Multiple sequence alignment - TraesCS5A01G078900

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 TraesCS5A01G078900 chr5A 100.000 3504 0 0 1 3504 97566424 97562921 0.000000e+00 6471
1 TraesCS5A01G078900 chr5D 91.501 2459 139 39 676 3120 102278550 102276148 0.000000e+00 3319
2 TraesCS5A01G078900 chr5D 94.737 399 16 2 3107 3504 102276129 102275735 1.790000e-172 616
3 TraesCS5A01G078900 chr5B 92.665 1595 75 22 1914 3504 111682043 111680487 0.000000e+00 2259
4 TraesCS5A01G078900 chr5B 89.776 802 57 16 771 1568 111683471 111682691 0.000000e+00 1003
5 TraesCS5A01G078900 chr5B 92.705 658 47 1 20 677 587458734 587459390 0.000000e+00 948
6 TraesCS5A01G078900 chr5B 88.889 477 35 10 1561 2034 111682504 111682043 3.920000e-159 571
7 TraesCS5A01G078900 chr2B 94.903 667 30 3 20 683 373097556 373096891 0.000000e+00 1040
8 TraesCS5A01G078900 chr2B 94.478 670 32 4 20 687 8072532 8071866 0.000000e+00 1027
9 TraesCS5A01G078900 chr2B 94.841 659 32 1 20 676 8228286 8227628 0.000000e+00 1027
10 TraesCS5A01G078900 chr2A 94.729 664 29 4 20 678 50050707 50050045 0.000000e+00 1027
11 TraesCS5A01G078900 chr2A 93.607 657 41 1 20 675 767550552 767551208 0.000000e+00 979
12 TraesCS5A01G078900 chr6D 94.946 653 32 1 30 681 433502707 433502055 0.000000e+00 1022
13 TraesCS5A01G078900 chr2D 93.646 661 42 0 20 680 101336023 101335363 0.000000e+00 989
14 TraesCS5A01G078900 chr2D 92.500 400 24 4 2421 2817 610857979 610858375 5.080000e-158 568
15 TraesCS5A01G078900 chr3A 93.161 658 41 4 20 676 162755135 162755789 0.000000e+00 963


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 TraesCS5A01G078900 chr5A 97562921 97566424 3503 True 6471.000000 6471 100.000000 1 3504 1 chr5A.!!$R1 3503
1 TraesCS5A01G078900 chr5D 102275735 102278550 2815 True 1967.500000 3319 93.119000 676 3504 2 chr5D.!!$R1 2828
2 TraesCS5A01G078900 chr5B 111680487 111683471 2984 True 1277.666667 2259 90.443333 771 3504 3 chr5B.!!$R1 2733
3 TraesCS5A01G078900 chr5B 587458734 587459390 656 False 948.000000 948 92.705000 20 677 1 chr5B.!!$F1 657
4 TraesCS5A01G078900 chr2B 373096891 373097556 665 True 1040.000000 1040 94.903000 20 683 1 chr2B.!!$R3 663
5 TraesCS5A01G078900 chr2B 8071866 8072532 666 True 1027.000000 1027 94.478000 20 687 1 chr2B.!!$R1 667
