Multiple sequence alignment - TraesCS4B01G368400

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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 TraesCS4B01G368400 chr4B 100.000 2390 0 0 1 2390 654732861 654730472 0.000000e+00 4414.0
1 TraesCS4B01G368400 chr4B 94.125 1515 58 10 880 2390 655077989 655076502 0.000000e+00 2276.0
2 TraesCS4B01G368400 chr4B 91.359 1111 70 4 404 1489 654807604 654806495 0.000000e+00 1496.0
3 TraesCS4B01G368400 chr4B 95.796 904 29 6 1492 2390 654806009 654805110 0.000000e+00 1450.0
4 TraesCS4B01G368400 chr4B 97.901 810 16 1 1582 2390 654605986 654605177 0.000000e+00 1400.0
5 TraesCS4B01G368400 chr4B 92.500 760 33 5 880 1638 655111506 655110770 0.000000e+00 1066.0
6 TraesCS4B01G368400 chr4B 95.819 574 20 3 1631 2203 655107455 655106885 0.000000e+00 924.0
7 TraesCS4B01G368400 chr4B 98.684 304 3 1 1902 2204 654834543 654834240 2.700000e-149 538.0
8 TraesCS4B01G368400 chr4B 88.583 254 20 3 560 806 655083919 655083668 1.390000e-77 300.0
9 TraesCS4B01G368400 chr4B 88.189 254 21 3 560 806 655111898 655111647 6.460000e-76 294.0
10 TraesCS4B01G368400 chr4B 85.567 194 23 2 1578 1771 654746083 654745895 5.210000e-47 198.0
11 TraesCS4B01G368400 chr4B 81.250 208 24 7 1578 1771 654706505 654706299 1.140000e-33 154.0
12 TraesCS4B01G368400 chr4B 90.000 120 7 2 1578 1697 654647118 654647004 1.480000e-32 150.0
13 TraesCS4B01G368400 chrUn 86.877 1044 102 17 957 1983 154567838 154568863 0.000000e+00 1136.0
14 TraesCS4B01G368400 chrUn 86.450 893 91 13 880 1771 154542496 154543359 0.000000e+00 952.0
15 TraesCS4B01G368400 chrUn 86.226 893 93 13 880 1771 201369050 201369913 0.000000e+00 941.0
16 TraesCS4B01G368400 chrUn 86.180 890 92 14 883 1771 189562010 189561151 0.000000e+00 933.0
17 TraesCS4B01G368400 chrUn 86.067 890 94 13 883 1771 189575698 189574838 0.000000e+00 929.0
18 TraesCS4B01G368400 chrUn 86.002 893 94 14 880 1771 279543188 279544050 0.000000e+00 928.0
19 TraesCS4B01G368400 chrUn 87.938 257 20 6 560 806 189576107 189575852 2.320000e-75 292.0
20 TraesCS4B01G368400 chrUn 87.938 257 20 6 560 806 201368644 201368899 2.320000e-75 292.0
21 TraesCS4B01G368400 chrUn 87.938 257 20 6 560 806 346445308 346445053 2.320000e-75 292.0
22 TraesCS4B01G368400 chrUn 87.938 257 20 6 560 806 363336362 363336617 2.320000e-75 292.0
23 TraesCS4B01G368400 chrUn 87.549 257 21 6 560 806 189562419 189562164 1.080000e-73 287.0
24 TraesCS4B01G368400 chrUn 87.549 257 21 6 560 806 377346081 377345826 1.080000e-73 287.0
25 TraesCS4B01G368400 chrUn 86.038 265 30 6 2097 2359 154569471 154569730 6.510000e-71 278.0
26 TraesCS4B01G368400 chrUn 78.531 177 23 7 126 293 154541927 154542097 4.200000e-18 102.0
