Multiple sequence alignment - TraesCS7D01G071400

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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 TraesCS7D01G071400 chr7D 100.000 3668 0 0 1 3668 41817463 41821130 0.000000e+00 6774
1 TraesCS7D01G071400 chr7D 91.120 2849 187 24 536 3353 42212717 42215530 0.000000e+00 3799
2 TraesCS7D01G071400 chr7D 90.886 2754 185 27 536 3265 42084305 42081594 0.000000e+00 3635
3 TraesCS7D01G071400 chr7D 89.954 2837 192 32 589 3389 42246232 42249011 0.000000e+00 3574
4 TraesCS7D01G071400 chr7D 91.321 2581 191 17 647 3220 42427415 42429969 0.000000e+00 3494
5 TraesCS7D01G071400 chr7D 90.240 1752 142 16 1473 3220 42423247 42424973 0.000000e+00 2261
6 TraesCS7D01G071400 chr7D 91.071 280 15 3 3118 3389 41875287 41875010 1.610000e-98 370
7 TraesCS7D01G071400 chr7D 84.861 251 15 10 1 231 42244594 42244841 7.920000e-57 231
8 TraesCS7D01G071400 chr7D 91.667 144 3 2 3254 3389 42435549 42435691 1.340000e-44 191
9 TraesCS7D01G071400 chr7D 96.552 116 3 1 3553 3668 61772897 61772783 1.340000e-44 191
10 TraesCS7D01G071400 chr7D 95.690 116 4 1 3554 3668 25675791 25675676 6.260000e-43 185
11 TraesCS7D01G071400 chr7D 92.248 129 9 1 3540 3668 561841436 561841309 8.090000e-42 182
12 TraesCS7D01G071400 chr4A 93.634 2969 135 20 434 3389 649007011 649009938 0.000000e+00 4386
13 TraesCS7D01G071400 chr4A 93.331 2969 151 24 434 3389 649056687 649059621 0.000000e+00 4342
14 TraesCS7D01G071400 chr4A 90.059 2887 220 24 538 3389 649144884 649147738 0.000000e+00 3679
15 TraesCS7D01G071400 chr4A 90.722 2091 162 21 1152 3237 649152536 649154599 0.000000e+00 2758
16 TraesCS7D01G071400 chr4A 92.777 443 28 3 1 440 649056202 649056643 3.990000e-179 638
17 TraesCS7D01G071400 chr4A 92.099 443 30 4 1 440 649006527 649006967 1.450000e-173 619
18 TraesCS7D01G071400 chr4A 89.135 451 23 12 2948 3389 649175927 649176360 4.170000e-149 538
19 TraesCS7D01G071400 chr4A 85.632 174 7 4 3381 3554 649059789 649059944 2.270000e-37 167
20 TraesCS7D01G071400 chr4A 84.483 174 9 3 3381 3554 649010105 649010260 4.900000e-34 156
21 TraesCS7D01G071400 chr7B 90.399 2885 211 29 536 3389 2564098 2561249 0.000000e+00 3733
22 TraesCS7D01G071400 chr7A 89.872 2883 234 28 536 3384 41619244 41622102 0.000000e+00 3653
23 TraesCS7D01G071400 chr7A 89.814 2896 220 34 536 3389 41626212 41629074 0.000000e+00 3644
24 TraesCS7D01G071400 chr7A 91.381 2599 186 19 648 3237 41746700 41749269 0.000000e+00 3524
25 TraesCS7D01G071400 chr7A 91.301 2598 191 18 648 3237 41775205 41777775 0.000000e+00 3513
26 TraesCS7D01G071400 chr7A 88.435 147 4 7 3254 3389 41791230 41791374 8.150000e-37 165
27 TraesCS7D01G071400 chr7A 96.721 61 2 0 122 182 41474837 41474897 6.480000e-18 102
28 TraesCS7D01G071400 chrUn 90.128 2725 215 19 536 3237 250935652 250932959 0.000000e+00 3493
29 TraesCS7D01G071400 chrUn 95.041 121 5 1 3549 3668 238793442 238793322 4.840000e-44 189