6 TraesCS5A01G078900 chr2B 8227628 8228286 658 True 1027.000000 1027 94.841000 20 676 1 chr2B.!!$R2 656
7 TraesCS5A01G078900 chr2A 50050045 50050707 662 True 1027.000000 1027 94.729000 20 678 1 chr2A.!!$R1 658
8 TraesCS5A01G078900 chr2A 767550552 767551208 656 False 979.000000 979 93.607000 20 675 1 chr2A.!!$F1 655
9 TraesCS5A01G078900 chr6D 433502055 433502707 652 True 1022.000000 1022 94.946000 30 681 1 chr6D.!!$R1 651
10 TraesCS5A01G078900 chr2D 101335363 101336023 660 True 989.000000 989 93.646000 20 680 1 chr2D.!!$R1 660
11 TraesCS5A01G078900 chr3A 162755135 162755789 654 False 963.000000 963 93.161000 20 676 1 chr3A.!!$F1 656

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
991 999 0.551879 CCCTCTCCGAGAACCCTAGA 59.448 60.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2712 3042 0.250424 CAAAGGGCAAGGCAAAAGGG 60.25 55.0 0.0 0.0 0.0 3.95 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
253 255 4.158384 CAATTTTACGTGATGACACAGGC 58.842 43.478 0.00 0.00 46.20 4.85
287 289 3.065233 TGCATCTTGTGTTGATATTCCGC 59.935 43.478 0.00 0.00 0.00 5.54
416 419 7.164122 GGAGGTAATTGAGATCATGCAGAATA 58.836 38.462 0.00 0.00 0.00 1.75
589 592 1.984570 CTGGAAGTCGGAGCCTCCA 60.985 63.158 12.13 0.00 35.91 3.86
602 605 3.518303 GGAGCCTCCAAGGTTTCTAGTAA 59.482 47.826 5.69 0.00 37.80 2.24
614 617 9.807386 CAAGGTTTCTAGTAAACGTTTTATCAG 57.193 33.333 20.19 11.31 36.47 2.90
615 618 8.543862 AGGTTTCTAGTAAACGTTTTATCAGG 57.456 34.615 20.19 5.59 0.00 3.86
639 642 6.302615 GCGATGTATCTTTATTCTCACATGC 58.697 40.000 0.00 0.00 0.00 4.06
701 707 2.368875 TGACAACAGAAAGAGAGGGACC 59.631 50.000 0.00 0.00 0.00 4.46
709 715 3.838903 AGAAAGAGAGGGACCGTGTAAAT 59.161 43.478 0.00 0.00 0.00 1.40
711 717 3.103080 AGAGAGGGACCGTGTAAATCT 57.897 47.619 0.00 0.00 0.00 2.40
752 759 3.740115 TCAAACCCTAGCTGTCTTTGTC 58.260 45.455 0.00 0.00 0.00 3.18
914 921 4.572870 CCTGGGCCTGGTATATCTGATCTA 60.573 50.000 20.63 0.00 0.00 1.98
991 999 0.551879 CCCTCTCCGAGAACCCTAGA 59.448 60.000 0.00 0.00 0.00 2.43
992 1000 1.477923 CCCTCTCCGAGAACCCTAGAG 60.478 61.905 0.00 0.00 34.71 2.43
999 1007 1.481363 CGAGAACCCTAGAGTTTCCCC 59.519 57.143 0.00 0.00 0.00 4.81
1062 1070 2.058595 CCTCGACAACCTCCCCGAT 61.059 63.158 0.00 0.00 0.00 4.18
1101 1109 1.640069 CGCCATGATCGAACAGCTG 59.360 57.895 13.48 13.48 0.00 4.24
