Multiple sequence alignment - TraesCS5B01G334400

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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 TraesCS5B01G334400 chr5B 100.000 5448 0 0 1 5448 517796697 517802144 0.000000e+00 10061
1 TraesCS5B01G334400 chr5B 84.412 3599 522 23 981 4562 517774893 517778469 0.000000e+00 3502
2 TraesCS5B01G334400 chr5B 83.785 3466 504 40 1133 4562 517694498 517697941 0.000000e+00 3234
3 TraesCS5B01G334400 chr5B 97.079 890 26 0 4559 5448 517811262 517812151 0.000000e+00 1500
4 TraesCS5B01G334400 chr5B 96.966 890 27 0 4559 5448 517813687 517814576 0.000000e+00 1495
5 TraesCS5B01G334400 chr5B 88.154 363 16 9 5112 5448 46124565 46124204 1.830000e-109 407
6 TraesCS5B01G334400 chr5B 95.000 80 4 0 178 257 517796953 517796874 5.730000e-25 126
7 TraesCS5B01G334400 chr5D 94.492 4720 195 38 132 4832 428669796 428674469 0.000000e+00 7215
8 TraesCS5B01G334400 chr5D 85.115 3406 490 15 1137 4529 428593106 428596507 0.000000e+00 3465
9 TraesCS5B01G334400 chr5D 84.367 3563 498 36 986 4529 428512205 428515727 0.000000e+00 3439
10 TraesCS5B01G334400 chr5D 83.773 3408 507 36 1127 4505 428565625 428569015 0.000000e+00 3188
11 TraesCS5B01G334400 chr5D 94.346 283 11 2 4830 5111 428674632 428674910 3.900000e-116 429
12 TraesCS5B01G334400 chr5A 92.658 4345 255 35 132 4460 544452058 544456354 0.000000e+00 6198
13 TraesCS5B01G334400 chr5A 84.767 3545 488 31 961 4469 544502313 544505841 0.000000e+00 3507
14 TraesCS5B01G334400 chr5A 86.106 2116 277 12 2411 4514 544246348 544248458 0.000000e+00 2263
15 TraesCS5B01G334400 chr5A 84.299 1726 253 11 1124 2837 544158649 544160368 0.000000e+00 1670
16 TraesCS5B01G334400 chr5A 83.467 1748 262 18 1017 2752 544461637 544463369 0.000000e+00 1602
17 TraesCS5B01G334400 chr5A 92.973 370 20 2 4461 4830 544511326 544511689 8.030000e-148 534
18 TraesCS5B01G334400 chr5A 93.310 284 11 5 4830 5111 544511847 544512124 3.930000e-111 412
19 TraesCS5B01G334400 chr7D 88.301 359 13 6 5110 5448 565218469 565218818 2.360000e-108 403
20 TraesCS5B01G334400 chr7D 93.258 89 6 0 169 257 199127712 199127624 1.230000e-26 132
21 TraesCS5B01G334400 chr7D 93.103 87 6 0 171 257 199127617 199127703 1.590000e-25 128
22 TraesCS5B01G334400 chr4A 88.056 360 17 7 5115 5448 711241800 711241441 2.360000e-108 403
23 TraesCS5B01G334400 chr4A 85.792 366 23 7 5112 5448 711176468 711176833 1.440000e-95 361
24 TraesCS5B01G334400 chr4A 84.647 241 15 5 5112 5340 699651793 699652023 2.550000e-53 220
25 TraesCS5B01G334400 chr1A 88.022 359 13 9 5110 5448 31961158 31960810 1.100000e-106 398
26 TraesCS5B01G334400 chr1A 85.580 319 35 2 5105 5412 11650382 11650064 1.890000e-84 324
27 TraesCS5B01G334400 chr1B 87.535 361 21 5 5112 5448 629802255 629802615 3.950000e-106 396