30 TraesCS7D01G071400 chr2B 89.476 2670 231 25 517 3154 784365255 784367906 0.000000e+00 3328
31 TraesCS7D01G071400 chr5D 97.479 119 3 0 3550 3668 443878490 443878372 1.730000e-48 204
32 TraesCS7D01G071400 chr6D 97.368 114 3 0 3555 3668 27188687 27188800 1.040000e-45 195
33 TraesCS7D01G071400 chr2D 97.368 114 3 0 3555 3668 617486431 617486318 1.040000e-45 195
34 TraesCS7D01G071400 chr2D 96.491 114 3 1 3555 3668 575791257 575791145 1.740000e-43 187
35 TraesCS7D01G071400 chr3D 95.726 117 5 0 3552 3668 54088067 54088183 4.840000e-44 189


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 TraesCS7D01G071400 chr7D 41817463 41821130 3667 False 6774.000000 6774 100.0000 1 3668 1 chr7D.!!$F1 3667
1 TraesCS7D01G071400 chr7D 42212717 42215530 2813 False 3799.000000 3799 91.1200 536 3353 1 chr7D.!!$F2 2817
2 TraesCS7D01G071400 chr7D 42081594 42084305 2711 True 3635.000000 3635 90.8860 536 3265 1 chr7D.!!$R3 2729
3 TraesCS7D01G071400 chr7D 42423247 42429969 6722 False 2877.500000 3494 90.7805 647 3220 2 chr7D.!!$F5 2573
4 TraesCS7D01G071400 chr7D 42244594 42249011 4417 False 1902.500000 3574 87.4075 1 3389 2 chr7D.!!$F4 3388
5 TraesCS7D01G071400 chr4A 649144884 649147738 2854 False 3679.000000 3679 90.0590 538 3389 1 chr4A.!!$F1 2851
6 TraesCS7D01G071400 chr4A 649152536 649154599 2063 False 2758.000000 2758 90.7220 1152 3237 1 chr4A.!!$F2 2085
7 TraesCS7D01G071400 chr4A 649006527 649010260 3733 False 1720.333333 4386 90.0720 1 3554 3 chr4A.!!$F4 3553
8 TraesCS7D01G071400 chr4A 649056202 649059944 3742 False 1715.666667 4342 90.5800 1 3554 3 chr4A.!!$F5 3553
9 TraesCS7D01G071400 chr7B 2561249 2564098 2849 True 3733.000000 3733 90.3990 536 3389 1 chr7B.!!$R1 2853
10 TraesCS7D01G071400 chr7A 41619244 41622102 2858 False 3653.000000 3653 89.8720 536 3384 1 chr7A.!!$F2 2848
11 TraesCS7D01G071400 chr7A 41626212 41629074 2862 False 3644.000000 3644 89.8140 536 3389 1 chr7A.!!$F3 2853
12 TraesCS7D01G071400 chr7A 41746700 41749269 2569 False 3524.000000 3524 91.3810 648 3237 1 chr7A.!!$F4 2589
13 TraesCS7D01G071400 chr7A 41775205 41777775 2570 False 3513.000000 3513 91.3010 648 3237 1 chr7A.!!$F5 2589
14 TraesCS7D01G071400 chrUn 250932959 250935652 2693 True 3493.000000 3493 90.1280 536 3237 1 chrUn.!!$R2 2701
15 TraesCS7D01G071400 chr2B 784365255 784367906 2651 False 3328.000000 3328 89.4760 517 3154 1 chr2B.!!$F1 2637

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
969 4507 0.611618 CAGCCTACCATTGCACCCAA 60.612 55.0 0.0 0.0 35.01 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2784 6365 0.107017 CAGGATCGGGGCAGAACAAT 60.107 55.0 0.0 0.0 0.0 2.71 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
75 83 3.920231 TGCATGCTCATAGTCTTCCTT 57.080 42.857 20.33 0.00 0.00 3.36
119 140 5.278604 AGCAAGTTGTTCAAATAACGGTTC 58.721 37.500 4.48 0.00 35.49 3.62
231 252 3.530910 CTTGGCCCTCCAACGTCGT 62.531 63.158 0.00 0.00 46.89 4.34