1191 1200 4.384247 CGTCATCTGATTTCGATAGCCTTC 59.616 45.833 5.63 0.00 0.00 3.46
1197 1206 0.526954 TTTCGATAGCCTTCGGTCGC 60.527 55.000 6.11 0.00 39.56 5.19
1218 1227 1.482593 AGCTTGTATCTTGCGCTACCT 59.517 47.619 9.73 0.00 0.00 3.08
1224 1233 4.513442 TGTATCTTGCGCTACCTGAAAAT 58.487 39.130 9.73 0.00 0.00 1.82
1227 1236 3.609853 TCTTGCGCTACCTGAAAATCAT 58.390 40.909 9.73 0.00 0.00 2.45
1240 1249 5.009010 CCTGAAAATCATTGATTAGGTCGGG 59.991 44.000 20.32 20.32 32.67 5.14
1297 1306 4.974645 TCATGGCGGAGGAATAAGTTAT 57.025 40.909 0.00 0.00 0.00 1.89
1298 1307 4.894784 TCATGGCGGAGGAATAAGTTATC 58.105 43.478 0.00 0.00 0.00 1.75
1365 1374 4.662468 TGATCTGTAGGAGATTGAGTGC 57.338 45.455 0.00 0.00 41.91 4.40
1367 1376 2.723273 TCTGTAGGAGATTGAGTGCGA 58.277 47.619 0.00 0.00 0.00 5.10
1396 1405 1.990563 GAACTAGCGCGCTTAGTTTCA 59.009 47.619 41.04 18.75 34.55 2.69
1417 1426 4.462483 TCAAGGTATCCACAGGATTTTTGC 59.538 41.667 3.55 0.00 39.79 3.68
1440 1449 1.039856 TTTGCAGCCCCTTCAAGTTC 58.960 50.000 0.00 0.00 0.00 3.01
1447 1456 1.202348 GCCCCTTCAAGTTCCAAATCG 59.798 52.381 0.00 0.00 0.00 3.34
1505 1514 6.817765 TTTGCTTAGATAGTTGAAACCTGG 57.182 37.500 0.00 0.00 0.00 4.45
1511 1520 7.773690 GCTTAGATAGTTGAAACCTGGGATTAA 59.226 37.037 0.00 0.00 0.00 1.40
1515 1524 8.971073 AGATAGTTGAAACCTGGGATTAATTTG 58.029 33.333 0.00 0.00 0.00 2.32
1520 1529 6.945218 TGAAACCTGGGATTAATTTGAATGG 58.055 36.000 0.00 0.00 0.00 3.16
1612 1818 3.244422 TGAGTTGGTTCGTGCCTATTCTT 60.244 43.478 0.40 0.00 0.00 2.52
1656 1862 6.189567 CGTTAAATAGCTTGTTGATTACCCG 58.810 40.000 0.00 0.00 0.00 5.28
1657 1863 4.632538 AAATAGCTTGTTGATTACCCGC 57.367 40.909 0.00 0.00 0.00 6.13
1658 1864 2.772077 TAGCTTGTTGATTACCCGCA 57.228 45.000 0.00 0.00 0.00 5.69
1660 1866 1.812571 AGCTTGTTGATTACCCGCAAG 59.187 47.619 0.00 0.00 39.40 4.01
1661 1867 1.810151 GCTTGTTGATTACCCGCAAGA 59.190 47.619 6.76 0.00 38.90 3.02
1666 1872 5.461032 TGTTGATTACCCGCAAGAAAAAT 57.539 34.783 0.00 0.00 43.02 1.82
1674 1880 5.006153 ACCCGCAAGAAAAATAAATAGCC 57.994 39.130 0.00 0.00 43.02 3.93
1675 1881 4.142026 ACCCGCAAGAAAAATAAATAGCCC 60.142 41.667 0.00 0.00 43.02 5.19
1676 1882 4.099419 CCCGCAAGAAAAATAAATAGCCCT 59.901 41.667 0.00 0.00 43.02 5.19
1689 1895 8.823220 AATAAATAGCCCTTTGATTGTGTAGT 57.177 30.769 0.00 0.00 0.00 2.73
