Multiple sequence alignment - TraesCS2D01G582000

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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 TraesCS2D01G582000 chr2D 100.000 3644 0 0 1 3644 643124986 643121343 0.000000e+00 6730.0
1 TraesCS2D01G582000 chr2D 92.304 1884 107 10 875 2725 643006935 643005057 0.000000e+00 2641.0
2 TraesCS2D01G582000 chr2D 98.675 830 8 1 2726 3552 9949878 9950707 0.000000e+00 1469.0
3 TraesCS2D01G582000 chr2D 92.352 863 57 2 1653 2509 642955320 642956179 0.000000e+00 1219.0
4 TraesCS2D01G582000 chr2D 91.829 514 13 6 73 586 643082926 643082442 0.000000e+00 689.0
5 TraesCS2D01G582000 chr2D 95.149 268 8 3 585 852 643082216 643081954 5.630000e-113 418.0
6 TraesCS2D01G582000 chr2D 88.839 224 14 8 595 816 643007337 643007123 7.760000e-67 265.0
7 TraesCS2D01G582000 chr2D 96.104 77 2 1 1 77 643083096 643083021 1.370000e-24 124.0
8 TraesCS2D01G582000 chr2D 93.103 58 2 1 881 938 643081864 643081809 2.330000e-12 84.2
9 TraesCS2D01G582000 chr2A 92.922 1879 92 10 875 2725 767986499 767984634 0.000000e+00 2695.0
10 TraesCS2D01G582000 chr2A 90.455 220 11 7 595 813 767986901 767986691 7.700000e-72 281.0
11 TraesCS2D01G582000 chrUn 92.602 1879 107 15 875 2724 31626608 31624733 0.000000e+00 2671.0
12 TraesCS2D01G582000 chrUn 91.715 857 68 1 1653 2509 31553763 31554616 0.000000e+00 1186.0
13 TraesCS2D01G582000 chrUn 91.791 268 22 0 1028 1295 183059007 183058740 1.240000e-99 374.0
14 TraesCS2D01G582000 chr7D 98.797 831 7 1 2725 3552 17207121 17206291 0.000000e+00 1476.0
15 TraesCS2D01G582000 chr7D 94.384 463 24 2 73 533 14651490 14651952 0.000000e+00 710.0
16 TraesCS2D01G582000 chr7D 94.667 75 3 1 3 77 14651322 14651395 8.270000e-22 115.0
17 TraesCS2D01G582000 chr6D 98.797 831 6 2 2725 3552 79645772 79646601 0.000000e+00 1476.0
18 TraesCS2D01G582000 chr6D 98.676 831 8 1 2725 3552 12174248 12173418 0.000000e+00 1471.0
19 TraesCS2D01G582000 chr6D 80.729 1427 240 22 1032 2436 382079601 382081014 0.000000e+00 1079.0
20 TraesCS2D01G582000 chr6D 95.000 460 21 2 73 532 473347876 473348333 0.000000e+00 721.0
21 TraesCS2D01G582000 chr3D 98.797 831 7 1 2725 3552 530277021 530277851 0.000000e+00 1476.0
22 TraesCS2D01G582000 chr3D 98.559 833 6 3 2724 3552 599952245 599953075 0.000000e+00 1467.0
23 TraesCS2D01G582000 chr5D 98.795 830 7 1 2726 3552 16152427 16153256 0.000000e+00 1474.0
