Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008942.1 Hibiscus syriacus cultivar Beakdansim tig00112261_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: 2383254
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:180784 original size:23 final size:23
Alignment explanation
Indices: 180734--180778 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
180724 TATCTATTTT
180734 ATTATATAAGCGCTACCTAATAC
1 ATTATATAAGCGCTACCTAATAC
180757 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
180779 TGTTATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:180786 original size:26 final size:24
Alignment explanation
Indices: 180732--180788 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 24
180722 AATATCTATT
180732 TTATTATATAAGCGCTACCTAATA
1 TTATTATATAAGCGCTACCTAATA
*
180756 -CATTATATAAGCGCTACCTAATA
1 TTATTATATAAGCGCTACCTAATA
180779 TGTTATTATA
1 --TTATTATA
180789 CTTAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 22 0.79
26 6 0.21
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.39
Consensus pattern (24 bp):
TTATTATATAAGCGCTACCTAATA
Found at i:181276 original size:21 final size:21
Alignment explanation
Indices: 181247--181352 Score: 133
Period size: 21 Copynumber: 5.1 Consensus size: 21
181237 AATATGTAAA
*
181247 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATATTCCAAAT
*
181268 TCGCGTTGCGATATTCCAAAT
1 TCGCATTGCGATATTCCAAAT
*
181289 TCGCGTTGCGATATTCCAAAT
1 TCGCATTGCGATATTCCAAAT
**
181310 TCGCATTGCGATATTTTAAAT
1 TCGCATTGCGATATTCCAAAT
** *
181331 TCGCAACGCGATAGT-CAAAT
1 TCGCATTGCGATATTCCAAAT
181351 TC
1 TC
181353 TCAACGCAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
20 6 0.08
21 70 0.92
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATATTCCAAAT
Found at i:181352 original size:20 final size:20
Alignment explanation
Indices: 181163--181417 Score: 130
Period size: 20 Copynumber: 12.7 Consensus size: 20
181153 AAATGACCAA
*
181163 CAAATTCGCAACGCGAT-GT
1 CAAATTCGCAACGCGATATT
*
181182 CAAATTTGCAACGCGA-ATT
1 CAAATTCGCAACGCGATATT
* *
181201 CCAATTTCGCAAC-CCAGT-TT
1 -CAAATTCGCAACGCGA-TATT
*
181221 CCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCG-ATAT-T
** *
181244 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGATATT
***
181262 CCAAATTCGCGTTGCGATATT
1 -CAAATTCGCAACGCGATATT
***
181283 CCAAATTCGCGTTGCGATATT
1 -CAAATTCGCAACGCGATATT
**
181304 CCAAATTCGCATTGCGATATTT
1 -CAAATTCGCAACGCGATA-TT
* *
181326 TAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATATT
* * * *
181346 CAAATTCTCAACGCAAAAGT
1 CAAATTCGCAACGCGATATT
* * *
181366 CAAATTCGCAATGCGAAAGT
1 CAAATTCGCAACGCGATATT
*
181386 CAAATTCGCAAC-TGA-ATTT
1 CAAATTCGCAACGCGATA-TT
181405 CAAATTCGCAACG
1 CAAATTCGCAACG
181418 TGAAAGTCAA
Statistics
Matches: 195, Mismatches: 27, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.01
19 36 0.18
20 81 0.42
21 71 0.36
22 4 0.02
23 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACGCGATATT
Found at i:181427 original size:20 final size:20
Alignment explanation
Indices: 181327--181429 Score: 127
Period size: 20 Copynumber: 5.2 Consensus size: 20
181317 GCGATATTTT
*
181327 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACGCGAAAGTC
* *
181347 AAATTCTCAACGCAAAAGTC
1 AAATTCGCAACGCGAAAGTC
*
181367 AAATTCGCAATGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
* **
181387 AAATTCGCAAC-TGAATTTC
1 AAATTCGCAACGCGAAAGTC
*
181406 AAATTCGCAACGTGAAAGTC
1 AAATTCGCAACGCGAAAGTC
181426 AAAT
1 AAAT
181430 ATTTTTACGC
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
19 16 0.23
20 54 0.77
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:181587 original size:22 final size:22
Alignment explanation
Indices: 181557--181602 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
181547 CTACGGCGAC
*
181557 ATCCGTCCCCATCTCCGACAAA
1 ATCCATCCCCATCTCCGACAAA
* *
181579 ATCCATCCCCATTTCCGACGAA
1 ATCCATCCCCATCTCCGACAAA
181601 AT
1 AT
181603 TCGTCTATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.41, G:0.09, T:0.22
Consensus pattern (22 bp):
ATCCATCCCCATCTCCGACAAA
Found at i:181830 original size:13 final size:13
Alignment explanation
Indices: 181812--181843 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
181802 AGTATTTGTC
181812 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
181825 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
181838 TTTGTT
1 TTTGTT
181844 GAAGAAACCC
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:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (13 bp):
TTTGTTTTGTCTT
Found at i:181963 original size:20 final size:20
Alignment explanation
Indices: 181882--181955 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
181872 TCGTAACACA
*
181882 AAAATGAAAATCGCAACACG
1 AAAATGAAAATCGCAACGCG
*
181902 AAAATGAAAATCTCAACGCG
1 AAAATGAAAATCGCAACGCG
181922 AAAATGAAAATCGCAACGCG
1 AAAATGAAAATCGCAACGCG
181942 AAAATGAAAATCGC
1 AAAATGAAAATCGC
181956 GTTGCGAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.53, C:0.19, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATGAAAATCGCAACGCG
Found at i:184357 original size:14 final size:14
Alignment explanation
Indices: 184338--184377 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
184328 TTTTGATTAA
184338 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
184352 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
184366 TTGATTTGTAAA
1 TTGATTTGTAAA
184378 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:184370 original size:61 final size:63
Alignment explanation
Indices: 184287--184425 Score: 149
Period size: 67 Copynumber: 2.2 Consensus size: 63
184277 TTTTACATTG
*
184287 AAAGTTAATTTGTTACAATTGATGAGGAAATAAG-ATTTATTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTACAATTGATGAGGAAATAAGAATTTATTTTCTTGATTAATTGATTTGTA
* ** * * *
184348 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTTTGCTTGTTTAATTGATTT
1 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-A--ATTTATTTT-CTTGATTAATTGATTT
184412 GTA
61 GTA
184415 AAAGTTGATTT
1 AAAGTTGATTT
184426 ATTGTTTCTA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
61 25 0.39
62 3 0.05
65 8 0.12
67 28 0.44
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.50
Consensus pattern (63 bp):
AAAGTTGATTTGTTACAATTGATGAGGAAATAAGAATTTATTTTCTTGATTAATTGATTTGTA
Found at i:184513 original size:20 final size:20
Alignment explanation
Indices: 184487--184544 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
184477 GTTGAAGGTA
*
184487 CAAATTCGTAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
184507 TAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
184527 CAAATTCGCAACGCGAAA
1 CAAATTCGCAACGCGAAA
184545 TAAGCGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:184624 original size:34 final size:34
Alignment explanation
Indices: 184586--184650 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
184576 AAAGTCAAAT
**
184586 TCGCAACGCGAT-TTTCGTTTTGCGAATTTGACTA
1 TCGCAACGC-ATATTTCGCGTTGCGAATTTGACTA
*
184620 TCGCAACGCTTATTTCGCGTTGCGAATTTGA
1 TCGCAACGCATATTTCGCGTTGCGAATTTGA
184651 ATTTCGCGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 1 0.04
34 26 0.96
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (34 bp):
TCGCAACGCATATTTCGCGTTGCGAATTTGACTA
Found at i:187303 original size:24 final size:24
Alignment explanation
Indices: 187269--187322 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
187259 CCATCACATC
187269 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
187293 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
187317 ATCAAA
1 ATCAAA
187323 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:187469 original size:12 final size:12
Alignment explanation
Indices: 187448--187481 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
187438 GGTTGTGGGT
*
187448 TTTGAGATTGTG
1 TTTGATATTGTG
187460 TTTGATATTGTG
1 TTTGATATTGTG
*
187472 TTTGGTATTG
1 TTTGATATTG
187482 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:188317 original size:21 final size:21
Alignment explanation
Indices: 188274--188317 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
188264 TTCGCGTTGA
* *
188274 GAATTTGGAATATCGTAACGC
1 GAATTTGGAAAATCGCAACGC
*
188295 GAATTTGGAAAATCGCAATGC
1 GAATTTGGAAAATCGCAACGC
188316 GA
1 GA
188318 TTTACATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (21 bp):
GAATTTGGAAAATCGCAACGC
Found at i:190003 original size:35 final size:35
Alignment explanation
Indices: 189962--190041 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
189952 AACACAGTCA
* * * *
189962 TCAATTATATTTTAAACCCCAAAATCTAAAATATT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
* *
189997 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
190032 TCAATTACAT
1 TCAATTACAT
190042 ACCCAACCCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAATACT
Found at i:190055 original size:35 final size:35
Alignment explanation
Indices: 189975--190057 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 35
189965 ATTATATTTT
* * * * *
189975 AAACCCCAAAATCTAAAATATTTCAATTACATTCT
1 AAACCCCAAATTCCAAAATACTTCAATTACATACC
*
190010 AAACCTCAAATTCCAAAATACTTCAATTACATACC
1 AAACCCCAAATTCCAAAATACTTCAATTACATACC
*
190045 CAACCCCAAATTC
1 AAACCCCAAATTC
190058 ATAATCCATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.27
Consensus pattern (35 bp):
AAACCCCAAATTCCAAAATACTTCAATTACATACC
Found at i:190417 original size:149 final size:148
Alignment explanation
Indices: 190211--190504 Score: 507
Period size: 149 Copynumber: 2.0 Consensus size: 148
190201 AAATAATCAA
