Multiple sequence alignment - TraesCS1A01G006300

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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 TraesCS1A01G006300 chr1A 100.000 5479 0 0 1 5479 3504929 3499451 0.000000e+00 10118.0
1 TraesCS1A01G006300 chr1A 85.317 3487 457 32 1037 4509 3491825 3488380 0.000000e+00 3552.0
2 TraesCS1A01G006300 chr1A 85.012 3356 480 20 1120 4467 3672437 3669097 0.000000e+00 3389.0
3 TraesCS1A01G006300 chr1A 82.345 2158 262 65 1 2094 3455862 3453760 0.000000e+00 1764.0
4 TraesCS1A01G006300 chr1A 87.927 762 44 22 4734 5479 3653107 3652378 0.000000e+00 854.0
5 TraesCS1A01G006300 chr1A 81.755 433 53 19 4770 5197 2979877 2980288 6.800000e-89 339.0
6 TraesCS1A01G006300 chr1A 82.230 287 36 11 4992 5265 3469849 3469565 3.300000e-57 233.0
7 TraesCS1A01G006300 chr1A 77.803 437 55 24 4770 5195 27218088 27218493 1.190000e-56 231.0
8 TraesCS1A01G006300 chr1A 90.370 135 4 4 4555 4685 3653698 3653569 9.440000e-38 169.0
9 TraesCS1A01G006300 chr1A 88.542 96 11 0 515 610 3696120 3696025 3.470000e-22 117.0
10 TraesCS1A01G006300 chr1A 84.444 90 9 4 5303 5391 3667670 3667585 3.520000e-12 84.2
11 TraesCS1A01G006300 chr1B 95.333 4264 155 27 314 4550 4094820 4099066 0.000000e+00 6732.0
12 TraesCS1A01G006300 chr1B 88.051 4427 466 41 1092 5479 3951180 3955582 0.000000e+00 5186.0
13 TraesCS1A01G006300 chr1B 85.856 3627 465 38 940 4550 3942264 3945858 0.000000e+00 3812.0
14 TraesCS1A01G006300 chr1B 85.611 3600 477 26 951 4535 4483775 4480202 0.000000e+00 3740.0
15 TraesCS1A01G006300 chr1B 85.463 3529 472 28 1037 4548 3964529 3968033 0.000000e+00 3637.0
16 TraesCS1A01G006300 chr1B 85.503 3442 476 20 1087 4520 4510812 4507386 0.000000e+00 3570.0
17 TraesCS1A01G006300 chr1B 87.383 1926 227 14 2638 4556 4566502 4564586 0.000000e+00 2196.0
18 TraesCS1A01G006300 chr1B 84.097 2138 265 39 121 2234 4857302 4855216 0.000000e+00 1995.0
19 TraesCS1A01G006300 chr1B 87.882 817 91 6 3745 4556 4842014 4841201 0.000000e+00 953.0
20 TraesCS1A01G006300 chr1B 83.008 359 22 17 1 333 4094463 4094808 6.940000e-74 289.0
21 TraesCS1A01G006300 chr1B 86.555 119 15 1 493 610 4859700 4859582 4.450000e-26 130.0
22 TraesCS1A01G006300 chr1D 85.297 4516 554 63 75 4536 622131 617672 0.000000e+00 4560.0
23 TraesCS1A01G006300 chr1D 88.724 807 42 19 4555 5354 651085 651849 0.000000e+00 941.0
24 TraesCS1A01G006300 chr1D 86.111 216 23 5 4987 5197 464141 464354 5.520000e-55 226.0
25 TraesCS1A01G006300 chr1D 80.986 142 15 5 4555 4693 694481 694349 9.710000e-18 102.0
26 TraesCS1A01G006300 chr3D 86.550 3487 431 32 1087 4556 560058089 560054624 0.000000e+00 3807.0
27 TraesCS1A01G006300 chr3D 78.348 448 64 21 4770 5191 560052981 560052541 5.440000e-65 259.0


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 TraesCS1A01G006300 chr1A 3499451 3504929 5478 True 10118.0 10118 100.0000 1 5479 1 chr1A.!!$R4 5478