24 TraesCS2D01G582000 chr5D 98.559 833 6 3 2725 3552 8259198 8258367 0.000000e+00 1467.0
25 TraesCS2D01G582000 chr5D 96.104 77 2 1 1 77 503733264 503733339 1.370000e-24 124.0
26 TraesCS2D01G582000 chr1D 98.199 833 11 2 2723 3552 389458232 389457401 0.000000e+00 1452.0
27 TraesCS2D01G582000 chr1D 93.319 464 27 3 72 532 25836187 25836649 0.000000e+00 682.0
28 TraesCS2D01G582000 chr1D 94.805 77 3 1 1 77 25836018 25836093 6.390000e-23 119.0
29 TraesCS2D01G582000 chr5B 95.248 463 19 1 73 532 74135171 74135633 0.000000e+00 730.0
30 TraesCS2D01G582000 chr5B 96.104 77 2 1 1 77 37778891 37778966 1.370000e-24 124.0
31 TraesCS2D01G582000 chr7A 93.333 465 27 3 73 533 13914704 13915168 0.000000e+00 684.0
32 TraesCS2D01G582000 chr7A 78.009 914 182 15 1481 2383 101433564 101434469 1.140000e-154 556.0
33 TraesCS2D01G582000 chr1B 89.914 466 37 9 73 532 4948068 4948529 3.130000e-165 592.0
34 TraesCS2D01G582000 chr1B 93.506 77 4 1 1 77 16819675 16819750 2.970000e-21 113.0
35 TraesCS2D01G582000 chr7B 89.655 464 41 7 73 532 654004111 654004571 5.240000e-163 584.0
36 TraesCS2D01G582000 chr7B 89.325 459 43 4 75 530 740433941 740434396 4.080000e-159 571.0
37 TraesCS2D01G582000 chr7B 89.009 464 45 6 73 532 652985716 652986177 1.470000e-158 569.0
38 TraesCS2D01G582000 chr7B 94.805 77 3 1 1 77 652985546 652985621 6.390000e-23 119.0
39 TraesCS2D01G582000 chr4B 75.191 915 191 30 1492 2391 663985678 663986571 2.040000e-107 399.0
40 TraesCS2D01G582000 chr5A 77.632 608 133 3 1785 2391 702898093 702897488 2.070000e-97 366.0
41 TraesCS2D01G582000 chr6B 94.805 77 3 1 1 77 648168893 648168818 6.390000e-23 119.0
42 TraesCS2D01G582000 chr6A 93.506 77 4 1 1 77 18654961 18654886 2.970000e-21 113.0


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 TraesCS2D01G582000 chr2D 643121343 643124986 3643 True 6730.0 6730 100.00000 1 3644 1 chr2D.!!$R1 3643
1 TraesCS2D01G582000 chr2D 9949878 9950707 829 False 1469.0 1469 98.67500 2726 3552 1 chr2D.!!$F1 826
2 TraesCS2D01G582000 chr2D 643005057 643007337 2280 True 1453.0 2641 90.57150 595 2725 2 chr2D.!!$R2 2130
3 TraesCS2D01G582000 chr2D 642955320 642956179 859 False 1219.0 1219 92.35200 1653 2509 1 chr2D.!!$F2 856
4 TraesCS2D01G582000 chr2D 643081809 643083096 1287 True 328.8 689 94.04625 1 938 4 chr2D.!!$R3 937
5 TraesCS2D01G582000 chr2A 767984634 767986901 2267 True 1488.0 2695 91.68850 595 2725 2 chr2A.!!$R1 2130