28 TraesCS5B01G334400 chr1B 91.011 89 7 1 170 257 187002141 187002229 9.590000e-23 119
29 TraesCS5B01G334400 chr2B 89.869 306 20 1 5112 5406 32047134 32046829 3.080000e-102 383
30 TraesCS5B01G334400 chr2B 95.062 81 4 0 177 257 675337153 675337233 1.590000e-25 128
31 TraesCS5B01G334400 chr2B 95.000 80 4 0 178 257 675337233 675337154 5.730000e-25 126
32 TraesCS5B01G334400 chr3D 89.251 307 22 1 5111 5406 604811446 604811140 1.850000e-99 374
33 TraesCS5B01G334400 chr3B 88.235 306 25 1 5112 5406 671506751 671507056 6.710000e-94 355
34 TraesCS5B01G334400 chr3B 85.598 368 20 12 5112 5448 758530351 758530716 6.710000e-94 355
35 TraesCS5B01G334400 chr3B 88.026 309 23 8 5109 5405 758518214 758518520 2.410000e-93 353
36 TraesCS5B01G334400 chr3B 87.000 300 24 6 5112 5398 758522259 758522556 1.890000e-84 324
37 TraesCS5B01G334400 chr3B 83.784 370 25 11 5112 5448 758526305 758526672 8.810000e-83 318
38 TraesCS5B01G334400 chr3B 79.076 368 21 23 5112 5448 758533147 758533489 9.250000e-48 202
39 TraesCS5B01G334400 chr3B 93.827 81 5 0 177 257 557093124 557093204 7.410000e-24 122
40 TraesCS5B01G334400 chr7A 83.702 362 23 7 5113 5448 140510751 140510400 5.300000e-80 309
41 TraesCS5B01G334400 chr4B 91.209 91 5 2 171 260 601766400 601766488 2.670000e-23 121
42 TraesCS5B01G334400 chr4D 86.916 107 6 4 159 264 30420770 30420869 4.460000e-21 113
43 TraesCS5B01G334400 chr6B 95.312 64 3 0 5343 5406 17592828 17592765 9.650000e-18 102


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 TraesCS5B01G334400 chr5B 517796697 517802144 5447 False 10061.0 10061 100.0000 1 5448 1 chr5B.!!$F3 5447
1 TraesCS5B01G334400 chr5B 517774893 517778469 3576 False 3502.0 3502 84.4120 981 4562 1 chr5B.!!$F2 3581
2 TraesCS5B01G334400 chr5B 517694498 517697941 3443 False 3234.0 3234 83.7850 1133 4562 1 chr5B.!!$F1 3429
3 TraesCS5B01G334400 chr5B 517811262 517814576 3314 False 1497.5 1500 97.0225 4559 5448 2 chr5B.!!$F4 889
4 TraesCS5B01G334400 chr5D 428669796 428674910 5114 False 3822.0 7215 94.4190 132 5111 2 chr5D.!!$F4 4979
5 TraesCS5B01G334400 chr5D 428593106 428596507 3401 False 3465.0 3465 85.1150 1137 4529 1 chr5D.!!$F3 3392
6 TraesCS5B01G334400 chr5D 428512205 428515727 3522 False 3439.0 3439 84.3670 986 4529 1 chr5D.!!$F1 3543
7 TraesCS5B01G334400 chr5D 428565625 428569015 3390 False 3188.0 3188 83.7730 1127 4505 1 chr5D.!!$F2 3378
8 TraesCS5B01G334400 chr5A 544452058 544456354 4296 False 6198.0 6198 92.6580 132 4460 1 chr5A.!!$F3 4328
9 TraesCS5B01G334400 chr5A 544502313 544505841 3528 False 3507.0 3507 84.7670 961 4469 1 chr5A.!!$F5 3508
10 TraesCS5B01G334400 chr5A 544246348 544248458 2110 False 2263.0 2263 86.1060 2411 4514 1 chr5A.!!$F2 2103
11 TraesCS5B01G334400 chr5A 544158649 544160368 1719 False 1670.0 1670 84.2990 1124 2837 1 chr5A.!!$F1 1713