27 TraesCS4B01G368400 chrUn 78.531 177 22 8 126 293 346445470 346445301 4.200000e-18 102.0
28 TraesCS4B01G368400 chrUn 78.531 177 22 8 126 293 363336200 363336369 4.200000e-18 102.0
29 TraesCS4B01G368400 chrUn 78.409 176 24 11 126 293 377346243 377346074 4.200000e-18 102.0
30 TraesCS4B01G368400 chrUn 78.771 179 17 10 126 293 201368483 201368651 1.510000e-17 100.0
31 TraesCS4B01G368400 chrUn 77.320 194 27 9 110 293 154567208 154567394 5.440000e-17 99.0
32 TraesCS4B01G368400 chrUn 77.966 177 23 9 126 293 189562581 189562412 1.960000e-16 97.1
33 TraesCS4B01G368400 chrUn 77.966 177 23 8 126 293 189576269 189576100 1.960000e-16 97.1
34 TraesCS4B01G368400 chrUn 77.401 177 24 9 126 293 279542620 279542789 9.100000e-15 91.6
35 TraesCS4B01G368400 chr2A 76.173 277 49 12 294 559 27997807 27998077 1.930000e-26 130.0
36 TraesCS4B01G368400 chr2A 82.456 114 19 1 294 406 726598185 726598298 5.440000e-17 99.0
37 TraesCS4B01G368400 chr3A 82.456 114 19 1 294 406 18968159 18968046 5.440000e-17 99.0
38 TraesCS4B01G368400 chr6A 83.077 65 7 3 294 358 541407331 541407271 3.320000e-04 56.5
39 TraesCS4B01G368400 chr6A 100.000 28 0 0 295 322 105637238 105637265 4.000000e-03 52.8
40 TraesCS4B01G368400 chr5D 94.444 36 1 1 373 408 51114813 51114779 1.000000e-03 54.7
41 TraesCS4B01G368400 chr5D 94.444 36 1 1 373 408 51132265 51132231 1.000000e-03 54.7
42 TraesCS4B01G368400 chr5D 94.444 36 1 1 373 408 51172107 51172073 1.000000e-03 54.7
43 TraesCS4B01G368400 chr5D 94.444 36 1 1 373 408 51191721 51191687 1.000000e-03 54.7


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 TraesCS4B01G368400 chr4B 654730472 654732861 2389 True 4414.000000 4414 100.000000 1 2390 1 chr4B.!!$R4 2389
1 TraesCS4B01G368400 chr4B 655076502 655077989 1487 True 2276.000000 2276 94.125000 880 2390 1 chr4B.!!$R7 1510
2 TraesCS4B01G368400 chr4B 654805110 654807604 2494 True 1473.000000 1496 93.577500 404 2390 2 chr4B.!!$R9 1986
3 TraesCS4B01G368400 chr4B 654605177 654605986 809 True 1400.000000 1400 97.901000 1582 2390 1 chr4B.!!$R1 808
4 TraesCS4B01G368400 chr4B 655106885 655111898 5013 True 761.333333 1066 92.169333 560 2203 3 chr4B.!!$R10 1643
5 TraesCS4B01G368400 chrUn 154541927 154543359 1432 False 527.000000 952 82.490500 126 1771 2 chrUn.!!$F1 1645
6 TraesCS4B01G368400 chrUn 279542620 279544050 1430 False 509.800000 928 81.701500 126 1771 2 chrUn.!!$F4 1645
7 TraesCS4B01G368400 chrUn 154567208 154569730 2522 False 504.333333 1136 83.411667 110 2359 3 chrUn.!!$F2 2249
8 TraesCS4B01G368400 chrUn 201368483 201369913 1430 False 444.333333 941 84.311667 126 1771 3 chrUn.!!$F3 1645
9 TraesCS4B01G368400 chrUn 189574838 189576269 1431 True 439.366667 929 83.990333 126 1771 3 chrUn.!!$R2 1645
