Multiple sequence alignment - TraesCS3B01G470700

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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 TraesCS3B01G470700 chr3B 100.000 3050 0 0 1 3050 718848990 718852039 0.000000e+00 5633.0
1 TraesCS3B01G470700 chr3B 87.500 56 5 2 2869 2923 320814532 320814478 2.540000e-06 63.9
2 TraesCS3B01G470700 chr3D 91.861 2654 79 55 219 2828 543007611 543010171 0.000000e+00 3578.0
3 TraesCS3B01G470700 chr3A 91.755 2559 93 52 535 3050 679694273 679696756 0.000000e+00 3448.0
4 TraesCS3B01G470700 chr3A 82.252 524 46 20 32 532 679692002 679692501 2.830000e-110 409.0
5 TraesCS3B01G470700 chr3A 79.545 88 16 2 2837 2923 644844624 644844710 9.130000e-06 62.1
6 TraesCS3B01G470700 chr3A 90.909 44 4 0 2889 2932 624424736 624424693 3.280000e-05 60.2
7 TraesCS3B01G470700 chr5D 88.710 186 21 0 1357 1542 205995774 205995959 8.510000e-56 228.0
8 TraesCS3B01G470700 chr5D 89.773 176 16 2 1360 1534 539014529 539014703 1.100000e-54 224.0
9 TraesCS3B01G470700 chr5A 88.172 186 22 0 1357 1542 264421494 264421679 3.960000e-54 222.0
10 TraesCS3B01G470700 chr5B 87.634 186 23 0 1357 1542 206102406 206102221 1.840000e-52 217.0
11 TraesCS3B01G470700 chr5B 87.097 62 7 1 2869 2929 463778129 463778068 5.460000e-08 69.4
12 TraesCS3B01G470700 chr2D 87.709 179 15 7 1360 1534 520537008 520536833 5.160000e-48 202.0
13 TraesCS3B01G470700 chr2B 88.764 89 10 0 2837 2925 764537698 764537610 3.220000e-20 110.0
14 TraesCS3B01G470700 chr7A 80.899 89 17 0 2835 2923 3860942 3861030 1.520000e-08 71.3
15 TraesCS3B01G470700 chr6A 85.965 57 6 2 2869 2924 10982423 10982368 3.280000e-05 60.2
16 TraesCS3B01G470700 chr7B 84.211 57 5 4 2869 2923 556634541 556634487 5.000000e-03 52.8


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 TraesCS3B01G470700 chr3B 718848990 718852039 3049 False 5633.0 5633 100.0000 1 3050 1 chr3B.!!$F1 3049
1 TraesCS3B01G470700 chr3D 543007611 543010171 2560 False 3578.0 3578 91.8610 219 2828 1 chr3D.!!$F1 2609
2 TraesCS3B01G470700 chr3A 679692002 679696756 4754 False 1928.5 3448 87.0035 32 3050 2 chr3A.!!$F2 3018

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
733 2556 0.035439 CCAGAAAGTGGGCGTGGTAT 60.035 55.0 0.0 0.0 43.63 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2297 4164 0.041833 AGGAGCAGCAGGAGTAGGAA 59.958 55.0 0.0 0.0 0.0 3.36 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
29 30 6.518208 TGGTGGGTTTAAAGTATATGTTGC 57.482 37.500 0.00 0.00 0.00 4.17
30 31 6.010850 TGGTGGGTTTAAAGTATATGTTGCA 58.989 36.000 0.00 0.00 0.00 4.08
