Multiple sequence alignment - TraesCS5A01G066500

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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 TraesCS5A01G066500 chr5A 100.000 4739 0 0 1 4739 74476882 74481620 0.000000e+00 8752
1 TraesCS5A01G066500 chr5A 73.913 1035 219 27 1233 2243 595144392 595145399 7.490000e-98 368
2 TraesCS5A01G066500 chr5D 94.578 4795 132 46 1 4739 77576559 77581281 0.000000e+00 7297
3 TraesCS5A01G066500 chr5D 73.694 1110 239 38 1466 2541 475692570 475693660 2.680000e-102 383
4 TraesCS5A01G066500 chr5B 94.281 4406 139 40 396 4739 87228123 87232477 0.000000e+00 6636
5 TraesCS5A01G066500 chr5B 89.779 362 10 15 1 355 87227778 87228119 5.630000e-119 438
6 TraesCS5A01G066500 chr5B 76.309 802 155 24 1456 2232 583176615 583177406 3.440000e-106 396
7 TraesCS5A01G066500 chr5B 93.939 132 7 1 4608 4739 672545669 672545539 1.040000e-46 198
8 TraesCS5A01G066500 chr6B 94.697 132 6 1 4608 4739 599816942 599817072 2.240000e-48 204
9 TraesCS5A01G066500 chr2B 94.697 132 6 1 4608 4739 183539326 183539196 2.240000e-48 204


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 TraesCS5A01G066500 chr5A 74476882 74481620 4738 False 8752 8752 100.000 1 4739 1 chr5A.!!$F1 4738
1 TraesCS5A01G066500 chr5A 595144392 595145399 1007 False 368 368 73.913 1233 2243 1 chr5A.!!$F2 1010
2 TraesCS5A01G066500 chr5D 77576559 77581281 4722 False 7297 7297 94.578 1 4739 1 chr5D.!!$F1 4738
3 TraesCS5A01G066500 chr5D 475692570 475693660 1090 False 383 383 73.694 1466 2541 1 chr5D.!!$F2 1075
4 TraesCS5A01G066500 chr5B 87227778 87232477 4699 False 3537 6636 92.030 1 4739 2 chr5B.!!$F2 4738
5 TraesCS5A01G066500 chr5B 583176615 583177406 791 False 396 396 76.309 1456 2232 1 chr5B.!!$F1 776

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
681 716 0.036388 AAGCTCCGAGAAAATCCGCA 60.036 50.0 0.0 0.0 0.00 5.69 F
752 801 0.541764 TGTTCTTGGTTGATGGGGGC 60.542 55.0 0.0 0.0 0.00 5.80 F
889 948 0.611896 CACCACCCACCCAGAAATCC 60.612 60.0 0.0 0.0 0.00 3.01 F
2322 2423 0.904649 ATCCAGTGCCTGATGTTCGA 59.095 50.0 4.0 0.0 32.44 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2382 2486 0.613777 GACCCGGGTCACTCTCAAAT 59.386 55.0 42.54 10.45 44.02 2.32 R
2487 2591 0.674895 AACAGTCCTCGCTGAATGCC 60.675 55.0 0.00 0.00 39.62 4.40 R
3108 3212 6.745794 TCATCATACCCATCACTTACATCA 57.254 37.5 0.00 0.00 0.00 3.07 R
