Multiple sequence alignment - TraesCS1B01G445500

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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 TraesCS1B01G445500 chr1B 100.000 3374 0 0 1 3374 665436939 665440312 0.000000e+00 6231.0
1 TraesCS1B01G445500 chr1B 90.909 44 4 0 1 44 581590774 581590817 3.640000e-05 60.2
2 TraesCS1B01G445500 chr1A 93.518 1882 112 3 463 2344 574392745 574394616 0.000000e+00 2791.0
3 TraesCS1B01G445500 chr1A 86.620 568 74 2 2336 2902 574397664 574398230 7.950000e-176 627.0
4 TraesCS1B01G445500 chr1A 87.613 331 27 6 3018 3341 574480565 574480888 4.110000e-99 372.0
5 TraesCS1B01G445500 chr1A 84.273 337 29 13 2709 3021 574479974 574480310 1.180000e-79 307.0
6 TraesCS1B01G445500 chr1A 90.323 186 12 3 218 398 574392552 574392736 4.350000e-59 239.0
7 TraesCS1B01G445500 chr1A 84.783 138 20 1 1 137 574387041 574387178 1.630000e-28 137.0
8 TraesCS1B01G445500 chr1D 91.032 959 56 18 231 1179 478180680 478181618 0.000000e+00 1267.0
9 TraesCS1B01G445500 chr1D 85.794 1070 118 12 2336 3374 478252368 478253434 0.000000e+00 1103.0
10 TraesCS1B01G445500 chr1D 86.796 568 73 2 2336 2902 478185196 478185762 1.710000e-177 632.0
11 TraesCS1B01G445500 chr1D 95.611 319 14 0 2026 2344 478182125 478182443 2.320000e-141 512.0
12 TraesCS1B01G445500 chr1D 86.937 222 18 5 1 212 478176493 478176713 4.350000e-59 239.0
13 TraesCS1B01G445500 chr1D 100.000 41 0 0 2109 2149 478181690 478181650 3.610000e-10 76.8
14 TraesCS1B01G445500 chr4B 79.600 250 32 10 708 948 31877207 31876968 9.690000e-36 161.0
15 TraesCS1B01G445500 chr4D 78.800 250 34 10 708 948 19409508 19409269 2.100000e-32 150.0
16 TraesCS1B01G445500 chr4D 85.714 84 6 2 1 84 87960711 87960788 2.160000e-12 84.2
17 TraesCS1B01G445500 chr4A 78.947 247 33 10 705 942 581481994 581482230 2.100000e-32 150.0
18 TraesCS1B01G445500 chr3B 96.226 53 2 0 1 53 738635585 738635533 1.670000e-13 87.9
19 TraesCS1B01G445500 chr3B 83.133 83 8 2 4 86 504676408 504676332 1.680000e-08 71.3
20 TraesCS1B01G445500 chr5B 85.185 81 6 2 3 83 653788526 653788600 1.000000e-10 78.7
21 TraesCS1B01G445500 chr5D 83.333 84 8 3 1 84 535902109 535902186 4.670000e-09 73.1
22 TraesCS1B01G445500 chr7B 83.133 83 8 5 1 83 496337512 496337588 1.680000e-08 71.3


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 TraesCS1B01G445500 chr1B 665436939 665440312 3373 False 6231.0 6231 100.000000 1 3374 1 chr1B.!!$F2 3373
1 TraesCS1B01G445500 chr1A 574392552 574398230 5678 False 1219.0 2791 90.153667 218 2902 3 chr1A.!!$F2 2684
2 TraesCS1B01G445500 chr1A 574479974 574480888 914 False 339.5 372 85.943000 2709 3341 2 chr1A.!!$F3 632
3 TraesCS1B01G445500 chr1D 478252368 478253434 1066 False 1103.0 1103 85.794000 2336 3374 1 chr1D.!!$F1 1038
4 TraesCS1B01G445500 chr1D 478176493 478185762 9269 False 662.5 1267 90.094000 1 2902 4 chr1D.!!$F2 2901

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
398 4361 0.473501 GCATCAGATCCTCCCTCCCT 60.474 60.0 0.00 0.00 0.00 4.20 F
1602 5571 0.599991 TCAACAGGTGCAGCTACGTG 60.600 55.0 19.71 15.98 41.02 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 5856 0.391661 TCTTGAGCCGTGGCATCTTC 60.392 55.0 14.29 2.18 44.88 2.87 R