* *
190211 TTCAGTTTATAAAATAATTGTCTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAGTTTATAAAATAATTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
* * *
190276 AAATTGAATTGAATTTTTGAGTTTTTGTTTAAATTTAATTATAAATATTTATCATATTATAATAT
66 AAATTGAATTGAATTTTTGAGTTTTTGTTTAAAATTAATTATAAATATTTATAATACTATAATAT
190341 TATTTGATTCTAATTCAG
131 TATTTGATTCTAATTCAG
*
190359 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGT
1 TTCAGTTTATAAAATAATTGACTCGAAA-TTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGT
**
190424 CGCATTGAATTGAATTTTTGAGTTTTTGTTTAAAATTAATTATAAATATTTATAATACTATAATA
65 CAAATTGAATTGAATTTTTGAGTTTTTGTTTAAAATTAATTATAAATATTTATAATACTATAATA
190489 TTATTTGATTCTAATT
130 TTATTTGATTCTAATT
190505 TAAATAATTT
Statistics
Matches: 137, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
148 26 0.19
149 111 0.81
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (148 bp):
TTCAGTTTATAAAATAATTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
AAATTGAATTGAATTTTTGAGTTTTTGTTTAAAATTAATTATAAATATTTATAATACTATAATAT
TATTTGATTCTAATTCAG
Found at i:191222 original size:11 final size:11
Alignment explanation
Indices: 191206--191252 Score: 78
Period size: 11 Copynumber: 4.4 Consensus size: 11
191196 ACAATCAACA
191206 AGAATCAAGAG
1 AGAATCAAGAG
191217 AGAATCAAGAG
1 AGAATCAAGAG
*
191228 AGAACCAAGAG
1 AGAATCAAGAG
191239 AGAATCAA-AG
1 AGAATCAAGAG
191249 AGAA
1 AGAA
191253 AACATCAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
10 6 0.18
11 28 0.82
ACGTcount: A:0.57, C:0.11, G:0.26, T:0.06
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:191236 original size:22 final size:21
Alignment explanation
Indices: 191198--191252 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
191188 AATTAACAAC
*
191198 AATCAACA-AGAATCAAGAGAG
1 AATCAA-AGAGAACCAAGAGAG
191219 AATCAAGAGAGAACCAAGAGAG
1 AATCAA-AGAGAACCAAGAGAG
191241 AATCAAAGAGAA
1 AATCAAAGAGAA
191253 AACATCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.58, C:0.13, G:0.22, T:0.07
Consensus pattern (21 bp):
AATCAAAGAGAACCAAGAGAG
Found at i:192238 original size:35 final size:36
Alignment explanation
Indices: 192180--192251 Score: 103
Period size: 35 Copynumber: 2.0 Consensus size: 36
192170 CATGTAAGTA
*
192180 AAGTATTTTTGGAATTTGAGGTTTATAATATAATTG
1 AAGTATTTTTGGAATTTGAGGTTTAGAATATAATTG
*
192216 AAGTA-TTTTGGAATTT-ATGGTTTAGAATGTAATTG
1 AAGTATTTTTGGAATTTGA-GGTTTAGAATATAATTG
192251 A
1 A
192252 TGATTGTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 1 0.03
35 27 0.82
36 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (36 bp):
AAGTATTTTTGGAATTTGAGGTTTAGAATATAATTG
Found at i:202439 original size:18 final size:18
Alignment explanation
Indices: 202416--202456 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
202406 GAATAATAAA
202416 TTTGTGAATAGTAAAAAT
1 TTTGTGAATAGTAAAAAT
202434 TTTGTGAATAGTAAAAAT
1 TTTGTGAATAGTAAAAAT
202452 TTTGT
1 TTTGT
202457 CGATGATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (18 bp):
TTTGTGAATAGTAAAAAT
Found at i:207815 original size:30 final size:31
Alignment explanation
Indices: 207763--207837 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 31
207753 TTAACCTGTG
*
207763 GTGATCACATCTTAAATAAATAAAAACAAAA
1 GTGATCATATCTTAAATAAATAAAAACAAAA
* * * *
207794 GTGATCATAT-TTAATTAAATAAGAACGAAT
1 GTGATCATATCTTAAATAAATAAAAACAAAA
*
207824 GTGACCATATCTTA
1 GTGATCATATCTTA
207838 TGTATTTTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 25 0.68
31 12 0.32
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.29
Consensus pattern (31 bp):
GTGATCATATCTTAAATAAATAAAAACAAAA
Found at i:213111 original size:13 final size:13
Alignment explanation
Indices: 213093--213118 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
213083 TACTGGCAGG
213093 GGAGTATCAATAC
1 GGAGTATCAATAC
213106 GGAGTATCAATAC
1 GGAGTATCAATAC
213119 TGCTCACACT
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:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GGAGTATCAATAC
Found at i:213417 original size:21 final size:21
Alignment explanation
Indices: 213391--213444 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
213381 TCTCAAGGCA
* *
213391 AATATCGGTACTGCCATGCCC
1 AATATCGGTACCGCCAGGCCC
213412 AATATCGGTACCGCCAGGCCC
1 AATATCGGTACCGCCAGGCCC
213433 AATATCGGTACC
1 AATATCGGTACC
213445 CTCATCATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.20
Consensus pattern (21 bp):
AATATCGGTACCGCCAGGCCC
Found at i:214625 original size:75 final size:75
Alignment explanation
Indices: 214493--214635 Score: 187
Period size: 75 Copynumber: 1.9 Consensus size: 75
214483 AACGTCGGAG
**
214493 AAGGAAAGACGTTAGCATTCACGACTTTCAACAATTACTTACCCGACATTGCAGTTGTTCCGCTA
1 AAGGAAAGACGTTAGCATTCACGACTTTCAACAACCACTTACCCGACATTGCAGTTGTTCCGCTA
214558 AACATTAGAA
66 AACATTAGAA
** * * *** **
214568 AAGGAAAGGTGTTAGCATTCACGACTTTCAACAGCCACTTGCCCGGTGTTGTGGTTGTTCCGCTA
1 AAGGAAAGACGTTAGCATTCACGACTTTCAACAACCACTTACCCGACATTGCAGTTGTTCCGCTA
214633 AAC
66 AAC
214636 CTCTTCACCT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
75 57 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.27
Consensus pattern (75 bp):
AAGGAAAGACGTTAGCATTCACGACTTTCAACAACCACTTACCCGACATTGCAGTTGTTCCGCTA
AACATTAGAA
Found at i:221748 original size:19 final size:19
Alignment explanation
Indices: 221724--221761 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
221714 TTAGGTATTT
*
221724 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
221743 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
221762 GATATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:221749 original size:44 final size:43
Alignment explanation
Indices: 221711--221848 Score: 145
Period size: 43 Copynumber: 3.4 Consensus size: 43
221701 TTTTATATTT
221711 GTTTTAGGTATTTTATTTTAAATAGGTTTTAGTATTTTAATTAA
1 GTTTTAGG-ATTTTATTTTAAATAGGTTTTAGTATTTTAATTAA
* * *
221755 GTTTTAGGATATTATTTT-TATA---TTT--TA-TGT--TT--
1 GTTTTAGGATTTTATTTTAAATAGGTTTTAGTATTTTAATTAA
221787 GTTTTAGGTATTTTATTTTAAATAGGTTTTAGTATTTTAATTAA
1 GTTTTAGG-ATTTTATTTTAAATAGGTTTTAGTATTTTAATTAA
*
221831 GTTTTAGGATATTATTTT
1 GTTTTAGGATTTTATTTT
221849 TATATTTTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
32 8 0.11
33 9 0.12
34 5 0.07
36 2 0.03
37 5 0.07
39 5 0.07
40 2 0.03
42 5 0.07
43 18 0.24
44 16 0.21
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (43 bp):
GTTTTAGGATTTTATTTTAAATAGGTTTTAGTATTTTAATTAA
Found at i:221824 original size:19 final size:19
Alignment explanation
Indices: 221800--221837 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
221790 TTAGGTATTT
*
221800 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
221819 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
221838 GATATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:221932 original size:75 final size:76
Alignment explanation
Indices: 221696--221904 Score: 368
Period size: 76 Copynumber: 2.8 Consensus size: 76
221686 ATTTTAAATA
221696 TTATATTTTATATTTGTTTTAGGTATTTTATTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATATTTGTTTTAGGTATTTTATTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
221761 GGATATTATTT
66 GGATATTATTT
*
221772 TTATATTTTATGTTTGTTTTAGGTATTTTATTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATATTTGTTTTAGGTATTTTATTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
221837 GGATATTATTT
66 GGATATTATTT
* *
221848 TTATATTTTATCTTT-TTTTAGGTATTTTATTTTAAATA-GTTTTAAGTGTTTTAATTA
1 TTATATTTTATATTTGTTTTAGGTATTTTATTTTAAATAGGTTTT-AGTATTTTAATTA
221905 GGATTTAAGA
Statistics
Matches: 129, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
74 5 0.04
75 35 0.27
76 89 0.69
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.61
Consensus pattern (76 bp):
TTATATTTTATATTTGTTTTAGGTATTTTATTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
GGATATTATTT
Found at i:222572 original size:15 final size:15
Alignment explanation
Indices: 222552--222609 Score: 52
Period size: 14 Copynumber: 4.0 Consensus size: 15
222542 TTAAAACCCC
*
222552 CTTTTATCTTTATTA
1 CTTTTATATTTATTA
222567 CTTTTAATATTTATTA
1 CTTTT-ATATTTATTA
222583 -TTTTAT-TATT-TTA
1 CTTTTATAT-TTATTA
*
222596 CTTGT-TATTTATTA
1 CTTTTATATTTATTA
222610 TTATCTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
13 7 0.19
14 11 0.31
15 9 0.25
16 9 0.25
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (15 bp):
CTTTTATATTTATTA
Found at i:222581 original size:16 final size:15
Alignment explanation
Indices: 222560--222593 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
222550 CCCTTTTATC
222560 TTTATTACTTTTAATA
1 TTTATTA-TTTTAATA
*
222576 TTTATTATTTTATTA
1 TTTATTATTTTAATA
222591 TTT
1 TTT
222594 TACTTGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTATTTTAATA
Found at i:228128 original size:16 final size:16
Alignment explanation
Indices: 228103--228145 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
228093 ATTTCATTCT
*
228103 ATTTTTTTTTTCTTTC
1 ATTTTATTTTTCTTTC
* *
228119 ATTTTATTTTTGTTTT
1 ATTTTATTTTTCTTTC
228135 ATTTTTATTTT
1 A-TTTTATTTT
228146 ATTTTTAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.81
Consensus pattern (16 bp):
ATTTTATTTTTCTTTC
Found at i:228134 original size:11 final size:11
Alignment explanation
Indices: 228102--228152 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
228092 CATTTCATTC
228102 TATTTTT-TTT
1 TATTTTTATTT
*
228112 T-TCTTTCATTT
1 TAT-TTTTATTT
*
228123 TATTTTTGTTT
1 TATTTTTATTT
228134 TATTTTTATTT
1 TATTTTTATTT
228145 TATTTTTA
1 TATTTTTA
228153 GCAAACTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 1 0.03