1730 1936 2.702478 AGATAGCCATTCAGCTGCAGTA 59.298 45.455 16.64 0.00 44.67 2.74
1737 1943 3.126514 CCATTCAGCTGCAGTAGTCTTTG 59.873 47.826 16.64 5.08 0.00 2.77
1757 1963 5.643379 TTGATTTTGGTGTAGATTCTGGC 57.357 39.130 0.00 0.00 0.00 4.85
1858 2064 6.013379 AGGTTACTCTCTGAATTGTTCCATCA 60.013 38.462 0.00 0.00 0.00 3.07
1915 2121 7.928103 TCTGTTATAGAACGTCTAGGTGATTC 58.072 38.462 0.00 0.00 38.51 2.52
1951 2157 7.389884 TGCCACAGGTAACGTAATTAACATTTA 59.610 33.333 0.00 0.00 46.39 1.40
2147 2475 8.574196 AGTTTTTACATTGTAACATCTGCAAC 57.426 30.769 8.75 4.61 31.94 4.17
2148 2476 8.413229 AGTTTTTACATTGTAACATCTGCAACT 58.587 29.630 8.75 6.37 31.94 3.16
2162 2490 3.882288 TCTGCAACTGAACAATGCTTACA 59.118 39.130 11.49 0.00 40.66 2.41
2164 2492 5.003692 TGCAACTGAACAATGCTTACAAA 57.996 34.783 11.49 0.00 40.66 2.83
2273 2601 0.318441 TGGACAAGCAAGAGGAGTCG 59.682 55.000 0.00 0.00 0.00 4.18
2321 2649 1.004044 CTGAAGCACTCCATGAGGGTT 59.996 52.381 0.00 0.00 35.18 4.11
2372 2700 2.612972 CGTTGCCACACCTGACTAATCT 60.613 50.000 0.00 0.00 0.00 2.40
2386 2714 7.092891 ACCTGACTAATCTAATGATGTGTTCCA 60.093 37.037 0.00 0.00 32.44 3.53
2409 2738 4.767409 AGCCCCTTCAAGTTTCTAACATTC 59.233 41.667 0.00 0.00 0.00 2.67
2418 2747 5.779241 AGTTTCTAACATTCCCCATCTGA 57.221 39.130 0.00 0.00 0.00 3.27
2454 2783 8.807581 GTTTGTAATCCTTGAAAGTTTTCAGTG 58.192 33.333 7.30 5.43 46.68 3.66
2458 2787 4.997565 TCCTTGAAAGTTTTCAGTGCTTG 58.002 39.130 7.30 0.00 46.68 4.01
2486 2815 4.139786 CCCACTGCTGCTTATCATGTTAT 58.860 43.478 0.00 0.00 0.00 1.89
2527 2856 3.917300 ACTGTATCGAATCCTTCCTCCT 58.083 45.455 0.00 0.00 0.00 3.69
2534 2864 3.451178 TCGAATCCTTCCTCCTGTTAAGG 59.549 47.826 0.00 0.00 46.06 2.69
2599 2929 8.286800 CCTTTGATATCTCGTCTAGTAGAGTTG 58.713 40.741 0.00 0.00 36.03 3.16
2657 2987 8.307483 TGGATCTCAACTTCTTTAGTAGACTTG 58.693 37.037 0.00 0.00 35.54 3.16
2658 2988 8.308207 GGATCTCAACTTCTTTAGTAGACTTGT 58.692 37.037 0.00 0.00 35.54 3.16
2659 2989 9.699703 GATCTCAACTTCTTTAGTAGACTTGTT 57.300 33.333 0.00 0.00 35.54 2.83
2695 3025 7.627088 GCTGTGTAATGCTGAAACATCATAGTT 60.627 37.037 0.00 0.00 0.00 2.24
2712 3042 6.349300 TCATAGTTCAAGATCTGTAAAGGCC 58.651 40.000 0.00 0.00 0.00 5.19
2763 3093 3.971032 ACTTTTGTTCGAGAGCAAAGG 57.029 42.857 17.88 17.88 41.33 3.11
2782 3112 4.890158 AGGATATTGGACGATGCACATA 57.110 40.909 0.00 0.00 0.00 2.29