4184 4295 0.035056 AGTGGAACATAGCAGTGGCC 60.035 55.0 0.00 0.00 44.52 5.36 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
44 45 4.155280 GTGTGACAGTACCAAACACTTTGT 59.845 41.667 10.03 0.00 38.44 2.83
150 162 3.595819 GCTCCAAAGCGAGGCAAT 58.404 55.556 0.00 0.00 39.10 3.56
158 170 0.745845 AAGCGAGGCAATGCAGTAGG 60.746 55.000 7.79 0.00 0.00 3.18
159 171 2.828128 GCGAGGCAATGCAGTAGGC 61.828 63.158 7.79 0.00 45.13 3.93
207 219 3.320129 AGTGTAGTACAAACAGGGGGAA 58.680 45.455 4.11 0.00 0.00 3.97
259 271 2.227194 GTGGTGTTGGTAGTTCTTGGG 58.773 52.381 0.00 0.00 0.00 4.12
260 272 1.244816 GGTGTTGGTAGTTCTTGGGC 58.755 55.000 0.00 0.00 0.00 5.36
355 367 2.841988 AGCGGGGAGGATCTGAGC 60.842 66.667 0.00 0.00 33.73 4.26
356 368 2.841988 GCGGGGAGGATCTGAGCT 60.842 66.667 0.00 0.00 33.73 4.09
357 369 2.866726 GCGGGGAGGATCTGAGCTC 61.867 68.421 6.82 6.82 33.73 4.09
370 382 0.607112 TGAGCTCTGAGTGAAGCCAG 59.393 55.000 16.19 0.00 0.00 4.85
371 383 0.607620 GAGCTCTGAGTGAAGCCAGT 59.392 55.000 6.43 0.00 0.00 4.00
372 384 0.321021 AGCTCTGAGTGAAGCCAGTG 59.679 55.000 6.53 0.00 0.00 3.66
373 385 0.319728 GCTCTGAGTGAAGCCAGTGA 59.680 55.000 6.53 0.00 0.00 3.41
374 386 1.672441 GCTCTGAGTGAAGCCAGTGAG 60.672 57.143 6.53 0.00 0.00 3.51
375 387 1.617850 CTCTGAGTGAAGCCAGTGAGT 59.382 52.381 0.00 0.00 30.37 3.41
385 397 1.735920 CCAGTGAGTGTGAGCGAGC 60.736 63.158 0.00 0.00 0.00 5.03
389 401 2.878520 GAGTGTGAGCGAGCGAGC 60.879 66.667 0.00 0.00 37.41 5.03
403 415 1.486644 GCGAGCGAGCTCCTTTCATC 61.487 60.000 18.19 0.00 39.77 2.92
438 473 3.349927 TGGTTTGAGAGAGCATTGATGG 58.650 45.455 0.00 0.00 0.00 3.51
439 474 2.098770 GGTTTGAGAGAGCATTGATGGC 59.901 50.000 0.00 0.00 0.00 4.40
500 535 2.163211 GGAGTCAAATCTTTGCTGAGGC 59.837 50.000 0.00 0.00 38.05 4.70
507 542 4.780275 AATCTTTGCTGAGGCTTCTTTC 57.220 40.909 0.00 0.00 39.59 2.62
515 550 4.037208 TGCTGAGGCTTCTTTCTTTCTTTG 59.963 41.667 0.00 0.00 39.59 2.77
516 551 4.037327 GCTGAGGCTTCTTTCTTTCTTTGT 59.963 41.667 0.00 0.00 35.22 2.83
517 552 5.451103 GCTGAGGCTTCTTTCTTTCTTTGTT 60.451 40.000 0.00 0.00 35.22 2.83
518 553 6.530019 TGAGGCTTCTTTCTTTCTTTGTTT 57.470 33.333 0.00 0.00 0.00 2.83
573 608 1.665599 CTGCCAAAAGCCAAAGCCG 60.666 57.895 0.00 0.00 42.71 5.52
579 614 0.178990 AAAAGCCAAAGCCGTCTCCT 60.179 50.000 0.00 0.00 41.25 3.69
618 653 2.512885 GAGCGTGTCATTGCATTTCAG 58.487 47.619 0.00 0.00 0.00 3.02
621 656 1.068402 CGTGTCATTGCATTTCAGGCA 60.068 47.619 0.00 0.00 40.00 4.75