10 4 0.12
11 28 0.82
12 1 0.03
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:228150 original size:16 final size:15
Alignment explanation
Indices: 228102--228152 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 15
228092 CATTTCATTC
228102 TATTTT-TTTTTTCTT
1 TATTTTATTTTTT-TT
228117 TCATTTTATTTTTGTTT
1 T-ATTTTATTTTT-TTT
228134 TATTTTTATTTTATTTT
1 TA-TTTTATTTT-TTTT
228151 TA
1 TA
228153 GCAAACTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 22 0.71
18 2 0.06
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (15 bp):
TATTTTATTTTTTTT
Found at i:228184 original size:20 final size:20
Alignment explanation
Indices: 228159--228201 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
228149 TTTAGCAAAC
*
228159 TTTATTTTCATT-ATATTTAT
1 TTTATTTTAATTAAT-TTTAT
228179 TTTATTTTAATTAATTTTAT
1 TTTATTTTAATTAATTTTAT
228199 TTT
1 TTT
228202 TTCTCTGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATTTTAATTAATTTTAT
Found at i:230465 original size:19 final size:20
Alignment explanation
Indices: 230437--230486 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
230427 TTAATATTTA
*
230437 TTATTTTATTATT-TCTCTT
1 TTATTTTATTATTATCTATT
230456 TT-TATTTATTATTATCTATT
1 TTAT-TTTATTATTATCTATT
230476 TTATTTTATTA
1 TTATTTTATTA
230487 AATCTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.04
19 11 0.41
20 14 0.52
21 1 0.04
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTTTATTATTATCTATT
Found at i:231635 original size:21 final size:22
Alignment explanation
Indices: 231611--231653 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
231601 AGGTATCGAT
*
231611 TTTTTTTA-AAGAGATCGATCC
1 TTTTTTCACAAGAGATCGATCC
*
231632 -TTTTTCACAAGGGATCGATCC
1 TTTTTTCACAAGAGATCGATCC
231653 T
1 T
231654 ATATTGGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40
Consensus pattern (22 bp):
TTTTTTCACAAGAGATCGATCC
Found at i:245680 original size:25 final size:25
Alignment explanation
Indices: 245629--245683 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
245619 TTACTTATAT
245629 AATAGTTTTAAAGATTATTTATAAA
1 AATAGTTTTAAAGATTATTTATAAA
*
245654 AATA-TTTTCAAGATTATTTATTCAAA
1 AATAGTTTTAAAGATTATTTA-T-AAA
245680 AATA
1 AATA
245684 TAAATTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 15 0.56
25 5 0.19
26 7 0.26
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (25 bp):
AATAGTTTTAAAGATTATTTATAAA
Found at i:245868 original size:13 final size:13
Alignment explanation
Indices: 245850--245874 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
245840 TACTTTTAAG
245850 ATATATATATATA
1 ATATATATATATA
245863 ATATATATATAT
1 ATATATATATAT
245875 GTTTGAACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Found at i:247962 original size:2 final size:2
Alignment explanation
Indices: 247910--247951 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
247900 ATTTATTAAG
247910 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
247952 TCACTTATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:248462 original size:16 final size:16
Alignment explanation
Indices: 248437--248479 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
248427 AACGTCTTTT
248437 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
248453 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
248470 ACAAAAATTT
1 AAAAAAATTT
248480 GATCTACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:250747 original size:25 final size:24
Alignment explanation
Indices: 250713--250862 Score: 210
Period size: 25 Copynumber: 6.0 Consensus size: 24
250703 TGGAAGGGGA
*
250713 TTAGGGTTTGAAACCCTAATTGGTT
1 TTAGGGTTTGAAACCCTAATT-GAT
250738 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAT-TGAT
*
250763 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCT-AATTGAT
*
250788 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCT-AATTGAT
250813 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAT-TGAT
*
250838 TTAGGGTTTAAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAT-TGAT
250863 GGGTTATTGG
Statistics
Matches: 118, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
24 2 0.02
25 113 0.96
26 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (24 bp):
TTAGGGTTTGAAACCCTAATTGAT
Found at i:250791 original size:50 final size:50
Alignment explanation
Indices: 250713--250862 Score: 239
Period size: 50 Copynumber: 3.0 Consensus size: 50
250703 TGGAAGGGGA
* *
250713 TTAGGGTTTGAAACCCT-AATTGGTTTTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACT-GATTTAGGGTTTGAAACCCTAATCTGAT
*
250763 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAATCTGAT
* *
250813 TTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTAAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAATCTGAT
250863 GGGTTATTGG
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 90 0.97
51 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (50 bp):
TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAATCTGAT
Found at i:250836 original size:75 final size:75
Alignment explanation
Indices: 250713--250862 Score: 248
Period size: 75 Copynumber: 2.0 Consensus size: 75
250703 TGGAAGGGGA
* * *
250713 TTAGGGTTTGAAACCCTAATTGGTTTTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTGAAACC
1 TTAGGGTTTGAAACCCTAACTGGATTTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTAAAACC
250778 CTAAACTGAT
66 CTAAACTGAT
250788 TTAGGGTTTGAAACCCTAAACT-GATTTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTAAAAC
1 TTAGGGTTTGAAACCCT-AACTGGATTTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTAAAAC
*
250852 CCTAATCTGAT
65 CCTAAACTGAT
250863 GGGTTATTGG
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
75 67 0.96
76 3 0.04
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (75 bp):
TTAGGGTTTGAAACCCTAACTGGATTTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTAAAACC
CTAAACTGAT
Found at i:250942 original size:3 final size:3
Alignment explanation
Indices: 250934--250994 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
250924 AAAAAATATG
* **
250934 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
250978 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
250995 CGATAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:250959 original size:28 final size:28
Alignment explanation
Indices: 250942--251000 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
250932 TGTAATAATA
*
250942 AATAATAATAAAATAATAAGATAACGAT
1 AATAATAATAAAATAATAAGATAACAAT
* *
250970 AATAATAATAATAATAATAAAATAACGAT
1 AATAATAATAA-AATAATAAGATAACAAT
250999 AA
1 AA
251001 AAAAAACCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.25
Consensus pattern (28 bp):
AATAATAATAAAATAATAAGATAACAAT
Found at i:251368 original size:87 final size:89
Alignment explanation
Indices: 251180--251576 Score: 525
Period size: 87 Copynumber: 4.4 Consensus size: 89
251170 ATGAAGAGGT
* * * * *
251180 CTGGTCATCTAAGGGTGACATGGCTCCTACGTGATGAGGAGATCTGGTCATCTAAAGGGATGATA
1 CTGGTTATCT-AGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGCCATCTAAAGGG-TGATA
* * *
251245 ACTCGGTTCCTACGTAATGAGGACGA
64 ACACGGTTCCTACGTGATGAGGACGG
*
251271 CTGGTTATC-AGGTTGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAA-GGTGATAAC
1 CTGGTTATCTAGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGCCATCTAAAGGGTGATAAC
251334 ACGGTTCCTACGTGATGAGGACGG
66 ACGGTTCCTACGTGATGAGGACGG
*
251358 CTGGTTATC-AGGTTGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAA-GGTGATAAC
1 CTGGTTATCTAGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGCCATCTAAAGGGTGATAAC
251421 ACGGTTCCTACGTGATGAGGACGG
66 ACGGTTCCTACGTGATGAGGACGG
* * *
251445 CTGGTTATCTATGGTTGACACGGCTCATACATGATGAAGA-ACTCTGGCCACCTTTAGGAAGGGT
1 CTGGTTATCTA-GGTTGACACGGCTCCTACGTGATGAAGAGA-TCTGGCCA--TCTA--AAGGGT
* *
251509 GATAACTCGGTTCCTACGTGATAAGGACGG
60 GATAACACGGTTCCTACGTGATGAGGACGG
*
251539 CTGGTTATCCTAATGTTGACACGGCTCCTACGTGATGA
1 CTGGTTAT-CT-AGGTTGACACGGCTCCTACGTGATGA
251577 GGAAGTCTGG
Statistics
Matches: 279, Mismatches: 17, Indels: 16
0.89 0.05 0.05
Matches are distributed among these distances:
87 124 0.44
88 4 0.01
89 74 0.27
91 11 0.04
93 2 0.01
94 39 0.14
95 24 0.09
96 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (89 bp):
CTGGTTATCTAGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGCCATCTAAAGGGTGATAAC
ACGGTTCCTACGTGATGAGGACGG
Found at i:251389 original size:41 final size:42
Alignment explanation
Indices: 251252--251579 Score: 162
Period size: 46 Copynumber: 7.4 Consensus size: 42
251242 ATAACTCGGT
* *
251252 TCCTACGTAATGAGGACGACTGGTTATC-AGGTTGACACGGC
1 TCCTACGTGATGAGGACGGCTGGTTATCAAGGTTGACACGGC
* * * ** * *
251293 TCTTACGTGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGT
1 TCCTACGTGATGAGGACG-GCTGGTTATC--AAGGT--TGACACGGC
251339 TCCTACGTGATGAGGACGGCTGGTTATC-AGGTTGACACGGC
1 TCCTACGTGATGAGGACGGCTGGTTATCAAGGTTGACACGGC
* * * ** * *
251380 TCTTACGTGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGT
1 TCCTACGTGATGAGGACG-GCTGGTTATC--AAGGT--TGACACGGC
*
251426 TCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGACGGCTGGTTATC-AAGGTTGACACGGC
* * * * ** * * *
251469 TCATACATGATGAAGAAC-TCTGGCCACCTTTAGGAAGGGTGATAACTCGGT
1 TCCTACGTGATG-AGGACGGCTGG------TTATCAA-GGT--TGACACGGC
* *
251520 TCCTACGTGATAAGGACGGCTGGTTATCCTAATGTTGACACGGC
1 TCCTACGTGATGAGGACGGCTGGTTAT-C-AAGGTTGACACGGC
251564 TCCTACGTGATGAGGA
1 TCCTACGTGATGAGGA
251580 AGTCTGGTCA
Statistics
Matches: 207, Mismatches: 53, Indels: 51
0.67 0.17 0.16
Matches are distributed among these distances:
40 2 0.01