31 32 6.071840 TGGTGGGTTTAAAGTATATGTTGCAC 60.072 38.462 0.00 0.00 0.00 4.57
32 33 6.071840 GGTGGGTTTAAAGTATATGTTGCACA 60.072 38.462 0.00 0.00 0.00 4.57
33 34 6.804783 GTGGGTTTAAAGTATATGTTGCACAC 59.195 38.462 0.00 0.00 0.00 3.82
34 35 6.025280 GGGTTTAAAGTATATGTTGCACACG 58.975 40.000 0.00 0.00 0.00 4.49
35 36 6.128227 GGGTTTAAAGTATATGTTGCACACGA 60.128 38.462 0.00 0.00 0.00 4.35
36 37 7.414762 GGGTTTAAAGTATATGTTGCACACGAT 60.415 37.037 0.00 0.00 0.00 3.73
37 38 7.966204 GGTTTAAAGTATATGTTGCACACGATT 59.034 33.333 0.00 0.00 0.00 3.34
38 39 9.976255 GTTTAAAGTATATGTTGCACACGATTA 57.024 29.630 0.00 0.00 0.00 1.75
51 52 5.106869 TGCACACGATTAATGTTGAACCTAC 60.107 40.000 0.00 0.00 0.00 3.18
64 65 8.908786 ATGTTGAACCTACAGAATATGTATGG 57.091 34.615 0.00 0.00 43.44 2.74
71 72 6.273260 ACCTACAGAATATGTATGGCTCCATT 59.727 38.462 6.73 0.00 43.44 3.16
72 73 6.596888 CCTACAGAATATGTATGGCTCCATTG 59.403 42.308 6.73 0.00 43.44 2.82
77 78 2.212812 TGTATGGCTCCATTGCAACA 57.787 45.000 0.00 2.67 37.82 3.33
81 82 1.081242 GGCTCCATTGCAACACACG 60.081 57.895 0.00 0.00 34.04 4.49
95 96 1.071699 ACACACGGACAATTAGCCAGT 59.928 47.619 0.00 0.00 0.00 4.00
101 102 0.447801 GACAATTAGCCAGTGCCACG 59.552 55.000 0.00 0.00 38.69 4.94
102 103 1.137404 CAATTAGCCAGTGCCACGC 59.863 57.895 0.00 0.00 38.69 5.34
123 124 3.303990 GCGTGTCTCAAAATGTGTGTCAT 60.304 43.478 0.00 0.00 38.57 3.06
128 129 7.097047 CGTGTCTCAAAATGTGTGTCATAAAAC 60.097 37.037 0.00 0.00 35.48 2.43
132 133 6.556212 TCAAAATGTGTGTCATAAAACGTGT 58.444 32.000 0.00 0.00 35.48 4.49
135 136 3.686128 TGTGTGTCATAAAACGTGTTGC 58.314 40.909 0.00 0.00 0.00 4.17
137 138 4.201960 TGTGTGTCATAAAACGTGTTGCAT 60.202 37.500 0.00 0.00 0.00 3.96
144 145 6.416455 GTCATAAAACGTGTTGCATTTTGAGA 59.584 34.615 0.00 1.53 0.00 3.27
147 148 3.773860 ACGTGTTGCATTTTGAGACAA 57.226 38.095 0.00 0.00 0.00 3.18
151 152 3.068024 GTGTTGCATTTTGAGACAAGGGA 59.932 43.478 0.00 0.00 0.00 4.20
155 156 4.922206 TGCATTTTGAGACAAGGGAGTAT 58.078 39.130 0.00 0.00 0.00 2.12
196 197 7.014134 TGTTGTATTTCTCTCAAAGCAATCCAA 59.986 33.333 0.00 0.00 0.00 3.53
203 204 6.507023 TCTCTCAAAGCAATCCAAAACTTTC 58.493 36.000 0.00 0.00 30.16 2.62
230 257 1.340889 TGCCAGTGAGCAATCCAAAAC 59.659 47.619 4.08 0.00 40.56 2.43
231 258 1.615392 GCCAGTGAGCAATCCAAAACT 59.385 47.619 0.00 0.00 0.00 2.66
232 259 2.036346 GCCAGTGAGCAATCCAAAACTT 59.964 45.455 0.00 0.00 0.00 2.66
233 260 3.493176 GCCAGTGAGCAATCCAAAACTTT 60.493 43.478 0.00 0.00 0.00 2.66
234 261 4.301628 CCAGTGAGCAATCCAAAACTTTC 58.698 43.478 0.00 0.00 0.00 2.62
268 295 5.192327 AGTGAGCAATCCAAAACTTTGAG 57.808 39.130 3.72 0.00 40.55 3.02