2571 10474 0.107703 TCACCATTGCCGTCCATCTC 60.108 55.0 0.00 0.00 0.00 2.75 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
137 142 7.833285 AAAGAAAGTTACATGGTGGTTACAT 57.167 32.000 0.00 0.00 0.00 2.29
165 170 4.335874 TCTCTCTTATAGTTCTCCGTGTGC 59.664 45.833 0.00 0.00 0.00 4.57
179 184 1.813513 GTGTGCCTGCATCTGTACTT 58.186 50.000 0.00 0.00 0.00 2.24
181 186 2.095567 GTGTGCCTGCATCTGTACTTTG 60.096 50.000 0.00 0.00 0.00 2.77
183 188 2.554032 GTGCCTGCATCTGTACTTTGTT 59.446 45.455 0.00 0.00 0.00 2.83
184 189 2.813754 TGCCTGCATCTGTACTTTGTTC 59.186 45.455 0.00 0.00 0.00 3.18
186 191 3.253188 GCCTGCATCTGTACTTTGTTCAA 59.747 43.478 0.00 0.00 0.00 2.69
187 192 4.261572 GCCTGCATCTGTACTTTGTTCAAA 60.262 41.667 0.00 0.00 0.00 2.69
188 193 5.455392 CCTGCATCTGTACTTTGTTCAAAG 58.545 41.667 19.56 19.56 35.93 2.77
189 194 5.239306 CCTGCATCTGTACTTTGTTCAAAGA 59.761 40.000 25.55 8.76 34.06 2.52
190 195 6.238731 CCTGCATCTGTACTTTGTTCAAAGAA 60.239 38.462 25.55 13.05 34.06 2.52
224 234 4.509970 TGATGCCGAATTCTTAATACGTGG 59.490 41.667 0.00 0.00 0.00 4.94
254 4213 9.417561 CCAAATATAATAGGCATCATGGATTCT 57.582 33.333 0.00 0.00 0.00 2.40
283 4242 2.761559 TGATTATGGTCCGCGGTAATG 58.238 47.619 27.15 0.00 0.00 1.90
364 4323 2.789409 GCCTGATCCGGCCTTTATAT 57.211 50.000 16.84 0.00 44.41 0.86
365 4324 2.359900 GCCTGATCCGGCCTTTATATG 58.640 52.381 16.84 0.00 44.41 1.78
366 4325 2.290323 GCCTGATCCGGCCTTTATATGT 60.290 50.000 16.84 0.00 44.41 2.29
367 4326 3.055385 GCCTGATCCGGCCTTTATATGTA 60.055 47.826 16.84 0.00 44.41 2.29
368 4327 4.504858 CCTGATCCGGCCTTTATATGTAC 58.495 47.826 0.00 0.00 0.00 2.90
384 4347 3.683365 TGTACAGAAGAAGCAGCATCA 57.317 42.857 0.00 0.00 0.00 3.07
385 4348 3.593096 TGTACAGAAGAAGCAGCATCAG 58.407 45.455 0.00 0.00 0.00 2.90
398 4361 0.473501 GCATCAGATCCTCCCTCCCT 60.474 60.000 0.00 0.00 0.00 4.20
399 4362 1.643310 CATCAGATCCTCCCTCCCTC 58.357 60.000 0.00 0.00 0.00 4.30
402 4365 1.311371 AGATCCTCCCTCCCTCCCT 60.311 63.158 0.00 0.00 0.00 4.20
404 4367 2.395180 GATCCTCCCTCCCTCCCTCC 62.395 70.000 0.00 0.00 0.00 4.30
405 4368 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
406 4369 4.548513 CTCCCTCCCTCCCTCCCG 62.549 77.778 0.00 0.00 0.00 5.14
408 4371 4.862823 CCCTCCCTCCCTCCCGTC 62.863 77.778 0.00 0.00 0.00 4.79
409 4372 4.862823 CCTCCCTCCCTCCCGTCC 62.863 77.778 0.00 0.00 0.00 4.79
427 4390 4.030452 GGTGCACTGCAAGCCGAC 62.030 66.667 17.98 1.40 41.47 4.79
429 4392 4.560743 TGCACTGCAAGCCGACCA 62.561 61.111 0.00 0.00 37.60 4.02
430 4393 4.030452 GCACTGCAAGCCGACCAC 62.030 66.667 0.00 0.00 37.60 4.16
431 4394 2.281070 CACTGCAAGCCGACCACT 60.281 61.111 0.00 0.00 37.60 4.00
432 4395 2.281070 ACTGCAAGCCGACCACTG 60.281 61.111 0.00 0.00 37.60 3.66
436 4399 2.738521 CAAGCCGACCACTGACCG 60.739 66.667 0.00 0.00 0.00 4.79
626 4589 3.324846 CCCATCACGATTCCTCCTTATCA 59.675 47.826 0.00 0.00 0.00 2.15
627 4590 4.310769 CCATCACGATTCCTCCTTATCAC 58.689 47.826 0.00 0.00 0.00 3.06
633 4596 0.744874 TTCCTCCTTATCACGCCGAG 59.255 55.000 0.00 0.00 0.00 4.63
637 4600 0.738975 TCCTTATCACGCCGAGACTG 59.261 55.000 0.00 0.00 0.00 3.51
656 4619 4.082523 CAGGACCGGCACCGTGAT 62.083 66.667 0.00 0.00 37.81 3.06