41 48 0.23
43 25 0.12
44 33 0.16
45 7 0.03
46 58 0.28
47 4 0.02
48 1 0.00
49 6 0.03
50 4 0.02
51 19 0.09
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (42 bp):
TCCTACGTGATGAGGACGGCTGGTTATCAAGGTTGACACGGC
Found at i:252562 original size:1 final size:1
Alignment explanation
Indices: 252558--252583 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
252548 TTCATTCCCC
252558 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
252584 AGGTGTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:263542 original size:16 final size:16
Alignment explanation
Indices: 263517--263559 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
263507 AACGTCTTTT
263517 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
263533 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
263550 ACAAAAATTT
1 AAAAAAATTT
263560 GATCTACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:265835 original size:25 final size:24
Alignment explanation
Indices: 265801--265950 Score: 192
Period size: 25 Copynumber: 6.0 Consensus size: 24
265791 TGGAAGGGGA
*
265801 TTAGGGTTTGAAACCCTAATTGGTT
1 TTAGGGTTTGAAACCCTAATT-GAT
*
265826 TTAGGGTTTGAAACCCTAATTGGTT
1 TTAGGGTTTGAAACCCTAATT-GAT
*
265851 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCT-AATTGAT
* *
265876 TTAGGGTTTAAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCT-AATTGAT
265901 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAT-TGAT
*
265926 TTAGGGTTTAAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAT-TGAT
265951 GGGTTGTTGG
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
24 2 0.02
25 112 0.96
26 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (24 bp):
TTAGGGTTTGAAACCCTAATTGAT
Found at i:265929 original size:75 final size:75
Alignment explanation
Indices: 265801--265950 Score: 214
Period size: 75 Copynumber: 2.0 Consensus size: 75
265791 TGGAAGGGGA
* * * * *
265801 TTAGGGTTTGAAACCCTAATTGGTTTTAGGGTTTGAAACCCTAATTGGTTTTAGGGTTTGAAACC
1 TTAGGGTTTAAAACCCTAACTGGATTTAGGGTTTGAAACCCTAATTGGATTTAGGGTTTAAAACC
265866 CTAAACTGAT
66 CTAAACTGAT
265876 TTAGGGTTTAAAACCCTAAACT-GATTTAGGGTTTGAAACCCTAATCT-GATTTAGGGTTTAAAA
1 TTAGGGTTTAAAACCCT-AACTGGATTTAGGGTTTGAAACCCTAAT-TGGATTTAGGGTTTAAAA
*
265939 CCCTAATCTGAT
64 CCCTAAACTGAT
265951 GGGTTGTTGG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
75 63 0.94
76 4 0.06
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (75 bp):
TTAGGGTTTAAAACCCTAACTGGATTTAGGGTTTGAAACCCTAATTGGATTTAGGGTTTAAAACC
CTAAACTGAT
Found at i:266030 original size:3 final size:3
Alignment explanation
Indices: 266022--266082 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
266012 AAAAAATATG
* **
266022 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
266066 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
266083 CGATAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:266047 original size:28 final size:28
Alignment explanation
Indices: 266030--266088 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
266020 TGTAATAATA
*
266030 AATAATAATAAAATAATAAGATAACGAT
1 AATAATAATAAAATAATAAGATAACAAT
* *
266058 AATAATAATAATAATAATAAAATAACGAT
1 AATAATAATAA-AATAATAAGATAACAAT
266087 AA
1 AA
266089 AAAAAACCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.25
Consensus pattern (28 bp):
AATAATAATAAAATAATAAGATAACAAT
Found at i:267153 original size:35 final size:35
Alignment explanation
Indices: 267042--267232 Score: 167
Period size: 35 Copynumber: 5.5 Consensus size: 35
267032 ACCTCCAGAG
* * *
267042 GCACCTCTTGGAGTGATAATACACGACTTTTGGAA
1 GCACCTCTTGGAGTGAAAAGACACGAATTTTGGAA
* * * * * *
267077 TCACCTATTGTAGTGAAAAAAC-CTGACA-TTTAGAG
1 GCACCTCTTGGAGTGAAAAGACAC-GA-ATTTTGGAA
*
267112 GCACCTCTTGGAGTGAAAAGACATGAATTTTGGAA
1 GCACCTCTTGGAGTGAAAAGACACGAATTTTGGAA
* * * *
267147 GGACCTCTTGGACTAAAAAGACACGACTTTTGGAA
1 GCACCTCTTGGAGTGAAAAGACACGAATTTTGGAA
* *
267182 GCACCTGTTGGAGTGAAAAGACAC-AACTTTTAGAA
1 GCACCTCTTGGAGTGAAAAGACACGAA-TTTTGGAA
*
267217 GCATCTCTT--AGTGAAA
1 GCACCTCTTGGAGTGAAA
267233 CATCATGTCC
Statistics
Matches: 123, Mismatches: 28, Indels: 12
0.75 0.17 0.07
Matches are distributed among these distances:
33 7 0.06
34 3 0.02
35 113 0.92
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (35 bp):
GCACCTCTTGGAGTGAAAAGACACGAATTTTGGAA
Found at i:271057 original size:16 final size:16
Alignment explanation
Indices: 271030--271077 Score: 87
Period size: 16 Copynumber: 2.9 Consensus size: 16
271020 CGAGGTATTC
271030 TAAAAGCTAACTAAATT
1 TAAAA-CTAACTAAATT
271047 TAAAACTAACTAAATT
1 TAAAACTAACTAAATT
271063 TAAAACTAACTAAAT
1 TAAAACTAACTAAAT
271078 CTTAGTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 26 0.84
17 5 0.16
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.29
Consensus pattern (16 bp):
TAAAACTAACTAAATT
Found at i:271937 original size:21 final size:22
Alignment explanation
Indices: 271899--271939 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
271889 ATTTTAGTAT
* *
271899 AAGCCCAAATAGATAGAAAATA
1 AAGCACAAAGAGATAGAAAATA
271921 AAGCACAAAGAGA-AGAAAA
1 AAGCACAAAGAGATAGAAAA
271940 ACACCCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.63, C:0.12, G:0.17, T:0.07
Consensus pattern (22 bp):
AAGCACAAAGAGATAGAAAATA
Found at i:274288 original size:21 final size:21
Alignment explanation
Indices: 274258--274311 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
274248 CGATTCAACT
274258 AGTATCGATACTGCTCATCCC
1 AGTATCGATACTGCTCATCCC
* * *
274279 AGTATTGATAATGTTCATCCC
1 AGTATCGATACTGCTCATCCC
274300 AGTATCGATACT
1 AGTATCGATACT
274312 CAAACTCTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (21 bp):
AGTATCGATACTGCTCATCCC
Found at i:277629 original size:2 final size:2
Alignment explanation
Indices: 277622--277654 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
277612 GCCAGTCTAT
*
277622 AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
277655 CCAAACAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:279122 original size:40 final size:40
Alignment explanation
Indices: 279067--279149 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
279057 GAGAGTTTAT
279067 ACCTAAGGGAACTTGAACTTTATCTTCTTGGAAGATTACA
1 ACCTAAGGGAACTTGAACTTTATCTTCTTGGAAGATTACA
279107 ACCTAAGGGAACTTGAACTTTATCTTCTTGGAAGATTACA
1 ACCTAAGGGAACTTGAACTTTATCTTCTTGGAAGATTACA
279147 ACC
1 ACC
279150 AAAGAAAGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (40 bp):
ACCTAAGGGAACTTGAACTTTATCTTCTTGGAAGATTACA
Found at i:284162 original size:36 final size:36
Alignment explanation
Indices: 284117--284186 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
284107 AAAGTATGAA
*
284117 TTTGAAATGATATGATTTCGAAA-AGAAAACTACAGT
1 TTTGAAATGATATGAATT-GAAATAGAAAACTACAGT
* *
284153 TTTGCAATGATATGAATTGAAATAGAAAAGTACA
1 TTTGAAATGATATGAATTGAAATAGAAAACTACA
284187 AATCCAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (36 bp):
TTTGAAATGATATGAATTGAAATAGAAAACTACAGT
Found at i:288326 original size:24 final size:24
Alignment explanation
Indices: 288299--288351 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
288289 GAGAAGCATC
*
288299 TCTATTTTACTTTCTACATCTCAA
1 TCTAGTTTACTTTCTACATCTCAA
288323 TCTAGTTTACTTTCTACATCTCAA
1 TCTAGTTTACTTTCTACATCTCAA
288347 TCTAG
1 TCTAG
288352 AGGTAATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.04, T:0.47
Consensus pattern (24 bp):
TCTAGTTTACTTTCTACATCTCAA
Found at i:289887 original size:12 final size:12
Alignment explanation
Indices: 289870--289911 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 12
289860 ACTCGTTTAC
289870 CCGACCCGTTGA
1 CCGACCCGTTGA
289882 CCGACCCGTTGA
1 CCGACCCGTTGA
289894 CCGTTGACCCGTTGA
1 CC---GACCCGTTGA
289909 CCG
1 CCG
289912 TTGACCGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 15 0.56
15 12 0.44
ACGTcount: A:0.14, C:0.40, G:0.26, T:0.19
Consensus pattern (12 bp):
CCGACCCGTTGA
Found at i:289899 original size:7 final size:7
Alignment explanation
Indices: 289887--289918 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
289877 GTTGACCGAC
289887 CCGTTGA
1 CCGTTGA
289894 CCGTTGA
1 CCGTTGA
289901 CCCGTTGA
1 -CCGTTGA
289909 CCGTTGA
1 CCGTTGA
289916 CCG
1 CCG
289919 GCATTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:289904 original size:15 final size:15
Alignment explanation
Indices: 289872--289917 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
289862 TCGTTTACCC
289872 GACCCGTTGACC---
1 GACCCGTTGACCGTT
289884 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
289899 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
289914 GACC
1 GACC
289918 GGCATTGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.37, G:0.26, T:0.22
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:292475 original size:24 final size:24
Alignment explanation
Indices: 292448--292562 Score: 128
Period size: 24 Copynumber: 4.8 Consensus size: 24
292438 TTCGATTTGA
292448 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
292472 ATTCTGATCTGATA-TCTAACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
292496 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
292520 ATTCTGATCT-ATTACTTGACCT-G
1 ATTCTGATCTGA-TACTTGACATGG
* * *
292543 ATTCCGATCTGTTTCTTGAC
1 ATTCTGATCTGATACTTGAC
292563 CTGATTTATG
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
23 19 0.24
24 58 0.74
25 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:295871 original size:30 final size:30
Alignment explanation
Indices: 295811--295895 Score: 73
Period size: 31 Copynumber: 2.8 Consensus size: 30
295801 CAACAATCTA
* * *
