 AAATGACCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
15 25 0.48
16 3 0.06
17 4 0.08
18 7 0.13
19 9 0.17
20 3 0.06
21 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (15 bp):
AATAAAAATATAAAT
Found at i:272063 original size:29 final size:29
Alignment explanation
Indices: 271972--272065 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
271962 GAACATAATG
* *
271972 AATAGTCAAGTGATCATTTTGTAACTTTT
1 AATAGTCAGGAGATCATTTTGTAACTTTT
** * *
272001 AATAGTC-GTGAGA-C-TTAAAAGCAAATTTCT
1 AATAGTCAG-GAGATCATT--TTGTAACTTT-T
272031 -ATAGTCAGGAGATCATTTTGTAACTTTT
1 AATAGTCAGGAGATCATTTTGTAACTTTT
272059 AATAGTC
1 AATAGTC
272066 GAGTTACTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 16
0.64 0.14 0.22
Matches are distributed among these distances:
27 2 0.04
28 2 0.04
29 38 0.81
30 3 0.06
31 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (29 bp):
AATAGTCAGGAGATCATTTTGTAACTTTT
Found at i:277762 original size:14 final size:15
Alignment explanation
Indices: 277745--277773 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
277735 TCATCAATAT
277745 TTTATCC-TCAAAAA
1 TTTATCCTTCAAAAA
277759 TTTATCCTTCAAAAA
1 TTTATCCTTCAAAAA
277774 AATTATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTATCCTTCAAAAA
Found at i:278066 original size:18 final size:17
Alignment explanation
Indices: 278024--278066 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
278014 TTTTAAATAA
278024 AATTTAAAAAATAAAAT
1 AATTTAAAAAATAAAAT
* *
278041 AATATTAAAAAACTTAACT
1 AAT-TTAAAAAA-TAAAAT
278060 AATTTAA
1 AATTTAA
278067 TTTTTCCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 12 0.55
19 7 0.32
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTTAAAAAATAAAAT
Found at i:284862 original size:177 final size:174
Alignment explanation
Indices: 284554--284890 Score: 588
Period size: 177 Copynumber: 1.9 Consensus size: 174
284544 ATAAAAATTA
284554 AATATTTTTAATTAAAAAAATAATTTCTAATTAATTTAAATAATATATAATTATAAAATAAAAAA
1 AATATTTTTAATTAAAAAAATAATTTCTAATTAATTTAAATAATATATAATTATAAAATAAAAAA
284619 TTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATTATT
66 TTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATTATT
284684 AATT-AGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATAT
131 AATTGA-GTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATAT
*
284728 AATATTTTTTAATTCAAAAAAATAGTTTAC-AATTAATTTAAATAATATATAATTATAAAATAAA
1 AATA-TTTTTAATT-AAAAAAATAATTT-CTAATTAATTTAAATAATATATAATTATAAAATAAA
* *
284792 AAATTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAATTTATTTGATCTTAAAT
63 AAA-TTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAAT
284857 TATTAATTGAGTTTTAAATGGTTTGGGCTGAGCC
127 TATTAATTGAGTTTTAAATGGTTTGGGCTGAGCC
284891 TTATATATAA
Statistics
Matches: 155, Mismatches: 3, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
174 4 0.03
175 9 0.06
176 49 0.32
177 92 0.59
178 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (174 bp):
AATATTTTTAATTAAAAAAATAATTTCTAATTAATTTAAATAATATATAATTATAAAATAAAAAA
TTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATTATT
AATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATAT
Found at i:286734 original size:16 final size:16
Alignment explanation
Indices: 286713--286743 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
286703 CTGTTTAATG
286713 AGTTTTAATAATAAAC
1 AGTTTTAATAATAAAC
286729 AGTTTTAATAATAAA
1 AGTTTTAATAATAAA
286744 AAAAATATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (16 bp):
AGTTTTAATAATAAAC
Found at i:290197 original size:60 final size:60
Alignment explanation
Indices: 290104--290227 Score: 248
Period size: 60 Copynumber: 2.1 Consensus size: 60
290094 GTTTCACTAT
290104 TCCACTGACATCACGGAGTATATTAACCACTCTTTTCTTCGAGGGGAAAAGCGTGATTAA
1 TCCACTGACATCACGGAGTATATTAACCACTCTTTTCTTCGAGGGGAAAAGCGTGATTAA
290164 TCCACTGACATCACGGAGTATATTAACCACTCTTTTCTTCGAGGGGAAAAGCGTGATTAA
1 TCCACTGACATCACGGAGTATATTAACCACTCTTTTCTTCGAGGGGAAAAGCGTGATTAA
290224 TCCA
1 TCCA
290228 ACAACTCCCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (60 bp):