286 308 0.749454 CCCACTATTGAGGGCTGCAC 60.749 60.000 0.50 0.00 37.28 4.57
314 336 1.484240 AGACTAGCATTCCTGTCCAGC 59.516 52.381 0.00 0.00 0.00 4.85
482 630 3.046374 AGAAACAAGGGTGGTCTACTGT 58.954 45.455 0.00 0.00 0.00 3.55
505 653 9.944663 CTGTAATTTCTGTTTAAGTTGTTGCTA 57.055 29.630 0.00 0.00 0.00 3.49
709 4235 3.254657 TCCAAAGCCGGTTGATAAGTTTG 59.745 43.478 1.90 0.00 0.00 2.93
969 4507 0.611618 CAGCCTACCATTGCACCCAA 60.612 55.000 0.00 0.00 35.01 4.12
1101 4639 0.855349 CCTATGTCATTGTCGAGCGC 59.145 55.000 0.00 0.00 0.00 5.92
1260 4798 8.492673 TTGTGAAATACTTGGATGACTATGTC 57.507 34.615 0.00 0.00 0.00 3.06
1327 4865 5.589855 TCATCCACATATGACAATGACCAAC 59.410 40.000 10.38 0.00 30.92 3.77
1381 4923 4.899352 AAGAGCACAATAGTCAGGTTCT 57.101 40.909 0.00 0.00 0.00 3.01
1461 5003 1.318576 CCGGACTGCAAAGTTTTCCT 58.681 50.000 0.00 0.00 0.00 3.36
1518 5060 2.935201 CAAGAGCTACTCTGGCATGAAC 59.065 50.000 0.00 0.00 40.28 3.18
1617 5159 2.064014 GTTATACGAAGCCCGGTATGC 58.936 52.381 0.00 0.00 43.93 3.14
1621 5163 2.173669 CGAAGCCCGGTATGCACAG 61.174 63.158 0.00 0.00 33.91 3.66
1709 5272 6.543831 CCCTATGGGCACTATATATTTTCAGC 59.456 42.308 0.00 0.00 35.35 4.26
1714 5277 4.392138 GGCACTATATATTTTCAGCGGGTC 59.608 45.833 0.00 0.00 0.00 4.46
1761 5334 5.652014 CACCACTAGAAGGGATGCAATTTTA 59.348 40.000 0.00 0.00 0.00 1.52
1884 5459 9.334693 CGAAAAATAACTCTTGAAAGAAGATGG 57.665 33.333 0.00 0.00 34.03 3.51
1954 5529 6.158598 ACATGTTTTATGGTTGCAGATTCAC 58.841 36.000 0.00 0.00 0.00 3.18
1957 5532 6.757237 TGTTTTATGGTTGCAGATTCACATT 58.243 32.000 0.00 0.00 0.00 2.71
2052 5627 4.511617 TTGTGATGGCTGCGAATTTAAA 57.488 36.364 0.00 0.00 0.00 1.52
2406 5983 1.389106 GCTCACGGTAACAACATCGAC 59.611 52.381 0.00 0.00 0.00 4.20
2419 5996 8.998989 GTAACAACATCGACATTTGAATATGTG 58.001 33.333 8.95 0.00 38.80 3.21
2435 6012 9.868277 TTGAATATGTGTGAGTTTGTTTTCTTT 57.132 25.926 0.00 0.00 0.00 2.52
2476 6057 8.970859 AATCTGCTAACAAGCTCTATGTTATT 57.029 30.769 9.36 0.92 41.13 1.40
2511 6092 7.337689 CAGAATGGTGAGAGGATGTTAAATGAA 59.662 37.037 0.00 0.00 0.00 2.57
2629 6210 1.462283 CAGATGCCAAGAATATCGCCG 59.538 52.381 0.00 0.00 0.00 6.46
2677 6258 7.352739 CACTATGTCCGGCTAAATTATCAAAC 58.647 38.462 0.00 0.00 0.00 2.93
2773 6354 3.732849 GGCTAAGGCAGGGGCACT 61.733 66.667 0.00 0.00 43.71 4.40
2810 6391 1.227383 GCCCCGATCCTGGAATGTT 59.773 57.895 0.00 0.00 0.00 2.71
2818 6399 3.539604 GATCCTGGAATGTTCACTGAGG 58.460 50.000 0.00 0.00 0.00 3.86
2830 6411 6.353404 TGTTCACTGAGGTGTATGATGTAA 57.647 37.500 0.00 0.00 43.41 2.41
2836 6417 8.536175 TCACTGAGGTGTATGATGTAATGTAAA 58.464 33.333 0.00 0.00 43.41 2.01
2837 6418 9.161629 CACTGAGGTGTATGATGTAATGTAAAA 57.838 33.333 0.00 0.00 38.54 1.52
2838 6419 9.162764 ACTGAGGTGTATGATGTAATGTAAAAC 57.837 33.333 0.00 0.00 0.00 2.43
2839 6420 9.383519 CTGAGGTGTATGATGTAATGTAAAACT 57.616 33.333 0.00 0.00 0.00 2.66
2922 6510 4.223659 GCCTTTTGCGTTTTCTCGATTTA 58.776 39.130 0.00 0.00 0.00 1.40
