Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold73
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: 1308442
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.31
Warning! 157727 characters in sequence are not A, C, G, or T
File 2 of 9
Found at i:161742 original size:13 final size:13
Alignment explanation
Indices: 161720--161749 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
161710 AATAAATTTT
161720 ATTT-TTTATTAA
1 ATTTATTTATTAA
161732 ATTTATTTATTAA
1 ATTTATTTATTAA
161745 ATTTA
1 ATTTA
161750 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTTATTTATTAA
Found at i:161759 original size:31 final size:29
Alignment explanation
Indices: 161712--161777 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
161702 ATCTTTCAAA
*
161712 TAAATTTTATTTTTTA-TTAAATTTATTTAT
1 TAAATTTAATTTTTTATTTAAATTT-TTT-T
161742 TAAATTTAATATTTTTATTTTAAATTTTTTT
1 TAAATTTAAT-TTTTTA-TTTAAATTTTTTT
161773 TAAAT
1 TAAAT
161778 ATTGAATGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 9 0.28
31 12 0.38
32 3 0.09
33 8 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
TAAATTTAATTTTTTATTTAAATTTTTTT
Found at i:163145 original size:33 final size:33
Alignment explanation
Indices: 163103--163168 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
163093 AATTTGCAAA
*
163103 GATGTCATTAGTGCAAAGACTTAAATCTGGCAT
1 GATGTCATTAGTGCAAAGACTTAAATCAGGCAT
* *
163136 GATGTCATTAGTGCAAGGACTTAATTCAGGCAT
1 GATGTCATTAGTGCAAAGACTTAAATCAGGCAT
163169 AGTTGTGCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (33 bp):
GATGTCATTAGTGCAAAGACTTAAATCAGGCAT
Found at i:168217 original size:2 final size:2
Alignment explanation
Indices: 168210--168248 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
168200 ACGTAATACG
168210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
168249 TCAACATTCG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:168802 original size:38 final size:38
Alignment explanation
Indices: 168751--168827 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
168741 ATTTGAGTGC
*
168751 CATAGTTTCTATATTCTCTAAGTACATTCGTAGGGTGG
1 CATAGTTTCTATATTCTCTAAGTACATTCGTAGGCTGG
168789 CATAGTTTCTATATTCTCTAAGTACATTCGTAGGCTGG
1 CATAGTTTCTATATTCTCTAAGTACATTCGTAGGCTGG
168827 C
1 C
168828 CATTATCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (38 bp):
CATAGTTTCTATATTCTCTAAGTACATTCGTAGGCTGG
Found at i:168989 original size:2 final size:2
Alignment explanation
Indices: 168982--169021 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
168972 GCCTATCAGA
168982 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
169022 TTTGTTGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:175625 original size:2 final size:2
Alignment explanation
Indices: 175618--175645 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
175608 CCGCGCTACC
175618 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
175646 GGCAGATGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:176067 original size:2 final size:2
Alignment explanation
Indices: 176060--176088 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
176050 ACCCTTGCTA
176060 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 A
176089 CAATCCACGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:176382 original size:19 final size:21
Alignment explanation
Indices: 176335--176382 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
176325 AATGTGATAC
176335 ATATATTAAACGTATTATATA
1 ATATATTAAACGTATTATATA
**
176356 ATTATATTAATTGTATT-TA-A
1 A-TATATTAAACGTATTATATA
176376 ATATATT
1 ATATATT
176383 TTATTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 3 0.12
22 13 0.54
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (21 bp):
ATATATTAAACGTATTATATA
Found at i:177282 original size:18 final size:18
Alignment explanation
Indices: 177251--177318 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 18
177241 AAAATTTTAT
* *
177251 ATAATTTTATTTAATAAA
1 ATAATATTAATTAATAAA
177269 ATAATATTAATTAATTAATTA
1 ATAATATTAATTAA-TAA--A
*
177290 ATAATATATAAATTTAT-AA
1 ATAATAT-T-AATTAATAAA
177309 ATAAT-TTAAT
1 ATAATATTAAT
177319 ATATCAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.07
17 1 0.02
18 13 0.31
19 9 0.21
21 9 0.21
22 2 0.05
23 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAATATTAATTAATAAA
Found at i:178480 original size:17 final size:18
Alignment explanation
Indices: 178444--178483 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
178434 ATTTTATTTA
178444 AATATAATAATAAATATT
1 AATATAATAATAAATATT
* *
178462 AATATAA-AATAATTTTT
1 AATATAATAATAAATATT
178479 AATAT
1 AATAT
178484 TATTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATAATAATAAATATT
Found at i:179121 original size:23 final size:24
Alignment explanation
Indices: 179077--179121 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
179067 GTTTACGTTA
* *
179077 TTTTTTGTATTATATTTTAATTAT
1 TTTTTTATATTATATTTCAATTAT
179101 TTTTTTATATTATA-TTCAATT
1 TTTTTTATATTATATTTCAATT
179122 CGAATTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTTTATATTATATTTCAATTAT
Found at i:179883 original size:25 final size:26
Alignment explanation
Indices: 179828--179885 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
179818 ATAATAATTT
*
179828 AATA-TAATTTAATTTAAATTATATA
1 AATATTAATTTAATTAAAATTATATA
* *
179853 ATTATTAATTTAATTAAAATT-TGTA
1 AATATTAATTTAATTAAAATTATATA
179878 AATATTAA
1 AATATTAA
179886 AAATATTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
AATATTAATTTAATTAAAATTATATA
Found at i:180078 original size:20 final size:20
Alignment explanation
Indices: 180049--180095 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
180039 AACAACTCCT
* *
180049 TTTAAAAAATAATTAAATTTA
1 TTTAAAAATTAAAT-AATTTA
180070 TTTAAAAATTAAATAATTTA
1 TTTAAAAATTAAATAATTTA
180090 TTTAAA
1 TTTAAA
180096 TTTATGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAAAATTAAATAATTTA
Found at i:182705 original size:50 final size:50
Alignment explanation
Indices: 182460--182704 Score: 355
Period size: 50 Copynumber: 4.9 Consensus size: 50
182450 TATACTTAGA
* * *
182460 GTCAACAATTATGGCCACCTTTCTCTATTGCCAAAGATTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
182510 GTCAACAATAATGGCCGCATCTTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* ** *
182560 GTCAACTATTACAGCCACCTCTCTCTATTGTCAAAGGTTGATGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
182610 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
182660 GTCAACAATTACGACCACCTCTCTCTGTTGTCAAAGGTTGGTGAA
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA
182705 AGATAGTTAA
Statistics
Matches: 172, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 172 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:187363 original size:50 final size:50
Alignment explanation
Indices: 187109--187353 Score: 373
Period size: 50 Copynumber: 4.9 Consensus size: 50
187099 TATACTTAGA
* * *
187109 GTCAACAATTATGGCCACCTTTCTCTATTGTCAAAAGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
187159 GTCAACAATAATGGCCACCTCTTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
187209 GTCAATAATTACGGCCACCTCTTTCAATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
187259 GTCAACAATTACGGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
187309 GTCAACAATTACGACCACCTCTCTCTATTGTCAAAGATTGATGAA
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA
187354 AGATAGTCAA
Statistics
Matches: 179, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 179 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (50 bp):
GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:189778 original size:2 final size:2
