Multiple sequence alignment - TraesCS2A01G459900

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 TraesCS2A01G459900 chr2A 100.000 3424 0 0 1 3424 706743787 706740364 0.000000e+00 6324
1 TraesCS2A01G459900 chr2A 91.656 755 38 10 1716 2445 706644620 706643866 0.000000e+00 1022
2 TraesCS2A01G459900 chr2A 87.228 689 65 14 459 1139 706645667 706644994 0.000000e+00 763
3 TraesCS2A01G459900 chr2B 91.208 2832 189 37 7 2815 679887643 679884849 0.000000e+00 3795
4 TraesCS2A01G459900 chr2B 92.236 747 34 6 1716 2440 679816094 679815350 0.000000e+00 1037
5 TraesCS2A01G459900 chr2B 91.734 617 49 2 2810 3424 679884604 679883988 0.000000e+00 856
6 TraesCS2A01G459900 chr2B 87.278 676 58 16 476 1139 679819499 679818840 0.000000e+00 747
7 TraesCS2A01G459900 chr2D 94.718 1382 60 7 1266 2643 566981039 566979667 0.000000e+00 2135
8 TraesCS2A01G459900 chr2D 92.118 812 31 15 465 1267 566981987 566981200 0.000000e+00 1114
9 TraesCS2A01G459900 chr2D 92.318 755 33 6 1716 2445 566836050 566835296 0.000000e+00 1050
10 TraesCS2A01G459900 chr2D 87.410 691 63 15 459 1139 566838270 566837594 0.000000e+00 773
11 TraesCS2A01G459900 chr2D 84.043 470 48 16 1 465 566982463 566982016 8.780000e-116 427
12 TraesCS2A01G459900 chr6D 83.480 454 64 9 2833 3277 83059387 83059838 2.460000e-111 412
13 TraesCS2A01G459900 chr6A 83.516 182 27 1 3099 3277 100095814 100095995 2.110000e-37 167


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 TraesCS2A01G459900 chr2A 706740364 706743787 3423 True 6324.000000 6324 100.000 1 3424 1 chr2A.!!$R1 3423
1 TraesCS2A01G459900 chr2A 706643866 706645667 1801 True 892.500000 1022 89.442 459 2445 2 chr2A.!!$R2 1986
2 TraesCS2A01G459900 chr2B 679883988 679887643 3655 True 2325.500000 3795 91.471 7 3424 2 chr2B.!!$R2 3417
3 TraesCS2A01G459900 chr2B 679815350 679819499 4149 True 892.000000 1037 89.757 476 2440 2 chr2B.!!$R1 1964
4 TraesCS2A01G459900 chr2D 566979667 566982463 2796 True 1225.333333 2135 90.293 1 2643 3 chr2D.!!$R2 2642
5 TraesCS2A01G459900 chr2D 566835296 566838270 2974 True 911.500000 1050 89.864 459 2445 2 chr2D.!!$R1 1986

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
228 230 0.394192 CGATGCAGAGGGCCTGATTA 59.606 55.0 12.95 0.0 45.78 1.75 F
1089 1150 0.389948 GTGTTCTGGCTACTGACCCG 60.390 60.0 0.00 0.0 0.00 5.28 F
