Multiple sequence alignment - TraesCS4B01G134700

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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 TraesCS4B01G134700 chr4B 100.000 3314 0 0 1 3314 175543184 175546497 0.000000e+00 6120.0
1 TraesCS4B01G134700 chr4D 95.525 2525 84 12 801 3314 115055085 115057591 0.000000e+00 4010.0
2 TraesCS4B01G134700 chr4D 93.284 268 15 1 1 268 115054053 115054317 3.100000e-105 392.0
3 TraesCS4B01G134700 chr4D 93.333 60 2 2 361 420 115054969 115055026 1.640000e-13 87.9
4 TraesCS4B01G134700 chr4D 94.545 55 1 2 315 368 115054318 115054371 2.120000e-12 84.2
5 TraesCS4B01G134700 chr4A 94.108 2512 120 12 812 3314 462212170 462209678 0.000000e+00 3794.0
6 TraesCS4B01G134700 chr4A 91.882 271 18 2 1 271 462212979 462212713 3.120000e-100 375.0
7 TraesCS4B01G134700 chr4A 81.423 253 37 8 533 777 717455061 717454811 7.250000e-47 198.0
8 TraesCS4B01G134700 chr4A 96.610 59 2 0 361 419 462212300 462212242 7.570000e-17 99.0
9 TraesCS4B01G134700 chr4A 96.429 56 1 1 315 370 462212715 462212661 1.270000e-14 91.6
10 TraesCS4B01G134700 chr3D 85.992 257 32 4 514 768 542849929 542849675 4.210000e-69 272.0
11 TraesCS4B01G134700 chr3A 79.133 369 54 15 421 768 427763977 427763611 1.990000e-57 233.0
12 TraesCS4B01G134700 chr3A 76.762 383 50 25 420 777 20350359 20349991 9.450000e-41 178.0
13 TraesCS4B01G134700 chr5B 82.946 258 30 10 519 773 268293942 268293696 1.550000e-53 220.0
14 TraesCS4B01G134700 chr5D 78.175 252 47 7 521 768 267840599 267840352 1.590000e-33 154.0
15 TraesCS4B01G134700 chr5D 78.261 230 43 6 543 770 555422718 555422494 1.240000e-29 141.0
16 TraesCS4B01G134700 chr5D 89.899 99 9 1 418 515 511950734 511950636 3.470000e-25 126.0
17 TraesCS4B01G134700 chr7D 85.567 97 11 3 421 515 617833788 617833883 7.570000e-17 99.0
18 TraesCS4B01G134700 chr6A 83.673 98 14 2 418 514 36950538 36950634 1.270000e-14 91.6
19 TraesCS4B01G134700 chr6A 94.872 39 2 0 444 482 36950146 36950184 9.930000e-06 62.1
20 TraesCS4B01G134700 chr1B 84.524 84 12 1 421 504 365446848 365446930 7.620000e-12 82.4
21 TraesCS4B01G134700 chr1A 86.667 60 6 2 424 482 566080306 566080248 7.680000e-07 65.8


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 TraesCS4B01G134700 chr4B 175543184 175546497 3313 False 6120.000 6120 100.00000 1 3314 1 chr4B.!!$F1 3313
1 TraesCS4B01G134700 chr4D 115054053 115057591 3538 False 1143.525 4010 94.17175 1 3314 4 chr4D.!!$F1 3313
2 TraesCS4B01G134700 chr4A 462209678 462212979 3301 True 1089.900 3794 94.75725 1 3314 4 chr4A.!!$R2 3313

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
310 311 0.454285 GCACACACACACACACACAC 60.454 55.0 0.00 0.0 0.0 3.82 F
705 878 0.678048 GGCGCCCAAGTTTGAGATCT 60.678 55.0 18.11 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2264 2562 0.464870 CTCAGCCACTGCAGAGCTAT 59.535 55.0 27.45 11.22 43.04 2.97 R
2591 2892 0.329596 ATCTGTGGCCAAAGGAGACC 59.670 55.0 23.27 0.35 0.00 3.85 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
125 126 4.298626 ACAGAGGTAATTAGCATCTCCCA 58.701 43.478 16.53 0.00 0.00 4.37
169 170 2.603075 TCTTCCATTTCTTGGTGGGG 57.397 50.000 0.00 0.00 46.52 4.96
170 171 1.077005 TCTTCCATTTCTTGGTGGGGG 59.923 52.381 0.00 0.00 46.52 5.40
202 203 4.463891 TCCTTCAGGAAAATGAATTGAGCC 59.536 41.667 0.00 0.00 42.18 4.70