2953 6541 4.953940 TTTACGTGTAGTTTACCAGGGT 57.046 40.909 0.00 0.00 0.00 4.34
3404 7191 2.703536 TCAGAACCACCTTCAGCAGTTA 59.296 45.455 0.00 0.00 0.00 2.24
3411 7198 3.206150 CACCTTCAGCAGTTAGTGTTGT 58.794 45.455 3.95 0.00 38.48 3.32
3421 7208 1.266989 GTTAGTGTTGTGCTGGGCTTC 59.733 52.381 0.00 0.00 0.00 3.86
3488 7275 0.965866 CCTACACCTCCAGCTCGTCA 60.966 60.000 0.00 0.00 0.00 4.35
3532 7319 0.629058 GTCCCTCTCCCTCTCTCTGT 59.371 60.000 0.00 0.00 0.00 3.41
3554 7341 3.244078 TGTGTGGAACCTGTCAGTACATC 60.244 47.826 0.00 0.00 34.36 3.06
3555 7342 2.969262 TGTGGAACCTGTCAGTACATCA 59.031 45.455 0.00 0.00 34.36 3.07
3556 7343 3.244078 TGTGGAACCTGTCAGTACATCAC 60.244 47.826 0.00 2.13 34.36 3.06
3557 7344 3.006967 GTGGAACCTGTCAGTACATCACT 59.993 47.826 0.00 0.00 38.32 3.41
3558 7345 7.472602 TGTGGAACCTGTCAGTACATCACTG 62.473 48.000 0.00 0.00 46.74 3.66
3586 7373 5.386958 AAAAAGCTCTTTAATCCCGGTTC 57.613 39.130 0.00 0.00 31.63 3.62
3587 7374 2.311124 AGCTCTTTAATCCCGGTTCG 57.689 50.000 0.00 0.00 0.00 3.95
3588 7375 0.656259 GCTCTTTAATCCCGGTTCGC 59.344 55.000 0.00 0.00 0.00 4.70
3589 7376 2.010043 GCTCTTTAATCCCGGTTCGCA 61.010 52.381 0.00 0.00 0.00 5.10
3590 7377 2.352388 CTCTTTAATCCCGGTTCGCAA 58.648 47.619 0.00 0.00 0.00 4.85
3591 7378 2.745281 CTCTTTAATCCCGGTTCGCAAA 59.255 45.455 0.00 0.00 0.00 3.68
3592 7379 2.745281 TCTTTAATCCCGGTTCGCAAAG 59.255 45.455 0.00 3.70 0.00 2.77
3593 7380 1.455248 TTAATCCCGGTTCGCAAAGG 58.545 50.000 0.00 0.00 0.00 3.11
3594 7381 1.027792 TAATCCCGGTTCGCAAAGGC 61.028 55.000 0.00 0.00 0.00 4.35
3597 7384 2.983592 CCGGTTCGCAAAGGCCTT 60.984 61.111 13.78 13.78 36.38 4.35
3598 7385 2.561037 CCGGTTCGCAAAGGCCTTT 61.561 57.895 25.47 25.47 36.38 3.11
3599 7386 1.238625 CCGGTTCGCAAAGGCCTTTA 61.239 55.000 29.94 12.86 36.38 1.85
3600 7387 0.168128 CGGTTCGCAAAGGCCTTTAG 59.832 55.000 29.94 24.65 36.38 1.85
3601 7388 1.244816 GGTTCGCAAAGGCCTTTAGT 58.755 50.000 29.94 6.35 36.38 2.24
3602 7389 1.199327 GGTTCGCAAAGGCCTTTAGTC 59.801 52.381 29.94 19.52 36.38 2.59
3603 7390 1.199327 GTTCGCAAAGGCCTTTAGTCC 59.801 52.381 29.94 16.69 36.38 3.85
3604 7391 0.322187 TCGCAAAGGCCTTTAGTCCC 60.322 55.000 29.94 14.43 36.38 4.46
3605 7392 1.644786 CGCAAAGGCCTTTAGTCCCG 61.645 60.000 29.94 21.01 36.38 5.14
3606 7393 1.313091 GCAAAGGCCTTTAGTCCCGG 61.313 60.000 29.94 16.67 0.00 5.73
3607 7394 1.001269 AAAGGCCTTTAGTCCCGGC 60.001 57.895 29.47 0.00 43.03 6.13
3608 7395 1.498176 AAAGGCCTTTAGTCCCGGCT 61.498 55.000 29.47 0.30 43.29 5.52
3609 7396 2.124695 GGCCTTTAGTCCCGGCTG 60.125 66.667 0.00 0.00 43.29 4.85
3610 7397 2.669240 GCCTTTAGTCCCGGCTGT 59.331 61.111 0.00 0.00 40.62 4.40
3611 7398 1.745489 GCCTTTAGTCCCGGCTGTG 60.745 63.158 0.00 0.00 40.62 3.66
3612 7399 1.745489 CCTTTAGTCCCGGCTGTGC 60.745 63.158 0.00 0.00 0.00 4.57
3613 7400 1.003839 CTTTAGTCCCGGCTGTGCA 60.004 57.895 0.00 0.00 0.00 4.57
3614 7401 0.605319 CTTTAGTCCCGGCTGTGCAA 60.605 55.000 0.00 0.00 0.00 4.08