6 TraesCS2D01G582000 chrUn 31624733 31626608 1875 True 2671.0 2671 92.60200 875 2724 1 chrUn.!!$R1 1849
7 TraesCS2D01G582000 chrUn 31553763 31554616 853 False 1186.0 1186 91.71500 1653 2509 1 chrUn.!!$F1 856
8 TraesCS2D01G582000 chr7D 17206291 17207121 830 True 1476.0 1476 98.79700 2725 3552 1 chr7D.!!$R1 827
9 TraesCS2D01G582000 chr7D 14651322 14651952 630 False 412.5 710 94.52550 3 533 2 chr7D.!!$F1 530
10 TraesCS2D01G582000 chr6D 79645772 79646601 829 False 1476.0 1476 98.79700 2725 3552 1 chr6D.!!$F1 827
11 TraesCS2D01G582000 chr6D 12173418 12174248 830 True 1471.0 1471 98.67600 2725 3552 1 chr6D.!!$R1 827
12 TraesCS2D01G582000 chr6D 382079601 382081014 1413 False 1079.0 1079 80.72900 1032 2436 1 chr6D.!!$F2 1404
13 TraesCS2D01G582000 chr3D 530277021 530277851 830 False 1476.0 1476 98.79700 2725 3552 1 chr3D.!!$F1 827
14 TraesCS2D01G582000 chr3D 599952245 599953075 830 False 1467.0 1467 98.55900 2724 3552 1 chr3D.!!$F2 828
15 TraesCS2D01G582000 chr5D 16152427 16153256 829 False 1474.0 1474 98.79500 2726 3552 1 chr5D.!!$F1 826
16 TraesCS2D01G582000 chr5D 8258367 8259198 831 True 1467.0 1467 98.55900 2725 3552 1 chr5D.!!$R1 827
17 TraesCS2D01G582000 chr1D 389457401 389458232 831 True 1452.0 1452 98.19900 2723 3552 1 chr1D.!!$R1 829
18 TraesCS2D01G582000 chr1D 25836018 25836649 631 False 400.5 682 94.06200 1 532 2 chr1D.!!$F1 531
19 TraesCS2D01G582000 chr7A 101433564 101434469 905 False 556.0 556 78.00900 1481 2383 1 chr7A.!!$F2 902
20 TraesCS2D01G582000 chr7B 652985546 652986177 631 False 344.0 569 91.90700 1 532 2 chr7B.!!$F3 531
21 TraesCS2D01G582000 chr4B 663985678 663986571 893 False 399.0 399 75.19100 1492 2391 1 chr4B.!!$F1 899
22 TraesCS2D01G582000 chr5A 702897488 702898093 605 True 366.0 366 77.63200 1785 2391 1 chr5A.!!$R1 606

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
873 1249 0.318762 GTGGCGACTCTGGAAACTCT 59.681 55.0 0.00 0.0 0.0 3.24 F
1380 1874 0.319211 GTCGTCACCAACACCGATGA 60.319 55.0 0.00 0.0 0.0 2.92 F
2012 2515 0.400213 TCTTCGGGAACATGGTGCTT 59.600 50.0 1.05 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 2425 0.678950 TGACCTGCGTGAACTCATCA 59.321 50.000 0.0 0.0 35.05 3.07 R
2624 3159 0.678950 TTGCATGACCGAGACACTCA 59.321 50.000 0.0 0.0 0.00 3.41 R
2884 3422 2.879462 GTCGTGGACGTGATCGGC 60.879 66.667 0.0 0.0 45.48 5.54 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