203 204 4.418392 CTTCAGGAAAATGAATTGAGCCG 58.582 43.478 0.00 0.00 38.47 5.52
213 214 4.174411 TGAATTGAGCCGGTAGATATCG 57.826 45.455 1.90 0.00 0.00 2.92
219 220 1.802960 AGCCGGTAGATATCGTACACG 59.197 52.381 1.90 0.00 41.45 4.49
227 228 6.310197 GGTAGATATCGTACACGGATGTAAC 58.690 44.000 1.39 0.00 42.99 2.50
247 248 5.712152 AACTGGCATCTTCCTAGTTTTTG 57.288 39.130 0.00 0.00 29.45 2.44
258 259 7.758495 TCTTCCTAGTTTTTGTTTGTGAAGAC 58.242 34.615 0.00 0.00 32.96 3.01
268 269 8.558973 TTTTGTTTGTGAAGACCATTTCATTT 57.441 26.923 0.00 0.00 39.13 2.32
271 272 7.776107 TGTTTGTGAAGACCATTTCATTTACA 58.224 30.769 0.00 0.00 39.13 2.41
272 273 7.704472 TGTTTGTGAAGACCATTTCATTTACAC 59.296 33.333 0.00 0.00 39.13 2.90
273 274 6.951062 TGTGAAGACCATTTCATTTACACA 57.049 33.333 0.00 0.00 39.13 3.72
274 275 6.734137 TGTGAAGACCATTTCATTTACACAC 58.266 36.000 0.00 0.00 39.13 3.82
275 276 6.319911 TGTGAAGACCATTTCATTTACACACA 59.680 34.615 0.00 0.00 39.13 3.72
276 277 6.636850 GTGAAGACCATTTCATTTACACACAC 59.363 38.462 0.00 0.00 39.13 3.82
277 278 5.356882 AGACCATTTCATTTACACACACG 57.643 39.130 0.00 0.00 0.00 4.49
278 279 3.896122 ACCATTTCATTTACACACACGC 58.104 40.909 0.00 0.00 0.00 5.34
279 280 2.908009 CCATTTCATTTACACACACGCG 59.092 45.455 3.53 3.53 0.00 6.01
280 281 3.550561 CATTTCATTTACACACACGCGT 58.449 40.909 5.58 5.58 0.00 6.01
282 283 1.854227 TCATTTACACACACGCGTGA 58.146 45.000 42.94 21.20 46.80 4.35
283 284 1.790043 TCATTTACACACACGCGTGAG 59.210 47.619 42.94 36.59 46.80 3.51
296 297 2.931386 GTGAGCTCACACGCACAC 59.069 61.111 36.23 11.79 45.75 3.82
297 298 1.882625 GTGAGCTCACACGCACACA 60.883 57.895 36.23 0.76 46.30 3.72
298 299 1.882625 TGAGCTCACACGCACACAC 60.883 57.895 13.74 0.00 0.00 3.82
299 300 1.882625 GAGCTCACACGCACACACA 60.883 57.895 9.40 0.00 0.00 3.72
300 301 2.094126 GAGCTCACACGCACACACAC 62.094 60.000 9.40 0.00 0.00 3.82
301 302 2.460275 GCTCACACGCACACACACA 61.460 57.895 0.00 0.00 0.00 3.72
302 303 1.348250 CTCACACGCACACACACAC 59.652 57.895 0.00 0.00 0.00 3.82
303 304 1.357991 CTCACACGCACACACACACA 61.358 55.000 0.00 0.00 0.00 3.72
304 305 1.225991 CACACGCACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
305 306 1.669437 ACACGCACACACACACACA 60.669 52.632 0.00 0.00 0.00 3.72
306 307 1.225991 CACGCACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
307 308 1.669437 ACGCACACACACACACACA 60.669 52.632 0.00 0.00 0.00 3.72
308 309 1.225991 CGCACACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
309 310 1.872468 GCACACACACACACACACA 59.128 52.632 0.00 0.00 0.00 3.72
310 311 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
311 312 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
312 313 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
313 314 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
314 315 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
315 316 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
316 317 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
317 318 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
321 322 3.559655 ACACACACACACACACACATATC 59.440 43.478 0.00 0.00 0.00 1.63
409 411 9.607285 GTTTCAACAGTATTATTTGTGTACTGG 57.393 33.333 14.14 0.96 45.92 4.00
410 412 9.562408 TTTCAACAGTATTATTTGTGTACTGGA 57.438 29.630 14.14 2.90 45.92 3.86
411 413 9.733556 TTCAACAGTATTATTTGTGTACTGGAT 57.266 29.630 14.14 2.84 45.92 3.41