TCCACTGACATCACGGAGTATATTAACCACTCTTTTCTTCGAGGGGAAAAGCGTGATTAA
Found at i:292813 original size:27 final size:27
Alignment explanation
Indices: 292759--292821 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
292749 ATTAAAAAAA
**
292759 TAATTTTTTAATAATTATAATTTAATT
1 TAATTTTTTAATAACGATAATTTAATT
* *
292786 TAATTTTTTAATAACGATTTATTTATTT
1 TAATTTTTTAATAACGA-TAATTTAATT
*
292814 TGATTTTT
1 TAATTTTT
292822 AAAAAATAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (27 bp):
TAATTTTTTAATAACGATAATTTAATT
Found at i:296874 original size:2 final size:2
Alignment explanation
Indices: 296867--296904 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
296857 ATTCACATTT
296867 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
296905 AGAAATGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:301840 original size:16 final size:16
Alignment explanation
Indices: 301819--301852 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
301809 TTACTATTCA
*
301819 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
301835 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
301851 CG
1 CG
301853 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:302620 original size:15 final size:16
Alignment explanation
Indices: 302602--302634 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
302592 GTGGCAGATC
302602 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
302617 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
302633 AA
1 AA
302635 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:308574 original size:31 final size:30
Alignment explanation
Indices: 308471--308575 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 30
308461 AGTTGAATTC
* *
308471 AGGGTTAAATTGATATTTTATCCAAAGTATA
1 AGGGTTAAATTAATATTTTATCTAAAGT-TA
* * * *
308502 TGGGTT-AATAAGATATTTCATCT-AAGTTT
1 AGGGTTAAATTA-ATATTTTATCTAAAGTTA
**
308531 AGAGGTCCAATTAATATTTTATCTAAAGTTA
1 AG-GGTTAAATTAATATTTTATCTAAAGTTA
308562 AGGGATTAAATTAA
1 AGGG-TTAAATTAA
308576 AATTAACCTC
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
29 2 0.04
30 22 0.39
31 32 0.57
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (30 bp):
AGGGTTAAATTAATATTTTATCTAAAGTTA
Found at i:316185 original size:29 final size:30
Alignment explanation
Indices: 316143--316234 Score: 82
Period size: 31 Copynumber: 3.1 Consensus size: 30
316133 ACTATTTTGT
* *
316143 TGAGTCTCTCGACTAATAAAAGTTATAAAA
1 TGAGTCACTTGACTAATAAAAGTTATAAAA
***
316173 TGA-TCA-TCTGACT-ATAGAAAGTTATTATGT
1 TGAGTCACT-TGACTAATA-AAAGTTA-TAAAA
*
316203 TGAGTCACTTGACTATTAAAAGTTATAAAA
1 TGAGTCACTTGACTAATAAAAGTTATAAAA
316233 TG
1 TG
316235 GTCGCCTGAC
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
28 4 0.09
29 13 0.28
30 12 0.26
31 15 0.32
32 3 0.06
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (30 bp):
TGAGTCACTTGACTAATAAAAGTTATAAAA
Found at i:316244 original size:60 final size:60
Alignment explanation
Indices: 316135--316247 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
316125 TATAATAGAC
* * *
316135 TATTTTGTTGAGTCTCTCGACTAATAAAAGTTATAAAATGATCATCTGACTATAGAAAGT
1 TATTATGTTGAGTCACTCGACTAATAAAAGTTATAAAATGATCACCTGACTATAGAAAGT
* * * *
316195 TATTATGTTGAGTCACTTGACTATTAAAAGTTATAAAATGGTCGCCTGACTAT
1 TATTATGTTGAGTCACTCGACTAATAAAAGTTATAAAATGATCACCTGACTAT
316248 TTATTATATT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (60 bp):
TATTATGTTGAGTCACTCGACTAATAAAAGTTATAAAATGATCACCTGACTATAGAAAGT
Found at i:317695 original size:17 final size:18
Alignment explanation
Indices: 317673--317712 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
317663 TAACTTATTT
317673 AATATT-TTTAAAAATAA
1 AATATTATTTAAAAATAA
**
317690 AATATTATTTAAATTTAA
1 AATATTATTTAAAAATAA
317708 AATAT
1 AATAT
317713 GAAGAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATATTATTTAAAAATAA
Found at i:317763 original size:15 final size:16
Alignment explanation
Indices: 317730--317762 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
317720 GAAAATATTC
317730 AAATATTTAAAAAATA