673 4636 3.528878 ATCGCCGCGACAGAGATCG 62.529 63.158 19.45 0.00 45.09 3.69
704 4667 1.227380 CAGGGAGAAAGATCGGGCG 60.227 63.158 0.00 0.00 0.00 6.13
705 4668 2.109181 GGGAGAAAGATCGGGCGG 59.891 66.667 0.00 0.00 0.00 6.13
706 4669 2.732619 GGGAGAAAGATCGGGCGGT 61.733 63.158 0.00 0.00 0.00 5.68
736 4699 1.306568 GGGAGAAGGAGCTGGAGGT 60.307 63.158 0.00 0.00 0.00 3.85
758 4721 2.760385 AGGGAGCAGTACCTCGGC 60.760 66.667 0.00 0.00 37.51 5.54
834 4797 4.803426 GACTGGGCGAGCACGGAG 62.803 72.222 13.72 0.00 40.15 4.63
1183 5152 3.384532 TCGACAGGGCCGGTTACC 61.385 66.667 11.53 3.22 0.00 2.85
1277 5246 4.069232 CGGCTCCGGCAAGACAGA 62.069 66.667 0.00 0.00 40.87 3.41
1278 5247 2.435059 GGCTCCGGCAAGACAGAC 60.435 66.667 0.00 0.00 40.87 3.51
1309 5278 1.713005 CCCCATGCTGGCCTACATCT 61.713 60.000 3.32 0.00 35.79 2.90
1425 5394 1.004440 GGAGACGGTGAAGCTTGCT 60.004 57.895 2.10 0.00 0.00 3.91
1588 5557 2.356553 GGTACGCCGTGCTCAACA 60.357 61.111 5.11 0.00 0.00 3.33
1593 5562 4.030452 GCCGTGCTCAACAGGTGC 62.030 66.667 0.00 0.00 36.55 5.01
1602 5571 0.599991 TCAACAGGTGCAGCTACGTG 60.600 55.000 19.71 15.98 41.02 4.49
1616 5585 4.039357 CGTGGTGCTCGACGAGGT 62.039 66.667 25.31 0.00 45.88 3.85
1638 5607 1.688735 GACAGGATGATCGACATGGGA 59.311 52.381 0.00 0.00 39.69 4.37
1647 5616 1.951130 CGACATGGGATTCGAGCCG 60.951 63.158 0.00 0.00 37.43 5.52
1695 5664 4.069232 TCGAGCCACCTGAAGCCG 62.069 66.667 0.00 0.00 0.00 5.52
1713 5682 2.100603 GAGAACGCGGACGAGGAG 59.899 66.667 12.47 0.00 43.93 3.69
1719 5688 4.500116 GCGGACGAGGAGCTGGAC 62.500 72.222 0.00 0.00 0.00 4.02
1731 5700 3.827898 CTGGACGAGGCGAGGACC 61.828 72.222 0.00 0.00 0.00 4.46
1737 5706 1.451567 CGAGGCGAGGACCTACAGA 60.452 63.158 0.00 0.00 41.32 3.41
1752 5721 1.878953 ACAGAACGACCCACATGTTC 58.121 50.000 0.00 0.00 41.71 3.18
1830 5799 4.773117 GTCGTCACCGTCGGCTCC 62.773 72.222 12.28 0.00 35.01 4.70
1862 5831 2.701780 CGGACCTCGTCACCCAGAG 61.702 68.421 0.00 0.00 33.68 3.35
1884 5853 0.692476 TGGTCATGGTGAAGGTCCAG 59.308 55.000 0.00 0.00 38.42 3.86
1887 5856 1.065854 GTCATGGTGAAGGTCCAGGAG 60.066 57.143 0.00 0.00 44.49 3.69
1911 5880 1.522580 GCCACGGCTCAAGAGGATC 60.523 63.158 0.00 0.00 38.26 3.36
1944 5913 1.153349 GAAGGACAGGACGGCCATC 60.153 63.158 11.69 6.54 36.29 3.51
1966 5935 1.400142 TGTTCTGCAACACCAAGAACG 59.600 47.619 9.49 0.00 40.99 3.95
1981 5950 3.916392 AACGCCGTGGAGAAGCTCG 62.916 63.158 0.00 0.00 0.00 5.03
2250 6260 2.159827 GCTCTCGACATCGTTTTTGACC 60.160 50.000 0.54 0.00 40.80 4.02
2257 6267 2.105821 ACATCGTTTTTGACCCTGGAGA 59.894 45.455 0.00 0.00 0.00 3.71
2382 10285 3.374988 TGTTCGCTCAATGATGATTGTCC 59.625 43.478 4.76 0.00 40.09 4.02
2399 10302 4.128925 TGTCCATGACAAGCTCTACATC 57.871 45.455 0.00 0.00 39.78 3.06
2403 10306 3.429410 CCATGACAAGCTCTACATCGTGA 60.429 47.826 0.00 0.00 0.00 4.35
2404 10307 3.217599 TGACAAGCTCTACATCGTGAC 57.782 47.619 0.00 0.00 0.00 3.67
2406 10309 1.893137 ACAAGCTCTACATCGTGACCA 59.107 47.619 0.00 0.00 0.00 4.02
2407 10310 2.094494 ACAAGCTCTACATCGTGACCAG 60.094 50.000 0.00 0.00 0.00 4.00
2412 10315 2.862536 CTCTACATCGTGACCAGCAATG 59.137 50.000 0.00 0.00 0.00 2.82