426 428 8.258007 TGTGTACTGGATAATTTGTAGGAAGAG 58.742 37.037 0.00 0.00 0.00 2.85
433 435 8.336235 TGGATAATTTGTAGGAAGAGGATTTGT 58.664 33.333 0.00 0.00 0.00 2.83
437 439 8.934023 AATTTGTAGGAAGAGGATTTGTAACA 57.066 30.769 0.00 0.00 0.00 2.41
441 443 6.727231 TGTAGGAAGAGGATTTGTAACACCTA 59.273 38.462 0.00 0.00 32.53 3.08
442 444 6.051179 AGGAAGAGGATTTGTAACACCTAC 57.949 41.667 0.00 0.00 32.53 3.18
444 446 5.476614 GAAGAGGATTTGTAACACCTACGT 58.523 41.667 0.00 0.00 32.65 3.57
445 447 6.350445 GGAAGAGGATTTGTAACACCTACGTA 60.350 42.308 0.00 0.00 32.65 3.57
447 449 5.713861 AGAGGATTTGTAACACCTACGTACT 59.286 40.000 0.00 0.00 32.65 2.73
449 451 5.105063 GGATTTGTAACACCTACGTACTCC 58.895 45.833 0.00 0.00 32.65 3.85
450 452 5.336690 GGATTTGTAACACCTACGTACTCCA 60.337 44.000 0.00 0.00 32.65 3.86
451 453 4.503741 TTGTAACACCTACGTACTCCAC 57.496 45.455 0.00 0.00 32.65 4.02
452 454 3.485394 TGTAACACCTACGTACTCCACA 58.515 45.455 0.00 0.00 32.65 4.17
471 610 6.837312 TCCACACCCCTATATGAACATTAAG 58.163 40.000 0.00 0.00 0.00 1.85
495 634 8.661352 AGTTCAAACAAATACCTGGAAATTTG 57.339 30.769 24.46 24.46 44.78 2.32
499 638 9.672673 TCAAACAAATACCTGGAAATTTGAAAA 57.327 25.926 28.95 16.69 42.90 2.29
500 639 9.715123 CAAACAAATACCTGGAAATTTGAAAAC 57.285 29.630 28.95 0.00 42.90 2.43
510 649 6.060788 TGGAAATTTGAAAACAAATCTGGGG 58.939 36.000 0.00 0.00 34.06 4.96
515 654 7.953005 ATTTGAAAACAAATCTGGGGTTTTT 57.047 28.000 0.00 0.00 42.79 1.94
516 655 6.993786 TTGAAAACAAATCTGGGGTTTTTC 57.006 33.333 0.00 0.00 42.79 2.29
519 659 6.541641 TGAAAACAAATCTGGGGTTTTTCATG 59.458 34.615 0.00 0.00 42.79 3.07
521 661 4.959723 ACAAATCTGGGGTTTTTCATGTG 58.040 39.130 0.00 0.00 0.00 3.21
525 665 6.438186 AATCTGGGGTTTTTCATGTGAAAT 57.562 33.333 8.82 0.00 42.83 2.17
527 667 6.245890 TCTGGGGTTTTTCATGTGAAATTT 57.754 33.333 8.82 0.00 42.83 1.82
528 668 6.287525 TCTGGGGTTTTTCATGTGAAATTTC 58.712 36.000 11.41 11.41 42.83 2.17
531 671 7.059156 TGGGGTTTTTCATGTGAAATTTCATT 58.941 30.769 23.05 11.72 42.83 2.57
532 672 7.559170 TGGGGTTTTTCATGTGAAATTTCATTT 59.441 29.630 23.05 11.38 42.83 2.32
618 790 9.492730 ACTATTTGGATGGATTTTAGTTTGGAT 57.507 29.630 0.00 0.00 0.00 3.41
636 808 5.621197 TGGATTGTATTTTCTTCACCACG 57.379 39.130 0.00 0.00 0.00 4.94
647 819 3.869065 TCTTCACCACGGATACATTTCC 58.131 45.455 0.00 0.00 0.00 3.13
649 821 3.992943 TCACCACGGATACATTTCCTT 57.007 42.857 0.00 0.00 33.30 3.36
652 825 4.223255 TCACCACGGATACATTTCCTTGTA 59.777 41.667 0.00 0.00 34.15 2.41
657 830 7.830201 ACCACGGATACATTTCCTTGTATTTTA 59.170 33.333 0.00 0.00 41.67 1.52
658 831 8.126700 CCACGGATACATTTCCTTGTATTTTAC 58.873 37.037 0.00 0.00 41.67 2.01
659 832 8.889717 CACGGATACATTTCCTTGTATTTTACT 58.110 33.333 0.00 0.00 41.67 2.24
689 862 2.422303 TACGGGAGTAGAATGGGCG 58.578 57.895 0.00 0.00 46.17 6.13
701 874 2.597217 TGGGCGCCCAAGTTTGAG 60.597 61.111 45.50 0.00 44.12 3.02
705 878 0.678048 GGCGCCCAAGTTTGAGATCT 60.678 55.000 18.11 0.00 0.00 2.75
770 943 9.463902 TCGAATTTAATTTTTGTATAGGGGTGA 57.536 29.630 0.00 0.00 0.00 4.02
807 1052 9.696572 TTGGTATAGATATATACTCCTGGTGAC 57.303 37.037 15.29 0.00 34.30 3.67
808 1053 8.842764 TGGTATAGATATATACTCCTGGTGACA 58.157 37.037 15.29 1.68 34.30 3.58
813 1058 8.282455 AGATATATACTCCTGGTGACATAACG 57.718 38.462 2.23 0.00 41.51 3.18