285 384 2.771943 TGGATGAATTCGAGGTAGGCTT 59.228 45.455 0.04 0.00 0.00 4.35
447 550 0.909623 TCTAGCCTAACAACCTGCCC 59.090 55.000 0.00 0.00 0.00 5.36
477 592 3.221771 ACAATACGCATGCAATACCCAT 58.778 40.909 19.57 0.00 0.00 4.00
586 701 3.829886 TTTGCTCGGCATACTTCTTTG 57.170 42.857 0.00 0.00 38.76 2.77
587 702 1.737838 TGCTCGGCATACTTCTTTGG 58.262 50.000 0.00 0.00 31.71 3.28
816 1161 3.942377 TAGTCGTAGGCCGCCACCA 62.942 63.158 13.15 0.00 36.19 4.17
863 1239 3.414700 CTGCGTTGGTGGCGACTC 61.415 66.667 0.00 0.00 0.00 3.36
868 1244 1.070786 GTTGGTGGCGACTCTGGAA 59.929 57.895 0.00 0.00 0.00 3.53
872 1248 0.670854 GGTGGCGACTCTGGAAACTC 60.671 60.000 0.00 0.00 0.00 3.01
873 1249 0.318762 GTGGCGACTCTGGAAACTCT 59.681 55.000 0.00 0.00 0.00 3.24
874 1250 0.603569 TGGCGACTCTGGAAACTCTC 59.396 55.000 0.00 0.00 0.00 3.20
875 1251 0.892063 GGCGACTCTGGAAACTCTCT 59.108 55.000 0.00 0.00 0.00 3.10
876 1252 1.135228 GGCGACTCTGGAAACTCTCTC 60.135 57.143 0.00 0.00 0.00 3.20
877 1253 1.542030 GCGACTCTGGAAACTCTCTCA 59.458 52.381 0.00 0.00 0.00 3.27
919 1397 2.943033 CTGGTTTTCTCGTCAGTTTGGT 59.057 45.455 0.00 0.00 0.00 3.67
920 1398 4.124238 CTGGTTTTCTCGTCAGTTTGGTA 58.876 43.478 0.00 0.00 0.00 3.25
947 1427 3.270877 GAGAAAGGGACGTGCACATAAT 58.729 45.455 18.64 0.00 0.00 1.28
973 1453 3.448301 TCAAAGGATGATGAAATGGCCAC 59.552 43.478 8.16 0.00 31.50 5.01
1013 1493 4.687018 CCACTACGTGCTGTAAATGTGTTA 59.313 41.667 0.00 0.00 31.20 2.41
1022 1502 1.469703 GTAAATGTGTTACCCGGCACC 59.530 52.381 0.00 0.00 34.94 5.01
1025 1505 2.670592 GTGTTACCCGGCACCACC 60.671 66.667 0.00 0.00 0.00 4.61
1026 1506 3.169242 TGTTACCCGGCACCACCA 61.169 61.111 0.00 0.00 39.03 4.17
1086 1580 4.208686 GGCCTACTCCACGCCTCG 62.209 72.222 0.00 0.00 39.70 4.63
1108 1602 0.392193 CTCTTGCCTGCGAGATGGTT 60.392 55.000 9.45 0.00 36.04 3.67
1190 1684 4.351938 CGCCGACTCCGTCCAACA 62.352 66.667 0.00 0.00 0.00 3.33
1320 1814 2.273179 TGCTTGTCGTAGAGGCCGT 61.273 57.895 0.00 0.00 36.95 5.68
1322 1816 1.880894 CTTGTCGTAGAGGCCGTCA 59.119 57.895 0.00 0.00 36.95 4.35
1336 1830 0.887836 CCGTCATCCCCGTCGATCTA 60.888 60.000 0.00 0.00 0.00 1.98
1380 1874 0.319211 GTCGTCACCAACACCGATGA 60.319 55.000 0.00 0.00 0.00 2.92
1484 1978 5.247792 ACTCCCGGGACATAAAATATAGGAC 59.752 44.000 22.63 0.00 0.00 3.85
1651 2145 2.281276 GAACTTCACCGCCCCGTT 60.281 61.111 0.00 0.00 0.00 4.44
1817 2320 4.143363 GTGCGCTTTACGGCCGAC 62.143 66.667 35.90 13.51 43.93 4.79