1 AAATATTTAAAAAATA
317746 AAATA-TT-AAAAATA
1 AAATATTTAAAAAATA
317760 AAA
1 AAA
317763 AATAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 10 0.59
15 2 0.12
16 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATATTTAAAAAATA
Found at i:318116 original size:20 final size:20
Alignment explanation
Indices: 318078--318116 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
318068 AACTAATGAT
*
318078 AAAATATATAATCTCATTTA
1 AAAATATATAATATCATTTA
318098 AAAATATTATAATAT-ATTT
1 AAAATA-TATAATATCATTT
318117 TCAATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATATATAATATCATTTA
Found at i:329777 original size:19 final size:19
Alignment explanation
Indices: 329753--329791 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
329743 TCAGAAAAAT
*
329753 TAAGAATATAAAGATTAAA
1 TAAGAATATAAAGACTAAA
329772 TAAGAATATAAAGACTAAA
1 TAAGAATATAAAGACTAAA
329791 T
1 T
329792 TCATGTACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (19 bp):
TAAGAATATAAAGACTAAA
Found at i:331052 original size:20 final size:20
Alignment explanation
Indices: 331044--331119 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
331034 ACACAGTTTC
331044 CAAAATCGCAACGCGGTTAT
1 CAAAATCGCAACGCGGTTAT
*
331064 CAAATTCGCAACGCGGTTAT
1 CAAAATCGCAACGCGGTTAT
* * *
331084 CAAATTCGCAACGCGATTCT
1 CAAAATCGCAACGCGGTTAT
331104 CCAAAATCGCAACGCG
1 -CAAAATCGCAACGCG
331120 TTGCGAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 37 0.73
21 14 0.27
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGGTTAT
Found at i:334671 original size:60 final size:60
Alignment explanation
Indices: 334597--334716 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
334587 CAATTGACCA
* *
334597 ATTTTGCAACTTTTAATAGTC-GAGAGACTCAACAATATAACT-CTCTATAGTT-GGAGGATT
1 ATTTTGCAACTTTTAATAGTCAAAG-GACTCAACAAAATAA-TACTCTATAGTTAGG-GGATT
* *
334657 ATTTTGTAATTTTTAATAGTCAAAGGACTCAACAAAATAATACTCTATAGTTAGGGGATT
1 ATTTTGCAACTTTTAATAGTCAAAGGACTCAACAAAATAATACTCTATAGTTAGGGGATT
334717 TGTGTGTACT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
59 1 0.02
60 48 0.91
61 4 0.08
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (60 bp):
ATTTTGCAACTTTTAATAGTCAAAGGACTCAACAAAATAATACTCTATAGTTAGGGGATT
Found at i:339505 original size:31 final size:29
Alignment explanation
Indices: 339413--339513 Score: 100
Period size: 31 Copynumber: 3.4 Consensus size: 29
339403 TATAGTGTGT
339413 AAATTCGGATATCGGATTTGATCTGATTCAA
1 AAATTCGGATATC-GA-TTGATCTGATTCAA
* * *
339444 AAACTCGAATATC-A-T-ATCCGATTCAA
1 AAATTCGGATATCGATTGATCTGATTCAA
*
339470 AAATTCGGATATCAGATCTGATCTGATCCAA
1 AAATTCGGATATC-GAT-TGATCTGATTCAA
*
339501 AAATTTGGATATC
1 AAATTCGGATATC
339514 TGAAAATAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
26 21 0.37
27 1 0.02
28 1 0.02
29 1 0.02
30 1 0.02
31 32 0.56
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (29 bp):
AAATTCGGATATCGATTGATCTGATTCAA
Found at i:339620 original size:2 final size:2
Alignment explanation
Indices: 339613--339665 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
339603 TAATTTGACA
339613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
339655 AT AT AT AT AT A
1 AT AT AT AT AT A
339666 ATTACTCACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:359629 original size:21 final size:21
Alignment explanation
Indices: 359604--359670 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
359594 GTATATGATT
*
359604 CTTAAGGGATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
*
359625 CTTAAGGAATGATATGTAGTC
1 CTTAAGGAATGATATGTGGTC
359646 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
359667 CTTA
1 CTTA
359671 TGGACATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.34
Consensus pattern (21 bp):
CTTAAGGAATGATATGTGGTC
Found at i:359729 original size:22 final size:22
Alignment explanation
Indices: 359687--359729 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
359677 TTATTATATG
**
359687 GCACTACGGTGCAATTCTACGT
1 GCACTACGGTGCAATGATACGT
*
359709 GCACTTCGGTGCAATGATACG
1 GCACTACGGTGCAATGATACG
359730 AGCTGTGGTG