280 307 8.795786 TCCAAAACTTTGAGATACAAAAATCG 57.204 30.769 3.72 0.00 45.97 3.34
292 319 6.765989 AGATACAAAAATCGTAGGCTGCAATA 59.234 34.615 2.89 0.00 0.00 1.90
310 337 4.143030 GCAATACAGATATAAGCAGCCACG 60.143 45.833 0.00 0.00 0.00 4.94
311 338 4.873746 ATACAGATATAAGCAGCCACGT 57.126 40.909 0.00 0.00 0.00 4.49
312 339 2.826428 ACAGATATAAGCAGCCACGTG 58.174 47.619 9.08 9.08 0.00 4.49
313 340 1.528586 CAGATATAAGCAGCCACGTGC 59.471 52.381 10.91 5.91 44.35 5.34
314 341 0.868406 GATATAAGCAGCCACGTGCC 59.132 55.000 10.91 0.00 45.20 5.01
315 342 0.180171 ATATAAGCAGCCACGTGCCA 59.820 50.000 10.91 0.00 45.20 4.92
316 343 0.461870 TATAAGCAGCCACGTGCCAG 60.462 55.000 10.91 0.00 45.20 4.85
317 344 3.776680 TATAAGCAGCCACGTGCCAGG 62.777 57.143 10.91 0.00 45.20 4.45
323 355 2.357517 CCACGTGCCAGGACTCAC 60.358 66.667 10.91 0.00 0.00 3.51
340 372 3.838317 ACTCACAGGCTGTAGTATTCCAA 59.162 43.478 21.59 0.00 0.00 3.53
344 376 6.346096 TCACAGGCTGTAGTATTCCAAATAC 58.654 40.000 21.59 2.32 0.00 1.89
345 377 6.156256 TCACAGGCTGTAGTATTCCAAATACT 59.844 38.462 21.59 14.75 38.32 2.12
346 378 7.343574 TCACAGGCTGTAGTATTCCAAATACTA 59.656 37.037 21.59 13.10 36.38 1.82
356 388 7.735917 AGTATTCCAAATACTACAGCATAGCA 58.264 34.615 9.95 0.00 33.45 3.49
431 477 1.001631 CCCCCTTTCCACCATTCCC 59.998 63.158 0.00 0.00 0.00 3.97
613 2436 1.210478 TGGACAAGATTAGCAGCTCCC 59.790 52.381 0.00 0.00 0.00 4.30
669 2492 0.539051 AAATGACAGCGGAGGAGGAG 59.461 55.000 0.00 0.00 0.00 3.69
670 2493 1.965754 AATGACAGCGGAGGAGGAGC 61.966 60.000 0.00 0.00 0.00 4.70
671 2494 3.071206 GACAGCGGAGGAGGAGCA 61.071 66.667 0.00 0.00 0.00 4.26
731 2554 2.113139 CCAGAAAGTGGGCGTGGT 59.887 61.111 0.00 0.00 43.63 4.16
732 2555 1.373435 CCAGAAAGTGGGCGTGGTA 59.627 57.895 0.00 0.00 43.63 3.25
733 2556 0.035439 CCAGAAAGTGGGCGTGGTAT 60.035 55.000 0.00 0.00 43.63 2.73
734 2557 1.369625 CAGAAAGTGGGCGTGGTATC 58.630 55.000 0.00 0.00 0.00 2.24
807 2635 0.745128 TCTCTCCTCGGCGTCTTCTC 60.745 60.000 6.85 0.00 0.00 2.87
808 2636 0.746563 CTCTCCTCGGCGTCTTCTCT 60.747 60.000 6.85 0.00 0.00 3.10
852 2683 3.071747 GGTCCATTATTGGTCTCCTCCTC 59.928 52.174 3.65 0.00 44.06 3.71
856 2687 3.508952 TTATTGGTCTCCTCCTCCCTT 57.491 47.619 0.00 0.00 0.00 3.95
993 2836 1.251527 TGGTTGTTTTGCGTGTGGGT 61.252 50.000 0.00 0.00 0.00 4.51
1090 2933 3.700350 CCACCTCCTCCCCCTCCT 61.700 72.222 0.00 0.00 0.00 3.69
1118 2961 4.960866 CCAGCACCACCAGCAGCA 62.961 66.667 0.00 0.00 0.00 4.41
1119 2962 3.362797 CAGCACCACCAGCAGCAG 61.363 66.667 0.00 0.00 0.00 4.24
1122 2965 3.667282 CACCACCAGCAGCAGCAC 61.667 66.667 3.17 0.00 45.49 4.40
