Multiple sequence alignment - TraesCS2D01G304200

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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 TraesCS2D01G304200 chr2D 100.000 3062 0 0 1 3062 389276266 389279327 0.000000e+00 5655.0
1 TraesCS2D01G304200 chr2D 96.226 53 2 0 2891 2943 389279105 389279157 1.510000e-13 87.9
2 TraesCS2D01G304200 chr2D 96.226 53 2 0 2840 2892 389279156 389279208 1.510000e-13 87.9
3 TraesCS2D01G304200 chr2B 93.056 1656 78 16 10 1651 461090675 461092307 0.000000e+00 2386.0
4 TraesCS2D01G304200 chr2B 91.207 671 40 6 2241 2892 461093146 461093816 0.000000e+00 894.0
5 TraesCS2D01G304200 chr2B 94.033 553 30 3 1692 2242 461092513 461093064 0.000000e+00 835.0
6 TraesCS2D01G304200 chr2B 95.349 172 8 0 2891 3062 461093764 461093935 1.080000e-69 274.0
7 TraesCS2D01G304200 chr2B 100.000 31 0 0 51 81 461090623 461090653 1.190000e-04 58.4
8 TraesCS2D01G304200 chr2A 97.005 1202 32 4 1692 2892 526064655 526065853 0.000000e+00 2017.0
9 TraesCS2D01G304200 chr2A 93.406 1016 44 8 333 1343 526063201 526064198 0.000000e+00 1483.0
10 TraesCS2D01G304200 chr2A 93.377 302 20 0 44 345 526062883 526063184 6.020000e-122 448.0
11 TraesCS2D01G304200 chr2A 93.004 243 15 2 1392 1633 526064196 526064437 1.350000e-93 353.0
12 TraesCS2D01G304200 chr2A 96.491 171 6 0 2891 3061 526065801 526065971 1.800000e-72 283.0
13 TraesCS2D01G304200 chr3A 78.261 276 58 2 401 674 691098942 691098667 3.140000e-40 176.0
14 TraesCS2D01G304200 chr7A 88.235 68 8 0 339 406 42260762 42260829 7.040000e-12 82.4
15 TraesCS2D01G304200 chr7A 96.875 32 0 1 2558 2588 50793000 50793031 6.000000e-03 52.8
16 TraesCS2D01G304200 chr7A 92.308 39 0 2 2558 2595 50815294 50815258 6.000000e-03 52.8
17 TraesCS2D01G304200 chr3B 91.111 45 3 1 310 354 705708155 705708198 3.300000e-05 60.2
18 TraesCS2D01G304200 chr7D 94.286 35 2 0 2554 2588 48259714 48259748 2.000000e-03 54.7


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 TraesCS2D01G304200 chr2D 389276266 389279327 3061 False 1943.60 5655 97.4840 1 3062 3 chr2D.!!$F1 3061
1 TraesCS2D01G304200 chr2B 461090623 461093935 3312 False 889.48 2386 94.7290 10 3062 5 chr2B.!!$F1 3052
2 TraesCS2D01G304200 chr2A 526062883 526065971 3088 False 916.80 2017 94.6566 44 3061 5 chr2A.!!$F1 3017

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
30 74 0.755698 GGTCCATAGGAGACGAGGCA 60.756 60.000 0.0 0.0 34.97 4.75 F
35 79 1.336440 CATAGGAGACGAGGCAGACTG 59.664 57.143 0.0 0.0 0.00 3.51 F
1581 1671 0.108138 CCTCGCTGAAGGATTTCGGT 60.108 55.000 0.0 0.0 41.01 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1223 1313 0.116541 TTCTCCTCCCCCGACTTCTT 59.883 55.0 0.0 0.0 0.00 2.52 R
1636 1726 0.392461 GGCAAGTGTTCCGGCATCTA 60.392 55.0 0.0 0.0 0.00 1.98 R