10 TraesCS4B01G368400 chrUn 189561151 189562581 1430 True 439.033333 933 83.898333 126 1771 3 chrUn.!!$R1 1645

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
287 318 0.109643 CACACCAACGACCATGCATG 60.11 55.0 20.19 20.19 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1554 0.107831 TGCTTGGCCGAGTACTTTGT 59.892 50.0 21.55 0.0 0.0 2.83 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
89 90 6.391227 TTTTTGGCTCTCTTTTTCTACAGG 57.609 37.500 0.00 0.00 0.00 4.00
90 91 4.706842 TTGGCTCTCTTTTTCTACAGGT 57.293 40.909 0.00 0.00 0.00 4.00
91 92 5.818678 TTGGCTCTCTTTTTCTACAGGTA 57.181 39.130 0.00 0.00 0.00 3.08
92 93 5.818678 TGGCTCTCTTTTTCTACAGGTAA 57.181 39.130 0.00 0.00 0.00 2.85
93 94 6.374417 TGGCTCTCTTTTTCTACAGGTAAT 57.626 37.500 0.00 0.00 0.00 1.89
94 95 6.779860 TGGCTCTCTTTTTCTACAGGTAATT 58.220 36.000 0.00 0.00 0.00 1.40
95 96 7.231467 TGGCTCTCTTTTTCTACAGGTAATTT 58.769 34.615 0.00 0.00 0.00 1.82
96 97 7.724061 TGGCTCTCTTTTTCTACAGGTAATTTT 59.276 33.333 0.00 0.00 0.00 1.82
97 98 8.577296 GGCTCTCTTTTTCTACAGGTAATTTTT 58.423 33.333 0.00 0.00 0.00 1.94
174 175 9.915629 TTTCACTACACATTAAACAGTTTTTGT 57.084 25.926 3.25 6.20 43.45 2.83
181 182 9.515020 ACACATTAAACAGTTTTTGTAGACATG 57.485 29.630 3.25 0.00 39.73 3.21
182 183 8.967218 CACATTAAACAGTTTTTGTAGACATGG 58.033 33.333 3.25 0.00 39.73 3.66
183 184 8.908903 ACATTAAACAGTTTTTGTAGACATGGA 58.091 29.630 3.25 0.00 39.73 3.41
184 185 9.398170 CATTAAACAGTTTTTGTAGACATGGAG 57.602 33.333 3.25 0.00 39.73 3.86
185 186 8.740123 TTAAACAGTTTTTGTAGACATGGAGA 57.260 30.769 3.25 0.00 39.73 3.71
186 187 7.823745 AAACAGTTTTTGTAGACATGGAGAT 57.176 32.000 0.00 0.00 39.73 2.75
187 188 7.440523 AACAGTTTTTGTAGACATGGAGATC 57.559 36.000 0.00 0.00 39.73 2.75
188 189 6.773638 ACAGTTTTTGTAGACATGGAGATCT 58.226 36.000 0.00 0.00 38.56 2.75
189 190 7.227156 ACAGTTTTTGTAGACATGGAGATCTT 58.773 34.615 0.00 0.00 38.56 2.40
190 191 7.389053 ACAGTTTTTGTAGACATGGAGATCTTC 59.611 37.037 0.00 0.00 38.56 2.87
191 192 7.605691 CAGTTTTTGTAGACATGGAGATCTTCT 59.394 37.037 1.86 0.72 0.00 2.85
192 193 7.821846 AGTTTTTGTAGACATGGAGATCTTCTC 59.178 37.037 1.86 0.00 42.66 2.87
193 194 7.487822 TTTTGTAGACATGGAGATCTTCTCT 57.512 36.000 1.86 0.00 42.95 3.10
194 195 6.462552 TTGTAGACATGGAGATCTTCTCTG 57.537 41.667 1.86 2.78 42.95 3.35
195 196 5.514169 TGTAGACATGGAGATCTTCTCTGT 58.486 41.667 1.86 6.06 42.95 3.41
196 197 6.663734 TGTAGACATGGAGATCTTCTCTGTA 58.336 40.000 1.86 0.00 42.95 2.74
200 201 7.754624 AGACATGGAGATCTTCTCTGTAGATA 58.245 38.462 1.86 0.00 42.95 1.98
203 204 7.230510 ACATGGAGATCTTCTCTGTAGATACAC 59.769 40.741 1.86 0.00 42.95 2.90
210 211 7.392494 TCTTCTCTGTAGATACACGTTGAAT 57.608 36.000 0.00 0.00 31.93 2.57