1091 1152 0.173708 GTTCTGGCTACTGACCCGAG 59.826 60.0 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1091 1152 1.078567 CAGAAGTCCTGGAGCTGGC 60.079 63.158 0.00 0.0 39.23 4.85 R
2270 5311 0.250814 AGTCGACGGTGTCCTTCTCT 60.251 55.000 10.46 0.0 0.00 3.10 R
2507 5574 0.518636 CGATCCACAAACACCTGCTG 59.481 55.000 0.00 0.0 0.00 4.41 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
24 25 4.546829 AGTATTCGTTGCTCTTTGGGTA 57.453 40.909 0.00 0.00 0.00 3.69
47 48 2.403252 CCAGTTGGAGATGGTACCAC 57.597 55.000 19.09 11.46 37.39 4.16
51 52 0.545787 TTGGAGATGGTACCACGGGT 60.546 55.000 19.09 0.00 40.16 5.28
86 87 4.521639 AGTGTGAGTGACGACCTAACAATA 59.478 41.667 0.00 0.00 0.00 1.90
142 144 8.339714 GCGGTAGTAATATATTGTGCTTTTGAA 58.660 33.333 8.28 0.00 0.00 2.69
191 193 8.902540 AGAACGGATACTTTGCAATCAATATA 57.097 30.769 0.00 0.00 31.33 0.86
198 200 9.956720 GATACTTTGCAATCAATATAAAGCTGT 57.043 29.630 0.00 0.00 32.97 4.40
223 225 1.147824 CAATCGATGCAGAGGGCCT 59.852 57.895 5.25 5.25 43.89 5.19
228 230 0.394192 CGATGCAGAGGGCCTGATTA 59.606 55.000 12.95 0.00 45.78 1.75
231 233 3.494332 GATGCAGAGGGCCTGATTAATT 58.506 45.455 12.95 0.00 45.78 1.40
304 310 8.987890 GTTGTAAAGCATAAAAACATTCCACAT 58.012 29.630 0.00 0.00 0.00 3.21
327 334 0.608035 TTTTGCTCACCCGATCACCC 60.608 55.000 0.00 0.00 0.00 4.61
329 336 3.458163 GCTCACCCGATCACCCGA 61.458 66.667 0.00 0.00 0.00 5.14
352 359 7.148171 CCGACATCTGCATCTAGAAGATATACA 60.148 40.741 5.32 0.00 40.92 2.29
353 360 7.909641 CGACATCTGCATCTAGAAGATATACAG 59.090 40.741 5.32 0.43 40.92 2.74
452 459 5.071788 TCCAAATAGTCTGGGCGATCTAATT 59.928 40.000 0.00 0.00 34.46 1.40
579 617 2.137523 TGGATCGATCGATGCATGTTG 58.862 47.619 38.19 0.00 45.60 3.33
595 633 6.689178 GCATGTTGCGAATAAAAAGAAGAA 57.311 33.333 0.00 0.00 31.71 2.52
596 634 6.745392 GCATGTTGCGAATAAAAAGAAGAAG 58.255 36.000 0.00 0.00 31.71 2.85
599 637 8.633408 CATGTTGCGAATAAAAAGAAGAAGAAG 58.367 33.333 0.00 0.00 0.00 2.85
605 643 9.323963 GCGAATAAAAAGAAGAAGAAGAAAGAG 57.676 33.333 0.00 0.00 0.00 2.85
614 652 7.053498 AGAAGAAGAAGAAAGAGCCATTATCC 58.947 38.462 0.00 0.00 0.00 2.59
661 699 3.687212 TGGTGTATGCATTAGTTTCCACG 59.313 43.478 3.54 0.00 0.00 4.94
685 723 5.298989 TGGATATTTAGGCACGTGGTTAT 57.701 39.130 18.88 0.00 0.00 1.89
761 801 5.589192 ACGTAAGCTAGCAATGTTAGTAGG 58.411 41.667 18.83 4.19 45.62 3.18
805 855 7.705325 GTCAAACTACACGGTGATATTAGTGAT 59.295 37.037 16.29 2.89 37.95 3.06