295811 CAACTTTTCCAAAATTA-ATGATTTGGTCCCC
1 CAACTTTTCAAAAATTATA-GA-ATGATCCCC
295842 CAACTTTTCAAAAATTATAGAATGATCCCC
1 CAACTTTTCAAAAATTATAGAATGATCCCC
* * * *
295872 AAATTTTTCGAAGACTTATAGAAT
1 CAACTTTTC-AAAAATTATAGAAT
295896 ACTTACTACA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
30 14 0.31
31 30 0.67
32 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (30 bp):
CAACTTTTCAAAAATTATAGAATGATCCCC
Found at i:298241 original size:39 final size:39
Alignment explanation
Indices: 298174--298252 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
298164 GAACAAAATC
* *
298174 TTACATGCTCACATATCGGGGGTAAAGTAAGTAAGAGAT
1 TTACATGCTCACATACCGAGGGTAAAGTAAGTAAGAGAT
*
298213 TTACATGCTCACATACCGAGGGTGAAGTAAGTAAGAGAT
1 TTACATGCTCACATACCGAGGGTAAAGTAAGTAAGAGAT
298252 T
1 T
298253 ATTAGGTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (39 bp):
TTACATGCTCACATACCGAGGGTAAAGTAAGTAAGAGAT
Found at i:301175 original size:25 final size:25
Alignment explanation
Indices: 301142--301196 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
301132 TCTATATCAA
* *
301142 ATATAAAGAAATATATATGTATTAT
1 ATATGAAGAAATATATAAGTATTAT
*
301167 ATATGAAGAAATATATAAGTATTGT
1 ATATGAAGAAATATATAAGTATTAT
301192 ATATG
1 ATATG
301197 GTTGTAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (25 bp):
ATATGAAGAAATATATAAGTATTAT
Found at i:301993 original size:157 final size:157
Alignment explanation
Indices: 301741--302160 Score: 497
Period size: 158 Copynumber: 2.7 Consensus size: 157
301731 ATTTATTCTC
* * * * * * *
301741 TAATTTCATTATTCTTTCAATTCCTCCATCATTTTAAATCTATTTTTTTACCAAATTTTAACCAC
1 TAATTTCCTTATTTTTTCAATTCATCCTTTATTTTAAGTC-ATTTTTTTACCAAATTTGAACCAC
* * * * * * *
301806 ATGCTCCTAAAACACAGTAGACTACATATGTACTTTTAATTCCT-CTTTTTGATAATAATTTTTT
65 ATGCTCATATAACACAATAGAATACCTATGTAC-TTAAATTCCTCCTTTTTGATAATAAATTTTT
* * *
301870 CTTTTACAATTTAGTCCCTCAATTTTTCA
129 ATTTTACAATTTAGTCCCTAAATATTTCA
* *
301899 TAATTTCCTTATTTTTTCAAGTCTTCCTTTATTTTAAGTCATTTTTTTACCAAATTTGAACCACA
1 TAATTTCCTTATTTTTTCAATTCATCCTTTATTTTAAGTCATTTTTTTACCAAATTTGAACCACA
** *
301964 AACTCATATACCACAATAGAATACCTATGTAACTTAAATTCCTCCTTTTTGATAATAAATTTTTA
66 TGCTCATATAACACAATAGAATACCTATGT-ACTTAAATTCCTCCTTTTTGATAATAAATTTTTA
*
302029 TTTTTCAATTTAGTCCCTAAATATTTCA
130 TTTTACAATTTAGTCCCTAAATATTTCA
* * *
302057 TAATTTCCTTATTTCTACAATTCATCCTTTATTTTAAGT--TCGTTTTTACCAAATTTGAACCAC
1 TAATTTCCTTATTTTTTCAATTCATCCTTTATTTTAAGTCAT-TTTTTTACCAAATTTGAACCAC
** *
302120 ATGCTCGA-ATATTACAATAGAATACCTATGTAACTTCAATT
65 ATGCTC-ATATAACACAATAGAATACCTATGT-ACTTAAATT
302161 TCTACATTTT
Statistics
Matches: 226, Mismatches: 32, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
156 1 0.00
157 110 0.49
158 115 0.51
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (157 bp):
TAATTTCCTTATTTTTTCAATTCATCCTTTATTTTAAGTCATTTTTTTACCAAATTTGAACCACA
TGCTCATATAACACAATAGAATACCTATGTACTTAAATTCCTCCTTTTTGATAATAAATTTTTAT
TTTACAATTTAGTCCCTAAATATTTCA
Found at i:302171 original size:158 final size:155
Alignment explanation
Indices: 301785--302160 Score: 470
Period size: 157 Copynumber: 2.4 Consensus size: 155
301775 TAAATCTATT
* * * * *
301785 TTTTTACCAAATTTTAACCACATGCTCCTAA-AACACAGTAGACTACATATGT-ACTTTTAATTC
1 TTTTTACCAAATTTGAACCACATGCT-C-AATAACACAATAGAATACCTATGTAAC-TTAAATTC
* * * *
301848 CTCTTTTTGATAATAATTTTTTCTTTTACAATTTAGTCCCTCAATTTTTCATAATTTCCTTATTT
63 CTCTTTTTGATAATAAATTTTTATTTTACAATTTAGTCCCTAAATATTTCATAATTTCCTTATTT
* * * *
301913 TTTCAAGTCTTCCTTTATTTTAAGTCATT
128 CTACAAGTCATCCTTTATTTTAAGTCA-G
** *
301942 TTTTTACCAAATTTGAACCACAAACTCATATACCACAATAGAATACCTATGTAACTTAAATTCCT
1 TTTTTACCAAATTTGAACCACATGCTCA-ATAACACAATAGAATACCTATGTAACTTAAATTCCT
*
302007 CCTTTTTGATAATAAATTTTTATTTTTCAATTTAGTCCCTAAATATTTCATAATTTCCTTATTTC
65 -CTTTTTGATAATAAATTTTTATTTTACAATTTAGTCCCTAAATATTTCATAATTTCCTTATTTC
*
302072 TACAATTCATCCTTTATTTTAAGTTC-G
129 TACAAGTCATCCTTTATTTTAAG-TCAG
** *
302099 TTTTTACCAAATTTGAACCACATGCTCGAATATTACAATAGAATACCTATGTAACTTCAATT
1 TTTTTACCAAATTTGAACCACATGCTC-AATAACACAATAGAATACCTATGTAACTTAAATT
302161 TCTACATTTT
Statistics
Matches: 190, Mismatches: 23, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
155 1 0.01
156 2 0.01
157 104 0.55
158 81 0.43
159 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.44
Consensus pattern (155 bp):
TTTTTACCAAATTTGAACCACATGCTCAATAACACAATAGAATACCTATGTAACTTAAATTCCTC
TTTTTGATAATAAATTTTTATTTTACAATTTAGTCCCTAAATATTTCATAATTTCCTTATTTCTA
CAAGTCATCCTTTATTTTAAGTCAG
Found at i:310298 original size:3 final size:3
Alignment explanation
Indices: 310290--310359 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
310280 TCCCAACATC
310290 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
310338 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
310360 TATTATTATT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:310366 original size:3 final size:3
Alignment explanation
Indices: 310360--310393 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
310350 AATAATAATA
310360 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
310394 TACAGGCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:318594 original size:15 final size:15
Alignment explanation
Indices: 318574--318625 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
318564 CTTCACTAGC
*
318574 CAATAAAGGCAACTA
1 CAATAAAGGCAATTA
318589 CAATAAAGTG-AATTA
1 CAATAAAG-GCAATTA
318604 CAATAAAGGCAATTA
1 CAATAAAGGCAATTA
318619 CAATAAA
1 CAATAAA
318626 TTAAATCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
14 1 0.03
15 32 0.94
16 1 0.03
ACGTcount: A:0.56, C:0.13, G:0.12, T:0.19
Consensus pattern (15 bp):
CAATAAAGGCAATTA
Found at i:319318 original size:44 final size:44
Alignment explanation
Indices: 319259--319398 Score: 176
Period size: 44 Copynumber: 3.2 Consensus size: 44
319249 AGAAATGATG
*
319259 AATGTTGGGGCACTTTTGAAGGACCATATCATCCAGAAGTAATG
1 AATGTTGGGGCACTTTTGAAGGACCATATCATCCAGAAGTAATA
* **
319303 AATGTTGGGGCACTTTTGAA-TATCTGTATCATCCAGAAGTAATA
1 AATGTTGGGGCACTTTTGAAGGA-CCATATCATCCAGAAGTAATA
* * * * *
319347 AATATTGGGGCA-TTTTGAAGGCCCATATCAGCAAGAAATAATA
1 AATGTTGGGGCACTTTTGAAGGACCATATCATCCAGAAGTAATA
319390 AATGTTGGG
1 AATGTTGGG
319399 ACATTTTTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
43 32 0.40
44 49 0.60
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (44 bp):
AATGTTGGGGCACTTTTGAAGGACCATATCATCCAGAAGTAATA
Found at i:320654 original size:38 final size:38
Alignment explanation
Indices: 320611--320922 Score: 374
Period size: 38 Copynumber: 8.1 Consensus size: 38
320601 AGTTGATTTT
* *
320611 TCTTTGTTATTATTGACTTCCTCTTGAAGAGAAGTCAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* ** * *
320649 TCTTTGTTACTCTTGACTTCCAAGTGAATAGAAGTAAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* * *
320687 TCTTTGTTACTCTTGACTTCCTCATAAAGAGAAGTCAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* * *
320725 TCTTTGTTATTTTTGATTTCTTCGTGAAGAGAAGTCAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* * *
320763 TCCTTGTTATTCTTGAATTCCTCATGAAGAGAAGTCAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* *
320801 TCTTTTTTATT-TTGACTTTCTCGTGAAGAGAAGTCAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* *
320838 TCTTTGTTATTCTTAACTTCCTCGTGAAGAAAAGTCAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* * *
320876 TCTTTCAATGTCATTCTTGACTTTCTCGTAAAGAGAAGTCAA
1 TC-TT---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
320918 TCTTT
1 TCTTT
320923 TAGTGTTGGC
Statistics
Matches: 231, Mismatches: 38, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
37 33 0.14
38 163 0.71
39 2 0.01
41 2 0.01
42 31 0.13
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (38 bp):
TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
Found at i:320946 original size:45 final size:45
Alignment explanation
Indices: 320847--321057 Score: 200
Period size: 45 Copynumber: 4.8 Consensus size: 45
320837 ATCTTTGTTA
* * * * * *
320847 TTCTTAACTTCCTCGTGAAGAAAAGTCAATCTTTCA---ATGTCA
1 TTCTTGACTTTCTCGTAAAGAGAAGTCAATCTTTCAGTGTTGTCC
* *
320889 TTCTTGACTTTCTCGTAAAGAGAAGTCAATCTTTTAGTGTTGGCC
1 TTCTTGACTTTCTCGTAAAGAGAAGTCAATCTTTCAGTGTTGTCC
* * *
320934 TTCTTAACTTTCT--TACGAAGAGGAA-TCAATCTTCCAGTGTCGTCC
1 TTCTTGACTTTCTCGTA--AAGA-GAAGTCAATCTTTCAGTGTTGTCC
* * * *
320979 TTCTTGACTTTCTCATGAAGGGAAGTCAATCTTTCAGTGTTGTCT
1 TTCTTGACTTTCTCGTAAAGAGAAGTCAATCTTTCAGTGTTGTCC
* *
321024 TTCTTGACTTTCTCGCAAAGAGGAGTCAATCTTT
1 TTCTTGACTTTCTCGTAAAGAGAAGTCAATCTTT
321058 TAGATTTGGT
Statistics
Matches: 136, Mismatches: 24, Indels: 15
0.78 0.14 0.09
Matches are distributed among these distances:
42 31 0.23
43 2 0.01
44 3 0.02
45 96 0.71
46 3 0.02
47 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.38
Consensus pattern (45 bp):
TTCTTGACTTTCTCGTAAAGAGAAGTCAATCTTTCAGTGTTGTCC
Found at i:321008 original size:90 final size:90
Alignment explanation
Indices: 320889--321056 Score: 237
Period size: 90 Copynumber: 1.9 Consensus size: 90
320879 TTCAATGTCA
* * * *
320889 TTCTTGACTTTCTCGTAAAGAGAAGTCAATCTTTTAGTGTTGGCCTTCTTAACTTTCTTACGAAG
1 TTCTTGACTTTCTCATAAAGAGAAGTCAATCTTTCAGTGTTGGCCTTCTTAACTTTCTCACAAAG
320954 AGGAATCAATCTTCCAGTGTCGTCC
66 AGGAATCAATCTTCCAGTGTCGTCC
* * * * * *
320979 TTCTTGACTTTCTCATGAAGGGAAGTCAATCTTTCAGTGTTGTCTTTCTTGACTTTCTCGCAAAG
1 TTCTTGACTTTCTCATAAAGAGAAGTCAATCTTTCAGTGTTGGCCTTCTTAACTTTCTCACAAAG
*
321044 AGGAGTCAATCTT
66 AGGAATCAATCTT
321057 TTAGATTTGG
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
90 67 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (90 bp):
TTCTTGACTTTCTCATAAAGAGAAGTCAATCTTTCAGTGTTGGCCTTCTTAACTTTCTCACAAAG
