Multiple sequence alignment - TraesCS1B01G238100

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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 TraesCS1B01G238100 chr1B 100.000 2690 0 0 1 2690 426073688 426070999 0.000000e+00 4968.0
1 TraesCS1B01G238100 chr1D 94.672 2290 81 12 409 2690 314575107 314572851 0.000000e+00 3515.0
2 TraesCS1B01G238100 chr1A 94.284 2152 102 13 409 2555 394853278 394851143 0.000000e+00 3273.0
3 TraesCS1B01G238100 chr1A 89.600 250 17 7 104 346 394853564 394853317 2.600000e-80 309.0
4 TraesCS1B01G238100 chr1A 89.474 133 5 2 2559 2690 394850980 394850856 2.770000e-35 159.0
5 TraesCS1B01G238100 chr1A 86.735 98 4 3 1 98 394853858 394853770 1.700000e-17 100.0
6 TraesCS1B01G238100 chr7B 84.395 801 119 2 746 1540 604034726 604035526 0.000000e+00 782.0
7 TraesCS1B01G238100 chr7A 83.697 687 106 3 734 1414 642253422 642254108 0.000000e+00 643.0
8 TraesCS1B01G238100 chr6D 88.923 325 33 3 1719 2042 12345466 12345144 5.400000e-107 398.0
9 TraesCS1B01G238100 chr6D 93.548 62 3 1 342 402 293177569 293177508 1.030000e-14 91.6
10 TraesCS1B01G238100 chr6B 82.895 456 51 6 1166 1621 22711663 22711235 4.200000e-103 385.0
11 TraesCS1B01G238100 chr6B 88.235 323 32 4 1719 2040 22711178 22710861 5.430000e-102 381.0
12 TraesCS1B01G238100 chr6B 93.220 59 3 1 345 402 560706183 560706125 4.770000e-13 86.1
13 TraesCS1B01G238100 chr6B 93.220 59 3 1 345 402 560745634 560745576 4.770000e-13 86.1
14 TraesCS1B01G238100 chr7D 92.537 67 4 1 337 402 21264610 21264544 7.930000e-16 95.3
15 TraesCS1B01G238100 chr5D 95.000 60 3 0 339 398 525738309 525738250 7.930000e-16 95.3
16 TraesCS1B01G238100 chr5D 94.737 57 3 0 342 398 320627431 320627375 3.690000e-14 89.8
17 TraesCS1B01G238100 chr3D 94.737 57 3 0 342 398 435678629 435678573 3.690000e-14 89.8
18 TraesCS1B01G238100 chr2B 94.737 57 2 1 343 398 248148814 248148870 1.330000e-13 87.9
19 TraesCS1B01G238100 chr3B 90.625 64 5 1 339 401 236510048 236509985 1.720000e-12 84.2


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 TraesCS1B01G238100 chr1B 426070999 426073688 2689 True 4968.00 4968 100.00000 1 2690 1 chr1B.!!$R1 2689
1 TraesCS1B01G238100 chr1D 314572851 314575107 2256 True 3515.00 3515 94.67200 409 2690 1 chr1D.!!$R1 2281
2 TraesCS1B01G238100 chr1A 394850856 394853858 3002 True 960.25 3273 90.02325 1 2690 4 chr1A.!!$R1 2689
3 TraesCS1B01G238100 chr7B 604034726 604035526 800 False 782.00 782 84.39500 746 1540 1 chr7B.!!$F1 794