3615 7402 0.887387 TTTAGTCCCGGCTGTGCAAC 60.887 55.000 0.00 0.00 37.35 4.17
3616 7403 2.741486 TTAGTCCCGGCTGTGCAACC 62.741 60.000 0.00 0.00 34.36 3.77
3622 7409 4.643387 GGCTGTGCAACCGGGACT 62.643 66.667 6.32 0.00 38.87 3.85
3623 7410 2.345991 GCTGTGCAACCGGGACTA 59.654 61.111 6.32 0.00 38.87 2.59
3624 7411 1.302192 GCTGTGCAACCGGGACTAA 60.302 57.895 6.32 0.00 38.87 2.24
3625 7412 0.887387 GCTGTGCAACCGGGACTAAA 60.887 55.000 6.32 0.00 38.87 1.85
3626 7413 1.821216 CTGTGCAACCGGGACTAAAT 58.179 50.000 6.32 0.00 38.87 1.40
3627 7414 2.937873 GCTGTGCAACCGGGACTAAATA 60.938 50.000 6.32 0.00 38.87 1.40
3628 7415 3.541632 CTGTGCAACCGGGACTAAATAT 58.458 45.455 6.32 0.00 38.87 1.28
3629 7416 3.275143 TGTGCAACCGGGACTAAATATG 58.725 45.455 6.32 0.00 38.87 1.78
3630 7417 2.032924 GTGCAACCGGGACTAAATATGC 59.967 50.000 6.32 2.60 34.56 3.14
3631 7418 1.263217 GCAACCGGGACTAAATATGCG 59.737 52.381 6.32 0.00 0.00 4.73
3632 7419 1.263217 CAACCGGGACTAAATATGCGC 59.737 52.381 6.32 0.00 0.00 6.09
3633 7420 0.599204 ACCGGGACTAAATATGCGCG 60.599 55.000 6.32 0.00 36.61 6.86
3634 7421 0.319211 CCGGGACTAAATATGCGCGA 60.319 55.000 12.10 0.00 38.72 5.87
3635 7422 0.782384 CGGGACTAAATATGCGCGAC 59.218 55.000 12.10 0.88 38.72 5.19
3636 7423 1.602165 CGGGACTAAATATGCGCGACT 60.602 52.381 12.10 0.00 38.72 4.18
3637 7424 2.351060 CGGGACTAAATATGCGCGACTA 60.351 50.000 12.10 0.00 38.72 2.59
3638 7425 3.645884 GGGACTAAATATGCGCGACTAA 58.354 45.455 12.10 0.00 0.00 2.24
3639 7426 4.053295 GGGACTAAATATGCGCGACTAAA 58.947 43.478 12.10 0.00 0.00 1.85
3640 7427 4.150098 GGGACTAAATATGCGCGACTAAAG 59.850 45.833 12.10 0.00 0.00 1.85
3641 7428 4.980434 GGACTAAATATGCGCGACTAAAGA 59.020 41.667 12.10 0.00 0.00 2.52
3642 7429 5.107951 GGACTAAATATGCGCGACTAAAGAC 60.108 44.000 12.10 0.00 0.00 3.01
3643 7430 4.743644 ACTAAATATGCGCGACTAAAGACC 59.256 41.667 12.10 0.00 0.00 3.85
3644 7431 2.150397 ATATGCGCGACTAAAGACCC 57.850 50.000 12.10 0.00 0.00 4.46
3645 7432 0.103572 TATGCGCGACTAAAGACCCC 59.896 55.000 12.10 0.00 0.00 4.95
3646 7433 2.510918 GCGCGACTAAAGACCCCC 60.511 66.667 12.10 0.00 0.00 5.40
3664 7451 3.782443 CCCCCTTTAGTCGCGGCT 61.782 66.667 20.79 20.79 0.00 5.52
3665 7452 2.202892 CCCCTTTAGTCGCGGCTC 60.203 66.667 20.54 2.06 0.00 4.70
3666 7453 2.722201 CCCCTTTAGTCGCGGCTCT 61.722 63.158 20.54 10.64 0.00 4.09
3667 7454 1.218316 CCCTTTAGTCGCGGCTCTT 59.782 57.895 20.54 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 212 6.808321 AGTGGCAAGATATTGGTCTACTTA 57.192 37.500 1.67 0.00 0.00 2.24
231 252 1.920325 CACCAGAGGGAGGAAGCCA 60.920 63.158 0.00 0.00 38.05 4.75
286 308 2.035704 AGGAATGCTAGTCTCGCATGAG 59.964 50.000 12.24 0.00 46.62 2.90
296 318 1.577736 AGCTGGACAGGAATGCTAGT 58.422 50.000 1.01 0.00 31.71 2.57
300 322 0.811616 CCGTAGCTGGACAGGAATGC 60.812 60.000 0.00 0.00 0.00 3.56
314 336 1.517257 CAGACTTGAGCGCCCGTAG 60.517 63.158 2.29 0.00 0.00 3.51