211 212 7.827701 TCTTCTCTGTAGATACACGTTGAATT 58.172 34.615 0.00 0.00 31.93 2.17
212 213 8.304596 TCTTCTCTGTAGATACACGTTGAATTT 58.695 33.333 0.00 0.00 31.93 1.82
213 214 8.827177 TTCTCTGTAGATACACGTTGAATTTT 57.173 30.769 0.00 0.00 31.93 1.82
251 282 9.712305 TGATGAACACTTTTCTTTAAAAACCAA 57.288 25.926 0.00 0.00 34.26 3.67
255 286 6.999456 ACACTTTTCTTTAAAAACCAATGCG 58.001 32.000 0.00 0.00 34.26 4.73
285 316 1.896183 CCACACCAACGACCATGCA 60.896 57.895 0.00 0.00 0.00 3.96
286 317 1.243342 CCACACCAACGACCATGCAT 61.243 55.000 0.00 0.00 0.00 3.96
287 318 0.109643 CACACCAACGACCATGCATG 60.110 55.000 20.19 20.19 0.00 4.06
288 319 0.537143 ACACCAACGACCATGCATGT 60.537 50.000 24.58 13.09 0.00 3.21
289 320 1.271108 ACACCAACGACCATGCATGTA 60.271 47.619 24.58 0.00 0.00 2.29
290 321 2.016318 CACCAACGACCATGCATGTAT 58.984 47.619 24.58 12.90 0.00 2.29
291 322 3.202097 CACCAACGACCATGCATGTATA 58.798 45.455 24.58 0.00 0.00 1.47
292 323 3.625313 CACCAACGACCATGCATGTATAA 59.375 43.478 24.58 0.00 0.00 0.98
293 324 4.275689 CACCAACGACCATGCATGTATAAT 59.724 41.667 24.58 5.88 0.00 1.28
294 325 5.468409 CACCAACGACCATGCATGTATAATA 59.532 40.000 24.58 0.00 0.00 0.98
295 326 6.149308 CACCAACGACCATGCATGTATAATAT 59.851 38.462 24.58 2.72 0.00 1.28
296 327 7.333174 CACCAACGACCATGCATGTATAATATA 59.667 37.037 24.58 0.00 0.00 0.86
297 328 7.333423 ACCAACGACCATGCATGTATAATATAC 59.667 37.037 24.58 3.56 0.00 1.47
298 329 7.201609 CCAACGACCATGCATGTATAATATACC 60.202 40.741 24.58 0.00 0.00 2.73
299 330 7.182817 ACGACCATGCATGTATAATATACCT 57.817 36.000 24.58 0.00 0.00 3.08
300 331 7.041721 ACGACCATGCATGTATAATATACCTG 58.958 38.462 24.58 9.12 0.00 4.00
301 332 6.479990 CGACCATGCATGTATAATATACCTGG 59.520 42.308 24.58 8.71 0.00 4.45
302 333 6.122277 ACCATGCATGTATAATATACCTGGC 58.878 40.000 24.58 11.97 0.00 4.85
303 334 5.532406 CCATGCATGTATAATATACCTGGCC 59.468 44.000 24.58 0.00 0.00 5.36
304 335 5.770685 TGCATGTATAATATACCTGGCCA 57.229 39.130 4.71 4.71 0.00 5.36
305 336 6.325993 TGCATGTATAATATACCTGGCCAT 57.674 37.500 5.51 0.00 0.00 4.40
306 337 6.121590 TGCATGTATAATATACCTGGCCATG 58.878 40.000 5.51 6.06 0.00 3.66
307 338 5.532406 GCATGTATAATATACCTGGCCATGG 59.468 44.000 5.51 13.05 0.00 3.66
308 339 5.708736 TGTATAATATACCTGGCCATGGG 57.291 43.478 20.97 16.10 0.00 4.00
356 387 3.174788 GGCACGAAATGTCCGACC 58.825 61.111 0.00 0.00 0.00 4.79
357 388 2.396157 GGCACGAAATGTCCGACCC 61.396 63.158 0.00 0.00 0.00 4.46
358 389 2.736682 GCACGAAATGTCCGACCCG 61.737 63.158 0.00 0.00 0.00 5.28
377 408 3.467226 TCGGGCCCGAGATTGTCC 61.467 66.667 42.66 0.00 44.01 4.02
378 409 3.781307 CGGGCCCGAGATTGTCCA 61.781 66.667 41.82 0.00 42.83 4.02
379 410 2.124695 GGGCCCGAGATTGTCCAC 60.125 66.667 5.69 0.00 0.00 4.02