2937 3267 2.447572 TGCTCCAGGTGGGTGTGA 60.448 61.111 0.00 0.00 38.11 3.58
2990 3320 1.347707 TGTCGATGGTGAAGGAAGCTT 59.652 47.619 0.00 0.00 0.00 3.74
2991 3321 2.565391 TGTCGATGGTGAAGGAAGCTTA 59.435 45.455 0.00 0.00 0.00 3.09
2996 3326 4.396166 CGATGGTGAAGGAAGCTTATTTGT 59.604 41.667 0.00 0.00 0.00 2.83
3030 3360 8.735692 TCTAATGCAATTATCATTGTGTCAGA 57.264 30.769 12.70 6.63 41.84 3.27
3112 3474 1.881973 TCTCTGCACTTGTGAATTGGC 59.118 47.619 4.79 0.00 0.00 4.52
3120 3482 3.503363 CACTTGTGAATTGGCTCTTGCTA 59.497 43.478 0.00 0.00 39.59 3.49
3127 3489 3.939740 ATTGGCTCTTGCTAATGAGGA 57.060 42.857 0.00 0.00 46.30 3.71
3187 3555 4.808895 CAGAGCATTTGTGGCTATTACGTA 59.191 41.667 0.00 0.00 42.78 3.57
3258 3628 1.494721 GTGGAAGGAGGAATATGGCCA 59.505 52.381 8.56 8.56 0.00 5.36
3264 3634 1.477558 GGAGGAATATGGCCACACAGG 60.478 57.143 8.16 0.00 41.84 4.00
3265 3635 1.490490 GAGGAATATGGCCACACAGGA 59.510 52.381 8.16 0.00 41.22 3.86
3282 3653 6.877855 CACACAGGAAGGAGGAATATCATATG 59.122 42.308 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.547671 CCACTGAGGGAGTCCTAGATTAA 58.452 47.826 9.58 0.00 45.05 1.40
1 2 4.186077 CCACTGAGGGAGTCCTAGATTA 57.814 50.000 9.58 0.00 45.05 1.75
2 3 3.039252 CCACTGAGGGAGTCCTAGATT 57.961 52.381 9.58 0.00 45.05 2.40
3 4 2.765689 CCACTGAGGGAGTCCTAGAT 57.234 55.000 9.58 0.00 45.05 1.98
14 15 2.202987 GCGATGCTCCCACTGAGG 60.203 66.667 0.00 0.00 41.73 3.86
15 16 2.202987 GGCGATGCTCCCACTGAG 60.203 66.667 0.00 0.00 44.47 3.35
16 17 3.002583 TGGCGATGCTCCCACTGA 61.003 61.111 0.00 0.00 0.00 3.41
17 18 2.513204 CTGGCGATGCTCCCACTG 60.513 66.667 0.00 0.00 0.00 3.66
18 19 2.527951 GAACTGGCGATGCTCCCACT 62.528 60.000 0.00 0.00 0.00 4.00
27 28 0.615331 ACCATGAGTGAACTGGCGAT 59.385 50.000 0.00 0.00 33.12 4.58
112 114 8.070034 TGATTCTCATATTTTTGGATTGTGCT 57.930 30.769 0.00 0.00 0.00 4.40
227 229 4.035675 TGTGTCATCACGTAAAATTGCACA 59.964 37.500 0.00 0.00 46.49 4.57
259 261 2.030371 TCAACACAAGATGCAGCCAAA 58.970 42.857 0.00 0.00 0.00 3.28
287 289 0.179134 GTCCCGACATCTTCCACGAG 60.179 60.000 0.00 0.00 0.00 4.18
589 592 8.996271 CCTGATAAAACGTTTACTAGAAACCTT 58.004 33.333 15.03 0.00 0.00 3.50
602 605 5.357257 AGATACATCGCCTGATAAAACGTT 58.643 37.500 0.00 0.00 32.18 3.99
614 617 6.619446 GCATGTGAGAATAAAGATACATCGCC 60.619 42.308 0.00 0.00 0.00 5.54