622 657 2.416296 CGTGTCATTGCATTTCAGGCAT 60.416 45.455 0.00 0.00 41.58 4.40
623 658 3.592059 GTGTCATTGCATTTCAGGCATT 58.408 40.909 0.00 0.00 41.58 3.56
624 659 3.998341 GTGTCATTGCATTTCAGGCATTT 59.002 39.130 0.00 0.00 41.58 2.32
625 660 4.092383 GTGTCATTGCATTTCAGGCATTTC 59.908 41.667 0.00 0.00 41.58 2.17
626 661 4.247258 GTCATTGCATTTCAGGCATTTCA 58.753 39.130 0.00 0.00 41.58 2.69
627 662 4.691685 GTCATTGCATTTCAGGCATTTCAA 59.308 37.500 0.00 0.00 41.58 2.69
628 663 4.932799 TCATTGCATTTCAGGCATTTCAAG 59.067 37.500 0.00 0.00 41.58 3.02
652 687 1.750399 CCACCCTCCGCCATTTCTG 60.750 63.158 0.00 0.00 0.00 3.02
655 690 1.379044 CCCTCCGCCATTTCTGCTT 60.379 57.895 0.00 0.00 0.00 3.91
657 692 0.677731 CCTCCGCCATTTCTGCTTCA 60.678 55.000 0.00 0.00 0.00 3.02
658 693 1.167851 CTCCGCCATTTCTGCTTCAA 58.832 50.000 0.00 0.00 0.00 2.69
659 694 1.541147 CTCCGCCATTTCTGCTTCAAA 59.459 47.619 0.00 0.00 0.00 2.69
660 695 1.541147 TCCGCCATTTCTGCTTCAAAG 59.459 47.619 0.00 0.00 0.00 2.77
661 696 1.541147 CCGCCATTTCTGCTTCAAAGA 59.459 47.619 0.00 0.00 0.00 2.52
662 697 2.030007 CCGCCATTTCTGCTTCAAAGAA 60.030 45.455 0.00 0.00 31.85 2.52
663 698 3.552684 CCGCCATTTCTGCTTCAAAGAAA 60.553 43.478 1.45 1.45 45.17 2.52
664 699 3.671928 CGCCATTTCTGCTTCAAAGAAAG 59.328 43.478 5.04 0.00 44.52 2.62
681 716 0.036388 AAGCTCCGAGAAAATCCGCA 60.036 50.000 0.00 0.00 0.00 5.69
690 725 1.203001 AGAAAATCCGCAGTTTCCCCA 60.203 47.619 0.00 0.00 37.31 4.96
699 734 2.026905 GCAGTTTCCCCACCTCAAACA 61.027 52.381 0.00 0.00 33.26 2.83
717 766 1.421268 ACACTGAGATTTCTGCACCCA 59.579 47.619 0.00 0.00 0.00 4.51
723 772 0.895100 GATTTCTGCACCCACAGCCA 60.895 55.000 0.00 0.00 37.59 4.75
746 795 1.620822 GGCCACTGTTCTTGGTTGAT 58.379 50.000 0.00 0.00 36.40 2.57
747 796 1.270550 GGCCACTGTTCTTGGTTGATG 59.729 52.381 0.00 0.00 36.40 3.07
748 797 1.270550 GCCACTGTTCTTGGTTGATGG 59.729 52.381 0.00 0.00 36.40 3.51
749 798 1.888512 CCACTGTTCTTGGTTGATGGG 59.111 52.381 0.00 0.00 0.00 4.00
750 799 1.888512 CACTGTTCTTGGTTGATGGGG 59.111 52.381 0.00 0.00 0.00 4.96
751 800 1.203050 ACTGTTCTTGGTTGATGGGGG 60.203 52.381 0.00 0.00 0.00 5.40
752 801 0.541764 TGTTCTTGGTTGATGGGGGC 60.542 55.000 0.00 0.00 0.00 5.80
753 802 1.304052 TTCTTGGTTGATGGGGGCG 60.304 57.895 0.00 0.00 0.00 6.13
754 803 3.451894 CTTGGTTGATGGGGGCGC 61.452 66.667 0.00 0.00 0.00 6.53
755 804 3.944250 CTTGGTTGATGGGGGCGCT 62.944 63.158 7.64 0.00 0.00 5.92
756 805 3.936772 TTGGTTGATGGGGGCGCTC 62.937 63.158 7.64 1.18 0.00 5.03
