Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008973.1 Hibiscus syriacus cultivar Beakdansim tig00112319_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: 2070395
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:188462 original size:15 final size:15
Alignment explanation
Indices: 188442--188495 Score: 72
Period size: 15 Copynumber: 3.4 Consensus size: 15
188432 TAATTTACTT
*
188442 TATATAGTTTTTATA
1 TATATAGTTTATATA
188457 TATATAGGTTATATATA
1 TATATA-GTT-TATATA
188474 TATATAGTTTATATA
1 TATATAGTTTATATA
188489 TACTATA
1 TA-TATA
188496 CATGGTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
15 14 0.40
16 10 0.29
17 11 0.31
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:188473 original size:17 final size:17
Alignment explanation
Indices: 188453--188495 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
188443 ATATAGTTTT
188453 TATATATATAGGTTATA
1 TATATATATAGGTTATA
*
188470 TATATATATAGTTTATA
1 TATATATATAGGTTATA
188487 TATACTATA
1 TATA-TATA
188496 CATGGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (17 bp):
TATATATATAGGTTATA
Found at i:188503 original size:20 final size:20
Alignment explanation
Indices: 188466--188511 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
188456 ATATATAGGT
*
188466 TATATA-TATATATAGTTTA
1 TATATACTATACATAGTTTA
*
188485 TATATACTATACATGGTTTA
1 TATATACTATACATAGTTTA
*
188505 TACATAC
1 TATATAC
188512 ATATTATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (20 bp):
TATATACTATACATAGTTTA
Found at i:189787 original size:2 final size:2
Alignment explanation
Indices: 189780--189815 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
189770 TTCTAGTGAA
189780 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
189816 CAAACCAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:195206 original size:27 final size:27
Alignment explanation
Indices: 195168--195223 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
195158 GCTACTTCAC
195168 TCAGTAGGACCTGGTGAGAGTCAATGG
1 TCAGTAGGACCTGGTGAGAGTCAATGG
195195 TCAGTAGGACCTGGTGAGAGTCAATGG
1 TCAGTAGGACCTGGTGAGAGTCAATGG
195222 TC
1 TC
195224 GCTACTTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.36, T:0.23
Consensus pattern (27 bp):
TCAGTAGGACCTGGTGAGAGTCAATGG
Found at i:197163 original size:21 final size:21
Alignment explanation
Indices: 197103--197163 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
197093 TTACATTAGG
* *
197103 GTTTATGGTTTA-GATTTTAA
1 GTTTAGGGTTTATGATTTAAA
*
197123 GATTTAGTGTTTAT-AGTTTAAA
1 G-TTTAGGGTTTATGA-TTTAAA
197145 GTTTAGGGTTTATGATTTA
1 GTTTAGGGTTTATGATTTA
197164 GGATTTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
20 1 0.03
21 25 0.76
22 7 0.21
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.52
Consensus pattern (21 bp):
GTTTAGGGTTTATGATTTAAA
Found at i:197263 original size:15 final size:15
Alignment explanation
Indices: 197243--197323 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
197233 TAATTTACTT
197243 TATATAGTTTATATA
1 TATATAGTTTATATA
*
197258 TATATAGGTTATATA
1 TATATAGTTTATATA
*
197273 TATAT-GTATATACTA
1 TATATAGTTTATA-TA
* * *
197288 TACATGGTTTATACA
1 TATATAGTTTATATA
* *
197303 TACATGGTTTATATA
1 TATATAGTTTATATA
197318 TATATA
1 TATATA
197324 TATATATAGT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
14 5 0.09
15 44 0.80
16 6 0.11
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:197347 original size:6 final size:7
Alignment explanation
Indices: 197332--197370 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
197322 TATATATATA
197332 GTTTAGG
1 GTTTAGG
*
197339 GGTTAGG
1 GTTTAGG
197346 GTTTAGG
1 GTTTAGG
197353 GTTTAGG
1 GTTTAGG
*
197360 GTTTAAG
1 GTTTAGG
197367 GTTT
1 GTTT
197371 CTATAAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:197741 original size:14 final size:14
Alignment explanation
Indices: 197718--197757 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
197708 TTATATTAGG
*
197718 GTTTAGGGTTTAAA
1 GTTTATGGTTTAAA
**
197732 GTTTATGGTTTATG
1 GTTTATGGTTTAAA
197746 GTTTATGGTTTA
1 GTTTATGGTTTA
197758 GGATTTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.53
Consensus pattern (14 bp):
GTTTATGGTTTAAA
Found at i:198272 original size:2 final size:2
Alignment explanation
Indices: 198265--198328 Score: 101
Period size: 2 Copynumber: 31.0 Consensus size: 2
198255 ACCCCTAATA
198265 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
*
198307 AT AGT TT AT AT AT ACT AT AT AT
1 AT A-T AT AT AT AT A-T AT AT AT
198329 GGTTTATACA
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 55 0.95
3 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:198333 original size:20 final size:18
Alignment explanation
Indices: 198265--198336 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
198255 ACCCCTAATA
* *
198265 ATATATATATATATATAT
1 ATATATATATGTTTATAT
* *
198283 ATATATATATATATATAT
1 ATATATATATGTTTATAT
198301 ATATATATA-GTTTATAT
1 ATATATATATGTTTATAT
198318 ATACTATATATGGTTTATA
1 ATA-TATATAT-GTTTATA
198337 CATACATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.18
18 33 0.67
20 7 0.14
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (18 bp):
ATATATATATGTTTATAT
Found at i:198341 original size:20 final size:20
Alignment explanation
Indices: 198266--198351 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 20
198256 CCCCTAATAA
* *
198266 TATATATA-TATATATATA-
1 TATATATAGTTTATACATAC
* *
198284 TATATATA-TATATATATA-
1 TATATATAGTTTATACATAC
*
198302 TATATATAGTTTATATATAC
1 TATATATAGTTTATACATAC
*
198322 TATATATGGTTTATACATAC
1 TATATATAGTTTATACATAC
198342 ATATTATATA
1 -TA-TATATA
198352 AAATTATTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
18 26 0.43
19 9 0.15
20 18 0.30
21 2 0.03
22 5 0.08
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TATATATAGTTTATACATAC
Found at i:198359 original size:13 final size:13
Alignment explanation
Indices: 198349--198374 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
198339 TACATATTAT
198349 ATAAAATTATTTA
1 ATAAAATTATTTA
198362 ATAAAATTATTTA
1 ATAAAATTATTTA
198375 GATGTTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:199227 original size:24 final size:25
Alignment explanation
Indices: 199174--199229 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
199164 TCCATATAAA
* *
199174 AAATCAGAACATAATTCAGGTAATG
1 AAATCAGAACATAATTCAAGCAATG
* *
199199 -TATCAGAACATAATTCAAGCCA-G
1 AAATCAGAACATAATTCAAGCAATG
199222 AAATCAGA
1 AAATCAGA
199230 TAAAATATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.21
Consensus pattern (25 bp):
AAATCAGAACATAATTCAAGCAATG
Found at i:203894 original size:24 final size:24
Alignment explanation
Indices: 203860--203930 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
203850 AAATGGAGAT
203860 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
203884 ATCAGATATCATAATAGAATCCAT
1 ATCAGAAATCAAAACAGAATTCAG
*
203908 ATCAGAAATCAGAACAGAATTCA
1 ATCAGAAATCAAAACAGAATTCA
203931 AGTAATGTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:203942 original size:48 final size:48
Alignment explanation
Indices: 203858--203968 Score: 129
Period size: 48 Copynumber: 2.3 Consensus size: 48
203848 GTAAATGGAG
* * *
203858 ATATCAGAAATCAAAACAGAATTCAGATCAGATATCATAATAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAATAGAATCC
**
203906 ATATCAGAAATCAGAACAGAATTCA-AGTAATG-TATCAGAATAGAATTT
1 ATATCAGAAATCAGAACAGAATTCAGA-TAA-GATATCAGAATAGAATCC
203954 A-AGTCAGAAATCAGA
1 ATA-TCAGAAATCAGA
203969 TAAAATATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
47 2 0.04
48 52 0.95
49 1 0.02
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.23
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAATAGAATCC
Found at i:203966 original size:24 final size:24
Alignment explanation
Indices: 203861--203968 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
203851 AATGGAGATA
*
203861 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * * *
203884 ATCAGATATCATAATAGAATCCATA-
1 -TCAGAAATCAGAACAGAATTCA-AG
203909 TCAGAAATCAGAACAGAATTCAAG
1 TCAGAAATCAGAACAGAATTCAAG
* * * *
203933 TAATG-TATCAGAATAGAATTTAAG
1 TCA-GAAATCAGAACAGAATTCAAG
203957 TCAGAAATCAGA
1 TCAGAAATCAGA
203969 TAAAATATTT
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
23 2 0.03
24 61 0.94
25 1 0.02
26 1 0.02
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:206533 original size:22 final size:23
Alignment explanation
Indices: 206501--206549 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
206491 CCACCTTTTG
*
206501 CAAATATTTACGA-AACTAACACC
1 CAAATATTTAC-ACAAATAACACC
206524 CAAAT-TTTACACAAATAACACC
1 CAAATATTTACACAAATAACACC
206546 CAAA
1 CAAA
206550 CAGAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 1 0.04
22 18 0.75
23 5 0.21
ACGTcount: A:0.51, C:0.27, G:0.02, T:0.20
Consensus pattern (23 bp):
CAAATATTTACACAAATAACACC
Found at i:208622 original size:24 final size:24
Alignment explanation
Indices: 208588--208659 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
208578 AAATAGAGAT
*
208588 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
208612 ATCAGATATCAGAATAGAATCCAT
1 ATCAGAAATCAGAACAGAATTCAG
*
208636 ATCATAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
208660 GTAATGTATC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:208652 original size:48 final size:48
Alignment explanation