2413 10316 2.495669 TCTACATCGTGACCAGCAATGA 59.504 45.455 0.00 0.00 0.00 2.57
2436 10339 6.778069 TGACTACATTTGTGGGTTGGATTTTA 59.222 34.615 0.00 0.00 0.00 1.52
2439 10342 9.315363 ACTACATTTGTGGGTTGGATTTTATTA 57.685 29.630 0.00 0.00 0.00 0.98
2441 10344 7.390823 ACATTTGTGGGTTGGATTTTATTACC 58.609 34.615 0.00 0.00 0.00 2.85
2458 10361 0.693049 ACCCCACATCCACAACTCTC 59.307 55.000 0.00 0.00 0.00 3.20
2460 10363 1.352352 CCCCACATCCACAACTCTCTT 59.648 52.381 0.00 0.00 0.00 2.85
2463 10366 3.496692 CCCACATCCACAACTCTCTTTCA 60.497 47.826 0.00 0.00 0.00 2.69
2465 10368 5.491070 CCACATCCACAACTCTCTTTCATA 58.509 41.667 0.00 0.00 0.00 2.15
2477 10380 5.086104 TCTCTTTCATAAAAGTCCCGGAG 57.914 43.478 0.73 0.00 42.17 4.63
2484 10387 4.285003 TCATAAAAGTCCCGGAGAAAGTCA 59.715 41.667 0.73 0.00 0.00 3.41
2485 10388 3.570912 AAAAGTCCCGGAGAAAGTCAA 57.429 42.857 0.73 0.00 0.00 3.18
2489 10392 1.301401 CCCGGAGAAAGTCAACGCA 60.301 57.895 0.73 0.00 0.00 5.24
2490 10393 0.882927 CCCGGAGAAAGTCAACGCAA 60.883 55.000 0.73 0.00 0.00 4.85
2503 10406 2.032054 TCAACGCAAACTTCAAGCTCTG 59.968 45.455 0.00 0.00 0.00 3.35
2508 10411 2.489329 GCAAACTTCAAGCTCTGGCATA 59.511 45.455 0.00 0.00 41.70 3.14
2525 10428 3.598299 GCATAGAGATGATTCTGGGCTC 58.402 50.000 0.00 0.00 34.73 4.70
2532 10435 3.136260 AGATGATTCTGGGCTCTTTCTCC 59.864 47.826 0.00 0.00 0.00 3.71
2538 10441 1.219393 GGGCTCTTTCTCCTCCACG 59.781 63.158 0.00 0.00 0.00 4.94
2549 10452 1.269998 CTCCTCCACGAAGACGAGTTT 59.730 52.381 0.00 0.00 42.66 2.66
2555 10458 3.005472 TCCACGAAGACGAGTTTCATCTT 59.995 43.478 0.00 0.00 42.66 2.40
2556 10459 3.741344 CCACGAAGACGAGTTTCATCTTT 59.259 43.478 0.00 0.00 42.66 2.52
2565 10468 3.364366 CGAGTTTCATCTTTGTGTCTGGC 60.364 47.826 0.00 0.00 0.00 4.85
2581 10484 2.105128 GCACCTCGAGATGGACGG 59.895 66.667 15.71 0.00 0.00 4.79
2585 10488 1.330655 ACCTCGAGATGGACGGCAAT 61.331 55.000 15.71 0.00 0.00 3.56
2613 10516 4.035102 GGTGGGAGCTGGTGGACC 62.035 72.222 0.00 0.00 0.00 4.46
2619 10522 1.671379 GAGCTGGTGGACCGGTTTC 60.671 63.158 9.42 5.08 44.34 2.78
2621 10524 1.671379 GCTGGTGGACCGGTTTCTC 60.671 63.158 9.42 5.46 44.34 2.87
2624 10527 0.827089 TGGTGGACCGGTTTCTCGTA 60.827 55.000 9.42 0.00 39.43 3.43
2629 10532 0.040067 GACCGGTTTCTCGTACGTGT 60.040 55.000 16.05 1.20 0.00 4.49
2636 10539 2.320805 TTCTCGTACGTGTAGCACAC 57.679 50.000 16.05 8.75 45.26 3.82
2637 10540 0.518636 TCTCGTACGTGTAGCACACC 59.481 55.000 16.05 0.98 45.93 4.16
2642 10545 1.454572 TACGTGTAGCACACCACCGT 61.455 55.000 0.00 9.54 45.93 4.83
2644 10547 2.019951 GTGTAGCACACCACCGTCG 61.020 63.158 7.86 0.00 43.05 5.12
2655 10558 1.343465 ACCACCGTCGTGAGAGATTTT 59.657 47.619 0.00 0.00 43.14 1.82
2663 10566 1.806542 CGTGAGAGATTTTGGGTGTGG 59.193 52.381 0.00 0.00 0.00 4.17
2666 10569 0.409484 AGAGATTTTGGGTGTGGGGG 59.591 55.000 0.00 0.00 0.00 5.40
2685 10588 1.221021 GTCGGGGAAGATGGTGGAC 59.779 63.158 0.00 0.00 0.00 4.02
2690 10593 1.913419 GGGGAAGATGGTGGACTTGTA 59.087 52.381 0.00 0.00 0.00 2.41
2701 10604 7.770897 AGATGGTGGACTTGTATTCTTATGTTC 59.229 37.037 0.00 0.00 0.00 3.18
2711 10614 5.872617 TGTATTCTTATGTTCGTGGACAAGG 59.127 40.000 0.00 0.00 32.47 3.61
2833 10736 2.626467 GGCCTCCCACCTTTCCCAT 61.626 63.158 0.00 0.00 0.00 4.00
