Multiple sequence alignment - TraesCS2B01G436100

Loading Multiple Alignment...

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 TraesCS2B01G436100 chr2B 100.000 3026 0 0 1 3026 626652900 626649875 0.000000e+00 5589.0
1 TraesCS2B01G436100 chr2B 87.595 1048 104 12 1000 2043 626884289 626883264 0.000000e+00 1192.0
2 TraesCS2B01G436100 chr2D 93.321 2635 103 37 419 3026 528474331 528471743 0.000000e+00 3823.0
3 TraesCS2B01G436100 chr2D 88.480 1033 98 8 1000 2029 528590054 528589040 0.000000e+00 1229.0
4 TraesCS2B01G436100 chr2D 86.850 327 23 11 1 310 528474678 528474355 6.210000e-92 348.0
5 TraesCS2B01G436100 chr2D 91.071 56 5 0 723 778 528590300 528590245 3.230000e-10 76.8
6 TraesCS2B01G436100 chr2A 92.390 1866 100 19 422 2272 673196685 673194847 0.000000e+00 2621.0
7 TraesCS2B01G436100 chr2A 88.953 1032 93 9 1000 2028 673277486 673276473 0.000000e+00 1254.0
8 TraesCS2B01G436100 chr2A 91.935 372 18 6 2612 2983 673194496 673194137 7.480000e-141 510.0
9 TraesCS2B01G436100 chr2A 84.848 231 11 11 101 310 673196935 673196708 8.500000e-51 211.0
10 TraesCS2B01G436100 chr2A 81.111 180 23 7 445 615 673278100 673277923 1.890000e-27 134.0
11 TraesCS2B01G436100 chr1D 84.286 210 27 5 1444 1650 307420830 307420624 1.840000e-47 200.0
12 TraesCS2B01G436100 chr1A 83.732 209 28 5 1444 1649 386480073 386479868 3.080000e-45 193.0
13 TraesCS2B01G436100 chr4D 83.799 179 27 2 1455 1632 479525194 479525371 5.190000e-38 169.0
14 TraesCS2B01G436100 chr4D 94.059 101 4 2 324 424 442748551 442748453 5.230000e-33 152.0
15 TraesCS2B01G436100 chr3B 100.000 87 0 0 333 419 802601561 802601647 8.680000e-36 161.0
16 TraesCS2B01G436100 chr7B 90.756 119 9 2 305 423 589394535 589394651 1.120000e-34 158.0
17 TraesCS2B01G436100 chr5A 91.964 112 7 2 313 423 126275737 126275627 4.040000e-34 156.0
18 TraesCS2B01G436100 chr6B 94.949 99 4 1 330 428 120317770 120317867 1.450000e-33 154.0
19 TraesCS2B01G436100 chr5D 95.833 96 3 1 326 421 373834939 373835033 1.450000e-33 154.0
20 TraesCS2B01G436100 chr7A 91.743 109 6 3 322 430 75869358 75869253 6.760000e-32 148.0
21 TraesCS2B01G436100 chr6D 93.939 99 4 2 321 418 383526411 383526508 6.760000e-32 148.0
22 TraesCS2B01G436100 chr5B 93.137 102 6 1 317 418 19454231 19454131 6.760000e-32 148.0
23 TraesCS2B01G436100 chr3D 78.049 164 33 3 1456 1619 330062839 330062679 1.920000e-17 100.0


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 TraesCS2B01G436100 chr2B 626649875 626652900 3025 True 5589.0 5589 100.000000 1 3026 1 chr2B.!!$R1 3025
1 TraesCS2B01G436100 chr2B 626883264 626884289 1025 True 1192.0 1192 87.595000 1000 2043 1 chr2B.!!$R2 1043
