Multiple sequence alignment - TraesCS2A01G522600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G522600 chr2A 100.000 2702 0 0 1 2702 744807890 744805189 0.000000e+00 4990
1 TraesCS2A01G522600 chr2A 90.112 445 43 1 1775 2218 133643436 133642992 6.490000e-161 577
2 TraesCS2A01G522600 chr7B 85.049 1545 220 10 217 1754 745608986 745610526 0.000000e+00 1563
3 TraesCS2A01G522600 chr7B 91.991 437 14 3 2211 2627 650233139 650232704 6.440000e-166 593
4 TraesCS2A01G522600 chr7B 88.739 444 50 0 1775 2218 415326191 415326634 6.580000e-151 544
5 TraesCS2A01G522600 chr2D 90.117 941 85 7 824 1760 88611482 88612418 0.000000e+00 1216
6 TraesCS2A01G522600 chr2D 83.494 830 106 19 2 812 88610441 88611258 0.000000e+00 745
7 TraesCS2A01G522600 chr6D 86.756 1042 134 4 720 1759 97146420 97145381 0.000000e+00 1157
8 TraesCS2A01G522600 chrUn 78.429 1706 319 37 72 1761 70179618 70177946 0.000000e+00 1066
9 TraesCS2A01G522600 chrUn 80.456 1315 235 19 457 1760 392136111 392134808 0.000000e+00 985
10 TraesCS2A01G522600 chr6A 97.289 627 16 1 1454 2080 121670451 121671076 0.000000e+00 1062
11 TraesCS2A01G522600 chr6A 92.996 514 16 1 2208 2701 121671219 121671732 0.000000e+00 732
12 TraesCS2A01G522600 chr6A 91.086 359 12 3 2364 2702 162188336 162188694 4.070000e-128 468
13 TraesCS2A01G522600 chr3D 78.169 1704 325 35 72 1760 419639808 419638137 0.000000e+00 1042
14 TraesCS2A01G522600 chr3D 78.657 1579 300 27 197 1760 355123206 355121650 0.000000e+00 1014
15 TraesCS2A01G522600 chr3D 90.039 512 31 3 2211 2702 419635664 419635153 0.000000e+00 645
16 TraesCS2A01G522600 chr5D 78.657 1579 301 27 197 1760 90281586 90283143 0.000000e+00 1016
17 TraesCS2A01G522600 chr5D 77.921 1703 325 38 72 1760 409710895 409712560 0.000000e+00 1014
18 TraesCS2A01G522600 chr5D 90.661 514 29 4 2208 2702 409715027 409715540 0.000000e+00 665
19 TraesCS2A01G522600 chr5D 91.904 457 37 0 1760 2216 154611169 154611625 8.160000e-180 640
20 TraesCS2A01G522600 chr5D 93.089 246 17 0 2208 2453 90285613 90285858 7.110000e-96 361
21 TraesCS2A01G522600 chr5B 87.425 668 68 6 288 949 627466971 627466314 0.000000e+00 754
22 TraesCS2A01G522600 chr3B 92.383 512 17 3 2211 2702 741391120 741390611 0.000000e+00 710
23 TraesCS2A01G522600 chr2B 92.383 512 17 3 2211 2702 652607704 652607195 0.000000e+00 710
24 TraesCS2A01G522600 chr6B 92.188 512 17 2 2211 2702 139417786 139417278 0.000000e+00 702
25 TraesCS2A01G522600 chr6B 96.386 249 9 0 2208 2456 707973330 707973578 6.960000e-111 411
26 TraesCS2A01G522600 chr7D 90.291 515 30 3 2208 2702 575649080 575649594 0.000000e+00 656
27 TraesCS2A01G522600 chr3A 89.865 444 45 0 1775 2218 98513748 98513305 3.020000e-159 571
28 TraesCS2A01G522600 chr3A 87.111 450 48 4 1769 2218 637957447 637957886 4.020000e-138 501
29 TraesCS2A01G522600 chr1A 88.444 450 52 0 1769 2218 177472548 177472997 6.580000e-151 544