322 344 2.743928 CCGGTGGCAGACTTGAGC 60.744 66.667 0.00 0.00 0.00 4.26
344 366 8.128322 ACAATAGGTTATGGTATTTGCAAACA 57.872 30.769 15.41 8.78 0.00 2.83
482 630 9.127277 AGGTAGCAACAACTTAAACAGAAATTA 57.873 29.630 0.00 0.00 0.00 1.40
505 653 2.437281 CTCAAGACATAGCCATCCAGGT 59.563 50.000 0.00 0.00 40.61 4.00
583 1743 4.944930 CCCCCGTCACAAATTACTTATGAA 59.055 41.667 0.00 0.00 0.00 2.57
585 1745 4.519213 TCCCCCGTCACAAATTACTTATG 58.481 43.478 0.00 0.00 0.00 1.90
587 1747 3.583966 ACTCCCCCGTCACAAATTACTTA 59.416 43.478 0.00 0.00 0.00 2.24
645 1809 8.940397 ACTCTTTAGAATTTCTTTCCATTCCA 57.060 30.769 3.86 0.00 34.67 3.53
969 4507 3.366052 AGAGTTGACAAAGTTGTGGGT 57.634 42.857 0.42 0.00 42.43 4.51
1101 4639 2.497628 GACGCGCTGCAACTTTCG 60.498 61.111 5.73 0.00 0.00 3.46
1260 4798 3.126171 TGGGTTGAATATTGAAACGCTCG 59.874 43.478 19.77 0.00 37.56 5.03
1324 4862 2.351641 CCACGATGGACCAACATTGTTG 60.352 50.000 20.31 20.31 41.55 3.33
1327 4865 0.171007 GCCACGATGGACCAACATTG 59.829 55.000 0.00 0.00 40.96 2.82
1381 4923 2.426738 CCACCACAAGAAACTTTGCTGA 59.573 45.455 0.00 0.00 0.00 4.26
1461 5003 0.541998 AGGAGTGGACGACATCACCA 60.542 55.000 0.00 0.00 34.67 4.17
1518 5060 2.549754 GCCAGATCCAATGACCAATACG 59.450 50.000 0.00 0.00 0.00 3.06
1641 5191 9.238368 CCTAGTGTTTCCAGGTCAAAATAATAA 57.762 33.333 0.00 0.00 0.00 1.40
1642 5192 7.832187 CCCTAGTGTTTCCAGGTCAAAATAATA 59.168 37.037 0.00 0.00 0.00 0.98
1643 5193 6.663523 CCCTAGTGTTTCCAGGTCAAAATAAT 59.336 38.462 0.00 0.00 0.00 1.28
1644 5194 6.007703 CCCTAGTGTTTCCAGGTCAAAATAA 58.992 40.000 0.00 0.00 0.00 1.40
1645 5195 5.515886 CCCCTAGTGTTTCCAGGTCAAAATA 60.516 44.000 0.00 0.00 0.00 1.40
1646 5196 4.407365 CCCTAGTGTTTCCAGGTCAAAAT 58.593 43.478 0.00 0.00 0.00 1.82
1672 5223 0.622154 CCATAGGGTGGGTGTGGGTA 60.622 60.000 0.00 0.00 44.79 3.69
1673 5224 1.928567 CCATAGGGTGGGTGTGGGT 60.929 63.158 0.00 0.00 44.79 4.51
1709 5272 0.676782 AAGAAATTGCCCTCGACCCG 60.677 55.000 0.00 0.00 0.00 5.28
1714 5277 7.095187 GGTGACTATAATAAGAAATTGCCCTCG 60.095 40.741 0.00 0.00 0.00 4.63
1957 5532 9.196139 CCCAACCTAATTAATTCCTTTGTCATA 57.804 33.333 3.39 0.00 0.00 2.15
1976 5551 0.251341 GCAAGTGTCATCCCCAACCT 60.251 55.000 0.00 0.00 0.00 3.50
2052 5627 4.487714 TGCTTCGATAGGTCTCCAAATT 57.512 40.909 0.00 0.00 0.00 1.82
2070 5647 2.517875 GCCTTCGGATGCCATGCT 60.518 61.111 0.00 0.00 0.00 3.79
2257 5834 2.634940 CCCATGTACCTGTAGGAGATGG 59.365 54.545 4.64 11.03 36.66 3.51
2327 5904 7.919313 ACACAATCGCATCAAATGATATTTC 57.081 32.000 0.00 0.00 32.63 2.17
2419 5996 5.176590 TGTTGCACAAAGAAAACAAACTCAC 59.823 36.000 0.00 0.00 29.96 3.51
2435 6012 4.039004 AGCAGATTTAACCATTGTTGCACA 59.961 37.500 0.00 0.00 35.87 4.57
2476 6057 5.252863 TCCTCTCACCATTCTGGGATAAAAA 59.747 40.000 0.00 0.00 43.37 1.94
2499 6080 6.633856 AGGCAGTCCATTTTCATTTAACATC 58.366 36.000 0.00 0.00 33.74 3.06
2511 6092 7.449704 GGATATTCTTTGATAGGCAGTCCATTT 59.550 37.037 0.00 0.00 33.74 2.32