12 TraesCS5B01G334400 chr5A 544461637 544463369 1732 False 1602.0 1602 83.4670 1017 2752 1 chr5A.!!$F4 1735
13 TraesCS5B01G334400 chr5A 544511326 544512124 798 False 473.0 534 93.1415 4461 5111 2 chr5A.!!$F6 650
14 TraesCS5B01G334400 chr3B 758518214 758533489 15275 False 310.4 355 84.6968 5109 5448 5 chr3B.!!$F3 339

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
825 839 0.101579 CGGCGAAACCAAAACCAAGT 59.898 50.000 0.0 0.0 39.03 3.16 F
1224 1264 1.308069 CCAAGCAACATCTGGGGACG 61.308 60.000 0.0 0.0 0.00 4.79 F
2748 2812 2.038863 TACCTTCTGAGCTTGGGGAA 57.961 50.000 0.0 0.0 0.00 3.97 F
3041 3113 3.157087 CTGGAAGTGTGGGCAATTTAGT 58.843 45.455 0.0 0.0 32.65 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 2415 0.392729 AGAGCCAGTGAGCTGATTGC 60.393 55.0 10.37 0.0 45.15 3.56 R
2814 2878 2.364972 ACAGGTTGCTTAACTTGCCT 57.635 45.0 2.71 0.0 33.62 4.75 R
4150 4238 0.318614 AACATTCTGCGCCCAAAACG 60.319 50.0 4.18 0.0 0.00 3.60 R
4521 4625 0.523519 GCTTAGCAGGCTTTGGACAC 59.476 55.0 0.00 0.0 0.00 3.67 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
31 32 3.453988 GCTGCTCGCTCCCTCTAT 58.546 61.111 0.00 0.00 35.14 1.98
32 33 1.288752 GCTGCTCGCTCCCTCTATC 59.711 63.158 0.00 0.00 35.14 2.08
34 35 0.881118 CTGCTCGCTCCCTCTATCTC 59.119 60.000 0.00 0.00 0.00 2.75
35 36 0.183731 TGCTCGCTCCCTCTATCTCA 59.816 55.000 0.00 0.00 0.00 3.27
36 37 1.202989 TGCTCGCTCCCTCTATCTCAT 60.203 52.381 0.00 0.00 0.00 2.90
40 41 4.439974 GCTCGCTCCCTCTATCTCATAATG 60.440 50.000 0.00 0.00 0.00 1.90
41 42 4.667573 TCGCTCCCTCTATCTCATAATGT 58.332 43.478 0.00 0.00 0.00 2.71
42 43 5.816682 TCGCTCCCTCTATCTCATAATGTA 58.183 41.667 0.00 0.00 0.00 2.29
44 45 6.375736 TCGCTCCCTCTATCTCATAATGTAAG 59.624 42.308 0.00 0.00 0.00 2.34
45 46 6.375736 CGCTCCCTCTATCTCATAATGTAAGA 59.624 42.308 0.00 0.00 0.00 2.10
46 47 7.543756 GCTCCCTCTATCTCATAATGTAAGAC 58.456 42.308 0.00 0.00 0.00 3.01
47 48 7.396055 GCTCCCTCTATCTCATAATGTAAGACT 59.604 40.741 0.00 0.00 0.00 3.24
48 49 9.308000 CTCCCTCTATCTCATAATGTAAGACTT 57.692 37.037 0.00 0.00 0.00 3.01
94 95 4.856664 CGTCTTACATTATAGGACGCACT 58.143 43.478 5.79 0.00 41.99 4.40
95 96 4.675565 CGTCTTACATTATAGGACGCACTG 59.324 45.833 5.79 0.00 41.99 3.66
96 97 4.444720 GTCTTACATTATAGGACGCACTGC 59.555 45.833 0.00 0.00 0.00 4.40
97 98 2.240493 ACATTATAGGACGCACTGCC 57.760 50.000 0.00 0.00 0.00 4.85
98 99 1.484653 ACATTATAGGACGCACTGCCA 59.515 47.619 0.00 0.00 0.00 4.92
101 102 2.772077 TATAGGACGCACTGCCAAAA 57.228 45.000 0.00 0.00 0.00 2.44
130 131 9.698309 ACATCTTACATTATATGACGAAAGGAG 57.302 33.333 0.00 0.00 0.00 3.69
188 189 2.444010 AGCTATCTTCTACTCCCTCCGT 59.556 50.000 0.00 0.00 0.00 4.69
189 190 2.815503 GCTATCTTCTACTCCCTCCGTC 59.184 54.545 0.00 0.00 0.00 4.79
190 191 3.497227 GCTATCTTCTACTCCCTCCGTCT 60.497 52.174 0.00 0.00 0.00 4.18