1461 3313 2.435059 GAGCTCGGCCACAAGTCC 60.435 66.667 2.24 0.00 0.00 3.85
1971 3823 2.253758 CCACCACCACGAACAGCAG 61.254 63.158 0.00 0.00 0.00 4.24
2184 4042 4.625972 CCTTTAGGTTGTTGTTGTTCGT 57.374 40.909 0.00 0.00 0.00 3.85
2193 4051 2.190161 GTTGTTGTTCGTTTCTTGGGC 58.810 47.619 0.00 0.00 0.00 5.36
2210 4068 5.596361 TCTTGGGCTTGTGATGAGTTTTTAA 59.404 36.000 0.00 0.00 0.00 1.52
2297 4164 1.008815 TGGATCAGGGTCATCCTCAGT 59.991 52.381 0.00 0.00 46.12 3.41
2354 4226 2.271777 TCCCTCCGGTTCAGGTAAAAT 58.728 47.619 0.00 0.00 0.00 1.82
2355 4227 2.237893 TCCCTCCGGTTCAGGTAAAATC 59.762 50.000 0.00 0.00 0.00 2.17
2357 4229 2.026636 CCTCCGGTTCAGGTAAAATCCA 60.027 50.000 0.00 0.00 0.00 3.41
2358 4230 3.371595 CCTCCGGTTCAGGTAAAATCCAT 60.372 47.826 0.00 0.00 0.00 3.41
2384 4256 1.582610 TTTCCGCATTCCGCTTGTCC 61.583 55.000 0.00 0.00 39.08 4.02
2388 4260 1.643832 GCATTCCGCTTGTCCGATC 59.356 57.895 0.00 0.00 37.77 3.69
2413 4285 1.973812 GCAGGGAGCTTGGTTGACC 60.974 63.158 0.00 0.00 41.15 4.02
2423 4295 1.207089 CTTGGTTGACCGATGAGCCTA 59.793 52.381 0.00 0.00 39.43 3.93
2424 4296 1.496060 TGGTTGACCGATGAGCCTAT 58.504 50.000 0.00 0.00 39.43 2.57
2425 4297 1.138859 TGGTTGACCGATGAGCCTATG 59.861 52.381 0.00 0.00 39.43 2.23
2426 4298 1.139058 GGTTGACCGATGAGCCTATGT 59.861 52.381 0.00 0.00 0.00 2.29
2427 4299 2.364324 GGTTGACCGATGAGCCTATGTA 59.636 50.000 0.00 0.00 0.00 2.29
2428 4300 3.006967 GGTTGACCGATGAGCCTATGTAT 59.993 47.826 0.00 0.00 0.00 2.29
2429 4301 3.942130 TGACCGATGAGCCTATGTATG 57.058 47.619 0.00 0.00 0.00 2.39
2430 4302 3.496331 TGACCGATGAGCCTATGTATGA 58.504 45.455 0.00 0.00 0.00 2.15
2431 4303 3.895041 TGACCGATGAGCCTATGTATGAA 59.105 43.478 0.00 0.00 0.00 2.57
2432 4304 4.528206 TGACCGATGAGCCTATGTATGAAT 59.472 41.667 0.00 0.00 0.00 2.57
2433 4305 4.825422 ACCGATGAGCCTATGTATGAATG 58.175 43.478 0.00 0.00 0.00 2.67
2442 4314 8.243426 TGAGCCTATGTATGAATGTTTGTTTTC 58.757 33.333 0.00 0.00 0.00 2.29
2450 4322 7.866898 TGTATGAATGTTTGTTTTCTGTCCATG 59.133 33.333 0.00 0.00 0.00 3.66
2491 4363 3.385755 TGAGAGCTGGATGATTTCGATCA 59.614 43.478 0.00 0.00 34.73 2.92
2550 4422 4.572389 GCAAGGTGTGTAGATATTCAGGTG 59.428 45.833 0.00 0.00 0.00 4.00
2639 4511 3.068732 GCTGGCAATTTTATCCTCCCTTC 59.931 47.826 0.00 0.00 0.00 3.46
2640 4512 3.638627 CTGGCAATTTTATCCTCCCTTCC 59.361 47.826 0.00 0.00 0.00 3.46
2783 4655 4.023279 TGTGTCGGACCAATGATTCTTTTG 60.023 41.667 5.55 0.00 0.00 2.44
2785 4657 4.824537 TGTCGGACCAATGATTCTTTTGAA 59.175 37.500 5.55 0.00 43.30 2.69
2831 4704 5.611374 AGTTGCACTACTTTCTCTTGCTTA 58.389 37.500 0.00 0.00 34.18 3.09