AGGAATCAATCTTCCAGTGTCGTCC
Found at i:321300 original size:136 final size:135
Alignment explanation
Indices: 321053--321661 Score: 731
Period size: 135 Copynumber: 4.5 Consensus size: 135
321043 GAGGAGTCAA
* * * * *
321053 TCTTTTAGATTTGGTCTTCCTGAAGAGCAACGAAGCAAATCAAGTTAGATTCAATCTTTCCTGAT
1 TCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAA
* * *
321118 GTGCAGCGAAGTGGATCAAAATTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGCAGAGCATATT
66 GAGCAGCGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCGCCTAAAGAGTAGCAGAGCATATT
321183 CTTCT
131 CTTCT
* * *
321188 TCTTTCAGATTTGGTCTTCCTGAAGAGCAGCAAAAGAAAATCAAGTTCGATTCAATCTTTCCTGA
1 TCTTTCAGATTTGGTCTTCCTGAAGAGCAGC-GAAGCAAATCAAGTTCGATTCAATCTTCCCTGA
* * * * *
321253 TGAGCAGCAAAGTGGATCAAAATTTTTCTCGAGTCTGATCTCGCCTAAAGAGTAGCAAAACATAT
65 AGAGCAGCGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCGCCTAAAGAGTAGCAGAGCATAT
*
321318 TCTTGT
130 TCTTCT
* * * * *
321324 TCTTTTAGATTTGGTCCTCCTGAAGAGAAGTGAAGCAAATCAAGTTCGATTTAATCTTCCCTGAA
1 TCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAA
* * * * *
321389 GAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTTGCCTAAAGAGTAGCGGACCAGATT
66 GAGCAGCGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCGCCTAAAGAGTAGCAGAGCATATT
321454 CTTCT
131 CTTCT
* * *
321459 TCTTTCAGATTTGGTCTTCCTAAAGAGCAGCGGAGCAAATCAAGTTCGATTCAATCTTCCCAGAA
1 TCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAA
* * *
321524 GAGTAGCGAAGTGGATCAAAA-TTTTATCAAGCCTGATCTC-CCTTAAAGAGTAGCGGAGTAG-A
66 GAGCAGCGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCGCC-TAAAGAGTAGC--AG-AGCA
* *
321586 TTTTCTTTT
127 TATTCTTCT
* ** * * ** * **
321595 TCTTTAAGATTTTATCTCCCTGAAGAGTAGTAAAGCAAATCGA-TTATTATTCAATCTTCCCTGA
1 TCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTT-CGATTCAATCTTCCCTGA
321659 AGA
65 AGA
321662 ACAGTGAAAT
Statistics
Matches: 408, Mismatches: 60, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
133 2 0.00
134 27 0.07
135 197 0.48
136 181 0.44
137 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (135 bp):
TCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAA
GAGCAGCGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCGCCTAAAGAGTAGCAGAGCATATT
CTTCT
Found at i:321619 original size:271 final size:271
Alignment explanation
Indices: 321053--321661 Score: 780
Period size: 271 Copynumber: 2.2 Consensus size: 271
321043 GAGGAGTCAA
* * *
321053 TCTTTTAGATTTGGTCTTCCTGAAGAGCAA-CGAAGCAAATCAAGTTAGATTCAATCTTTCCTGA
1 TCTTTTAGATTTGGTCTCCCTGAAGAG-AAGTGAAGCAAATCAAGTTAGATTCAATCTTCCCTGA
* * * * * *
321117 TGTGCAGCGAAGTGGATCAAAATTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGCAGAGCATAT
65 AGAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCCCCTAAAGAGTAGCAGACCAGAT
*
321182 TCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGCAAAAGAAAATCAAGTTCGATTCAATCTT
130 TCTTCTTCTTTCAGATTTGGTCTTCCTAAAGAGCAGCAAAAGAAAATCAAGTTCGATTCAATCTT
* * * * * *
321247 TCCTGATGAGCAGCAAAGTGGATCAAAATTTTTCTCGAGTCTGATCTCGCCTAAAGAGTAGCAAA
195 CCCAGAAGAGCAGCAAAGTGGATCAAAATTTTTATCAAGCCTGATCTCGCCTAAAGAGTAGCAAA
321312 ACATATTCTTGT
260 ACATATTCTTGT
* *
321324 TCTTTTAGATTTGGTC-CTCCTGAAGAGAAGTGAAGCAAATCAAGTTCGATTTAATCTTCCCTGA
1 TCTTTTAGATTTGGTCTC-CCTGAAGAGAAGTGAAGCAAATCAAGTTAGATTCAATCTTCCCTGA
** *
321388 AGAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTTGCCTAAAGAGTAGCGGACCAGAT
65 AGAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCCCCTAAAGAGTAGCAGACCAGAT
** *
321453 TCTTCTTCTTTCAGATTTGGTCTTCCTAAAGAGCAGC-GGAGCAAATCAAGTTCGATTCAATCTT
130 TCTTCTTCTTTCAGATTTGGTCTTCCTAAAGAGCAGCAAAAGAAAATCAAGTTCGATTCAATCTT
* *
321517 CCCAGAAGAGTAGCGAAGTGGATCAAAA-TTTTATCAAGCCTGATCTC-CCTTAAAGAGTAGCGG
195 CCCAGAAGAGCAGCAAAGTGGATCAAAATTTTTATCAAGCCTGATCTCGCC-TAAAGAGTAGC--
** * * *
321580 AGTAGATTTTCTTTT
257 AAAACATATTCTTGT
* ** * * * *
321595 TCTTTAAGATTTTATCTCCCTGAAGAGTAGTAAAGCAAATCGA-TTATTATTCAATCTTCCCTGA
1 TCTTTTAGATTTGGTCTCCCTGAAGAGAAGTGAAGCAAATCAAGTTA-GATTCAATCTTCCCTGA
321659 AGA
65 AGA
321662 ACAGTGAAAT
Statistics
Matches: 291, Mismatches: 40, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
268 2 0.01
269 27 0.09
270 51 0.18
271 210 0.72
272 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (271 bp):
TCTTTTAGATTTGGTCTCCCTGAAGAGAAGTGAAGCAAATCAAGTTAGATTCAATCTTCCCTGAA
GAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCCCCTAAAGAGTAGCAGACCAGATT
CTTCTTCTTTCAGATTTGGTCTTCCTAAAGAGCAGCAAAAGAAAATCAAGTTCGATTCAATCTTC
CCAGAAGAGCAGCAAAGTGGATCAAAATTTTTATCAAGCCTGATCTCGCCTAAAGAGTAGCAAAA
CATATTCTTGT
Found at i:324979 original size:22 final size:22
Alignment explanation
Indices: 324954--324996 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
324944 TGAAAGCTTC
324954 TATACACATTATTTGCAACTTA
1 TATACACATTATTTGCAACTTA
324976 TATACACATTATTTGCAACTT
1 TATACACATTATTTGCAACTT
324997 CTACTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.42
Consensus pattern (22 bp):
TATACACATTATTTGCAACTTA
Found at i:331253 original size:3 final size:3
Alignment explanation
Indices: 331247--331274 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
331237 TAGGGTTTTT
331247 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
331275 ATAGTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:332504 original size:21 final size:21
Alignment explanation
Indices: 332443--332504 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
332433 GATACTTAAG
**
332443 GGAGTATCGATACTAGGGGTA
1 GGAGTATCGATACTAGGAATA
***
332464 -GAGTATCGATACTCTCAATA
1 GGAGTATCGATACTAGGAATA
332484 GGAGTATCGATACTAGGAATA
1 GGAGTATCGATACTAGGAATA
332505 ATTTTGAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.34, C:0.13, G:0.27, T:0.26
Consensus pattern (21 bp):
GGAGTATCGATACTAGGAATA
Found at i:335618 original size:21 final size:21
Alignment explanation
Indices: 335566--335619 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
335556 ATTGATACCT
* *
335566 TGGTATCCATACAGGATGAAG
1 TGGTATCTATACAGGATGAAC
* *
335587 TGGCATTTATATC-GGATGAAC
1 TGGTATCTATA-CAGGATGAAC
335608 TGGTATCTATAC
1 TGGTATCTATAC
335620 CAGAGAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (21 bp):
TGGTATCTATACAGGATGAAC
Found at i:337426 original size:45 final size:45
Alignment explanation
Indices: 337375--337601 Score: 269
Period size: 45 Copynumber: 5.0 Consensus size: 45
337365 CATTAAGCAC
*
337375 TTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCATATGCA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* *
337420 TTTCAACTATAGTATACTTTTCTGTTGATAATCCATCCATATGCA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* * * * *
337465 TTTCAACTATAATATACTCTTCTGTTGATTATGTACCCATATACA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* * * * *
337510 TTTCAACTATAGTATACATTTATGTTGATAATGTACCTATATACA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* * **
337555 TTTCAACTAT-G-ACATCCTTTCATGCCGATAATGCACCCATATGCA
1 TTTCAACTATAGTATA-CTTTTC-TGTTGATAATGCACCCATATGCA
337600 TT
1 TT
337602 ATTATTTTCA
Statistics
Matches: 156, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
43 2 0.01
44 5 0.03
45 149 0.96
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (45 bp):
TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
Found at i:344318 original size:45 final size:45
Alignment explanation
Indices: 344267--344493 Score: 287
Period size: 45 Copynumber: 5.0 Consensus size: 45
344257 CATTAAGCAC
* *
344267 TTTCAACTATAGCATACTTTTCTATTGATAATGCATCCATATGCA
1 TTTCAACTATAGTATACTTTTCTATTGATAATGCACCCATATGCA
*
344312 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
1 TTTCAACTATAGTATACTTTTCTATTGATAATGCACCCATATGCA
* * * * *
344357 TTTCAACTATATTATACTCTTCTTTTGATAATGGACCCATATACA
1 TTTCAACTATAGTATACTTTTCTATTGATAATGCACCCATATGCA
* * * *
344402 TTTCAACTATAGTTTACTTTTCTGTTGATAATGTACCCATATACA
1 TTTCAACTATAGTATACTTTTCTATTGATAATGCACCCATATGCA
* * *
344447 TTTCAACTATAGCAT-CCTTTC-ATGCCGATAATGCACCCATATGCA
1 TTTCAACTATAGTATACTTTTCTAT--TGATAATGCACCCATATGCA
344492 TT
1 TT
344494 ATTATTTTCA
Statistics
Matches: 160, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
43 1 0.01
44 5 0.03
45 154 0.96
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (45 bp):
TTTCAACTATAGTATACTTTTCTATTGATAATGCACCCATATGCA
Found at i:347450 original size:12 final size:12
Alignment explanation
Indices: 347433--347457 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
347423 AAGAGATACC
347433 AACAAAATCTAT
1 AACAAAATCTAT
347445 AACAAAATCTAT
1 AACAAAATCTAT
347457 A
1 A
347458 TCCATTGTCC
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:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
AACAAAATCTAT
Found at i:354858 original size:2 final size:2
Alignment explanation
Indices: 354841--354886 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
354831 TGAATAAAAG
354841 TA TA TA -A TA T- TA -A 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
354880 TA TA TA T
1 TA TA TA T
354887 GTGTGTGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:354891 original size:2 final size:2
Alignment explanation
Indices: 354886--354916 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
354876 TATATATATA
354886 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 T
354917 ATCTTTGTGA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:358500 original size:22 final size:22
Alignment explanation
Indices: 358449--358502 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
358439 ACTAAAAATG
358449 TTAAACTCATGTATTCACAGAA
1 TTAAACTCATGTATTCACAGAA
* *
358471 TCT-TACTCATGTATTCA-ATATA