380 411 2.668632 GGCCCGAGATTGTCCACA 59.331 61.111 0.00 0.00 0.00 4.17
381 412 1.450312 GGCCCGAGATTGTCCACAG 60.450 63.158 0.00 0.00 0.00 3.66
382 413 1.450312 GCCCGAGATTGTCCACAGG 60.450 63.158 0.00 0.00 0.00 4.00
383 414 1.450312 CCCGAGATTGTCCACAGGC 60.450 63.158 0.00 0.00 0.00 4.85
384 415 1.450312 CCGAGATTGTCCACAGGCC 60.450 63.158 0.00 0.00 0.00 5.19
385 416 1.811266 CGAGATTGTCCACAGGCCG 60.811 63.158 0.00 0.00 0.00 6.13
386 417 1.450312 GAGATTGTCCACAGGCCGG 60.450 63.158 0.00 0.00 0.00 6.13
387 418 2.438434 GATTGTCCACAGGCCGGG 60.438 66.667 8.08 6.31 0.00 5.73
388 419 4.740822 ATTGTCCACAGGCCGGGC 62.741 66.667 22.67 22.67 0.00 6.13
415 446 3.877735 GCCTAGATTTTGAAGAGGCCCAA 60.878 47.826 0.00 0.00 45.80 4.12
418 449 1.550524 GATTTTGAAGAGGCCCAACCC 59.449 52.381 0.00 0.00 40.58 4.11
421 452 1.497309 TTGAAGAGGCCCAACCCGAT 61.497 55.000 0.00 0.00 40.58 4.18
441 472 1.303317 CCTGGCGGGCTTTTACACT 60.303 57.895 0.00 0.00 0.00 3.55
442 473 1.586154 CCTGGCGGGCTTTTACACTG 61.586 60.000 0.00 0.00 0.00 3.66
445 476 1.495951 GCGGGCTTTTACACTGTCG 59.504 57.895 0.00 0.00 0.00 4.35
471 502 2.672961 GCTTGGGGCCTGATTTTTAC 57.327 50.000 0.84 0.00 34.27 2.01
472 503 1.899142 GCTTGGGGCCTGATTTTTACA 59.101 47.619 0.84 0.00 34.27 2.41
475 506 1.191535 GGGGCCTGATTTTTACACCC 58.808 55.000 0.84 0.00 34.99 4.61
482 513 1.158434 GATTTTTACACCCGACGCCA 58.842 50.000 0.00 0.00 0.00 5.69
503 534 1.538047 GGCCTGAGTTTTCTGCATCA 58.462 50.000 0.00 0.00 0.00 3.07
510 541 1.891150 AGTTTTCTGCATCAGGCTTGG 59.109 47.619 0.00 0.00 45.15 3.61
522 553 2.669240 GCTTGGTTAGGCCCGTCT 59.331 61.111 0.00 0.00 36.04 4.18
528 559 1.318158 GGTTAGGCCCGTCTCGAAGA 61.318 60.000 0.00 0.00 0.00 2.87
532 563 3.745803 GCCCGTCTCGAAGACCGT 61.746 66.667 8.73 0.00 42.12 4.83
535 566 2.097918 CGTCTCGAAGACCGTCCG 59.902 66.667 8.73 0.00 42.12 4.79
536 567 2.385875 CGTCTCGAAGACCGTCCGA 61.386 63.158 8.73 0.00 42.12 4.55
598 636 7.286546 AGCTAGCTATGAATAGTTGACTTCTCA 59.713 37.037 17.69 0.00 32.96 3.27
607 645 3.172339 AGTTGACTTCTCATGCTCTCCT 58.828 45.455 0.00 0.00 0.00 3.69
608 646 3.582208 AGTTGACTTCTCATGCTCTCCTT 59.418 43.478 0.00 0.00 0.00 3.36
1004 1161 0.253044 AGGCTAGCTTTCGCAATGGA 59.747 50.000 15.72 0.00 39.10 3.41
1179 1338 3.205536 TGCGCCAACGTGCTGAAA 61.206 55.556 4.18 0.00 46.08 2.69
1394 1554 2.125552 CTGCCCGCACTGATCGAA 60.126 61.111 0.00 0.00 0.00 3.71
1406 1566 3.608506 CACTGATCGAACAAAGTACTCGG 59.391 47.826 0.00 0.00 33.44 4.63
1458 1618 1.502231 CATGCAGCCGTCTATACACC 58.498 55.000 0.00 0.00 0.00 4.16
1567 2210 6.094048 GTGATCACTAGGTAGGTACGTAAACA 59.906 42.308 18.83 0.00 0.00 2.83
1659 5628 4.665833 TCATCTGAAATACTGTACCGGG 57.334 45.455 6.32 0.00 0.00 5.73