4 TraesCS1B01G238100 chr7A 642253422 642254108 686 False 643.00 643 83.69700 734 1414 1 chr7A.!!$F1 680
5 TraesCS1B01G238100 chr6B 22710861 22711663 802 True 383.00 385 85.56500 1166 2040 2 chr6B.!!$R3 874

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
804 1021 0.179018 AAGCCTTCTTCGCCTTGTGT 60.179 50.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2631 3042 0.332632 AGCTTGGCTGCCATTAGGAA 59.667 50.0 24.03 5.13 37.57 3.36 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
21 22 1.508088 GCACTTTGGCAGGATTCCG 59.492 57.895 0.00 0.00 0.00 4.30
22 23 0.960364 GCACTTTGGCAGGATTCCGA 60.960 55.000 0.00 0.00 0.00 4.55
43 44 1.666189 GAGTAGGAAAAGCGTCCATGC 59.334 52.381 6.86 0.00 40.48 4.06
53 54 1.001745 GCGTCCATGCCGTGTTTTTC 61.002 55.000 5.15 0.00 0.00 2.29
54 55 0.591170 CGTCCATGCCGTGTTTTTCT 59.409 50.000 0.00 0.00 0.00 2.52
55 56 1.001815 CGTCCATGCCGTGTTTTTCTT 60.002 47.619 0.00 0.00 0.00 2.52
56 57 2.542824 CGTCCATGCCGTGTTTTTCTTT 60.543 45.455 0.00 0.00 0.00 2.52
57 58 3.049912 GTCCATGCCGTGTTTTTCTTTC 58.950 45.455 0.00 0.00 0.00 2.62
58 59 2.050691 CCATGCCGTGTTTTTCTTTCG 58.949 47.619 0.00 0.00 0.00 3.46
59 60 2.542824 CCATGCCGTGTTTTTCTTTCGT 60.543 45.455 0.00 0.00 0.00 3.85
60 61 2.923605 TGCCGTGTTTTTCTTTCGTT 57.076 40.000 0.00 0.00 0.00 3.85
61 62 2.788030 TGCCGTGTTTTTCTTTCGTTC 58.212 42.857 0.00 0.00 0.00 3.95
62 63 2.420722 TGCCGTGTTTTTCTTTCGTTCT 59.579 40.909 0.00 0.00 0.00 3.01
98 99 6.772078 ACTGCAAACGTACTAGCAATAAATC 58.228 36.000 0.00 0.00 36.44 2.17
100 101 7.094975 ACTGCAAACGTACTAGCAATAAATCAA 60.095 33.333 0.00 0.00 36.44 2.57
101 102 7.240674 TGCAAACGTACTAGCAATAAATCAAG 58.759 34.615 0.00 0.00 33.48 3.02
102 103 7.118535 TGCAAACGTACTAGCAATAAATCAAGA 59.881 33.333 0.00 0.00 33.48 3.02
117 318 5.930837 AATCAAGACCCAAGTTCAAACAA 57.069 34.783 0.00 0.00 0.00 2.83
129 330 2.203337 AAACAAGCTCAGCCCGCA 60.203 55.556 0.00 0.00 0.00 5.69
159 360 2.125952 TGTGCAGATGCTCGACCG 60.126 61.111 6.35 0.00 42.66 4.79
161 362 3.068064 TGCAGATGCTCGACCGGA 61.068 61.111 9.46 0.00 42.66 5.14
232 440 3.945285 TCAAAAGAACCTGAAGTGTGTCC 59.055 43.478 0.00 0.00 0.00 4.02
234 442 2.622064 AGAACCTGAAGTGTGTCCAC 57.378 50.000 0.00 0.00 42.17 4.02
277 485 3.563808 GCACTGTTGTGGACACTAAATGA 59.436 43.478 3.91 0.00 43.97 2.57
296 504 6.347061 AATGATAAAACCTCCCCAAGAGAT 57.653 37.500 0.00 0.00 46.50 2.75
300 508 3.441500 AAACCTCCCCAAGAGATTGAC 57.558 47.619 0.00 0.00 46.50 3.18
325 533 3.758023 CACAATACAGACAAGCCATCCAA 59.242 43.478 0.00 0.00 0.00 3.53