1 TraesCS1A01G006300 chr1A 3488380 3491825 3445 True 3552.0 3552 85.3170 1037 4509 1 chr1A.!!$R3 3472
2 TraesCS1A01G006300 chr1A 3453760 3455862 2102 True 1764.0 1764 82.3450 1 2094 1 chr1A.!!$R1 2093
3 TraesCS1A01G006300 chr1A 3667585 3672437 4852 True 1736.6 3389 84.7280 1120 5391 2 chr1A.!!$R7 4271
4 TraesCS1A01G006300 chr1A 3652378 3653698 1320 True 511.5 854 89.1485 4555 5479 2 chr1A.!!$R6 924
5 TraesCS1A01G006300 chr1B 3951180 3955582 4402 False 5186.0 5186 88.0510 1092 5479 1 chr1B.!!$F2 4387
6 TraesCS1A01G006300 chr1B 3942264 3945858 3594 False 3812.0 3812 85.8560 940 4550 1 chr1B.!!$F1 3610
7 TraesCS1A01G006300 chr1B 4480202 4483775 3573 True 3740.0 3740 85.6110 951 4535 1 chr1B.!!$R1 3584
8 TraesCS1A01G006300 chr1B 3964529 3968033 3504 False 3637.0 3637 85.4630 1037 4548 1 chr1B.!!$F3 3511
9 TraesCS1A01G006300 chr1B 4507386 4510812 3426 True 3570.0 3570 85.5030 1087 4520 1 chr1B.!!$R2 3433
10 TraesCS1A01G006300 chr1B 4094463 4099066 4603 False 3510.5 6732 89.1705 1 4550 2 chr1B.!!$F4 4549
11 TraesCS1A01G006300 chr1B 4564586 4566502 1916 True 2196.0 2196 87.3830 2638 4556 1 chr1B.!!$R3 1918
12 TraesCS1A01G006300 chr1B 4855216 4859700 4484 True 1062.5 1995 85.3260 121 2234 2 chr1B.!!$R5 2113
13 TraesCS1A01G006300 chr1B 4841201 4842014 813 True 953.0 953 87.8820 3745 4556 1 chr1B.!!$R4 811
14 TraesCS1A01G006300 chr1D 617672 622131 4459 True 4560.0 4560 85.2970 75 4536 1 chr1D.!!$R1 4461
15 TraesCS1A01G006300 chr1D 651085 651849 764 False 941.0 941 88.7240 4555 5354 1 chr1D.!!$F2 799
16 TraesCS1A01G006300 chr3D 560052541 560058089 5548 True 2033.0 3807 82.4490 1087 5191 2 chr3D.!!$R1 4104

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
353 2684 0.176680 AGCCACTGCCTCGTATTCTG 59.823 55.000 0.00 0.0 38.69 3.02 F
633 2974 0.534203 TCAAACCAACCAGAGGACGC 60.534 55.000 0.00 0.0 0.00 5.19 F
1083 3455 1.747355 AGCAAAATGCCATCTTCCTCG 59.253 47.619 0.00 0.0 46.52 4.63 F
1109 3496 2.254546 TTGTTGTACCTCTGCCTGTG 57.745 50.000 0.00 0.0 0.00 3.66 F
3336 5730 2.079925 CTCTCTGGCCTACAACTTTGC 58.920 52.381 3.32 0.0 0.00 3.68 F
3424 5818 0.034756 GGTGGTGGGTTTTGGCATTC 59.965 55.000 0.00 0.0 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 4169 7.824779 GGTATAGGCCCTGAAAGTTGATTATAG 59.175 40.741 0.00 0.00 0.00 1.31 R
2400 4790 3.473625 CCCAAGTCGAACAAGGTTTACT 58.526 45.455 0.00 0.00 0.00 2.24 R
2658 5048 1.216427 AGATTTTGGGAGATCTGCCCC 59.784 52.381 28.47 20.05 45.40 5.80 R
3405 5799 0.034756 GAATGCCAAAACCCACCACC 59.965 55.000 0.00 0.00 0.00 4.61 R
4296 6706 0.995024 ACCAGCATAGCTTGTTCCCT 59.005 50.000 0.00 0.00 36.40 4.20 R
4602 7061 1.412710 CGTGTGGCATACAGGAGGTAT 59.587 52.381 14.87 0.00 45.61 2.73 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
34 37 4.420522 AGTACCGAGTCTACCTTAGAGG 57.579 50.000 0.00 0.00 42.49 3.69