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:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GCACTACGGTGCAATGATACGT
Found at i:364873 original size:21 final size:21
Alignment explanation
Indices: 364848--364914 Score: 125
Period size: 21 Copynumber: 3.2 Consensus size: 21
364838 GTATATGATT
364848 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
*
364869 CTTAAGGAATGATATGTAGTC
1 CTTAAGGAATGATATGTGGTC
364890 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
364911 CTTA
1 CTTA
364915 TGGACATTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.34
Consensus pattern (21 bp):
CTTAAGGAATGATATGTGGTC
Found at i:364973 original size:22 final size:22
Alignment explanation
Indices: 364931--364973 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
364921 TTATTATATG
**
364931 GCACTACGGTGCAATTCTACGT
1 GCACTACGGTGCAATGATACGT
*
364953 GCACTTCGGTGCAATGATACG
1 GCACTACGGTGCAATGATACG
364974 AGCTGTGGTG
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:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GCACTACGGTGCAATGATACGT
Found at i:365212 original size:21 final size:21
Alignment explanation
Indices: 365166--365213 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
365156 TAAATAATTC
*
365166 GATGATAATGATAATAATATA
1 GATGATAATGATAAGAATATA
* *
365187 TATGATAATGCTAAGAA-AGTA
1 GATGATAATGATAAGAATA-TA
365208 GATGAT
1 GATGAT
365214 GATATATGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.48, C:0.02, G:0.19, T:0.31
Consensus pattern (21 bp):
GATGATAATGATAAGAATATA
Found at i:370099 original size:21 final size:21
Alignment explanation
Indices: 370074--370182 Score: 191
Period size: 21 Copynumber: 5.2 Consensus size: 21
370064 GTATATGATT
* *
370074 CTTAAGGGATGATATGTGGTC
1 CTTAAGGAATGATATGTAGTC
370095 CTTAAGGAATGATATGTAGTC
1 CTTAAGGAATGATATGTAGTC
370116 CTTAAGGAATGATATGTAGTC
1 CTTAAGGAATGATATGTAGTC
370137 CTTAAGGAATGATATGTAGTC
1 CTTAAGGAATGATATGTAGTC
*
370158 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTAGTC
370179 CTTA
1 CTTA
370183 TGGACATTAT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 85 1.00
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (21 bp):
CTTAAGGAATGATATGTAGTC
Found at i:375829 original size:19 final size:19
Alignment explanation
Indices: 375805--375841 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
375795 ATGACTAACA
*
375805 AAATCGCAATGCGATCTCT
1 AAATCGCAAAGCGATCTCT
375824 AAATCGCAAAGCGATCTC
1 AAATCGCAAAGCGATCTC
375842 CAGTATCGCA
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:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAAAGCGATCTCT
Found at i:375851 original size:20 final size:19
Alignment explanation
Indices: 375805--375853 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
375795 ATGACTAACA
* *
375805 AAATCGCAATGCGATCTCT
1 AAATCGCAAAGCGATCTCC
375824 AAATCGCAAAGCGATCTCC
1 AAATCGCAAAGCGATCTCC
*
375843 AGTATCGCAAA
1 A-AATCGCAAA
375854 TTAGTTTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.20
Consensus pattern (19 bp):
AAATCGCAAAGCGATCTCC
Found at i:375932 original size:21 final size:21
Alignment explanation
Indices: 375892--375932 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
375882 GACTATCCCA
* *
375892 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTACAAAATCGCG
*
375913 TTGCGATTTTAGAAAATCGC
1 TTGCGATTTTACAAAATCGC
375933 AATGCGAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (21 bp):
TTGCGATTTTACAAAATCGCG
Found at i:375971 original size:20 final size:20
Alignment explanation
Indices: 375948--376038 Score: 112
Period size: 20 Copynumber: 4.5 Consensus size: 20
375938 GAATATGTAA
*
375948 ATCGCAACGCAATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
375968 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
*
375988 AATCGCAACTCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
376009 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
376029 GTCGCAACGC
1 ATCGCAACGC
376039 TGAATTTCAA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.03