195 196 3.165087 TCTACTCCCTCCGTCTCAAAA 57.835 47.619 0.00 0.00 0.00 2.44
199 200 6.607970 TCTACTCCCTCCGTCTCAAAATATA 58.392 40.000 0.00 0.00 0.00 0.86
200 201 7.064866 TCTACTCCCTCCGTCTCAAAATATAA 58.935 38.462 0.00 0.00 0.00 0.98
201 202 6.163135 ACTCCCTCCGTCTCAAAATATAAG 57.837 41.667 0.00 0.00 0.00 1.73
202 203 5.897824 ACTCCCTCCGTCTCAAAATATAAGA 59.102 40.000 0.00 0.00 0.00 2.10
203 204 6.383147 ACTCCCTCCGTCTCAAAATATAAGAA 59.617 38.462 0.00 0.00 0.00 2.52
204 205 6.579865 TCCCTCCGTCTCAAAATATAAGAAC 58.420 40.000 0.00 0.00 0.00 3.01
205 206 5.462398 CCCTCCGTCTCAAAATATAAGAACG 59.538 44.000 0.00 0.00 0.00 3.95
206 207 6.040878 CCTCCGTCTCAAAATATAAGAACGT 58.959 40.000 0.00 0.00 0.00 3.99
207 208 6.534079 CCTCCGTCTCAAAATATAAGAACGTT 59.466 38.462 0.00 0.00 0.00 3.99
211 221 8.837059 CCGTCTCAAAATATAAGAACGTTTTTG 58.163 33.333 13.87 12.46 38.17 2.44
244 254 8.696175 GTGTCAAAAACGTTCTTATATTTTGGG 58.304 33.333 15.53 0.00 39.94 4.12
245 255 8.630917 TGTCAAAAACGTTCTTATATTTTGGGA 58.369 29.630 15.53 4.35 39.94 4.37
246 256 9.124807 GTCAAAAACGTTCTTATATTTTGGGAG 57.875 33.333 15.53 0.00 39.94 4.30
247 257 8.301002 TCAAAAACGTTCTTATATTTTGGGAGG 58.699 33.333 15.53 0.00 39.94 4.30
257 267 2.680439 TTTTGGGAGGGAGGGAGTAT 57.320 50.000 0.00 0.00 0.00 2.12
267 277 5.094387 GAGGGAGGGAGTATCATATTCCAA 58.906 45.833 8.41 0.00 36.38 3.53
268 278 5.680327 AGGGAGGGAGTATCATATTCCAAT 58.320 41.667 8.41 0.00 36.38 3.16
269 279 5.490357 AGGGAGGGAGTATCATATTCCAATG 59.510 44.000 8.41 0.00 36.38 2.82
279 289 3.389656 TCATATTCCAATGGACGCCACTA 59.610 43.478 0.00 0.00 35.80 2.74
289 299 4.739587 TGGACGCCACTACACAAATATA 57.260 40.909 0.00 0.00 0.00 0.86
290 300 5.284861 TGGACGCCACTACACAAATATAT 57.715 39.130 0.00 0.00 0.00 0.86
294 304 7.934665 TGGACGCCACTACACAAATATATATTT 59.065 33.333 13.85 13.85 36.39 1.40
296 306 8.896320 ACGCCACTACACAAATATATATTTCA 57.104 30.769 16.25 3.80 33.88 2.69
323 333 5.232463 AGCAATTTCAGGCACAAACATTAG 58.768 37.500 0.00 0.00 0.00 1.73
325 335 5.107375 GCAATTTCAGGCACAAACATTAGTG 60.107 40.000 0.00 0.00 38.74 2.74
326 336 5.789643 ATTTCAGGCACAAACATTAGTGT 57.210 34.783 0.00 0.00 41.28 3.55
349 362 5.845391 TGTCCATATCAGAACACATACGA 57.155 39.130 0.00 0.00 0.00 3.43
350 363 5.588240 TGTCCATATCAGAACACATACGAC 58.412 41.667 0.00 0.00 0.00 4.34
366 379 1.871039 ACGACTTCATTTGAACCGTGG 59.129 47.619 12.35 4.89 37.08 4.94
367 380 2.139917 CGACTTCATTTGAACCGTGGA 58.860 47.619 0.00 0.00 0.00 4.02
368 381 2.096417 CGACTTCATTTGAACCGTGGAC 60.096 50.000 0.00 0.00 0.00 4.02
370 383 0.589223 TTCATTTGAACCGTGGACGC 59.411 50.000 0.00 0.00 38.18 5.19
371 384 1.154488 CATTTGAACCGTGGACGCG 60.154 57.895 3.53 3.53 38.18 6.01
384 397 2.096713 GTGGACGCGCTAAATCATCATC 60.097 50.000 5.73 0.00 0.00 2.92