30 TraesCS2A01G522600 chr7A 90.859 361 12 7 2362 2702 99587083 99586724 5.270000e-127 464


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G522600 chr2A 744805189 744807890 2701 True 4990.0 4990 100.0000 1 2702 1 chr2A.!!$R2 2701
1 TraesCS2A01G522600 chr7B 745608986 745610526 1540 False 1563.0 1563 85.0490 217 1754 1 chr7B.!!$F2 1537
2 TraesCS2A01G522600 chr2D 88610441 88612418 1977 False 980.5 1216 86.8055 2 1760 2 chr2D.!!$F1 1758
3 TraesCS2A01G522600 chr6D 97145381 97146420 1039 True 1157.0 1157 86.7560 720 1759 1 chr6D.!!$R1 1039
4 TraesCS2A01G522600 chrUn 70177946 70179618 1672 True 1066.0 1066 78.4290 72 1761 1 chrUn.!!$R1 1689
5 TraesCS2A01G522600 chrUn 392134808 392136111 1303 True 985.0 985 80.4560 457 1760 1 chrUn.!!$R2 1303
6 TraesCS2A01G522600 chr6A 121670451 121671732 1281 False 897.0 1062 95.1425 1454 2701 2 chr6A.!!$F2 1247
7 TraesCS2A01G522600 chr3D 355121650 355123206 1556 True 1014.0 1014 78.6570 197 1760 1 chr3D.!!$R1 1563
8 TraesCS2A01G522600 chr3D 419635153 419639808 4655 True 843.5 1042 84.1040 72 2702 2 chr3D.!!$R2 2630
9 TraesCS2A01G522600 chr5D 409710895 409715540 4645 False 839.5 1014 84.2910 72 2702 2 chr5D.!!$F3 2630
10 TraesCS2A01G522600 chr5D 90281586 90285858 4272 False 688.5 1016 85.8730 197 2453 2 chr5D.!!$F2 2256
11 TraesCS2A01G522600 chr5B 627466314 627466971 657 True 754.0 754 87.4250 288 949 1 chr5B.!!$R1 661
12 TraesCS2A01G522600 chr3B 741390611 741391120 509 True 710.0 710 92.3830 2211 2702 1 chr3B.!!$R1 491
13 TraesCS2A01G522600 chr2B 652607195 652607704 509 True 710.0 710 92.3830 2211 2702 1 chr2B.!!$R1 491
14 TraesCS2A01G522600 chr6B 139417278 139417786 508 True 702.0 702 92.1880 2211 2702 1 chr6B.!!$R1 491
15 TraesCS2A01G522600 chr7D 575649080 575649594 514 False 656.0 656 90.2910 2208 2702 1 chr7D.!!$F1 494

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
977 1262 0.034186 CTTATGCCAGCCACCCTGAA 60.034 55.0 0.0 0.0 44.64 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 4709 1.237285 GGCGTTGCTGTCCTTGATGT 61.237 55.0 0.0 0.0 0.0 3.06 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.397482 CTGAGTCCCTTGTTTGAGAGTG 58.603 50.000 0.00 0.00 0.00 3.51
41 42 0.258774 TGCCCCTTTTCTCCTATGGC 59.741 55.000 0.00 0.00 37.90 4.40
47 48 2.498167 CTTTTCTCCTATGGCCCATCG 58.502 52.381 0.00 0.00 0.00 3.84
66 67 2.636412 GCCTTTTTCCAGGGCCGAC 61.636 63.158 0.00 0.00 39.96 4.79
67 68 1.977009 CCTTTTTCCAGGGCCGACC 60.977 63.158 0.00 0.00 40.67 4.79
86 87 2.851071 CGCCGGCCCTCTCTCTTAG 61.851 68.421 23.46 0.00 0.00 2.18
89 90 1.739049 CGGCCCTCTCTCTTAGCTG 59.261 63.158 0.00 0.00 0.00 4.24
90 91 1.743321 CGGCCCTCTCTCTTAGCTGG 61.743 65.000 0.00 0.00 0.00 4.85
106 107 2.058829 CTGGTCACACGCACCAAACC 62.059 60.000 0.00 0.00 43.56 3.27
133 134 3.876274 TCTCTTCCTTGGATTCGTCTG 57.124 47.619 0.00 0.00 0.00 3.51
150 198 3.813724 GCTCACCCCATCCCCCTG 61.814 72.222 0.00 0.00 0.00 4.45
158 206 4.851252 CATCCCCCTGCCCCCTCT 62.851 72.222 0.00 0.00 0.00 3.69