Indices: 208586--208679 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
208576 GTAAATAGAG
*
208586 ATATCAGAAATCAAAACAGAATTCAGATCA-GATATCAGAATAGAATCC
1 ATATCAGAAATCAAAACAGAATTCAGATAATG-TATCAGAATAGAATCC
* * *
208634 ATATCATAAATCAGAACAGAATTCAGGTAATGTATCAGAATAGAAT
1 ATATCAGAAATCAAAACAGAATTCAGATAATGTATCAGAATAGAAT
208680 TTAAGTTGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 40 0.98
49 1 0.02
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAGAATTCAGATAATGTATCAGAATAGAATCC
Found at i:211143 original size:17 final size:18
Alignment explanation
Indices: 211121--211163 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
211111 CGTTTAATTT
* *
211121 ACGGTCAACTG-TGGTTA
1 ACGGTCAACTGCAGGTCA
211138 ACGGTCAA-TGCAGGTCA
1 ACGGTCAACTGCAGGTCA
211155 ACGGTCAAC
1 ACGGTCAAC
211164 AGTCGACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (18 bp):
ACGGTCAACTGCAGGTCA
Found at i:215940 original size:57 final size:57
Alignment explanation
Indices: 215845--216016 Score: 263
Period size: 57 Copynumber: 3.0 Consensus size: 57
215835 GTTGGAGGAA
* * * *
215845 GAATACTTGCGGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTTGTGACGGGGTT
1 GAATACTTGCAGGTTCCTTGGCTTTGTGCTGAGGGCCTTACTGTTCGTGACGGGGTT
* * *
215902 GAATACTTGTAGGTTCCTTGACTTTGTGTTGAGGGCCTTACTGTTCGTGACGGGGTT
1 GAATACTTGCAGGTTCCTTGGCTTTGTGCTGAGGGCCTTACTGTTCGTGACGGGGTT
* *
215959 GAATACTTGCAGGTTCCTTGGCTTTGTGCTCAGGGCCTTACTGTTCGTGATGGGGTT
1 GAATACTTGCAGGTTCCTTGGCTTTGTGCTGAGGGCCTTACTGTTCGTGACGGGGTT
216016 G
1 G
216017 TATGGTTATA
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 103 1.00
ACGTcount: A:0.13, C:0.18, G:0.33, T:0.37
Consensus pattern (57 bp):
GAATACTTGCAGGTTCCTTGGCTTTGTGCTGAGGGCCTTACTGTTCGTGACGGGGTT
Found at i:216191 original size:27 final size:27
Alignment explanation
Indices: 216161--216220 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
216151 ATTATGATCT
216161 CCTGAACCTAGACATCTGAAATATTTC
1 CCTGAACCTAGACATCTGAAATATTTC
216188 CCTGAACCTAGACATCTGAAATATTTC
1 CCTGAACCTAGACATCTGAAATATTTC
216215 CCTGAA
1 CCTGAA
216221 ATAAACTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (27 bp):
CCTGAACCTAGACATCTGAAATATTTC
Found at i:217321 original size:42 final size:42
Alignment explanation
Indices: 217276--217519 Score: 353
Period size: 42 Copynumber: 5.8 Consensus size: 42
217266 GGTTTTATCC
* * *
217276 TTGCACACAGCAAAGGAACCTGGGAAATTGTAATGCTTACCC
1 TTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCT
*
217318 TTGCACACAACAAAGGAACCTGGGGAAACTGTAAGGCTTACCT
1 TTGCACACAGCAAAGGAACCT-GGGAAACTGTAAGGCTTACCT
* * **
217361 TTTCACACAGCAAAAGAACCTGGGAAACTGTAATACTTACCT
1 TTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCT
* * *
217403 TTTCACATAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCT
1 TTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCT
*
217445 TTGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCT
1 TTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCT
* *
217487 TTGCACACAGTAAATGAACCTGGGAAACTGTAA
1 TTGCACACAGCAAAGGAACCTGGGAAACTGTAA
217520 CGGTAATTAA
Statistics
Matches: 182, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 146 0.80
43 36 0.20
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (42 bp):
TTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCT
Found at i:217499 original size:22 final size:22
Alignment explanation
Indices: 217432--217499 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
217422 CTGGGAAACT
217432 GTAAGGCTTACCTTTGCACACA
1 GTAAGGCTTACCTTTGCACACA
* * * * * *
217454 GCAAAGG--GACC-TGGGAAACT
1 G-TAAGGCTTACCTTTGCACACA
217474 GTAAGGCTTACCTTTGCACACA
1 GTAAGGCTTACCTTTGCACACA
217496 GTAA
1 GTAA
217500 ATGAACCTGG
Statistics
Matches: 30, Mismatches: 12, Indels: 8
0.60 0.24 0.16
Matches are distributed among these distances:
19 4 0.13
20 6 0.20
21 6 0.20
22 10 0.33
23 4 0.13
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (22 bp):
GTAAGGCTTACCTTTGCACACA
Found at i:221562 original size:21 final size:20
Alignment explanation
Indices: 221537--221590 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
221527 TTTATATTAA
*
221537 GGTTTAGGGTTTAATGTTTAG
1 GGTTTAGGGTTTAAAGTTT-G
* *
221558 TGTTTATGGTTTAAAGTTTG
1 GGTTTAGGGTTTAAAGTTTG
221578 GGTTTTAGGGTTT
1 GG-TTTAGGGTTT
221591 CTATAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (20 bp):
GGTTTAGGGTTTAAAGTTTG
Found at i:221679 original size:2 final size:2
Alignment explanation
Indices: 221674--221726 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
221664 TTATATAGTT
* * * * *
221674 TA TA TA TA TA TA TA TG TA TA TG TA TA TG TA TA TG TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
221716 TA TA TA CTA TA
1 TA TA TA -TA TA
221727 CATGGTTTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (2 bp):
TA
Found at i:221699 original size:12 final size:12
Alignment explanation
Indices: 221678--221711 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
221668 ATAGTTTATA
*
221678 TATATATATATG
1 TATATGTATATG
221690 TATATGTATATG
1 TATATGTATATG
221702 TATATGTATA
1 TATATGTATA
221712 AATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (12 bp):
TATATGTATATG
Found at i:221717 original size:18 final size:18
Alignment explanation
Indices: 221677--221721 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
221667 TATAGTTTAT
*
221677 ATATATATATATGTATAT
1 ATATATATATATGTATAA
* *
221695 GTATATGTATATGTATAA
1 ATATATATATATGTATAA
221713 ATATATATA
1 ATATATATA
221722 CTATACATGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (18 bp):
ATATATATATATGTATAA
Found at i:222114 original size:14 final size:14
Alignment explanation
Indices: 222095--222138 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
222085 TCTATTTATA
222095 TTAGGGTTTATAGT
1 TTAGGGTTTATAGT
222109 TTAGGGTTTA-ATGT
1 TTAGGGTTTATA-GT
*
222123 TTAGTGTTTAT-GT
1 TTAGGGTTTATAGT
222136 TTA
1 TTA
222139 AAGTTTAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (14 bp):
TTAGGGTTTATAGT
Found at i:222139 original size:20 final size:20
Alignment explanation
Indices: 222114--222151 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
222104 ATAGTTTAGG
* *
222114 GTTTAATGTTTAGTGTTTAT
1 GTTTAAAGTTTAGGGTTTAT
222134 GTTTAAAGTTTAGGGTTT
1 GTTTAAAGTTTAGGGTTT
222152 CTATAAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (20 bp):
GTTTAAAGTTTAGGGTTTAT
Found at i:222248 original size:17 final size:18
Alignment explanation
Indices: 222226--222264 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
222216 TAATTTACTT
*
222226 TATATATTTTATATATA-
1 TATATAGTTTATATATAC
222243 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
222261 TATA
1 TATA
222265 CATGGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:222272 original size:20 final size:20
Alignment explanation
Indices: 222235--222280 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
222225 TTATATATTT
*
222235 TATATA-TATATATAGTTTA
1 TATATACTATACATAGTTTA
*
222254 TATATACTATACATGGTTTA
1 TATATACTATACATAGTTTA
*
222274 TACATAC
1 TATATAC
222281 ACATTATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (20 bp):
TATATACTATACATAGTTTA
Found at i:222749 original size:561 final size:558
Alignment explanation
Indices: 221293--222692 Score: 2063
Period size: 538 Copynumber: 2.5 Consensus size: 558
221283 GGTTACATGG
* *
221293 TTCATAAATGGTAGTACATGCCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTA
1 TTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTA
* *
221358 GGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATAAATAAGTTATAATAAAACCCAAAAA
66 GGTTAATTCACATTAATAGCCCATTTATTTTGTTATTATGAATAAGTTATAATAAAACCCAAAAA
* *
221423 TAAGTCCATTTGCATTAGTGCTAGTTCATTTACAGTAGTTTACATAGGCCCAATACATAAGCCCA
131 T-AGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCA
* *
221488 CCCTTTTATTACAAATATATATGCATTAGTGCTAGTC-----CATT--TATATTAAGGTTTAGGG
195 CTCTTTTATTACAAATATATATGCATTAGTGCTAGTCATTTACATTAGTAT-TTATGGTTTAGGG
*
221546 TTTAATGTTTAGTGTTTATGGTTTAAAGTTTGGGTTTTAGGGTTTCTATA-AAA-TATATACTTT
259 TTTAATGTTTAGTGTTTAT-GTTTAAAGTTTAGGTTTTA-GGTTTCTATATAAACTATATACTTT
*
221609 ATTACTTTATATAGTTTATGAATAATGTTTCTATAAACTATATAAGTAATTTATTTTATATAGTT
322 ATTACTTTATATAGTTTATGAATAATGTTTCTATAAACTATATAAGTAA--TA--TTATATACTT
221674 TATATATATATATATGTATATGTATATGTATATGTATAAATATATATACTATACATGGTTTATAC
383 TATATATATATATA-GTATA-GTATA-GTATATGTAT--ATATATATACTATACATGGTTTATAC
*
221739 ATACATATTATATAAAATTATTTAATAAAATTAATAAAATAATTTAAATGTAAATTATATAAAAC
443 ATACACATTATATAAAATTATTTAATAAAATTAATAAAATAATTTAAATGTAAATTATATAAAAC
***
221804 ATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGG
508 ATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATACAC
* * *
221855 TTCATAAATAGTTGTATATGTCATATTAATTTCATTTGCATAATTAATATTTTAGTTGCATGTTA
1 TTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTA
*
221920 GGTTAATTCCCATTAATAGCCCATTTATTTTGTTATTATGAATAAGTTATAATAAAACCCAAAAA
66 GGTTAATTCACATTAATAGCCCATTTATTTTGTTATTATGAATAAGTTATAATAAAACCCAAAAA
221985 TATGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCA
131 TA-GTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCA
* * ** *
222050 CTCTTTTATTACAAATATATATGCATTAATGCTAGTCTATTTATATTAGGGTTTATAGTTTAGGG
195 CTCTTTTATTACAAATATATATGCATTAGTGCTAGTC-ATTTACATTAGTATTTATGGTTTAGGG
222115 TTTAATGTTTAGTGTTTATGTTTAAAGTTTA-G-----GGTTTC--TATAAACTATATACTTTAT
259 TTTAATGTTTAGTGTTTATGTTTAAAGTTTAGGTTTTAGGTTTCTATATAAACTATATACTTTAT