393 406 5.536260 CGCTAAATCATCATCCAAGAGAGA 58.464 41.667 0.00 0.00 0.00 3.10
438 451 3.002348 GCACGGTAAGCACCATATCTTTC 59.998 47.826 0.00 0.00 46.14 2.62
440 453 4.876107 CACGGTAAGCACCATATCTTTCTT 59.124 41.667 0.00 0.00 46.14 2.52
542 555 3.713858 TTGTCAGCATTGAAACCAGTG 57.286 42.857 0.00 0.00 34.49 3.66
545 558 2.622942 GTCAGCATTGAAACCAGTGGAA 59.377 45.455 18.40 0.00 34.49 3.53
546 559 3.068024 GTCAGCATTGAAACCAGTGGAAA 59.932 43.478 18.40 5.01 34.49 3.13
602 615 2.760799 TGGTCCCGTCCCGTATGG 60.761 66.667 0.00 0.00 0.00 2.74
645 658 1.451067 ACGTAGTCGAGGTCTTCCAG 58.549 55.000 0.00 0.00 29.74 3.86
825 839 0.101579 CGGCGAAACCAAAACCAAGT 59.898 50.000 0.00 0.00 39.03 3.16
897 911 8.585881 TCTTCTTAGCTATTATTATCGCACCTT 58.414 33.333 0.00 0.00 0.00 3.50
1167 1204 2.444706 CTGAGATCCCAGGCCGGA 60.445 66.667 5.05 8.48 36.56 5.14
1197 1234 4.326826 TCCACTGGAAATCATCAGTCAAC 58.673 43.478 0.00 0.00 41.71 3.18
1212 1249 2.972713 AGTCAACTACTCCTCCAAGCAA 59.027 45.455 0.00 0.00 30.33 3.91
1215 1255 3.327757 TCAACTACTCCTCCAAGCAACAT 59.672 43.478 0.00 0.00 0.00 2.71
1224 1264 1.308069 CCAAGCAACATCTGGGGACG 61.308 60.000 0.00 0.00 0.00 4.79
1665 1726 3.882326 ATCCCATGGCAGCTCGGG 61.882 66.667 6.09 7.76 40.32 5.14
2080 2144 2.224670 TGGGGTAACAACATCACTGGAC 60.225 50.000 0.00 0.00 39.74 4.02
2241 2305 2.464459 GGAATTGCCGACCGAGCTG 61.464 63.158 0.00 0.00 0.00 4.24
2351 2415 7.546358 AGTATGAGAGAAATGAGACTGTTCAG 58.454 38.462 0.00 0.00 0.00 3.02
2748 2812 2.038863 TACCTTCTGAGCTTGGGGAA 57.961 50.000 0.00 0.00 0.00 3.97
2814 2878 8.929260 TGAATAGTGAGATACCGGTAGAAATA 57.071 34.615 20.91 9.00 0.00 1.40
3006 3078 9.166173 TCATTATATATGCATAACAACAGCCTC 57.834 33.333 11.13 0.00 0.00 4.70
3041 3113 3.157087 CTGGAAGTGTGGGCAATTTAGT 58.843 45.455 0.00 0.00 32.65 2.24
3128 3200 6.514063 TCAGCAAACTAGAGATGATGATCTG 58.486 40.000 0.00 0.00 39.19 2.90
3704 3780 7.465353 TCCAGCATGAGATTGAAATGTTAAA 57.535 32.000 0.00 0.00 39.69 1.52
4179 4267 2.484264 GCGCAGAATGTTCCTACACTTT 59.516 45.455 0.30 0.00 39.31 2.66
4228 4316 0.821711 GCTTTGGTGTGGTGGTGCTA 60.822 55.000 0.00 0.00 0.00 3.49
4235 4323 0.685097 TGTGGTGGTGCTAGAGGTTC 59.315 55.000 0.00 0.00 0.00 3.62
4521 4625 5.241728 AGAACAAAACTTAAGCTGCCTTAGG 59.758 40.000 1.29 0.00 36.86 2.69
4928 7636 2.020720 TGCAAAACAGTGTTCCGACAT 58.979 42.857 9.40 0.00 38.23 3.06
5044 7755 5.180680 GGTGCTTCCTACGAACATAAAAACT 59.819 40.000 0.00 0.00 0.00 2.66
5118 12145 1.076332 CCTGAAATCGACGGGTCAAC 58.924 55.000 0.00 0.00 0.00 3.18
5181 12219 3.273434 GAGAAATAGCTCATGTGCACCA 58.727 45.455 20.92 2.61 35.01 4.17
5290 12330 5.104485 ACAGGGGGTCAAACTAATCAGTATC 60.104 44.000 0.00 0.00 33.48 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.183731 TGAGATAGAGGGAGCGAGCA 59.816 55.000 0.00 0.00 0.00 4.26