615 618 6.073602 TGCATGTGAGAATAAAGATACATCGC 60.074 38.462 0.00 0.00 0.00 4.58
691 697 3.103080 AGATTTACACGGTCCCTCTCT 57.897 47.619 0.00 0.00 0.00 3.10
701 707 1.202031 GGCCGCTGAAAGATTTACACG 60.202 52.381 0.00 0.00 34.07 4.49
764 771 9.356433 GATTTTTAGTCCGGCTATCTTATACTC 57.644 37.037 0.00 0.00 0.00 2.59
836 843 1.479757 GCCCTTTGGGTTTCACCTGTA 60.480 52.381 4.42 0.00 46.51 2.74
839 846 1.152333 GGCCCTTTGGGTTTCACCT 60.152 57.895 4.42 0.00 46.51 4.00
840 847 1.152333 AGGCCCTTTGGGTTTCACC 60.152 57.895 0.00 0.00 46.51 4.02
914 921 7.287005 AGGGACTCGTTTTTCCTTTCTTTTATT 59.713 33.333 0.00 0.00 31.90 1.40
991 999 2.032071 CGCACGAAGGGGGAAACT 59.968 61.111 0.00 0.00 0.00 2.66
992 1000 3.053896 CCGCACGAAGGGGGAAAC 61.054 66.667 7.61 0.00 46.16 2.78
1062 1070 0.036105 ACATGCGCATCTTGTCCTCA 60.036 50.000 22.51 0.00 0.00 3.86
1101 1109 0.389817 TGTACCTGTCACGCATCTGC 60.390 55.000 0.00 0.00 37.78 4.26
1130 1138 3.827302 GAGAGGCCGTATTATCAGAGGAA 59.173 47.826 0.00 0.00 0.00 3.36
1131 1139 3.422796 GAGAGGCCGTATTATCAGAGGA 58.577 50.000 0.00 0.00 0.00 3.71
1134 1143 3.136009 TCGAGAGGCCGTATTATCAGA 57.864 47.619 0.00 0.00 0.00 3.27
1191 1200 0.647410 CAAGATACAAGCTGCGACCG 59.353 55.000 0.00 0.00 0.00 4.79
1218 1227 5.588648 GTCCCGACCTAATCAATGATTTTCA 59.411 40.000 14.15 0.00 33.95 2.69
1224 1233 3.371034 TGAGTCCCGACCTAATCAATGA 58.629 45.455 0.00 0.00 0.00 2.57
1227 1236 3.104512 ACATGAGTCCCGACCTAATCAA 58.895 45.455 0.00 0.00 0.00 2.57
1240 1249 3.006323 AGTCAGAGGAACACACATGAGTC 59.994 47.826 0.00 0.00 0.00 3.36
1297 1306 2.495669 TGCCACAGATACACATCTTCGA 59.504 45.455 0.00 0.00 39.62 3.71
1298 1307 2.604914 GTGCCACAGATACACATCTTCG 59.395 50.000 0.00 0.00 39.62 3.79
1314 1323 1.275856 GAAATCATTGCCCAAGTGCCA 59.724 47.619 0.00 0.00 0.00 4.92
1365 1374 1.723384 GCGCTAGTTCTATCGAGCTCG 60.723 57.143 30.03 30.03 41.45 5.03
1367 1376 0.236187 CGCGCTAGTTCTATCGAGCT 59.764 55.000 5.56 0.00 34.73 4.09
1383 1392 2.284417 GGATACCTTGAAACTAAGCGCG 59.716 50.000 0.00 0.00 0.00 6.86
1396 1405 3.443681 CGCAAAAATCCTGTGGATACCTT 59.556 43.478 0.00 0.00 42.27 3.50
1417 1426 1.172180 TTGAAGGGGCTGCAAACTCG 61.172 55.000 0.50 0.00 0.00 4.18
1440 1449 0.597637 ACCTATCTCGCGCGATTTGG 60.598 55.000 34.86 30.74 0.00 3.28
1447 1456 5.151632 TCAAATTTAAACCTATCTCGCGC 57.848 39.130 0.00 0.00 0.00 6.86