62 65 7.759489 TGTTTAAGATGCAACCAGTCTAATT 57.241 32.000 0.00 0.00 0.00 1.40
69 72 5.682943 TGCAACCAGTCTAATTTACACAC 57.317 39.130 0.00 0.00 0.00 3.82
73 76 6.427150 CAACCAGTCTAATTTACACACACAC 58.573 40.000 0.00 0.00 0.00 3.82
84 87 1.597195 ACACACACACACACATAAGCG 59.403 47.619 0.00 0.00 0.00 4.68
87 90 1.197492 CACACACACACATAAGCGCAT 59.803 47.619 11.47 0.00 0.00 4.73
90 93 0.523968 CACACACATAAGCGCATGCC 60.524 55.000 13.15 4.99 44.31 4.40
91 94 0.959867 ACACACATAAGCGCATGCCA 60.960 50.000 13.15 0.00 44.31 4.92
110 120 1.003580 CACACTTGGAGCTACATGGGT 59.996 52.381 13.87 13.87 32.99 4.51
164 2443 5.121221 ACTTGTATTTACAAAGTGCTGGC 57.879 39.130 4.82 0.00 44.67 4.85
172 2451 1.342174 ACAAAGTGCTGGCCAATCAAG 59.658 47.619 7.01 0.00 0.00 3.02
237 2536 4.949856 ACTTGAGCTTGGAACTTTTCTTCA 59.050 37.500 0.00 0.00 0.00 3.02
243 2542 4.576463 GCTTGGAACTTTTCTTCAGTCAGA 59.424 41.667 0.00 0.00 0.00 3.27
284 2585 3.268334 TGGCTGTATTCCCCACTTGTATT 59.732 43.478 0.00 0.00 0.00 1.89
352 2683 1.409427 GTAGCCACTGCCTCGTATTCT 59.591 52.381 0.00 0.00 38.69 2.40
353 2684 0.176680 AGCCACTGCCTCGTATTCTG 59.823 55.000 0.00 0.00 38.69 3.02
355 2686 1.676014 GCCACTGCCTCGTATTCTGTT 60.676 52.381 0.00 0.00 0.00 3.16
401 2732 5.195756 ACTTGGGGTCCAGGATTTGTATTAT 59.804 40.000 3.03 0.00 34.05 1.28
402 2733 5.742562 TGGGGTCCAGGATTTGTATTATT 57.257 39.130 0.00 0.00 0.00 1.40
421 2753 9.581099 GTATTATTACCAAAATTCAACACAGGG 57.419 33.333 0.00 0.00 0.00 4.45
425 2757 2.037121 CCAAAATTCAACACAGGGACCC 59.963 50.000 0.59 0.59 0.00 4.46
426 2758 2.009681 AAATTCAACACAGGGACCCC 57.990 50.000 7.00 1.17 0.00 4.95
429 2761 1.822425 TTCAACACAGGGACCCCTTA 58.178 50.000 7.00 0.00 45.70 2.69
430 2762 2.053747 TCAACACAGGGACCCCTTAT 57.946 50.000 7.00 0.00 45.70 1.73
433 2765 3.264964 TCAACACAGGGACCCCTTATTAC 59.735 47.826 7.00 0.00 45.70 1.89
481 2819 4.535526 ATTTTCCCATGGTTAGTTGCAC 57.464 40.909 11.73 0.00 0.00 4.57
488 2829 2.332654 GGTTAGTTGCACTGCCCCG 61.333 63.158 0.00 0.00 0.00 5.73
631 2972 4.287766 ACTATCAAACCAACCAGAGGAC 57.712 45.455 0.00 0.00 0.00 3.85
632 2973 2.185004 ATCAAACCAACCAGAGGACG 57.815 50.000 0.00 0.00 0.00 4.79
633 2974 0.534203 TCAAACCAACCAGAGGACGC 60.534 55.000 0.00 0.00 0.00 5.19
646 2987 2.363680 AGAGGACGCACCATCAGATAAG 59.636 50.000 2.21 0.00 42.04 1.73
680 3021 6.088085 CGCAATGTTAACTCAAAAGTCCATTC 59.912 38.462 7.22 0.00 33.48 2.67
824 3169 4.886489 AGGCATGAGGAAAGAAAATAGAGC 59.114 41.667 0.00 0.00 0.00 4.09
903 3251 3.269381 AGAAAAATGGGGCAGAGATGGTA 59.731 43.478 0.00 0.00 0.00 3.25
932 3280 5.171339 ACTGAAAACTACTCATCCAGCAT 57.829 39.130 0.00 0.00 0.00 3.79
933 3281 6.299805 ACTGAAAACTACTCATCCAGCATA 57.700 37.500 0.00 0.00 0.00 3.14
935 3283 7.341805 ACTGAAAACTACTCATCCAGCATAAT 58.658 34.615 0.00 0.00 0.00 1.28
936 3284 7.831193 ACTGAAAACTACTCATCCAGCATAATT 59.169 33.333 0.00 0.00 0.00 1.40