2847 4720 4.866508 TGCTTATAATGTACTCCCTCCG 57.133 45.455 0.00 0.00 0.00 4.63
2849 4722 4.280174 TGCTTATAATGTACTCCCTCCGAC 59.720 45.833 0.00 0.00 0.00 4.79
2855 4728 1.133575 TGTACTCCCTCCGACCCATAG 60.134 57.143 0.00 0.00 0.00 2.23
2862 4735 2.385803 CCTCCGACCCATAGTAAGTGT 58.614 52.381 0.00 0.00 0.00 3.55
2864 4737 3.021695 CTCCGACCCATAGTAAGTGTCA 58.978 50.000 0.00 0.00 0.00 3.58
2866 4739 4.795469 TCCGACCCATAGTAAGTGTCATA 58.205 43.478 0.00 0.00 0.00 2.15
2867 4740 5.391256 TCCGACCCATAGTAAGTGTCATAT 58.609 41.667 0.00 0.00 0.00 1.78
2919 4792 8.742125 ATTACACTTATTATGGATCAGAGGGA 57.258 34.615 0.00 0.00 0.00 4.20
2920 4793 6.678568 ACACTTATTATGGATCAGAGGGAG 57.321 41.667 0.00 0.00 0.00 4.30
2921 4794 6.146760 ACACTTATTATGGATCAGAGGGAGT 58.853 40.000 0.00 0.00 0.00 3.85
2922 4795 7.306013 ACACTTATTATGGATCAGAGGGAGTA 58.694 38.462 0.00 0.00 0.00 2.59
2923 4796 7.453126 ACACTTATTATGGATCAGAGGGAGTAG 59.547 40.741 0.00 0.00 0.00 2.57
2924 4797 7.453126 CACTTATTATGGATCAGAGGGAGTAGT 59.547 40.741 0.00 0.00 0.00 2.73
2925 4798 8.013667 ACTTATTATGGATCAGAGGGAGTAGTT 58.986 37.037 0.00 0.00 0.00 2.24
2926 4799 8.798975 TTATTATGGATCAGAGGGAGTAGTTT 57.201 34.615 0.00 0.00 0.00 2.66
2927 4800 9.892444 TTATTATGGATCAGAGGGAGTAGTTTA 57.108 33.333 0.00 0.00 0.00 2.01
2928 4801 8.980832 ATTATGGATCAGAGGGAGTAGTTTAT 57.019 34.615 0.00 0.00 0.00 1.40
2929 4802 8.798975 TTATGGATCAGAGGGAGTAGTTTATT 57.201 34.615 0.00 0.00 0.00 1.40
2930 4803 7.698163 ATGGATCAGAGGGAGTAGTTTATTT 57.302 36.000 0.00 0.00 0.00 1.40
2931 4804 6.889198 TGGATCAGAGGGAGTAGTTTATTTG 58.111 40.000 0.00 0.00 0.00 2.32
2932 4805 6.672218 TGGATCAGAGGGAGTAGTTTATTTGA 59.328 38.462 0.00 0.00 0.00 2.69
2933 4806 6.987404 GGATCAGAGGGAGTAGTTTATTTGAC 59.013 42.308 0.00 0.00 0.00 3.18
2934 4807 7.147637 GGATCAGAGGGAGTAGTTTATTTGACT 60.148 40.741 0.00 0.00 0.00 3.41
3006 4879 5.426833 AGGATAAGGCAGTAGAATGTTCAGT 59.573 40.000 0.00 0.00 0.00 3.41
3014 4887 7.288852 AGGCAGTAGAATGTTCAGTAGATGTAT 59.711 37.037 0.00 0.00 0.00 2.29
3038 4911 7.831691 TTCAGGATGGTGAAATGTTTTTAGA 57.168 32.000 0.00 0.00 33.41 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.856103 GCAACATATACTTTAAACCCACCATAT 58.144 33.333 0.00 0.00 0.00 1.78
4 5 7.834681 TGCAACATATACTTTAAACCCACCATA 59.165 33.333 0.00 0.00 0.00 2.74
5 6 6.665680 TGCAACATATACTTTAAACCCACCAT 59.334 34.615 0.00 0.00 0.00 3.55
7 8 6.071840 TGTGCAACATATACTTTAAACCCACC 60.072 38.462 0.00 0.00 45.67 4.61
8 9 6.915349 TGTGCAACATATACTTTAAACCCAC 58.085 36.000 0.00 0.00 45.67 4.61
25 26 4.381566 GGTTCAACATTAATCGTGTGCAAC 59.618 41.667 0.00 0.00 37.35 4.17