1505 1514 7.043192 CGAACTGCAATCCATTCAAATTAATCC 60.043 37.037 0.00 0.00 0.00 3.01
1511 1520 4.789012 ACGAACTGCAATCCATTCAAAT 57.211 36.364 0.00 0.00 0.00 2.32
1515 1524 5.505286 CAGATAACGAACTGCAATCCATTC 58.495 41.667 0.00 0.00 0.00 2.67
1543 1552 0.954452 GCCACTCAACCCAAGTGAAG 59.046 55.000 4.89 0.00 45.64 3.02
1612 1818 1.089112 CAAGGATGCACGCTTCATCA 58.911 50.000 12.25 0.00 41.46 3.07
1633 1839 5.969435 GCGGGTAATCAACAAGCTATTTAAC 59.031 40.000 0.00 0.00 0.00 2.01
1656 1862 8.722480 ATCAAAGGGCTATTTATTTTTCTTGC 57.278 30.769 0.00 0.00 0.00 4.01
1660 1866 9.435688 ACACAATCAAAGGGCTATTTATTTTTC 57.564 29.630 0.00 0.00 0.00 2.29
1666 1872 8.644374 AAACTACACAATCAAAGGGCTATTTA 57.356 30.769 0.00 0.00 0.00 1.40
1713 1919 0.617413 ACTACTGCAGCTGAATGGCT 59.383 50.000 20.43 0.00 44.10 4.75
1715 1921 2.687700 AGACTACTGCAGCTGAATGG 57.312 50.000 20.43 6.00 0.00 3.16
1716 1922 3.999001 TCAAAGACTACTGCAGCTGAATG 59.001 43.478 20.43 8.71 0.00 2.67
1723 1929 5.009010 ACACCAAAATCAAAGACTACTGCAG 59.991 40.000 13.48 13.48 0.00 4.41
1730 1936 7.175641 CCAGAATCTACACCAAAATCAAAGACT 59.824 37.037 0.00 0.00 0.00 3.24
1737 1943 4.986622 GTGCCAGAATCTACACCAAAATC 58.013 43.478 4.73 0.00 0.00 2.17
1757 1963 5.048504 AACATATGTTCTTGCACTTCTGGTG 60.049 40.000 15.47 0.00 40.41 4.17
1858 2064 6.721318 TCCTTTATCAACTCCAGCATAAACT 58.279 36.000 0.00 0.00 0.00 2.66
1951 2157 6.603201 ACCATCGAACATCTTTATTTCACCAT 59.397 34.615 0.00 0.00 0.00 3.55
1963 2169 7.687941 ACTATTTTCAAACCATCGAACATCT 57.312 32.000 0.00 0.00 0.00 2.90
1969 2175 6.183360 GGGCAATACTATTTTCAAACCATCGA 60.183 38.462 0.00 0.00 0.00 3.59
2005 2211 6.713903 CCGACTATATACACAAGGACTAAGGA 59.286 42.308 0.00 0.00 0.00 3.36
2128 2456 6.484977 TGTTCAGTTGCAGATGTTACAATGTA 59.515 34.615 0.00 0.00 0.00 2.29
2147 2475 6.774354 AGCAAATTTGTAAGCATTGTTCAG 57.226 33.333 19.03 0.00 0.00 3.02
2148 2476 7.408123 CAAAGCAAATTTGTAAGCATTGTTCA 58.592 30.769 19.03 0.00 42.84 3.18
2162 2490 7.009174 CGTAGACTGAAACAACAAAGCAAATTT 59.991 33.333 0.00 0.00 0.00 1.82
2164 2492 5.971202 CGTAGACTGAAACAACAAAGCAAAT 59.029 36.000 0.00 0.00 0.00 2.32
2321 2649 1.804598 CTCAGCAAATCGCATGCCA 59.195 52.632 13.15 0.00 44.91 4.92
2363 2691 6.763135 GCTGGAACACATCATTAGATTAGTCA 59.237 38.462 0.00 0.00 30.20 3.41