938 3286 8.461222 TGAAAACTACTCATCCAGCATAATTTG 58.539 33.333 0.00 0.00 0.00 2.32
960 3320 2.700371 TGTGTGTTGACTGACTGAGGAT 59.300 45.455 0.00 0.00 0.00 3.24
970 3330 5.359292 TGACTGACTGAGGATCTCATAACAG 59.641 44.000 16.37 16.37 39.92 3.16
1017 3385 2.698803 TCAATGGTGTCCACAGAATCG 58.301 47.619 0.00 0.00 35.80 3.34
1032 3400 2.092212 AGAATCGCATCCTCCAACCAAT 60.092 45.455 0.00 0.00 0.00 3.16
1033 3401 3.136443 AGAATCGCATCCTCCAACCAATA 59.864 43.478 0.00 0.00 0.00 1.90
1034 3402 2.620251 TCGCATCCTCCAACCAATAG 57.380 50.000 0.00 0.00 0.00 1.73
1083 3455 1.747355 AGCAAAATGCCATCTTCCTCG 59.253 47.619 0.00 0.00 46.52 4.63
1109 3496 2.254546 TTGTTGTACCTCTGCCTGTG 57.745 50.000 0.00 0.00 0.00 3.66
1152 3542 3.349006 CAAGAAGCACACGCGGCT 61.349 61.111 12.47 6.83 45.49 5.52
1779 4169 7.446319 ACCCAACTAAATACTTTGTACCTGTTC 59.554 37.037 0.00 0.00 0.00 3.18
2400 4790 4.353383 TCCTCGAGAATTCGGAGATCTA 57.647 45.455 23.13 9.11 46.67 1.98
2658 5048 4.505922 GCCTTGTCATCAAATAGACTCTCG 59.494 45.833 0.00 0.00 35.81 4.04
3336 5730 2.079925 CTCTCTGGCCTACAACTTTGC 58.920 52.381 3.32 0.00 0.00 3.68
3405 5799 4.496175 GGTTTGCTTTTGCCAATTGTTCTG 60.496 41.667 4.43 0.00 46.87 3.02
3424 5818 0.034756 GGTGGTGGGTTTTGGCATTC 59.965 55.000 0.00 0.00 0.00 2.67
3461 5855 9.244799 TGTTGTCATAATAATGCTTAGTCGTAG 57.755 33.333 0.00 0.00 32.76 3.51
3723 6117 4.424061 TCGCAGTGAAATGGAAATCTTG 57.576 40.909 0.00 0.00 0.00 3.02
3847 6241 3.609853 CGGATGTTGGAAAATGAGGAGA 58.390 45.455 0.00 0.00 0.00 3.71
3854 6248 3.415212 TGGAAAATGAGGAGACAGCAAG 58.585 45.455 0.00 0.00 0.00 4.01
3870 6264 1.278699 GCAAGGGAATTGGATTGGCAA 59.721 47.619 0.68 0.68 39.47 4.52
4122 6522 0.969894 ACCTTCCTTCTCACGTCTGG 59.030 55.000 0.00 0.00 0.00 3.86
4123 6523 0.247736 CCTTCCTTCTCACGTCTGGG 59.752 60.000 0.00 0.00 0.00 4.45
4124 6524 0.390472 CTTCCTTCTCACGTCTGGGC 60.390 60.000 0.00 0.00 0.00 5.36
4125 6525 1.118965 TTCCTTCTCACGTCTGGGCA 61.119 55.000 0.00 0.00 0.00 5.36
4126 6526 0.904865 TCCTTCTCACGTCTGGGCAT 60.905 55.000 0.00 0.00 0.00 4.40
4127 6527 0.742281 CCTTCTCACGTCTGGGCATG 60.742 60.000 0.00 0.00 0.00 4.06
4129 6529 1.204704 CTTCTCACGTCTGGGCATGTA 59.795 52.381 0.00 0.00 0.00 2.29
4130 6530 1.485124 TCTCACGTCTGGGCATGTAT 58.515 50.000 0.00 0.00 0.00 2.29
4131 6531 1.409064 TCTCACGTCTGGGCATGTATC 59.591 52.381 0.00 0.00 0.00 2.24
4133 6533 2.623416 CTCACGTCTGGGCATGTATCTA 59.377 50.000 0.00 0.00 0.00 1.98
4135 6535 4.403734 TCACGTCTGGGCATGTATCTATA 58.596 43.478 0.00 0.00 0.00 1.31
4139 6540 7.996644 TCACGTCTGGGCATGTATCTATATATA 59.003 37.037 0.00 0.00 0.00 0.86
4296 6706 7.660112 TCTATTAGACGGTAGTTTGTCAAACA 58.340 34.615 26.19 12.32 43.79 2.83
4464 6874 2.432146 GCATACCAGACACTCATCCAGA 59.568 50.000 0.00 0.00 0.00 3.86
4465 6875 3.118629 GCATACCAGACACTCATCCAGAA 60.119 47.826 0.00 0.00 0.00 3.02