940 995 4.977963 CACAATTACCAAGCTCAAACACTG 59.022 41.667 0.00 0.00 0.00 3.66
1056 1117 0.468585 TGGTGGTACTCGTGGTCTGT 60.469 55.000 0.00 0.00 0.00 3.41
1089 1150 0.389948 GTGTTCTGGCTACTGACCCG 60.390 60.000 0.00 0.00 0.00 5.28
1091 1152 0.173708 GTTCTGGCTACTGACCCGAG 59.826 60.000 0.00 0.00 0.00 4.63
1168 1231 4.925390 AAGAAGAAGATTTGCTCCCTCT 57.075 40.909 0.00 0.00 0.00 3.69
1180 1243 5.767816 TTGCTCCCTCTTTTTCAACTTAC 57.232 39.130 0.00 0.00 0.00 2.34
1209 1272 8.917415 AAGTTCTAGCTTTTTCTTTGTCAAAG 57.083 30.769 17.73 17.73 39.88 2.77
1333 1558 3.410631 TTTGGAACGGAAGCTACATGA 57.589 42.857 0.00 0.00 0.00 3.07
1575 4400 6.455360 ACATCAAGTGAACTGTTTCATTGT 57.545 33.333 0.00 0.00 43.72 2.71
1579 4404 6.554419 TCAAGTGAACTGTTTCATTGTTCAG 58.446 36.000 7.85 0.00 46.82 3.02
1619 4444 6.927416 TCACTTAGGTTAGTCGAAGCAATAA 58.073 36.000 0.00 0.00 38.05 1.40
1868 4909 1.301716 GTTGAACGCTCAGGGCTCA 60.302 57.895 0.00 0.00 39.13 4.26
2270 5311 1.675310 CGCCAAGGCCTTCATGACA 60.675 57.895 17.29 0.00 37.98 3.58
2501 5568 3.252701 ACAGAGTGTGGTGTAGTAAGTCG 59.747 47.826 0.00 0.00 0.00 4.18
2507 5574 3.253188 TGTGGTGTAGTAAGTCGTGTACC 59.747 47.826 0.00 0.00 0.00 3.34
2566 5635 1.873863 CTAGCACTCGGTCGTGTCA 59.126 57.895 0.00 0.00 37.24 3.58
2668 5737 9.435688 GGTTTGGTCATAATTTTTGCTAATTCT 57.564 29.630 0.00 0.00 0.00 2.40
2688 5757 6.392625 TTCTCAATCGACGGAGAAATATCT 57.607 37.500 21.74 0.00 44.67 1.98
2693 5762 4.815040 TCGACGGAGAAATATCTGAGTC 57.185 45.455 0.00 0.00 35.54 3.36
2708 5777 0.807496 GAGTCTCAGCCAACCATTGC 59.193 55.000 0.00 0.00 0.00 3.56
2726 5795 6.507023 CCATTGCCTGGTGTTATTTAGATTC 58.493 40.000 0.00 0.00 40.49 2.52
2729 5798 5.250200 TGCCTGGTGTTATTTAGATTCGTT 58.750 37.500 0.00 0.00 0.00 3.85
2739 5808 9.917129 TGTTATTTAGATTCGTTCTGAAGTACA 57.083 29.630 0.00 5.33 40.65 2.90
2776 5848 5.531634 AGTACTTATTTTTCGGTCGTCACA 58.468 37.500 0.00 0.00 0.00 3.58
2787 5859 1.406887 GGTCGTCACATGGCTTATGGT 60.407 52.381 0.00 0.00 41.25 3.55
2799 5871 5.106876 TGGCTTATGGTAGTAGGGTTTTC 57.893 43.478 0.00 0.00 0.00 2.29
2801 5873 5.252164 TGGCTTATGGTAGTAGGGTTTTCTT 59.748 40.000 0.00 0.00 0.00 2.52
2802 5874 5.821470 GGCTTATGGTAGTAGGGTTTTCTTC 59.179 44.000 0.00 0.00 0.00 2.87
2803 5875 6.352823 GGCTTATGGTAGTAGGGTTTTCTTCT 60.353 42.308 0.00 0.00 0.00 2.85
2804 5876 6.539103 GCTTATGGTAGTAGGGTTTTCTTCTG 59.461 42.308 0.00 0.00 0.00 3.02