771 820 1.021390 CGCTCGGGCTCTGACATTTT 61.021 55.000 5.36 0.00 36.09 1.82
772 821 0.729690 GCTCGGGCTCTGACATTTTC 59.270 55.000 0.00 0.00 35.22 2.29
773 822 1.677217 GCTCGGGCTCTGACATTTTCT 60.677 52.381 0.00 0.00 35.22 2.52
774 823 2.005451 CTCGGGCTCTGACATTTTCTG 58.995 52.381 0.00 0.00 0.00 3.02
775 824 1.623311 TCGGGCTCTGACATTTTCTGA 59.377 47.619 0.00 0.00 0.00 3.27
776 825 2.237143 TCGGGCTCTGACATTTTCTGAT 59.763 45.455 0.00 0.00 32.19 2.90
790 839 6.379417 ACATTTTCTGATCCCCATTTTCTCTC 59.621 38.462 0.00 0.00 0.00 3.20
889 948 0.611896 CACCACCCACCCAGAAATCC 60.612 60.000 0.00 0.00 0.00 3.01
2319 2420 3.499338 TGAAAATCCAGTGCCTGATGTT 58.501 40.909 4.00 0.00 32.44 2.71
2322 2423 0.904649 ATCCAGTGCCTGATGTTCGA 59.095 50.000 4.00 0.00 32.44 3.71
2397 2501 2.232452 AGAGACATTTGAGAGTGACCCG 59.768 50.000 0.00 0.00 0.00 5.28
2487 2591 2.060383 TGAGGTGATGAGGAGCCCG 61.060 63.158 0.00 0.00 0.00 6.13
3108 3212 6.169094 GTCTGGATATCCATTTCGTGATGAT 58.831 40.000 24.73 0.00 46.46 2.45
3183 3293 5.002464 AGATAATTTGCAGGCACATTGAC 57.998 39.130 14.15 8.75 30.26 3.18
3189 3299 0.171903 GCAGGCACATTGACCATGTC 59.828 55.000 0.00 0.00 43.17 3.06
3539 3649 6.404293 GCTTCCTTTTATAAGAATGGTCGCAA 60.404 38.462 0.00 0.00 32.92 4.85
3675 3785 1.347707 TCATTCCTGGAAAGTGAGCGT 59.652 47.619 14.03 0.00 0.00 5.07
3705 3815 2.019156 GCTACTGACCAAATGGAGGCC 61.019 57.143 6.42 0.00 38.94 5.19
3753 3863 7.428020 GGCAAATTTGAGCTTGATGTATGATA 58.572 34.615 22.31 0.00 0.00 2.15
3947 4058 4.998671 CTCATCAGTAGAGCTCCTTTCA 57.001 45.455 10.93 0.00 0.00 2.69
4007 4118 8.220755 TGAAATAGTTTTGAGTGCTTTGTACT 57.779 30.769 0.00 0.00 0.00 2.73
4041 4152 4.157105 TCATGATGCAGTTTTCACATCCTG 59.843 41.667 0.00 0.00 39.55 3.86
4043 4154 3.503363 TGATGCAGTTTTCACATCCTGTC 59.497 43.478 0.00 0.00 39.55 3.51
4051 4162 7.327032 GCAGTTTTCACATCCTGTCTTAAAATC 59.673 37.037 0.00 0.00 0.00 2.17
4057 4168 6.934645 TCACATCCTGTCTTAAAATCGTCTTT 59.065 34.615 0.00 0.00 0.00 2.52
4059 4170 7.535258 CACATCCTGTCTTAAAATCGTCTTTTG 59.465 37.037 8.17 0.00 0.00 2.44
4062 4173 7.806690 TCCTGTCTTAAAATCGTCTTTTGATG 58.193 34.615 8.17 0.00 36.81 3.07
4081 4192 6.137794 TGATGTATTTTTGTTCGTGGTTGT 57.862 33.333 0.00 0.00 0.00 3.32
4137 4248 9.590451 CTTTTATAATCAATCAATGTTGCTGGT 57.410 29.630 0.00 0.00 0.00 4.00
4143 4254 4.022935 TCAATCAATGTTGCTGGTTGACTC 60.023 41.667 0.00 0.00 34.98 3.36
4162 4273 6.070656 TGACTCTCCTTTTTGTTCATGGAAT 58.929 36.000 0.00 0.00 0.00 3.01