* * *
222172 TACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATGAGT-A-A-T-T-TACTTTATATA
324 TACTTTATATAGTTTATGAATAATGTTTCTATAAACTATATAAGTAATATTATATACTTTATATA
222232 T-T-T-TA-TATA-TATA-TATA-GT-T-TATATATACTATACATGGTTTATACATACACATTAT
389 TATATATAGTATAGTATAGTATATGTATATATATATACTATACATGGTTTATACATACACATTAT
222288 ATAAAATTATTTAATAAAATTAATAAAAGT-ATTTAAATGTAAATTATATAAAACATGATTAATT
454 ATAAAATTATTTAATAAAATTAATAAAA-TAATTTAAATGTAAATTATATAAAACATGATTAATT
*
222352 AGGTGTTAAATAATTAGTATGTCGCATTGCATATTATACAC
518 AGGTGTTAAATAATTAGTATGTCACATTGCATATTATACAC
*
222393 TTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTTGTTGCATGTTA
1 TTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTA
* * * *
222458 GGTTAATTCACATTAATAGCCCATTTATTTTGTTCTTATGAATAAGTAATAAAAAAACCAAAAAA
66 GGTTAATTCACATTAATAGCCCATTTATTTTGTTATTATGAATAAGTTATAATAAAACCCAAAAA
* *
222523 TCAGTCTATTTGCATTAGTGCTAGTCCAGTTACATTAGTTTACATAGGCCCAATACATAAGCCCA
131 T-AGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCA
*
222588 CTCTTTTATTAAAAATATATATGCATTAGTGCTAGTCAGTTTACATTAGTATTTATGGTTTAGGG
195 CTCTTTTATTACAAATATATATGCATTAGTGCTAGTCA-TTTACATTAGTATTTATGGTTTAGGG
* * *
222653 TTTAGTATTTAGTGTGTATGATTTAAAGTTTAGGTTTTAG
259 TTTAATGTTTAGTGTTTATG-TTTAAAGTTTAGGTTTTAG
222693 AGTATAGGGT
Statistics
Matches: 770, Mismatches: 47, Indels: 59
0.88 0.05 0.07
Matches are distributed among these distances:
537 1 0.00
538 390 0.51
539 13 0.02
540 1 0.00
541 1 0.00
542 2 0.00
543 4 0.01
545 5 0.01
547 4 0.01
549 2 0.00
550 1 0.00
551 1 0.00
552 11 0.01
553 1 0.00
554 1 0.00
557 1 0.00
559 2 0.00
560 4 0.01
561 61 0.08
562 218 0.28
567 1 0.00
568 14 0.02
569 30 0.04
570 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (558 bp):
TTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTA
GGTTAATTCACATTAATAGCCCATTTATTTTGTTATTATGAATAAGTTATAATAAAACCCAAAAA
TAGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCAC
TCTTTTATTACAAATATATATGCATTAGTGCTAGTCATTTACATTAGTATTTATGGTTTAGGGTT
TAATGTTTAGTGTTTATGTTTAAAGTTTAGGTTTTAGGTTTCTATATAAACTATATACTTTATTA
CTTTATATAGTTTATGAATAATGTTTCTATAAACTATATAAGTAATATTATATACTTTATATATA
TATATAGTATAGTATAGTATATGTATATATATATACTATACATGGTTTATACATACACATTATAT
AAAATTATTTAATAAAATTAATAAAATAATTTAAATGTAAATTATATAAAACATGATTAATTAGG
TGTTAAATAATTAGTATGTCACATTGCATATTATACAC
Found at i:222756 original size:13 final size:13
Alignment explanation
Indices: 222738--222767 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
222728 TAATTTACTT
*
222738 TATATAGTTTATA
1 TATATAGGTTATA
222751 TATATAGGTTATA
1 TATATAGGTTATA
222764 TATA
1 TATA
222768 CTATACATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (13 bp):
TATATAGGTTATA
Found at i:223294 original size:17 final size:17
Alignment explanation
Indices: 223272--223323 Score: 95
Period size: 17 Copynumber: 3.1 Consensus size: 17
223262 ATAATTTACC
223272 ATATATAGTTTATATAT
1 ATATATAGTTTATATAT
*
223289 ATATATAGGTTATATAT
1 ATATATAGTTTATATAT
223306 ATATATAGTTTATATAT
1 ATATATAGTTTATATAT
223323 A
1 A
223324 CTAGACATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (17 bp):
ATATATAGTTTATATAT
Found at i:223495 original size:2 final size:2
Alignment explanation
Indices: 223456--223487 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
223446 TTCTATAAAC
223456 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
223488 CGTATATAAT
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):
TA
Found at i:223782 original size:7 final size:7
Alignment explanation
Indices: 223770--223820 Score: 84
Period size: 7 Copynumber: 7.3 Consensus size: 7
223760 TTCATTTACA
223770 TTAGGGT
1 TTAGGGT
223777 TTAGGGT
1 TTAGGGT
223784 TTAGGGT
1 TTAGGGT
223791 TTAGGGT
1 TTAGGGT
223798 TTAGGGT
1 TTAGGGT
**
223805 TTAAAGT
1 TTAGGGT
223812 TTAGGGT
1 TTAGGGT
223819 TT
1 TT
223821 CTATAAACTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:223917 original size:17 final size:17
Alignment explanation
Indices: 223895--223950 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
223885 TAATTTACTT
* *
223895 TATATAATTTACATATA
1 TATATAGTTTATATATA
*
223912 TATATAGGTTATATATA
1 TATATAGTTTATATATA
223929 TATATAGTTTATATATA
1 TATATAGTTTATATATA
223946 CTATA
1 -TATA
223951 CATGGTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 30 0.88
18 4 0.12
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (17 bp):
TATATAGTTTATATATA
Found at i:223958 original size:20 final size:20
Alignment explanation
Indices: 223921--223966 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
223911 ATATATAGGT
*
223921 TATATA-TATATATAGTTTA
1 TATATACTATACATAGTTTA
*
223940 TATATACTATACATGGTTTA
1 TATATACTATACATAGTTTA
*
223960 TACATAC
1 TATATAC
223967 ATATTATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (20 bp):
TATATACTATACATAGTTTA
Found at i:224316 original size:14 final size:14
Alignment explanation
Indices: 224297--224340 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
224287 TCTATTTATA
224297 TTAGGGTTTATAGT
1 TTAGGGTTTATAGT
224311 TTAGGGTTTA-ATGT
1 TTAGGGTTTATA-GT
*
224325 TTAGTGTTTAT-GT
1 TTAGGGTTTATAGT
224338 TTA
1 TTA
224341 AAGTTTAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (14 bp):
TTAGGGTTTATAGT
Found at i:224341 original size:20 final size:20
Alignment explanation
Indices: 224316--224353 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
224306 ATAGTTTAGG
* *
224316 GTTTAATGTTTAGTGTTTAT
1 GTTTAAAGTTTAGGGTTTAT
224336 GTTTAAAGTTTAGGGTTT
1 GTTTAAAGTTTAGGGTTT
224354 CTATAAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (20 bp):
GTTTAAAGTTTAGGGTTTAT
Found at i:224475 original size:19 final size:19
Alignment explanation
Indices: 224436--224479 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
224426 TTTATATATT
*
224436 TTATATATATATATATAGG
1 TTATATATATATACATAGG
224455 TTATATATACTATACAT-GG
1 TTATATATA-TATACATAGG
224474 TT-TATA
1 TTATATA
224480 CATACACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 6 0.26
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (19 bp):
TTATATATATATACATAGG
Found at i:224537 original size:25 final size:25
Alignment explanation
Indices: 224487--224547 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
224477 ATACATACAC
*
224487 ATTATATAAAATTATTTAATAATAAA
1 ATTATATAAAAGTATTTAATAAT-AA
*
224513 ATTA-ATAAAAGTATTTAA-ATGTAA
1 ATTATATAAAAGTATTTAATA-ATAA
224537 ATTATATAAAA
1 ATTATATAAAA
224548 CATGATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 7 0.23
25 20 0.65
26 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (25 bp):
ATTATATAAAAGTATTTAATAATAA
Found at i:224788 original size:13 final size:13
Alignment explanation
Indices: 224770--224820 Score: 93
Period size: 13 Copynumber: 3.9 Consensus size: 13
224760 TACATTAGTT
*
224770 TACATAGGCCCAA
1 TACATAAGCCCAA
224783 TACATAAGCCCAA
1 TACATAAGCCCAA
224796 TACATAAGCCCAA
1 TACATAAGCCCAA
224809 TACATAAGCCCA
1 TACATAAGCCCA
224821 CTCTTTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.43, C:0.31, G:0.10, T:0.16
Consensus pattern (13 bp):
TACATAAGCCCAA
Found at i:224917 original size:35 final size:35
Alignment explanation
Indices: 224878--224944 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
224868 AGTATTTATG
* * * *
224878 GTTTAGGGTTTAGTGTTTAGTGTGTATGATTTAAA
1 GTTTAGGGTTTAGAGTATAGGGTCTATGATTTAAA
*
224913 GTTTAGGTTTTAGAGTATAGGGTCTATGATTT
1 GTTTAGGGTTTAGAGTATAGGGTCTATGATTT
224945 CTATAAACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.48
Consensus pattern (35 bp):
GTTTAGGGTTTAGAGTATAGGGTCTATGATTTAAA
Found at i:224991 original size:15 final size:15
Alignment explanation
Indices: 224971--225024 Score: 81
Period size: 15 Copynumber: 3.4 Consensus size: 15
224961 TAATTTACTT
224971 TATATAGTTTATATA
1 TATATAGTTTATATA
224986 TATATAGGTTATATATA
1 TATATA-GTT-TATATA
225003 TATATAGTTTATATA
1 TATATAGTTTATATA
225018 TACTATA
1 TA-TATA
225025 CATGGTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
15 14 0.39
16 10 0.28
17 12 0.33
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:225000 original size:17 final size:17
Alignment explanation
Indices: 224971--225024 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
224961 TAATTTACTT
224971 TATATA-GTT-TATATA
1 TATATAGGTTATATATA
224986 TATATAGGTTATATATA
1 TATATAGGTTATATATA
*
225003 TATATAGTTTATATATA
1 TATATAGGTTATATATA
225020 CTATA
1 -TATA
225025 CATGGTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
15 6 0.17
16 3 0.09
17 22 0.63
18 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (17 bp):
TATATAGGTTATATATA
Found at i:225032 original size:20 final size:20
Alignment explanation
Indices: 224995--225040 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
224985 ATATATAGGT
*
224995 TATATA-TATATATAGTTTA
1 TATATACTATACATAGTTTA
*
225014 TATATACTATACATGGTTTA
1 TATATACTATACATAGTTTA
*
225034 TACATAC
1 TATATAC
225041 ATATTATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (20 bp):
TATATACTATACATAGTTTA
Found at i:225249 original size:553 final size:558
Alignment explanation
Indices: 224234--225347 Score: 1569
Period size: 553 Copynumber: 2.0 Consensus size: 558
224224 GTTTACAAAG
* * * *
224234 GCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCTATTTATATT
1 GCCCAATACATAAGCCCACTCTTTTATTAAAAATATATATGCATTAGTGCTAGTCCAGTTACATT
* *
224299 AGGGTTTATAGTTTAGGGTTTAATGTTTAGTGTTTATGTTTAAAGTTTAGGGTTTCTATAAACTA
66 AGGATTTATAGTTTAGGGTTTAATGTTTAGTGTGTATGTTTAAAGTTTAGGGTTTCTATAAACTA