2012 2515 0.400213 TCTTCGGGAACATGGTGCTT 59.600 50.000 1.05 0.00 0.00 3.91
2021 2524 1.367102 CATGGTGCTTTGGGCGTTT 59.633 52.632 0.00 0.00 45.43 3.60
2411 2929 3.067461 CGACCTTCTACTCCTTGGATGAG 59.933 52.174 0.00 0.00 35.92 2.90
2461 2979 5.667539 TGCTCCCTCTAATCATACATAGC 57.332 43.478 0.00 0.00 0.00 2.97
2464 2982 5.395103 GCTCCCTCTAATCATACATAGCTGG 60.395 48.000 0.00 0.00 0.00 4.85
2624 3159 6.676950 TGTGTAAACAAATCTGCGAATTCAT 58.323 32.000 6.22 0.00 0.00 2.57
2635 3170 1.590238 GCGAATTCATGAGTGTCTCGG 59.410 52.381 11.31 0.00 32.35 4.63
2636 3171 2.881074 CGAATTCATGAGTGTCTCGGT 58.119 47.619 6.22 0.00 32.35 4.69
2637 3172 2.854777 CGAATTCATGAGTGTCTCGGTC 59.145 50.000 6.22 0.00 32.35 4.79
2638 3173 3.673323 CGAATTCATGAGTGTCTCGGTCA 60.673 47.826 6.22 0.00 32.35 4.02
2807 3343 4.659111 TTTTATTAGCCGTCCGATCTGA 57.341 40.909 0.00 0.00 0.00 3.27
2823 3359 6.044989 TCCGATCTGATGGGGGATTAAAAATA 59.955 38.462 17.23 0.00 0.00 1.40
3259 3800 1.739067 ACTTTGATTCGTAGCCTGCC 58.261 50.000 0.00 0.00 0.00 4.85
3355 3896 4.304537 ACATCTCTGATCACGTCTGATG 57.695 45.455 12.87 12.87 37.24 3.07
3552 4093 1.065491 TGCAGGAAGACATGGCGTATT 60.065 47.619 0.00 0.00 0.00 1.89
3553 4094 1.599542 GCAGGAAGACATGGCGTATTC 59.400 52.381 0.00 0.00 43.70 1.75
3556 4097 2.622064 GAAGACATGGCGTATTCCCT 57.378 50.000 0.00 0.00 39.47 4.20
3557 4098 3.746045 GAAGACATGGCGTATTCCCTA 57.254 47.619 0.00 0.00 39.47 3.53
3558 4099 3.654414 GAAGACATGGCGTATTCCCTAG 58.346 50.000 0.00 0.00 39.47 3.02
3559 4100 2.679082 AGACATGGCGTATTCCCTAGT 58.321 47.619 0.00 0.00 0.00 2.57
3560 4101 2.365617 AGACATGGCGTATTCCCTAGTG 59.634 50.000 0.00 0.00 0.00 2.74
3561 4102 1.202651 ACATGGCGTATTCCCTAGTGC 60.203 52.381 0.00 0.00 0.00 4.40
3562 4103 1.128200 ATGGCGTATTCCCTAGTGCA 58.872 50.000 0.00 0.00 0.00 4.57
3563 4104 1.128200 TGGCGTATTCCCTAGTGCAT 58.872 50.000 0.00 0.00 0.00 3.96
3564 4105 1.488812 TGGCGTATTCCCTAGTGCATT 59.511 47.619 0.00 0.00 0.00 3.56
3565 4106 2.092646 TGGCGTATTCCCTAGTGCATTT 60.093 45.455 0.00 0.00 0.00 2.32
3566 4107 2.949644 GGCGTATTCCCTAGTGCATTTT 59.050 45.455 0.00 0.00 0.00 1.82
3567 4108 3.380320 GGCGTATTCCCTAGTGCATTTTT 59.620 43.478 0.00 0.00 0.00 1.94
3568 4109 4.577283 GGCGTATTCCCTAGTGCATTTTTA 59.423 41.667 0.00 0.00 0.00 1.52
3569 4110 5.240844 GGCGTATTCCCTAGTGCATTTTTAT 59.759 40.000 0.00 0.00 0.00 1.40
3570 4111 6.238925 GGCGTATTCCCTAGTGCATTTTTATT 60.239 38.462 0.00 0.00 0.00 1.40