2650 6231 3.275617 AATTTAGCCGGACATAGTGCA 57.724 42.857 5.05 0.00 0.00 4.57
2677 6258 1.445410 TCGAAGACGCATTCACCGG 60.445 57.895 0.00 0.00 39.58 5.28
2784 6365 0.107017 CAGGATCGGGGCAGAACAAT 60.107 55.000 0.00 0.00 0.00 2.71
2937 6525 4.992951 CACACTAACCCTGGTAAACTACAC 59.007 45.833 0.00 0.00 0.00 2.90
2953 6541 6.299805 AGAATCAACCATCTAGCACACTAA 57.700 37.500 0.00 0.00 0.00 2.24
3404 7191 0.764890 TAGAAGCCCAGCACAACACT 59.235 50.000 0.00 0.00 0.00 3.55
3411 7198 2.662596 CACCGTAGAAGCCCAGCA 59.337 61.111 0.00 0.00 0.00 4.41
3421 7208 2.417516 CCGGATCCAGCACCGTAG 59.582 66.667 13.41 0.00 46.53 3.51
3449 7236 4.309950 ACGAGGCCCCGTGTTGAC 62.310 66.667 13.12 0.00 41.70 3.18
3450 7237 3.998672 GACGAGGCCCCGTGTTGA 61.999 66.667 20.23 0.00 43.49 3.18
3451 7238 3.934391 GAGACGAGGCCCCGTGTTG 62.934 68.421 20.23 0.00 43.49 3.33
3452 7239 3.692406 GAGACGAGGCCCCGTGTT 61.692 66.667 20.23 4.80 43.49 3.32
3455 7242 3.736224 TAGGAGACGAGGCCCCGT 61.736 66.667 13.96 13.96 46.43 5.28
3459 7246 1.380112 AGGTGTAGGAGACGAGGCC 60.380 63.158 0.00 0.00 0.00 5.19
3488 7275 2.980233 GTTGACCTTGCCGCAGCT 60.980 61.111 0.00 0.00 40.80 4.24
3532 7319 2.112190 TGTACTGACAGGTTCCACACA 58.888 47.619 7.51 0.00 0.00 3.72
3564 7351 4.082949 CGAACCGGGATTAAAGAGCTTTTT 60.083 41.667 6.32 7.46 34.23 1.94
3565 7352 3.439129 CGAACCGGGATTAAAGAGCTTTT 59.561 43.478 6.32 0.00 34.23 2.27
3566 7353 3.007635 CGAACCGGGATTAAAGAGCTTT 58.992 45.455 6.32 0.74 36.63 3.51
3567 7354 2.629051 CGAACCGGGATTAAAGAGCTT 58.371 47.619 6.32 0.00 0.00 3.74
3568 7355 1.742750 GCGAACCGGGATTAAAGAGCT 60.743 52.381 6.32 0.00 0.00 4.09
3569 7356 0.656259 GCGAACCGGGATTAAAGAGC 59.344 55.000 6.32 0.00 0.00 4.09
3570 7357 2.018542 TGCGAACCGGGATTAAAGAG 57.981 50.000 6.32 0.00 0.00 2.85
3571 7358 2.476126 TTGCGAACCGGGATTAAAGA 57.524 45.000 6.32 0.00 0.00 2.52
3572 7359 2.159435 CCTTTGCGAACCGGGATTAAAG 60.159 50.000 6.32 9.66 0.00 1.85
3573 7360 1.813786 CCTTTGCGAACCGGGATTAAA 59.186 47.619 6.32 0.00 0.00 1.52
3574 7361 1.455248 CCTTTGCGAACCGGGATTAA 58.545 50.000 6.32 0.00 0.00 1.40
3575 7362 1.027792 GCCTTTGCGAACCGGGATTA 61.028 55.000 6.32 0.00 0.00 1.75
3576 7363 2.340328 GCCTTTGCGAACCGGGATT 61.340 57.895 6.32 0.00 0.00 3.01
3577 7364 2.750237 GCCTTTGCGAACCGGGAT 60.750 61.111 6.32 0.00 0.00 3.85
3580 7367 1.238625 TAAAGGCCTTTGCGAACCGG 61.239 55.000 35.99 0.00 38.85 5.28
3581 7368 0.168128 CTAAAGGCCTTTGCGAACCG 59.832 55.000 35.99 14.04 38.85 4.44
3582 7369 1.199327 GACTAAAGGCCTTTGCGAACC 59.801 52.381 35.99 17.08 38.85 3.62
3583 7370 1.199327 GGACTAAAGGCCTTTGCGAAC 59.801 52.381 35.99 23.16 38.85 3.95
3584 7371 1.530323 GGACTAAAGGCCTTTGCGAA 58.470 50.000 35.99 18.29 38.85 4.70
3585 7372 0.322187 GGGACTAAAGGCCTTTGCGA 60.322 55.000 35.99 18.65 38.85 5.10
3586 7373 1.644786 CGGGACTAAAGGCCTTTGCG 61.645 60.000 35.99 27.79 38.85 4.85
3587 7374 1.313091 CCGGGACTAAAGGCCTTTGC 61.313 60.000 35.99 24.64 34.23 3.68