20 42 0.70
21 14 0.23
22 2 0.03
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:377118 original size:15 final size:14
Alignment explanation
Indices: 377100--377135 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
377090 GAAAAAGAAA
377100 AAGAATAAATCCCCG
1 AAGAA-AAATCCCCG
*
377115 AAGAAAAGTCCCCG
1 AAGAAAAATCCCCG
377129 AAGAAAA
1 AAGAAAA
377136 TGTCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.53, C:0.22, G:0.17, T:0.08
Consensus pattern (14 bp):
AAGAAAAATCCCCG
Found at i:379516 original size:140 final size:140
Alignment explanation
Indices: 379264--379546 Score: 512
Period size: 140 Copynumber: 2.0 Consensus size: 140
379254 GTAAACGTTG
*
379264 TATTATGTGTATTTTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTATAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
* * *
379329 TTGAACATTGTTATGATCTGTTTAGTTGTTATCACTTATTATACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
379394 CGAATTTGAC
131 CGAATTTGAC
* *
379404 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGATT
1 TATTATGTGTATTTTATGTATAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
379469 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
379534 CGAATTTGAC
131 CGAATTTGAC
379544 TAT
1 TAT
379547 CGCAACGGGA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTATAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:379542 original size:20 final size:20
Alignment explanation
Indices: 379517--379573 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
379507 TTACACATTC
*
379517 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
379537 ATTTGACTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
379557 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
379574 AGAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:381213 original size:21 final size:21
Alignment explanation
Indices: 381189--381290 Score: 89
Period size: 21 Copynumber: 4.9 Consensus size: 21
381179 GTGGGAGGGA
*
381189 CCTCTTCAACGATGACAGAGG
1 CCTCTTGAACGATGACAGAGG
** *
381210 CCTCTTGAACGATGGGAGGGG
1 CCTCTTGAACGATGACAGAGG
* ** * *
381231 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGACAGAGG
* *
381252 CCTCTTTAACGAT-AGGAGAGG
1 CCTCTTGAACGATGA-CAGAGG
381273 CCTCTTGAACGATGACAG
1 CCTCTTGAACGATGACAG
381291 GTGAGTCGGG
Statistics
Matches: 62, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 1 0.02
21 60 0.97
22 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.22
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGAGG
Found at i:381228 original size:42 final size:42
Alignment explanation
Indices: 381169--381290 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 42
381159 ATGAATCGGG
* * *
381169 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGAGGC
1 CTCTTGAACGATGGGAGGGACCTCTTGAACGATGACAGAGGC
** * *
381211 CTCTTGAACGATGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGATGGGA-GGGACCTCTTGAACGATGACAGAGGC
* *
381253 CTCTTTAACGATAGGAGAGG-CCTCTTGAACGATGACAG
1 CTCTTGAACGATGGGAG-GGACCTCTTGAACGATGACAG
381291 GTGAGTCGGG
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
41 1 0.02
42 60 0.92
43 4 0.06
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGATGGGAGGGACCTCTTGAACGATGACAGAGGC
Found at i:381792 original size:20 final size:20
Alignment explanation
Indices: 381767--381810 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
381757 AATAGTTTCT
381767 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
381787 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
381807 GAAA
1 GAAA
381811 ATGACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:381820 original size:20 final size:20
Alignment explanation
Indices: 381797--381864 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
381787 GAAACTTAAA
381797 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
381817 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
381837 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
381857 ATCGCAAC
1 ATCGCAAC
381865 AAGATAATCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:382025 original size:20 final size:20