* * * * * * ** *
224364 TATACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATGAGTAATTTACTTT
131 TAGACTCTATGACTTTATAAACTATAT-CATAGTGAATCTAT-AACTATATGAGTAATTTACTAT
**
224429 ATATATTTTATATATATATATATAGGTTATATATACTATACATGGTTTATACATACACATTATAT
194 ATATATGGTATATATATATATATAGGTTATATATACTATACATGGTTTATACATACACATTATAT
* *
224494 AAAATTATTTAATAATAAAATTAATAAAAGTATTTAAATGTAAATTATATAAAACATGATTAATT
259 AAAATTATTT-ATAATAAAATTAAAAAAATTATTTAAATGTAAATTATATAAAACATGATTAATT
*
224559 AGGTGTTAAATAATTAGTATGTCACATTGCATATTATATACTTCATAAATAGTAGTACATGTCAT
323 AGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGCTTCATAAATAGTAGTACATGTCAT
*
224624 ATTAATTTCATTTGCATAATTAGTATTTTTGTTGCATGTTAGGTTAATTCACATTAATAGCCCAT
388 ATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCAT
* *
224689 TTATTTTGTTCTTATGAATAAGTAATAATAAAACCAAAAAATAAGTCTAATTGCATTAGTGCTAG
453 TTATTTTGTTCTTATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATTAGTGCTAG
*
224754 TCCAGTTACATTAGTTTACATAGGCCCAATACATAAGCCCAATACATAA
518 TCCATTTACATTAGTTTACATAGGCCCAATACATAAG-CC----C---A
*
224803 GCCCAATACATAAGCCCACTCTTTTATTAAAAATATATATGCATTAGTGCTAGTCCGGTTACATT
1 GCCCAATACATAAGCCCACTCTTTTATTAAAAATATATATGCATTAGTGCTAGTCCAGTTACATT
* * * * *
224868 AGTATTTATGGTTTAGGGTTTAGTGTTTAGTGTGTATGATTTAAAGTTTA-GG-TT-T-TAGAGT
66 AGGATTTATAGTTTAGGGTTTAATGTTTAGTGTGTATG-TTTAAAGTTTAGGGTTTCTATAAACT
** * * *
224929 ATAGGGTCTATGATTTCTATAAACTATAT-A-AGT-AAT-T-T-ACTTTAT-A-TAGTTTA-TAT
130 ATAGACTCTATGACTT-TATAAACTATATCATAGTGAATCTATAACTATATGAGTAATTTACTAT
* *
224985 ATATATAGGT-TATATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTATA
194 ATATAT-GGTATATATATATATATAGGTTATATATACTATACATGGTTTATACATACACATTATA
*
225049 TAAAATTA-TT-TAATAAAATTAAAAAAATTATTTAAATGTAAATGATATAAAACATGATTAATT
258 TAAAATTATTTATAATAAAATTAAAAAAATTATTTAAATGTAAATTATATAAAACATGATTAATT
* * *
225112 AGGTGTTAAATAATTAGTATGTCACATTGCATAATATATGTTTCTTAAATAGTAGTACATGTCAT
323 AGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGCTTCATAAATAGTAGTACATGTCAT
* *
225177 ATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTAACATTAATAACCCAT
388 ATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCAT
* *
225242 TTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAA-TACCATTTGCAATAGTGCTA
453 TTATTTTGTTCTTATGAATAAGTAATAATAAAACCAAAAAATAAGT-CCATTTGCATTAGTGCTA
225306 GTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCA
517 GTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCCCA
225348 CTCTTTTATT
Statistics
Matches: 496, Mismatches: 45, Indels: 32
0.87 0.08 0.06
Matches are distributed among these distances:
545 1 0.00
548 1 0.00
552 3 0.01
553 268 0.54
555 2 0.00
556 68 0.14
557 7 0.01
558 1 0.00
559 6 0.01
561 1 0.00
562 1 0.00
563 1 0.00
564 3 0.01
565 1 0.00
566 14 0.03
567 10 0.02
568 2 0.00
569 95 0.19
570 11 0.02
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (558 bp):
GCCCAATACATAAGCCCACTCTTTTATTAAAAATATATATGCATTAGTGCTAGTCCAGTTACATT
AGGATTTATAGTTTAGGGTTTAATGTTTAGTGTGTATGTTTAAAGTTTAGGGTTTCTATAAACTA
TAGACTCTATGACTTTATAAACTATATCATAGTGAATCTATAACTATATGAGTAATTTACTATAT
ATATGGTATATATATATATATAGGTTATATATACTATACATGGTTTATACATACACATTATATAA
AATTATTTATAATAAAATTAAAAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGG
TGTTAAATAATTAGTATGTCACATTGCATATTATATGCTTCATAAATAGTAGTACATGTCATATT
AATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTA
TTTTGTTCTTATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATTAGTGCTAGTCC
ATTTACATTAGTTTACATAGGCCCAATACATAAGCCCA
Found at i:225529 original size:2 final size:2
Alignment explanation
Indices: 225524--225588 Score: 69
Period size: 2 Copynumber: 32.0 Consensus size: 2
225514 AATAATTTAC
* **
225524 TA TA TA TA GTT TA TA TA TA TA TA TA TA TA GG T- 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
*
225566 TA TA TA TA TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA
225589 CTAGACATGG
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
1 1 0.02
2 50 0.94
3 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:225538 original size:25 final size:23
Alignment explanation
Indices: 225514--225584 Score: 83
Period size: 25 Copynumber: 3.0 Consensus size: 23
225504 AAACTATATA
*
225514 AATAATTTACTATATATAGTTTAT
1 AATAATATA-TATATATAGTTTAT
*
225538 -AT-ATATATATATATAGGTTAT
1 AATAATATATATATATAGTTTAT
225559 ATATATATATATATATATAGTTTAT
1 A-ATA-ATATATATATATAGTTTAT
225584 A
1 A
225585 TATACTAGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 13 0.32
22 4 0.10
23 4 0.10
25 19 0.47
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (23 bp):
AATAATATATATATATAGTTTAT
Found at i:225550 original size:21 final size:21
Alignment explanation
Indices: 225524--225588 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 21
225514 AATAATTTAC
225524 TATATATAGTTTATATATATA
1 TATATATAGTTTATATATATA
225545 TATATATAGGTTATATATATATATA
1 TATATATA-G-T-T-TATATATATA
225570 TATATATAGTTTATATATA
1 TATATATAGTTTATATATA
225589 CTAGACATGG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
21 16 0.40
22 2 0.05
23 2 0.05
24 2 0.05
25 18 0.45
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (21 bp):
TATATATAGTTTATATATATA
Found at i:225585 original size:25 final size:25
Alignment explanation
Indices: 225535--225588 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
225525 ATATATAGTT
225535 TATATATATATATATATAGGTTATA
1 TATATATATATATATATAGGTTATA
*
225560 TATATATATATATATATAGTTTATA
1 TATATATATATATATATAGGTTATA
225585 TATA
1 TATA
225589 CTAGACATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (25 bp):
TATATATATATATATATAGGTTATA
Found at i:226035 original size:7 final size:7
Alignment explanation
Indices: 226019--226056 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
226009 TTCATTTACA
226019 TTAGGGT
1 TTAGGGT
*
226026 TTATGGT
1 TTAGGGT
*
226033 TTAGTGT
1 TTAGGGT
226040 TTAGGGT
1 TTAGGGT
226047 TTAGGGT
1 TTAGGGT
226054 TTA
1 TTA
226057 AAGTTTAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (7 bp):
TTAGGGT
Found at i:226062 original size:14 final size:14
Alignment explanation
Indices: 226019--226069 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
226009 TTCATTTACA
*
226019 TTAGGGTTTATGGT
1 TTAGGGTTTAAGGT
* *
226033 TTAGTGTTTAGGGT
1 TTAGGGTTTAAGGT
*
226047 TTAGGGTTTAAAGT
1 TTAGGGTTTAAGGT
*
226061 TTAAGGTTT
1 TTAGGGTTT
226070 CTATAAACTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
TTAGGGTTTAAGGT
Found at i:226062 original size:21 final size:21
Alignment explanation
Indices: 226019--226069 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
226009 TTCATTTACA
* **
226019 TTAGGGTTTATGGTTTAGTGT
1 TTAGGGTTTAGGGTTTAAAGT
226040 TTAGGGTTTAGGGTTTAAAGT
1 TTAGGGTTTAGGGTTTAAAGT
*
226061 TTAAGGTTT
1 TTAGGGTTT
226070 CTATAAACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (21 bp):
TTAGGGTTTAGGGTTTAAAGT
Found at i:226161 original size:2 final size:2
Alignment explanation
Indices: 226156--226207 Score: 52
Period size: 2 Copynumber: 25.5 Consensus size: 2
226146 TATAATTTAC
* * *
226156 AT AT AT AT AT AT AT AT AT AT AG GT -T AT AT AT AT AT AGT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
226198 AT AT ACT AT A
1 AT AT A-T AT A
226208 CATGGTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
1 1 0.02
2 38 0.90
3 3 0.07
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:226164 original size:15 final size:15
Alignment explanation
Indices: 226144--226207 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
226134 TAATTTACTT
*
226144 TATATAATTTACATA
1 TATATAATTTATATA
226159 TATAT-A--TATATA
1 TATATAATTTATATA
**
226171 TATATAGGTTATATA
1 TATATAATTTATATA
*
226186 TATATAGTTTATATA
1 TATATAATTTATATA
226201 TACTATA
1 TA-TATA
226208 CATGGTTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
12 10 0.24
14 1 0.02
15 27 0.64
16 4 0.10
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (15 bp):
TATATAATTTATATA
Found at i:226185 original size:13 final size:14
Alignment explanation
Indices: 226156--226202 Score: 64
Period size: 15 Copynumber: 3.5 Consensus size: 14
226146 TATAATTTAC
226156 ATATATATA--TAT
1 ATATATATAGTTAT
226168 ATATATATAGGTTAT
1 ATATATATA-GTTAT
226183 ATATATATAGTT-T
1 ATATATATAGTTAT
226196 ATATATA
1 ATATATA
226203 CTATACATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.28
13 8 0.25
14 3 0.09
15 12 0.38
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (14 bp):
ATATATATAGTTAT
Found at i:226523 original size:14 final size:14
Alignment explanation
Indices: 226504--226547 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
226494 TCTAATTATA
226504 TTAGGGTTTATAGT
1 TTAGGGTTTATAGT
226518 TTAGGGTTTA-ATGT
1 TTAGGGTTTATA-GT
*
226532 TTAGTGTTTAT-GT
1 TTAGGGTTTATAGT
226545 TTA
1 TTA
226548 AAGTTTAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (14 bp):
TTAGGGTTTATAGT
Found at i:226548 original size:20 final size:20
Alignment explanation
Indices: 226523--226560 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
226513 ATAGTTTAGG
* *
226523 GTTTAATGTTTAGTGTTTAT
1 GTTTAAAGTTTAGGGTTTAT
226543 GTTTAAAGTTTAGGGTTT
1 GTTTAAAGTTTAGGGTTT
226561 CTATAAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (20 bp):
GTTTAAAGTTTAGGGTTTAT
Found at i:226655 original size:15 final size:15
Alignment explanation
Indices: 226635--226671 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
226625 TAATTTACTT