2 TraesCS2B01G436100 chr2D 528471743 528474678 2935 True 2085.5 3823 90.085500 1 3026 2 chr2D.!!$R1 3025
3 TraesCS2B01G436100 chr2D 528589040 528590300 1260 True 652.9 1229 89.775500 723 2029 2 chr2D.!!$R2 1306
4 TraesCS2B01G436100 chr2A 673194137 673196935 2798 True 1114.0 2621 89.724333 101 2983 3 chr2A.!!$R1 2882
5 TraesCS2B01G436100 chr2A 673276473 673278100 1627 True 694.0 1254 85.032000 445 2028 2 chr2A.!!$R2 1583

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
846 983 0.32483 CCTTCCCGTCTCCTTCCTCT 60.325 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2737 2988 0.039527 GCATGGGGTCAAACGTTCAC 60.04 55.0 0.0 1.05 0.0 3.18 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
56 57 3.629438 CATTGATATGCATGGCAACGA 57.371 42.857 10.16 0.00 43.62 3.85
61 62 1.581934 TATGCATGGCAACGAGCTAC 58.418 50.000 10.16 0.00 43.62 3.58
62 63 1.097547 ATGCATGGCAACGAGCTACC 61.098 55.000 0.00 0.00 43.62 3.18
63 64 2.813179 GCATGGCAACGAGCTACCG 61.813 63.158 0.00 0.00 44.79 4.02
72 73 3.255725 CAACGAGCTACCGTAATTTGGA 58.744 45.455 0.39 0.00 42.54 3.53
78 79 1.790623 CTACCGTAATTTGGATCGCCG 59.209 52.381 3.62 0.00 36.79 6.46
79 80 1.278637 CCGTAATTTGGATCGCCGC 59.721 57.895 0.00 0.00 36.79 6.53
80 81 1.278637 CGTAATTTGGATCGCCGCC 59.721 57.895 0.00 0.00 36.79 6.13
92 93 3.892581 GCCGCCTTGTGCTATGCC 61.893 66.667 0.00 0.00 38.05 4.40
166 175 4.548991 ACAGCTAGGACGATTAGTAACG 57.451 45.455 0.00 0.00 0.00 3.18
174 183 2.872370 ACGATTAGTAACGTCAGCACC 58.128 47.619 0.00 0.00 38.34 5.01
175 184 2.490903 ACGATTAGTAACGTCAGCACCT 59.509 45.455 0.00 0.00 38.34 4.00
176 185 3.106672 CGATTAGTAACGTCAGCACCTC 58.893 50.000 0.00 0.00 0.00 3.85
177 186 3.427098 CGATTAGTAACGTCAGCACCTCA 60.427 47.826 0.00 0.00 0.00 3.86
181 199 0.391228 TAACGTCAGCACCTCAGCAA 59.609 50.000 0.00 0.00 36.85 3.91
196 214 2.373169 TCAGCAACTGTCTTCCCATTCT 59.627 45.455 0.00 0.00 32.61 2.40
204 222 5.805728 ACTGTCTTCCCATTCTATCGTTTT 58.194 37.500 0.00 0.00 0.00 2.43
301 324 5.176407 GTCATACTGACACTGCCTAGTAG 57.824 47.826 2.48 0.00 46.22 2.57
302 325 4.641094 GTCATACTGACACTGCCTAGTAGT 59.359 45.833 2.48 0.00 46.22 2.73
303 326 5.821470 GTCATACTGACACTGCCTAGTAGTA 59.179 44.000 2.48 0.00 46.22 1.82
304 327 6.487331 GTCATACTGACACTGCCTAGTAGTAT 59.513 42.308 2.48 0.00 46.22 2.12
305 328 7.660617 GTCATACTGACACTGCCTAGTAGTATA 59.339 40.741 2.48 0.00 46.22 1.47
306 329 8.215736 TCATACTGACACTGCCTAGTAGTATAA 58.784 37.037 0.00 0.00 35.51 0.98
307 330 6.945938 ACTGACACTGCCTAGTAGTATAAG 57.054 41.667 0.00 0.00 34.74 1.73
308 331 6.660800 ACTGACACTGCCTAGTAGTATAAGA 58.339 40.000 0.00 0.00 34.74 2.10
309 332 7.117397 ACTGACACTGCCTAGTAGTATAAGAA 58.883 38.462 0.00 0.00 34.74 2.52