Alignment explanation
Indices: 189771--189802 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
189761 ATTTAACCTC
189771 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
189803 GTATGTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:190598 original size:50 final size:50
Alignment explanation
Indices: 190531--190689 Score: 266
Period size: 50 Copynumber: 3.2 Consensus size: 50
190521 AGGTGTTGCC
* *
190531 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGCTGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCTGTA
190581 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGG-TCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCT-GTA
**
190631 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCTGTA
190681 ATTGTTGAC
1 ATTGTTGAC
190690 TCTAAGTATA
Statistics
Matches: 103, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
49 1 0.01
50 102 0.99
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCTGTA
Found at i:195161 original size:50 final size:49
Alignment explanation
Indices: 195050--195206 Score: 235
Period size: 50 Copynumber: 3.2 Consensus size: 49
195040 AGTTGTTGTC
* *
195050 ATTGTTGACTATCCTTCACCAACCTTTGACAAT-AGAGAGGTGGCCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAAGAGAGGTGGCCGTA
* *
195098 ATTGTTGATGATTCTTCACCAACCTTTGACAATAAAGAGTGGTGGCCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAT-AAGAGAGGTGGCCGTA
**
195148 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCTATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATA-AGAGAGGTGGCCGTA
195198 ATTGTTGAC
1 ATTGTTGAC
195207 TCTATGTATA
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
48 30 0.31
49 1 0.01
50 67 0.68
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (49 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAAGAGAGGTGGCCGTA
Found at i:197761 original size:3 final size:3
Alignment explanation
Indices: 197745--197778 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
197735 ATATGTACCC
* *
197745 ATA ATA TTA TTA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
197779 CAACGACCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:199750 original size:2 final size:2
Alignment explanation
Indices: 199745--199775 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
199735 TTTTTACATT
199745 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
199776 TATGTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:200391 original size:15 final size:15
Alignment explanation
Indices: 200368--200397 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
200358 CTACGGATAC
*
200368 TTTATATTAAATTAT
1 TTTAGATTAAATTAT
200383 TTTAGATTAAATTAT
1 TTTAGATTAAATTAT
200398 ATTTTATTTT
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:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TTTAGATTAAATTAT
Found at i:201236 original size:222 final size:224
Alignment explanation
Indices: 200762--201370 Score: 877
Period size: 225 Copynumber: 2.8 Consensus size: 224
200752 TTGAATAGTT
200762 GTGAAACAAATAGGCTCGCCCAATGACATGGGAAAACTGTTCTGTTTTTTTTTTTTTTAACCCTA
1 GTGAAACAAATAGGCTCGCCCAATGACATGGGAAAACTGTTCTGTTTTTTTTTTTTTTAACCCTA
* *
200827 TGTAGATGGTCCATGTTTCTCCCTTGTACGTAACACATACGTGATCTTATATGAGACAATAATTT
66 TGTAGATGGTCCATGTTTCTCCCTTGTACGTAACACAAACGTGATCTTATATGAAACAATAATTT
* * *
200892 TTAATTAAAATAATATATATTTTTATTTAAATTTAATTA-AAGTTTTTGACCTAAGCGAAAATGA
131 TTAATTAAAATAATATATATTTTTATTTAAATTTAATTATAA--ATTTGAACTAAGAGAAAATGA
*
200956 CATGAATTATTGAATAGTTGTCCTTTTACAC
194 CATGAATTACTGAATAGTTGTCCTTTTACAC
200987 GTGAAACAAATAGGCTCGCCCAATGACATGGGAAAACTGTTCTGTTTTTTTTTTTTTTAACCCTA
1 GTGAAACAAATAGGCTCGCCCAATGACATGGGAAAACTGTTCTGTTTTTTTTTTTTTTAACCCTA
* * *
201052 TGCAGATGGTCCATGTTTCTCCCTTGTACGTAACACAAACGTGATCTTATATAAAAAAATAATTT
66 TGTAGATGGTCCATGTTTCTCCCTTGTACGTAACACAAACGTGATCTTATATGAAACAATAATTT
* * **** *
201117 TTAATTAAAATAGTATATATTTTTATTTAAATTTAATTATAAATTT-AATTAA-AGTTCTTGACC
131 TTAATTAAAATAATATATATTTTTATTTAAATTTAATTATAAATTTGAACTAAGAGAAAATGACA
201180 TGAATTACTGAATAGTTGTCCTTTTACAC
196 TGAATTACTGAATAGTTGTCCTTTTACAC
* * *
201209 GTGAAACAAATAGGCTTGCCCAATGACATGGGAAAA--G---TG-----TTCTTTTTTAACCCTG
1 GTGAAACAAATAGGCTCGCCCAATGACATGGGAAAACTGTTCTGTTTTTTTTTTTTTTAACCCTA
* * * **
201264 TGTAGATGGTCCATGTTTCTCCCTCGTACGTAACACACACGTGGTCTTGCATGAAACAATAA-TT
66 TGTAGATGGTCCATGTTTCTCCCTTGTACGTAACACAAACGTGATCTTATATGAAACAATAATTT
*
201328 TTAATTAAAATAATATATATATTTATTTAAATTTAATTATAAA
131 TTAATTAAAATAATATATATTTTTATTTAAATTTAATTATAAA
201371 ATATATTAAC
Statistics
Matches: 354, Mismatches: 29, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
211 43 0.12
212 68 0.19
217 2 0.01
220 1 0.00
222 68 0.19
223 4 0.01
224 3 0.01
225 163 0.46
226 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (224 bp):
GTGAAACAAATAGGCTCGCCCAATGACATGGGAAAACTGTTCTGTTTTTTTTTTTTTTAACCCTA
TGTAGATGGTCCATGTTTCTCCCTTGTACGTAACACAAACGTGATCTTATATGAAACAATAATTT
TTAATTAAAATAATATATATTTTTATTTAAATTTAATTATAAATTTGAACTAAGAGAAAATGACA
TGAATTACTGAATAGTTGTCCTTTTACAC
Found at i:201399 original size:21 final size:22
Alignment explanation
Indices: 201360--201400 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
201350 TTATTTAAAT
* *
201360 TTAATTATAAAATATATTAACA
1 TTAATTATAAAAGAAATTAACA
201382 TTAA-TATAAAAGAAATTAA
1 TTAATTATAAAAGAAATTAA
201401 TATTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
TTAATTATAAAAGAAATTAACA
Found at i:201791 original size:3 final size:3
Alignment explanation
Indices: 201783--201807 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
201773 TCATAGAAAA
201783 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
201808 GTAAATTATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:202143 original size:2 final size:2
Alignment explanation
Indices: 202136--202181 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
202126 TATAGGCAAG
202136 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
202178 AT AT
1 AT AT
202182 TATTCATCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:204346 original size:27 final size:28
Alignment explanation
Indices: 204310--204362 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
204300 ATATATTACT
204310 TAATATATTTTTATAAAT-TTAAATATAA
1 TAATATATTTTTA-AAATATTAAATATAA
*
204338 TAAT-TATTTTTAAAATATTATATAT
1 TAATATATTTTTAAAATATTAAATAT
204363 TATATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 15 0.65
28 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TAATATATTTTTAAAATATTAAATATAA
Found at i:205643 original size:2 final size:2
Alignment explanation
Indices: 205638--205678 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
205628 TAGGTATATA
205638 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
205679 ATGTATGATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:208944 original size:25 final size:24
Alignment explanation
Indices: 208899--208949 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
208889 TTATAAGATA
* *
208899 AAAATTATATAATATATATAATAC
1 AAAATTATATAATATAAATAAAAC
208923 AAAATTACTATTAAT-TAAATAAAAC
1 AAAATTA-TA-TAATATAAATAAAAC
208948 AA
1 AA
208950 GTTTGGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.30
25 12 0.52
26 4 0.17
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAATTATATAATATAAATAAAAC
Found at i:209243 original size:13 final size:14
Alignment explanation
Indices: 209225--209256 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
209215 TTTATGTTTT
209225 TTTTTAA-ATTTAA
1 TTTTTAATATTTAA
209238 TTTTTAATATTTAA
1 TTTTTAATATTTAA
209252 TTTTT
1 TTTTT
209257 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTAATATTTAA
Found at i:210722 original size:14 final size:14
Alignment explanation
Indices: 210699--210740 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
210689 TGTAACTAAT
*
210699 AAATTTATTTTTCA
1 AAATTTATTTTTAA
*
210713 AAATTAATTTTATAA
1 AAATTTATTTT-TAA
210728 AAATTTATTTTTA
1 AAATTTATTTTTA
210741 TGAAATAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
AAATTTATTTTTAA
Found at i:210921 original size:15 final size:15
Alignment explanation
Indices: 210901--210930 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
210891 TTTTTTACAA
210901 AATAATAATAATAAC
1 AATAATAATAATAAC
210916 AATAATAATAATAAC
1 AATAATAATAATAAC
210931 CAGGACCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAATAATAATAAC
Found at i:213264 original size:19 final size:19
Alignment explanation
Indices: 213207--213265 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
213197 AGATAATTTT
213207 AATATA-TATAATATAT-AA
1 AATATATTA-AATATATAAA
*
213225 AA-A-ATT-AATATATATA
1 AATATATTAAATATATAAA
*
213241 TATATATTAAATATATAAA
1 AATATATTAAATATATAAA
213260 AATATA
1 AATATA
213266 ATATTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
15 7 0.22
16 3 0.09
17 3 0.09
18 5 0.16
19 14 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATATTAAATATATAAA
Found at i:213268 original size:15 final size:16
Alignment explanation
Indices: 213210--213269 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 16
213200 TAATTTTAAT
213210 ATATATAATATATAAAA
1 ATAT-TAATATATAAAA
*
213227 A-ATTAATATATATATAT
1 ATATTAATATATA-A-AA
213244 ATATTAAATATATAAAA
1 ATATT-AATATATAAAA
213261 ATA-TAATAT
1 ATATTAATAT
213270 TTTAATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 14 0.38
16 4 0.11
17 7 0.19
18 4 0.11
19 8 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATTAATATATAAAA
Found at i:213285 original size:32 final size:32
Alignment explanation
Indices: 213202--213289 Score: 99
Period size: 34 Copynumber: 2.7 Consensus size: 32
213192 TATGAAGATA
*
213202 ATTTTAATATATATAATATATAAAAAATTAAT
1 ATTTTAATATATAAAATATATAAAAAATTAAT
* *
213234 ATATATATATATATTAAATATAT-AAAAATATAAT
1 AT-TTTA-ATATATAAAATATATAAAAAAT-TAAT
*
213268 ATTTTAATAAATAAAATA-ATAA
1 ATTTTAATATATAAAATATATAA
213290 TTTAAAAAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
31 2 0.04
32 13 0.28
33 12 0.26
34 19 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
ATTTTAATATATAAAATATATAAAAAATTAAT
Found at i:214103 original size:20 final size:20
Alignment explanation
Indices: 214066--214101 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
214056 AATAATTTAT
214066 TTTATTACTTATTTATATTA
1 TTTATTACTTATTTATATTA
214086 TTTATTA-TT-TTTATAT
1 TTTATTACTTATTTATAT
214102 ATAAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 2 0.12
20 7 0.44
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTACTTATTTATATTA
Found at i:215707 original size:22 final size:22
Alignment explanation
Indices: 215679--215721 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
215669 TAAACTATTA
* *
215679 TTTTATATTAATATTTAAATAT
1 TTTTATAATAAAATTTAAATAT
215701 TTTTATAATAAAATTTAAATA
1 TTTTATAATAAAATTTAAATA
215722 AATTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTATAATAAAATTTAAATAT
Found at i:216538 original size:28 final size:26
Alignment explanation
Indices: 216477--216539 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
216467 TCAGATTATG
* *
216477 ATTTATATTTTTAAAATTTTAAATTT
1 ATTTATATTTTTAAAATATTAAATAT
216503 ATTT-TATTATTTAAAAAATATTAAA-AT
1 ATTTATATT-TTT--AAAATATTAAATAT
216530 ATTTATATTT
1 ATTTATATTT
216540 ATATATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
25 4 0.13
26 7 0.23
27 6 0.19
28 14 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTATATTTTTAAAATATTAAATAT
Found at i:217642 original size:20 final size:20
Alignment explanation
Indices: 217617--217666 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
217607 TTTTTTATAT
217617 ATTTTAAAT-AATAAAATAAA
1 ATTTTAAATAAATAAAA-AAA
217637 ATTTTAAATTTAAATAAAAAAA
1 ATTTTAAA--TAAATAAAAAAA
217659 A-TTTAAAT
1 ATTTTAAAT
217667 TCAACTTAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 1 0.04
20 8 0.30
21 6 0.22
22 5 0.19
23 7 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTTTAAATAAATAAAAAAA
Found at i:217663 original size:21 final size:23
Alignment explanation
Indices: 217626--217667 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
217616 TATTTTAAAT
217626 AATAAAATAAAATTTTAAATTTA
1 AATAAAATAAAATTTTAAATTTA
217649 AATAAAA-AAAA-TTTAAATT
1 AATAAAATAAAATTTTAAATT
217668 CAACTTAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AATAAAATAAAATTTTAAATTTA
Found at i:218069 original size:22 final size:22
Alignment explanation
Indices: 218038--218083 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
218028 ACATATTTTT
*
218038 ATATTTTAAAATTT-ATTTTAA
1 ATATTTTAAAATTTAATCTTAA
218059 ATATCTTTAAAATTTAATCTTAA
1 ATAT-TTTAAAATTTAATCTTAA
218082 AT
1 AT
218084 CAAAAAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 10 0.45
23 8 0.36
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTTTAAAATTTAATCTTAA
Found at i:218074 original size:29 final size:29
Alignment explanation
Indices: 218010--218075 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
218000 TATATCGATA
* *
218010 TAAAA-TT-AAATTAATTTTACATATTTT
1 TAAAATTTAAAATTAATTTTAAATATCTT
* * *
218037 TATATTTTAAAATTTATTTTAAATATCTT
1 TAAAATTTAAAATTAATTTTAAATATCTT
218066 TAAAATTTAA
1 TAAAATTTAA
218076 TCTTAAATCA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
27 3 0.10
28 2 0.07
29 25 0.83
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (29 bp):
TAAAATTTAAAATTAATTTTAAATATCTT
Found at i:218153 original size:34 final size:34
Alignment explanation
Indices: 218098--218188 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 34
218088 AAATCGAGTT
***
218098 TTTTAAATTTGATCCCGAATCTACTTAAAAAATC
1 TTTTAAATTTGATCTTAAATCTACTTAAAAAATC
* * * * *
218132 TTTTAAATTTGATCTTAAATCTATTTTAAGATTT
1 TTTTAAATTTGATCTTAAATCTACTTAAAAAATC
*
218166 TTTTAAACTTAGATCTTAAATCT
1 TTTTAAA-TTTGATCTTAAATCT
218189 GCTTTAAGGG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
34 33 0.70
35 14 0.30
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.47
Consensus pattern (34 bp):
TTTTAAATTTGATCTTAAATCTACTTAAAAAATC
Found at i:221958 original size:22 final size:22
Alignment explanation
Indices: 221930--221972 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
221920 AATTAAATTT
221930 TAAAAATTATTTTTA-TATTAAA
1 TAAAAA-TATTTTTATTATTAAA
221952 TAAAAATATTTTTATTATTAA
1 TAAAAATATTTTTATTATTAA
221973 TTAATCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAAAATATTTTTATTATTAAA
Found at i:222319 original size:16 final size:16
Alignment explanation
Indices: 222286--222319 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
222276 TTCTTTTTAC
*
222286 TTTTATTTTATTAAAT
1 TTTTATTTTAATAAAT
*
222302 TTTTATTTTAATATAT
1 TTTTATTTTAATAAAT
222318 TT
1 TT
222320 AAATATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTTTAATAAAT
Found at i:222321 original size:22 final size:21
Alignment explanation
Indices: 222279--222342 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
222269 TTTTACCTTC
* *
222279 TTTTTACTTTTATTTTATTAAA
1 TTTTTA-TTTTAATATATTAAA
222301 TTTTTATTTTAATATATTTAAA
1 TTTTTATTTTAATATA-TTAAA
* *
222323 -TATTA-TTTAATATAATAAA
1 TTTTTATTTTAATATATTAAA
222342 T
1 T
222343 AAACTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 4 0.11
20 9 0.25
21 12 0.33
22 11 0.31
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTATTTTAATATATTAAA
Found at i:222578 original size:17 final size:18