2805 5877 7.563724 TTATGGTAGTAGGGTTTTCTTCTGT 57.436 36.000 0.00 0.00 0.00 3.41
2807 5879 6.999705 TGGTAGTAGGGTTTTCTTCTGTAA 57.000 37.500 0.00 0.00 0.00 2.41
2864 6187 2.822399 CCTCCCCTCCGATTTCCG 59.178 66.667 0.00 0.00 38.18 4.30
2898 6221 6.970484 CCATATGGTGCTCCTAATAACAAAC 58.030 40.000 14.09 0.00 34.23 2.93
2921 6244 8.579682 AACTAAAGCATAAAAGAAAACAGCAG 57.420 30.769 0.00 0.00 0.00 4.24
2927 6250 2.712057 AAAGAAAACAGCAGCATCCG 57.288 45.000 0.00 0.00 0.00 4.18
2928 6251 1.896220 AAGAAAACAGCAGCATCCGA 58.104 45.000 0.00 0.00 0.00 4.55
2930 6253 0.874390 GAAAACAGCAGCATCCGACA 59.126 50.000 0.00 0.00 0.00 4.35
2947 6270 7.522073 GCATCCGACAATTAACATCCATTACAT 60.522 37.037 0.00 0.00 0.00 2.29
2961 6284 4.907269 TCCATTACATCAGATAGCCCAAGA 59.093 41.667 0.00 0.00 0.00 3.02
2992 6315 2.027469 ACCAAAAGCTAGACTAACCCCG 60.027 50.000 0.00 0.00 0.00 5.73
3016 6339 3.981308 CCAAAGGGCAACGACGAT 58.019 55.556 0.00 0.00 37.60 3.73
3030 6353 0.778815 GACGATGCGCGAGGATTAAG 59.221 55.000 12.10 0.00 44.47 1.85
3065 6388 6.846283 GTGACTGCAAAGTTTATATACATCGC 59.154 38.462 0.00 0.00 0.00 4.58
3073 6396 9.950680 CAAAGTTTATATACATCGCCAAAAGAT 57.049 29.630 0.00 0.00 0.00 2.40
3080 6403 1.402968 CATCGCCAAAAGATGAGGGTG 59.597 52.381 0.28 0.00 46.09 4.61
3106 6429 6.823678 ACTAGAAGTCAAACAAACACTACG 57.176 37.500 0.00 0.00 0.00 3.51
3113 6436 3.685272 TCAAACAAACACTACGAACAGCA 59.315 39.130 0.00 0.00 0.00 4.41
3118 6441 2.370281 ACACTACGAACAGCATCCAG 57.630 50.000 0.00 0.00 0.00 3.86
3154 6477 5.293814 ACAAAGCATCATCTTCGATCTTCAG 59.706 40.000 0.00 0.00 0.00 3.02
3155 6478 3.992643 AGCATCATCTTCGATCTTCAGG 58.007 45.455 0.00 0.00 0.00 3.86
3156 6479 3.640498 AGCATCATCTTCGATCTTCAGGA 59.360 43.478 0.00 0.00 0.00 3.86
3160 6483 4.218312 TCATCTTCGATCTTCAGGATCCA 58.782 43.478 15.82 0.00 45.90 3.41
3164 6487 1.414181 TCGATCTTCAGGATCCAAGCC 59.586 52.381 15.82 4.59 45.90 4.35
3171 6494 0.747283 CAGGATCCAAGCCTGCAGAC 60.747 60.000 17.39 2.52 45.66 3.51
3189 6512 4.223700 GCAGACACCATATCTCCATCCATA 59.776 45.833 0.00 0.00 0.00 2.74
3218 6541 6.226787 GCCTTGTATATCTCACTTGCTACAT 58.773 40.000 0.00 0.00 0.00 2.29
3222 6545 6.820335 TGTATATCTCACTTGCTACATGCTT 58.180 36.000 0.00 0.00 43.37 3.91
3234 6557 3.916776 GCTACATGCTTGAGAAGTTTTGC 59.083 43.478 6.60 0.00 38.95 3.68