310 333 7.614583 ACTGACACTGCCTAGTAGTATAAGAAA 59.385 37.037 0.00 0.00 34.74 2.52
311 334 8.534954 TGACACTGCCTAGTAGTATAAGAAAT 57.465 34.615 0.00 0.00 34.74 2.17
339 362 9.884814 AAGAATGATACTAGTATTGTACTCCCT 57.115 33.333 16.46 4.41 40.14 4.20
341 364 8.653036 AATGATACTAGTATTGTACTCCCTCC 57.347 38.462 16.46 0.57 40.14 4.30
342 365 6.236409 TGATACTAGTATTGTACTCCCTCCG 58.764 44.000 16.46 0.00 40.14 4.63
343 366 4.516652 ACTAGTATTGTACTCCCTCCGT 57.483 45.455 0.00 0.00 40.14 4.69
344 367 4.864726 ACTAGTATTGTACTCCCTCCGTT 58.135 43.478 0.00 0.00 40.14 4.44
345 368 4.886489 ACTAGTATTGTACTCCCTCCGTTC 59.114 45.833 0.00 0.00 40.14 3.95
346 369 3.029570 AGTATTGTACTCCCTCCGTTCC 58.970 50.000 0.00 0.00 32.47 3.62
347 370 1.946984 ATTGTACTCCCTCCGTTCCA 58.053 50.000 0.00 0.00 0.00 3.53
348 371 1.719529 TTGTACTCCCTCCGTTCCAA 58.280 50.000 0.00 0.00 0.00 3.53
349 372 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
350 373 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
351 374 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
352 375 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
353 376 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
354 377 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
355 378 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
356 379 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
357 380 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
358 381 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
359 382 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
360 383 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
361 384 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
362 385 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
363 386 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
364 387 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
365 388 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
366 389 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
367 390 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
368 391 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
369 392 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
370 393 7.893302 TCCAAAATAGATGACCCAACTTTGTAT 59.107 33.333 0.00 0.00 0.00 2.29
371 394 8.531146 CCAAAATAGATGACCCAACTTTGTATT 58.469 33.333 0.00 0.00 0.00 1.89
375 398 9.975218 AATAGATGACCCAACTTTGTATTAACT 57.025 29.630 0.00 0.00 0.00 2.24
376 399 9.975218 ATAGATGACCCAACTTTGTATTAACTT 57.025 29.630 0.00 0.00 0.00 2.66
377 400 8.706322 AGATGACCCAACTTTGTATTAACTTT 57.294 30.769 0.00 0.00 0.00 2.66
378 401 9.802039 AGATGACCCAACTTTGTATTAACTTTA 57.198 29.630 0.00 0.00 0.00 1.85