Alignment explanation
Indices: 381961--382028 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
381951 CGATTATCTT
**
381961 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGC
* *
381981 GTTGTGATAGTCATTTCCGC
1 GTTGCGATAGTCATTTTCGC
* *
382001 ATTGCGATAGTCATTTTTGC
1 GTTGCGATAGTCATTTTCGC
382021 GTTGCGAT
1 GTTGCGAT
382029 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGC
Found at i:384133 original size:21 final size:21
Alignment explanation
Indices: 384107--384157 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
384097 AAACAAAGAC
384107 AAATACTAACTTTACAGGGTT
1 AAATACTAACTTTACAGGGTT
384128 AAATACTAACTTTACAGGGTT
1 AAATACTAACTTTACAGGGTT
*
384149 AAAGACTAA
1 AAATACTAA
384158 ACAGTTTAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (21 bp):
AAATACTAACTTTACAGGGTT
Found at i:384424 original size:22 final size:22
Alignment explanation
Indices: 384390--384454 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
384380 TCTGAGAGAT
384390 GGAGATA--GACGGATTTCGCC
1 GGAGATAGGGACGGATTTCGCC
* *
384410 GGAGATGGGGACGGATTTCGTC
1 GGAGATAGGGACGGATTTCGCC
* * *
384432 GGGGATAGGGATGGATGTCGCC
1 GGAGATAGGGACGGATTTCGCC
384454 G
1 G
384455 TAGAGAGTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 6 0.17
22 30 0.83
ACGTcount: A:0.20, C:0.15, G:0.45, T:0.20
Consensus pattern (22 bp):
GGAGATAGGGACGGATTTCGCC
Found at i:384645 original size:20 final size:20
Alignment explanation
Indices: 384622--384724 Score: 118
Period size: 20 Copynumber: 5.1 Consensus size: 20
384612 TTATCGCAAC
384622 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
*
384642 GCGATAGTCAGAATCTCGTT
1 GCGATAGTCAGAATCGCGTT
384662 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
* * * **
384682 ACGAT-TTACTAAAATCGCAAT
1 GCGATAGT-C-AGAATCGCGTT
*
384703 GCGATAGTCAAAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
384723 GC
1 GC
384725 AATTTTGTTG
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.01
20 54 0.78
21 13 0.19
22 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:386701 original size:22 final size:22
Alignment explanation
Indices: 386676--386718 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
386666 TAACTCCCGA
* *
386676 AATTATATCAAGTAACCCCTGG
1 AATTAAATCAAATAACCCCTGG
*
386698 AATTAAATCAAATAACTCCTG
1 AATTAAATCAAATAACCCCTG
386719 TAACTCCTGA
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:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (22 bp):
AATTAAATCAAATAACCCCTGG
Found at i:387004 original size:6 final size:6
Alignment explanation
Indices: 386993--387035 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
386983 GACACGTATT
* * *
386993 ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
387036 GCCGAGCCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.28, C:0.49, G:0.16, T:0.07
Consensus pattern (6 bp):
ACCACG
Found at i:387043 original size:5 final size:5
Alignment explanation
Indices: 387033--387076 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
387023 ACCACGACCA
* *
387033 CGAGC CGAGC CGAGC CGAGC CGTGC CGAGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
387077 ACGGACGGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.20, C:0.36, G:0.41, T:0.02
Consensus pattern (5 bp):
CGAGC
Found at i:392950 original size:6 final size:6
Alignment explanation
Indices: 392939--392981 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
392929 GACACGTATT
*
392939 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
392982 GCCGAGCCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:392989 original size:5 final size:5
Alignment explanation
Indices: 392979--393027 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
392969 ACCACGACCA
* * *
392979 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
393028 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.22, C:0.35, G:0.41, T:0.02
Consensus pattern (5 bp):
CGAGC
Found at i:395004 original size:21 final size:21
Alignment explanation