3238 6561 1.332195 GCTTGAGAAGTTTTGCCCCT 58.668 50.000 0.00 0.00 0.00 4.79
3283 6606 3.388308 CTCCTTCTGCAATATCGACCAG 58.612 50.000 0.00 0.00 0.00 4.00
3304 6627 2.213499 CCCACGATCCAGTAGCAAATC 58.787 52.381 0.00 0.00 0.00 2.17
3326 6649 5.759059 TCAGCTTAATCAGAATCAATGGGT 58.241 37.500 0.00 0.00 0.00 4.51
3328 6651 4.818546 AGCTTAATCAGAATCAATGGGTCG 59.181 41.667 0.00 0.00 0.00 4.79
3329 6652 4.023707 GCTTAATCAGAATCAATGGGTCGG 60.024 45.833 0.00 0.00 0.00 4.79
3389 6712 4.884164 ACTTCCAAAGAGTCCAGAAAACAG 59.116 41.667 0.00 0.00 0.00 3.16
3390 6713 3.214328 TCCAAAGAGTCCAGAAAACAGC 58.786 45.455 0.00 0.00 0.00 4.40
3410 6733 1.263217 CAGCCGAACCAACAAGTACAC 59.737 52.381 0.00 0.00 0.00 2.90
3411 6734 0.233848 GCCGAACCAACAAGTACACG 59.766 55.000 0.00 0.00 0.00 4.49
3412 6735 0.233848 CCGAACCAACAAGTACACGC 59.766 55.000 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.274602 TGTACCCAAAGAGCAACGAATA 57.725 40.909 0.00 0.00 0.00 1.75
10 11 2.293399 CTGGTTGTACCCAAAGAGCAAC 59.707 50.000 0.00 0.00 37.50 4.17
14 15 2.884639 CCAACTGGTTGTACCCAAAGAG 59.115 50.000 11.73 0.00 37.50 2.85
18 19 2.128535 TCTCCAACTGGTTGTACCCAA 58.871 47.619 11.73 0.00 37.50 4.12
24 25 2.039879 GGTACCATCTCCAACTGGTTGT 59.960 50.000 7.15 0.00 43.21 3.32
44 45 6.764085 TCACACTAATTGAATATAACCCGTGG 59.236 38.462 0.00 0.00 0.00 4.94
47 48 7.709182 TCACTCACACTAATTGAATATAACCCG 59.291 37.037 0.00 0.00 0.00 5.28
51 52 9.297586 GTCGTCACTCACACTAATTGAATATAA 57.702 33.333 0.00 0.00 0.00 0.98
98 99 4.481463 ACCGCAACAAAATTACATGTAGC 58.519 39.130 5.56 2.76 0.00 3.58
142 144 8.159344 CTTACAGAATTGGAAGAACAGAAAGT 57.841 34.615 0.00 0.00 46.47 2.66
161 163 5.856126 TTGCAAAGTATCCGTTCTTACAG 57.144 39.130 0.00 0.00 0.00 2.74
171 173 9.403110 CAGCTTTATATTGATTGCAAAGTATCC 57.597 33.333 1.71 0.00 37.59 2.59
172 174 9.956720 ACAGCTTTATATTGATTGCAAAGTATC 57.043 29.630 1.71 0.00 37.59 2.24
191 193 3.921119 TCGATTGATGCAAACAGCTTT 57.079 38.095 0.00 0.00 45.94 3.51
317 324 1.068083 CAGATGTCGGGTGATCGGG 59.932 63.158 0.00 0.00 0.00 5.14
327 334 7.756558 TGTATATCTTCTAGATGCAGATGTCG 58.243 38.462 13.49 0.00 35.37 4.35
329 336 8.876303 TCTGTATATCTTCTAGATGCAGATGT 57.124 34.615 13.49 10.26 35.98 3.06
362 369 7.833682 TCATCAAACAATGTGGTAGTCCAATAT 59.166 33.333 0.00 0.00 46.15 1.28
363 370 7.171653 TCATCAAACAATGTGGTAGTCCAATA 58.828 34.615 0.00 0.00 46.15 1.90