*
226635 TATATATTTTATATA
1 TATATAGTTTATATA
226650 TATATAGTTTATATA
1 TATATAGTTTATATA
226665 TACTATA
1 TA-TATA
226672 CATGGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:226716 original size:23 final size:25
Alignment explanation
Indices: 226690--226747 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 25
226680 ATACATACAC
*
226690 ATTATATAAAATTATTT-AAT-AAA
1 ATTATATAAAAGTATTTAAATGAAA
* *
226713 ATTA-ATATAAGTATTTAAATGTAA
1 ATTATATAAAAGTATTTAAATGAAA
226737 ATTATATAAAA
1 ATTATATAAAA
226748 ACATGATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 10 0.36
23 7 0.25
24 6 0.21
25 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATATAAAAGTATTTAAATGAAA
Found at i:226989 original size:13 final size:13
Alignment explanation
Indices: 226971--227008 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
226961 TACATTAGTT
*
226971 TACATAGGCCCAA
1 TACATAAGCCCAA
226984 TACATAAGCCCAA
1 TACATAAGCCCAA
*
226997 TATATAAGCCCA
1 TACATAAGCCCA
227009 CTCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.42, C:0.29, G:0.11, T:0.18
Consensus pattern (13 bp):
TACATAAGCCCAA
Found at i:227181 original size:17 final size:17
Alignment explanation
Indices: 227159--227216 Score: 89
Period size: 17 Copynumber: 3.2 Consensus size: 17
227149 TAATTTACTT
227159 TATATAGTTTATATATA
1 TATATAGTTTATATATA
227176 TATATAGGTTATATATATA
1 TATATA-GTT-TATATATA
227195 TATATAGTTTATATATA
1 TATATAGTTTATATATA
227212 CTATA
1 -TATA
227217 CATGGTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.37
18 10 0.26
19 14 0.37
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (17 bp):
TATATAGTTTATATATA
Found at i:227190 original size:19 final size:19
Alignment explanation
Indices: 227159--227216 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
227149 TAATTTACTT
227159 TATATA-GTT-TATATATA
1 TATATAGGTTATATATATA
227176 TATATAGGTTATATATATA
1 TATATAGGTTATATATATA
*
227195 TATATAGTTTATATATACTA
1 TATATAGGTTATATATA-TA
227215 TA
1 TA
227217 CATGGTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
17 6 0.16
18 3 0.08
19 24 0.65
20 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (19 bp):
TATATAGGTTATATATATA
Found at i:227612 original size:14 final size:14
Alignment explanation
Indices: 227593--227629 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
227583 ACTTTAGGGT
*
227593 TTTATGGTTTAGAG
1 TTTATGGTTTAAAG
227607 TTTATGGTTTAAAG
1 TTTATGGTTTAAAG
*
227621 TTTAGGGTT
1 TTTATGGTT
227630 CAAGGTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (14 bp):
TTTATGGTTTAAAG
Found at i:227722 original size:2 final size:2
Alignment explanation
Indices: 227717--227789 Score: 85
Period size: 2 Copynumber: 36.0 Consensus size: 2
227707 AATAATTTAC
* **
227717 TA TA TA TA GTT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GG
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
227760 T- TA TA TA TA TA TA TA TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
227790 CTAGACATGG
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
1 1 0.02
2 58 0.95
3 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:227739 original size:33 final size:34
Alignment explanation
Indices: 227701--227789 Score: 126
Period size: 33 Copynumber: 2.6 Consensus size: 34
227691 TTCTATAAAC
* *
227701 TATATAAATAATTTACTATATATAGTTTATATATA
1 TATATATATAATTTA-TATATATAGGTTATATATA
*
227736 TATATATAT-ATATATATATATAGGTTATATATA
1 TATATATATAATTTATATATATAGGTTATATATA
*
227769 TATATATATAGTTTATATATA
1 TATATATATAATTTATATATA
227790 CTAGACATGG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 27 0.56
34 13 0.27
35 8 0.17
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (34 bp):
TATATATATAATTTATATATATAGGTTATATATA
Found at i:227743 original size:21 final size:20
Alignment explanation
Indices: 227717--227789 Score: 85
Period size: 19 Copynumber: 3.6 Consensus size: 20
227707 AATAATTTAC
*
227717 TATATATAGTTTATATATATA
1 TATATATA-TATATATATATA
227738 TATATATATATATATATATA
1 TATATATATATATATATATA
**
227758 GGT-TATATATATATATATA
1 TATATATATATATATATATA
*
227777 TAGTTTATATATA
1 TA-TATATATATA
227790 CTAGACATGG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
19 16 0.36
20 13 0.29
21 16 0.36
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TATATATATATATATATATA
Found at i:228247 original size:7 final size:7
Alignment explanation
Indices: 228231--228281 Score: 66
Period size: 7 Copynumber: 7.3 Consensus size: 7
228221 TTCATTTACA
228231 TTAGGGT
1 TTAGGGT
*
228238 TTATGGT
1 TTAGGGT
*
228245 TTAGTGT
1 TTAGGGT
*
228252 TTATGGT
1 TTAGGGT
228259 TTAGGGT
1 TTAGGGT
*
228266 TTAAGGT
1 TTAGGGT
228273 TTAGGGT
1 TTAGGGT
228280 TT
1 TT
228282 CTATAAACTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (7 bp):
TTAGGGT
Found at i:228253 original size:14 final size:14
Alignment explanation
Indices: 228231--228281 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
228221 TTCATTTACA
228231 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
228245 TTAGTGTTTATGGT
1 TTAGGGTTTATGGT
*
228259 TTAGGGTTTAAGGT
1 TTAGGGTTTATGGT
228273 TTAGGGTTT
1 TTAGGGTTT
228282 CTATAAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:228378 original size:17 final size:17
Alignment explanation
Indices: 228356--228411 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
228346 TAATTTACTT
* *
228356 TATATAATTTACATATA
1 TATATAGTTTATATATA
*
228373 TATATAGGTTATATATA
1 TATATAGTTTATATATA
228390 TATATAGTTTATATATA
1 TATATAGTTTATATATA
228407 CTATA
1 -TATA
228412 CATGGTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 30 0.88
18 4 0.12
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (17 bp):
TATATAGTTTATATATA
Found at i:228419 original size:20 final size:20
Alignment explanation
Indices: 228382--228427 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
228372 ATATATAGGT
*
228382 TATATA-TATATATAGTTTA
1 TATATACTATACATAGTTTA
*
228401 TATATACTATACATGGTTTA
1 TATATACTATACATAGTTTA
*
228421 TACATAC
1 TATATAC
228428 ATATTATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (20 bp):
TATATACTATACATAGTTTA
Found at i:228780 original size:7 final size:7
Alignment explanation
Indices: 228758--228823 Score: 51
Period size: 7 Copynumber: 9.4 Consensus size: 7
228748 TCTAGTTATA
228758 TTAGGGT
1 TTAGGGT
**
228765 TTATAGT
1 TTAGGGT
228772 TTAGGGT
1 TTAGGGT
*
228779 TTAGTGT
1 TTAGGGT
**
228786 TTAGTAT
1 TTAGGGT
*
228793 TTATGGT
1 TTAGGGT
***
228800 TTAAAAT
1 TTAGGGT
228807 TTAGGGT
1 TTAGGGT
228814 TTAGGGT
1 TTAGGGT
228821 TTA
1 TTA
228824 TAGTTTCTAT
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (7 bp):
TTAGGGT
Found at i:228918 original size:2 final size:2
Alignment explanation
Indices: 228913--228954 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
228903 TTATATAGTT
**
228913 TA TA TA TA TA TA TA TA TA GG T- TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
228955 CATGATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Found at i:228930 original size:21 final size:21
Alignment explanation
Indices: 228904--228949 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
228894 TAATCTACAT
*
228904 TATATAGTTTATATATATATA
1 TATATAGGTTATATATATATA
228925 TATATAGGTTATATATATATA
1 TATATAGGTTATATATATATA
228946 TATA
1 TATA
228950 GTATACATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TATATAGGTTATATATATATA
Found at i:229380 original size:21 final size:21
Alignment explanation
Indices: 229340--229386 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
229330 TATCATTCAG
* *
229340 GGTTTAATGTTTAGTGTTTAT
1 GGTTTAAAGTTTAGTGTTTAC
229361 GGTTTAAAGTTTAG-GTTTTAC
1 GGTTTAAAGTTTAGTG-TTTAC
229382 GGTTT
1 GGTTT
229387 CTATAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.19, C:0.02, G:0.26, T:0.53
Consensus pattern (21 bp):
GGTTTAAAGTTTAGTGTTTAC
Found at i:229780 original size:13 final size:13
Alignment explanation
Indices: 229762--229799 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
229752 TATATTAGTT
*
229762 TACATAGGCCCAA
1 TACATAAGCCCAA
229775 TACATAAGCCCAA
1 TACATAAGCCCAA
229788 TACATAAGCCCA
1 TACATAAGCCCA
229800 CTCTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.42, C:0.32, G:0.11, T:0.16
Consensus pattern (13 bp):
TACATAAGCCCAA
Found at i:229864 original size:14 final size:14
Alignment explanation
Indices: 229845--229889 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
229835 TCCATTTATA
229845 TTAGGGTTAATGGT
1 TTAGGGTTAATGGT
229859 TTAGGGTTTAAT-GT
1 TTAGGG-TTAATGGT
* *
229873 TTAGTGTTTATGGT
1 TTAGGGTTAATGGT
229887 TTA
1 TTA
229890 AAGTTTAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 4 0.15
14 18 0.67
15 5 0.19
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (14 bp):
TTAGGGTTAATGGT
Found at i:229887 original size:21 final size:21
Alignment explanation
Indices: 229856--229902 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
229846 TAGGGTTAAT
*
229856 GGTTTAGGGTTTAATGTTTAG
1 GGTTTAGGGTTTAAAGTTTAG
* *
229877 TGTTTATGGTTTAAAGTTTAG
1 GGTTTAGGGTTTAAAGTTTAG
229898 GGTTT
1 GGTTT
229903 CTATAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (21 bp):
GGTTTAGGGTTTAAAGTTTAG
Found at i:230008 original size:17 final size:17
Alignment explanation
Indices: 229986--230025 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
229976 TTATATAGTT
229986 TATATATATAGAGGTTA
1 TATATATATAGAGGTTA
* * *
230003 TATATATGTATAGTTTA