814 1059 7.889073 AGATATATACTCCTGGTGACATAACGT 59.111 37.037 2.23 0.00 41.51 3.99
1000 1295 1.557099 CTAGGCTCCTGGTGTACACA 58.443 55.000 26.51 12.27 0.00 3.72
1011 1306 3.745799 TGGTGTACACATGTTAACCTGG 58.254 45.455 26.51 6.78 34.95 4.45
1019 1314 4.225042 ACACATGTTAACCTGGAGCTCATA 59.775 41.667 17.19 2.65 0.00 2.15
1501 1799 1.671742 GTGAGGGTGTCCATGTCGT 59.328 57.895 0.00 0.00 34.83 4.34
1570 1868 3.306019 GGTCCAAATTCGCAGTCCAAATT 60.306 43.478 0.00 0.00 0.00 1.82
1608 1906 3.201290 GACCATCTGCAACCTACTGATG 58.799 50.000 3.51 3.51 40.92 3.07
1672 1970 2.672996 CCCCAAGTGGAAGCACCG 60.673 66.667 0.00 0.00 42.61 4.94
1977 2275 2.991190 CAGCTTGAAATGGACAATGTGC 59.009 45.455 0.00 0.00 0.00 4.57
2007 2305 5.738783 GCTCTCTTTCTGGGTCTATGTCATC 60.739 48.000 0.00 0.00 0.00 2.92
2043 2341 1.990160 TTCGTTGGGTCTGGCCACTT 61.990 55.000 0.00 0.00 39.65 3.16
2084 2382 2.039418 TCACAGGGGGTTATCTGATCG 58.961 52.381 0.00 0.00 35.20 3.69
2103 2401 2.632996 TCGTCAAGTCAATGGGAAGACT 59.367 45.455 0.00 0.00 46.45 3.24
2117 2415 4.164030 TGGGAAGACTATTGCTGCTAATCA 59.836 41.667 0.00 0.00 0.00 2.57
2132 2430 4.100373 GCTAATCAGGGTGGAGGAGATAT 58.900 47.826 0.00 0.00 0.00 1.63
2169 2467 0.842635 AGGGATCATCAAGAGGTGGC 59.157 55.000 0.00 0.00 0.00 5.01
2177 2475 2.031516 CAAGAGGTGGCGCTGTGAG 61.032 63.158 7.64 0.00 0.00 3.51
2218 2516 1.477105 GAGGAAAGCACAACAAACGC 58.523 50.000 0.00 0.00 0.00 4.84
2264 2562 1.676746 CTCGATGAGGGGTCGTCTTA 58.323 55.000 0.00 0.00 39.91 2.10
2315 2613 3.839654 TCGACGACGAATCATAGGC 57.160 52.632 7.68 0.00 45.74 3.93
2396 2694 3.727970 GCTGTAAAGTTTATGCTGACCGC 60.728 47.826 13.10 1.94 39.77 5.68
2398 2696 4.823157 TGTAAAGTTTATGCTGACCGCTA 58.177 39.130 0.00 0.00 40.11 4.26
2422 2720 1.001815 ACAGTTTGTTACACGCCATGC 60.002 47.619 0.00 0.00 0.00 4.06
2517 2818 2.037772 ACTAATCGATAAGCTGCAGGGG 59.962 50.000 17.12 0.00 0.00 4.79
2556 2857 5.506730 TCCTTATTCATGTTGGTACCACA 57.493 39.130 16.04 16.19 0.00 4.17
2590 2891 3.244526 TGGTTGACATGAGCTGTGTATGT 60.245 43.478 0.00 0.00 38.54 2.29
2591 2892 3.125829 GGTTGACATGAGCTGTGTATGTG 59.874 47.826 0.00 0.00 38.54 3.21
2603 2904 2.084546 GTGTATGTGGTCTCCTTTGGC 58.915 52.381 0.00 0.00 0.00 4.52
2626 2927 4.063689 CACAGATGTTGGATAGATGAGGC 58.936 47.826 0.00 0.00 0.00 4.70
2644 2945 2.498078 AGGCTGGAGTAGTAGCTTGTTC 59.502 50.000 0.00 0.00 39.80 3.18
2680 2983 1.065564 AGGTCAGCCTCTCAGCAATTC 60.066 52.381 0.00 0.00 42.67 2.17
2722 3025 7.215719 TCTAGTCATGGAGATTATAACCACG 57.784 40.000 0.00 0.00 36.49 4.94
2837 3151 9.578439 AGCATTTTATGTAAATTCTTTCTCAGC 57.422 29.630 0.00 0.00 34.19 4.26
2838 3152 9.578439 GCATTTTATGTAAATTCTTTCTCAGCT 57.422 29.630 0.00 0.00 34.19 4.24
2919 3234 5.922544 GTCAGATGGTTGAAAATCCAACTTG 59.077 40.000 0.00 0.00 44.24 3.16
2970 3285 7.176515 CCAATTCATTCGGTTTATGGGATCATA 59.823 37.037 0.00 0.00 34.96 2.15
3039 3354 2.431454 GCAAACTTCCTTCAGAGAGGG 58.569 52.381 0.00 0.00 37.41 4.30
3070 3385 3.960571 AGATGACAGGGACAATTTCAGG 58.039 45.455 0.00 0.00 0.00 3.86
3071 3386 2.584835 TGACAGGGACAATTTCAGGG 57.415 50.000 0.00 0.00 0.00 4.45
3101 3417 5.363292 AGCCATATCATTTTTGTGGTATGCA 59.637 36.000 0.00 0.00 40.33 3.96
3170 3487 6.049790 AGAGACTGGAAATTAAATCGTAGCC 58.950 40.000 0.00 0.00 0.00 3.93
3242 3559 5.754890 TGCTGTCATAGTACACATAAGCATG 59.245 40.000 0.00 0.00 38.21 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.292103 CCAAATGGGCCGTGTAATTG 57.708 50.000 0.00 0.00 0.00 2.32