370 377 6.573664 TTCCTTCATCAAACAATGTGGTAG 57.426 37.500 0.00 0.00 0.00 3.18
373 380 6.457355 TGATTTCCTTCATCAAACAATGTGG 58.543 36.000 0.00 0.00 0.00 4.17
452 459 7.898014 TCTTTGGTAGTAGATGCTGATTCTA 57.102 36.000 0.00 0.00 0.00 2.10
579 617 9.323963 CTCTTTCTTCTTCTTCTTTTTATTCGC 57.676 33.333 0.00 0.00 0.00 4.70
581 619 9.619316 GGCTCTTTCTTCTTCTTCTTTTTATTC 57.381 33.333 0.00 0.00 0.00 1.75
584 622 8.697507 ATGGCTCTTTCTTCTTCTTCTTTTTA 57.302 30.769 0.00 0.00 0.00 1.52
585 623 7.594351 ATGGCTCTTTCTTCTTCTTCTTTTT 57.406 32.000 0.00 0.00 0.00 1.94
586 624 7.594351 AATGGCTCTTTCTTCTTCTTCTTTT 57.406 32.000 0.00 0.00 0.00 2.27
587 625 8.876303 ATAATGGCTCTTTCTTCTTCTTCTTT 57.124 30.769 0.00 0.00 0.00 2.52
588 626 7.555914 GGATAATGGCTCTTTCTTCTTCTTCTT 59.444 37.037 0.00 0.00 0.00 2.52
589 627 7.053498 GGATAATGGCTCTTTCTTCTTCTTCT 58.947 38.462 0.00 0.00 0.00 2.85
590 628 7.053498 AGGATAATGGCTCTTTCTTCTTCTTC 58.947 38.462 0.00 0.00 0.00 2.87
591 629 6.967897 AGGATAATGGCTCTTTCTTCTTCTT 58.032 36.000 0.00 0.00 0.00 2.52
592 630 6.573712 AGGATAATGGCTCTTTCTTCTTCT 57.426 37.500 0.00 0.00 0.00 2.85
593 631 6.601217 ACAAGGATAATGGCTCTTTCTTCTTC 59.399 38.462 0.00 0.00 0.00 2.87
594 632 6.488715 ACAAGGATAATGGCTCTTTCTTCTT 58.511 36.000 0.00 0.00 0.00 2.52
595 633 6.072199 ACAAGGATAATGGCTCTTTCTTCT 57.928 37.500 0.00 0.00 0.00 2.85
596 634 5.882557 TGACAAGGATAATGGCTCTTTCTTC 59.117 40.000 0.00 0.00 0.00 2.87
599 637 5.649831 ACTTGACAAGGATAATGGCTCTTTC 59.350 40.000 19.16 0.00 0.00 2.62
605 643 5.163612 GGAAGAACTTGACAAGGATAATGGC 60.164 44.000 19.16 1.52 0.00 4.40
614 652 2.930950 TGGGTGGAAGAACTTGACAAG 58.069 47.619 13.77 13.77 0.00 3.16
644 682 5.029807 TCCATCGTGGAAACTAATGCATA 57.970 39.130 0.00 0.00 45.00 3.14
661 699 3.740115 ACCACGTGCCTAAATATCCATC 58.260 45.455 10.91 0.00 0.00 3.51
685 723 6.427547 CCCACTAACTGTTTGTTTATACGGAA 59.572 38.462 4.89 0.00 39.89 4.30
761 801 2.885266 TGACTAGGCATCCACGATACTC 59.115 50.000 0.00 0.00 0.00 2.59
805 855 5.515797 ACACTAGCAACAGCTATAATCGA 57.484 39.130 0.00 0.00 39.92 3.59
940 995 1.137282 GTCTGTCAGGGTAAGCTAGCC 59.863 57.143 12.13 0.00 46.53 3.93
1080 1141 2.037367 AGCTGGCTCGGGTCAGTA 59.963 61.111 19.91 0.00 46.03 2.74
1089 1150 1.220477 GAAGTCCTGGAGCTGGCTC 59.780 63.158 13.56 13.56 42.04 4.70
1091 1152 1.078567 CAGAAGTCCTGGAGCTGGC 60.079 63.158 0.00 0.00 39.23 4.85
1309 1534 3.811083 TGTAGCTTCCGTTCCAAAAAGA 58.189 40.909 0.00 0.00 0.00 2.52