Alignment explanation
Indices: 222545--222581 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
222535 AACATATACA
222545 ACTATTAATTTTAATTTT
1 ACTATTAATTTTAATTTT
* *
222563 ACTATTATTTTTATTTTT
1 ACTATTAATTTTAATTTT
222581 A
1 A
222582 ATTTTATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (18 bp):
ACTATTAATTTTAATTTT
Found at i:223837 original size:21 final size:21
Alignment explanation
Indices: 223813--223853 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
223803 TAATAAAAAA
223813 ATATTTTAT-ATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
223834 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
223854 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:223869 original size:16 final size:16
Alignment explanation
Indices: 223843--223946 Score: 75
Period size: 16 Copynumber: 6.0 Consensus size: 16
223833 TATATTTTAT
223843 AATTAAATTTAATTAAA
1 AATT-AATTTAATTAAA
*
223860 AAATAATTTAATTATTAA
1 AATTAATTTAATTA--AA
223878 ATATTAATTTAAATTAAA
1 A-ATTAATTT-AATTAAA
223896 TCAATTAATTTAATTTATAA
1 --AATTAATTTAA-TTA-AA
* *
223916 AA-AAATTTATTTAAA
1 AATTAATTTAATTAAA
* *
223931 ATTTAATTTTATTAAA
1 AATTAATTTAATTAAA
223947 TTAAATAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
15 3 0.04
16 23 0.33
17 9 0.13
18 9 0.13
19 18 0.26
20 8 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTAATTTAATTAAA
Found at i:223878 original size:19 final size:19
Alignment explanation
Indices: 223854--223921 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
223844 ATTAAATTTA
223854 ATTAAAAAATAATTTAATT
1 ATTAAAAAATAATTTAATT
* *
223873 ATTAAATATTAATTTAA--
1 ATTAAAAAATAATTTAATT
*
223890 ATTAAATCAATTAATTTAATTT
1 ATTAAA--AAATAATTTAA-TT
*
223912 ATAAAAAAAT
1 ATTAAAAAAT
223922 TTATTTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
17 6 0.15
19 25 0.64
20 3 0.08
22 5 0.13
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTAAAAAATAATTTAATT
Found at i:223904 original size:49 final size:51
Alignment explanation
Indices: 223798--223905 Score: 118
Period size: 49 Copynumber: 2.2 Consensus size: 51
223788 ATTTTTATTT
* * ** *
223798 ATAATTAATAAAAAAATATTTTATATTAATATTTATATATTTTATAATTAA
1 ATAATTAATTAAAAAATAATTTATATTAATAAATATATAATTTATAATTAA
*
223849 AT--TTAATTAAAAAATAATTTA-ATTATTAAATAT-TAATTTA-AATTAA
1 ATAATTAATTAAAAAATAATTTATATTAATAAATATATAATTTATAATTAA
223895 ATCAATTAATT
1 AT-AATTAATT
223906 TAATTTATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
46 8 0.17
47 6 0.12
48 9 0.19
49 23 0.48
51 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (51 bp):
ATAATTAATTAAAAAATAATTTATATTAATAAATATATAATTTATAATTAA
Found at i:224051 original size:24 final size:24
Alignment explanation
Indices: 224018--224063 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
224008 AAAAATATTA
*
224018 AAATATTATTTTATAATTAAATTT
1 AAATAATATTTTATAATTAAATTT
*
224042 AAATAATATTTTTTAATTAAAT
1 AAATAATATTTTATAATTAAAT
224064 AATTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AAATAATATTTTATAATTAAATTT
Found at i:224685 original size:12 final size:14
Alignment explanation
Indices: 224646--224720 Score: 64
Period size: 15 Copynumber: 5.3 Consensus size: 14
224636 ACGTTATGTT
**
224646 TATATTTATATCGA
1 TATATTTATATTTA
224660 -ATATTTATATTTA
1 TATATTTATATTTA
224673 TATATTT-TATTATA
1 TATATTTATATT-TA
* *
224687 TTATAATTATATTAA
1 -TATATTTATATTTA
*
224702 AATATTTTATATTTA
1 TATA-TTTATATTTA
224717 TATA
1 TATA
224721 AATTTTTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
13 15 0.31
14 11 0.23
15 18 0.38
16 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (14 bp):
TATATTTATATTTA
Found at i:224721 original size:29 final size:29
Alignment explanation
Indices: 224664--224718 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
224654 TATCGAATAT
* *
224664 TTATATTTATATATTTTATTATATTATAA
1 TTATATTAAAATATTTTATTATATTATAA
224693 TTATATTAAAATATTTTA-TAT-TTATA
1 TTATATTAAAATATTTTATTATATTATA
224719 TAAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 3 0.12
29 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TTATATTAAAATATTTTATTATATTATAA
Found at i:224723 original size:19 final size:20
Alignment explanation
Indices: 224644--224761 Score: 73
Period size: 21 Copynumber: 5.7 Consensus size: 20
224634 TGACGTTATG
*
224644 TTTATATTTATATCGAATA-
1 TTTATATTTATATCAAATAT
*
224663 TTTATATTTATAT-ATTTTATTAT
1 TTTATATTTATATCA----AATAT
* * *
224686 ATTATAATTATATTAAAATAT
1 TTTATATTTATA-TCAAATAT
224707 TTTATATTTATAT-AAAT-T
1 TTTATATTTATATCAAATAT
224725 TTTAAATATTTATATCAAATCAT
1 TTT--ATATTTATATCAAAT-AT
*
224748 ATTATATATTATAT
1 TTTATAT-TTATAT
224762 ATTCTTACAC
Statistics
Matches: 78, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
18 4 0.05
19 17 0.22
20 11 0.14
21 22 0.28
22 9 0.12
23 13 0.17
24 1 0.01
25 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.56
Consensus pattern (20 bp):
TTTATATTTATATCAAATAT
Found at i:224961 original size:3 final size:3
Alignment explanation
Indices: 224953--224992 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
224943 GTATTTTTTA
224953 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
224993 AATGGGCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:225277 original size:2 final size:2
Alignment explanation
Indices: 225268--225302 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
225258 TTAAAGTTAG
225268 AT AT -T 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
225303 TCTTAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:229039 original size:20 final size:20
Alignment explanation
Indices: 229016--229073 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 20
229006 TAAATTATTT
229016 TATATTTATATAAAATTTAA
1 TATATTTATATAAAATTTAA
* *
229036 TATATTAATAATAAATATTAAA
1 TATATTTAT-ATAAA-ATTTAA
*
229058 TAAATTT-T-TAAAATTT
1 TATATTTATATAAAATTT
229074 TTAAATTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 3 0.10
19 4 0.13
20 8 0.26
21 6 0.19
22 10 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATTTATATAAAATTTAA
Found at i:229436 original size:2 final size:2
Alignment explanation
Indices: 229429--229453 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
229419 AAGGAAAATA
229429 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 A
229454 AATAGTGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:229584 original size:22 final size:23
Alignment explanation
Indices: 229537--229603 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 23
229527 GAGAATATAA
* *
229537 ATATAAAAATATTTTTATTAAAT
1 ATATAATAATATTTTTATAAAAT
229560 ATATAATAA-ATTTTTA-AAAATT
1 ATATAATAATATTTTTATAAAA-T
229582 ATATATATAATATATCTTTATA
1 ATATA-ATAATAT-T-TTTATA
229604 TTTGATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
21 3 0.08
22 13 0.36
23 12 0.33
24 2 0.06
25 1 0.03
26 4 0.11
27 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATAATAATATTTTTATAAAAT
Found at i:229825 original size:19 final size:19
Alignment explanation
Indices: 229801--229838 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
229791 TTATTTACTA
229801 TATTATTAAAATT-TATTTT
1 TATTATT-AAATTATATTTT
229820 TATTATTAAATTATATTTT
1 TATTATTAAATTATATTTT
229839 AAATCAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTATTAAATTATATTTT
Found at i:229841 original size:31 final size:30
Alignment explanation
Indices: 229774--229841 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
229764 GTTGTTTGAG
*
229774 TTTAAAATTTTATTTTATTATTTACTATAT
1 TTTAAAATTTTATTTTATTATTAACTATAT
*
229804 TATTAAAA-TTTATTTTTATTATTAAATTATAT
1 T-TTAAAATTTTA-TTTTATTATT-AACTATAT
229836 TTTAAA
1 TTTAAA
229842 TCAAGTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 5 0.15