1660 5629 2.973694 TCTGAAATACTGTACCGGGC 57.026 50.000 6.32 0.00 0.00 6.13
1661 5630 1.135527 TCTGAAATACTGTACCGGGCG 59.864 52.381 6.32 0.00 0.00 6.13
1662 5631 0.460635 TGAAATACTGTACCGGGCGC 60.461 55.000 6.32 0.00 0.00 6.53
1749 5718 7.923878 TGTTACATATATATTGCCGCGTCATAT 59.076 33.333 4.92 6.28 0.00 1.78
1758 5727 0.939577 CCGCGTCATATTCCACTCCG 60.940 60.000 4.92 0.00 0.00 4.63
1765 5735 4.201685 CGTCATATTCCACTCCGAAAACAC 60.202 45.833 0.00 0.00 0.00 3.32
1940 5926 3.002791 CGATGTTTATATCGGCTGGCAT 58.997 45.455 1.08 0.00 44.56 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 5.891551 ACCTGTAGAAAAAGAGAGCCAAAAA 59.108 36.000 0.00 0.00 0.00 1.94
67 68 5.445964 ACCTGTAGAAAAAGAGAGCCAAAA 58.554 37.500 0.00 0.00 0.00 2.44
68 69 5.048846 ACCTGTAGAAAAAGAGAGCCAAA 57.951 39.130 0.00 0.00 0.00 3.28
69 70 4.706842 ACCTGTAGAAAAAGAGAGCCAA 57.293 40.909 0.00 0.00 0.00 4.52
70 71 5.818678 TTACCTGTAGAAAAAGAGAGCCA 57.181 39.130 0.00 0.00 0.00 4.75
71 72 7.689446 AAATTACCTGTAGAAAAAGAGAGCC 57.311 36.000 0.00 0.00 0.00 4.70
162 163 7.721399 AGATCTCCATGTCTACAAAAACTGTTT 59.279 33.333 0.00 0.00 39.64 2.83
170 171 6.438741 ACAGAGAAGATCTCCATGTCTACAAA 59.561 38.462 0.00 0.00 44.42 2.83
171 172 5.954752 ACAGAGAAGATCTCCATGTCTACAA 59.045 40.000 0.00 0.00 44.42 2.41
172 173 5.514169 ACAGAGAAGATCTCCATGTCTACA 58.486 41.667 0.00 0.00 44.42 2.74
173 174 6.995686 TCTACAGAGAAGATCTCCATGTCTAC 59.004 42.308 0.00 0.00 44.42 2.59
174 175 7.142995 TCTACAGAGAAGATCTCCATGTCTA 57.857 40.000 0.00 0.00 44.42 2.59
175 176 6.012337 TCTACAGAGAAGATCTCCATGTCT 57.988 41.667 0.00 0.00 44.42 3.41
176 177 6.899393 ATCTACAGAGAAGATCTCCATGTC 57.101 41.667 0.00 0.00 44.42 3.06
177 178 7.230510 GTGTATCTACAGAGAAGATCTCCATGT 59.769 40.741 0.00 1.97 44.42 3.21
178 179 7.572910 CGTGTATCTACAGAGAAGATCTCCATG 60.573 44.444 0.00 0.00 44.42 3.66
179 180 6.429692 CGTGTATCTACAGAGAAGATCTCCAT 59.570 42.308 0.00 0.00 44.42 3.41
180 181 5.760743 CGTGTATCTACAGAGAAGATCTCCA 59.239 44.000 0.00 0.00 44.42 3.86
181 182 5.761234 ACGTGTATCTACAGAGAAGATCTCC 59.239 44.000 0.00 0.00 44.42 3.71
182 183 6.854496 ACGTGTATCTACAGAGAAGATCTC 57.146 41.667 0.00 0.00 43.70 2.75
183 184 6.824196 TCAACGTGTATCTACAGAGAAGATCT 59.176 38.462 0.00 0.00 39.56 2.75
184 185 7.017498 TCAACGTGTATCTACAGAGAAGATC 57.983 40.000 0.00 0.00 36.78 2.75
185 186 7.392494 TTCAACGTGTATCTACAGAGAAGAT 57.608 36.000 0.00 0.00 36.78 2.40
186 187 6.812879 TTCAACGTGTATCTACAGAGAAGA 57.187 37.500 0.00 0.00 36.78 2.87
187 188 8.467402 AAATTCAACGTGTATCTACAGAGAAG 57.533 34.615 0.00 0.00 36.78 2.85
188 189 8.827177 AAAATTCAACGTGTATCTACAGAGAA 57.173 30.769 0.00 0.00 36.78 2.87
189 190 8.827177 AAAAATTCAACGTGTATCTACAGAGA 57.173 30.769 0.00 0.00 36.78 3.10