2855 10758 7.371159 CCATTTTGAATGATGAGGATGATCAG 58.629 38.462 0.09 0.00 43.33 2.90
2895 10798 3.754323 TGTTTAACCATTCGCCTTGGTAG 59.246 43.478 4.50 0.00 46.75 3.18
2902 10805 1.485294 TTCGCCTTGGTAGGAGCCAA 61.485 55.000 0.00 0.00 45.05 4.52
2936 10863 4.272991 GTCATGCTCTTTTGCCTCTATGAG 59.727 45.833 0.00 0.00 0.00 2.90
2946 10873 5.682234 TTGCCTCTATGAGAAGACATTGA 57.318 39.130 0.00 0.00 32.99 2.57
2951 10878 7.288621 TGCCTCTATGAGAAGACATTGAGATTA 59.711 37.037 16.76 5.11 45.55 1.75
3046 11231 9.869757 ACCTTGTAATGCTTTTATTTGGTTATC 57.130 29.630 0.00 0.00 0.00 1.75
3149 11334 4.981812 AGTAGAAAACAAAGTTCCCCGAT 58.018 39.130 0.00 0.00 0.00 4.18
3150 11335 5.382616 AGTAGAAAACAAAGTTCCCCGATT 58.617 37.500 0.00 0.00 0.00 3.34
3163 11348 5.104277 AGTTCCCCGATTGATAAACCATGTA 60.104 40.000 0.00 0.00 0.00 2.29
3191 11376 1.531522 GCGTTGTTCAGCTTTGCACG 61.532 55.000 0.00 0.00 0.00 5.34
3220 11405 2.346803 TGTATCTTGGCAGCTTCGTTC 58.653 47.619 0.00 0.00 0.00 3.95
3237 11422 3.690139 TCGTTCTGAGCTAGAATTCGTCT 59.310 43.478 0.00 0.00 46.50 4.18
3295 11481 0.438445 ATGACGAACGATGCAACACG 59.562 50.000 0.14 9.16 0.00 4.49
3343 11535 6.494893 TGCGCCCAATATATTTCATACTTC 57.505 37.500 4.18 0.00 0.00 3.01
3346 11538 6.348213 GCGCCCAATATATTTCATACTTCGTT 60.348 38.462 0.00 0.00 0.00 3.85
3347 11539 7.581476 CGCCCAATATATTTCATACTTCGTTT 58.419 34.615 0.00 0.00 0.00 3.60
3355 11547 5.759506 TTTCATACTTCGTTTGAAAGCCA 57.240 34.783 8.02 0.00 38.09 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 27 8.078060 TCATGATAGTACCAAGAACATCAGAA 57.922 34.615 0.00 0.00 0.00 3.02
89 91 2.668457 CGTGAGAACCAGCATGTAACTC 59.332 50.000 0.00 0.00 0.00 3.01
91 93 2.683968 TCGTGAGAACCAGCATGTAAC 58.316 47.619 0.00 0.00 37.03 2.50
92 94 3.394674 TTCGTGAGAACCAGCATGTAA 57.605 42.857 0.00 0.00 46.92 2.41
137 142 9.186837 ACACGGAGAACTATAAGAGAGAAATTA 57.813 33.333 0.00 0.00 0.00 1.40
161 166 2.153645 CAAAGTACAGATGCAGGCACA 58.846 47.619 0.00 0.00 0.00 4.57
165 170 5.239306 TCTTTGAACAAAGTACAGATGCAGG 59.761 40.000 21.39 0.00 45.88 4.85
208 218 3.625764 TGGCTGCCACGTATTAAGAATTC 59.374 43.478 19.30 0.00 0.00 2.17
212 222 2.772077 TTGGCTGCCACGTATTAAGA 57.228 45.000 23.30 0.00 30.78 2.10
213 223 5.689383 ATATTTGGCTGCCACGTATTAAG 57.311 39.130 23.30 0.00 30.78 1.85
214 224 7.753309 ATTATATTTGGCTGCCACGTATTAA 57.247 32.000 23.30 12.46 30.78 1.40
215 225 7.551262 CCTATTATATTTGGCTGCCACGTATTA 59.449 37.037 23.30 15.67 30.78 0.98
216 226 6.374333 CCTATTATATTTGGCTGCCACGTATT 59.626 38.462 23.30 10.61 30.78 1.89
224 234 5.902613 TGATGCCTATTATATTTGGCTGC 57.097 39.130 17.17 11.26 45.11 5.25
254 4213 1.136690 GACCATAATCATCGCGCGAA 58.863 50.000 38.07 22.71 0.00 4.70
283 4242 2.125952 GGCTGAAAATGGCGGCAC 60.126 61.111 16.34 1.16 39.38 5.01
346 4305 3.703001 ACATATAAAGGCCGGATCAGG 57.297 47.619 5.05 7.64 0.00 3.86
355 4314 6.293135 GCTGCTTCTTCTGTACATATAAAGGC 60.293 42.308 0.00 0.00 0.00 4.35
357 4316 7.776933 TGCTGCTTCTTCTGTACATATAAAG 57.223 36.000 0.00 0.15 0.00 1.85
358 4317 7.986889 TGATGCTGCTTCTTCTGTACATATAAA 59.013 33.333 15.38 0.00 0.00 1.40
359 4318 7.500141 TGATGCTGCTTCTTCTGTACATATAA 58.500 34.615 15.38 0.00 0.00 0.98