17 18 1.544724 ATGAGATAGAGGGAGCGAGC 58.455 55.000 0.00 0.00 0.00 5.03
18 19 4.704540 ACATTATGAGATAGAGGGAGCGAG 59.295 45.833 0.00 0.00 0.00 5.03
20 21 6.375736 TCTTACATTATGAGATAGAGGGAGCG 59.624 42.308 0.00 0.00 0.00 5.03
21 22 7.396055 AGTCTTACATTATGAGATAGAGGGAGC 59.604 40.741 0.00 0.00 0.00 4.70
22 23 8.877864 AGTCTTACATTATGAGATAGAGGGAG 57.122 38.462 0.00 0.00 0.00 4.30
23 24 9.661954 AAAGTCTTACATTATGAGATAGAGGGA 57.338 33.333 0.00 0.00 0.00 4.20
73 74 4.444720 GCAGTGCGTCCTATAATGTAAGAC 59.555 45.833 0.00 0.00 0.00 3.01
74 75 4.500887 GGCAGTGCGTCCTATAATGTAAGA 60.501 45.833 9.45 0.00 0.00 2.10
75 76 3.741344 GGCAGTGCGTCCTATAATGTAAG 59.259 47.826 9.45 0.00 0.00 2.34
77 78 2.696187 TGGCAGTGCGTCCTATAATGTA 59.304 45.455 9.45 0.00 0.00 2.29
78 79 1.484653 TGGCAGTGCGTCCTATAATGT 59.515 47.619 9.45 0.00 0.00 2.71
79 80 2.238942 TGGCAGTGCGTCCTATAATG 57.761 50.000 9.45 0.00 0.00 1.90
80 81 3.275617 TTTGGCAGTGCGTCCTATAAT 57.724 42.857 9.45 0.00 0.00 1.28
81 82 2.772077 TTTGGCAGTGCGTCCTATAA 57.228 45.000 9.45 0.00 0.00 0.98
82 83 2.772077 TTTTGGCAGTGCGTCCTATA 57.228 45.000 9.45 0.00 0.00 1.31
83 84 1.904287 TTTTTGGCAGTGCGTCCTAT 58.096 45.000 9.45 0.00 0.00 2.57
84 85 3.405689 TTTTTGGCAGTGCGTCCTA 57.594 47.368 9.45 0.00 0.00 2.94
85 86 4.251246 TTTTTGGCAGTGCGTCCT 57.749 50.000 9.45 0.00 0.00 3.85
104 105 9.698309 CTCCTTTCGTCATATAATGTAAGATGT 57.302 33.333 0.00 0.00 0.00 3.06
118 119 9.915629 GTCTTGATATATTACTCCTTTCGTCAT 57.084 33.333 0.00 0.00 0.00 3.06
119 120 8.358148 GGTCTTGATATATTACTCCTTTCGTCA 58.642 37.037 0.00 0.00 0.00 4.35
120 121 8.358148 TGGTCTTGATATATTACTCCTTTCGTC 58.642 37.037 0.00 0.00 0.00 4.20
121 122 8.246430 TGGTCTTGATATATTACTCCTTTCGT 57.754 34.615 0.00 0.00 0.00 3.85
122 123 9.360093 GATGGTCTTGATATATTACTCCTTTCG 57.640 37.037 0.00 0.00 0.00 3.46
158 159 8.620177 AGGGAGTAGAAGATAGCTCAATAGTAT 58.380 37.037 0.00 0.00 0.00 2.12
160 161 6.858941 AGGGAGTAGAAGATAGCTCAATAGT 58.141 40.000 0.00 0.00 0.00 2.12
169 170 4.202377 TGAGACGGAGGGAGTAGAAGATAG 60.202 50.000 0.00 0.00 0.00 2.08
174 175 2.893215 TTGAGACGGAGGGAGTAGAA 57.107 50.000 0.00 0.00 0.00 2.10
181 182 5.462398 CGTTCTTATATTTTGAGACGGAGGG 59.538 44.000 0.00 0.00 0.00 4.30
195 196 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
220 230 9.124807 CTCCCAAAATATAAGAACGTTTTTGAC 57.875 33.333 13.87 0.00 38.79 3.18
226 236 6.069705 TCCCTCCCAAAATATAAGAACGTT 57.930 37.500 0.00 0.00 0.00 3.99
227 237 5.397559 CCTCCCTCCCAAAATATAAGAACGT 60.398 44.000 0.00 0.00 0.00 3.99
228 238 5.063880 CCTCCCTCCCAAAATATAAGAACG 58.936 45.833 0.00 0.00 0.00 3.95
229 239 5.133830 TCCCTCCCTCCCAAAATATAAGAAC 59.866 44.000 0.00 0.00 0.00 3.01
231 241 4.913968 CTCCCTCCCTCCCAAAATATAAGA 59.086 45.833 0.00 0.00 0.00 2.10
233 243 4.652628 ACTCCCTCCCTCCCAAAATATAA 58.347 43.478 0.00 0.00 0.00 0.98