31 21 0.64
32 7 0.21
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTAAAATTTTATTTTATTATTAACTATAT
Found at i:230920 original size:23 final size:23
Alignment explanation
Indices: 230876--230929 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
230866 ATCTAATCAG
230876 ATTATTATTTTAATTAATATTTT
1 ATTATTATTTTAATTAATATTTT
*
230899 ATTATT-TTTATATATTAA-ATTTAA
1 ATTATTATTT-TA-ATTAATATTT-T
230923 ATTATTA
1 ATTATTA
230930 AATTATAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.12
23 12 0.46
24 11 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTATTATTTTAATTAATATTTT
Found at i:230959 original size:41 final size:41
Alignment explanation
Indices: 230913--230997 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
230903 TTTTTATATA
* *
230913 TTAAATTTAAATTATT-AAATTATAGTTAAATT-TAATTAAAT
1 TTAAATTTAAATT-TTAAAATT-TAATCAAATTATAATTAAAT
* *
230954 TTAAATTTATATTTTAAAATTTAATCAAATTATAATTTAAT
1 TTAAATTTAAATTTTAAAATTTAATCAAATTATAATTAAAT
230995 TTA
1 TTA
230998 TAAATAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 10 0.26
41 28 0.74
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (41 bp):
TTAAATTTAAATTTTAAAATTTAATCAAATTATAATTAAAT
Found at i:230976 original size:30 final size:30
Alignment explanation
Indices: 230940--231001 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
230930 AATTATAGTT
*
230940 AAATTTAATTAAATT-TAAATTTATATTT-TA
1 AAATTTAATCAAATTAT-AATTTA-ATTTATA
230970 AAATTTAATCAAATTATAATTTAATTTATA
1 AAATTTAATCAAATTATAATTTAATTTATA
231000 AA
1 AA
231002 TAAATTTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 4 0.14
30 24 0.83
31 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
AAATTTAATCAAATTATAATTTAATTTATA
Found at i:234847 original size:61 final size:61
Alignment explanation
Indices: 234773--234894 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
234763 TTTTAAGCAT
234773 AGTAAATATTATCGTGATCAATTATTAAATTTTGATAATGAATATCAGCAGTGAAGAAAAC
1 AGTAAATATTATCGTGATCAATTATTAAATTTTGATAATGAATATCAGCAGTGAAGAAAAC
*
234834 AGTAAATATTATCGTGATCAATTATTAAATTTTGATAATGAATATCAGCAGTGGAGAAAAC
1 AGTAAATATTATCGTGATCAATTATTAAATTTTGATAATGAATATCAGCAGTGAAGAAAAC
234895 TAAAGTTGTG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (61 bp):
AGTAAATATTATCGTGATCAATTATTAAATTTTGATAATGAATATCAGCAGTGAAGAAAAC
Found at i:237236 original size:22 final size:24
Alignment explanation
Indices: 237195--237248 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
237185 AATATTAAAA
* *
237195 AATATTTT-ATATTAATATTT-AT
1 AATATTTTAAAATTAAAATTTAAT
237217 -ATATTTTAAAATTAAAATTTAAT
1 AATATTTTAAAATTAAAATTTAAT
237240 AATATTTTA
1 AATATTTTA
237249 TTTTATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 7 0.26
22 10 0.37
23 2 0.07
24 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATATTTTAAAATTAAAATTTAAT
Found at i:237668 original size:29 final size:28
Alignment explanation
Indices: 237633--237711 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 28
237623 TTAATTTGAT
*
237633 TTTAATTTTTATTTAATAATATTATTTA
1 TTTAAATTTTATTTAATAATATTATTTA
* *
237661 TTTAAATTTAATTATAA-AATATATATTAA
1 TTTAAATTTTATT-TAATAATAT-TATTTA
*
237690 TATAAATTTT-TTTAATAATATT
1 TTTAAATTTTATTTAATAATATT
237712 TAATTAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 4 0.09
28 23 0.53
29 16 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTAAATTTTATTTAATAATATTATTTA
Found at i:237717 original size:29 final size:28
Alignment explanation
Indices: 237639--237725 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 28
237629 TGATTTTAAT
* *
237639 TTTTATTTAATAATA-TTATTTATTTAAA
1 TTTT-TTTAATAATATTTATTAATATAAA
* *
237667 TTTAATTATAA-AATATATATTAATATAAA
1 TTT--TTTTAATAATATTTATTAATATAAA
237696 TTTTTTTAATAATATTTAATTAATA-AAA
1 TTTTTTTAATAATATTT-ATTAATATAAA
237724 TT
1 TT
237726 GATTAACAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
27 5 0.10
28 18 0.38
29 24 0.50
30 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTTTTTAATAATATTTATTAATATAAA
Found at i:245161 original size:3 final size:3
Alignment explanation
Indices: 245153--245187 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
245143 AACATTTAGA
* *
245153 AAG AAG AAG AAG AAG ACG AGG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
245188 AAAAAACCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.63, C:0.03, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:246481 original size:19 final size:19
Alignment explanation
Indices: 246457--246532 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
246447 ATATAATAAA
246457 AAAATAATATAAATATATT
1 AAAATAATATAAATATATT
* *
246476 AAAATATTA-AAATTTATAT
1 AAAATAATATAAATATAT-T
246495 AAAATATATTATAAA-ATATT
1 AAAATA-A-TATAAATATATT
*
246515 AAAATTTATATAAATATA
1 AAAA-TAATATAAATATA
246533 AAATTTTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
18 7 0.15
19 21 0.46
20 9 0.20
21 6 0.13
22 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAATATAAATATATT
Found at i:246482 original size:10 final size:10
Alignment explanation
Indices: 246467--246532 Score: 59
Period size: 10 Copynumber: 6.7 Consensus size: 10
246457 AAAATAATAT
246467 AAATATATT-
1 AAATATATTA
246476 AAA-ATATTA
1 AAATATATTA
*
246485 AAATTTATATA
1 AAATATAT-TA
246496 AAATATATTA
1 AAATATATTA
246506 TAAA-ATATTA
1 -AAATATATTA
*
246516 AAATTTA-TA
1 AAATATATTA
246525 TAAATATA
1 -AAATATA
246533 AAATTTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
8 5 0.11
9 11 0.23
10 19 0.40
11 12 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AAATATATTA
Found at i:246507 original size:12 final size:11
Alignment explanation
Indices: 246457--246532 Score: 55
Period size: 10 Copynumber: 7.7 Consensus size: 11
246447 ATATAATAAA
246457 AAAATA-ATAT
1 AAAATATATAT
246467 -AAATATAT-T
1 AAAATATATAT
246476 -AAA-ATAT-T
1 AAAATATATAT
*
246484 AAAATTTATAT
1 AAAATATATAT
246495 AAAATATAT-T
1 AAAATATATAT
246505 ATAAA-ATAT-T
1 A-AAATATATAT
*
246515 AAAATTTATAT
1 AAAATATATAT
246526 -AAATATA
1 AAAATATA
246533 AAATTTTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
8 5 0.09
9 15 0.27
10 22 0.40
11 13 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAAATATATAT
Found at i:246513 original size:31 final size:28
Alignment explanation
Indices: 246463--246532 Score: 113
Period size: 31 Copynumber: 2.4 Consensus size: 28
246453 TAAAAAAATA
246463 ATATAAATATATTAAAATATTAAAATTT
1 ATATAAATATATTAAAATATTAAAATTT
246491 ATATAAAATATATTATAAAATATTAAAATTT
1 ATAT-AAATATA-T-TAAAATATTAAAATTT
246522 ATATAAATATA
1 ATATAAATATA
246533 AAATTTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 4 0.10
29 7 0.18
30 8 0.21
31 20 0.51
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATATAAATATATTAAAATATTAAAATTT
Found at i:246519 original size:20 final size:20
Alignment explanation
Indices: 246464--246576 Score: 67
Period size: 20 Copynumber: 5.5 Consensus size: 20
246454 AAAAAAATAA
246464 TATAAATATATT-AAA-ATAT
1 TATAAA-ATATTAAAATATAT
*
246483 TA-AAATTTATATAAAATATAT
1 TATAAA-ATAT-TAAAATATAT
246504 TATAAAATATTAAAATTTATAT
1 TATAAAATATTAAAA--TATAT
* *
246526 AAATATAAAAT-TTTAAATACGAT
1 ---TATAAAATATTAAAATA-TAT
246549 TATAAAATA-TAAAA-ATAT
1 TATAAAATATTAAAATATAT
246567 TATATAAATA
1 TATA-AAATA
246577 CATAATATTT
Statistics
Matches: 76, Mismatches: 6, Indels: 24
0.72 0.06 0.23
Matches are distributed among these distances:
18 13 0.17
19 9 0.12
20 20 0.26
21 9 0.12
22 10 0.13
23 2 0.03
24 5 0.07
25 8 0.11
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (20 bp):
TATAAAATATTAAAATATAT
Found at i:246534 original size:25 final size:26
Alignment explanation