380 403 8.983702 TGACCCAACTTTGTATTAACTTTAGT 57.016 30.769 0.00 0.00 0.00 2.24
404 427 9.408648 AGTATAAAGTTGGGTCATCTATTTTGG 57.591 33.333 0.00 0.00 0.00 3.28
405 428 7.660030 ATAAAGTTGGGTCATCTATTTTGGG 57.340 36.000 0.00 0.00 0.00 4.12
406 429 4.946160 AGTTGGGTCATCTATTTTGGGA 57.054 40.909 0.00 0.00 0.00 4.37
407 430 4.600062 AGTTGGGTCATCTATTTTGGGAC 58.400 43.478 0.00 0.00 0.00 4.46
408 431 3.275617 TGGGTCATCTATTTTGGGACG 57.724 47.619 0.00 0.00 0.00 4.79
409 432 2.092646 TGGGTCATCTATTTTGGGACGG 60.093 50.000 0.00 0.00 0.00 4.79
410 433 2.171870 GGGTCATCTATTTTGGGACGGA 59.828 50.000 0.00 0.00 0.00 4.69
411 434 3.467803 GGTCATCTATTTTGGGACGGAG 58.532 50.000 0.00 0.00 0.00 4.63
412 435 3.467803 GTCATCTATTTTGGGACGGAGG 58.532 50.000 0.00 0.00 0.00 4.30
413 436 2.438021 TCATCTATTTTGGGACGGAGGG 59.562 50.000 0.00 0.00 0.00 4.30
414 437 2.257391 TCTATTTTGGGACGGAGGGA 57.743 50.000 0.00 0.00 0.00 4.20
415 438 2.116238 TCTATTTTGGGACGGAGGGAG 58.884 52.381 0.00 0.00 0.00 4.30
416 439 1.838077 CTATTTTGGGACGGAGGGAGT 59.162 52.381 0.00 0.00 0.00 3.85
417 440 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
523 553 3.643763 CTCTCCTGCGCGTCTTATTAAT 58.356 45.455 8.43 0.00 0.00 1.40
598 628 2.753966 CGCGCCCCTGTTCTTCATG 61.754 63.158 0.00 0.00 0.00 3.07
625 744 3.589988 GACTCAGGAAAATTCTCAGCGA 58.410 45.455 0.00 0.00 0.00 4.93
654 773 4.679373 TTGAACAGGATATCTCAGCTCC 57.321 45.455 2.05 0.00 0.00 4.70
802 931 4.157840 GGGTAATCCTGTTGGTCAAATCAC 59.842 45.833 0.00 0.00 34.23 3.06
805 934 5.649782 AATCCTGTTGGTCAAATCACATC 57.350 39.130 0.00 0.00 34.23 3.06
813 942 3.577415 TGGTCAAATCACATCAAATGCCA 59.423 39.130 0.00 0.00 0.00 4.92
814 943 4.178540 GGTCAAATCACATCAAATGCCAG 58.821 43.478 0.00 0.00 0.00 4.85
815 944 4.082081 GGTCAAATCACATCAAATGCCAGA 60.082 41.667 0.00 0.00 0.00 3.86
846 983 0.324830 CCTTCCCGTCTCCTTCCTCT 60.325 60.000 0.00 0.00 0.00 3.69
847 984 1.107945 CTTCCCGTCTCCTTCCTCTC 58.892 60.000 0.00 0.00 0.00 3.20
867 1004 2.621998 TCAGCTGGCCTATAAGTACGTC 59.378 50.000 15.13 0.00 0.00 4.34
872 1009 1.000938 GGCCTATAAGTACGTCCACCG 60.001 57.143 0.00 0.00 44.03 4.94
877 1014 1.876497 TAAGTACGTCCACCGCCACC 61.876 60.000 0.00 0.00 41.42 4.61
894 1031 2.048222 CGCGCTTTGTCCTCAGGA 60.048 61.111 5.56 0.00 0.00 3.86
934 1071 4.009675 AGCAGAACTCACAAACAAACTCA 58.990 39.130 0.00 0.00 0.00 3.41
939 1076 4.946784 ACTCACAAACAAACTCACAGAC 57.053 40.909 0.00 0.00 0.00 3.51
940 1077 3.689649 ACTCACAAACAAACTCACAGACC 59.310 43.478 0.00 0.00 0.00 3.85
1239 1430 2.711542 CAAGGTTACATGGACCTGACC 58.288 52.381 19.94 6.14 46.60 4.02
1263 1454 0.117340 AGTACCTGAACTCCTGCCCT 59.883 55.000 0.00 0.00 0.00 5.19