347 555 4.080969 CGGCATAGTCCGTCTATTCTAC 57.919 50.000 0.00 0.00 44.18 2.59
348 556 3.752222 CGGCATAGTCCGTCTATTCTACT 59.248 47.826 0.00 0.00 44.18 2.57
349 557 4.142859 CGGCATAGTCCGTCTATTCTACTC 60.143 50.000 0.00 0.00 44.18 2.59
350 558 4.156373 GGCATAGTCCGTCTATTCTACTCC 59.844 50.000 0.00 0.00 37.26 3.85
351 559 4.156373 GCATAGTCCGTCTATTCTACTCCC 59.844 50.000 0.00 0.00 37.26 4.30
352 560 5.562635 CATAGTCCGTCTATTCTACTCCCT 58.437 45.833 0.00 0.00 37.26 4.20
353 561 4.089408 AGTCCGTCTATTCTACTCCCTC 57.911 50.000 0.00 0.00 0.00 4.30
354 562 3.148412 GTCCGTCTATTCTACTCCCTCC 58.852 54.545 0.00 0.00 0.00 4.30
356 564 2.486907 CCGTCTATTCTACTCCCTCCGT 60.487 54.545 0.00 0.00 0.00 4.69
357 565 2.807392 CGTCTATTCTACTCCCTCCGTC 59.193 54.545 0.00 0.00 0.00 4.79
359 567 2.107901 TCTATTCTACTCCCTCCGTCCC 59.892 54.545 0.00 0.00 0.00 4.46
360 568 0.635009 ATTCTACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
361 569 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
362 570 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
364 572 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
367 575 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
368 576 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
370 578 5.847817 ACTCCCTCCGTCCCATAATATAAAA 59.152 40.000 0.00 0.00 0.00 1.52
371 579 6.330778 ACTCCCTCCGTCCCATAATATAAAAA 59.669 38.462 0.00 0.00 0.00 1.94
372 580 6.536447 TCCCTCCGTCCCATAATATAAAAAC 58.464 40.000 0.00 0.00 0.00 2.43
373 581 5.410439 CCCTCCGTCCCATAATATAAAAACG 59.590 44.000 0.00 0.00 0.00 3.60
374 582 5.993441 CCTCCGTCCCATAATATAAAAACGT 59.007 40.000 0.00 0.00 0.00 3.99
375 583 6.484308 CCTCCGTCCCATAATATAAAAACGTT 59.516 38.462 0.00 0.00 0.00 3.99
376 584 7.012610 CCTCCGTCCCATAATATAAAAACGTTT 59.987 37.037 7.96 7.96 0.00 3.60
377 585 8.278729 TCCGTCCCATAATATAAAAACGTTTT 57.721 30.769 20.26 20.26 0.00 2.43
428 636 1.132436 CATGTGCAAACGCGACGAT 59.868 52.632 15.93 0.00 0.00 3.73
441 649 2.657427 CGCGACGATGAACATGCATAAG 60.657 50.000 0.00 0.00 0.00 1.73
600 814 2.358737 CACCGTTCCAGACCAGCC 60.359 66.667 0.00 0.00 0.00 4.85
621 835 1.227853 AGGACACGCCAGAAACCAC 60.228 57.895 0.00 0.00 40.02 4.16
714 928 3.430556 TCCGACACATACACATCAAAACG 59.569 43.478 0.00 0.00 0.00 3.60
804 1021 0.179018 AAGCCTTCTTCGCCTTGTGT 60.179 50.000 0.00 0.00 0.00 3.72
993 1210 1.449778 GAGCCGGTAGTTGCCCTTC 60.450 63.158 1.90 0.00 0.00 3.46
1128 1345 2.568956 AGCAGTGAATACAGCCTTCTCA 59.431 45.455 0.00 0.00 39.88 3.27