2560 2900 0.251297 CAGTTCCCCTGCATGGTTCA 60.251 55.0 7.3 0.0 33.59 3.18 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
30 74 0.755698 GGTCCATAGGAGACGAGGCA 60.756 60.000 0.00 0.00 34.97 4.75
35 79 1.336440 CATAGGAGACGAGGCAGACTG 59.664 57.143 0.00 0.00 0.00 3.51
41 85 2.143594 GACGAGGCAGACTGACGGTT 62.144 60.000 6.65 0.00 0.00 4.44
314 369 6.518493 TGATTCCGTAAAACACTACTCACTT 58.482 36.000 0.00 0.00 0.00 3.16
519 604 1.409427 CTCGAAGGCCGGAATAAGTCT 59.591 52.381 5.05 0.00 39.14 3.24
688 774 3.006672 CTTTGTCAAGCACGACCCT 57.993 52.632 0.00 0.00 34.88 4.34
732 818 5.389859 TGATCAGGTTTTAGGTGCAAATG 57.610 39.130 0.00 0.00 0.00 2.32
749 835 5.473846 TGCAAATGCCAATTGTGAAATCAAT 59.526 32.000 4.43 0.00 41.18 2.57
794 881 4.011698 TCAAGACTGGTACTGCGTATGTA 58.988 43.478 0.00 0.00 0.00 2.29
795 882 4.103357 CAAGACTGGTACTGCGTATGTAC 58.897 47.826 0.00 0.00 39.43 2.90
796 883 3.349927 AGACTGGTACTGCGTATGTACA 58.650 45.455 0.00 0.00 41.27 2.90
797 884 3.760151 AGACTGGTACTGCGTATGTACAA 59.240 43.478 0.00 5.00 41.27 2.41
798 885 4.401519 AGACTGGTACTGCGTATGTACAAT 59.598 41.667 0.00 0.00 41.27 2.71
799 886 5.080969 ACTGGTACTGCGTATGTACAATT 57.919 39.130 0.00 0.00 41.27 2.32
800 887 5.484715 ACTGGTACTGCGTATGTACAATTT 58.515 37.500 0.00 0.00 41.27 1.82
801 888 5.579511 ACTGGTACTGCGTATGTACAATTTC 59.420 40.000 0.00 0.00 41.27 2.17
1114 1204 1.846007 CGATATCTCCTCCCCTCCTG 58.154 60.000 0.34 0.00 0.00 3.86
1254 1344 3.706373 GGAGAAGGAGGCGCACCA 61.706 66.667 21.48 0.00 39.06 4.17
1312 1402 1.463214 TTCACCCTCCTCAAGCCCA 60.463 57.895 0.00 0.00 0.00 5.36
1341 1431 1.822990 CCCAAGGTACGAAGCTCTGTA 59.177 52.381 0.00 0.00 31.54 2.74
1419 1509 2.757686 TTGTGCATTTTGACGCGTTA 57.242 40.000 15.53 6.34 0.00 3.18
1420 1510 2.308347 TGTGCATTTTGACGCGTTAG 57.692 45.000 15.53 0.00 0.00 2.34
1422 1512 1.069500 GTGCATTTTGACGCGTTAGGT 60.069 47.619 15.53 0.00 0.00 3.08
1424 1514 2.239201 GCATTTTGACGCGTTAGGTTC 58.761 47.619 15.53 0.00 0.00 3.62
1426 1516 3.608474 GCATTTTGACGCGTTAGGTTCTT 60.608 43.478 15.53 0.00 0.00 2.52
1427 1517 3.865224 TTTTGACGCGTTAGGTTCTTC 57.135 42.857 15.53 0.00 0.00 2.87
1429 1519 0.592637 TGACGCGTTAGGTTCTTCGA 59.407 50.000 15.53 0.00 0.00 3.71
1539 1629 3.862309 AGGGGAGTAACAATATTGGGGTT 59.138 43.478 19.37 7.59 0.00 4.11
1571 1661 1.977009 TTCGCCTCTCCTCGCTGAA 60.977 57.895 0.00 0.00 0.00 3.02
1581 1671 0.108138 CCTCGCTGAAGGATTTCGGT 60.108 55.000 0.00 0.00 41.01 4.69
1599 1689 1.227292 TACACCGCAGTTTGTCGCA 60.227 52.632 0.00 0.00 0.00 5.10
1633 1723 4.390264 ACAGGCAGAGAAGAAAAAGGTAC 58.610 43.478 0.00 0.00 0.00 3.34
1635 1725 4.453819 CAGGCAGAGAAGAAAAAGGTACTG 59.546 45.833 0.00 0.00 40.86 2.74
1636 1726 4.103311 AGGCAGAGAAGAAAAAGGTACTGT 59.897 41.667 0.00 0.00 40.86 3.55
1637 1727 5.307196 AGGCAGAGAAGAAAAAGGTACTGTA 59.693 40.000 0.00 0.00 40.86 2.74
1638 1728 5.639931 GGCAGAGAAGAAAAAGGTACTGTAG 59.360 44.000 0.00 0.00 40.86 2.74