Indices: 394978--395019 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
394968 CCGATCAAAT
394978 AGTTATCTGACACAAATTAAC
1 AGTTATCTGACACAAATTAAC
394999 AGTTATCTGACACAAATTAAC
1 AGTTATCTGACACAAATTAAC
395020 TTTCACACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (21 bp):
AGTTATCTGACACAAATTAAC
Found at i:411039 original size:13 final size:13
Alignment explanation
Indices: 411010--411044 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
411000 ATAACTAATA
*
411010 ATATTAAAT-ATT
1 ATATTAAATAAAT
411022 ATATTAAATAAAT
1 ATATTAAATAAAT
411035 ATATTAAATA
1 ATATTAAATA
411045 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:414053 original size:8 final size:8
Alignment explanation
Indices: 414040--414080 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
414030 CTCATTTTCA
414040 GAGAATTT
1 GAGAATTT
414048 GAGAATTT
1 GAGAATTT
*
414056 -AGAGTTT
1 GAGAATTT
*
414063 GGGAATTT
1 GAGAATTT
414071 GAGAATTT
1 GAGAATTT
414079 GA
1 GA
414081 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:414373 original size:126 final size:126
Alignment explanation
Indices: 414148--414752 Score: 1156
Period size: 126 Copynumber: 4.8 Consensus size: 126
414138 CTATAATCGG
414148 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
414213 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
414274 TTCACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
414339 TCAGTGCCTTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
414400 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
414465 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
414526 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
414591 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
414652 TTCACTATTCACATGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
414717 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
414753 ATAACTTAAA
Statistics
Matches: 471, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 471 1.00
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:415217 original size:32 final size:34
Alignment explanation
Indices: 415139--415236 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 34
415129 AAATTTAATG
*
415139 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * *
415173 TTAAATTT-GAATAATATTATTT-T-TTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
415204 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
415237 AACATTTATC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
31 14 0.26
32 14 0.26
33 13 0.24
34 13 0.24
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:415843 original size:21 final size:21
Alignment explanation
Indices: 415755--415848 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
415745 TATGGTATAA
*
415755 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
415776 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
415797 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
415818 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
415839 AACCCTGCGG
1 AACCCTGCGG
415849 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:415878 original size:21 final size:21
Alignment explanation
Indices: 415852--415899 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
415842 CCTGCGGAGA
*
415852 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
415873 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
415894 GGGCAT
1 TGGCAT
415900 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:417654 original size:29 final size:30
Alignment explanation
Indices: 417622--417689 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
417612 AATTCTAAAT
* *
417622 AAATAATAATTATATAAATATTTTAATA-A
1 AAATAATAATTACATAAATATATTAATATA
*
417651 AAATAATATTTACATAAATATATTAATATA
1 AAATAATAATTACATAAATATATTAATATA
417681 AAA-AATAAT
1 AAATAATAAT
417690 AACTATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (30 bp):
AAATAATAATTACATAAATATATTAATATA
Found at i:422472 original size:5 final size:5
Alignment explanation