360 4319 7.014615 TCTGATGCTGCTTCTTCTGTACATATA 59.985 37.037 15.38 0.00 0.00 0.86
361 4320 5.922053 TGATGCTGCTTCTTCTGTACATAT 58.078 37.500 15.38 0.00 0.00 1.78
363 4322 4.081254 TCTGATGCTGCTTCTTCTGTACAT 60.081 41.667 15.38 0.00 0.00 2.29
364 4323 3.259123 TCTGATGCTGCTTCTTCTGTACA 59.741 43.478 15.38 0.00 0.00 2.90
365 4324 3.854666 TCTGATGCTGCTTCTTCTGTAC 58.145 45.455 15.38 0.00 0.00 2.90
366 4325 4.442612 GGATCTGATGCTGCTTCTTCTGTA 60.443 45.833 15.38 0.00 0.00 2.74
367 4326 3.533547 GATCTGATGCTGCTTCTTCTGT 58.466 45.455 15.38 0.00 0.00 3.41
368 4327 2.873472 GGATCTGATGCTGCTTCTTCTG 59.127 50.000 15.38 5.42 0.00 3.02
384 4347 1.311371 AGGGAGGGAGGGAGGATCT 60.311 63.158 0.00 0.00 33.73 2.75
385 4348 1.157513 GAGGGAGGGAGGGAGGATC 59.842 68.421 0.00 0.00 0.00 3.36
405 4368 3.716006 CTTGCAGTGCACCGGACG 61.716 66.667 19.58 0.00 38.71 4.79
406 4369 4.030452 GCTTGCAGTGCACCGGAC 62.030 66.667 19.58 0.00 38.71 4.79
410 4373 4.030452 GTCGGCTTGCAGTGCACC 62.030 66.667 19.58 16.02 38.71 5.01
411 4374 4.030452 GGTCGGCTTGCAGTGCAC 62.030 66.667 19.58 9.40 38.71 4.57
412 4375 4.560743 TGGTCGGCTTGCAGTGCA 62.561 61.111 15.37 15.37 36.47 4.57
413 4376 4.030452 GTGGTCGGCTTGCAGTGC 62.030 66.667 8.58 8.58 0.00 4.40
414 4377 2.281070 AGTGGTCGGCTTGCAGTG 60.281 61.111 0.00 0.00 0.00 3.66
415 4378 2.281070 CAGTGGTCGGCTTGCAGT 60.281 61.111 0.00 0.00 0.00 4.40
416 4379 2.031012 TCAGTGGTCGGCTTGCAG 59.969 61.111 0.00 0.00 0.00 4.41
607 4570 3.553096 GCGTGATAAGGAGGAATCGTGAT 60.553 47.826 0.00 0.00 0.00 3.06
627 4590 4.803426 GTCCTGGCAGTCTCGGCG 62.803 72.222 14.43 0.00 0.00 6.46
656 4619 4.237809 CGATCTCTGTCGCGGCGA 62.238 66.667 22.69 22.69 34.56 5.54
736 4699 1.781786 GAGGTACTGCTCCCTGATCA 58.218 55.000 0.00 0.00 41.55 2.92
758 4721 1.373570 GCTTCTTGTCCTTGGATCCG 58.626 55.000 7.39 0.00 0.00 4.18
878 4847 4.880537 CGTAGAGCAGCAGGGCGG 62.881 72.222 0.00 0.00 39.27 6.13
1005 4974 2.108157 GTCCAGTGCGTGTCCACA 59.892 61.111 0.00 0.00 38.18 4.17
1039 5008 2.202623 GTCGCGCTCCGTCATCTT 60.203 61.111 5.56 0.00 38.35 2.40
1185 5154 4.508128 TGGATCGGCGTCGGCTTC 62.508 66.667 17.35 12.78 39.81 3.86
1191 5160 2.663188 GCCATCTGGATCGGCGTC 60.663 66.667 6.85 3.71 35.79 5.19
1260 5229 4.069232 TCTGTCTTGCCGGAGCCG 62.069 66.667 5.05 1.06 38.69 5.52
1278 5247 4.473520 ATGGGGAGCACGAAGGCG 62.474 66.667 0.00 0.00 44.79 5.52
1302 5271 1.665916 CGGCATGCGGGAGATGTAG 60.666 63.158 16.98 0.00 0.00 2.74
1401 5370 1.251527 GCTTCACCGTCTCCCTCTCA 61.252 60.000 0.00 0.00 0.00 3.27
1482 5451 1.817099 GGCCTGCTTCTGGATCGTG 60.817 63.158 0.00 0.00 0.00 4.35
1485 5454 1.823041 GCTGGCCTGCTTCTGGATC 60.823 63.158 25.99 0.00 0.00 3.36
1588 5557 2.343758 CACCACGTAGCTGCACCT 59.656 61.111 1.02 0.00 0.00 4.00
1593 5562 1.801913 GTCGAGCACCACGTAGCTG 60.802 63.158 13.18 6.89 42.04 4.24
1616 5585 1.338020 CCATGTCGATCATCCTGTCGA 59.662 52.381 0.00 0.00 43.79 4.20
1638 5607 3.760035 ACGACCTGCGGCTCGAAT 61.760 61.111 16.93 0.00 46.49 3.34
1695 5664 3.398353 CTCCTCGTCCGCGTTCTCC 62.398 68.421 4.92 0.00 39.49 3.71
1713 5682 4.500116 GTCCTCGCCTCGTCCAGC 62.500 72.222 0.00 0.00 0.00 4.85
1719 5688 1.030488 TTCTGTAGGTCCTCGCCTCG 61.030 60.000 0.00 0.00 39.94 4.63