169 170 5.373812 TTTTCCTGAAGGATGATACTCCC 57.626 43.478 0.00 0.00 44.98 4.30
170 171 6.595682 TCATTTTCCTGAAGGATGATACTCC 58.404 40.000 0.00 0.00 44.98 3.85
171 172 8.688747 ATTCATTTTCCTGAAGGATGATACTC 57.311 34.615 0.00 0.00 44.98 2.59
176 177 6.127535 GCTCAATTCATTTTCCTGAAGGATGA 60.128 38.462 0.00 0.00 44.98 2.92
184 185 2.493278 ACCGGCTCAATTCATTTTCCTG 59.507 45.455 0.00 0.00 0.00 3.86
202 203 3.434641 ACATCCGTGTACGATATCTACCG 59.565 47.826 5.91 8.09 43.02 4.02
203 204 6.148480 AGTTACATCCGTGTACGATATCTACC 59.852 42.308 5.91 0.00 40.40 3.18
213 214 2.373540 TGCCAGTTACATCCGTGTAC 57.626 50.000 0.00 0.00 40.40 2.90
219 220 3.567478 AGGAAGATGCCAGTTACATCC 57.433 47.619 0.00 0.00 44.08 3.51
227 228 5.712152 AACAAAAACTAGGAAGATGCCAG 57.288 39.130 0.00 0.00 0.00 4.85
247 248 7.704472 TGTGTAAATGAAATGGTCTTCACAAAC 59.296 33.333 0.00 0.00 38.12 2.93
258 259 2.908009 CGCGTGTGTGTAAATGAAATGG 59.092 45.455 0.00 0.00 0.00 3.16
268 269 1.371267 GAGCTCACGCGTGTGTGTA 60.371 57.895 35.74 17.62 46.49 2.90
271 272 2.658593 GTGAGCTCACGCGTGTGT 60.659 61.111 35.74 23.42 46.49 3.72
280 281 1.882625 GTGTGTGCGTGTGAGCTCA 60.883 57.895 13.74 13.74 38.15 4.26
281 282 1.882625 TGTGTGTGCGTGTGAGCTC 60.883 57.895 6.82 6.82 38.13 4.09
282 283 2.173669 GTGTGTGTGCGTGTGAGCT 61.174 57.895 0.00 0.00 38.13 4.09
283 284 2.324477 GTGTGTGTGCGTGTGAGC 59.676 61.111 0.00 0.00 37.71 4.26
284 285 1.348250 GTGTGTGTGTGCGTGTGAG 59.652 57.895 0.00 0.00 0.00 3.51
285 286 1.374758 TGTGTGTGTGTGCGTGTGA 60.375 52.632 0.00 0.00 0.00 3.58
286 287 1.225991 GTGTGTGTGTGTGCGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
287 288 1.669437 TGTGTGTGTGTGTGCGTGT 60.669 52.632 0.00 0.00 0.00 4.49
288 289 1.225991 GTGTGTGTGTGTGTGCGTG 60.226 57.895 0.00 0.00 0.00 5.34
289 290 1.669437 TGTGTGTGTGTGTGTGCGT 60.669 52.632 0.00 0.00 0.00 5.24
290 291 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
291 292 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
292 293 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
293 294 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
294 295 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
295 296 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
296 297 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
297 298 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
298 299 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
299 300 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
300 301 3.058983 GGATATGTGTGTGTGTGTGTGTG 60.059 47.826 0.00 0.00 0.00 3.82
301 302 3.138304 GGATATGTGTGTGTGTGTGTGT 58.862 45.455 0.00 0.00 0.00 3.72
302 303 3.137533 TGGATATGTGTGTGTGTGTGTG 58.862 45.455 0.00 0.00 0.00 3.82
303 304 3.402110 CTGGATATGTGTGTGTGTGTGT 58.598 45.455 0.00 0.00 0.00 3.72
304 305 2.160219 GCTGGATATGTGTGTGTGTGTG 59.840 50.000 0.00 0.00 0.00 3.82
305 306 2.224499 TGCTGGATATGTGTGTGTGTGT 60.224 45.455 0.00 0.00 0.00 3.72
306 307 2.425539 TGCTGGATATGTGTGTGTGTG 58.574 47.619 0.00 0.00 0.00 3.82
307 308 2.857186 TGCTGGATATGTGTGTGTGT 57.143 45.000 0.00 0.00 0.00 3.72
308 309 4.877823 ACTTATGCTGGATATGTGTGTGTG 59.122 41.667 6.87 0.00 0.00 3.82
309 310 5.102953 ACTTATGCTGGATATGTGTGTGT 57.897 39.130 6.87 0.00 0.00 3.72