1343 1534 3.069980 GCGAGCCGTCTCCTGTGAT 62.070 63.158 0.00 0.00 35.94 3.06
1344 1535 1.725557 GCGAGCCGTCTCCTGTGATA 61.726 60.000 0.00 0.00 35.94 2.15
1731 1922 4.166523 CGAACACACGTAAGAGATCACAT 58.833 43.478 0.00 0.00 43.62 3.21
1914 2105 2.582436 GGATTTCCTCCGACGCCA 59.418 61.111 0.00 0.00 33.29 5.69
2029 2220 4.259690 CGCAGCTCACCGTTAGTTAATTAC 60.260 45.833 0.00 0.00 0.00 1.89
2052 2246 2.423538 AGGCGGTTAATTGCTGTGAATC 59.576 45.455 2.49 0.00 0.00 2.52
2184 2378 1.864711 GTGCGTTTGCTAAGAGACACA 59.135 47.619 0.00 0.00 43.34 3.72
2304 2498 9.609346 TGAAGTTACTCCTAGCAAATTATAACC 57.391 33.333 0.00 0.00 0.00 2.85
2306 2500 9.969001 AAGTTACTCCTAGCAAATTATAACCAA 57.031 29.630 0.00 0.00 0.00 3.67
2737 2988 4.152223 TGATGTGTGTGTTTCTAGATTGCG 59.848 41.667 0.00 0.00 0.00 4.85
2743 2994 3.183574 TGTGTTTCTAGATTGCGTGAACG 59.816 43.478 0.00 0.00 43.27 3.95
2744 2995 3.183775 GTGTTTCTAGATTGCGTGAACGT 59.816 43.478 4.59 0.00 42.22 3.99
2888 3139 7.461363 TCTGGTAGTAGTATATGATCTCCCTCA 59.539 40.741 0.00 0.00 0.00 3.86
2895 3146 6.619464 AGTATATGATCTCCCTCACAACTCT 58.381 40.000 0.00 0.00 0.00 3.24
3010 3265 8.843308 TTTATAGGGTACTTAGCTCCACTTAA 57.157 34.615 0.00 0.00 0.00 1.85
3013 3268 5.092259 AGGGTACTTAGCTCCACTTAAGTT 58.908 41.667 5.07 0.00 34.89 2.66
3014 3269 6.259123 AGGGTACTTAGCTCCACTTAAGTTA 58.741 40.000 5.07 0.00 34.89 2.24
3015 3270 6.154192 AGGGTACTTAGCTCCACTTAAGTTAC 59.846 42.308 5.07 2.79 34.89 2.50
3016 3271 6.032717 GGTACTTAGCTCCACTTAAGTTACG 58.967 44.000 5.07 0.00 34.89 3.18
3017 3272 5.718724 ACTTAGCTCCACTTAAGTTACGT 57.281 39.130 5.07 0.00 29.40 3.57
3019 3274 7.219484 ACTTAGCTCCACTTAAGTTACGTAA 57.781 36.000 5.07 3.29 29.40 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.037326 ACATGCACGGTCCAGTACTG 60.037 55.000 16.34 16.34 40.63 2.74
56 57 2.480845 GCGATCCAAATTACGGTAGCT 58.519 47.619 0.00 0.00 0.00 3.32
61 62 1.278637 GCGGCGATCCAAATTACGG 59.721 57.895 12.98 0.00 0.00 4.02
62 63 1.157870 AGGCGGCGATCCAAATTACG 61.158 55.000 12.98 0.00 0.00 3.18
63 64 1.021968 AAGGCGGCGATCCAAATTAC 58.978 50.000 12.98 0.00 0.00 1.89
78 79 2.438434 ACCGGCATAGCACAAGGC 60.438 61.111 0.00 0.00 45.30 4.35
79 80 2.764314 GCACCGGCATAGCACAAGG 61.764 63.158 0.00 0.00 40.72 3.61
80 81 2.793946 GCACCGGCATAGCACAAG 59.206 61.111 0.00 0.00 40.72 3.16
112 114 1.452651 CTTCCCATGCTGGCGACAT 60.453 57.895 0.00 0.00 41.51 3.06
136 138 2.816087 TCGTCCTAGCTGTTACGAGTTT 59.184 45.455 13.17 0.00 39.25 2.66
166 175 0.533755 ACAGTTGCTGAGGTGCTGAC 60.534 55.000 2.91 0.00 35.18 3.51
168 177 0.250209 AGACAGTTGCTGAGGTGCTG 60.250 55.000 2.91 0.00 35.18 4.41
169 178 0.471617 AAGACAGTTGCTGAGGTGCT 59.528 50.000 2.91 0.00 35.18 4.40