1731 5700 2.743636 ACATGTGGGTCGTTCTGTAG 57.256 50.000 0.00 0.00 0.00 2.74
1737 5706 1.227999 CGCTGAACATGTGGGTCGTT 61.228 55.000 0.00 0.00 0.00 3.85
1862 5831 1.298859 GACCTTCACCATGACCACGC 61.299 60.000 0.00 0.00 0.00 5.34
1884 5853 1.522580 GAGCCGTGGCATCTTCTCC 60.523 63.158 14.29 0.00 44.88 3.71
1887 5856 0.391661 TCTTGAGCCGTGGCATCTTC 60.392 55.000 14.29 2.18 44.88 2.87
2023 5992 2.579201 CGACTTCCCTCCGTGCAT 59.421 61.111 0.00 0.00 0.00 3.96
2178 6188 4.460505 CGATACGATGCGTGTACAGATAA 58.539 43.478 0.00 0.00 41.39 1.75
2179 6189 3.120442 CCGATACGATGCGTGTACAGATA 60.120 47.826 0.00 0.00 41.39 1.98
2250 6260 4.392940 AGAAAATGTCAGTGTTCTCCAGG 58.607 43.478 0.00 0.00 0.00 4.45
2257 6267 6.867662 AAGATCGAAGAAAATGTCAGTGTT 57.132 33.333 0.00 0.00 43.58 3.32
2294 6304 1.141881 ACGGGACTATTGCTCTGCG 59.858 57.895 0.00 0.00 0.00 5.18
2345 10248 2.159986 GCGAACAAAATTTGATGGCACG 60.160 45.455 13.19 8.97 37.19 5.34
2353 10256 6.693761 TCATCATTGAGCGAACAAAATTTG 57.306 33.333 3.89 3.89 33.44 2.32
2382 10285 3.549471 GTCACGATGTAGAGCTTGTCATG 59.451 47.826 0.00 0.00 0.00 3.07
2399 10302 2.078849 TGTAGTCATTGCTGGTCACG 57.921 50.000 0.00 0.00 0.00 4.35
2403 10306 3.507233 CCACAAATGTAGTCATTGCTGGT 59.493 43.478 0.00 0.00 42.60 4.00
2404 10307 3.119388 CCCACAAATGTAGTCATTGCTGG 60.119 47.826 0.00 0.00 42.60 4.85
2406 10309 3.766545 ACCCACAAATGTAGTCATTGCT 58.233 40.909 0.00 0.00 42.60 3.91
2407 10310 4.236935 CAACCCACAAATGTAGTCATTGC 58.763 43.478 0.00 0.00 42.60 3.56
2412 10315 5.722021 AAATCCAACCCACAAATGTAGTC 57.278 39.130 0.00 0.00 0.00 2.59
2413 10316 7.790782 ATAAAATCCAACCCACAAATGTAGT 57.209 32.000 0.00 0.00 0.00 2.73
2436 10339 2.919602 AGAGTTGTGGATGTGGGGTAAT 59.080 45.455 0.00 0.00 0.00 1.89
2439 10342 0.693049 GAGAGTTGTGGATGTGGGGT 59.307 55.000 0.00 0.00 0.00 4.95
2441 10344 2.867109 AAGAGAGTTGTGGATGTGGG 57.133 50.000 0.00 0.00 0.00 4.61
2458 10361 5.705905 ACTTTCTCCGGGACTTTTATGAAAG 59.294 40.000 21.60 21.60 46.17 2.62
2460 10363 5.221762 TGACTTTCTCCGGGACTTTTATGAA 60.222 40.000 0.00 0.00 0.00 2.57
2463 10366 4.903045 TGACTTTCTCCGGGACTTTTAT 57.097 40.909 0.00 0.00 0.00 1.40
2465 10368 3.211865 GTTGACTTTCTCCGGGACTTTT 58.788 45.455 0.00 0.00 0.00 2.27
2477 10380 3.240631 GCTTGAAGTTTGCGTTGACTTTC 59.759 43.478 0.00 0.00 36.31 2.62
2484 10387 1.334869 CCAGAGCTTGAAGTTTGCGTT 59.665 47.619 0.00 0.00 0.00 4.84
2485 10388 0.947244 CCAGAGCTTGAAGTTTGCGT 59.053 50.000 0.00 0.00 0.00 5.24
2489 10392 4.260170 CTCTATGCCAGAGCTTGAAGTTT 58.740 43.478 0.00 0.00 44.34 2.66
2490 10393 3.871485 CTCTATGCCAGAGCTTGAAGTT 58.129 45.455 0.00 0.00 44.34 2.66
2503 10406 2.305343 AGCCCAGAATCATCTCTATGCC 59.695 50.000 0.00 0.00 32.03 4.40
2508 10411 4.039339 AGAAAGAGCCCAGAATCATCTCT 58.961 43.478 0.00 0.00 35.82 3.10
2525 10428 1.540267 TCGTCTTCGTGGAGGAGAAAG 59.460 52.381 0.00 0.00 38.33 2.62
2532 10435 2.417339 TGAAACTCGTCTTCGTGGAG 57.583 50.000 0.00 0.00 38.33 3.86
2565 10468 2.105128 GCCGTCCATCTCGAGGTG 59.895 66.667 19.14 19.14 0.00 4.00
2569 10472 1.143838 CCATTGCCGTCCATCTCGA 59.856 57.895 0.00 0.00 0.00 4.04
2571 10474 0.107703 TCACCATTGCCGTCCATCTC 60.108 55.000 0.00 0.00 0.00 2.75