1 TATATATATAGAGGTTA
230020 TATATA
1 TATATA
230026 CTATGCATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
TATATATATAGAGGTTA
Found at i:230021 original size:15 final size:15
Alignment explanation
Indices: 229977--230025 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
229967 TAATTTACTT
229977 TATATAGTTTATATA
1 TATATAGTTTATATA
*
229992 TATAGAGGTTATATATA
1 TATATA-GTT-TATATA
*
230009 TGTATAGTTTATATA
1 TATATAGTTTATATA
230024 TA
1 TA
230026 CTATGCATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
16 6 0.21
17 10 0.36
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:230038 original size:20 final size:20
Alignment explanation
Indices: 230001--230046 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
229991 ATATAGAGGT
*
230001 TATATA-TATGTATAGTTTA
1 TATATACTATGCATAGTTTA
*
230020 TATATACTATGCATGGTTTA
1 TATATACTATGCATAGTTTA
*
230040 TACATAC
1 TATATAC
230047 ATATTATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (20 bp):
TATATACTATGCATAGTTTA
Found at i:230144 original size:21 final size:21
Alignment explanation
Indices: 230120--230160 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
230110 TATATTAGGG
230120 TTTAGGGTTTAGGGTTTAATA
1 TTTAGGGTTTAGGGTTTAATA
* *
230141 TTTAGTGTTTATGGTTTAAT
1 TTTAGGGTTTAGGGTTTAAT
230161 GTTTCTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTAATA
Found at i:230246 original size:262 final size:263
Alignment explanation
Indices: 229815--230346 Score: 908
Period size: 262 Copynumber: 2.0 Consensus size: 263
229805 TTATTACAAA
* *
229815 TATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTAATGGTTTAGGGTTTAATGTTTAGTGT
1 TATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTAAGGGTTTAGGGTTTAATATTTAGTGT
229880 TTATGGTTTAAAGTTTAGGGTTTCTATAAACTATATAATTTAGTACTTTATATAGTTTATGCATA
66 TTATGGTTTAAA--TT--GGTTTCTATAAACTATATAATTTAGTACTTTATATAGTTTATGCATA
229945 GTGGTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATAGAGGTTATATATAT
127 GTGGTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATAGAGGTTATATATAT
*
230010 GTATAGTTTATATATACTATGCATGGTTTATACATACATATTATATAAAATTATTTAATAAAATT
192 GTATAGTTTATATATACTATACAT-GTTTATACATACATATTATATAAAATTATTTAATAAAATT
230075 AATAAAATT
256 AAT-AAATT
*
230084 TATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTAGGGTTTAGGGTTTAATATTTAGTGT
1 TATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTAAGGGTTTAGGGTTTAATATTTAGTGT
* * * *
230149 TTATGGTTT-AA-T-GTTTCTATAAACTATATACTTTATTAGTTTATATAGTTTATGCATAGTGT
66 TTATGGTTTAAATTGGTTTCTATAAACTATATAATTTAGTACTTTATATAGTTTATGCATAGTGG
*
230211 TTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATAGGTTATATATATGTAT
131 TTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATAGAGGTTATATATATGTAT
230276 AGTTTATATATACTATACATGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAA
196 AGTTTATATATACTATACATGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAA
230341 ATT
261 ATT
230344 TAT
1 TAT
230347 TTAAATGTAA
Statistics
Matches: 254, Mismatches: 9, Indels: 9
0.93 0.03 0.03
Matches are distributed among these distances:
260 8 0.03
261 43 0.17
262 129 0.51
265 1 0.00
268 2 0.01
269 71 0.28
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.47
Consensus pattern (263 bp):
TATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTAAGGGTTTAGGGTTTAATATTTAGTGT
TTATGGTTTAAATTGGTTTCTATAAACTATATAATTTAGTACTTTATATAGTTTATGCATAGTGG
TTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATAGAGGTTATATATATGTAT
AGTTTATATATACTATACATGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAA
ATT
Found at i:230259 original size:15 final size:15
Alignment explanation
Indices: 230239--230292 Score: 72
Period size: 15 Copynumber: 3.4 Consensus size: 15
230229 TAATTTACTT
230239 TATATAGTTTATATA
1 TATATAGTTTATATA
230254 TATATAGGTTATATATA
1 TATATA-GTT-TATATA
*
230271 TGTATAGTTTATATA
1 TATATAGTTTATATA
230286 TACTATA
1 TA-TATA
230293 CATGTTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 13 0.38
16 10 0.29
17 11 0.32
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:230268 original size:17 final size:17
Alignment explanation
Indices: 230239--230292 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
230229 TAATTTACTT
230239 TATATA-GTT-TATATA
1 TATATAGGTTATATATA
230254 TATATAGGTTATATATA
1 TATATAGGTTATATATA
* *
230271 TGTATAGTTTATATATA
1 TATATAGGTTATATATA
230288 CTATA
1 -TATA
230293 CATGTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 6 0.18
16 3 0.09
17 21 0.64
18 3 0.09
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (17 bp):
TATATAGGTTATATATA
Found at i:230703 original size:14 final size:14
Alignment explanation
Indices: 230660--230704 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
230650 TTCATTTATA
*
230660 TTAGGGTTTATGGT
1 TTAGTGTTTATGGT
*
230674 TTAATGTTTAAT-GT
1 TTAGTGTTT-ATGGT
230688 TTAGTGTTTATGGT
1 TTAGTGTTTATGGT
230702 TTA
1 TTA
230705 AAGCATAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (14 bp):
TTAGTGTTTATGGT
Found at i:230819 original size:15 final size:15
Alignment explanation
Indices: 230799--230850 Score: 79
Period size: 15 Copynumber: 3.4 Consensus size: 15
230789 TAATTTACTT
230799 TATATAGTTTATATA
1 TATATAGTTTATATA
230814 TATATA-TGTTATATA
1 TATATAGT-TTATATA
230829 TATATAGTTTATATA
1 TATATAGTTTATATA
230844 TACTATA
1 TA-TATA
230851 CATGGTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.03
15 28 0.82
16 5 0.15
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:231215 original size:14 final size:14
Alignment explanation
Indices: 231196--231227 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
231186 TCCATTTATA
231196 TTAGGGCTTATGGT
1 TTAGGGCTTATGGT
*
231210 TTAGGGTTTATGGT
1 TTAGGGCTTATGGT
231224 TTAG
1 TTAG
231228 TATATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.03, G:0.34, T:0.47
Consensus pattern (14 bp):
TTAGGGCTTATGGT
Found at i:240450 original size:12 final size:12
Alignment explanation
Indices: 240433--240457 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
240423 TAGTGTTTCT
240433 ATAAACTATATA
1 ATAAACTATATA
240445 ATAAACTATATA
1 ATAAACTATATA
240457 A
1 A
240458 GTAATTTACT
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAACTATATA
Found at i:240921 original size:14 final size:15
Alignment explanation
Indices: 240857--240921 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 15
240847 TCCATTTATA
240857 TTAGGGTTTATGG-T
1 TTAGGGTTTATGGTT
*
240871 TTAGGATTTAAT-G-T
1 TTAGGGTTT-ATGGTT
*
240885 TTAGTGTTTATGGTT
1 TTAGGGTTTATGGTT
* *
240900 TGA-AGTTTA-GGTT
1 TTAGGGTTTATGGTT
240913 TTAGGGTTT
1 TTAGGGTTT
240922 CTATAAACTA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
13 8 0.20
14 27 0.68
15 5 0.12
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.52
Consensus pattern (15 bp):
TTAGGGTTTATGGTT
Found at i:241020 original size:19 final size:19
Alignment explanation
Indices: 240996--241040 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
240986 TAATTTACTT
* *
240996 TATATAATTTATATATATA
1 TATATAAATAATATATATA
241015 TATATAAATAATATATATA
1 TATATAAATAATATATATA
241034 TACTATA
1 TA-TATA
241041 CATGATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATAAATAATATATATA
Found at i:241101 original size:15 final size:13
Alignment explanation
Indices: 241064--241089 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
241054 TACATATTAT
241064 ATAAAATTATTTA
1 ATAAAATTATTTA
241077 ATAAAATTATTTA
1 ATAAAATTATTTA
241090 GATGTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:241412 original size:7 final size:7
Alignment explanation
Indices: 241400--241460 Score: 68
Period size: 7 Copynumber: 8.7 Consensus size: 7
241390 TCTATTTATA
241400 TTAGGGT
1 TTAGGGT
241407 TTAGGGT
1 TTAGGGT
**
241414 TTAGTAT
1 TTAGGGT
*
241421 TTAGTGT
1 TTAGGGT
*
241428 TTAGTGT
1 TTAGGGT
* *
241435 ATATGGT
1 TTAGGGT
241442 TTAGGGT
1 TTAGGGT
241449 TTAGGGT
1 TTAGGGT
241456 TTAGG
1 TTAGG
241461 ATTTTAATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (7 bp):
TTAGGGT
Found at i:241605 original size:13 final size:13
Alignment explanation
Indices: 241595--241633 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
241585 TATATATTAT
241595 ATAAAATTATTTA
1 ATAAAATTATTTA
241608 ATAAAATTATTTA
1 ATAAAATTATTTA
241621 ATAAAATTATTTA
1 ATAAAATTATTTA
241634 GATGTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:241653 original size:544 final size:540
Alignment explanation
Indices: 240347--242096 Score: 2592
Period size: 544 Copynumber: 3.2 Consensus size: 540
240337 GAGGGTTACA
* * **
240347 TAGTGTGTATGGTTTGAAGTTTAAGGTTTAGGGTTTCTATAATTTATATACTTTATTACTTTATA
1 TAGTGTTTATGGTTTGAAGTTTAGGGTTTAGGGTTTCTATAAACTATATACTTTATTACTTTATA
* * * *
240412 TAGTTTATGCTTAGTGTTTCTATAAACTATATAA-TAA---ACTATATAAGTAATTTACTTTATA
66 TAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATTTACTTTAT-A-T-ATATA-TATATA
** * * *
240473 TAGTTTTTATATATATTGTTTATATACATACATATTATATAAAATAATTTAAT-AAA--A-TTAA
127 TA--TAATATATATAATGATTATATACATACATATTATATAAAATTATTTAATAAAATTATTTAA
* * *
240534 TAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTGGGTGTTAAATAATTAGTATGCCA
190 TAAAATTATTTAGATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCA
* *
240599 CGTTGCATATTATATGGTTCATAAATAGTAGTACATGCCATATTAATTTCATTTGCATAATTAGT
255 CATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGT
* * * *