4188 4299 1.656587 ACTGAGAATAGTGTGGGCCA 58.343 50.000 0.00 0.00 0.00 5.36
4208 4320 3.614092 CACTGCTATGTTCCACTTCCAT 58.386 45.455 0.00 0.00 0.00 3.41
4228 4340 9.709495 CTTCCATTTTGATTTTATTCCAGTCAA 57.291 29.630 0.00 0.00 0.00 3.18
4279 4391 8.055279 TGAAATAGAACCATTCAGTTGGATTC 57.945 34.615 0.00 0.00 39.25 2.52
4287 4399 5.106157 ACCATTCAGTTGGATTCGAAATGTC 60.106 40.000 0.00 0.00 39.25 3.06
4458 4570 6.126536 ACCTGATCTGAAGAAGCATTAGGAAT 60.127 38.462 0.38 0.00 30.45 3.01
4563 4675 3.624861 CAGTGGGCTCACATGAATAAGAC 59.375 47.826 21.13 0.00 45.91 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.155280 ACAAAGTGTTTGGTACTGTCACAC 59.845 41.667 4.52 8.99 44.81 3.82
120 132 3.311966 CTTTGGAGCTGCAAAAGTAAGC 58.688 45.455 29.71 0.00 37.20 3.09
166 178 1.004080 ACCACTGCTGCAGCTACTG 60.004 57.895 36.61 26.38 42.66 2.74
169 181 1.294459 CTCACCACTGCTGCAGCTA 59.706 57.895 36.61 22.60 42.66 3.32
177 189 3.380479 TTGTACTACACTCACCACTGC 57.620 47.619 0.00 0.00 0.00 4.40
178 190 4.689071 TGTTTGTACTACACTCACCACTG 58.311 43.478 0.00 0.00 0.00 3.66
180 192 4.056050 CCTGTTTGTACTACACTCACCAC 58.944 47.826 0.00 0.00 0.00 4.16
181 193 3.070446 CCCTGTTTGTACTACACTCACCA 59.930 47.826 0.00 0.00 0.00 4.17
207 219 6.194967 TCACTCTCCTTTTCCTTTCCTTTTT 58.805 36.000 0.00 0.00 0.00 1.94
218 230 4.035675 CACACCAACTTCACTCTCCTTTTC 59.964 45.833 0.00 0.00 0.00 2.29
223 235 1.141053 ACCACACCAACTTCACTCTCC 59.859 52.381 0.00 0.00 0.00 3.71
229 241 1.272203 ACCAACACCACACCAACTTCA 60.272 47.619 0.00 0.00 0.00 3.02
259 271 0.460109 GGGGTTGCATTCATTTCCGC 60.460 55.000 0.00 0.00 0.00 5.54
260 272 0.175531 GGGGGTTGCATTCATTTCCG 59.824 55.000 0.00 0.00 0.00 4.30
301 313 3.977244 GTGGTTTGGGGCGCACTG 61.977 66.667 10.74 0.00 0.00 3.66
309 321 3.411351 CGTCGCGAGTGGTTTGGG 61.411 66.667 10.24 0.00 0.00 4.12
355 367 1.617850 ACTCACTGGCTTCACTCAGAG 59.382 52.381 0.00 0.00 35.20 3.35
356 368 1.342496 CACTCACTGGCTTCACTCAGA 59.658 52.381 0.00 0.00 35.20 3.27
357 369 1.069823 ACACTCACTGGCTTCACTCAG 59.930 52.381 0.00 0.00 37.07 3.35
370 382 1.799519 CTCGCTCGCTCACACTCAC 60.800 63.158 0.00 0.00 0.00 3.51
371 383 2.563427 CTCGCTCGCTCACACTCA 59.437 61.111 0.00 0.00 0.00 3.41
372 384 2.878520 GCTCGCTCGCTCACACTC 60.879 66.667 0.00 0.00 0.00 3.51
373 385 4.767841 CGCTCGCTCGCTCACACT 62.768 66.667 0.00 0.00 0.00 3.55
374 386 4.760840 TCGCTCGCTCGCTCACAC 62.761 66.667 0.00 0.00 0.00 3.82