3571 4112 7.200455 GCGTATTCCCTAGTGCATTTTTATTT 58.800 34.615 0.00 0.00 0.00 1.40
3572 4113 7.704899 GCGTATTCCCTAGTGCATTTTTATTTT 59.295 33.333 0.00 0.00 0.00 1.82
3573 4114 9.233232 CGTATTCCCTAGTGCATTTTTATTTTC 57.767 33.333 0.00 0.00 0.00 2.29
3577 4118 9.434420 TTCCCTAGTGCATTTTTATTTTCAATG 57.566 29.630 0.00 0.00 0.00 2.82
3578 4119 8.592809 TCCCTAGTGCATTTTTATTTTCAATGT 58.407 29.630 0.00 0.00 31.60 2.71
3579 4120 9.218440 CCCTAGTGCATTTTTATTTTCAATGTT 57.782 29.630 0.00 0.00 31.60 2.71
3583 4124 9.733219 AGTGCATTTTTATTTTCAATGTTTTGG 57.267 25.926 0.00 0.00 33.44 3.28
3584 4125 9.727627 GTGCATTTTTATTTTCAATGTTTTGGA 57.272 25.926 0.00 0.00 33.44 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
285 384 7.010160 ACCCTTTCTTCTTTCATGGTAATCAA 58.990 34.615 0.00 0.00 0.00 2.57
447 550 5.402464 TGCATGCGTATTGTTGTGTATAG 57.598 39.130 14.09 0.00 0.00 1.31
477 592 3.133901 AGTGTCACGATGGGTATATTGCA 59.866 43.478 0.00 0.00 0.00 4.08
564 679 4.545610 CAAAGAAGTATGCCGAGCAAAAA 58.454 39.130 2.68 0.00 43.62 1.94
607 949 5.659463 TCTTGTGGTTTCAACTTTCAATGG 58.341 37.500 0.00 0.00 0.00 3.16
789 1134 4.115279 CTACGACTACGGAGCCGA 57.885 61.111 11.40 0.00 43.65 5.54
839 1214 2.280524 CACCAACGCAGACCCGAA 60.281 61.111 0.00 0.00 0.00 4.30
859 1235 2.894126 TGGTGAGAGAGTTTCCAGAGTC 59.106 50.000 0.00 0.00 0.00 3.36
863 1239 2.772287 GGTTGGTGAGAGAGTTTCCAG 58.228 52.381 0.00 0.00 0.00 3.86
868 1244 0.471211 TCCCGGTTGGTGAGAGAGTT 60.471 55.000 0.00 0.00 34.77 3.01
872 1248 0.320771 CAGTTCCCGGTTGGTGAGAG 60.321 60.000 0.00 0.00 34.77 3.20
873 1249 1.752198 CAGTTCCCGGTTGGTGAGA 59.248 57.895 0.00 0.00 34.77 3.27
874 1250 1.966451 GCAGTTCCCGGTTGGTGAG 60.966 63.158 0.00 0.00 34.77 3.51
875 1251 1.122632 TAGCAGTTCCCGGTTGGTGA 61.123 55.000 0.00 0.00 34.77 4.02
876 1252 0.250553 TTAGCAGTTCCCGGTTGGTG 60.251 55.000 0.00 0.00 34.77 4.17
877 1253 0.475044 TTTAGCAGTTCCCGGTTGGT 59.525 50.000 0.00 1.48 34.77 3.67
919 1397 3.056678 TGCACGTCCCTTTCTCGTTTATA 60.057 43.478 0.00 0.00 35.62 0.98
920 1398 2.289195 TGCACGTCCCTTTCTCGTTTAT 60.289 45.455 0.00 0.00 35.62 1.40
947 1427 5.939296 GGCCATTTCATCATCCTTTGAAAAA 59.061 36.000 0.00 0.00 43.04 1.94
973 1453 6.015688 ACGTAGTGGTGTATATATGAACCCAG 60.016 42.308 13.34 5.77 42.51 4.45
1013 1493 3.319198 CTAGTGGTGGTGCCGGGT 61.319 66.667 2.18 0.00 41.21 5.28
1025 1505 1.802880 CGCCTCCATTTCGACCTAGTG 60.803 57.143 0.00 0.00 0.00 2.74