240664 ATTTTAGTTGCATGTTAGGTAAATTCACAATAATAGAACCATTTATTTTGTTGTTATAAATAAGT
320 ATTTTAGTTGCATGTTAGGTTAATTCACATTAATAG-CCCATTTATTTTGTTGTTATGAATAAGT
* * * *
240729 TATAATAAAACCCAAAAATAAGTCCATTAGCATTAGTGCTAGTCCATTTCCATTAGTTCACATAG
384 TATAATAAAACCCAAAAATATGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATAG
* * * *
240794 GACCAATACATAAGCCCACCCTTTTATTACAAATATATATGTATTAGTGCTAGTCCATTTATATT
449 GCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCTATTTATATT
240859 AGGGTTTATGGTTTAGGATTTAATGTT
514 AGGGTTTATGGTTTAGGATTTAATGTT
*
240886 TAGTGTTTATGGTTTGAAGTTTAGGTTTTAGGGTTTCTATAAACTATATACTTTATTACTTTATA
1 TAGTGTTTATGGTTTGAAGTTTAGGGTTTAGGGTTTCTATAAACTATATACTTTATTACTTTATA
* * *
240951 TAATTTATGCATAGTGTTTCAATAAACTATATAAGTAATTTACTTTATATA-ATTTATATATATA
66 TAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATATATATATATATATA
*
241015 TATATAAATAAT-ATATATATACTATACATGATT-TATACATACA-TA-TTATATAAAATTATTT
131 -ATATATATAATGAT-TATATAC-ATACAT-ATTATATA-A-A-ATTATTTA-ATAAAATTATTT
241076 AATAAAATTATTTAGATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGT
188 AATAAAATTATTTAGATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGT
*
241141 CACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCAAATTAATTTCATTTGCATAATTA
253 CACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTA
* *
241206 GTATTTTTGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGACTAAG
318 GTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAG
* * *
241271 TTATAATAAAACCCAAAAATATGTCCATTTGCATTAGTTCTAGTCCATTTACATTATTTTACGTA
383 TTATAATAAAACCCAAAAATATGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATA
241336 GGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCTATTTATAT
448 GGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCTATTTATAT
* * *
241401 TAGGGTTTAGGGTTTAGTATTTAGTGTT
513 TAGGGTTTATGGTTTAGGATTTAATGTT
* * *
241429 TAGTGTATATGGTTT-AGGGTTTAGGGTTTAGGATTT-TAATAAACTATATACTTTATTACTTTA
1 TAGTGTTTATGGTTTGA-AGTTTAGGGTTTAGGGTTTCT-ATAAACTATATACTTTATTACTTTA
*
241492 TATAGTTTATGAATAGTGTTTCTATAAACTATATAAGTAAATTTACTTTATATATATATATATAT
64 TATAGTTTATGCATAGTGTTTCTATAAACTATATAAGT-AATTTACTTTATATATATATATATAT
* *
241557 ACTAACTATACTATACATGGTT-TATACATATATATTATATAAAATTATTTAATAAAATTATTTA
128 A-TAA-TATA-TATA-ATGATTATATACATACATATTATATAAAATTATTTAATAAAATTATTTA
241621 ATAAAATTATTTAGATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTC
189 ATAAAATTATTTAGATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTC
*
241686 ACATTGCATATTATATGATTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAG
254 ACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAG
241751 TATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGT
319 TATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGT
* * *
241816 TATAATAAAACCCAAAAATATGTCCATTTGCGTTAGTGCTAGCCCATTTATATTAGTTTACATAG
384 TATAATAAAACCCAAAAATATGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATAG
241881 GCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCTATTTATATT
449 GCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCTATTTATATT
* * *
241946 AGGGTTAATGGTTTAGGGTTTACTGTT
514 AGGGTTTATGGTTTAGGATTTAATGTT
*
241973 TAGTGTTTATGGTTT-AA----A--GTTTAGGGTTTCTATAAACTATATACTTTAGTACTTTATA
1 TAGTGTTTATGGTTTGAAGTTTAGGGTTTAGGGTTTCTATAAACTATATACTTTATTACTTTATA
* *
242031 TAGTTTATGCATAGTGTTTCTGTAAACTATATAAGTAATTTACTTTATATAGTTTATATATATAT
66 TAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATA-TATATATATATAT
242096 A
130 A
242097 TAGGTTATAT
Statistics
Matches: 1104, Mismatches: 77, Indels: 63
0.89 0.06 0.05
Matches are distributed among these distances:
536 19 0.02
537 96 0.09
538 18 0.02
539 100 0.09
540 8 0.01
541 5 0.00
542 3 0.00
543 266 0.24
544 544 0.49
545 18 0.02
546 15 0.01
547 8 0.01
548 3 0.00
549 1 0.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (540 bp):
TAGTGTTTATGGTTTGAAGTTTAGGGTTTAGGGTTTCTATAAACTATATACTTTATTACTTTATA
TAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATATATATATATATATA
ATATATATAATGATTATATACATACATATTATATAAAATTATTTAATAAAATTATTTAATAAAAT
TATTTAGATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGC
ATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTA
GTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTTATAATA
AAACCCAAAAATATGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACATAGGCCCAAT
ACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCTATTTATATTAGGGTTT
ATGGTTTAGGATTTAATGTT
Found at i:241994 original size:21 final size:21
Alignment explanation
Indices: 241955--242001 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
241945 TAGGGTTAAT
**
241955 GGTTTAGGGTTTACTGTTTAG
1 GGTTTAGGGTTTAAAGTTTAG
* *
241976 TGTTTATGGTTTAAAGTTTAG
1 GGTTTAGGGTTTAAAGTTTAG
241997 GGTTT
1 GGTTT
242002 CTATAAACTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.17, C:0.02, G:0.30, T:0.51
Consensus pattern (21 bp):
GGTTTAGGGTTTAAAGTTTAG
Found at i:242037 original size:49 final size:50
Alignment explanation
Indices: 241984--242086 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 50
241974 AGTGTTTATG
** ** *
241984 GTTTAAAGTTTAGGGTTTCTATAAACTATATACTTTA-GTACTTTATATA
1 GTTTAAAGCATAGGGTTTCTATAAACTATATAAGTAATGTACTTTATATA
* * * *
242033 GTTT-ATGCATAGTGTTTCTGTAAACTATATAAGTAATTTACTTTATATA
1 GTTTAAAGCATAGGGTTTCTATAAACTATATAAGTAATGTACTTTATATA
242082 GTTTA
1 GTTTA
242087 TATATATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
48 24 0.56
49 19 0.44
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.48
Consensus pattern (50 bp):
GTTTAAAGCATAGGGTTTCTATAAACTATATAAGTAATGTACTTTATATA
Found at i:242098 original size:17 final size:17
Alignment explanation
Indices: 242076--242142 Score: 89
Period size: 17 Copynumber: 3.8 Consensus size: 17
242066 TAATTTACTT
242076 TATATAGTTTATATATA
1 TATATAGTTTATATATA
*
242093 TATATAGGTTATATATA
1 TATATAGTTTATATATA
*
242110 TGTATAGTTTATATATA
1 TATATAGTTTATATATA
242127 TTATACATAGTTTATA
1 -TAT--ATAGTTTATA
242143 CATACATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
17 31 0.72
18 2 0.05
20 10 0.23
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (17 bp):
TATATAGTTTATATATA
Found at i:242273 original size:21 final size:21
Alignment explanation
Indices: 242215--242279 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
242205 TCCATTTATA
*
242215 TTAAGGTTTATGG-TTTATGGT
1 TTAATGTTTA-GGTTTTATGGT
* *
242236 TTAATATTT-TGTGTTTATGGT
1 TTAATGTTTAGGT-TTTATGGT
*
242257 TTAATGTTTAGGTTTTAAGGT
1 TTAATGTTTAGGTTTTATGGT
242278 TT
1 TT
242280 CTATAAACTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 1 0.03
21 32 0.91
22 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (21 bp):
TTAATGTTTAGGTTTTATGGT
Found at i:242396 original size:37 final size:35
Alignment explanation
Indices: 242376--242453 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
242366 GGTTTATGGT
242376 TATATATATAGGCTATATATAGTTTATATAGTTTA
1 TATATATATAGGCTATATATAGTTTATATAGTTTA
*
242411 TATATATATAGGCTATATATA---TGTATAGTTTA
1 TATATATATAGGCTATATATAGTTTATATAGTTTA
242443 TATATACTATA
1 TATATA-TATA
242454 TATGGTTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
32 16 0.39
33 4 0.10
35 21 0.51
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.47
Consensus pattern (35 bp):
TATATATATAGGCTATATATAGTTTATATAGTTTA
Found at i:242444 original size:15 final size:15
Alignment explanation
Indices: 242400--242453 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
242390 ATATATAGTT
242400 TATATAGTTTATATA
1 TATATAGTTTATATA
*
242415 TATATAGGCTATATATA
1 TATATA-G-TTTATATA
*
242432 TGTATAGTTTATATA
1 TATATAGTTTATATA
242447 TACTATA
1 TA-TATA
242454 TATGGTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 14 0.44
16 6 0.19
17 12 0.38
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:242463 original size:20 final size:20
Alignment explanation
Indices: 242378--242479 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 20
242368 TTTATGGTTA
242378 TATATATAGGCTATATATAGTT
1 TATATATA--CTATATATAGTT
* *
242400 TATATAGT-TTATATATA-TA
1 TATATA-TACTATATATAGTT
*
242419 TAGGCTATATA-TATGTATAGTT
1 TA---TATATACTATATATAGTT
*
242441 TATATATACTATATATGGTT
1 TATATATACTATATATAGTT
*
242461 TATACATACATATTATATA
1 TATATATAC-TA-TATATA
242480 AAATTATTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
19 9 0.14
20 25 0.40
21 10 0.16
22 18 0.29
23 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (20 bp):
TATATATACTATATATAGTT
Found at i:242844 original size:14 final size:14
Alignment explanation
Indices: 242822--242864 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
242812 TCCATTTATA
*
242822 TTAGGGTTTATGGT
1 TTAGTGTTTATGGT
242836 TTAGTGTTTAAT-GT
1 TTAGTGTTT-ATGGT
242850 TTAGTGTTTATGGT
1 TTAGTGTTTATGGT
242864 T
1 T
242865 GAAAGCTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (14 bp):
TTAGTGTTTATGGT
Found at i:243016 original size:13 final size:13
Alignment explanation
Indices: 243006--243032 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
242996 TATATATTAT
243006 ATAAAATTATTTA
1 ATAAAATTATTTA
243019 ATAAAATTATTTA
1 ATAAAATTATTTA
243032 A
1 A
243033 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:243042 original size:15 final size:14
Alignment explanation
Indices: 243006--243048 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
242996 TATATATTAT
243006 ATAAAATTATTT-A
1 ATAAAATTATTTAA
243019 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