170 218 4.400251 CCCTCTCCCCGTCCACCT 62.400 72.222 0.00 0.00 0.00 4.00
171 219 2.284699 CCTCTCCCCGTCCACCTT 60.285 66.667 0.00 0.00 0.00 3.50
172 220 1.001248 CCTCTCCCCGTCCACCTTA 59.999 63.158 0.00 0.00 0.00 2.69
173 221 1.328430 CCTCTCCCCGTCCACCTTAC 61.328 65.000 0.00 0.00 0.00 2.34
174 222 1.305549 TCTCCCCGTCCACCTTACC 60.306 63.158 0.00 0.00 0.00 2.85
175 223 1.305887 CTCCCCGTCCACCTTACCT 60.306 63.158 0.00 0.00 0.00 3.08
176 224 1.305549 TCCCCGTCCACCTTACCTC 60.306 63.158 0.00 0.00 0.00 3.85
177 225 2.364780 CCCCGTCCACCTTACCTCC 61.365 68.421 0.00 0.00 0.00 4.30
178 226 1.305887 CCCGTCCACCTTACCTCCT 60.306 63.158 0.00 0.00 0.00 3.69
179 227 0.908180 CCCGTCCACCTTACCTCCTT 60.908 60.000 0.00 0.00 0.00 3.36
180 228 0.535797 CCGTCCACCTTACCTCCTTC 59.464 60.000 0.00 0.00 0.00 3.46
181 229 1.558233 CGTCCACCTTACCTCCTTCT 58.442 55.000 0.00 0.00 0.00 2.85
182 230 1.204941 CGTCCACCTTACCTCCTTCTG 59.795 57.143 0.00 0.00 0.00 3.02
209 257 4.340666 TCTCTCCTTATCTGCTTACAGCTG 59.659 45.833 13.48 13.48 44.10 4.24
227 275 2.855180 CTGCTTTACGTTGGATGCTTG 58.145 47.619 0.00 0.00 0.00 4.01
246 294 0.321653 GTCCAAACGCACCAGATCCT 60.322 55.000 0.00 0.00 0.00 3.24
264 312 2.053244 CCTTGGATAGCCACATCCTCT 58.947 52.381 0.00 0.00 45.94 3.69
265 313 3.116746 TCCTTGGATAGCCACATCCTCTA 60.117 47.826 0.00 0.00 45.94 2.43
330 378 5.222233 CCTCCTCTCCAGATCCATTACTCTA 60.222 48.000 0.00 0.00 0.00 2.43
333 381 5.835819 CCTCTCCAGATCCATTACTCTAACA 59.164 44.000 0.00 0.00 0.00 2.41
334 382 6.496565 CCTCTCCAGATCCATTACTCTAACAT 59.503 42.308 0.00 0.00 0.00 2.71
335 383 7.309744 CCTCTCCAGATCCATTACTCTAACATC 60.310 44.444 0.00 0.00 0.00 3.06
337 385 5.833667 TCCAGATCCATTACTCTAACATCGT 59.166 40.000 0.00 0.00 0.00 3.73
343 392 5.350365 TCCATTACTCTAACATCGTTGTTGC 59.650 40.000 19.62 0.00 45.56 4.17
389 441 4.637977 GCAAATCTACCTCCCTCTCTTTTG 59.362 45.833 0.00 0.00 0.00 2.44
418 481 2.354003 GCCTTTGACCACCCATGATTTG 60.354 50.000 0.00 0.00 0.00 2.32
420 483 4.085733 CCTTTGACCACCCATGATTTGTA 58.914 43.478 0.00 0.00 0.00 2.41
426 489 4.589908 ACCACCCATGATTTGTACTTCTC 58.410 43.478 0.00 0.00 0.00 2.87
433 496 5.122869 CCATGATTTGTACTTCTCAGGTGTG 59.877 44.000 0.00 0.00 0.00 3.82
445 508 3.005554 CTCAGGTGTGCAGTCTATTTGG 58.994 50.000 0.00 0.00 0.00 3.28
478 545 0.178975 ACGGCCAGGAGATCCTAGAG 60.179 60.000 2.24 0.00 46.65 2.43
511 579 4.559704 CGGACTGAAGGTATATTCCTCTGC 60.560 50.000 0.75 0.00 36.74 4.26
534 602 1.064906 CCAGATCCACATCCAGCTGTT 60.065 52.381 13.81 0.00 0.00 3.16
550 618 5.156355 CAGCTGTTTCTTTAATTCATGCGT 58.844 37.500 5.25 0.00 0.00 5.24
659 729 8.846211 ACGGCAGCAAAATATATAATTTACTGT 58.154 29.630 18.48 8.38 32.48 3.55
734 807 6.673154 AACTTCAACTTAACAAGCTACGTT 57.327 33.333 0.00 6.67 0.00 3.99
857 1142 8.761689 TGTTCATAGCCTCATGATATTATAGCA 58.238 33.333 0.00 0.00 34.95 3.49
884 1169 5.469373 TTCATGATGCACTTAGTAAAGCG 57.531 39.130 0.00 0.00 36.05 4.68