1655 1756 0.392461 TAGATGCCGGAACACTTGCC 60.392 55.000 5.05 0.00 0.00 4.52
1666 1767 1.117142 ACACTTGCCATTTGCCAGCT 61.117 50.000 0.00 0.00 36.19 4.24
1671 1772 0.033306 TGCCATTTGCCAGCTCCATA 60.033 50.000 0.00 0.00 40.16 2.74
1679 1780 6.127814 CCATTTGCCAGCTCCATACTATATTG 60.128 42.308 0.00 0.00 0.00 1.90
1680 1781 3.942829 TGCCAGCTCCATACTATATTGC 58.057 45.455 0.00 0.00 0.00 3.56
1681 1782 3.584406 TGCCAGCTCCATACTATATTGCT 59.416 43.478 0.00 0.00 0.00 3.91
1682 1783 4.777366 TGCCAGCTCCATACTATATTGCTA 59.223 41.667 0.00 0.00 0.00 3.49
1683 1784 5.112686 GCCAGCTCCATACTATATTGCTAC 58.887 45.833 0.00 0.00 0.00 3.58
1685 1786 5.423610 CCAGCTCCATACTATATTGCTACCT 59.576 44.000 0.00 0.00 0.00 3.08
1689 1790 8.440771 AGCTCCATACTATATTGCTACCTTTTT 58.559 33.333 0.00 0.00 0.00 1.94
1690 1791 8.507249 GCTCCATACTATATTGCTACCTTTTTG 58.493 37.037 0.00 0.00 0.00 2.44
1718 1973 1.803555 GAGCTCCTTCTGTTGTTGCTC 59.196 52.381 0.87 0.00 38.58 4.26
1725 1980 5.316167 TCCTTCTGTTGTTGCTCATAATGT 58.684 37.500 0.00 0.00 0.00 2.71
1734 1989 6.866010 TGTTGCTCATAATGTATGGTGATC 57.134 37.500 0.00 0.00 36.81 2.92
1770 2025 4.141959 CCACATTTTGGGAAAGTTCAGTGT 60.142 41.667 0.00 0.00 42.54 3.55
1781 2036 6.935208 GGGAAAGTTCAGTGTTAGTATTGTCT 59.065 38.462 0.00 0.00 0.00 3.41
2086 2342 7.659390 AGTTTCTTTCTCTTAACAGGAGATGTG 59.341 37.037 0.00 0.00 43.00 3.21
2192 2448 6.650427 AAAGGTTACAAATGTTCTTCTCCC 57.350 37.500 0.00 0.00 0.00 4.30
2558 2898 1.606668 TGACAACATGCCGGTCTTTTC 59.393 47.619 1.90 0.00 32.84 2.29
2560 2900 2.293399 GACAACATGCCGGTCTTTTCTT 59.707 45.455 1.90 0.00 0.00 2.52
2847 3205 0.976641 CTGGTGTCTAGTGCCAGGAA 59.023 55.000 16.64 0.00 44.36 3.36
2889 3247 5.065988 TGTGCTCTCAAACTGTTTTTAGTCC 59.934 40.000 2.41 1.94 0.00 3.85
2890 3248 5.297029 GTGCTCTCAAACTGTTTTTAGTCCT 59.703 40.000 2.41 0.00 0.00 3.85
2891 3249 5.296780 TGCTCTCAAACTGTTTTTAGTCCTG 59.703 40.000 2.41 0.00 0.00 3.86
2892 3250 5.297029 GCTCTCAAACTGTTTTTAGTCCTGT 59.703 40.000 2.41 0.00 0.00 4.00
2893 3251 6.511929 GCTCTCAAACTGTTTTTAGTCCTGTC 60.512 42.308 2.41 0.00 0.00 3.51
2894 3252 6.411376 TCTCAAACTGTTTTTAGTCCTGTCA 58.589 36.000 2.41 0.00 0.00 3.58
2895 3253 6.538742 TCTCAAACTGTTTTTAGTCCTGTCAG 59.461 38.462 2.41 0.00 0.00 3.51
2896 3254 5.588648 TCAAACTGTTTTTAGTCCTGTCAGG 59.411 40.000 13.21 13.21 36.46 3.86
2897 3255 5.367945 AACTGTTTTTAGTCCTGTCAGGA 57.632 39.130 18.15 18.15 43.43 3.86
2905 3263 3.257627 TCCTGTCAGGACTGGGTTT 57.742 52.632 18.15 0.00 46.54 3.27
2906 3264 1.056660 TCCTGTCAGGACTGGGTTTC 58.943 55.000 18.15 0.00 46.54 2.78
2907 3265 0.036875 CCTGTCAGGACTGGGTTTCC 59.963 60.000 14.26 0.00 43.94 3.13
2908 3266 1.059913 CTGTCAGGACTGGGTTTCCT 58.940 55.000 0.65 0.00 44.97 3.36
2909 3267 1.421646 CTGTCAGGACTGGGTTTCCTT 59.578 52.381 0.65 0.00 40.95 3.36