243033 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
243048 A
1 A
243049 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:243399 original size:9 final size:9
Alignment explanation
Indices: 243366--243403 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
243356 TTAGGGTTTC
243366 TATA-TTTA
1 TATACTTTA
243374 TATACTTTA
1 TATACTTTA
243383 T-TACTTTA
1 TATACTTTA
*
243391 TATAGTTTA
1 TATACTTTA
243400 TATA
1 TATA
243404 TATATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 12 0.44
9 15 0.56
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (9 bp):
TATACTTTA
Found at i:243463 original size:2 final size:2
Alignment explanation
Indices: 243398--243453 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
243388 TTATATAGTT
243398 TA TA 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 TA TA
**
243440 GG T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
243454 TGTTTATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:244366 original size:14 final size:14
Alignment explanation
Indices: 244344--244401 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
244334 TCCATTTATA
*
244344 TTAGAGTTTATGGT
1 TTAGGGTTTATGGT
244358 TTAGGGTTTAAT-GT
1 TTAGGGTTT-ATGGT
* **
244372 TTAGTGAATATGGT
1 TTAGGGTTTATGGT
*
244386 TTAGGGTTTAGGGT
1 TTAGGGTTTATGGT
244400 TT
1 TT
244402 TTATAAACTA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
13 2 0.06
14 30 0.88
15 2 0.06
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:244979 original size:2 final size:2
Alignment explanation
Indices: 244974--245046 Score: 60
Period size: 2 Copynumber: 36.5 Consensus size: 2
244964 ATAAGTAATA
* * *
244974 AT AT AT AT AT AT AT AT AT AG GT -T AT AT AT AT AT AT AGT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
245016 AT AT AT AGT TT AT AT AC AT AC AT AT -T AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A
245047 AAATTATTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
1 2 0.04
2 52 0.93
3 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:244987 original size:496 final size:503
Alignment explanation
Indices: 243493--244990 Score: 2003
Period size: 523 Copynumber: 2.9 Consensus size: 503
243483 TATTTAATAA
* *
243493 AATTA-ATAAAATAATTTAAATGTAAATTATATAAAACTTGATTAATTAGGTGTTAAATAATTAG
1 AATTATATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAG
* * *
243557 TATGTCACGTTGCATATTATATGGTTTATAAATAGTAGTACATGCCATATTAATTTCATTTGCAT
66 TATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGC--
* * * * *
243622 AATTAGTATTTTAGTTGCATGTTAGGTTAATTCACAATACTAGAACCATTTATTTTGTTGTTATA
129 -ATTAGTATTTTTGTTGCATGTTAGGTTAATTCACATTAATAG-CCCATTTATTTTGTTGTTATG
* *
243687 AATAAGTTATAATTAAAACCAAAAATAAGTCCATTAGCATTAGTGCTAGTCCATTTCCATTAGTT
192 AATAAGTTATAA-TAAAACCAAAAATAAGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTT
** *
243752 TACAAAGGCCCAATACATAAGCCCA-TCCTTTTATTATAAATATATATGCATTAGTGCTAGTCCA
256 TACGTAGGCCCAATACATAAGCCCACT-CTTTTATTACAAATATATATGCATTAGTGCTAGTCCA
* *
243816 TTTATATTAGGGCTTATGGTTTAGGATTTAGGGTTTATGTA--TACAGTTTGAAG-TT--G---A
320 TTTATATTAGGGTTTATGGTTTAGGATTTAAGGTTTA-GTATGTA-AGTTTGAAGTTTAGGTTTA
* *
243873 GGGTTTCTATAAACTATAGACTTTATTACTTTATATAGTTTATGCATAGTATTTCTATAAACTAT
383 GGGTTTCTATAAACTATAAACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTAT
*
243938 ATAAGTAATTTACTTTATATAGTTTATATTTATATATATATATTATACATGGTTTATACATATAT
448 ATAAGT-A---A--TTATATA---TATA--TATATATACATATTATACATGGTTTATAC----A-
*
244003 ATTATAT
497 ATTACAT
244010 AAATTATTTTAGTAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATA
1 -AATTA---TA-TAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATA
*
244075 ATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCAAATTAATTTCATT
61 ATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATT
244140 TGCATAATTAGTATTTTTGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGT
126 TGC---ATTAGTATTTTTGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGT
* * *
244205 TATGACTAAGTTATAATAAAACCCAAAAATATGTCCATTTGCATTAGTTCTAGTCCATTTACATT
188 TATGAATAAGTTATAATAAAA-CCAAAAATAAGTCCATTTGCATTAGTGCTAGTCCATTTACATT
*
244270 ATTTTACGTAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGT
252 AGTTTACGTAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGT
* * * *
244335 CCATTTATATTAGAGTTTATGGTTTAGGGTTTAATGTTTAG--TG-AA-TATG--GTTTAGGGTT
317 CCATTTATATTAGGGTTTATGGTTTAGGATTTAAGGTTTAGTATGTAAGTTTGAAGTTTA-GGTT
*
244394 TAGGGTTTTTATAAACTATAAACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACT
381 TAGGGTTTCTATAAACTATAAACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACT
* * * * ** *
244459 ATATTAGTAATT-TACTTTATATAGTTTATATATACAATAAATGGTTTATAC-A-TACAT
446 ATATAAGTAATTATA-TATATATA-TATATACATATTATACATGGTTTATACAATTACAT
*
244516 -ATTATATAAAATTATTTAAATGTAAATTATATTAAACATGATTAATTAGGTGTTAAATAATTAG
1 AATTATATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAG
* *
244580 TATGTCACATTGGATATTATATGCTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGC-T
66 TATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCAT
*
244644 TAGTATTTTTGTTGCATTTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATA
131 TAGTATTTTTGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATA
* * * * *
244709 AGTAATAATAAAACTAAAAAATAAATCTATTTGCATTAGTGCTAGTCCAATTACATTAGTTTACG
196 AGTTATAATAAAAC-CAAAAATAAGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACG
* * * *
244774 TAGGCCCAATATATAAGCCTACTCTTTTATTACAAATATATAAGCATTAGTGCTAGTCCATTTAC
260 TAGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTAT
*
244839 ATTAGGGTTTATGGTTTAGGATTTACGGTTTAGTATGTAAGGTTTGAAGTTTAGGTTTTAGGGTT
325 ATTAGGGTTTATGGTTTAGGATTTAAGGTTTAGTATGTAA-GTTTGAAGTTTAGG-TTTAGGGTT
* *
244904 TCTATAAAATATATACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAG
388 TCTATAAACTATAAACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAG
*
244969 TAATAATATATATATATATATA
453 TAATTATATATATATATATATA
244991 TAGGTTATAT
Statistics
Matches: 886, Mismatches: 66, Indels: 72
0.87 0.06 0.07
Matches are distributed among these distances:
495 1 0.00
496 209 0.24
498 2 0.00
499 2 0.00
500 117 0.13
501 5 0.01
502 7 0.01
503 86 0.10
504 6 0.01
506 4 0.00
507 1 0.00
512 2 0.00
513 23 0.03
514 4 0.00
516 3 0.00
517 5 0.01
518 8 0.01
519 2 0.00
520 2 0.00
521 6 0.01
522 165 0.19
523 226 0.26
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.43
Consensus pattern (503 bp):
AATTATATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAG
TATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCAT
TAGTATTTTTGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATA
AGTTATAATAAAACCAAAAATAAGTCCATTTGCATTAGTGCTAGTCCATTTACATTAGTTTACGT
AGGCCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTATA
TTAGGGTTTATGGTTTAGGATTTAAGGTTTAGTATGTAAGTTTGAAGTTTAGGTTTAGGGTTTCT
ATAAACTATAAACTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAA
TTATATATATATATATATACATATTATACATGGTTTATACAATTACAT
Found at i:245001 original size:17 final size:17
Alignment explanation
Indices: 244979--245022 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
244969 TAATAATATA
244979 TATATATATATATAGGT
1 TATATATATATATAGGT
*
244996 TATATATATATATAGTT
1 TATATATATATATAGGT
245013 TATATATATA
1 TATATATATA
245023 GTTTATATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (17 bp):
TATATATATATATAGGT
Found at i:245016 original size:13 final size:13
Alignment explanation
Indices: 245000--245031 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
244990 ATAGGTTATA
245000 TATATATATAGTT
1 TATATATATAGTT
245013 TATATATATAGTT
1 TATATATATAGTT
245026 TATATA
1 TATATA
245032 CATACATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (13 bp):
TATATATATAGTT
Found at i:245054 original size:13 final size:13
Alignment explanation
Indices: 245044--245070 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
245034 TACATATTAT
245044 ATAAAATTATTTA
1 ATAAAATTATTTA
245057 ATAAAATTATTTA
1 ATAAAATTATTTA
245070 A
1 A
245071 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:245080 original size:15 final size:14
Alignment explanation
Indices: 245044--245086 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
245034 TACATATTAT
245044 ATAAAATTATTT-A
1 ATAAAATTATTTAA
245057 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
245071 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
245086 A
1 A
245087 ACATTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:245462 original size:2 final size:2
Alignment explanation
Indices: 245457--245507 Score: 57
Period size: 2 Copynumber: 24.0 Consensus size: 2
245447 TTATATAGTT
* *
245457 TA TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA TA GTT 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
245501 TA CTA TA
1 TA -TA TA
245508 CATGGTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 38 0.90
3 4 0.10
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:245466 original size:13 final size:13
Alignment explanation
Indices: 245448--245502 Score: 94
Period size: 13 Copynumber: 4.3 Consensus size: 13
245438 TAATTTACTT
245448 TATATAGTTTATA
1 TATATAGTTTATA
*
245461 TATATA-TATATA
1 TATATAGTTTATA
245473 TATATAGTTTATA
1 TATATAGTTTATA
245486 TATATAGTTTATA
1 TATATAGTTTATA
245499 TATA
1 TATA
245503 CTATACATGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.28
13 28 0.72
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Done.