1 T-TAAACTCATGTATTCACAGA-A
358493 TTAAACTCAT
1 TTAAACTCAT
358503 AGTCTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
21 3 0.12
22 22 0.85
23 1 0.04
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.39
Consensus pattern (22 bp):
TTAAACTCATGTATTCACAGAA
Found at i:362304 original size:29 final size:29
Alignment explanation
Indices: 362252--362328 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
362242 TTTTTTTGTC
*
362252 ATATTTAGAG-TTTTTCTTTTTTGTTACA
1 ATATTCAGAGTTTTTTCTTTTTTGTTACA
362280 ATATTCAGAGTTTTTTCTTTTTTGTTACA
1 ATATTCAGAGTTTTTTCTTTTTTGTTACA
362309 ATATTCAGAGTTTTTT-TTTT
1 ATATTCAGAGTTTTTTCTTTT
362329 CTCTAAAATC
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 13 0.28
29 34 0.72
ACGTcount: A:0.21, C:0.08, G:0.10, T:0.61
Consensus pattern (29 bp):
ATATTCAGAGTTTTTTCTTTTTTGTTACA
Found at i:362598 original size:21 final size:21
Alignment explanation
Indices: 362557--362598 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
362547 ATAGCTACTT
*
362557 TTTTCTTCACCATATTAGTAA
1 TTTTCTTCACCAGATTAGTAA
*
362578 TTTTCTTGACCAGGATT-GTAA
1 TTTTCTTCACCA-GATTAGTAA
362599 ATGAGATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (21 bp):
TTTTCTTCACCAGATTAGTAA
Found at i:363255 original size:31 final size:32
Alignment explanation
Indices: 363198--363262 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 32
363188 ATTCAAAAAA
**
363198 AATATTTGGCCACTTTTGTTTTTTATTTAATT
1 AATATTTGGCCACTTTTCATTTTTATTTAATT
*
363230 AATATTTGGTCAC-TTTCATTTTTATTTAATT
1 AATATTTGGCCACTTTTCATTTTTATTTAATT
363261 AA
1 AA
363263 GATGTAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.26, C:0.09, G:0.08, T:0.57
Consensus pattern (32 bp):
AATATTTGGCCACTTTTCATTTTTATTTAATT
Found at i:365962 original size:76 final size:76
Alignment explanation
Indices: 365836--365990 Score: 274
Period size: 76 Copynumber: 2.0 Consensus size: 76
365826 AATGTCATTT
* * *
365836 AATAATAACTAAGGAGAAGATGTATTTTAACACAGAGAGAGAGAGAGGGCCTAAATATGCCCAAA
1 AATAATAACCAAGGAGAAGATGTATTTGAACACACAGAGAGAGAGAGGGCCTAAATATGCCCAAA
365901 AGAGAAAAGGC
66 AGAGAAAAGGC
*
365912 AATAATAACCAAGGAGAAGATGTATTTGAACACACAGAGAGAGAGAGGGCCTTAATATGCCCAAA
1 AATAATAACCAAGGAGAAGATGTATTTGAACACACAGAGAGAGAGAGGGCCTAAATATGCCCAAA
365977 AGAGAAAAGGC
66 AGAGAAAAGGC
365988 AAT
1 AAT
365991 GTTGTATAAT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.47, C:0.13, G:0.25, T:0.15
Consensus pattern (76 bp):
AATAATAACCAAGGAGAAGATGTATTTGAACACACAGAGAGAGAGAGGGCCTAAATATGCCCAAA
AGAGAAAAGGC
Found at i:367452 original size:30 final size:29
Alignment explanation
Indices: 367393--367457 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
367383 ATTATTATTA
* *
367393 TTATTTTGCCCATTAGGGCATTCCCGTTTT
1 TTATTTAGCCCATTAGGGCATTCCAG-TTT
367423 TTATTTAGCCCATTAGGGCA-TCCGAGTTT
1 TTATTTAGCCCATTAGGGCATTCC-AGTTT
367452 TTATTT
1 TTATTT
367458 CGAGAATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 12 0.38
30 20 0.62
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (29 bp):
TTATTTAGCCCATTAGGGCATTCCAGTTT
Found at i:369762 original size:20 final size:21
Alignment explanation
Indices: 369732--369771 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
369722 AGCCGTTGGG
369732 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
369753 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
369772 CTATACAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:374220 original size:16 final size:16
Alignment explanation
Indices: 374196--374236 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
374186 TAATAAAATT
374196 ATTAATTTAATTTTTA
1 ATTAATTTAATTTTTA
* *
374212 ATTATTTTATTTTTTA
1 ATTAATTTAATTTTTA
374228 A--AATTTAAT
1 ATTAATTTAAT
374237 CCAGTCGAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
14 6 0.29
16 15 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTAATTTAATTTTTA
Found at i:374484 original size:30 final size:30
Alignment explanation
Indices: 374419--374501 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
374409 ACCCTAGTGT
** * **
374419 CCTAATGGATTAAATAAAAAATCTGCGTGC
1 CCTAATGGGCTAAATAAAAAATTTGAATGC
*
374449 ACTAATGGGCTAAATAAAAAATTTGAATGC
1 CCTAATGGGCTAAATAAAAAATTTGAATGC
*
374479 CCTAATGGGCCAAA-AAACAAATT
1 CCTAATGGGCTAAATAAA-AAATT
374502 ATTTTTTTAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 3 0.07
30 41 0.93
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.24
Consensus pattern (30 bp):
CCTAATGGGCTAAATAAAAAATTTGAATGC
Found at i:375372 original size:20 final size:20
Alignment explanation
Indices: 375334--375373 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
375324 ATGTTCACCG
375334 ATAAACGAGTGAATGTTATT
1 ATAAACGAGTGAATGTTATT
*
375354 ATAAATGAGATGAAT-TTATT
1 ATAAACGAG-TGAATGTTATT
375374 TTATGATAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (20 bp):
ATAAACGAGTGAATGTTATT
Found at i:376774 original size:41 final size:41
Alignment explanation
Indices: 376724--376843 Score: 125
Period size: 41 Copynumber: 2.9 Consensus size: 41
376714 CCAATTTTTA
* * * *
376724 ATATCGATACCAAATCATCTGGTATGGATA-CAAATCCTTCG
1 ATATGGATACCAATTCATCTGGTATGGATAGC-AACCCTACG
* * ***
376765 ATATGGATACTAGTTCATCCCTTATGGATAGCAACCCTACG
1 ATATGGATACCAATTCATCTGGTATGGATAGCAACCCTACG
* *
376806 ATATGGATACCAATTCATCTGGTATGGAAACCAACCCT
1 ATATGGATACCAATTCATCTGGTATGGATAGCAACCCT
376844 CCGGTATTGG
Statistics
Matches: 62, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 61 0.98
42 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (41 bp):
ATATGGATACCAATTCATCTGGTATGGATAGCAACCCTACG
Found at i:376833 original size:21 final size:20
Alignment explanation
Indices: 376724--376839 Score: 54
Period size: 21 Copynumber: 5.7 Consensus size: 20
376714 CCAATTTTTA
* *
376724 ATATCGATACCAAATCATCTG
1 ATATGGATACCAATTCATC-G
* * * *
376745 GTATGGATACAAATCCTTCG
1 ATATGGATACCAATTCATCG
* * *
376765 ATATGGATACTAGTTCATCCC
1 ATATGGATACCAATTCAT-CG
* * * *
376786 TTATGGATAGCAA-CCCTACG
1 ATATGGATACCAATTCAT-CG
376806 ATATGGATACCAATTCATCTG
1 ATATGGATACCAATTCATC-G
* *
376827 GTATGGAAACCAA
1 ATATGGATACCAA
376840 CCCTCCGGTA
Statistics
Matches: 66, Mismatches: 26, Indels: 6
0.67 0.27 0.06
Matches are distributed among these distances:
20 29 0.44
21 37 0.56
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (20 bp):
ATATGGATACCAATTCATCG
Found at i:379874 original size:25 final size:25
Alignment explanation
Indices: 379832--379879 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
379822 ACAAGTGAGA
379832 TAACAACTAGAAAAAATAATAATAG
1 TAACAACTAGAAAAAATAATAATAG
* *
379857 TAACAACTATAAATAATAATAAT
1 TAACAACTAGAAAAAATAATAAT
379880 TAGTTTGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.25
Consensus pattern (25 bp):
TAACAACTAGAAAAAATAATAATAG
Found at i:380368 original size:32 final size:31
Alignment explanation
Indices: 380310--380442 Score: 117
Period size: 32 Copynumber: 4.2 Consensus size: 31
380300 ACGAGTCATA
* * * *
380310 ATAGAGTTATTATTGCATTCAAATAATGTAC
1 ATAGAGTTAGTATTGAATTTAGATAATGTAC
** * *
380341 ATCAGAGTTACCATGGAATTTAGATAATACATA-
1 AT-AGAGTTAGTATTGAATTTAGATAAT--GTAC
*
380374 ATAGAGTTAGTATTGAATTTAGATAATGCAC
1 ATAGAGTTAGTATTGAATTTAGATAATGTAC
* *
380405 AATATAGTTAGTATTGAATTTAGATAATGCAC
1 -ATAGAGTTAGTATTGAATTTAGATAATGTAC
380437 A-AGAGT
1 ATAGAGT
380443 GTTAGTGTCA
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
30 5 0.06
31 3 0.04
32 71 0.86
33 2 0.02
34 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.35
Consensus pattern (31 bp):
ATAGAGTTAGTATTGAATTTAGATAATGTAC
Found at i:380414 original size:64 final size:64
Alignment explanation
Indices: 380306--380432 Score: 157
Period size: 64 Copynumber: 2.0 Consensus size: 64
380296 GTTTACGAGT
* * *
380306 CATAATAGAGTTATTATTGCATTCAAATAATGTACATCAGAGTTACCATGGAATTTAGATAATA
1 CATAATAGAGTTAGTATTGAATTCAAATAATGCACATCAGAGTTACCATGGAATTTAGATAATA
* * * ** *
380370 CATAATAGAGTTAGTATTGAATTTAGATAATGCACAAT-ATAGTTAGTATTGAATTTAGATAAT
1 CATAATAGAGTTAGTATTGAATTCAAATAATGCAC-ATCAGAGTTACCATGGAATTTAGATAAT
380433 GCACAAGAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 51 0.96
65 2 0.04
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (64 bp):
CATAATAGAGTTAGTATTGAATTCAAATAATGCACATCAGAGTTACCATGGAATTTAGATAATA
Found at i:380447 original size:32 final size:32
Alignment explanation
Indices: 380356--380448 Score: 134
Period size: 32 Copynumber: 2.9 Consensus size: 32
380346 AGTTACCATG
* * *
380356 GAATTTAGATAATACATAATAGAGTTAGTATT
1 GAATTTAGATAATGCACAATAGTGTTAGTATT
380388 GAATTTAGATAATGCACAATA-TAGTTAGTATT
1 GAATTTAGATAATGCACAATAGT-GTTAGTATT
*
380420 GAATTTAGATAATGCACAAGAGTGTTAGT
1 GAATTTAGATAATGCACAATAGTGTTAGT
380449 GTCACATTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
32 54 0.98
33 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.35
Consensus pattern (32 bp):
GAATTTAGATAATGCACAATAGTGTTAGTATT
Found at i:380458 original size:32 final size:32
Alignment explanation
Indices: 380357--380466 Score: 98
Period size: 32 Copynumber: 3.4 Consensus size: 32
380347 GTTACCATGG
* * * * * *
380357 AATTTAGATAATACATAATAGAGTTAGTATTG
1 AATTTAGATAATGCACAAGATAGTTAGTAGTC
* * *
380389 AATTTAGATAATGCACAATATAGTTAGTATTG
1 AATTTAGATAATGCACAAGATAGTTAGTAGTC
380421 AATTTAGATAATGCACAAGAGT-GTTAGT-GTC
1 AATTTAGATAATGCACAAGA-TAGTTAGTAGTC
*
380452 ACATTTAGACAATGC
1 A-ATTTAGATAATGC
380467 GGCTTAGAGT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
31 2 0.03
32 66 0.96
33 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (32 bp):
AATTTAGATAATGCACAAGATAGTTAGTAGTC
Found at i:385953 original size:20 final size:20