244 254 4.689062 TGGAATATGATACTCCCTCCCTC 58.311 47.826 0.00 0.00 0.00 4.30
245 255 4.785173 TGGAATATGATACTCCCTCCCT 57.215 45.455 0.00 0.00 0.00 4.20
246 256 5.339530 CCATTGGAATATGATACTCCCTCCC 60.340 48.000 0.00 0.00 0.00 4.30
247 257 5.488919 TCCATTGGAATATGATACTCCCTCC 59.511 44.000 1.94 0.00 0.00 4.30
257 267 2.172505 AGTGGCGTCCATTGGAATATGA 59.827 45.455 7.05 0.00 35.28 2.15
267 277 2.489938 ATTTGTGTAGTGGCGTCCAT 57.510 45.000 1.90 0.00 35.28 3.41
268 278 3.620427 ATATTTGTGTAGTGGCGTCCA 57.380 42.857 0.00 0.00 0.00 4.02
269 279 7.900782 AATATATATTTGTGTAGTGGCGTCC 57.099 36.000 1.91 0.00 0.00 4.79
289 299 7.286087 TGTGCCTGAAATTGCTAGATGAAATAT 59.714 33.333 0.00 0.00 0.00 1.28
290 300 6.602803 TGTGCCTGAAATTGCTAGATGAAATA 59.397 34.615 0.00 0.00 0.00 1.40
294 304 3.954200 TGTGCCTGAAATTGCTAGATGA 58.046 40.909 0.00 0.00 0.00 2.92
296 306 4.523943 TGTTTGTGCCTGAAATTGCTAGAT 59.476 37.500 0.00 0.00 0.00 1.98
323 333 6.237835 CGTATGTGTTCTGATATGGACAACAC 60.238 42.308 6.34 6.34 39.37 3.32
325 335 6.019801 GTCGTATGTGTTCTGATATGGACAAC 60.020 42.308 0.00 0.00 0.00 3.32
326 336 6.040247 GTCGTATGTGTTCTGATATGGACAA 58.960 40.000 0.00 0.00 0.00 3.18
330 340 6.273071 TGAAGTCGTATGTGTTCTGATATGG 58.727 40.000 0.00 0.00 0.00 2.74
349 362 1.871039 CGTCCACGGTTCAAATGAAGT 59.129 47.619 0.00 0.00 34.27 3.01
350 363 1.399727 GCGTCCACGGTTCAAATGAAG 60.400 52.381 0.55 0.00 40.23 3.02
366 379 2.135139 TGGATGATGATTTAGCGCGTC 58.865 47.619 8.43 0.00 0.00 5.19
367 380 2.238942 TGGATGATGATTTAGCGCGT 57.761 45.000 8.43 0.00 0.00 6.01
368 381 2.802247 TCTTGGATGATGATTTAGCGCG 59.198 45.455 0.00 0.00 0.00 6.86
370 383 5.404968 GTCTCTCTTGGATGATGATTTAGCG 59.595 44.000 0.00 0.00 0.00 4.26
371 384 5.700373 GGTCTCTCTTGGATGATGATTTAGC 59.300 44.000 0.00 0.00 0.00 3.09
384 397 5.835113 TTCTTTGTTTTGGTCTCTCTTGG 57.165 39.130 0.00 0.00 0.00 3.61
393 406 4.050553 CGACATGCATTCTTTGTTTTGGT 58.949 39.130 0.00 0.00 0.00 3.67
453 466 2.432206 TGACGATCGTGCTTTCAAGA 57.568 45.000 28.12 0.00 35.30 3.02
454 467 4.105486 TCTATGACGATCGTGCTTTCAAG 58.895 43.478 28.12 15.13 0.00 3.02
455 468 4.104696 TCTATGACGATCGTGCTTTCAA 57.895 40.909 28.12 6.97 0.00 2.69
484 497 0.539051 GGTCACTGGCTCACTGCTAT 59.461 55.000 0.00 0.00 42.39 2.97
485 498 1.544825 GGGTCACTGGCTCACTGCTA 61.545 60.000 0.00 0.00 42.39 3.49
494 507 4.035102 GAGGTGGGGGTCACTGGC 62.035 72.222 0.00 0.00 45.38 4.85
495 508 3.706373 CGAGGTGGGGGTCACTGG 61.706 72.222 0.00 0.00 45.38 4.00
496 509 3.706373 CCGAGGTGGGGGTCACTG 61.706 72.222 0.00 0.00 45.38 3.66
542 555 4.252971 TGTGCGACCTAGCTATATTTCC 57.747 45.455 0.00 0.00 38.13 3.13
545 558 3.756963 TCGATGTGCGACCTAGCTATATT 59.243 43.478 0.00 0.00 45.59 1.28
546 559 3.344515 TCGATGTGCGACCTAGCTATAT 58.655 45.455 0.00 0.00 45.59 0.86
645 658 2.042831 ATGCAGCCCAAGTCTTCGC 61.043 57.895 0.00 0.00 0.00 4.70