1140 1357 1.406069 GCCTTCTCATTCTCTTCGCCA 60.406 52.381 0.00 0.00 0.00 5.69
1224 1441 1.177401 GGGCAGAACTCCCATTGTTC 58.823 55.000 0.00 0.00 43.37 3.18
1226 1446 0.804989 GCAGAACTCCCATTGTTCGG 59.195 55.000 0.00 0.00 45.84 4.30
1671 1891 0.798776 CTGTAACTTCTGCCTTGCCG 59.201 55.000 0.00 0.00 0.00 5.69
1708 1928 2.180276 GAGAGGGTGCTTCAGTTAGGA 58.820 52.381 0.00 0.00 0.00 2.94
1845 2093 2.435586 GCTGATGGCTGCTGACGT 60.436 61.111 0.00 0.00 38.06 4.34
2027 2275 3.614870 GCCATCCTTACAAGTTTTGGCTG 60.615 47.826 14.79 0.00 38.91 4.85
2068 2320 7.229306 ACATCAACAAACTGAAGAGAGCATAAA 59.771 33.333 0.00 0.00 0.00 1.40
2102 2354 5.534278 TGAAGAAGTAACCATGCAACATCAA 59.466 36.000 0.00 0.00 0.00 2.57
2112 2364 5.128171 ACCATGCAACATCAAAGATTAGCAT 59.872 36.000 0.00 0.00 41.64 3.79
2168 2420 4.162320 TCTTTTTGTATTGCACCAACCCAA 59.838 37.500 0.00 0.00 0.00 4.12
2187 2439 8.458843 CAACCCAACTACAGAATAAACCATAAG 58.541 37.037 0.00 0.00 0.00 1.73
2209 2461 6.538945 AGGCAAACTAAAAAGTTGAAAGGA 57.461 33.333 0.00 0.00 31.64 3.36
2212 2464 7.549134 AGGCAAACTAAAAAGTTGAAAGGAAAG 59.451 33.333 0.00 0.00 31.64 2.62
2213 2465 7.201609 GGCAAACTAAAAAGTTGAAAGGAAAGG 60.202 37.037 0.00 0.00 31.64 3.11
2233 2485 5.904362 AGGGAAGCAAACATGAATACTTC 57.096 39.130 0.00 7.19 34.23 3.01
2291 2543 9.750125 GACTAAACAAGATTTGTGAAGGAAAAT 57.250 29.630 0.00 0.00 44.59 1.82
2301 2553 6.418057 TTGTGAAGGAAAATTATGTTGCCT 57.582 33.333 0.00 0.00 0.00 4.75
2315 2567 3.065019 GTTGCCTATAACAACATGCCG 57.935 47.619 11.56 0.00 45.35 5.69
2364 2616 4.909696 TGCGAAACAAATCTTTTCCTGA 57.090 36.364 0.00 0.00 30.44 3.86
2445 2697 2.513897 GCCATGCGTCCCCAGTAC 60.514 66.667 0.00 0.00 0.00 2.73
2472 2724 1.374758 CAGACAACTCCCGCTGTCC 60.375 63.158 0.00 0.00 42.45 4.02
2474 2726 2.526873 ACAACTCCCGCTGTCCCT 60.527 61.111 0.00 0.00 0.00 4.20
2484 2736 1.016130 CGCTGTCCCTCACATGTCAC 61.016 60.000 0.00 0.00 33.23 3.67
2485 2737 0.035317 GCTGTCCCTCACATGTCACA 59.965 55.000 0.00 0.00 33.23 3.58
2489 2741 2.903135 TGTCCCTCACATGTCACATGTA 59.097 45.455 23.13 10.77 0.00 2.29
2545 2797 8.487028 AGGTACTATTTAACAGCTAAAGCAGAT 58.513 33.333 4.54 0.00 40.12 2.90
2547 2799 9.922305 GTACTATTTAACAGCTAAAGCAGATTG 57.078 33.333 4.54 0.00 45.16 2.67
2555 2808 7.493743 ACAGCTAAAGCAGATTGATTCTATG 57.506 36.000 4.54 0.00 45.16 2.23
2631 3042 9.799106 CCCAAATATACTGATGTAGAGGAAAAT 57.201 33.333 0.00 0.00 31.51 1.82
2659 3070 4.709840 AGCCAAGCTGCAGTAGTG 57.290 55.556 16.64 10.68 37.57 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.984230 TCTCGGAATCCTGCCAAAGT 59.016 50.000 0.00 0.00 0.00 2.66