Alignment explanation
Indices: 385924--386036 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
385914 CAAGAGTATA
385924 CATACTTTGGTAAAAGTTTC
1 CATACTTTGGTAAAAGTTTC
* * *
385944 CATGCTTTGGTAAGAGTATC
1 CATACTTTGGTAAAAGTTTC
* * *
385964 TATACTTTCGTCAAAA-TTTT
1 CATACTTTGGT-AAAAGTTTC
** *
385984 TGTACTTTGGTAAGAGTATT-
1 CATACTTTGGTAAAAGT-TTC
* *
386004 CATAATTTGGTAAAAGTTTT
1 CATACTTTGGTAAAAGTTTC
386024 CATACTTTGGTAA
1 CATACTTTGGTAA
386037 GAGTATCAAT
Statistics
Matches: 72, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
19 5 0.07
20 62 0.86
21 5 0.07
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (20 bp):
CATACTTTGGTAAAAGTTTC
Found at i:385970 original size:40 final size:40
Alignment explanation
Indices: 385915--386053 Score: 158
Period size: 40 Copynumber: 3.5 Consensus size: 40
385905 ATACTAGTGC
* *
385915 AAGAGTATAC-ATACTTTGGTAAAAGTTTCCATGCTTTGGT
1 AAGAGTAT-CTATACTTTGGTAAAAGTTTTCATACTTTGGT
* **
385955 AAGAGTATCTATACTTTCGTCAAAA-TTTTTGTACTTTGGT
1 AAGAGTATCTATACTTTGGT-AAAAGTTTTCATACTTTGGT
*
385995 AAGAGTAT-TCATAATTTGGTAAAAGTTTTCATACTTTGGT
1 AAGAGTATCT-ATACTTTGGTAAAAGTTTTCATACTTTGGT
* *
386035 AAGAGTATCAATAGTTTGG
1 AAGAGTATCTATACTTTGG
386054 CAAGAGTATC
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
39 6 0.07
40 73 0.88
41 4 0.05
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (40 bp):
AAGAGTATCTATACTTTGGTAAAAGTTTTCATACTTTGGT
Found at i:386052 original size:20 final size:19
Alignment explanation
Indices: 385989--386064 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
385979 ATTTTTGTAC
385989 TTTGGTAAGAGTATTCATAA
1 TTTGGTAAGAGTA-TCATAA
* * *
386009 TTTGGTAAAAGTTTTCATAC
1 TTTGGTAAGAG-TATCATAA
*
386029 TTTGGTAAGAGTATCAATAG
1 TTTGGTAAGAGTATC-ATAA
*
386049 TTTGGCAAGAGTATCA
1 TTTGGTAAGAGTATCA
386065 ATACATTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 4 0.09
20 42 0.89
21 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (19 bp):
TTTGGTAAGAGTATCATAA
Found at i:388905 original size:35 final size:35
Alignment explanation
Indices: 388831--388905 Score: 100
Period size: 33 Copynumber: 2.2 Consensus size: 35
388821 GTTCAGGTTT
*
388831 TGTTTTGGGTAAAAGATATATATTTTCGAATCGGA
1 TGTTTCGGGTAAAAGATATATATTTTCGAATCGGA
* **
388866 --TTTCGGGTGAAAGATATATATTTTCGGGTCGGA
1 TGTTTCGGGTAAAAGATATATATTTTCGAATCGGA
388899 TGTTTCG
1 TGTTTCG
388906 ACCTGACCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
33 29 0.85
35 5 0.15
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (35 bp):
TGTTTCGGGTAAAAGATATATATTTTCGAATCGGA
Found at i:389402 original size:29 final size:29
Alignment explanation
Indices: 389334--389402 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
389324 CAAACTAAAT
*
389334 TGATGTCATTACTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
*
389363 AGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
389392 TGATGTCATTG
1 TGATGTCATTG
389403 ACATAAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAATTAA
Found at i:394050 original size:27 final size:27
Alignment explanation
Indices: 394016--394070 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
394006 TCATACTTAC
394016 ATCATTTAATTAAAGATGTCATTGCTT
1 ATCATTTAATTAAAGATGTCATTGCTT
*
394043 ATCATTTAATTAATGATGTCATTGCTT
1 ATCATTTAATTAAAGATGTCATTGCTT
394070 A
1 A
394071 CATAAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (27 bp):
ATCATTTAATTAAAGATGTCATTGCTT
Found at i:396305 original size:17 final size:16
Alignment explanation
Indices: 396264--396305 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
396254 AAATACATTT
396264 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
396280 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
396297 TAAAA-AATT
1 TAAAATAATT
396306 GATATGCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:396601 original size:2 final size:2
Alignment explanation
Indices: 396594--396638 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
396584 TTTGGAAACA
396594 AT AT AT AT AT AT AT AT AT -T 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
396635 AT AT
1 AT AT
396639 TATCCAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:398264 original size:82 final size:81
Alignment explanation
Indices: 398138--398573 Score: 486
Period size: 82 Copynumber: 5.4 Consensus size: 81
398128 AAGGAGTACG
*
398138 AGTCTGCTCCACTATTCTTTCAGGGAGACCAGACTTGATATGTTCCTCTTTCTT-GGGTAGTCAG
1 AGTCTGCTCCACTATTCTTTCAGGGAGATCAGACTTGATATGTTCCTCTTT-TTCGGGTAGTCAG
* *
398202 ATCAATTTCGGAAAACA
65 ATCAATTTTGGAAGACA
* * * *
398219 AGTCTGCTCCATTATTCTTTCGGGGGAGATCAGACTTGA-ATTGTTCCTCTCTTTCAGGTAGTCA
1 AGTCTGCTCCACTATTCTTTC-AGGGAGATCAGACTTGATA-TGTTCCTCTTTTTCGGGTAGTCA
*
398283 GATCAATTTTGGAAGA-T
64 GATCAATTTTGGAAGACA
* * * *
398300 AGATTTGCTCCACTAATCTTTCAAGGGAGATCAGACTTGATATGTTCCTTTTTTTCAGGTAGTCA
1 AG-TCTGCTCCACTATTCTTTC-AGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCA
* **
398365 GATCAATTTTAGAAGATG
64 GATCAATTTTGGAAGACA
* * * * *
398383 AGTATGCTCCACTATTCTTTTAGGGGAGATCAAACTTGATTTGTTCTTCTTTTTCGGGTAGTCAG
1 AGTCTGCTCCACTATTCTTTCA-GGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAG
* *
398448 ATCAATTTCGGAAGACG
65 ATCAATTTTGGAAGACA
* * * * * *
398465 GGT-TGCTCTATTATTCTTTCAGGGAGATCAAATTTGATCT-TTGCCTCTTTTTCGGGTAGTCAG
1 AGTCTGCTCCACTATTCTTTCAGGGAGATCAGACTTGATATGTT-CCTCTTTTTCGGGTAGTCAG
* *
398528 AACAATTTTGGAAAACA
65 ATCAATTTTGGAAGACA
* *
398545 AGTCTGCTCCACTCTTCTTTCACGGAGAT
1 AGTCTGCTCCACTATTCTTTCAGGGAGAT
398574 AAGTCTCAAG
Statistics
Matches: 302, Mismatches: 44, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
79 2 0.01
80 51 0.17
81 62 0.21
82 184 0.61
83 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (81 bp):
AGTCTGCTCCACTATTCTTTCAGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGA
TCAATTTTGGAAGACA
Found at i:398340 original size:164 final size:162
Alignment explanation
Indices: 398137--398566 Score: 540
Period size: 164 Copynumber: 2.6 Consensus size: 162
398127 GAAGGAGTAC
*
398137 GAGTCTGCTCCACTATTCTTTCAGGGAGACCAGACTTGATATGTTCCTCTTTCTT-GGGTAGTCA
1 GAGT-TGCTCCACTATTCTTTCAGGGAGATCAGACTTGATATGTTCCTCTTT-TTCGGGTAGTCA
* * * *
398201 GATCAATTTCGGAAAACAAGTCTGCTCCATTATTCTTTCGGGGGAGATCAGACTTGAATTGTTCC
64 GATCAATTTTGGAAAACAAGTCTGCTCCACTATTCTTTCAGGGGAGATCAAACTTGAATTGTTCC
*
398266 TCTCTTTCAGGTAGTCAGATCAATTTTGGAAGATA
129 TCTCTTTCAGGTAGTCAGATCAATTTCGGAAGA-A
* * * *
398301 GATTTGCTCCACTAATCTTTCAAGGGAGATCAGACTTGATATGTTCCTTTTTTTCAGGTAGTCAG
1 GAGTTGCTCCACTATTCTTTC-AGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAG
* * ** * * * *
398366 ATCAATTTTAGAAGATGAGTATGCTCCACTATTCTTTTAGGGGAGATCAAACTTGATTTGTTCTT
65 ATCAATTTTGGAAAACAAGTCTGCTCCACTATTCTTTCAGGGGAGATCAAACTTGAATTGTTCCT
* * *
398431 CTTTTTCGGGTAGTCAGATCAATTTCGGAAGAC
130 CTCTTTCAGGTAGTCAGATCAATTTCGGAAGAA
* * * * * *
398464 GGGTTGCTCTATTATTCTTTCAGGGAGATCAAATTTGATCT-TTGCCTCTTTTTCGGGTAGTCAG
1 GAGTTGCTCCACTATTCTTTCAGGGAGATCAGACTTGATATGTT-CCTCTTTTTCGGGTAGTCAG
* *
398528 AACAATTTTGGAAAACAAGTCTGCTCCACTCTTCTTTCA
65 ATCAATTTTGGAAAACAAGTCTGCTCCACTATTCTTTCA
398567 CGGAGATAAG
Statistics
Matches: 224, Mismatches: 39, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
161 2 0.01
162 66 0.29
163 34 0.15
164 122 0.54
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (162 bp):
GAGTTGCTCCACTATTCTTTCAGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGA
TCAATTTTGGAAAACAAGTCTGCTCCACTATTCTTTCAGGGGAGATCAAACTTGAATTGTTCCTC
TCTTTCAGGTAGTCAGATCAATTTCGGAAGAA
Found at i:398824 original size:89 final size:89
Alignment explanation
Indices: 398716--398948 Score: 224
Period size: 89 Copynumber: 2.6 Consensus size: 89
398706 ACTATTCTGA
** * * * * * *
398716 GGAGATCTA-ACTCGAGATTGATTTTCTTCACTACTCTTTTGGGAATACCAAATTTCAAATAAAA
1 GGAGATC-AGACTCGAGATTGATTTAATTCACTACTATTTCGGAAAGACCAAATCTCAAAGAAAA
**
398780 AGAATCTACTCCACTACGT-TT-TTG
65 AGAATCTACTCCACTAC-TCTTCCAG
* * *
398804 GGAAGATCATACTCGAGATTGATTTAATTCTCTACTATTTCGGAAAGACCAAATCTGAAAGAAAA
1 GG-AGATCAGACTCGAGATTGATTTAATTCACTACTATTTCGGAAAGACCAAATCTCAAAGAAAA
* *
398869 AGAATCTGCTCCACTTCTCTTCCAG
65 AGAATCTACTCCACTACTCTTCCAG
* * *
398894 GGAGATCAGACTCGAGATTGATTTGATTCGCTGCT-TCTTCAGG-AAGACCAAATCT
1 GGAGATCAGACTCGAGATTGATTTAATTCACTACTAT-TTC-GGAAAGACCAAATCT
398949 AACCTAATTT
Statistics
Matches: 121, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
88 5 0.04
89 111 0.92
90 5 0.04
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (89 bp):
GGAGATCAGACTCGAGATTGATTTAATTCACTACTATTTCGGAAAGACCAAATCTCAAAGAAAAA
GAATCTACTCCACTACTCTTCCAG
Found at i:399027 original size:29 final size:29
Alignment explanation
Indices: 398990--399058 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
398980 ATCAAATCAG
* *
398990 AAAGATTGACTTATATTCACGAGGAAGTC
1 AAAGATTGAATTATATTAACGAGGAAGTC
* * *
399019 AAAGGTTGAATTATTTTAATGAGGAAGTC
1 AAAGATTGAATTATATTAACGAGGAAGTC
*
399048 AAGGATTGAAT
1 AAAGATTGAAT
399059 CCTCTTCACG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (29 bp):
AAAGATTGAATTATATTAACGAGGAAGTC
Found at i:399071 original size:29 final size:29
Alignment explanation
Indices: 399005--399082 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
398995 TTGACTTATA
* *
399005 TTCACGAGGAAGTCAAAGG-TTGAATTATT
1 TTCACGAGGAAGTC-AAGGATTGAATCATC
* * *
399034 TTAATGAGGAAGTCAAGGATTGAATCCTC
1 TTCACGAGGAAGTCAAGGATTGAATCATC
* *
399063 TTCACGAGGGAGTCATGGAT
1 TTCACGAGGAAGTCAAGGAT
399083 AACAAATATT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
28 4 0.10
29 35 0.90
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (29 bp):
TTCACGAGGAAGTCAAGGATTGAATCATC
Done.