2581 10484 0.883833 CCACCTGTCTTCACCATTGC 59.116 55.000 0.00 0.00 0.00 3.56
2585 10488 1.768684 GCTCCCACCTGTCTTCACCA 61.769 60.000 0.00 0.00 0.00 4.17
2609 10512 0.730494 CACGTACGAGAAACCGGTCC 60.730 60.000 24.41 2.58 0.00 4.46
2613 10516 1.253999 GCTACACGTACGAGAAACCG 58.746 55.000 24.41 4.43 0.00 4.44
2629 10532 2.137425 CTCACGACGGTGGTGTGCTA 62.137 60.000 20.33 3.20 44.50 3.49
2636 10539 1.726791 CAAAATCTCTCACGACGGTGG 59.273 52.381 0.00 0.00 44.50 4.61
2637 10540 1.726791 CCAAAATCTCTCACGACGGTG 59.273 52.381 0.00 0.00 45.78 4.94
2642 10545 2.549992 CCACACCCAAAATCTCTCACGA 60.550 50.000 0.00 0.00 0.00 4.35
2644 10547 2.162681 CCCACACCCAAAATCTCTCAC 58.837 52.381 0.00 0.00 0.00 3.51
2663 10566 3.489513 CCATCTTCCCCGACCCCC 61.490 72.222 0.00 0.00 0.00 5.40
2666 10569 1.993391 TCCACCATCTTCCCCGACC 60.993 63.158 0.00 0.00 0.00 4.79
2670 10573 0.698818 ACAAGTCCACCATCTTCCCC 59.301 55.000 0.00 0.00 0.00 4.81
2671 10574 3.933861 ATACAAGTCCACCATCTTCCC 57.066 47.619 0.00 0.00 0.00 3.97
2685 10588 6.961359 TGTCCACGAACATAAGAATACAAG 57.039 37.500 0.00 0.00 0.00 3.16
2690 10593 5.046591 TCTCCTTGTCCACGAACATAAGAAT 60.047 40.000 0.00 0.00 0.00 2.40
2701 10604 1.751351 TGATAGCTCTCCTTGTCCACG 59.249 52.381 0.00 0.00 0.00 4.94
2711 10614 5.523188 CAGGTCAACAGAAATGATAGCTCTC 59.477 44.000 0.00 0.00 0.00 3.20
2795 10698 4.043435 GGCCAGATAGTCATAAGGGGAAAT 59.957 45.833 0.00 0.00 0.00 2.17
2833 10736 6.544931 GTCCTGATCATCCTCATCATTCAAAA 59.455 38.462 0.00 0.00 29.78 2.44
2855 10758 2.277084 ACAATGCGAGGTTATTCGTCC 58.723 47.619 0.00 0.00 42.38 4.79
2902 10805 9.333750 GGCAAAAGAGCATGACTACAAAAGTCT 62.334 40.741 0.00 0.00 44.89 3.24
2916 10843 4.767578 TCTCATAGAGGCAAAAGAGCAT 57.232 40.909 0.00 0.00 35.83 3.79
2936 10863 5.973651 TCGCATGTAATCTCAATGTCTTC 57.026 39.130 0.00 0.00 0.00 2.87
2951 10878 9.638239 ATGTTCAAGTTTTAATATTTCGCATGT 57.362 25.926 0.00 0.00 0.00 3.21
3046 11231 0.456221 ATGCGAGGTCAAGTAGTCCG 59.544 55.000 0.00 0.00 0.00 4.79
3138 11323 4.310022 TGGTTTATCAATCGGGGAACTT 57.690 40.909 0.00 0.00 0.00 2.66
3144 11329 6.494842 CACTTTACATGGTTTATCAATCGGG 58.505 40.000 0.00 0.00 0.00 5.14
3149 11334 6.098679 GCATGCACTTTACATGGTTTATCAA 58.901 36.000 14.21 0.00 44.12 2.57
3150 11335 5.649557 GCATGCACTTTACATGGTTTATCA 58.350 37.500 14.21 0.00 44.12 2.15
3163 11348 1.865248 GCTGAACAACGCATGCACTTT 60.865 47.619 19.57 4.34 0.00 2.66
3191 11376 5.594926 AGCTGCCAAGATACAATTAATTGC 58.405 37.500 24.82 11.24 41.38 3.56
3220 11405 4.103365 ACACAGACGAATTCTAGCTCAG 57.897 45.455 3.52 0.00 31.12 3.35
3237 11422 1.199789 GCATCTCGATTGGCAAACACA 59.800 47.619 3.01 0.00 0.00 3.72
3278 11464 0.448861 CACGTGTTGCATCGTTCGTC 60.449 55.000 7.58 0.00 38.23 4.20
3295 11481 2.473376 CGTTAATTCTTTCCGGTCGCAC 60.473 50.000 0.00 0.00 0.00 5.34
3303 11489 2.659757 GCGCAAACCGTTAATTCTTTCC 59.340 45.455 0.30 0.00 39.71 3.13
3343 11535 0.667993 TTGCTCCTGGCTTTCAAACG 59.332 50.000 0.00 0.00 42.39 3.60
3346 11538 2.596346 TCAATTGCTCCTGGCTTTCAA 58.404 42.857 0.00 0.00 42.39 2.69
3347 11539 2.291209 TCAATTGCTCCTGGCTTTCA 57.709 45.000 0.00 0.00 42.39 2.69


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

AutoCloner maintained by Alex Coulton.