170 179 0.871057 GAAGACAGTTGCTGAGGTGC 59.129 55.000 2.91 0.00 35.18 5.01
171 180 1.517242 GGAAGACAGTTGCTGAGGTG 58.483 55.000 2.91 0.00 35.18 4.00
172 181 0.398318 GGGAAGACAGTTGCTGAGGT 59.602 55.000 2.91 0.00 35.18 3.85
173 182 0.397941 TGGGAAGACAGTTGCTGAGG 59.602 55.000 2.91 0.00 35.18 3.86
174 183 2.486472 ATGGGAAGACAGTTGCTGAG 57.514 50.000 2.91 0.00 35.18 3.35
175 184 2.373169 AGAATGGGAAGACAGTTGCTGA 59.627 45.455 2.91 0.00 35.18 4.26
176 185 2.787994 AGAATGGGAAGACAGTTGCTG 58.212 47.619 0.00 0.00 37.52 4.41
177 186 4.681781 CGATAGAATGGGAAGACAGTTGCT 60.682 45.833 0.00 0.00 39.76 3.91
181 199 5.422214 AAACGATAGAATGGGAAGACAGT 57.578 39.130 0.00 0.00 41.38 3.55
196 214 5.404096 TCACAACTAGCGATCAAAACGATA 58.596 37.500 0.00 0.00 33.17 2.92
204 222 5.106712 GGAAATTGTTCACAACTAGCGATCA 60.107 40.000 0.00 0.00 38.86 2.92
326 349 2.762327 TGGAACGGAGGGAGTACAATAC 59.238 50.000 0.00 0.00 0.00 1.89
334 357 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
335 358 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
337 360 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
338 361 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
339 362 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
341 364 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
342 365 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
343 366 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
344 367 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
345 368 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
349 372 9.975218 AGTTAATACAAAGTTGGGTCATCTATT 57.025 29.630 0.00 0.00 0.00 1.73
350 373 9.975218 AAGTTAATACAAAGTTGGGTCATCTAT 57.025 29.630 0.00 0.00 0.00 1.98
351 374 9.802039 AAAGTTAATACAAAGTTGGGTCATCTA 57.198 29.630 0.00 0.00 0.00 1.98
352 375 8.706322 AAAGTTAATACAAAGTTGGGTCATCT 57.294 30.769 0.00 0.00 0.00 2.90
354 377 9.582648 ACTAAAGTTAATACAAAGTTGGGTCAT 57.417 29.630 0.00 0.00 0.00 3.06
355 378 8.983702 ACTAAAGTTAATACAAAGTTGGGTCA 57.016 30.769 0.00 0.00 0.00 4.02
378 401 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
379 402 8.630037 CCCAAAATAGATGACCCAACTTTATAC 58.370 37.037 0.00 0.00 0.00 1.47
380 403 8.561769 TCCCAAAATAGATGACCCAACTTTATA 58.438 33.333 0.00 0.00 0.00 0.98
381 404 7.342026 GTCCCAAAATAGATGACCCAACTTTAT 59.658 37.037 0.00 0.00 0.00 1.40
382 405 6.661805 GTCCCAAAATAGATGACCCAACTTTA 59.338 38.462 0.00 0.00 0.00 1.85
383 406 5.480422 GTCCCAAAATAGATGACCCAACTTT 59.520 40.000 0.00 0.00 0.00 2.66
384 407 5.016831 GTCCCAAAATAGATGACCCAACTT 58.983 41.667 0.00 0.00 0.00 2.66
385 408 4.600062 GTCCCAAAATAGATGACCCAACT 58.400 43.478 0.00 0.00 0.00 3.16