7 8 0.984230 ACTCTCGGAATCCTGCCAAA 59.016 50.000 0.00 0.00 0.00 3.28
21 22 3.190874 CATGGACGCTTTTCCTACTCTC 58.809 50.000 0.00 0.00 36.51 3.20
22 23 2.678190 GCATGGACGCTTTTCCTACTCT 60.678 50.000 0.00 0.00 36.51 3.24
43 44 6.384178 AAAAAGAACGAAAGAAAAACACGG 57.616 33.333 0.00 0.00 0.00 4.94
98 99 3.131046 AGCTTGTTTGAACTTGGGTCTTG 59.869 43.478 0.00 0.00 0.00 3.02
100 101 2.952310 GAGCTTGTTTGAACTTGGGTCT 59.048 45.455 0.00 0.00 0.00 3.85
101 102 2.687935 TGAGCTTGTTTGAACTTGGGTC 59.312 45.455 0.00 0.00 0.00 4.46
102 103 2.689983 CTGAGCTTGTTTGAACTTGGGT 59.310 45.455 0.00 0.00 0.00 4.51
117 318 1.617018 TATCAAGTGCGGGCTGAGCT 61.617 55.000 3.72 0.00 35.28 4.09
129 330 4.394300 GCATCTGCACACTCTTTATCAAGT 59.606 41.667 0.00 0.00 41.59 3.16
232 440 4.142902 CCATCTTGCCACTAGTTTTACGTG 60.143 45.833 0.00 0.00 0.00 4.49
234 442 3.181510 GCCATCTTGCCACTAGTTTTACG 60.182 47.826 0.00 0.00 0.00 3.18
247 455 0.038892 CCACAACAGTGCCATCTTGC 60.039 55.000 0.00 0.00 31.87 4.01
248 456 1.267806 GTCCACAACAGTGCCATCTTG 59.732 52.381 0.00 0.00 31.87 3.02
249 457 1.133823 TGTCCACAACAGTGCCATCTT 60.134 47.619 0.00 0.00 32.81 2.40
250 458 0.473755 TGTCCACAACAGTGCCATCT 59.526 50.000 0.00 0.00 32.81 2.90
277 485 5.254032 AGTCAATCTCTTGGGGAGGTTTTAT 59.746 40.000 0.00 0.00 42.22 1.40
296 504 4.515191 GGCTTGTCTGTATTGTGAAGTCAA 59.485 41.667 0.00 0.00 0.00 3.18
300 508 4.095483 GGATGGCTTGTCTGTATTGTGAAG 59.905 45.833 0.00 0.00 0.00 3.02
337 545 3.148412 GGACGGAGGGAGTAGAATAGAC 58.852 54.545 0.00 0.00 0.00 2.59
346 554 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
347 555 6.368779 TTTTATATTATGGGACGGAGGGAG 57.631 41.667 0.00 0.00 0.00 4.30
348 556 6.536447 GTTTTTATATTATGGGACGGAGGGA 58.464 40.000 0.00 0.00 0.00 4.20
349 557 5.410439 CGTTTTTATATTATGGGACGGAGGG 59.590 44.000 0.00 0.00 0.00 4.30
350 558 5.993441 ACGTTTTTATATTATGGGACGGAGG 59.007 40.000 0.00 0.00 33.95 4.30
351 559 7.486802 AACGTTTTTATATTATGGGACGGAG 57.513 36.000 0.00 0.00 33.95 4.63
352 560 7.862512 AAACGTTTTTATATTATGGGACGGA 57.137 32.000 7.96 0.00 33.95 4.69
353 561 8.800031 CAAAAACGTTTTTATATTATGGGACGG 58.200 33.333 32.12 15.00 38.23 4.79
354 562 9.557338 TCAAAAACGTTTTTATATTATGGGACG 57.443 29.630 32.12 18.06 38.23 4.79
383 591 7.584108 TCATCTTTGTGTTTGCACTAATGTAG 58.416 34.615 0.00 0.00 45.44 2.74
384 592 7.503521 TCATCTTTGTGTTTGCACTAATGTA 57.496 32.000 0.00 0.00 45.44 2.29
385 593 6.389830 TCATCTTTGTGTTTGCACTAATGT 57.610 33.333 0.00 0.00 45.44 2.71