4466 6876 4.691175 CATACCAGACACTCATCCAGAAG 58.309 47.826 0.00 0.00 0.00 2.85
4467 6877 2.894731 ACCAGACACTCATCCAGAAGA 58.105 47.619 0.00 0.00 0.00 2.87
4470 6880 2.093764 CAGACACTCATCCAGAAGACCC 60.094 54.545 0.00 0.00 0.00 4.46
4552 6977 2.289002 GACATGTGATCCGAATTCTGGC 59.711 50.000 1.15 0.00 0.00 4.85
4559 7018 0.323629 TCCGAATTCTGGCGAGGTTT 59.676 50.000 3.52 0.00 0.00 3.27
4573 7032 2.352421 CGAGGTTTCCGCTTTAGACTCA 60.352 50.000 0.00 0.00 0.00 3.41
4743 8810 3.270877 AGCTAGGTGCAGGAAAATTACG 58.729 45.455 0.00 0.00 45.94 3.18
4842 8990 8.362639 AGTTTCTTGTATTTCATTGCTCACATT 58.637 29.630 0.00 0.00 0.00 2.71
4843 8991 9.624697 GTTTCTTGTATTTCATTGCTCACATTA 57.375 29.630 0.00 0.00 0.00 1.90
4844 8992 9.624697 TTTCTTGTATTTCATTGCTCACATTAC 57.375 29.630 0.00 0.00 0.00 1.89
4845 8993 8.334263 TCTTGTATTTCATTGCTCACATTACA 57.666 30.769 0.00 0.00 0.00 2.41
4846 8994 8.236586 TCTTGTATTTCATTGCTCACATTACAC 58.763 33.333 0.00 0.00 0.00 2.90
4847 8995 7.686438 TGTATTTCATTGCTCACATTACACT 57.314 32.000 0.00 0.00 0.00 3.55
4851 8999 6.968131 TTCATTGCTCACATTACACTAGAC 57.032 37.500 0.00 0.00 0.00 2.59
4871 9019 4.528206 AGACCCATCATCTCGTATTGCATA 59.472 41.667 0.00 0.00 0.00 3.14
4884 9032 2.591753 GCATACCCTGCCTGCAGA 59.408 61.111 20.29 0.98 46.30 4.26
4885 9033 1.150081 GCATACCCTGCCTGCAGAT 59.850 57.895 20.29 10.38 46.30 2.90
5014 9187 7.224949 CAGGATGCTGCATACATCTATATCTTG 59.775 40.741 25.71 8.14 42.88 3.02
5026 9271 8.718158 ACATCTATATCTTGAATCCTGACAGA 57.282 34.615 3.32 0.00 0.00 3.41
5032 9277 3.708631 TCTTGAATCCTGACAGATCCCTC 59.291 47.826 3.32 0.00 0.00 4.30
5135 9457 8.341173 GCTAGAATCCAAATCTAACATGAACTG 58.659 37.037 0.00 0.00 0.00 3.16
5146 9468 6.650120 TCTAACATGAACTGGATAGGAAACC 58.350 40.000 0.00 0.00 0.00 3.27
5254 9614 7.185304 AGGGAAGGCATATGGAATACAGATATT 59.815 37.037 4.56 0.00 33.47 1.28
5255 9615 8.494433 GGGAAGGCATATGGAATACAGATATTA 58.506 37.037 4.56 0.00 30.77 0.98
5256 9616 9.553064 GGAAGGCATATGGAATACAGATATTAG 57.447 37.037 4.56 0.00 30.77 1.73
5259 9619 9.271921 AGGCATATGGAATACAGATATTAGACA 57.728 33.333 4.56 0.00 30.77 3.41
5267 9627 9.509855 GGAATACAGATATTAGACATTAGAGCG 57.490 37.037 0.00 0.00 30.77 5.03
5382 9880 9.319060 TCAACTAGATTCAGGATTCAGCTATAT 57.681 33.333 0.00 0.00 0.00 0.86
5391 9889 6.665680 TCAGGATTCAGCTATATACCTTCTCC 59.334 42.308 0.00 0.00 0.00 3.71
5404 9902 8.817092 ATATACCTTCTCCTATTCAGCTAGAC 57.183 38.462 0.00 0.00 0.00 2.59
5448 9954 0.174617 GCGGGAAGAGAGGTGAAGAG 59.825 60.000 0.00 0.00 0.00 2.85
5452 9965 2.530701 GGAAGAGAGGTGAAGAGGACA 58.469 52.381 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.351706 AGCCTCTAAGGTAGACTCGG 57.648 55.000 0.00 0.00 37.80 4.63
18 19 4.391155 ACATAGCCTCTAAGGTAGACTCG 58.609 47.826 0.00 0.00 37.80 4.18
34 37 5.355350 AGACTGGTTGCATCTTAAACATAGC 59.645 40.000 0.00 0.00 0.00 2.97