375 387 4.467062 CTCGCTCGCTCGCTCACA 62.467 66.667 0.00 0.00 0.00 3.58
385 397 0.102120 AGATGAAAGGAGCTCGCTCG 59.898 55.000 7.83 0.00 43.59 5.03
389 401 1.753649 TCCAGAGATGAAAGGAGCTCG 59.246 52.381 7.83 0.00 32.80 5.03
438 473 0.954452 CACCACCACCAAGAAGAAGC 59.046 55.000 0.00 0.00 0.00 3.86
439 474 1.133792 ACCACCACCACCAAGAAGAAG 60.134 52.381 0.00 0.00 0.00 2.85
507 542 8.628630 AGAGGGATAGAAAGAAACAAAGAAAG 57.371 34.615 0.00 0.00 0.00 2.62
655 690 4.455877 GGATTTTCTCGGAGCTTTCTTTGA 59.544 41.667 0.00 0.00 0.00 2.69
657 692 3.437049 CGGATTTTCTCGGAGCTTTCTTT 59.563 43.478 0.00 0.00 0.00 2.52
658 693 3.003480 CGGATTTTCTCGGAGCTTTCTT 58.997 45.455 0.00 0.00 0.00 2.52
659 694 2.622436 CGGATTTTCTCGGAGCTTTCT 58.378 47.619 0.00 0.00 0.00 2.52
660 695 1.062733 GCGGATTTTCTCGGAGCTTTC 59.937 52.381 0.00 0.00 0.00 2.62
661 696 1.087501 GCGGATTTTCTCGGAGCTTT 58.912 50.000 0.00 0.00 0.00 3.51
662 697 0.036388 TGCGGATTTTCTCGGAGCTT 60.036 50.000 0.00 0.00 0.00 3.74
663 698 0.460987 CTGCGGATTTTCTCGGAGCT 60.461 55.000 0.00 0.00 37.94 4.09
664 699 0.741221 ACTGCGGATTTTCTCGGAGC 60.741 55.000 0.00 0.00 46.22 4.70
681 716 1.569072 AGTGTTTGAGGTGGGGAAACT 59.431 47.619 0.00 0.00 32.01 2.66
699 734 1.421268 TGTGGGTGCAGAAATCTCAGT 59.579 47.619 0.00 0.00 0.00 3.41
723 772 2.281761 CAAGAACAGTGGCCGGCT 60.282 61.111 28.56 4.40 0.00 5.52
751 800 4.521062 ATGTCAGAGCCCGAGCGC 62.521 66.667 0.00 0.00 46.67 5.92
752 801 1.021390 AAAATGTCAGAGCCCGAGCG 61.021 55.000 0.00 0.00 46.67 5.03
753 802 0.729690 GAAAATGTCAGAGCCCGAGC 59.270 55.000 0.00 0.00 40.32 5.03
754 803 2.005451 CAGAAAATGTCAGAGCCCGAG 58.995 52.381 0.00 0.00 0.00 4.63
755 804 1.623311 TCAGAAAATGTCAGAGCCCGA 59.377 47.619 0.00 0.00 0.00 5.14
756 805 2.099141 TCAGAAAATGTCAGAGCCCG 57.901 50.000 0.00 0.00 0.00 6.13
771 820 2.780010 GGGAGAGAAAATGGGGATCAGA 59.220 50.000 0.00 0.00 0.00 3.27
772 821 2.158549 GGGGAGAGAAAATGGGGATCAG 60.159 54.545 0.00 0.00 0.00 2.90
773 822 1.852965 GGGGAGAGAAAATGGGGATCA 59.147 52.381 0.00 0.00 0.00 2.92
774 823 1.145945 GGGGGAGAGAAAATGGGGATC 59.854 57.143 0.00 0.00 0.00 3.36
775 824 1.235756 GGGGGAGAGAAAATGGGGAT 58.764 55.000 0.00 0.00 0.00 3.85
776 825 2.723305 GGGGGAGAGAAAATGGGGA 58.277 57.895 0.00 0.00 0.00 4.81
992 1072 2.879070 GAGAGATGCATGTGCCGCG 61.879 63.158 2.46 0.00 41.18 6.46
1071 1151 4.465446 CCTCCTCCTCCTCCGCCA 62.465 72.222 0.00 0.00 0.00 5.69
1869 1970 2.436109 GCCTTCCTCTTGCCCACA 59.564 61.111 0.00 0.00 0.00 4.17