Indices: 422462--422514 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
422452 AACGGTCAAC
* *
422462 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
422511 GGTC
1 GGTC
422515 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:422477 original size:17 final size:17
Alignment explanation
Indices: 422455--422515 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
422445 AACGGTCAAC
422455 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
422472 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
422494 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
422511 GGTCA
1 GGTCA
422516 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:422482 original size:7 final size:7
Alignment explanation
Indices: 422435--422465 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
422425 GTCAAAGAAA
422435 GTCAACG
1 GTCAACG
*
422442 ATCAACG
1 GTCAACG
422449 GTCAACG
1 GTCAACG
422456 GTCAACG
1 GTCAACG
422463 GTC
1 GTC
422466 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:422490 original size:22 final size:22
Alignment explanation
Indices: 422448--422514 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
422438 AACGATCAAC
*
422448 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
422472 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
422494 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
422515 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:422535 original size:19 final size:19
Alignment explanation
Indices: 422513--422598 Score: 86
Period size: 19 Copynumber: 4.5 Consensus size: 19
422503 TCGGGTCGGG
*
422513 TCAGACCGGTCAAACTGGC
1 TCAGACCGGTCAAACCGGC
*
422532 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGC
* *
422551 TCAGACCGATCAAACCGGT
1 TCAGACCGGTCAAACCGGC
*
422570 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGC
*
422589 TCAAACCGGT
1 TCAGACCGGT
422599 TTCCAGCAGC
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
18 2 0.03
19 48 0.83
20 8 0.14
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGC
Found at i:422550 original size:9 final size:9
Alignment explanation
Indices: 422511--422598 Score: 77
Period size: 9 Copynumber: 9.3 Consensus size: 9
422501 GGTCGGGTCG
*
422511 GGTCAGACC
1 GGTCAAACC
*
422520 GGTCAAACT
1 GGTCAAACC
*
422529 GGCTCAGACC
1 GG-TCAAACC
422539 GGTCAAACC
1 GGTCAAACC
*
422548 GGTTCAGACC
1 GG-TCAAACC
*
422558 GATCAAACC
1 GGTCAAACC
*
422567 GGTTCGAACC
1 GG-TCAAACC
*
422577 GGTTGAAACC
1 GG-TCAAACC
422587 GGTCAAACC
1 GGTCAAACC
422596 GGT
1 GGT
422599 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
9 33 0.52
10 30 0.48
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:422578 original size:38 final size:39
Alignment explanation
Indices: 422513--422589 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 39
422503 TCGGGTCGGG
* *
422513 TCAGACCGGTCAAACTGGCTCAGACCGG-TCAAACCGGT
1 TCAGACCGATCAAACCGGCTCAGACCGGTTCAAACCGGT
* *
422551 TCAGACCGATCAAACCGGTTC-GAACCGGTTGAAACCGGT
1 TCAGACCGATCAAACCGGCTCAG-ACCGGTTCAAACCGGT
422590 CAAACCGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 1 0.03
38 23 0.70
39 9 0.27
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.17
Consensus pattern (39 bp):
TCAGACCGATCAAACCGGCTCAGACCGGTTCAAACCGGT
Found at i:428086 original size:30 final size:30
Alignment explanation
Indices: 428052--428109 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
428042 TGTTTGTGAG
*
428052 CTTCCGAGTTTCGATTTTGGCCATTAAAAT
1 CTTCCGAGTTTCGATTTTGACCATTAAAAT
*
428082 CTTCCGTGTTTCGATTTTGACCATTAAA
1 CTTCCGAGTTTCGATTTTGACCATTAAA
428110 TTTTTTTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (30 bp):
CTTCCGAGTTTCGATTTTGACCATTAAAAT
Found at i:429273 original size:14 final size:15
Alignment explanation
Indices: 429254--429291 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
429244 TCCCCATCTC
429254 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
429268 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
429284 TAATTTTT
1 TAATTTTT
429292 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Done.