1333 1558 7.276218 CGACCATGTTGCATGAAAGAAATTAAT 59.724 33.333 10.34 0.00 0.00 1.40
1382 4200 9.528018 CAAACAAATAACAGGAAACACAATACT 57.472 29.630 0.00 0.00 0.00 2.12
1383 4201 9.522804 TCAAACAAATAACAGGAAACACAATAC 57.477 29.630 0.00 0.00 0.00 1.89
1575 4400 4.690748 GTGATCGAAACATGAAGTCCTGAA 59.309 41.667 0.00 0.00 0.00 3.02
1579 4404 5.292101 CCTAAGTGATCGAAACATGAAGTCC 59.708 44.000 0.00 0.00 0.00 3.85
1701 4739 2.823984 TGTTGCAGCAATTTCCAAGTG 58.176 42.857 11.96 0.00 0.00 3.16
1982 5023 4.877619 AGGATCTCGGAGCCGCGA 62.878 66.667 8.23 3.91 43.66 5.87
2270 5311 0.250814 AGTCGACGGTGTCCTTCTCT 60.251 55.000 10.46 0.00 0.00 3.10
2461 5528 2.687935 CTGTTTACCAGTGGCTTGTTGT 59.312 45.455 9.78 0.00 36.37 3.32
2462 5529 2.948979 TCTGTTTACCAGTGGCTTGTTG 59.051 45.455 9.78 0.00 42.19 3.33
2501 5568 1.333619 CACAAACACCTGCTGGTACAC 59.666 52.381 15.70 0.00 46.60 2.90
2507 5574 0.518636 CGATCCACAAACACCTGCTG 59.481 55.000 0.00 0.00 0.00 4.41
2566 5635 5.736951 TGCACTTTGGGCACTATTTATTT 57.263 34.783 0.00 0.00 36.11 1.40
2653 5722 6.747280 CCGTCGATTGAGAATTAGCAAAAATT 59.253 34.615 0.00 0.00 0.00 1.82
2655 5724 5.410132 TCCGTCGATTGAGAATTAGCAAAAA 59.590 36.000 0.00 0.00 0.00 1.94
2668 5737 5.299531 ACTCAGATATTTCTCCGTCGATTGA 59.700 40.000 0.00 0.00 0.00 2.57
2671 5740 5.067273 AGACTCAGATATTTCTCCGTCGAT 58.933 41.667 0.00 0.00 35.15 3.59
2673 5742 4.273724 TGAGACTCAGATATTTCTCCGTCG 59.726 45.833 0.00 0.00 35.15 5.12
2688 5757 1.883638 GCAATGGTTGGCTGAGACTCA 60.884 52.381 4.78 4.78 0.00 3.41
2708 5777 6.816640 TCAGAACGAATCTAAATAACACCAGG 59.183 38.462 0.00 0.00 36.32 4.45
2744 5813 8.907222 ACCGAAAAATAAGTACTCACCTTAAA 57.093 30.769 0.00 0.00 0.00 1.52
2754 5823 5.827568 TGTGACGACCGAAAAATAAGTAC 57.172 39.130 0.00 0.00 0.00 2.73
2776 5848 5.432060 AGAAAACCCTACTACCATAAGCCAT 59.568 40.000 0.00 0.00 0.00 4.40
2827 6148 5.363868 GGAGGCCCTTCTTATGCTAATTTTT 59.636 40.000 0.00 0.00 0.00 1.94
2828 6149 4.895889 GGAGGCCCTTCTTATGCTAATTTT 59.104 41.667 0.00 0.00 0.00 1.82
2829 6150 4.474394 GGAGGCCCTTCTTATGCTAATTT 58.526 43.478 0.00 0.00 0.00 1.82
2830 6151 3.181428 GGGAGGCCCTTCTTATGCTAATT 60.181 47.826 0.00 0.00 41.34 1.40
2831 6152 2.376855 GGGAGGCCCTTCTTATGCTAAT 59.623 50.000 0.00 0.00 41.34 1.73
2854 6176 4.387598 TGGTTTCTTTAACGGAAATCGGA 58.612 39.130 6.21 0.00 44.45 4.55