1026 1506 0.460311 CGCCTCCATTTCGACCTAGT 59.540 55.000 0.00 0.00 0.00 2.57
1086 1580 3.397613 ATCTCGCAGGCAAGAGGGC 62.398 63.158 4.52 0.00 43.80 5.19
1097 1591 2.125552 CAGCGGAACCATCTCGCA 60.126 61.111 9.51 0.00 43.32 5.10
1108 1602 2.035155 TCGAAGAGGGTCAGCGGA 59.965 61.111 0.00 0.00 0.00 5.54
1190 1684 4.416738 GCCCTCCTTGAGCGCCTT 62.417 66.667 2.29 0.00 28.31 4.35
1320 1814 1.235281 CGCTAGATCGACGGGGATGA 61.235 60.000 0.00 0.00 0.00 2.92
1322 1816 0.956410 CTCGCTAGATCGACGGGGAT 60.956 60.000 0.00 0.00 34.46 3.85
1361 1855 0.319211 TCATCGGTGTTGGTGACGAC 60.319 55.000 0.00 0.00 45.61 4.34
1380 1874 1.073199 GGCACTGCAGGGTACAGTT 59.927 57.895 19.18 0.00 46.01 3.16
1577 2071 0.613853 AGGTGCTAACGGAGTAGCCA 60.614 55.000 11.16 0.08 45.00 4.75
1651 2145 2.782222 CCGCGATCGAGGAAAGGGA 61.782 63.158 31.31 0.00 37.24 4.20
1817 2320 1.150567 CCTTGAGCTCGGCGATGAAG 61.151 60.000 11.27 6.38 0.00 3.02
1922 2425 0.678950 TGACCTGCGTGAACTCATCA 59.321 50.000 0.00 0.00 35.05 3.07
2012 2515 1.456705 AAGCCTTGGAAACGCCCAA 60.457 52.632 4.74 4.74 43.42 4.12
2456 2974 2.386661 AACGACCTTCACCAGCTATG 57.613 50.000 0.00 0.00 0.00 2.23
2608 3143 4.978186 ACACTCATGAATTCGCAGATTTG 58.022 39.130 0.00 2.44 35.04 2.32
2624 3159 0.678950 TTGCATGACCGAGACACTCA 59.321 50.000 0.00 0.00 0.00 3.41
2635 3170 7.031372 ACACACATGAGATTTATTTGCATGAC 58.969 34.615 0.00 0.00 38.82 3.06
2636 3171 7.160547 ACACACATGAGATTTATTTGCATGA 57.839 32.000 0.00 0.00 38.82 3.07
2637 3172 8.186163 AGTACACACATGAGATTTATTTGCATG 58.814 33.333 0.00 0.00 41.44 4.06
2638 3173 8.284945 AGTACACACATGAGATTTATTTGCAT 57.715 30.769 0.00 0.00 0.00 3.96
2712 3248 8.393366 CCGTAAAAGGGCTCTAAGTTAAATAAC 58.607 37.037 0.00 0.00 36.46 1.89
2884 3422 2.879462 GTCGTGGACGTGATCGGC 60.879 66.667 0.00 0.00 45.48 5.54
3259 3800 9.892130 ATGACTAAACAAATCTAAGTAGGAAGG 57.108 33.333 0.00 0.00 0.00 3.46
3355 3896 3.059800 GCAAGATCGGACGGCTAATAAAC 60.060 47.826 0.00 0.00 0.00 2.01
3552 4093 8.592809 ACATTGAAAATAAAAATGCACTAGGGA 58.407 29.630 0.00 0.00 35.20 4.20
3553 4094 8.776376 ACATTGAAAATAAAAATGCACTAGGG 57.224 30.769 0.00 0.00 35.20 3.53
3557 4098 9.733219 CCAAAACATTGAAAATAAAAATGCACT 57.267 25.926 0.00 0.00 35.20 4.40
3558 4099 9.727627 TCCAAAACATTGAAAATAAAAATGCAC 57.272 25.926 0.00 0.00 35.20 4.57


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

AutoCloner maintained by Alex Coulton.