Indices: 246504--246568 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
246494 TAAAATATAT
*
246504 TATAAAATATTAAA-A-TTTATATAAA
1 TATAAAATATTAAATACATTATA-AAA
*
246529 TATAAAATTTTAAATACGATTATAAAA
1 TATAAAATATTAAATAC-ATTATAAAA
246556 TATAAAAATATTA
1 TAT-AAAATATTA
246569 TATAAATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 13 0.39
26 1 0.03
27 6 0.18
28 13 0.39
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
TATAAAATATTAAATACATTATAAAA
Found at i:249620 original size:24 final size:25
Alignment explanation
Indices: 249593--249736 Score: 75
Period size: 28 Copynumber: 5.4 Consensus size: 25
249583 TGTATGGACA
249593 TAATTAAAATAATTAAATAA-AAAT
1 TAATTAAAATAATTAAATAATAAAT
*
249617 TAATT-AATTAATTAAATTAATTATATAT
1 TAATTAAAATAATTAAA-TAA-TA-A-AT
249645 TAA--AAAATAATTATAAATAATATAAT
1 TAATTAAAATAA-T-TAAATAATA-AAT
249671 TATGAGTTAAATAAATAATTAAATAA-AAA-
1 TA--A-TT--A-AAATAATTAAATAATAAAT
* *
249700 TAATTAATATAATTTAAATATAACAAAT
1 TAATTAAAATAA-TT-AA-ATAATAAAT
249728 TAATTAAAA
1 TAATTAAAA
249737 ATTATTTATT
Statistics
Matches: 95, Mismatches: 4, Indels: 38
0.69 0.03 0.28
Matches are distributed among these distances:
23 15 0.16
24 11 0.12
25 2 0.02
26 11 0.12
27 14 0.15
28 18 0.19
29 6 0.06
30 2 0.02
31 1 0.01
32 7 0.07
33 2 0.02
34 6 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (25 bp):
TAATTAAAATAATTAAATAATAAAT
Found at i:249629 original size:32 final size:35
Alignment explanation
Indices: 249610--249736 Score: 86
Period size: 33 Copynumber: 3.7 Consensus size: 35
249600 AATAATTAAA
* *
249610 TAAAAATTAATTAATTAATTAAATTAATTATATAT
1 TAAAAAATAATTAATTAATTAAAATAATTATATAT
* * *
249645 TAAAAAATAATT-A-TAAATAATATAATTATGA-GT
1 TAAAAAATAATTAATTAATTAAAATAATTAT-ATAT
*
249678 TAAATAAATAATT-A--AATAAAAATAATTAATATAAT
1 TAAA-AAATAATTAATTAATTAAAATAATT-ATAT-AT
* * **
249713 TTAAATATAACAAATTAATTAAAA
1 TAAAAAATAATTAATTAATTAAAA
249737 ATTATTTATT
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
33 29 0.41
34 18 0.26
35 16 0.23
37 7 0.10
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.38
Consensus pattern (35 bp):
TAAAAAATAATTAATTAATTAAAATAATTATATAT
Found at i:249702 original size:14 final size:15
Alignment explanation
Indices: 249598--249711 Score: 60
Period size: 15 Copynumber: 7.1 Consensus size: 15
249588 GGACATAATT
249598 AAAATAATTAA-ATA
1 AAAATAATTAATATA
249612 AAAATTAATTAAT-TA
1 AAAA-TAATTAATATA
249627 ATTAAATTAATTATATATTAA
1 A--AAA-TAATTA-ATA-T-A
249648 AAAATAATT-ATA-A
1 AAAATAATTAATATA
249661 ATAATATAATT-ATGAGTTAA
1 A-AA-ATAATTAAT-A--T-A
249681 ATAAATAATTAA-ATA
1 A-AAATAATTAATATA
249696 AAAATAATTAATATA
1 AAAATAATTAATATA
249711 A
1 A
249712 TTTAAATATA
Statistics
Matches: 83, Mismatches: 0, Indels: 33
0.72 0.00 0.28
Matches are distributed among these distances:
13 2 0.02
14 16 0.19
15 24 0.29
16 5 0.06
17 10 0.12
18 8 0.10
19 9 0.11
20 7 0.08
21 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
AAAATAATTAATATA
Found at i:249702 original size:18 final size:18
Alignment explanation
Indices: 249679--249738 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
249669 ATTATGAGTT
*
249679 AAATAAATAATTAAATAA
1 AAATAAATAATTAATTAA
*
249697 AAATAATTAATATAATTTAA
1 AAATAAATAAT-TAA-TTAA
*
249717 ATATAACA-AATTAATTAA
1 AAATAA-ATAATTAATTAA
249735 AAAT
1 AAAT
249739 TATTTATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 17 0.50
19 6 0.18
20 11 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAATAATTAATTAA
Found at i:249732 original size:42 final size:41
Alignment explanation
Indices: 249602--249735 Score: 114
Period size: 42 Copynumber: 3.2 Consensus size: 41
249592 ATAATTAAAA
249602 TAATTAAATAAAAATTAATTAAT-TAA-TTAAATTAATTATATAT
1 TAATTAAATAAAAA-TAATTAATATAATTTAAATTAA--ATA-AT
* ** * * * *
249645 TAA-AAAATAATTATAAATAATATAATTATGAGTTAAATAAA
1 TAATTAAATAAAAATAATTAATATAATT-TAAATTAAATAAT
249686 TAATTAAATAAAAATAATTAATATAATTTAAATATAACA-AAT
1 TAATTAAATAAAAATAATTAATATAATTTAAAT-TAA-ATAAT
249728 TAATTAAA
1 TAATTAAA
249736 AATTATTTAT
Statistics
Matches: 71, Mismatches: 14, Indels: 13
0.72 0.14 0.13
Matches are distributed among these distances:
41 14 0.20
42 46 0.65
43 5 0.07
44 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (41 bp):
TAATTAAATAAAAATAATTAATATAATTTAAATTAAATAAT
Found at i:250667 original size:14 final size:14
Alignment explanation
Indices: 250643--250692 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
250633 TATGTCATGT
250643 TAAATAA-TTAATA
1 TAAATAATTTAATA
*
250656 TAAATAATTTAATG
1 TAAATAATTTAATA
250670 TAAATAATTTGAA-A
1 TAAATAATTT-AATA
*
250684 TAAAAAATT
1 TAAATAATT
250693 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 7 0.22
14 23 0.72
15 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (14 bp):
TAAATAATTTAATA
Found at i:250694 original size:27 final size:28
Alignment explanation
Indices: 250619--250694 Score: 68
Period size: 28 Copynumber: 2.7 Consensus size: 28
250609 TTATATTTAT
* *
250619 ATTTGATAATAAAATATGTCATGTTAAATA
1 ATTTGA-AATAAAAAAT-TAATGTTAAATA
*
250649 A-TT-AATATAAATAATTTAATG-TAAATA
1 ATTTGAA-ATAAA-AAATTAATGTTAAATA
250676 ATTTGAAATAAAAAATTAA
1 ATTTGAAATAAAAAATTAA
250695 AATAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
27 14 0.37
28 17 0.45
29 6 0.16
30 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (28 bp):
ATTTGAAATAAAAAATTAATGTTAAATA
Found at i:250765 original size:14 final size:14
Alignment explanation
Indices: 250748--250790 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
250738 ACTAATAAAA
250748 TTAATATAAATAAT
1 TTAATATAAATAAT
*
250762 TTAATGTAAATAAT
1 TTAATATAAATAAT
*
250776 TTGAA-ATAAAAAAT
1 TT-AATATAAATAAT
250790 T
1 T
250791 AAATTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 23 0.92
15 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (14 bp):
TTAATATAAATAAT
Found at i:251125 original size:36 final size:35
Alignment explanation
Indices: 251049--251135 Score: 88
Period size: 36 Copynumber: 2.5 Consensus size: 35
251039 CTTACCCTTA
** *
251049 ATATAATTATTAATATATTAATAATTTATATAAAT
1 ATATAATTATTAATATATTAATAATAAATAAAAAT
* *
251084 TTATAATATTTTAATATAATT-ATAATAAATAAAAAT
1 ATATAAT-TATTAATAT-ATTAATAATAAATAAAAAT
*
251120 ATATAAATA-TAATATA
1 ATATAATTATTAATATA
251136 AATTTATGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
33 1 0.02
34 6 0.14
35 7 0.17
36 25 0.60
37 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAATTATTAATATATTAATAATAAATAAAAAT
Found at i:251895 original size:2 final size:2
Alignment explanation
Indices: 251888--251956 Score: 53
Period size: 2 Copynumber: 38.0 Consensus size: 2
251878 TTTGACAATT
* * *
251888 TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA TA TA TT TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
251928 TA T- TA -A T- TA TA TA AA TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
251957 AATTATTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
1 7 0.13
2 48 0.87
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:258240 original size:2 final size:2
Alignment explanation
Indices: 258228--258269 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
258218 TAGTAGTAAT
*
258228 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
258268 TA
1 TA
258270 CTTTAGTACA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:258425 original size:14 final size:15
Alignment explanation
Indices: 258401--258429 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
258391 ATATTTTATT
258401 AATTATATAAATATA
1 AATTATATAAATATA
258416 AATTAT-TAAATATA
1 AATTATATAAATATA
258430 TTATAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTATATAAATATA
Found at i:258757 original size:20 final size:20
Alignment explanation
Indices: 258717--258755 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
258707 TAGATAGTTA
*
258717 AAAAATTTAAATTTAAATTT
1 AAAAATTTAAAGTTAAATTT
258737 AAAAATTT-AAGTTAAATTT
1 AAAAATTTAAAGTTAAATTT
258756 TATTGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
AAAAATTTAAAGTTAAATTT
Found at i:258777 original size:13 final size:13
Alignment explanation
Indices: 258719--258777 Score: 52
Period size: 14 Copynumber: 4.6 Consensus size: 13
258709 GATAGTTAAA
258719 AAATTT-AAATTT
1 AAATTTAAAATTT
258731 AAATTTAAAAATTT
1 AAATTT-AAAATTT
*
258745 -AAGTT-AAATTT
1 AAATTTAAAATTT
* *
258756 TATTGTTAAAATTT
1 AAAT-TTAAAATTT
258770 AAATTTAA
1 AAATTTAA
258778 TTTGATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
11 6 0.16
12 7 0.19
13 10 0.27
14 14 0.38
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:259965 original size:21 final size:21
Alignment explanation
Indices: 259923--259965 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
259913 GATTAAAAAT
* *
259923 TTTAAATATTAAATTTATTAA
1 TTTAAATATTAAAATAATTAA
259944 TTTAAA-ATTAAAATAATGTAA
1 TTTAAATATTAAAATAAT-TAA
259965 T
1 T
259966 GATTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTAAATATTAAAATAATTAA
Found at i:260814 original size:3 final size:3
Alignment explanation
Indices: 260806--260840 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
260796 GGTCAGCTCT
260806 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
260841 TATATTAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:265890 original size:14 final size:14
Alignment explanation
Indices: 265871--265909 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 14
265861 TATGATTAAA
265871 AAAAATAATATAAT
1 AAAAATAATATAAT
265885 AAAAAT--TAT-AT
1 AAAAATAATATAAT
265896 AAAAATAATATAAT
1 AAAAATAATATAAT
265910 TATGTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 8 0.36
12 3 0.14
13 3 0.14
14 8 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAATAATATAAT
Found at i:265965 original size:20 final size:20
Alignment explanation
Indices: 265942--265987 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
265932 ATTTAAATTG
265942 ATATAAACAATATTAT-T-AAT
1 ATATAAA-AAT-TTATATAAAT
*
265962 ATATTAAAATTTATATAAAT
1 ATATAAAAATTTATATAAAT
265982 ATATAA
1 ATATAA
265988 TATTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAAAAATTTATATAAAT
Found at i:266443 original size:3 final size:3
Alignment explanation
Indices: 266432--266464 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
266422 CTATTACTAC
*
266432 TAT TCT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
266465 AGTTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:267036 original size:15 final size:15
Alignment explanation
Indices: 266990--267038 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
266980 ATTCAAGCTA
*
266990 AAATTACTTAAATTT
1 AAATTATTTAAATTT
*
267005 TAATTATTTTAAATTT
1 AAATTA-TTTAAATTT
267021 AAATTA-TTAAAGTTT
1 AAATTATTTAAA-TTT
267036 AAA
1 AAA
267039 ATCAAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 5 0.17
15 11 0.38
16 13 0.45
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
AAATTATTTAAATTT
Found at i:267204 original size:2 final size:2
Alignment explanation
Indices: 267197--267224 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
267187 AATTAAAAAC
267197 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
267225 AAAACAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:268182 original size:7 final size:7
Alignment explanation
Indices: 268170--268203 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
268160 TGATTGAAAA
268170 AAATGCT
1 AAATGCT
268177 AAATGCT
1 AAATGCT
*
268184 AAATACT
1 AAATGCT
*
268191 AAATACT
1 AAATGCT
268198 AAATGC
1 AAATGC
268204 GAGCCGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (7 bp):
AAATGCT
Found at i:270405 original size:2 final size:2
Alignment explanation
Indices: 270398--270425 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
270388 TATATTAGTG
270398 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
270426 GATGAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:272797 original size:20 final size:20
Alignment explanation
Indices: 272759--272797 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
272749 TTGGTTTTTA
* *
272759 TATTTAATTTTTAATTTAAT
1 TATTTAATTTTAAAATTAAT
*
272779 TATTTGATTTTAAAATTAA
1 TATTTAATTTTAAAATTAA
272798 ATTTAAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTTAATTTTAAAATTAAT
Found at i:283098 original size:28 final size:28
Alignment explanation
Indices: 283060--283129 Score: 92
Period size: 27 Copynumber: 2.5 Consensus size: 28
283050 AAACAAGCCT
*
283060 CCATATTTGACAAATC-CAAAGGA-AACCA
1 CCATTTTTGACAAATCACAAA--ATAACCA
283088 CCATTTTTGACAAA-CACAAAATAACCA
1 CCATTTTTGACAAATCACAAAATAACCA
283115 CCATTTTTGACAAAT
1 CCATTTTTGACAAAT
283130 AAATGGGTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.24
Consensus pattern (28 bp):
CCATTTTTGACAAATCACAAAATAACCA
Found at i:284155 original size:19 final size:21
Alignment explanation
Indices: 284116--284165 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
284106 TAATTAGTTG
284116 ATATATTAATTACAATATATA
1 ATATATTAATTACAATATATA
*
284137 ATAT-TTAATTA-AATGTATA
1 ATATATTAATTACAATATATA
*
284156 AT-TAATAATT
1 ATATATTAATT
284166 TTATTTATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 14 0.54
20 7 0.27
21 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
ATATATTAATTACAATATATA
Found at i:284592 original size:20 final size:19
Alignment explanation
Indices: 284560--284604 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
284550 TTCATATATT
*
284560 ATTATATATTAAAAAAATTA
1 ATTA-ATATTAAAAAAACTA
*
284580 ATTAATATCTAAAAACACTA
1 ATTAATAT-TAAAAAAACTA
284600 ATTAA
1 ATTAA
284605 AACTATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAATATTAAAAAAACTA
Found at i:284680 original size:21 final size:19
Alignment explanation
Indices: 284636--284683 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
284626 TTTTTAAAAA
284636 AATT-AATAAAAATAATAT
1 AATTAAATAAAAATAATAT
284654 -ATTAAATACAAAATAATTAT
1 AATTAAATA-AAAATAA-TAT
284674 AATTAAATAA
1 AATTAAATAA
284684 TTTTAATCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.12
18 4 0.15
19 7 0.27
20 4 0.15
21 8 0.31
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTAAATAAAAATAATAT
Found at i:284918 original size:14 final size:15
Alignment explanation
Indices: 284890--284984 Score: 51
Period size: 16 Copynumber: 6.4 Consensus size: 15
284880 TATTTTCAAG
284890 TTATT-TAATATATA
1 TTATTATAATATATA
*
284904 TTATTATAATAATATT
1 TTATTATAAT-ATATA
284920 TTATT-TAA-ATATAA
1 TTATTATAATATAT-A
* *
284934 TAATTAATAAT-TTTA
1 TTATT-ATAATATATA
284949 TTTATTATTTAA-ATATA
1 -TTATTA--TAATATATA
*
284966 TTA-AATAA-ATATA
1 TTATTATAATATATA
284979 TTATTA
1 TTATTA
284985 AAAAAATTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 22
0.67 0.09 0.24
Matches are distributed among these distances:
13 15 0.24
14 10 0.16
15 10 0.16
16 21 0.34
17 6 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATTATAATATATA
Found at i:284930 original size:13 final size:13
Alignment explanation
Indices: 284890--284983 Score: 56
Period size: 13 Copynumber: 7.4 Consensus size: 13
284880 TATTTTCAAG
284890 TTATTTAATATATA
1 TTATTTAA-ATATA
*
284904 TTATTATAATAATATT
1 TTATT-T-A-AATATA
284920 TTATTTAAATATA
1 TTATTTAAATATA
* *
284933 ATAATT-AATA-A
1 TTATTTAAATATA
*
284944 -T-TTT--ATTTA
1 TTATTTAAATATA
284953 TTATTTAAATATA
1 TTATTTAAATATA
**
284966 TTAAATAAATATA