310 311 6.441093 AAACTTATGCTGGATATGTGTGTG 57.559 37.500 8.16 0.00 0.00 3.82
311 312 5.590259 GGAAACTTATGCTGGATATGTGTGT 59.410 40.000 8.16 0.00 0.00 3.72
312 313 5.589855 TGGAAACTTATGCTGGATATGTGTG 59.410 40.000 8.16 0.00 0.00 3.82
313 314 5.754782 TGGAAACTTATGCTGGATATGTGT 58.245 37.500 8.16 3.55 0.00 3.72
314 315 6.698008 TTGGAAACTTATGCTGGATATGTG 57.302 37.500 8.16 0.00 0.00 3.21
315 316 7.615365 TCTTTTGGAAACTTATGCTGGATATGT 59.385 33.333 2.53 2.53 0.00 2.29
316 317 7.999679 TCTTTTGGAAACTTATGCTGGATATG 58.000 34.615 1.38 1.38 0.00 1.78
317 318 8.593945 TTCTTTTGGAAACTTATGCTGGATAT 57.406 30.769 0.00 0.00 0.00 1.63
321 322 6.331369 TCTTCTTTTGGAAACTTATGCTGG 57.669 37.500 0.00 0.00 33.07 4.85
383 385 9.607285 CCAGTACACAAATAATACTGTTGAAAC 57.393 33.333 9.18 0.00 42.79 2.78
384 386 9.562408 TCCAGTACACAAATAATACTGTTGAAA 57.438 29.630 9.18 0.00 42.79 2.69
385 387 9.733556 ATCCAGTACACAAATAATACTGTTGAA 57.266 29.630 9.18 0.00 42.79 2.69
397 399 9.747898 TTCCTACAAATTATCCAGTACACAAAT 57.252 29.630 0.00 0.00 0.00 2.32
398 400 9.226606 CTTCCTACAAATTATCCAGTACACAAA 57.773 33.333 0.00 0.00 0.00 2.83
399 401 8.598916 TCTTCCTACAAATTATCCAGTACACAA 58.401 33.333 0.00 0.00 0.00 3.33
400 402 8.141298 TCTTCCTACAAATTATCCAGTACACA 57.859 34.615 0.00 0.00 0.00 3.72
401 403 7.711339 CCTCTTCCTACAAATTATCCAGTACAC 59.289 40.741 0.00 0.00 0.00 2.90
402 404 7.622081 TCCTCTTCCTACAAATTATCCAGTACA 59.378 37.037 0.00 0.00 0.00 2.90
403 405 8.019656 TCCTCTTCCTACAAATTATCCAGTAC 57.980 38.462 0.00 0.00 0.00 2.73
404 406 8.798975 ATCCTCTTCCTACAAATTATCCAGTA 57.201 34.615 0.00 0.00 0.00 2.74
405 407 7.698163 ATCCTCTTCCTACAAATTATCCAGT 57.302 36.000 0.00 0.00 0.00 4.00
406 408 8.844244 CAAATCCTCTTCCTACAAATTATCCAG 58.156 37.037 0.00 0.00 0.00 3.86
407 409 8.336235 ACAAATCCTCTTCCTACAAATTATCCA 58.664 33.333 0.00 0.00 0.00 3.41
408 410 8.753497 ACAAATCCTCTTCCTACAAATTATCC 57.247 34.615 0.00 0.00 0.00 2.59
412 414 8.793592 GTGTTACAAATCCTCTTCCTACAAATT 58.206 33.333 0.00 0.00 0.00 1.82
413 415 7.393515 GGTGTTACAAATCCTCTTCCTACAAAT 59.606 37.037 0.00 0.00 0.00 2.32
414 416 6.713450 GGTGTTACAAATCCTCTTCCTACAAA 59.287 38.462 0.00 0.00 0.00 2.83
415 417 6.043938 AGGTGTTACAAATCCTCTTCCTACAA 59.956 38.462 0.00 0.00 0.00 2.41
416 418 5.546499 AGGTGTTACAAATCCTCTTCCTACA 59.454 40.000 0.00 0.00 0.00 2.74
417 419 6.051179 AGGTGTTACAAATCCTCTTCCTAC 57.949 41.667 0.00 0.00 0.00 3.18
418 420 6.127535 CGTAGGTGTTACAAATCCTCTTCCTA 60.128 42.308 0.00 0.00 32.27 2.94
419 421 5.337330 CGTAGGTGTTACAAATCCTCTTCCT 60.337 44.000 0.00 0.00 32.27 3.36
426 428 5.105063 GGAGTACGTAGGTGTTACAAATCC 58.895 45.833 0.00 0.00 30.05 3.01
433 435 2.819608 GGTGTGGAGTACGTAGGTGTTA 59.180 50.000 0.00 0.00 0.00 2.41
435 437 1.251251 GGTGTGGAGTACGTAGGTGT 58.749 55.000 0.00 0.00 0.00 4.16
437 439 0.613012 GGGGTGTGGAGTACGTAGGT 60.613 60.000 0.00 0.00 0.00 3.08
441 443 3.117398 TCATATAGGGGTGTGGAGTACGT 60.117 47.826 0.00 0.00 0.00 3.57
442 444 3.493334 TCATATAGGGGTGTGGAGTACG 58.507 50.000 0.00 0.00 0.00 3.67
444 446 4.886163 TGTTCATATAGGGGTGTGGAGTA 58.114 43.478 0.00 0.00 0.00 2.59
445 447 3.731431 TGTTCATATAGGGGTGTGGAGT 58.269 45.455 0.00 0.00 0.00 3.85
447 449 6.388689 ACTTAATGTTCATATAGGGGTGTGGA 59.611 38.462 0.00 0.00 0.00 4.02
471 610 8.655651 TCAAATTTCCAGGTATTTGTTTGAAC 57.344 30.769 20.07 0.00 40.74 3.18