887 1172 3.334691 TGATGCACTTAGTAAAGCGCTT 58.665 40.909 18.98 18.98 40.65 4.68
952 1237 5.585500 TTATTCTTACCGCGCATTGTATC 57.415 39.130 8.75 0.00 0.00 2.24
961 1246 2.993220 CGCGCATTGTATCTATGCCTTA 59.007 45.455 8.75 0.00 44.25 2.69
970 1255 1.139439 TCTATGCCTTATGCCAGCCA 58.861 50.000 0.00 0.00 40.16 4.75
977 1262 0.034186 CTTATGCCAGCCACCCTGAA 60.034 55.000 0.00 0.00 44.64 3.02
1023 1308 1.076533 AATTGGTCGAGCTACGCACG 61.077 55.000 16.64 0.00 43.31 5.34
1058 1343 2.694628 AGGCAATGTTTGACAAGCTTGA 59.305 40.909 32.50 8.75 42.71 3.02
1147 1432 4.466827 TCACCATACCAGAGAGCGTTATA 58.533 43.478 0.00 0.00 0.00 0.98
1191 1476 5.726980 AATTGTTGAGCCATACATGTGTT 57.273 34.783 9.11 0.00 0.00 3.32
1195 1480 3.625649 TGAGCCATACATGTGTTAGCA 57.374 42.857 9.11 0.00 0.00 3.49
1248 1533 9.754382 GATCAAGCAATTACATACATGGAAAAT 57.246 29.630 0.00 0.00 33.64 1.82
1317 1602 6.039781 CAAGAAAAACAATCTTGTGCAAGG 57.960 37.500 11.47 0.00 45.53 3.61
1326 1611 2.867624 TCTTGTGCAAGGCTTTCAGAT 58.132 42.857 11.47 0.00 38.88 2.90
1328 1613 3.753272 TCTTGTGCAAGGCTTTCAGATAC 59.247 43.478 11.47 0.00 38.88 2.24
1329 1614 2.436417 TGTGCAAGGCTTTCAGATACC 58.564 47.619 0.00 0.00 0.00 2.73
1340 1625 5.108517 GCTTTCAGATACCTTGTCAGAGAG 58.891 45.833 0.00 0.00 0.00 3.20
1344 1629 4.396478 TCAGATACCTTGTCAGAGAGAACG 59.604 45.833 0.00 0.00 0.00 3.95
1345 1630 4.396478 CAGATACCTTGTCAGAGAGAACGA 59.604 45.833 0.00 0.00 0.00 3.85
1351 1636 4.683781 CCTTGTCAGAGAGAACGAAAGAAG 59.316 45.833 0.00 0.00 0.00 2.85
1376 1661 1.028330 CAGCGCAACCAGACCATCAT 61.028 55.000 11.47 0.00 0.00 2.45
1638 1923 2.871022 CGATGGGCTTTCTGATGAAGAG 59.129 50.000 0.00 0.00 35.91 2.85
1652 1937 5.354767 TGATGAAGAGACCGATGAAGATTG 58.645 41.667 0.00 0.00 0.00 2.67
1714 1999 1.661341 CCCATGAGCACTGTCTAAGC 58.339 55.000 0.00 0.00 0.00 3.09
1777 2063 4.730903 GCTTCATGATGACAATGCTCACTG 60.731 45.833 12.54 0.00 0.00 3.66
1818 2104 4.877823 TGTCATATTGAGCCTGCTAAACTG 59.122 41.667 0.00 0.00 0.00 3.16
1833 2119 3.996150 AAACTGTCTCTTTGCCATGTG 57.004 42.857 0.00 0.00 0.00 3.21
1865 2151 0.750850 TATGGCTTCACCGCTAGGAC 59.249 55.000 0.00 0.00 43.94 3.85
1950 2236 5.372373 ACTCATAGCTTTGGCCTAGAAATC 58.628 41.667 3.32 0.00 39.73 2.17
2013 2320 4.565166 TGAAGTCTGTGTTGACGTGTTAAG 59.435 41.667 0.00 0.00 41.47 1.85
2080 2387 8.244494 TGTGATTCTTCTTTTCAGTATCTTCG 57.756 34.615 0.00 0.00 0.00 3.79
2089 2396 9.647797 TTCTTTTCAGTATCTTCGCTATAAACA 57.352 29.630 0.00 0.00 0.00 2.83
2103 2410 8.153479 TCGCTATAAACATACATTCATTTGCT 57.847 30.769 0.00 0.00 0.00 3.91
2112 2419 8.761575 ACATACATTCATTTGCTTTAACCTTG 57.238 30.769 0.00 0.00 0.00 3.61
2115 2422 6.054295 ACATTCATTTGCTTTAACCTTGCAA 58.946 32.000 0.00 0.00 43.69 4.08
2116 2423 6.203338 ACATTCATTTGCTTTAACCTTGCAAG 59.797 34.615 19.93 19.93 45.52 4.01
2135 2442 4.456566 GCAAGGCCAAATCAATGAACATTT 59.543 37.500 5.01 0.00 0.00 2.32
2137 2444 4.004982 AGGCCAAATCAATGAACATTTGC 58.995 39.130 5.01 0.14 38.26 3.68