2372 2700 1.922447 AGGGGCTGGAACACATCATTA 59.078 47.619 0.00 0.00 0.00 1.90
2386 2714 3.876309 TGTTAGAAACTTGAAGGGGCT 57.124 42.857 0.00 0.00 0.00 5.19
2418 2747 6.962182 TCAAGGATTACAAACTGATCCTGAT 58.038 36.000 4.99 0.00 46.81 2.90
2454 2783 0.524862 CAGCAGTGGGTTCATCAAGC 59.475 55.000 0.00 0.00 0.00 4.01
2458 2787 2.113860 TAAGCAGCAGTGGGTTCATC 57.886 50.000 0.00 0.00 0.00 2.92
2527 2856 0.965439 GCACAATGTGGCCCTTAACA 59.035 50.000 15.78 0.00 33.64 2.41
2534 2864 5.123227 TCTATTAAGTAGCACAATGTGGCC 58.877 41.667 15.78 0.00 33.64 5.36
2657 2987 5.354234 AGCATTACACAGCAATACCAGTAAC 59.646 40.000 0.00 0.00 0.00 2.50
2658 2988 5.353956 CAGCATTACACAGCAATACCAGTAA 59.646 40.000 0.00 0.00 0.00 2.24
2659 2989 4.875536 CAGCATTACACAGCAATACCAGTA 59.124 41.667 0.00 0.00 0.00 2.74
2660 2990 3.691118 CAGCATTACACAGCAATACCAGT 59.309 43.478 0.00 0.00 0.00 4.00
2695 3025 2.562296 AGGGGCCTTTACAGATCTTGA 58.438 47.619 0.84 0.00 0.00 3.02
2712 3042 0.250424 CAAAGGGCAAGGCAAAAGGG 60.250 55.000 0.00 0.00 0.00 3.95
2763 3093 6.136071 GTGTTTATGTGCATCGTCCAATATC 58.864 40.000 0.00 0.00 0.00 1.63
2782 3112 3.615592 GCTGTTGATGGCATGATGTGTTT 60.616 43.478 3.81 0.00 0.00 2.83
2937 3267 6.432403 AACCCACATGGATGTAAAACAATT 57.568 33.333 0.00 0.00 39.39 2.32
2990 3320 6.023357 TGCATTAGAGCAAGCAAACAAATA 57.977 33.333 0.00 0.00 42.46 1.40
2991 3321 4.885413 TGCATTAGAGCAAGCAAACAAAT 58.115 34.783 0.00 0.00 42.46 2.32
3030 3360 6.294176 GCATAGAACAACTCACAATCTTGGTT 60.294 38.462 0.00 0.00 0.00 3.67
3093 3423 1.884579 AGCCAATTCACAAGTGCAGAG 59.115 47.619 0.00 0.00 0.00 3.35
3112 3474 7.621428 TCATTTTCTTCCTCATTAGCAAGAG 57.379 36.000 0.00 0.00 0.00 2.85
3120 3482 7.114754 TGCAGAGTATCATTTTCTTCCTCATT 58.885 34.615 0.00 0.00 37.82 2.57
3136 3504 8.970859 AACATAGCTCTTAATTTGCAGAGTAT 57.029 30.769 0.00 5.37 39.10 2.12
3187 3555 3.932545 TTTTATTTGTGTGATGCCGCT 57.067 38.095 0.00 0.00 0.00 5.52
3258 3628 6.013032 CCATATGATATTCCTCCTTCCTGTGT 60.013 42.308 3.65 0.00 0.00 3.72
3264 3634 6.314896 CGAAAGCCATATGATATTCCTCCTTC 59.685 42.308 3.65 0.00 0.00 3.46
3265 3635 6.176183 CGAAAGCCATATGATATTCCTCCTT 58.824 40.000 3.65 0.00 0.00 3.36
3282 3653 0.321996 AGGTCTCCAGAACGAAAGCC 59.678 55.000 0.00 0.00 36.72 4.35


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

AutoCloner maintained by Alex Coulton.