225 226 9.712305 TTGGTTTTTAAAGAAAAGTGTTCATCA 57.288 25.926 0.00 0.00 35.96 3.07
234 235 6.256757 TCCACGCATTGGTTTTTAAAGAAAAG 59.743 34.615 1.37 0.00 46.97 2.27
262 293 0.462937 TGGTCGTTGGTGTGGACAAG 60.463 55.000 0.00 0.00 32.39 3.16
263 294 0.181587 ATGGTCGTTGGTGTGGACAA 59.818 50.000 0.00 0.00 32.39 3.18
285 316 5.399038 GCCCATGGCCAGGTATATTATACAT 60.399 44.000 17.55 5.78 44.06 2.29
286 317 4.080015 GCCCATGGCCAGGTATATTATACA 60.080 45.833 17.55 0.00 44.06 2.29
287 318 4.461198 GCCCATGGCCAGGTATATTATAC 58.539 47.826 17.55 5.42 44.06 1.47
288 319 4.788925 GCCCATGGCCAGGTATATTATA 57.211 45.455 17.55 0.00 44.06 0.98
289 320 3.669939 GCCCATGGCCAGGTATATTAT 57.330 47.619 17.55 0.00 44.06 1.28
333 364 2.736682 GACATTTCGTGCCGGGTCG 61.737 63.158 2.18 1.52 0.00 4.79
334 365 2.396157 GGACATTTCGTGCCGGGTC 61.396 63.158 2.18 0.00 0.00 4.46
335 366 2.359478 GGACATTTCGTGCCGGGT 60.359 61.111 2.18 0.00 0.00 5.28
336 367 3.496131 CGGACATTTCGTGCCGGG 61.496 66.667 2.18 0.00 41.05 5.73
337 368 2.433491 TCGGACATTTCGTGCCGG 60.433 61.111 0.00 0.00 43.27 6.13
338 369 2.736682 GGTCGGACATTTCGTGCCG 61.737 63.158 10.76 0.00 43.93 5.69
339 370 2.396157 GGGTCGGACATTTCGTGCC 61.396 63.158 10.76 0.00 30.82 5.01
340 371 2.736682 CGGGTCGGACATTTCGTGC 61.737 63.158 10.76 0.00 0.00 5.34
341 372 3.470267 CGGGTCGGACATTTCGTG 58.530 61.111 10.76 0.00 0.00 4.35
358 389 3.735037 GACAATCTCGGGCCCGACC 62.735 68.421 42.66 21.77 44.01 4.79
359 390 2.202892 GACAATCTCGGGCCCGAC 60.203 66.667 42.66 27.49 44.01 4.79
360 391 3.467226 GGACAATCTCGGGCCCGA 61.467 66.667 42.62 42.62 46.87 5.14
361 392 3.781307 TGGACAATCTCGGGCCCG 61.781 66.667 39.13 39.13 41.35 6.13
362 393 2.124695 GTGGACAATCTCGGGCCC 60.125 66.667 13.57 13.57 0.00 5.80
363 394 1.450312 CTGTGGACAATCTCGGGCC 60.450 63.158 0.00 0.00 0.00 5.80
364 395 1.450312 CCTGTGGACAATCTCGGGC 60.450 63.158 0.00 0.00 0.00 6.13
365 396 1.450312 GCCTGTGGACAATCTCGGG 60.450 63.158 0.00 0.00 0.00 5.14
366 397 1.450312 GGCCTGTGGACAATCTCGG 60.450 63.158 0.00 0.00 0.00 4.63
367 398 1.811266 CGGCCTGTGGACAATCTCG 60.811 63.158 0.00 0.00 0.00 4.04
368 399 1.450312 CCGGCCTGTGGACAATCTC 60.450 63.158 0.00 0.00 0.00 2.75
369 400 2.671070 CCGGCCTGTGGACAATCT 59.329 61.111 0.00 0.00 0.00 2.40
370 401 2.438434 CCCGGCCTGTGGACAATC 60.438 66.667 0.00 0.00 0.00 2.67
371 402 4.740822 GCCCGGCCTGTGGACAAT 62.741 66.667 0.00 0.00 0.00 2.71
387 418 2.027385 CTTCAAAATCTAGGCCCAGGC 58.973 52.381 0.00 0.00 41.06 4.85
388 419 3.549794 CTCTTCAAAATCTAGGCCCAGG 58.450 50.000 0.00 0.00 0.00 4.45
389 420 3.549794 CCTCTTCAAAATCTAGGCCCAG 58.450 50.000 0.00 0.00 0.00 4.45
390 421 2.357154 GCCTCTTCAAAATCTAGGCCCA 60.357 50.000 0.00 0.00 45.69 5.36