2140 2447 5.292589 GGCCAAATCAATGAACATTTGCTAG 59.707 40.000 0.00 0.00 38.26 3.42
2142 2449 5.870433 CCAAATCAATGAACATTTGCTAGCA 59.130 36.000 14.93 14.93 38.26 3.49
2143 2450 6.537301 CCAAATCAATGAACATTTGCTAGCAT 59.463 34.615 20.13 2.09 38.26 3.79
2184 3589 4.998051 TGCCCTTTTTACTCAATTCTCCT 58.002 39.130 0.00 0.00 0.00 3.69
2186 3591 5.243730 TGCCCTTTTTACTCAATTCTCCTTG 59.756 40.000 0.00 0.00 0.00 3.61
2187 3592 5.243954 GCCCTTTTTACTCAATTCTCCTTGT 59.756 40.000 0.00 0.00 0.00 3.16
2188 3593 6.239317 GCCCTTTTTACTCAATTCTCCTTGTT 60.239 38.462 0.00 0.00 0.00 2.83
2192 3597 9.971922 CTTTTTACTCAATTCTCCTTGTTCATT 57.028 29.630 0.00 0.00 0.00 2.57
2196 3601 6.240894 ACTCAATTCTCCTTGTTCATTAGCA 58.759 36.000 0.00 0.00 0.00 3.49
2197 3602 6.373774 ACTCAATTCTCCTTGTTCATTAGCAG 59.626 38.462 0.00 0.00 0.00 4.24
2198 3603 6.475504 TCAATTCTCCTTGTTCATTAGCAGA 58.524 36.000 0.00 0.00 0.00 4.26
2199 3604 7.114754 TCAATTCTCCTTGTTCATTAGCAGAT 58.885 34.615 0.00 0.00 0.00 2.90
2200 3605 7.281774 TCAATTCTCCTTGTTCATTAGCAGATC 59.718 37.037 0.00 0.00 0.00 2.75
2201 3606 5.682234 TCTCCTTGTTCATTAGCAGATCA 57.318 39.130 0.00 0.00 0.00 2.92
2203 3608 6.475504 TCTCCTTGTTCATTAGCAGATCAAA 58.524 36.000 0.00 0.00 0.00 2.69
2204 3609 6.942005 TCTCCTTGTTCATTAGCAGATCAAAA 59.058 34.615 0.00 0.00 0.00 2.44
2205 3610 7.448161 TCTCCTTGTTCATTAGCAGATCAAAAA 59.552 33.333 0.00 0.00 0.00 1.94
2206 3611 7.370383 TCCTTGTTCATTAGCAGATCAAAAAC 58.630 34.615 0.00 0.00 0.00 2.43
2209 3614 9.844790 CTTGTTCATTAGCAGATCAAAAACATA 57.155 29.630 0.00 0.00 0.00 2.29
2294 4709 1.381076 GGTTCCCCGGGATCAACAA 59.619 57.895 26.32 1.08 0.00 2.83
2360 4775 6.061441 TCACCAGTTGTAGTTCATTCATTGT 58.939 36.000 0.00 0.00 0.00 2.71
2517 4952 8.684386 TTTGAATGAGGTGATGTTGTAGTAAA 57.316 30.769 0.00 0.00 0.00 2.01
2659 5094 0.392461 GTGGCGCCTACAAGAATGGA 60.392 55.000 29.70 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.768275 TCTCAAACAAGGGACTCAGCA 59.232 47.619 0.00 0.00 38.49 4.41
14 15 2.489073 GGAGAAAAGGGGCACTCTCAAA 60.489 50.000 6.80 0.00 36.78 2.69
17 18 0.988063 AGGAGAAAAGGGGCACTCTC 59.012 55.000 0.00 0.00 34.75 3.20
23 24 0.468214 GGCCATAGGAGAAAAGGGGC 60.468 60.000 0.00 0.00 39.18 5.80
41 42 1.322538 CCTGGAAAAAGGCCGATGGG 61.323 60.000 0.00 0.00 0.00 4.00
69 70 3.133946 CTAAGAGAGAGGGCCGGC 58.866 66.667 21.18 21.18 0.00 6.13
84 85 2.034048 TTGGTGCGTGTGACCAGCTA 62.034 55.000 0.00 0.00 44.36 3.32
86 87 2.477176 TTTGGTGCGTGTGACCAGC 61.477 57.895 0.00 0.00 44.36 4.85
89 90 2.719354 GGTTTGGTGCGTGTGACC 59.281 61.111 0.00 0.00 0.00 4.02
90 91 0.533308 TAGGGTTTGGTGCGTGTGAC 60.533 55.000 0.00 0.00 0.00 3.67
106 107 5.069781 ACGAATCCAAGGAAGAGAAGATAGG 59.930 44.000 0.00 0.00 0.00 2.57
133 134 3.813724 CAGGGGGATGGGGTGAGC 61.814 72.222 0.00 0.00 0.00 4.26
158 206 1.305549 GAGGTAAGGTGGACGGGGA 60.306 63.158 0.00 0.00 0.00 4.81
160 208 0.908180 AAGGAGGTAAGGTGGACGGG 60.908 60.000 0.00 0.00 0.00 5.28