62 65 3.246463 CGCTTATGTGTGTGTGTGTGTAA 59.754 43.478 0.00 0.00 0.00 2.41
69 72 1.886037 CATGCGCTTATGTGTGTGTG 58.114 50.000 9.73 0.00 0.00 3.82
73 76 0.523968 GTGGCATGCGCTTATGTGTG 60.524 55.000 12.44 0.00 38.60 3.82
84 87 0.677731 TAGCTCCAAGTGTGGCATGC 60.678 55.000 9.90 9.90 45.54 4.06
87 90 0.692476 ATGTAGCTCCAAGTGTGGCA 59.308 50.000 0.00 0.00 45.54 4.92
90 93 1.003580 ACCCATGTAGCTCCAAGTGTG 59.996 52.381 0.00 0.00 0.00 3.82
91 94 1.003580 CACCCATGTAGCTCCAAGTGT 59.996 52.381 0.00 0.00 0.00 3.55
164 2443 6.652481 TCTTCTAGCACTTTCTTCTTGATTGG 59.348 38.462 0.00 0.00 0.00 3.16
172 2451 8.996024 ATTCTACTTCTTCTAGCACTTTCTTC 57.004 34.615 0.00 0.00 0.00 2.87
237 2536 4.696455 CAAAATTTTTGGCCACTCTGACT 58.304 39.130 3.88 0.00 0.00 3.41
243 2542 2.950975 CCAAGCAAAATTTTTGGCCACT 59.049 40.909 20.36 8.46 37.85 4.00
284 2585 5.105567 TGAAGAAAGGTACAACTTGTGGA 57.894 39.130 4.57 0.00 0.00 4.02
295 2596 1.064003 TGGCTGGCTGAAGAAAGGTA 58.936 50.000 2.00 0.00 0.00 3.08
333 2664 1.409064 CAGAATACGAGGCAGTGGCTA 59.591 52.381 20.63 4.42 38.98 3.93
352 2683 1.208706 TGGAAGTCCTGTGTCCAACA 58.791 50.000 0.00 0.00 38.50 3.33
353 2684 2.341846 TTGGAAGTCCTGTGTCCAAC 57.658 50.000 0.25 0.00 44.57 3.77
355 2686 1.208706 TGTTGGAAGTCCTGTGTCCA 58.791 50.000 0.00 0.00 39.70 4.02
401 2732 4.342665 GGTCCCTGTGTTGAATTTTGGTAA 59.657 41.667 0.00 0.00 0.00 2.85
402 2733 3.892588 GGTCCCTGTGTTGAATTTTGGTA 59.107 43.478 0.00 0.00 0.00 3.25
420 2752 4.154942 TCGATGGTAGTAATAAGGGGTCC 58.845 47.826 0.00 0.00 0.00 4.46
421 2753 5.997384 ATCGATGGTAGTAATAAGGGGTC 57.003 43.478 0.00 0.00 0.00 4.46
425 2757 9.804758 GGAATTCTATCGATGGTAGTAATAAGG 57.195 37.037 8.54 0.00 0.00 2.69
429 2761 8.651589 TCTGGAATTCTATCGATGGTAGTAAT 57.348 34.615 8.54 0.00 0.00 1.89
430 2762 8.473358 TTCTGGAATTCTATCGATGGTAGTAA 57.527 34.615 8.54 0.00 0.00 2.24
433 2765 6.815641 CCATTCTGGAATTCTATCGATGGTAG 59.184 42.308 8.54 0.00 40.96 3.18
488 2829 4.773323 ACAAAAGATTAGCTCAAGTGGC 57.227 40.909 0.00 0.00 0.00 5.01
604 2945 6.318900 CCTCTGGTTGGTTTGATAGTATTTCC 59.681 42.308 0.00 0.00 0.00 3.13
631 2972 3.801050 CAGAGTTCTTATCTGATGGTGCG 59.199 47.826 0.00 0.00 45.80 5.34
632 2973 3.559242 GCAGAGTTCTTATCTGATGGTGC 59.441 47.826 7.13 0.00 45.80 5.01
633 2974 4.125703 GGCAGAGTTCTTATCTGATGGTG 58.874 47.826 7.13 0.00 45.80 4.17
646 2987 2.484264 AGTTAACATTGCGGCAGAGTTC 59.516 45.455 20.40 10.95 0.00 3.01
680 3021 3.845178 TCCGTCTACAACTTATGCACTG 58.155 45.455 0.00 0.00 0.00 3.66
716 3057 2.686915 ACAGCGTACGCCTACTCTTATT 59.313 45.455 34.88 11.10 43.17 1.40
720 3061 1.654954 CCACAGCGTACGCCTACTCT 61.655 60.000 34.88 14.27 43.17 3.24
783 3128 2.615912 GCCTGTGGAAATATGACAGAGC 59.384 50.000 0.00 0.00 39.64 4.09
824 3169 1.998315 CTTCAGCGTCACCATCTCTTG 59.002 52.381 0.00 0.00 0.00 3.02
903 3251 7.907389 TGGATGAGTAGTTTTCAGTATCTGTT 58.093 34.615 0.00 0.00 32.61 3.16