2319 2420 1.664649 CAGCTGTGAGCCGTTTCGA 60.665 57.895 5.25 0.00 43.77 3.71
2322 2423 2.980233 GGCAGCTGTGAGCCGTTT 60.980 61.111 16.64 0.00 43.77 3.60
2382 2486 0.613777 GACCCGGGTCACTCTCAAAT 59.386 55.000 42.54 10.45 44.02 2.32
2397 2501 2.433318 GAGCTGCTGTCACGACCC 60.433 66.667 7.01 0.00 0.00 4.46
2487 2591 0.674895 AACAGTCCTCGCTGAATGCC 60.675 55.000 0.00 0.00 39.62 4.40
3108 3212 6.745794 TCATCATACCCATCACTTACATCA 57.254 37.500 0.00 0.00 0.00 3.07
3183 3293 1.280133 AGCCCCATCATATCGACATGG 59.720 52.381 3.42 5.77 37.42 3.66
3189 3299 2.037641 TCTGTTGAGCCCCATCATATCG 59.962 50.000 0.00 0.00 0.00 2.92
3675 3785 5.366482 TTTGGTCAGTAGCTATGGCAATA 57.634 39.130 3.10 0.00 41.70 1.90
3753 3863 7.002879 CCTTCCACTCCTTCATTGATCAATAT 58.997 38.462 20.32 0.00 0.00 1.28
3757 3867 3.588842 ACCTTCCACTCCTTCATTGATCA 59.411 43.478 0.00 0.00 0.00 2.92
3947 4058 5.519927 GCTGCTTTACAAACATTGTTCAGTT 59.480 36.000 1.83 0.00 42.22 3.16
4007 4118 3.827876 ACTGCATCATGAACACATTCCAA 59.172 39.130 0.00 0.00 33.49 3.53
4051 4162 7.357206 CCACGAACAAAAATACATCAAAAGACG 60.357 37.037 0.00 0.00 0.00 4.18
4057 4168 6.565234 ACAACCACGAACAAAAATACATCAA 58.435 32.000 0.00 0.00 0.00 2.57
4059 4170 6.561350 GCAACAACCACGAACAAAAATACATC 60.561 38.462 0.00 0.00 0.00 3.06
4062 4173 4.801516 AGCAACAACCACGAACAAAAATAC 59.198 37.500 0.00 0.00 0.00 1.89
4073 4184 3.765026 ACAACTTTAAGCAACAACCACG 58.235 40.909 0.00 0.00 0.00 4.94
4104 4215 5.666969 TGATTGATTATAAAAGGTCGGCG 57.333 39.130 0.00 0.00 0.00 6.46
4115 4226 8.190122 GTCAACCAGCAACATTGATTGATTATA 58.810 33.333 0.00 0.00 34.98 0.98
4137 4248 5.445069 TCCATGAACAAAAAGGAGAGTCAA 58.555 37.500 0.00 0.00 0.00 3.18
4143 4254 6.016024 TGTGAGATTCCATGAACAAAAAGGAG 60.016 38.462 0.00 0.00 0.00 3.69
4184 4295 0.035056 AGTGGAACATAGCAGTGGCC 60.035 55.000 0.00 0.00 44.52 5.36
4188 4299 4.307032 AATGGAAGTGGAACATAGCAGT 57.693 40.909 0.00 0.00 44.52 4.40
4191 4302 5.643379 TCAAAATGGAAGTGGAACATAGC 57.357 39.130 0.00 0.00 44.52 2.97
4195 4306 9.487790 GAATAAAATCAAAATGGAAGTGGAACA 57.512 29.630 0.00 0.00 41.43 3.18
4228 4340 7.322664 ACAAGACAAAAACATGTTGAACAGAT 58.677 30.769 12.82 0.00 32.57 2.90
4279 4391 8.912787 AAGTGATAGTACTTACAGACATTTCG 57.087 34.615 0.00 0.00 39.03 3.46
4287 4399 9.360093 CAAGAAGGAAAGTGATAGTACTTACAG 57.640 37.037 0.00 0.00 39.86 2.74


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

AutoCloner maintained by Alex Coulton.