161 209 0.535797 GAAGGAGGTAAGGTGGACGG 59.464 60.000 0.00 0.00 0.00 4.79
162 210 1.204941 CAGAAGGAGGTAAGGTGGACG 59.795 57.143 0.00 0.00 0.00 4.79
163 211 1.066071 GCAGAAGGAGGTAAGGTGGAC 60.066 57.143 0.00 0.00 0.00 4.02
164 212 1.203313 AGCAGAAGGAGGTAAGGTGGA 60.203 52.381 0.00 0.00 0.00 4.02
165 213 1.208293 GAGCAGAAGGAGGTAAGGTGG 59.792 57.143 0.00 0.00 0.00 4.61
166 214 2.167487 GAGAGCAGAAGGAGGTAAGGTG 59.833 54.545 0.00 0.00 0.00 4.00
167 215 2.043801 AGAGAGCAGAAGGAGGTAAGGT 59.956 50.000 0.00 0.00 0.00 3.50
168 216 2.693074 GAGAGAGCAGAAGGAGGTAAGG 59.307 54.545 0.00 0.00 0.00 2.69
169 217 3.631250 AGAGAGAGCAGAAGGAGGTAAG 58.369 50.000 0.00 0.00 0.00 2.34
170 218 3.626222 GGAGAGAGAGCAGAAGGAGGTAA 60.626 52.174 0.00 0.00 0.00 2.85
171 219 2.092103 GGAGAGAGAGCAGAAGGAGGTA 60.092 54.545 0.00 0.00 0.00 3.08
172 220 1.341976 GGAGAGAGAGCAGAAGGAGGT 60.342 57.143 0.00 0.00 0.00 3.85
173 221 1.063717 AGGAGAGAGAGCAGAAGGAGG 60.064 57.143 0.00 0.00 0.00 4.30
174 222 2.442236 AGGAGAGAGAGCAGAAGGAG 57.558 55.000 0.00 0.00 0.00 3.69
175 223 2.917713 AAGGAGAGAGAGCAGAAGGA 57.082 50.000 0.00 0.00 0.00 3.36
176 224 4.279169 CAGATAAGGAGAGAGAGCAGAAGG 59.721 50.000 0.00 0.00 0.00 3.46
177 225 4.261741 GCAGATAAGGAGAGAGAGCAGAAG 60.262 50.000 0.00 0.00 0.00 2.85
178 226 3.636300 GCAGATAAGGAGAGAGAGCAGAA 59.364 47.826 0.00 0.00 0.00 3.02
179 227 3.117550 AGCAGATAAGGAGAGAGAGCAGA 60.118 47.826 0.00 0.00 0.00 4.26
180 228 3.225104 AGCAGATAAGGAGAGAGAGCAG 58.775 50.000 0.00 0.00 0.00 4.24
181 229 3.311167 AGCAGATAAGGAGAGAGAGCA 57.689 47.619 0.00 0.00 0.00 4.26
182 230 4.582656 TGTAAGCAGATAAGGAGAGAGAGC 59.417 45.833 0.00 0.00 0.00 4.09
209 257 2.414161 GGACAAGCATCCAACGTAAAGC 60.414 50.000 0.00 0.00 38.77 3.51
227 275 0.321653 AGGATCTGGTGCGTTTGGAC 60.322 55.000 0.00 0.00 35.37 4.02
264 312 1.211969 GCACTGCGGAGACTCGTTA 59.788 57.895 12.26 0.00 0.00 3.18
265 313 2.049063 GCACTGCGGAGACTCGTT 60.049 61.111 12.26 0.00 0.00 3.85
365 414 2.035632 AGAGAGGGAGGTAGATTTGCG 58.964 52.381 0.00 0.00 0.00 4.85
418 481 2.297597 AGACTGCACACCTGAGAAGTAC 59.702 50.000 0.00 0.00 0.00 2.73
420 483 1.418334 AGACTGCACACCTGAGAAGT 58.582 50.000 0.00 0.00 0.00 3.01
426 489 2.086869 CCCAAATAGACTGCACACCTG 58.913 52.381 0.00 0.00 0.00 4.00
433 496 3.350219 TGGAAGACCCAAATAGACTGC 57.650 47.619 0.00 0.00 43.29 4.40
511 579 1.489649 AGCTGGATGTGGATCTGGAAG 59.510 52.381 0.00 0.00 0.00 3.46
610 680 8.515414 CCGTTATGAGAGTACATCATTCATAGA 58.485 37.037 16.06 0.00 38.36 1.98
634 704 9.329913 GACAGTAAATTATATATTTTGCTGCCG 57.670 33.333 28.89 17.11 44.41 5.69
718 791 4.506654 CACTGACAACGTAGCTTGTTAAGT 59.493 41.667 0.00 0.16 33.41 2.24
734 807 2.571653 AGGTAAAGCATAGGCACTGACA 59.428 45.455 0.67 0.00 44.61 3.58
819 892 3.432749 GGCTATGAACAGAGGCAATCAGA 60.433 47.826 15.95 0.00 43.61 3.27
857 1142 7.756722 GCTTTACTAAGTGCATCATGAAACAAT 59.243 33.333 0.00 0.00 33.74 2.71