386 409 3.377172 CGTCCCAAAATAGATGACCCAAC 59.623 47.826 0.00 0.00 0.00 3.77
387 410 3.616219 CGTCCCAAAATAGATGACCCAA 58.384 45.455 0.00 0.00 0.00 4.12
388 411 2.092646 CCGTCCCAAAATAGATGACCCA 60.093 50.000 0.00 0.00 0.00 4.51
389 412 2.171870 TCCGTCCCAAAATAGATGACCC 59.828 50.000 0.00 0.00 0.00 4.46
390 413 3.467803 CTCCGTCCCAAAATAGATGACC 58.532 50.000 0.00 0.00 0.00 4.02
391 414 3.467803 CCTCCGTCCCAAAATAGATGAC 58.532 50.000 0.00 0.00 0.00 3.06
392 415 2.438021 CCCTCCGTCCCAAAATAGATGA 59.562 50.000 0.00 0.00 0.00 2.92
393 416 2.438021 TCCCTCCGTCCCAAAATAGATG 59.562 50.000 0.00 0.00 0.00 2.90
394 417 2.706190 CTCCCTCCGTCCCAAAATAGAT 59.294 50.000 0.00 0.00 0.00 1.98
395 418 2.116238 CTCCCTCCGTCCCAAAATAGA 58.884 52.381 0.00 0.00 0.00 1.98
396 419 1.838077 ACTCCCTCCGTCCCAAAATAG 59.162 52.381 0.00 0.00 0.00 1.73
397 420 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
398 421 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
399 422 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
400 423 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
401 424 4.571362 GGATATATACTCCCTCCGTCCCAA 60.571 50.000 0.00 0.00 0.00 4.12
402 425 3.053095 GGATATATACTCCCTCCGTCCCA 60.053 52.174 0.00 0.00 0.00 4.37
403 426 3.564264 GGATATATACTCCCTCCGTCCC 58.436 54.545 0.00 0.00 0.00 4.46
404 427 3.212685 CGGATATATACTCCCTCCGTCC 58.787 54.545 11.84 0.00 42.93 4.79
408 431 6.210984 ACAGAAAACGGATATATACTCCCTCC 59.789 42.308 0.00 0.00 0.00 4.30
409 432 7.091443 CACAGAAAACGGATATATACTCCCTC 58.909 42.308 0.00 0.00 0.00 4.30
410 433 6.553852 ACACAGAAAACGGATATATACTCCCT 59.446 38.462 0.00 0.00 0.00 4.20
411 434 6.645415 CACACAGAAAACGGATATATACTCCC 59.355 42.308 0.00 0.00 0.00 4.30
412 435 7.431249 TCACACAGAAAACGGATATATACTCC 58.569 38.462 0.00 0.00 0.00 3.85
413 436 8.867112 TTCACACAGAAAACGGATATATACTC 57.133 34.615 0.00 0.00 32.05 2.59
523 553 2.798283 CCGCTCACACTTTACGAGAAAA 59.202 45.455 0.00 0.00 0.00 2.29
598 628 3.665190 AGAATTTTCCTGAGTCGTGTCC 58.335 45.455 0.00 0.00 0.00 4.02
625 744 7.630082 GCTGAGATATCCTGTTCAAATTTGCTT 60.630 37.037 13.54 0.00 0.00 3.91
654 773 2.187946 GGGATCGTGCACCCAGAG 59.812 66.667 12.15 0.00 44.96 3.35
687 806 2.126071 TTGCGCCGCTCTACTGTC 60.126 61.111 11.67 0.00 0.00 3.51
694 816 2.099062 CTTCATGTTGCGCCGCTC 59.901 61.111 11.67 4.14 0.00 5.03
802 931 5.238868 CCTATGTTCTCTCTGGCATTTGATG 59.761 44.000 0.00 0.00 0.00 3.07
805 934 3.314635 GCCTATGTTCTCTCTGGCATTTG 59.685 47.826 0.00 0.00 40.04 2.32
813 942 2.403561 GGGAAGGCCTATGTTCTCTCT 58.596 52.381 5.16 0.00 0.00 3.10
814 943 1.069358 CGGGAAGGCCTATGTTCTCTC 59.931 57.143 5.16 0.00 0.00 3.20
815 944 1.123928 CGGGAAGGCCTATGTTCTCT 58.876 55.000 5.16 0.00 0.00 3.10