869 883 9.372369 GGTGCGATAATAATAGCTAAGAAGAAT 57.628 33.333 0.00 0.00 35.03 2.40
887 901 6.101650 AGACATGATGATTAAGGTGCGATA 57.898 37.500 0.00 0.00 0.00 2.92
888 902 4.965814 AGACATGATGATTAAGGTGCGAT 58.034 39.130 0.00 0.00 0.00 4.58
890 904 5.490139 AAAGACATGATGATTAAGGTGCG 57.510 39.130 0.00 0.00 0.00 5.34
891 905 7.093322 AGAAAAGACATGATGATTAAGGTGC 57.907 36.000 0.00 0.00 0.00 5.01
892 906 9.565213 GAAAGAAAAGACATGATGATTAAGGTG 57.435 33.333 0.00 0.00 0.00 4.00
893 907 8.454106 CGAAAGAAAAGACATGATGATTAAGGT 58.546 33.333 0.00 0.00 0.00 3.50
894 908 7.430502 GCGAAAGAAAAGACATGATGATTAAGG 59.569 37.037 0.00 0.00 0.00 2.69
897 911 7.376435 TGCGAAAGAAAAGACATGATGATTA 57.624 32.000 0.00 0.00 0.00 1.75
1069 1097 2.431454 CCTGGAAGCAAGGAGAAGAAC 58.569 52.381 0.00 0.00 36.91 3.01
1146 1183 2.420890 GCCTGGGATCTCAGCGAG 59.579 66.667 17.80 5.00 33.64 5.03
1167 1204 0.326264 ATTTCCAGTGGAGAAGCGCT 59.674 50.000 12.67 2.64 31.21 5.92
1197 1234 3.529533 CAGATGTTGCTTGGAGGAGTAG 58.470 50.000 0.00 0.00 0.00 2.57
1212 1249 0.972983 CTCTCCACGTCCCCAGATGT 60.973 60.000 0.00 0.00 43.24 3.06
1215 1255 1.304217 GTCTCTCCACGTCCCCAGA 60.304 63.158 0.00 0.00 0.00 3.86
1224 1264 1.517257 CATGCCGTCGTCTCTCCAC 60.517 63.158 0.00 0.00 0.00 4.02
1665 1726 3.254166 TCTTTCTCATGTTTCCAAGCTGC 59.746 43.478 0.00 0.00 0.00 5.25
2241 2305 3.431673 TCCAAATTTGCCAAATTCCCC 57.568 42.857 15.31 0.00 40.05 4.81
2351 2415 0.392729 AGAGCCAGTGAGCTGATTGC 60.393 55.000 10.37 0.00 45.15 3.56
2409 2473 5.981315 CAGCTTGTTGTCATTCAGTTCAATT 59.019 36.000 0.00 0.00 0.00 2.32
2814 2878 2.364972 ACAGGTTGCTTAACTTGCCT 57.635 45.000 2.71 0.00 33.62 4.75
3041 3113 2.433604 TCAAACATGCTTTGCAGGGAAA 59.566 40.909 8.97 0.00 45.01 3.13
4150 4238 0.318614 AACATTCTGCGCCCAAAACG 60.319 50.000 4.18 0.00 0.00 3.60
4179 4267 5.421056 ACATCACATTTCTCCGTAACTAGGA 59.579 40.000 0.00 0.00 36.20 2.94
4228 4316 1.425066 TGTTTGCCCATCAGAACCTCT 59.575 47.619 0.00 0.00 0.00 3.69
4235 4323 1.108776 CCTGGATGTTTGCCCATCAG 58.891 55.000 9.47 0.00 42.47 2.90
4521 4625 0.523519 GCTTAGCAGGCTTTGGACAC 59.476 55.000 0.00 0.00 0.00 3.67
4928 7636 3.582647 TGTAATTGAGGAACTGAGAGCCA 59.417 43.478 0.00 0.00 41.55 4.75
4972 7681 5.001232 GTCACTACAAATTGGTAGGAAGCA 58.999 41.667 21.55 0.93 43.99 3.91
5044 7755 6.175471 ACAATCTGAATGATTACTCAGTGCA 58.825 36.000 0.00 0.00 43.00 4.57
5080 7791 0.685097 GGGCCGCAGTCCAATATCTA 59.315 55.000 0.00 0.00 0.00 1.98
5081 7792 1.451936 GGGCCGCAGTCCAATATCT 59.548 57.895 0.00 0.00 0.00 1.98
5118 12145 1.945387 AATGTGTCGCATAGGAGCTG 58.055 50.000 0.00 0.00 36.67 4.24
5290 12330 4.887957 TGGGACCCACTACCAGAG 57.112 61.111 9.95 0.00 0.00 3.35
5313 12353 1.069090 GCGGGGAATCGATGCACTA 59.931 57.895 5.40 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.