3588 7375 1.313091 GCCGGGACTAAAGGCCTTTG 61.313 60.000 35.99 26.94 44.80 2.77
3589 7376 1.001269 GCCGGGACTAAAGGCCTTT 60.001 57.895 32.37 32.37 44.80 3.11
3590 7377 2.675371 GCCGGGACTAAAGGCCTT 59.325 61.111 13.78 13.78 44.80 4.35
3594 7381 1.745489 GCACAGCCGGGACTAAAGG 60.745 63.158 2.18 0.00 0.00 3.11
3595 7382 0.605319 TTGCACAGCCGGGACTAAAG 60.605 55.000 2.18 0.00 0.00 1.85
3596 7383 0.887387 GTTGCACAGCCGGGACTAAA 60.887 55.000 2.18 0.00 0.00 1.85
3597 7384 1.302192 GTTGCACAGCCGGGACTAA 60.302 57.895 2.18 0.00 0.00 2.24
3598 7385 2.345991 GTTGCACAGCCGGGACTA 59.654 61.111 2.18 0.00 0.00 2.59
3599 7386 4.643387 GGTTGCACAGCCGGGACT 62.643 66.667 2.18 0.00 0.00 3.85
3605 7392 2.741486 TTAGTCCCGGTTGCACAGCC 62.741 60.000 0.00 0.00 0.00 4.85
3606 7393 0.887387 TTTAGTCCCGGTTGCACAGC 60.887 55.000 0.00 0.00 0.00 4.40
3607 7394 1.821216 ATTTAGTCCCGGTTGCACAG 58.179 50.000 0.00 0.00 0.00 3.66
3608 7395 3.275143 CATATTTAGTCCCGGTTGCACA 58.725 45.455 0.00 0.00 0.00 4.57
3609 7396 2.032924 GCATATTTAGTCCCGGTTGCAC 59.967 50.000 0.00 0.00 0.00 4.57
3610 7397 2.294074 GCATATTTAGTCCCGGTTGCA 58.706 47.619 0.00 0.00 0.00 4.08
3611 7398 1.263217 CGCATATTTAGTCCCGGTTGC 59.737 52.381 0.00 0.00 0.00 4.17
3612 7399 1.263217 GCGCATATTTAGTCCCGGTTG 59.737 52.381 0.30 0.00 0.00 3.77
3613 7400 1.589803 GCGCATATTTAGTCCCGGTT 58.410 50.000 0.30 0.00 0.00 4.44
3614 7401 0.599204 CGCGCATATTTAGTCCCGGT 60.599 55.000 8.75 0.00 0.00 5.28
3615 7402 0.319211 TCGCGCATATTTAGTCCCGG 60.319 55.000 8.75 0.00 0.00 5.73
3616 7403 0.782384 GTCGCGCATATTTAGTCCCG 59.218 55.000 8.75 0.00 0.00 5.14
3617 7404 2.150397 AGTCGCGCATATTTAGTCCC 57.850 50.000 8.75 0.00 0.00 4.46
3618 7405 4.980434 TCTTTAGTCGCGCATATTTAGTCC 59.020 41.667 8.75 0.00 0.00 3.85
3619 7406 5.107951 GGTCTTTAGTCGCGCATATTTAGTC 60.108 44.000 8.75 0.00 0.00 2.59
3620 7407 4.743644 GGTCTTTAGTCGCGCATATTTAGT 59.256 41.667 8.75 0.00 0.00 2.24
3621 7408 4.150098 GGGTCTTTAGTCGCGCATATTTAG 59.850 45.833 8.75 0.00 0.00 1.85
3622 7409 4.053295 GGGTCTTTAGTCGCGCATATTTA 58.947 43.478 8.75 0.00 0.00 1.40
3623 7410 2.870411 GGGTCTTTAGTCGCGCATATTT 59.130 45.455 8.75 0.00 0.00 1.40
3624 7411 2.480845 GGGTCTTTAGTCGCGCATATT 58.519 47.619 8.75 0.00 0.00 1.28
3625 7412 1.270147 GGGGTCTTTAGTCGCGCATAT 60.270 52.381 8.75 0.00 0.00 1.78
3626 7413 0.103572 GGGGTCTTTAGTCGCGCATA 59.896 55.000 8.75 0.00 0.00 3.14
3627 7414 1.153429 GGGGTCTTTAGTCGCGCAT 60.153 57.895 8.75 0.00 0.00 4.73
3628 7415 2.263540 GGGGTCTTTAGTCGCGCA 59.736 61.111 8.75 0.00 0.00 6.09
3629 7416 2.510918 GGGGGTCTTTAGTCGCGC 60.511 66.667 0.00 0.00 0.00 6.86
3647 7434 3.735037 GAGCCGCGACTAAAGGGGG 62.735 68.421 8.23 0.00 41.41 5.40
3648 7435 2.202892 GAGCCGCGACTAAAGGGG 60.203 66.667 8.23 0.00 43.62 4.79
3649 7436 1.218316 AAGAGCCGCGACTAAAGGG 59.782 57.895 8.23 0.00 0.00 3.95
3650 7437 4.913126 AAGAGCCGCGACTAAAGG 57.087 55.556 8.23 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.