26 27 4.277174 AGGTTCAACATTAATCGTGTGCAA 59.723 37.500 0.00 0.00 0.00 4.08
27 28 3.818210 AGGTTCAACATTAATCGTGTGCA 59.182 39.130 0.00 0.00 0.00 4.57
28 29 4.419522 AGGTTCAACATTAATCGTGTGC 57.580 40.909 0.00 0.00 0.00 4.57
29 30 6.367695 TCTGTAGGTTCAACATTAATCGTGTG 59.632 38.462 0.00 0.00 0.00 3.82
30 31 6.460781 TCTGTAGGTTCAACATTAATCGTGT 58.539 36.000 0.00 0.00 0.00 4.49
31 32 6.961359 TCTGTAGGTTCAACATTAATCGTG 57.039 37.500 0.00 0.00 0.00 4.35
32 33 9.832445 ATATTCTGTAGGTTCAACATTAATCGT 57.168 29.630 0.00 0.00 0.00 3.73
38 39 9.342308 CCATACATATTCTGTAGGTTCAACATT 57.658 33.333 0.00 0.00 43.44 2.71
51 52 4.763279 TGCAATGGAGCCATACATATTCTG 59.237 41.667 1.81 0.00 35.31 3.02
64 65 1.081242 CCGTGTGTTGCAATGGAGC 60.081 57.895 0.59 0.00 0.00 4.70
71 72 1.265635 GCTAATTGTCCGTGTGTTGCA 59.734 47.619 0.00 0.00 0.00 4.08
72 73 1.401018 GGCTAATTGTCCGTGTGTTGC 60.401 52.381 0.00 0.00 0.00 4.17
77 78 1.808411 CACTGGCTAATTGTCCGTGT 58.192 50.000 0.00 0.00 0.00 4.49
81 82 0.811281 GTGGCACTGGCTAATTGTCC 59.189 55.000 11.13 0.00 40.87 4.02
95 96 1.163420 ATTTTGAGACACGCGTGGCA 61.163 50.000 43.29 31.63 42.32 4.92
101 102 2.031560 TGACACACATTTTGAGACACGC 59.968 45.455 0.00 0.00 0.00 5.34
102 103 3.942539 TGACACACATTTTGAGACACG 57.057 42.857 0.00 0.00 0.00 4.49
123 124 5.641709 TGTCTCAAAATGCAACACGTTTTA 58.358 33.333 0.00 0.00 43.99 1.52
128 129 3.044986 CCTTGTCTCAAAATGCAACACG 58.955 45.455 0.00 0.00 0.00 4.49
132 133 3.565307 ACTCCCTTGTCTCAAAATGCAA 58.435 40.909 0.00 0.00 0.00 4.08
164 165 7.229306 TGCTTTGAGAGAAATACAACATCACTT 59.771 33.333 0.00 0.00 0.00 3.16
168 169 7.699812 GGATTGCTTTGAGAGAAATACAACATC 59.300 37.037 0.00 0.00 34.65 3.06
211 238 1.615392 AGTTTTGGATTGCTCACTGGC 59.385 47.619 0.00 0.00 0.00 4.85
214 241 4.218312 AGGAAAGTTTTGGATTGCTCACT 58.782 39.130 0.00 0.00 0.00 3.41
243 270 1.537202 AGTTTTGGATTGCTCACTCGC 59.463 47.619 0.00 0.00 0.00 5.03
245 272 5.009010 TCTCAAAGTTTTGGATTGCTCACTC 59.991 40.000 4.89 0.00 38.66 3.51
268 295 4.875544 TGCAGCCTACGATTTTTGTATC 57.124 40.909 0.00 0.00 0.00 2.24
280 307 6.166279 TGCTTATATCTGTATTGCAGCCTAC 58.834 40.000 0.00 0.00 44.66 3.18
292 319 2.826428 CACGTGGCTGCTTATATCTGT 58.174 47.619 7.95 0.00 0.00 3.41
307 334 1.665916 CTGTGAGTCCTGGCACGTG 60.666 63.158 12.28 12.28 37.83 4.49
310 337 2.359230 GCCTGTGAGTCCTGGCAC 60.359 66.667 18.34 0.00 45.74 5.01
312 339 1.544825 TACAGCCTGTGAGTCCTGGC 61.545 60.000 7.83 16.59 46.53 4.85
313 340 0.534412 CTACAGCCTGTGAGTCCTGG 59.466 60.000 7.83 0.00 0.00 4.45
314 341 1.261480 ACTACAGCCTGTGAGTCCTG 58.739 55.000 7.83 0.00 0.00 3.86