474 613 9.715123 GTTTTCAAATTTCCAGGTATTTGTTTG 57.285 29.630 20.07 10.55 40.74 2.93
495 634 6.542005 ACATGAAAAACCCCAGATTTGTTTTC 59.458 34.615 0.00 0.00 40.29 2.29
499 638 4.653341 TCACATGAAAAACCCCAGATTTGT 59.347 37.500 0.00 0.00 0.00 2.83
500 639 5.212532 TCACATGAAAAACCCCAGATTTG 57.787 39.130 0.00 0.00 0.00 2.32
532 672 8.679100 CCACGGATACATTTCCTTGTATTTTTA 58.321 33.333 0.00 0.00 41.67 1.52
541 711 2.799126 TGCCACGGATACATTTCCTT 57.201 45.000 0.00 0.00 33.30 3.36
595 767 8.605065 ACAATCCAAACTAAAATCCATCCAAAT 58.395 29.630 0.00 0.00 0.00 2.32
607 779 9.974980 GGTGAAGAAAATACAATCCAAACTAAA 57.025 29.630 0.00 0.00 0.00 1.85
608 780 9.137459 TGGTGAAGAAAATACAATCCAAACTAA 57.863 29.630 0.00 0.00 0.00 2.24
612 784 6.442952 CGTGGTGAAGAAAATACAATCCAAA 58.557 36.000 0.00 0.00 0.00 3.28
618 790 6.231951 TGTATCCGTGGTGAAGAAAATACAA 58.768 36.000 0.00 0.00 0.00 2.41
652 825 8.851541 TCCCGTATGAAGTTTTGTAGTAAAAT 57.148 30.769 0.00 0.00 0.00 1.82
657 830 5.479124 ACTCCCGTATGAAGTTTTGTAGT 57.521 39.130 0.00 0.00 0.00 2.73
658 831 6.860080 TCTACTCCCGTATGAAGTTTTGTAG 58.140 40.000 0.00 0.00 0.00 2.74
659 832 6.839124 TCTACTCCCGTATGAAGTTTTGTA 57.161 37.500 0.00 0.00 0.00 2.41
661 834 6.037172 CCATTCTACTCCCGTATGAAGTTTTG 59.963 42.308 0.00 0.00 0.00 2.44
662 835 6.113411 CCATTCTACTCCCGTATGAAGTTTT 58.887 40.000 0.00 0.00 0.00 2.43
671 844 1.741327 GCGCCCATTCTACTCCCGTA 61.741 60.000 0.00 0.00 0.00 4.02
683 856 1.978617 CTCAAACTTGGGCGCCCAT 60.979 57.895 46.94 32.19 46.64 4.00
687 860 0.729690 GAGATCTCAAACTTGGGCGC 59.270 55.000 18.11 0.00 0.00 6.53
783 1028 9.869667 ATGTCACCAGGAGTATATATCTATACC 57.130 37.037 0.00 0.00 40.35 2.73
807 1052 4.637968 CTTTTGTCACCATCGACGTTATG 58.362 43.478 0.00 0.00 38.84 1.90
808 1053 3.124636 GCTTTTGTCACCATCGACGTTAT 59.875 43.478 0.00 0.00 38.84 1.89
810 1055 1.263217 GCTTTTGTCACCATCGACGTT 59.737 47.619 0.00 0.00 38.84 3.99
811 1056 0.865769 GCTTTTGTCACCATCGACGT 59.134 50.000 0.00 0.00 38.84 4.34
812 1057 0.179250 CGCTTTTGTCACCATCGACG 60.179 55.000 0.00 0.00 38.84 5.12
813 1058 0.165944 CCGCTTTTGTCACCATCGAC 59.834 55.000 0.00 0.00 36.40 4.20
814 1059 0.250124 ACCGCTTTTGTCACCATCGA 60.250 50.000 0.00 0.00 0.00 3.59
816 1061 1.335872 CCAACCGCTTTTGTCACCATC 60.336 52.381 0.00 0.00 0.00 3.51
817 1062 0.673437 CCAACCGCTTTTGTCACCAT 59.327 50.000 0.00 0.00 0.00 3.55
818 1063 2.010582 GCCAACCGCTTTTGTCACCA 62.011 55.000 0.00 0.00 0.00 4.17
819 1064 1.299850 GCCAACCGCTTTTGTCACC 60.300 57.895 0.00 0.00 0.00 4.02
866 1158 4.065281 GAGGGGTCCACGTGTCGG 62.065 72.222 15.65 0.00 0.00 4.79
1000 1295 3.136626 GGGTATGAGCTCCAGGTTAACAT 59.863 47.826 12.15 0.00 0.00 2.71
1011 1306 1.205893 GGATCCATCGGGTATGAGCTC 59.794 57.143 6.95 6.82 37.86 4.09
1019 1314 1.766461 GGTCCTGGATCCATCGGGT 60.766 63.158 16.63 0.00 34.93 5.28
1501 1799 2.033141 GGAGTCTGGCAGCAGCAA 59.967 61.111 10.34 0.00 44.61 3.91
1570 1868 6.434028 CAGATGGTCAGGTTAAATTCCAAGAA 59.566 38.462 0.00 0.00 0.00 2.52
1608 1906 4.394729 TGTGAGGTTTTAACAGATGGGAC 58.605 43.478 0.00 0.00 0.00 4.46
1672 1970 2.821366 CTGGGTGGCTGATGCGAC 60.821 66.667 0.00 0.00 45.32 5.19
1692 1990 1.927174 CTCTTGTACCGCAGCATGTAC 59.073 52.381 13.07 13.07 39.31 2.90
1977 2275 0.671781 CCCAGAAAGAGAGCCACACG 60.672 60.000 0.00 0.00 0.00 4.49
2043 2341 1.146041 GTCCCATGCAGATACCGCA 59.854 57.895 0.00 0.00 44.94 5.69