916 3264 6.886459 ACACAAATTATGCTGGATGAGTAGTT 59.114 34.615 0.00 0.00 0.00 2.24
918 3266 6.317140 ACACACAAATTATGCTGGATGAGTAG 59.683 38.462 0.00 0.00 0.00 2.57
921 3269 5.106038 ACACACACAAATTATGCTGGATGAG 60.106 40.000 0.00 0.00 0.00 2.90
932 3280 5.877564 TCAGTCAGTCAACACACACAAATTA 59.122 36.000 0.00 0.00 0.00 1.40
933 3281 4.699735 TCAGTCAGTCAACACACACAAATT 59.300 37.500 0.00 0.00 0.00 1.82
935 3283 3.669536 TCAGTCAGTCAACACACACAAA 58.330 40.909 0.00 0.00 0.00 2.83
936 3284 3.261580 CTCAGTCAGTCAACACACACAA 58.738 45.455 0.00 0.00 0.00 3.33
938 3286 2.159099 TCCTCAGTCAGTCAACACACAC 60.159 50.000 0.00 0.00 0.00 3.82
960 3320 4.100963 AGTGTGTTGTCCACTGTTATGAGA 59.899 41.667 0.00 0.00 44.81 3.27
970 3330 5.995897 AGTATTTAAGGAGTGTGTTGTCCAC 59.004 40.000 0.00 0.00 44.78 4.02
1017 3385 2.092429 TGGACTATTGGTTGGAGGATGC 60.092 50.000 0.00 0.00 0.00 3.91
1032 3400 5.532779 TGTTTGCATGTTGTGTATTGGACTA 59.467 36.000 0.00 0.00 0.00 2.59
1033 3401 4.340666 TGTTTGCATGTTGTGTATTGGACT 59.659 37.500 0.00 0.00 0.00 3.85
1034 3402 4.444056 GTGTTTGCATGTTGTGTATTGGAC 59.556 41.667 0.00 0.00 0.00 4.02
1083 3455 2.484264 GCAGAGGTACAACAATGGTGTC 59.516 50.000 7.41 0.00 36.80 3.67
1117 3507 1.597742 TGCAAGAGAAGAAGGCACAC 58.402 50.000 0.00 0.00 0.00 3.82
1152 3542 1.008815 AGTGAGATCCCTCCATGGTGA 59.991 52.381 15.47 9.34 38.66 4.02
1779 4169 7.824779 GGTATAGGCCCTGAAAGTTGATTATAG 59.175 40.741 0.00 0.00 0.00 1.31
2400 4790 3.473625 CCCAAGTCGAACAAGGTTTACT 58.526 45.455 0.00 0.00 0.00 2.24
2658 5048 1.216427 AGATTTTGGGAGATCTGCCCC 59.784 52.381 28.47 20.05 45.40 5.80
3405 5799 0.034756 GAATGCCAAAACCCACCACC 59.965 55.000 0.00 0.00 0.00 4.61
3424 5818 9.069078 CATTATTATGACAACAGTTGCAGAAAG 57.931 33.333 13.56 5.09 33.37 2.62
3461 5855 4.110036 ACTTCTTGTGGTTTTGTCTTGC 57.890 40.909 0.00 0.00 0.00 4.01
3741 6135 7.434307 CAGAATCCATACATTTTGACAATGCTC 59.566 37.037 0.00 0.00 0.00 4.26
3847 6241 2.181975 CCAATCCAATTCCCTTGCTGT 58.818 47.619 0.00 0.00 33.20 4.40
3854 6248 3.515104 TCTCTTTTGCCAATCCAATTCCC 59.485 43.478 0.00 0.00 0.00 3.97
4296 6706 0.995024 ACCAGCATAGCTTGTTCCCT 59.005 50.000 0.00 0.00 36.40 4.20
4464 6874 4.134933 AGAGGAACTACAAGAGGGTCTT 57.865 45.455 0.00 0.00 41.55 3.01
4465 6875 3.837399 AGAGGAACTACAAGAGGGTCT 57.163 47.619 0.00 0.00 41.55 3.85
4466 6876 3.196039 GGAAGAGGAACTACAAGAGGGTC 59.804 52.174 0.00 0.00 41.55 4.46
4467 6877 3.174779 GGAAGAGGAACTACAAGAGGGT 58.825 50.000 0.00 0.00 41.55 4.34
4470 6880 3.839293 CACGGAAGAGGAACTACAAGAG 58.161 50.000 0.00 0.00 41.55 2.85
4552 6977 2.260481 GAGTCTAAAGCGGAAACCTCG 58.740 52.381 0.00 0.00 0.00 4.63
4559 7018 2.891580 AGTGACTTGAGTCTAAAGCGGA 59.108 45.455 12.00 0.00 44.99 5.54
4573 7032 3.701205 TGTGTGGCATATGAGTGACTT 57.299 42.857 6.97 0.00 0.00 3.01
4600 7059 3.258372 CGTGTGGCATACAGGAGGTATAT 59.742 47.826 14.87 0.00 45.61 0.86