315 342 2.901338 TACTACAGCCTGTGAGTCCT 57.099 50.000 7.83 0.00 0.00 3.85
316 343 3.181474 GGAATACTACAGCCTGTGAGTCC 60.181 52.174 7.83 7.24 0.00 3.85
317 344 3.447586 TGGAATACTACAGCCTGTGAGTC 59.552 47.826 7.83 1.59 0.00 3.36
319 346 4.471904 TTGGAATACTACAGCCTGTGAG 57.528 45.455 7.83 3.87 0.00 3.51
349 381 1.167851 TCCAACAACAGCTGCTATGC 58.832 50.000 15.27 0.00 0.00 3.14
350 382 2.751259 ACATCCAACAACAGCTGCTATG 59.249 45.455 15.27 13.20 0.00 2.23
351 383 3.077484 ACATCCAACAACAGCTGCTAT 57.923 42.857 15.27 0.00 0.00 2.97
356 388 5.590530 TTTTGTTACATCCAACAACAGCT 57.409 34.783 1.12 0.00 45.52 4.24
360 392 5.177327 CAGGCATTTTGTTACATCCAACAAC 59.823 40.000 1.12 0.00 45.52 3.32
361 393 5.069648 TCAGGCATTTTGTTACATCCAACAA 59.930 36.000 0.00 0.00 44.50 2.83
362 394 4.586421 TCAGGCATTTTGTTACATCCAACA 59.414 37.500 0.00 0.00 36.65 3.33
364 396 5.798125 TTCAGGCATTTTGTTACATCCAA 57.202 34.783 0.00 0.00 0.00 3.53
431 477 2.423064 GCAGGCGGGGTAAAATGGG 61.423 63.158 0.00 0.00 0.00 4.00
669 2492 0.179179 GCGATGTCTTTTCCTGCTGC 60.179 55.000 0.00 0.00 0.00 5.25
670 2493 1.129998 CTGCGATGTCTTTTCCTGCTG 59.870 52.381 0.00 0.00 0.00 4.41
671 2494 1.446907 CTGCGATGTCTTTTCCTGCT 58.553 50.000 0.00 0.00 0.00 4.24
772 2599 0.411848 GAGAGAGATAGGGGAGGGGG 59.588 65.000 0.00 0.00 0.00 5.40
777 2605 1.982226 CGAGGAGAGAGAGATAGGGGA 59.018 57.143 0.00 0.00 0.00 4.81
780 2608 1.821216 GCCGAGGAGAGAGAGATAGG 58.179 60.000 0.00 0.00 0.00 2.57
781 2609 1.270625 ACGCCGAGGAGAGAGAGATAG 60.271 57.143 0.00 0.00 0.00 2.08
783 2611 0.534203 GACGCCGAGGAGAGAGAGAT 60.534 60.000 0.00 0.00 0.00 2.75
807 2635 0.034616 GATGGCGATGGGGAGAGAAG 59.965 60.000 0.00 0.00 0.00 2.85
808 2636 0.399091 AGATGGCGATGGGGAGAGAA 60.399 55.000 0.00 0.00 0.00 2.87
852 2683 1.413118 AAACCAGGCAAGAACAAGGG 58.587 50.000 0.00 0.00 0.00 3.95
856 2687 1.484240 CCCAAAAACCAGGCAAGAACA 59.516 47.619 0.00 0.00 0.00 3.18
1107 2950 4.960866 TGGTGCTGCTGCTGGTGG 62.961 66.667 17.00 0.00 40.48 4.61
1114 2957 3.362797 CTGCTGGTGGTGCTGCTG 61.363 66.667 0.00 0.00 0.00 4.41
1117 2960 3.362797 CTGCTGCTGGTGGTGCTG 61.363 66.667 0.00 0.00 0.00 4.41
1120 2963 3.362797 CTGCTGCTGCTGGTGGTG 61.363 66.667 17.00 0.00 40.48 4.17
1341 3193 1.580845 CCTTGTTGGAGCTCCGCTTG 61.581 60.000 27.43 15.40 39.88 4.01
1419 3271 4.880537 AGCTGGAAGATCCGCGCG 62.881 66.667 25.67 25.67 40.17 6.86
1939 3791 4.974721 GTGGTGCTGGTGGGGGTG 62.975 72.222 0.00 0.00 0.00 4.61
1942 3794 4.974721 GTGGTGGTGCTGGTGGGG 62.975 72.222 0.00 0.00 0.00 4.96
1943 3795 4.974721 GGTGGTGGTGCTGGTGGG 62.975 72.222 0.00 0.00 0.00 4.61