386 594 6.696583 TGTTCATCTTTGTGTTTGCACTAATG 59.303 34.615 0.00 0.00 45.44 1.90
387 595 6.804677 TGTTCATCTTTGTGTTTGCACTAAT 58.195 32.000 0.00 0.00 45.44 1.73
388 596 6.201226 TGTTCATCTTTGTGTTTGCACTAA 57.799 33.333 0.00 0.00 45.44 2.24
389 597 5.826601 TGTTCATCTTTGTGTTTGCACTA 57.173 34.783 0.00 0.00 45.44 2.74
390 598 4.717233 TGTTCATCTTTGTGTTTGCACT 57.283 36.364 0.00 0.00 45.44 4.40
391 599 4.805192 ACATGTTCATCTTTGTGTTTGCAC 59.195 37.500 0.00 0.00 45.44 4.57
392 600 4.804665 CACATGTTCATCTTTGTGTTTGCA 59.195 37.500 0.00 0.00 0.00 4.08
393 601 4.318263 GCACATGTTCATCTTTGTGTTTGC 60.318 41.667 0.00 0.00 0.00 3.68
394 602 4.804665 TGCACATGTTCATCTTTGTGTTTG 59.195 37.500 0.00 0.00 0.00 2.93
395 603 5.008619 TGCACATGTTCATCTTTGTGTTT 57.991 34.783 0.00 0.00 0.00 2.83
396 604 4.652421 TGCACATGTTCATCTTTGTGTT 57.348 36.364 0.00 0.00 0.00 3.32
397 605 4.652421 TTGCACATGTTCATCTTTGTGT 57.348 36.364 0.00 0.00 0.00 3.72
398 606 4.085466 CGTTTGCACATGTTCATCTTTGTG 60.085 41.667 0.00 0.00 0.00 3.33
399 607 4.043750 CGTTTGCACATGTTCATCTTTGT 58.956 39.130 0.00 0.00 0.00 2.83
400 608 3.121261 GCGTTTGCACATGTTCATCTTTG 60.121 43.478 0.00 0.00 42.15 2.77
401 609 3.052036 GCGTTTGCACATGTTCATCTTT 58.948 40.909 0.00 0.00 42.15 2.52
402 610 2.664916 GCGTTTGCACATGTTCATCTT 58.335 42.857 0.00 0.00 42.15 2.40
403 611 1.400113 CGCGTTTGCACATGTTCATCT 60.400 47.619 0.00 0.00 42.97 2.90
404 612 0.976963 CGCGTTTGCACATGTTCATC 59.023 50.000 0.00 0.00 42.97 2.92
405 613 0.590682 TCGCGTTTGCACATGTTCAT 59.409 45.000 5.77 0.00 42.97 2.57
406 614 0.316607 GTCGCGTTTGCACATGTTCA 60.317 50.000 5.77 0.00 42.97 3.18
407 615 1.320382 CGTCGCGTTTGCACATGTTC 61.320 55.000 5.77 0.00 42.97 3.18
428 636 5.122711 CACATCACTGTCTTATGCATGTTCA 59.877 40.000 10.16 2.72 31.62 3.18
441 649 3.257393 GAGTCATCACCACATCACTGTC 58.743 50.000 0.00 0.00 31.62 3.51
600 814 1.507141 GGTTTCTGGCGTGTCCTGTG 61.507 60.000 0.00 0.00 35.49 3.66
621 835 6.618287 AAAACATATCGTACCCATGTCATG 57.382 37.500 5.79 5.79 31.82 3.07
732 946 1.083209 GGCGTCCGACGTTTGAAAC 60.083 57.895 21.37 0.00 44.73 2.78
804 1021 1.071987 CAAGGCTGCAGTGGAGACA 59.928 57.895 20.80 0.00 38.70 3.41
1128 1345 3.744660 AGTTGAAACTGGCGAAGAGAAT 58.255 40.909 0.00 0.00 37.98 2.40
1140 1357 0.111253 CAGAGGGCCCAGTTGAAACT 59.889 55.000 27.56 0.00 40.60 2.66
1224 1441 0.523072 CTTTCAACATGGGTGCTCCG 59.477 55.000 0.00 0.00 38.76 4.63
1226 1446 2.229784 CCTTCTTTCAACATGGGTGCTC 59.770 50.000 0.00 0.00 0.00 4.26