4601 7060 2.626266 CGTGTGGCATACAGGAGGTATA 59.374 50.000 14.87 0.00 45.61 1.47
4602 7061 1.412710 CGTGTGGCATACAGGAGGTAT 59.587 52.381 14.87 0.00 45.61 2.73
4743 8810 5.297029 AGTCAACTAGTTTTCCTTGCTGTTC 59.703 40.000 5.07 0.00 0.00 3.18
4808 8956 9.916397 CAATGAAATACAAGAAACTATCGGTAC 57.084 33.333 0.00 0.00 0.00 3.34
4842 8990 4.166246 ACGAGATGATGGGTCTAGTGTA 57.834 45.455 0.00 0.00 31.62 2.90
4843 8991 3.019799 ACGAGATGATGGGTCTAGTGT 57.980 47.619 0.00 0.00 31.62 3.55
4844 8992 5.465051 CAATACGAGATGATGGGTCTAGTG 58.535 45.833 0.00 0.00 34.21 2.74
4845 8993 4.021894 GCAATACGAGATGATGGGTCTAGT 60.022 45.833 0.00 0.00 35.97 2.57
4846 8994 4.021981 TGCAATACGAGATGATGGGTCTAG 60.022 45.833 0.00 0.00 0.00 2.43
4847 8995 3.895041 TGCAATACGAGATGATGGGTCTA 59.105 43.478 0.00 0.00 0.00 2.59
4871 9019 2.694397 TCTATAATCTGCAGGCAGGGT 58.306 47.619 20.19 11.26 43.75 4.34
4879 9027 5.543790 TCCATACCTGCTTCTATAATCTGCA 59.456 40.000 0.00 0.00 0.00 4.41
4880 9028 6.042638 TCCATACCTGCTTCTATAATCTGC 57.957 41.667 0.00 0.00 0.00 4.26
4881 9029 8.316946 TGAATCCATACCTGCTTCTATAATCTG 58.683 37.037 0.00 0.00 0.00 2.90
4882 9030 8.441311 TGAATCCATACCTGCTTCTATAATCT 57.559 34.615 0.00 0.00 0.00 2.40
4883 9031 8.535335 TCTGAATCCATACCTGCTTCTATAATC 58.465 37.037 0.00 0.00 0.00 1.75
4884 9032 8.441311 TCTGAATCCATACCTGCTTCTATAAT 57.559 34.615 0.00 0.00 0.00 1.28
4885 9033 7.855784 TCTGAATCCATACCTGCTTCTATAA 57.144 36.000 0.00 0.00 0.00 0.98
4975 9145 3.820467 CAGCATCCTGTTGTTTACCAGAA 59.180 43.478 0.00 0.00 34.31 3.02
5014 9187 2.402564 TGGAGGGATCTGTCAGGATTC 58.597 52.381 0.00 0.00 0.00 2.52
5026 9271 2.107901 GAGCTGAAATGGATGGAGGGAT 59.892 50.000 0.00 0.00 0.00 3.85
5032 9277 5.738208 GCCAATAAAGAGCTGAAATGGATGG 60.738 44.000 0.00 0.00 0.00 3.51
5135 9457 2.802719 TGTTGCCTTGGTTTCCTATCC 58.197 47.619 0.00 0.00 0.00 2.59
5146 9468 3.988379 AACACACTGTATGTTGCCTTG 57.012 42.857 3.26 0.00 40.64 3.61
5254 9614 8.905660 ATAGAGAAACTACGCTCTAATGTCTA 57.094 34.615 0.00 0.00 44.33 2.59
5255 9615 7.499563 TGATAGAGAAACTACGCTCTAATGTCT 59.500 37.037 0.00 0.00 44.33 3.41
5256 9616 7.640852 TGATAGAGAAACTACGCTCTAATGTC 58.359 38.462 0.00 0.00 44.33 3.06
5257 9617 7.499563 TCTGATAGAGAAACTACGCTCTAATGT 59.500 37.037 0.00 0.00 44.33 2.71
5258 9618 7.866729 TCTGATAGAGAAACTACGCTCTAATG 58.133 38.462 0.00 0.00 44.33 1.90
5259 9619 8.630054 ATCTGATAGAGAAACTACGCTCTAAT 57.370 34.615 0.00 0.00 44.33 1.73
5260 9620 9.557061 TTATCTGATAGAGAAACTACGCTCTAA 57.443 33.333 0.00 0.00 44.33 2.10
5331 9827 9.850628 GACGTGCTTTCATACACCTATATATTA 57.149 33.333 0.00 0.00 33.09 0.98
5382 9880 6.268855 AGTCTAGCTGAATAGGAGAAGGTA 57.731 41.667 0.00 0.00 0.00 3.08
5383 9881 5.137412 AGTCTAGCTGAATAGGAGAAGGT 57.863 43.478 0.00 0.00 0.00 3.50
5404 9902 6.019237 CACACTATTCGATGAAATGTCCTCAG 60.019 42.308 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.