884 1169 5.277058 CGACATGCAGTAAGGATCTAAAAGC 60.277 44.000 0.00 0.00 0.00 3.51
887 1172 5.592104 TCGACATGCAGTAAGGATCTAAA 57.408 39.130 0.00 0.00 0.00 1.85
939 1224 3.955429 GCATAGATACAATGCGCGG 57.045 52.632 8.83 0.00 40.27 6.46
961 1246 2.036256 GTTCAGGGTGGCTGGCAT 59.964 61.111 7.33 0.00 0.00 4.40
970 1255 5.077564 GGTTTCAAAAGATAGGTTCAGGGT 58.922 41.667 0.00 0.00 0.00 4.34
977 1262 6.139679 TGAGGATGGTTTCAAAAGATAGGT 57.860 37.500 0.00 0.00 0.00 3.08
1023 1308 1.538047 TTGCCTCAGCCAAAGATGTC 58.462 50.000 0.00 0.00 38.69 3.06
1058 1343 1.351350 GGTAAACTGGTCTTGGGAGCT 59.649 52.381 0.00 0.00 40.29 4.09
1155 1440 1.060308 CAATTTAGTCCGGCGTGCG 59.940 57.895 6.01 0.00 0.00 5.34
1191 1476 0.179702 CCATTGCTGCCTCTCTGCTA 59.820 55.000 0.00 0.00 39.95 3.49
1195 1480 1.141254 CTGATCCATTGCTGCCTCTCT 59.859 52.381 0.00 0.00 0.00 3.10
1248 1533 6.707440 TCAGCAAGAACCTTGTTTTCATTA 57.293 33.333 8.29 0.00 0.00 1.90
1317 1602 5.078411 TCTCTGACAAGGTATCTGAAAGC 57.922 43.478 0.00 0.00 0.00 3.51
1326 1611 4.825634 TCTTTCGTTCTCTCTGACAAGGTA 59.174 41.667 0.00 0.00 0.00 3.08
1328 1613 4.244425 TCTTTCGTTCTCTCTGACAAGG 57.756 45.455 0.00 0.00 0.00 3.61
1329 1614 5.285651 ACTTCTTTCGTTCTCTCTGACAAG 58.714 41.667 0.00 0.00 0.00 3.16
1340 1625 2.348591 CGCTGGTTGACTTCTTTCGTTC 60.349 50.000 0.00 0.00 0.00 3.95
1344 1629 0.944386 TGCGCTGGTTGACTTCTTTC 59.056 50.000 9.73 0.00 0.00 2.62
1345 1630 1.065551 GTTGCGCTGGTTGACTTCTTT 59.934 47.619 9.73 0.00 0.00 2.52
1351 1636 1.891919 TCTGGTTGCGCTGGTTGAC 60.892 57.895 9.73 0.00 0.00 3.18
1376 1661 3.380637 GGACGCCTCTTTAGTCATCTGTA 59.619 47.826 0.00 0.00 36.68 2.74
1638 1923 2.564771 TGATGGCAATCTTCATCGGTC 58.435 47.619 2.00 0.00 41.78 4.79
1652 1937 3.252701 GTCATCATCCATGTCTTGATGGC 59.747 47.826 20.62 17.77 44.34 4.40
1777 2063 0.179073 CACTCATGGGGATCGGACAC 60.179 60.000 0.00 0.00 0.00 3.67
1818 2104 2.095364 CAGCTTCACATGGCAAAGAGAC 60.095 50.000 0.00 0.00 0.00 3.36
1833 2119 4.802876 GAAGCCATACATACACAGCTTC 57.197 45.455 6.78 6.78 46.38 3.86
1865 2151 2.085262 CAGCAGACACAGAGACGCG 61.085 63.158 3.53 3.53 0.00 6.01
1869 2155 2.988010 AAACACAGCAGACACAGAGA 57.012 45.000 0.00 0.00 0.00 3.10
1871 2157 3.384789 AGACTAAACACAGCAGACACAGA 59.615 43.478 0.00 0.00 0.00 3.41
1950 2236 7.118971 CCAGAGTCAAGTTCAGAAAGGATAAAG 59.881 40.741 0.00 0.00 0.00 1.85
2085 2392 9.777297 AAGGTTAAAGCAAATGAATGTATGTTT 57.223 25.926 0.00 0.00 0.00 2.83
2086 2393 9.206870 CAAGGTTAAAGCAAATGAATGTATGTT 57.793 29.630 0.00 0.00 0.00 2.71
2089 2396 7.385267 TGCAAGGTTAAAGCAAATGAATGTAT 58.615 30.769 0.00 0.00 34.97 2.29
2091 2398 5.609423 TGCAAGGTTAAAGCAAATGAATGT 58.391 33.333 0.00 0.00 34.97 2.71
2092 2399 6.347888 CCTTGCAAGGTTAAAGCAAATGAATG 60.348 38.462 33.46 4.92 46.30 2.67
2093 2400 5.702209 CCTTGCAAGGTTAAAGCAAATGAAT 59.298 36.000 33.46 0.00 46.30 2.57
2096 2403 4.996062 CCTTGCAAGGTTAAAGCAAATG 57.004 40.909 33.46 6.71 46.30 2.32
2112 2419 3.042871 TGTTCATTGATTTGGCCTTGC 57.957 42.857 3.32 0.00 0.00 4.01