1671 1891 4.054671 CCTCTCAACTTGTTGAGTCAGAC 58.945 47.826 30.49 0.00 46.37 3.51
1845 2093 3.592059 CCGGAAGATTGTAAAGGTTCGA 58.408 45.455 0.00 0.00 0.00 3.71
2068 2320 9.476202 GCATGGTTACTTCTTCAAACTATTTTT 57.524 29.630 0.00 0.00 0.00 1.94
2080 2332 6.265196 TCTTTGATGTTGCATGGTTACTTCTT 59.735 34.615 0.00 0.00 0.00 2.52
2125 2377 9.649167 AAAAAGAAGGAATCTGCATAATCAAAG 57.351 29.630 0.00 0.00 38.79 2.77
2168 2420 7.888546 AGTTTGCCTTATGGTTTATTCTGTAGT 59.111 33.333 0.00 0.00 35.27 2.73
2187 2439 7.201609 CCTTTCCTTTCAACTTTTTAGTTTGCC 60.202 37.037 0.00 0.00 0.00 4.52
2209 2461 6.670695 AAGTATTCATGTTTGCTTCCCTTT 57.329 33.333 0.00 0.00 0.00 3.11
2301 2553 7.575414 AATTACCATTCGGCATGTTGTTATA 57.425 32.000 0.00 0.00 34.57 0.98
2313 2565 3.130340 CCAACCCAGAAATTACCATTCGG 59.870 47.826 0.00 0.00 38.77 4.30
2315 2567 3.428862 CGCCAACCCAGAAATTACCATTC 60.429 47.826 0.00 0.00 0.00 2.67
2342 2594 5.241506 TCTCAGGAAAAGATTTGTTTCGCAT 59.758 36.000 0.00 0.00 36.11 4.73
2345 2597 5.909610 GTGTCTCAGGAAAAGATTTGTTTCG 59.090 40.000 0.00 0.00 36.11 3.46
2472 2724 4.064388 TGTTGTACATGTGACATGTGAGG 58.936 43.478 34.35 9.64 33.76 3.86
2474 2726 7.626028 GCATAATGTTGTACATGTGACATGTGA 60.626 37.037 34.35 21.02 37.97 3.58
2489 2741 9.573166 TGGCTATATCTTTAAGCATAATGTTGT 57.427 29.630 0.00 0.00 38.01 3.32
2523 2775 8.792830 TCAATCTGCTTTAGCTGTTAAATAGT 57.207 30.769 0.00 0.00 42.66 2.12
2531 2783 6.017275 GCATAGAATCAATCTGCTTTAGCTGT 60.017 38.462 0.00 0.00 42.66 4.40
2545 2797 6.979465 TGTCATTGTTGTTGCATAGAATCAA 58.021 32.000 0.00 0.00 0.00 2.57
2547 2799 7.872163 TTTGTCATTGTTGTTGCATAGAATC 57.128 32.000 0.00 0.00 0.00 2.52
2555 2808 8.710551 TGATTGAATATTTGTCATTGTTGTTGC 58.289 29.630 0.00 0.00 0.00 4.17
2602 3013 9.442062 TTCCTCTACATCAGTATATTTGGGTAA 57.558 33.333 0.00 0.00 0.00 2.85
2631 3042 0.332632 AGCTTGGCTGCCATTAGGAA 59.667 50.000 24.03 5.13 37.57 3.36
2656 3067 2.223876 CCAATCAAGTTTGCACTGCACT 60.224 45.455 2.26 0.00 38.71 4.40
2657 3068 2.129607 CCAATCAAGTTTGCACTGCAC 58.870 47.619 2.26 0.00 38.71 4.57
2658 3069 1.538634 GCCAATCAAGTTTGCACTGCA 60.539 47.619 0.00 0.00 36.47 4.41
2659 3070 1.142474 GCCAATCAAGTTTGCACTGC 58.858 50.000 0.00 0.00 31.60 4.40
2660 3071 2.512485 TGCCAATCAAGTTTGCACTG 57.488 45.000 0.00 0.00 31.60 3.66
2661 3072 2.289195 CCATGCCAATCAAGTTTGCACT 60.289 45.455 0.00 0.00 33.11 4.40
2662 3073 2.070783 CCATGCCAATCAAGTTTGCAC 58.929 47.619 0.00 0.00 0.00 4.57
2663 3074 1.608542 GCCATGCCAATCAAGTTTGCA 60.609 47.619 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.