2047 2345 2.093500 TGTGACTGTCCCATGCAGATAC 60.093 50.000 5.17 5.10 37.40 2.24
2084 2382 5.163713 GCAATAGTCTTCCCATTGACTTGAC 60.164 44.000 0.00 0.00 42.67 3.18
2103 2401 2.777114 TCCACCCTGATTAGCAGCAATA 59.223 45.455 0.00 0.00 43.50 1.90
2117 2415 1.079658 GGCCTATATCTCCTCCACCCT 59.920 57.143 0.00 0.00 0.00 4.34
2132 2430 1.117994 CTCATGTGAGCTCTGGCCTA 58.882 55.000 16.19 0.00 39.73 3.93
2169 2467 2.997315 TCCCTCCACCTCACAGCG 60.997 66.667 0.00 0.00 0.00 5.18
2177 2475 1.687493 CCTCTCCTGTCCCTCCACC 60.687 68.421 0.00 0.00 0.00 4.61
2264 2562 0.464870 CTCAGCCACTGCAGAGCTAT 59.535 55.000 27.45 11.22 43.04 2.97
2307 2605 1.150081 GCAGGTGGCTGCCTATGAT 59.850 57.895 21.03 0.00 43.99 2.45
2396 2694 4.212425 TGGCGTGTAACAAACTGTGATTAG 59.788 41.667 0.00 0.00 35.74 1.73
2398 2696 2.946329 TGGCGTGTAACAAACTGTGATT 59.054 40.909 0.00 0.00 35.74 2.57
2422 2720 1.698506 AGCCCTTCAGATCTCCTACG 58.301 55.000 0.00 0.00 0.00 3.51
2453 2751 7.010091 GCCATTTATTTGCGTTATTATATGCCC 59.990 37.037 0.00 0.00 0.00 5.36
2497 2798 2.613977 CCCCCTGCAGCTTATCGATTAG 60.614 54.545 8.66 4.88 0.00 1.73
2517 2818 1.802365 AGGAACGCAAATTACGTGACC 59.198 47.619 15.81 15.81 44.30 4.02
2556 2857 6.680378 GCTCATGTCAACCAAACACTAAAAGT 60.680 38.462 0.00 0.00 0.00 2.66
2590 2891 1.059584 TCTGTGGCCAAAGGAGACCA 61.060 55.000 23.27 5.64 0.00 4.02
2591 2892 0.329596 ATCTGTGGCCAAAGGAGACC 59.670 55.000 23.27 0.35 0.00 3.85
2603 2904 4.639334 CCTCATCTATCCAACATCTGTGG 58.361 47.826 0.00 0.00 0.00 4.17
2626 2927 2.159226 CGGGAACAAGCTACTACTCCAG 60.159 54.545 0.00 0.00 0.00 3.86
2644 2945 2.143925 GACCTGAAAGTCTGAAACGGG 58.856 52.381 0.00 0.00 33.79 5.28
2680 2983 6.646653 TGACTAGAAAGTGTGCAAAGACATAG 59.353 38.462 0.00 0.00 35.56 2.23
2722 3025 6.759497 AAAATAGGTATCACAGGAAAGCAC 57.241 37.500 0.00 0.00 0.00 4.40
2825 3139 6.545298 CCTAAGCCATAAAGCTGAGAAAGAAT 59.455 38.462 0.00 0.00 43.26 2.40
2826 3140 5.882557 CCTAAGCCATAAAGCTGAGAAAGAA 59.117 40.000 0.00 0.00 43.26 2.52
2828 3142 5.431765 TCCTAAGCCATAAAGCTGAGAAAG 58.568 41.667 0.00 0.00 43.26 2.62
2829 3143 5.189736 TCTCCTAAGCCATAAAGCTGAGAAA 59.810 40.000 0.00 0.00 43.26 2.52
2830 3144 4.716784 TCTCCTAAGCCATAAAGCTGAGAA 59.283 41.667 0.00 0.00 43.26 2.87
2831 3145 4.290093 TCTCCTAAGCCATAAAGCTGAGA 58.710 43.478 0.00 0.00 43.26 3.27
2832 3146 4.679373 TCTCCTAAGCCATAAAGCTGAG 57.321 45.455 0.00 0.00 44.11 3.35
2833 3147 4.655649 TCATCTCCTAAGCCATAAAGCTGA 59.344 41.667 0.00 0.00 44.11 4.26
2834 3148 4.965814 TCATCTCCTAAGCCATAAAGCTG 58.034 43.478 0.00 0.00 44.11 4.24
2836 3150 6.699575 TTTTCATCTCCTAAGCCATAAAGC 57.300 37.500 0.00 0.00 0.00 3.51
2837 3151 7.255730 CCCATTTTCATCTCCTAAGCCATAAAG 60.256 40.741 0.00 0.00 0.00 1.85
2838 3152 6.550854 CCCATTTTCATCTCCTAAGCCATAAA 59.449 38.462 0.00 0.00 0.00 1.40
2839 3153 6.070656 CCCATTTTCATCTCCTAAGCCATAA 58.929 40.000 0.00 0.00 0.00 1.90
3001 3316 9.774742 GAAGTTTGCGAATGATTAAAATACTCT 57.225 29.630 0.00 0.00 0.00 3.24
3039 3354 9.574516 AATTGTCCCTGTCATCTTTATATAACC 57.425 33.333 0.00 0.00 0.00 2.85
3071 3386 3.047796 CAAAAATGATATGGCTCGCTGC 58.952 45.455 0.00 0.00 41.94 5.25
3170 3487 1.927174 GATGACGATGGGAACTTCACG 59.073 52.381 0.00 0.00 34.30 4.35
3242 3559 5.220605 GCGAAGAAAATGACATGGTAGGTAC 60.221 44.000 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.