1 TTATTTAAATATA
284979 TTATT
1 TTATT
284984 AAAAAAATTA
Statistics
Matches: 61, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
8 2 0.03
9 3 0.05
10 2 0.03
11 4 0.07
12 4 0.07
13 27 0.44
14 6 0.10
15 2 0.03
16 10 0.16
17 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATTTAAATATA
Found at i:284973 original size:30 final size:28
Alignment explanation
Indices: 284890--284973 Score: 78
Period size: 33 Copynumber: 2.8 Consensus size: 28
284880 TATTTTCAAG
*
284890 TTATTTAATATATATTATTATAATAATATT
1 TTATTTAA-ATATATTA-AATAATAATATT
* *
284920 TTATTTAAATATAATAATTAATAATTTTATTT
1 TTATTTAAATATATTAAATAATAA---TA-TT
284952 ATTATTTAAATATATTAAATAA
1 -TTATTTAAATATATTAAATAA
284974 ATATATTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 6 0.14
29 7 0.16
30 8 0.18
31 2 0.05
32 2 0.05
33 19 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTATTTAAATATATTAAATAATAATATT
Found at i:284983 original size:33 final size:33
Alignment explanation
Indices: 284920--284983 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
284910 TAATAATATT
* *
284920 TTATTTAAATATAATAATTAATAATTTTATTTA
1 TTATTTAAATATAATAATAAATAATATTATTTA
*
284953 TTATTTAAATATATTAAATAAAT-ATATTATT
1 TTATTTAAATATAAT-AATAAATAATATTATT
284984 AAAAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTATTTAAATATAATAATAAATAATATTATTTA
Found at i:285020 original size:21 final size:20
Alignment explanation
Indices: 284968--285022 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
284958 TAAATATATT
*
284968 AAATAAATATATTATTAAAA
1 AAATTAATATATTATTAAAA
* *
284988 AAATTAACATATTACTTAATA
1 AAATTAATATATTA-TTAAAA
*
285009 AAATTTATATATTA
1 AAATTAATATATTA
285023 AATATTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATTAATATATTATTAAAA
Found at i:285954 original size:31 final size:29
Alignment explanation
Indices: 285910--286053 Score: 115
Period size: 31 Copynumber: 5.1 Consensus size: 29
285900 TTTTTAGATT
*
285910 TTTTTAAGGTTAAATTATTTTAAATTTAATA
1 TTTTTAA-TTTAAATTATTTTAAATTTAA-A
* **
285941 ATTTTATATTTAAATTATTTTATTTTTAAA
1 TTTTTA-ATTTAAATTATTTTAAATTTAAA
*
285971 TTATTTAAGTTTAAATTA-ATTAAATTTAAA
1 TT-TTTAA-TTTAAATTATTTTAAATTTAAA
*
286001 TTTTTAATTT--ATTA---T--ATTTAAT
1 TTTTTAATTTAAATTATTTTAAATTTAAA
* *
286023 TTTTTAATTAAAATTATTTTAAATTAAAA
1 TTTTTAATTTAAATTATTTTAAATTTAAA
286052 TT
1 TT
286054 ATTTTTAAAG
Statistics
Matches: 91, Mismatches: 12, Indels: 22
0.73 0.10 0.18
Matches are distributed among these distances:
22 15 0.16
24 5 0.05
26 4 0.04
27 1 0.01
28 3 0.03
29 12 0.13
30 14 0.15
31 36 0.40
32 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTTTAATTTAAATTATTTTAAATTTAAA
Found at i:285983 original size:15 final size:15
Alignment explanation
Indices: 285919--286058 Score: 97
Period size: 16 Copynumber: 9.8 Consensus size: 15
285909 TTTTTTAAGG
285919 TTAAATTATTTTAAAT
1 TTAAATTATTTT-AAT
*
285935 TT-AATAATTTTATAT
1 TTAAATTATTTTA-AT
*
285950 TTAAATTATTTTATTT
1 TTAAATTATTTTA-AT
285966 TTAAATTA-TTTAAGT
1 TTAAATTATTTTAA-T
* *
285981 TTAAATTAATTAAAT
1 TTAAATTATTTTAAT
285996 TTAAA-T-TTTTAAT
1 TTAAATTATTTTAAT
286009 TT--ATTA---T-AT
1 TTAAATTATTTTAAT
286018 TT-AATT-TTTTAAT
1 TTAAATTATTTTAAT
*
286031 TAAAATTATTTTAAAT
1 TTAAATTATTTT-AAT
*
286047 TAAAATTATTTT
1 TTAAATTATTTT
286059 TAAAGATCGA
Statistics
Matches: 102, Mismatches: 8, Indels: 28
0.74 0.06 0.20
Matches are distributed among these distances:
9 4 0.04
10 4 0.04
11 1 0.01
12 2 0.02
13 10 0.10
14 6 0.06
15 35 0.34
16 40 0.39
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (15 bp):
TTAAATTATTTTAAT
Found at i:286014 original size:22 final size:22
Alignment explanation
Indices: 285948--286031 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 22
285938 ATAATTTTAT
*
285948 ATTTAAATTATTTTATTT-TTAA
1 ATTTAAATT-TTTAATTTATTAA
* * * *
285970 ATTATTTAAGTTTAAATTAATTAA
1 A-T-TTAAATTTTTAATTTATTAA
*
285994 ATTTAAATTTTTAATTTATTAT
1 ATTTAAATTTTTAATTTATTAA
*
286016 ATTTAATTTTTTAATT
1 ATTTAAATTTTTAATT
286032 AAAATTATTT
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
22 31 0.65
23 7 0.15
24 10 0.21
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (22 bp):
ATTTAAATTTTTAATTTATTAA
Found at i:288718 original size:20 final size:19
Alignment explanation
Indices: 288680--288718 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
288670 CTAATTAGCA
* *
288680 ATTTCACATATTGTTGATT
1 ATTTCAAATATTCTTGATT
288699 ATTTCAAATATTCCTTGATT
1 ATTTCAAATATT-CTTGATT
288719 GGTTCTGCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (19 bp):
ATTTCAAATATTCTTGATT
Found at i:291789 original size:24 final size:24
Alignment explanation
Indices: 291762--291816 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
291752 TGCACATGAG
291762 ATATATATATA-TAT-AAATATAA
1 ATATATATATATTATCAAATATAA
*
291784 ATATATATATATTATCAAATTTAA
1 ATATATATATATTATCAAATATAA
*
291808 TTATATATA
1 ATATATATA
291817 ATAATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 11 0.38
23 3 0.10
24 15 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATATATATATTATCAAATATAA
Found at i:291814 original size:2 final size:2
Alignment explanation
Indices: 291762--291795 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
291752 TGCACATGAG
* *
291762 AT AT AT AT AT AT AT AA AT AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
291796 TATCAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:297082 original size:20 final size:21
Alignment explanation
Indices: 297053--297114 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
297043 TTTATTATTT
297053 AAAATATATTAAAATATTAAA
1 AAAATATATTAAAATATTAAA
** *
297074 AAAAT-TATTTTATTATTAAA
1 AAAATATATTAAAATATTAAA
* *
297094 ATAATATCTTAAAATCATTAA
1 AAAATATATTAAAAT-ATTAA
297115 TAATTATTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 16 0.52
21 10 0.32
22 5 0.16
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATATATTAAAATATTAAA
Found at i:297638 original size:2 final size:2
Alignment explanation
Indices: 297631--297667 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
297621 CTTCAACCGA
297631 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 A
297668 CACGTGACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:303314 original size:28 final size:29
Alignment explanation
Indices: 303259--303332 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 29
303249 TTATATAAAT
* *
303259 TTTTAAATATATTATTATATTTATATCATA
1 TTTTAATTAT-TTTTTATATTTATATCATA
* * *
303289 -TTTATTTTATTTTTTATA-TTGTATCATC
1 TTTTA-ATTATTTTTTATATTTATATCATA
303317 TTTTAATTATTTTTTA
1 TTTTAATTATTTTTTA
303333 ACTATATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
28 18 0.50
29 15 0.42
30 3 0.08
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (29 bp):
TTTTAATTATTTTTTATATTTATATCATA
Found at i:305464 original size:11 final size:11
Alignment explanation
Indices: 305450--305490 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
305440 TTTTTTTAAA
305450 TAAAATTTATT
1 TAAAATTTATT
305461 TAAAATTTATT
1 TAAAATTTATT
*
305472 T-TAATTTAATT
1 TAAAATTT-ATT
305483 TAAAATTT
1 TAAAATTT
305491 TATTAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 5 0.19
11 16 0.62
12 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TAAAATTTATT
Found at i:305496 original size:21 final size:21
Alignment explanation
Indices: 305453--305497 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
305443 TTTTAAATAA
*
305453 AATTTATTTAAAATTTATTTT
1 AATTTATTTAAAATTTATATT
305474 AATTTAATTTAAAATTT-TATT
1 AATTT-ATTTAAAATTTATATT
305495 AAT
1 AAT
305498 AATTATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTTATTTAAAATTTATATT
Done.