846 983 2.621998 GACGTACTTATAGGCCAGCTGA 59.378 50.000 17.39 0.00 0.00 4.26
847 984 2.288273 GGACGTACTTATAGGCCAGCTG 60.288 54.545 6.78 6.78 0.00 4.24
877 1014 2.048222 TCCTGAGGACAAAGCGCG 60.048 61.111 0.00 0.00 0.00 6.86
878 1015 0.320771 TTCTCCTGAGGACAAAGCGC 60.321 55.000 0.00 0.00 0.00 5.92
879 1016 2.275318 GATTCTCCTGAGGACAAAGCG 58.725 52.381 0.00 0.00 0.00 4.68
880 1017 2.093973 TCGATTCTCCTGAGGACAAAGC 60.094 50.000 0.00 0.00 0.00 3.51
881 1018 3.876274 TCGATTCTCCTGAGGACAAAG 57.124 47.619 0.00 0.00 0.00 2.77
894 1031 1.800805 CTGTGGTGCTGTTCGATTCT 58.199 50.000 0.00 0.00 0.00 2.40
934 1071 4.008933 GCGGTGGCAGAGGTCTGT 62.009 66.667 8.74 0.00 45.45 3.41
940 1077 4.147449 TCGATGGCGGTGGCAGAG 62.147 66.667 0.00 0.00 42.43 3.35
1076 1255 4.832608 GGTTAGCCGTCGCCAGGG 62.833 72.222 0.00 0.00 34.57 4.45
1158 1337 1.005037 CTGCTGGTACGCTTGTGGA 60.005 57.895 0.00 0.00 0.00 4.02
1208 1387 1.009829 GTAACCTTGCATCTGCTCCG 58.990 55.000 3.53 0.00 42.66 4.63
1263 1454 2.599281 TCAGGGACGTCGGCAGAA 60.599 61.111 9.92 0.00 0.00 3.02
1715 1906 4.498850 CCTCCTCATGTGATCTCTTACGTG 60.499 50.000 0.00 0.00 35.63 4.49
1731 1922 3.933048 GACGTCGGGGTCCTCCTCA 62.933 68.421 0.00 0.00 32.73 3.86
1842 2033 2.358247 GAGGCTGTTTCCCGCGAA 60.358 61.111 8.23 0.00 0.00 4.70
1851 2042 2.600769 ACCGTCGAGGAGGCTGTT 60.601 61.111 6.70 0.00 45.00 3.16
1899 2090 1.227263 CGATGGCGTCGGAGGAAAT 60.227 57.895 21.01 0.00 46.47 2.17
2029 2220 0.096976 CACAGCAATTAACCGCCTCG 59.903 55.000 0.00 0.00 0.00 4.63
2052 2246 3.829601 TGTTTATTGGTTAACCCCAGCTG 59.170 43.478 21.97 6.78 35.49 4.24
2304 2498 7.650504 CCATTTACAGCAAATATCACATCCTTG 59.349 37.037 0.00 0.00 34.99 3.61
2306 2500 6.266103 CCCATTTACAGCAAATATCACATCCT 59.734 38.462 0.00 0.00 34.99 3.24
2392 2638 0.597377 GCCACTTTCCGTTTTGCTGG 60.597 55.000 0.00 0.00 0.00 4.85
2513 2759 4.392754 TCAGAGCAGAAACATACGTACGTA 59.607 41.667 28.62 28.62 34.87 3.57
2569 2816 3.334583 TTCAGTGATCCAGGCACTTAC 57.665 47.619 0.00 0.00 43.67 2.34
2607 2854 4.458989 GTGTCCCTTGCTGTCAATTATTCA 59.541 41.667 0.00 0.00 0.00 2.57
2725 2976 4.508492 TCAAACGTTCACGCAATCTAGAAA 59.492 37.500 0.00 0.00 44.43 2.52
2737 2988 0.039527 GCATGGGGTCAAACGTTCAC 60.040 55.000 0.00 1.05 0.00 3.18
2743 2994 0.623723 TCTAGGGCATGGGGTCAAAC 59.376 55.000 0.00 0.00 0.00 2.93
2744 2995 0.623723 GTCTAGGGCATGGGGTCAAA 59.376 55.000 0.00 0.00 0.00 2.69
2872 3123 6.491745 TGAGAGTTGTGAGGGAGATCATATAC 59.508 42.308 0.00 0.00 0.00 1.47
2888 3139 4.439700 GCATATGCATTGCTTGAGAGTTGT 60.440 41.667 22.84 0.00 41.59 3.32


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

AutoCloner maintained by Alex Coulton.