1993 3851 3.141488 CTCGTCCTCCCCGTCCTG 61.141 72.222 0.00 0.00 0.00 3.86
2184 4042 3.228188 ACTCATCACAAGCCCAAGAAA 57.772 42.857 0.00 0.00 0.00 2.52
2193 4051 9.450807 AAAATCGACTTAAAAACTCATCACAAG 57.549 29.630 0.00 0.00 0.00 3.16
2297 4164 0.041833 AGGAGCAGCAGGAGTAGGAA 59.958 55.000 0.00 0.00 0.00 3.36
2354 4226 2.734755 ATGCGGAAAAGGATCATGGA 57.265 45.000 0.00 0.00 0.00 3.41
2355 4227 2.035066 GGAATGCGGAAAAGGATCATGG 59.965 50.000 0.00 0.00 0.00 3.66
2357 4229 1.949525 CGGAATGCGGAAAAGGATCAT 59.050 47.619 0.00 0.00 0.00 2.45
2358 4230 1.378531 CGGAATGCGGAAAAGGATCA 58.621 50.000 0.00 0.00 0.00 2.92
2384 4256 0.942962 GCTCCCTGCTCAAATGATCG 59.057 55.000 0.00 0.00 38.95 3.69
2413 4285 6.203530 ACAAACATTCATACATAGGCTCATCG 59.796 38.462 0.00 0.00 0.00 3.84
2423 4295 7.950512 TGGACAGAAAACAAACATTCATACAT 58.049 30.769 0.00 0.00 0.00 2.29
2424 4296 7.340122 TGGACAGAAAACAAACATTCATACA 57.660 32.000 0.00 0.00 0.00 2.29
2425 4297 7.867403 ACATGGACAGAAAACAAACATTCATAC 59.133 33.333 0.00 0.00 0.00 2.39
2426 4298 7.950512 ACATGGACAGAAAACAAACATTCATA 58.049 30.769 0.00 0.00 0.00 2.15
2427 4299 6.819284 ACATGGACAGAAAACAAACATTCAT 58.181 32.000 0.00 0.00 0.00 2.57
2428 4300 6.219417 ACATGGACAGAAAACAAACATTCA 57.781 33.333 0.00 0.00 0.00 2.57
2429 4301 6.509997 GCAACATGGACAGAAAACAAACATTC 60.510 38.462 0.00 0.00 0.00 2.67
2430 4302 5.294060 GCAACATGGACAGAAAACAAACATT 59.706 36.000 0.00 0.00 0.00 2.71
2431 4303 4.810491 GCAACATGGACAGAAAACAAACAT 59.190 37.500 0.00 0.00 0.00 2.71
2432 4304 4.180057 GCAACATGGACAGAAAACAAACA 58.820 39.130 0.00 0.00 0.00 2.83
2433 4305 4.180057 TGCAACATGGACAGAAAACAAAC 58.820 39.130 0.00 0.00 0.00 2.93
2442 4314 2.183478 TACACCTGCAACATGGACAG 57.817 50.000 0.00 1.11 0.00 3.51
2450 4322 5.601662 TCTCAGCTATTATACACCTGCAAC 58.398 41.667 0.00 0.00 0.00 4.17
2491 4363 0.908198 GCACTCACTCAAGGGAGGAT 59.092 55.000 13.62 0.00 45.81 3.24
2550 4422 2.019984 CACCTCCCTAGCTGCAAAATC 58.980 52.381 1.02 0.00 0.00 2.17
2831 4704 2.090943 TGGGTCGGAGGGAGTACATTAT 60.091 50.000 0.00 0.00 0.00 1.28
2893 4766 9.837681 TCCCTCTGATCCATAATAAGTGTAATA 57.162 33.333 0.00 0.00 0.00 0.98
2895 4768 7.789831 ACTCCCTCTGATCCATAATAAGTGTAA 59.210 37.037 0.00 0.00 0.00 2.41
2896 4769 7.306013 ACTCCCTCTGATCCATAATAAGTGTA 58.694 38.462 0.00 0.00 0.00 2.90
2913 4786 9.411189 CTACTAGTCAAATAAACTACTCCCTCT 57.589 37.037 0.00 0.00 0.00 3.69
3006 4879 7.805163 ACATTTCACCATCCTGAATACATCTA 58.195 34.615 0.00 0.00 30.19 1.98
3014 4887 7.831691 TCTAAAAACATTTCACCATCCTGAA 57.168 32.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.