2115 2422 4.004982 GCAAATGTTCATTGATTTGGCCT 58.995 39.130 3.32 0.00 39.14 5.19
2116 2423 4.004982 AGCAAATGTTCATTGATTTGGCC 58.995 39.130 11.30 0.00 39.14 5.36
2117 2424 5.220529 GCTAGCAAATGTTCATTGATTTGGC 60.221 40.000 10.63 5.14 39.14 4.52
2119 2426 6.954616 TGCTAGCAAATGTTCATTGATTTG 57.045 33.333 16.84 6.79 40.87 2.32
2156 2463 8.422577 AGAATTGAGTAAAAAGGGCAAATAGT 57.577 30.769 0.00 0.00 0.00 2.12
2157 2464 7.976175 GGAGAATTGAGTAAAAAGGGCAAATAG 59.024 37.037 0.00 0.00 0.00 1.73
2158 2465 7.673926 AGGAGAATTGAGTAAAAAGGGCAAATA 59.326 33.333 0.00 0.00 0.00 1.40
2163 2470 5.243954 ACAAGGAGAATTGAGTAAAAAGGGC 59.756 40.000 0.00 0.00 34.20 5.19
2164 2471 6.901081 ACAAGGAGAATTGAGTAAAAAGGG 57.099 37.500 0.00 0.00 34.20 3.95
2165 2472 7.940850 TGAACAAGGAGAATTGAGTAAAAAGG 58.059 34.615 0.00 0.00 34.20 3.11
2170 3575 7.882791 TGCTAATGAACAAGGAGAATTGAGTAA 59.117 33.333 0.00 0.00 34.20 2.24
2175 3580 6.748333 TCTGCTAATGAACAAGGAGAATTG 57.252 37.500 0.00 0.00 37.27 2.32
2177 3582 6.656902 TGATCTGCTAATGAACAAGGAGAAT 58.343 36.000 0.00 0.00 42.46 2.40
2184 3589 9.624697 GTATGTTTTTGATCTGCTAATGAACAA 57.375 29.630 0.00 0.00 0.00 2.83
2186 3591 8.462016 AGGTATGTTTTTGATCTGCTAATGAAC 58.538 33.333 0.00 0.00 0.00 3.18
2187 3592 8.579850 AGGTATGTTTTTGATCTGCTAATGAA 57.420 30.769 0.00 0.00 0.00 2.57
2188 3593 8.049117 AGAGGTATGTTTTTGATCTGCTAATGA 58.951 33.333 0.00 0.00 0.00 2.57
2192 3597 7.394016 TGAAGAGGTATGTTTTTGATCTGCTA 58.606 34.615 0.00 0.00 0.00 3.49
2193 3598 6.240894 TGAAGAGGTATGTTTTTGATCTGCT 58.759 36.000 0.00 0.00 0.00 4.24
2194 3599 6.500684 TGAAGAGGTATGTTTTTGATCTGC 57.499 37.500 0.00 0.00 0.00 4.26
2196 3601 9.171877 GAGATTGAAGAGGTATGTTTTTGATCT 57.828 33.333 0.00 0.00 0.00 2.75
2197 3602 8.950210 TGAGATTGAAGAGGTATGTTTTTGATC 58.050 33.333 0.00 0.00 0.00 2.92
2198 3603 8.868522 TGAGATTGAAGAGGTATGTTTTTGAT 57.131 30.769 0.00 0.00 0.00 2.57
2199 3604 8.156820 TCTGAGATTGAAGAGGTATGTTTTTGA 58.843 33.333 0.00 0.00 0.00 2.69
2200 3605 8.327941 TCTGAGATTGAAGAGGTATGTTTTTG 57.672 34.615 0.00 0.00 0.00 2.44
2201 3606 9.171877 GATCTGAGATTGAAGAGGTATGTTTTT 57.828 33.333 0.00 0.00 0.00 1.94
2203 3608 7.855375 TGATCTGAGATTGAAGAGGTATGTTT 58.145 34.615 0.00 0.00 0.00 2.83
2204 3609 7.429374 TGATCTGAGATTGAAGAGGTATGTT 57.571 36.000 0.00 0.00 0.00 2.71
2205 3610 7.429374 TTGATCTGAGATTGAAGAGGTATGT 57.571 36.000 0.00 0.00 0.00 2.29
2206 3611 8.728337 TTTTGATCTGAGATTGAAGAGGTATG 57.272 34.615 0.00 0.00 0.00 2.39
2209 3614 8.108364 AGATTTTTGATCTGAGATTGAAGAGGT 58.892 33.333 0.00 0.00 0.00 3.85
2291 4706 1.603802 CGTTGCTGTCCTTGATGTTGT 59.396 47.619 0.00 0.00 0.00 3.32
2294 4709 1.237285 GGCGTTGCTGTCCTTGATGT 61.237 55.000 0.00 0.00 0.00 3.06
2376 4791 2.288152 GGCGATGGAGCAAAACTGAAAA 60.288 45.455 0.00 0.00 39.27 2.29
2659 5094 4.995624 AGAAAAGTTACAGGTAGGCCTT 57.004 40.909 12.58 0.00 44.18 4.35


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.