2855 6177 4.752661 TGGTTTCTTTAACGGAAATCGG 57.247 40.909 6.21 0.00 44.45 4.18
2898 6221 6.642131 TGCTGCTGTTTTCTTTTATGCTTTAG 59.358 34.615 0.00 0.00 0.00 1.85
2921 6244 4.836125 ATGGATGTTAATTGTCGGATGC 57.164 40.909 0.00 0.00 0.00 3.91
2930 6253 9.236006 GGCTATCTGATGTAATGGATGTTAATT 57.764 33.333 0.00 0.00 0.00 1.40
2947 6270 2.501723 GTCTTGGTCTTGGGCTATCTGA 59.498 50.000 0.00 0.00 0.00 3.27
2961 6284 2.159179 AGCTTTTGGTTGGTCTTGGT 57.841 45.000 0.00 0.00 0.00 3.67
3016 6339 1.521457 CCTGCTTAATCCTCGCGCA 60.521 57.895 8.75 0.00 0.00 6.09
3030 6353 3.660621 GCAGTCACTGGAACCTGC 58.339 61.111 7.00 0.00 42.94 4.85
3065 6388 5.560724 TCTAGTTTCACCCTCATCTTTTGG 58.439 41.667 0.00 0.00 0.00 3.28
3073 6396 5.104693 TGTTTGACTTCTAGTTTCACCCTCA 60.105 40.000 0.00 0.00 0.00 3.86
3074 6397 5.365619 TGTTTGACTTCTAGTTTCACCCTC 58.634 41.667 0.00 0.00 0.00 4.30
3080 6403 7.844653 CGTAGTGTTTGTTTGACTTCTAGTTTC 59.155 37.037 0.00 0.00 0.00 2.78
3106 6429 0.723981 GTTCTCGCTGGATGCTGTTC 59.276 55.000 0.00 0.00 40.11 3.18
3127 6450 4.809958 AGATCGAAGATGATGCTTTGTCTG 59.190 41.667 0.00 0.00 45.12 3.51
3154 6477 1.028868 GTGTCTGCAGGCTTGGATCC 61.029 60.000 20.86 4.20 0.00 3.36
3155 6478 1.028868 GGTGTCTGCAGGCTTGGATC 61.029 60.000 20.86 0.00 0.00 3.36
3156 6479 1.001641 GGTGTCTGCAGGCTTGGAT 60.002 57.895 20.86 0.00 0.00 3.41
3160 6483 1.842562 AGATATGGTGTCTGCAGGCTT 59.157 47.619 20.86 4.45 0.00 4.35
3164 6487 3.556633 GGATGGAGATATGGTGTCTGCAG 60.557 52.174 7.63 7.63 45.24 4.41
3168 6491 4.464244 CGTATGGATGGAGATATGGTGTCT 59.536 45.833 0.00 0.00 0.00 3.41
3171 6494 4.675408 CGTCGTATGGATGGAGATATGGTG 60.675 50.000 0.00 0.00 0.00 4.17
3189 6512 2.950309 AGTGAGATATACAAGGCGTCGT 59.050 45.455 0.00 0.00 0.00 4.34
3218 6541 1.039856 GGGGCAAAACTTCTCAAGCA 58.960 50.000 0.00 0.00 0.00 3.91
3222 6545 2.200373 GCTAGGGGCAAAACTTCTCA 57.800 50.000 0.00 0.00 41.35 3.27
3234 6557 1.207791 AGAGGTGTTGATGCTAGGGG 58.792 55.000 0.00 0.00 0.00 4.79
3238 6561 3.008375 AGCAAGAAGAGGTGTTGATGCTA 59.992 43.478 0.00 0.00 40.78 3.49
3283 6606 0.392461 TTTGCTACTGGATCGTGGGC 60.392 55.000 0.00 0.00 0.00 5.36
3304 6627 5.277683 CGACCCATTGATTCTGATTAAGCTG 60.278 44.000 0.00 0.00 0.00 4.24
3389 6712 0.237498 GTACTTGTTGGTTCGGCTGC 59.763 55.000 0.00 0.00 0.00 5.25
3390 6713 1.263217 GTGTACTTGTTGGTTCGGCTG 59.737 52.381 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.