391 422 2.302260 GCCTCTTCAAAATCTAGGCCC 58.698 52.381 0.00 0.00 45.69 5.80
394 425 3.652057 TGGGCCTCTTCAAAATCTAGG 57.348 47.619 4.53 0.00 0.00 3.02
395 426 3.696548 GGTTGGGCCTCTTCAAAATCTAG 59.303 47.826 4.53 0.00 0.00 2.43
396 427 3.563479 GGGTTGGGCCTCTTCAAAATCTA 60.563 47.826 4.53 0.00 37.43 1.98
397 428 2.529632 GGTTGGGCCTCTTCAAAATCT 58.470 47.619 4.53 0.00 0.00 2.40
398 429 1.550524 GGGTTGGGCCTCTTCAAAATC 59.449 52.381 4.53 0.00 37.43 2.17
399 430 1.644509 GGGTTGGGCCTCTTCAAAAT 58.355 50.000 4.53 0.00 37.43 1.82
400 431 0.825840 CGGGTTGGGCCTCTTCAAAA 60.826 55.000 4.53 0.00 37.43 2.44
401 432 1.228429 CGGGTTGGGCCTCTTCAAA 60.228 57.895 4.53 0.00 37.43 2.69
402 433 1.497309 ATCGGGTTGGGCCTCTTCAA 61.497 55.000 4.53 0.00 37.43 2.69
457 488 0.815095 CGGGTGTAAAAATCAGGCCC 59.185 55.000 0.00 0.00 0.00 5.80
482 513 0.407139 ATGCAGAAAACTCAGGCCCT 59.593 50.000 0.00 0.00 0.00 5.19
487 518 2.434428 AGCCTGATGCAGAAAACTCAG 58.566 47.619 5.87 5.87 44.83 3.35
510 541 0.179142 GTCTTCGAGACGGGCCTAAC 60.179 60.000 0.84 0.00 35.28 2.34
522 553 3.437795 GGCTCGGACGGTCTTCGA 61.438 66.667 8.23 8.53 42.43 3.71
544 575 6.712547 GGCTTATACATTATATCTGGCCATCC 59.287 42.308 5.51 0.00 36.31 3.51
547 578 6.634889 TGGCTTATACATTATATCTGGCCA 57.365 37.500 4.71 4.71 42.66 5.36
598 636 6.927381 GCAAATGCATATTAAAAGGAGAGCAT 59.073 34.615 0.00 0.00 42.62 3.79
675 719 1.750206 TGACGATTTTCATGCCATGGG 59.250 47.619 15.13 0.00 0.00 4.00
689 733 4.366586 CTGAAGATATGCTGTGTGACGAT 58.633 43.478 0.00 0.00 0.00 3.73
1004 1161 0.107945 GAAGAGCTTGGTCGATGGCT 60.108 55.000 0.00 0.00 37.77 4.75
1135 1293 1.792367 CAGCTTCAACGTGTCAATCGA 59.208 47.619 0.00 0.00 0.00 3.59
1168 1326 1.331756 CTTCAGCAGTTTCAGCACGTT 59.668 47.619 0.00 0.00 0.00 3.99
1394 1554 0.107831 TGCTTGGCCGAGTACTTTGT 59.892 50.000 21.55 0.00 0.00 2.83
1458 1618 4.155826 TGAACTCAAACACAAACTGGAGTG 59.844 41.667 0.00 0.00 41.40 3.51
1567 2210 5.532406 ACTTGACACACTTTCATGCACTTAT 59.468 36.000 0.00 0.00 0.00 1.73
1660 5629 0.905357 AAGCTAGGGGCATATAGGCG 59.095 55.000 2.88 0.00 45.36 5.52
1661 5630 1.630878 ACAAGCTAGGGGCATATAGGC 59.369 52.381 0.00 0.00 44.79 3.93
1662 5631 4.716784 TGATACAAGCTAGGGGCATATAGG 59.283 45.833 0.00 0.00 44.79 2.57
1749 5718 4.345859 AGTATGTGTTTTCGGAGTGGAA 57.654 40.909 0.00 0.00 0.00 3.53
1758 5727 3.496884 TCTCGGTGCAAGTATGTGTTTTC 59.503 43.478 0.00 0.00 0.00 2.29
1765 5735 3.242543 GCTTTGATCTCGGTGCAAGTATG 60.243 47.826 0.00 0.00 0.00 2.39
1940 5926 9.778741 GTAACTGGATGTAAGGATGATATGAAA 57.221 33.333 0.00 0.00 0.00 2.69
2023 6009 5.468746 TCCACTTCTTTTACAATGACTTCCG 59.531 40.000 0.00 0.00 0.00 4.30
2273 6765 8.688747 TGGATGCAAATAAAATTTGAAAAGGT 57.311 26.923 14.83 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.