2910 3268 1.420138 TGTCAGGACTGGGTTTCCTTC 59.580 52.381 0.65 0.00 40.95 3.46
2911 3269 1.700186 GTCAGGACTGGGTTTCCTTCT 59.300 52.381 0.00 0.00 40.95 2.85
2912 3270 2.106684 GTCAGGACTGGGTTTCCTTCTT 59.893 50.000 0.00 0.00 40.95 2.52
2913 3271 2.783510 TCAGGACTGGGTTTCCTTCTTT 59.216 45.455 0.00 0.00 40.95 2.52
2914 3272 2.887152 CAGGACTGGGTTTCCTTCTTTG 59.113 50.000 0.00 0.00 40.95 2.77
2915 3273 2.158460 AGGACTGGGTTTCCTTCTTTGG 60.158 50.000 0.00 0.00 40.95 3.28
2916 3274 2.424379 GGACTGGGTTTCCTTCTTTGGT 60.424 50.000 0.00 0.00 0.00 3.67
2917 3275 2.623416 GACTGGGTTTCCTTCTTTGGTG 59.377 50.000 0.00 0.00 0.00 4.17
2918 3276 2.024369 ACTGGGTTTCCTTCTTTGGTGT 60.024 45.455 0.00 0.00 0.00 4.16
2919 3277 2.362077 CTGGGTTTCCTTCTTTGGTGTG 59.638 50.000 0.00 0.00 0.00 3.82
2920 3278 1.068588 GGGTTTCCTTCTTTGGTGTGC 59.931 52.381 0.00 0.00 0.00 4.57
2921 3279 2.031870 GGTTTCCTTCTTTGGTGTGCT 58.968 47.619 0.00 0.00 0.00 4.40
2922 3280 2.034685 GGTTTCCTTCTTTGGTGTGCTC 59.965 50.000 0.00 0.00 0.00 4.26
2923 3281 2.952310 GTTTCCTTCTTTGGTGTGCTCT 59.048 45.455 0.00 0.00 0.00 4.09
2924 3282 2.550830 TCCTTCTTTGGTGTGCTCTC 57.449 50.000 0.00 0.00 0.00 3.20
2925 3283 1.768275 TCCTTCTTTGGTGTGCTCTCA 59.232 47.619 0.00 0.00 0.00 3.27
2926 3284 2.172505 TCCTTCTTTGGTGTGCTCTCAA 59.827 45.455 0.00 0.00 0.00 3.02
2927 3285 2.951642 CCTTCTTTGGTGTGCTCTCAAA 59.048 45.455 7.32 7.32 0.00 2.69
2928 3286 3.243201 CCTTCTTTGGTGTGCTCTCAAAC 60.243 47.826 4.58 0.00 0.00 2.93
2929 3287 3.281727 TCTTTGGTGTGCTCTCAAACT 57.718 42.857 4.58 0.00 31.03 2.66
2930 3288 2.945008 TCTTTGGTGTGCTCTCAAACTG 59.055 45.455 4.58 0.00 31.03 3.16
2931 3289 2.418368 TTGGTGTGCTCTCAAACTGT 57.582 45.000 0.00 0.00 31.03 3.55
2932 3290 2.418368 TGGTGTGCTCTCAAACTGTT 57.582 45.000 0.00 0.00 31.03 3.16
2933 3291 2.722094 TGGTGTGCTCTCAAACTGTTT 58.278 42.857 0.00 0.00 31.03 2.83
2934 3292 3.088532 TGGTGTGCTCTCAAACTGTTTT 58.911 40.909 2.41 0.00 31.03 2.43
2935 3293 3.509575 TGGTGTGCTCTCAAACTGTTTTT 59.490 39.130 2.41 0.00 31.03 1.94
2936 3294 4.702612 TGGTGTGCTCTCAAACTGTTTTTA 59.297 37.500 2.41 0.00 31.03 1.52
2937 3295 5.163663 TGGTGTGCTCTCAAACTGTTTTTAG 60.164 40.000 2.41 4.72 31.03 1.85
2938 3296 5.163652 GGTGTGCTCTCAAACTGTTTTTAGT 60.164 40.000 2.41 0.00 31.03 2.24
2939 3297 5.965918 GTGTGCTCTCAAACTGTTTTTAGTC 59.034 40.000 2.41 2.88 0.00 2.59
3049 3407 3.830755 GGGTACAGAGAACTGAACTACCA 59.169 47.826 13.48 0.00 46.03 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.795360 TCCTATGGACCTAGGACATGGA 59.205 50.000 24.83 23.47 41.89 3.41
1 2 3.169099 CTCCTATGGACCTAGGACATGG 58.831 54.545 24.44 22.10 41.89 3.66
4 5 2.158652 CGTCTCCTATGGACCTAGGACA 60.159 54.545 17.98 14.48 41.89 4.02
5 6 2.106166 TCGTCTCCTATGGACCTAGGAC 59.894 54.545 17.98 9.70 41.89 3.85
6 7 2.372504 CTCGTCTCCTATGGACCTAGGA 59.627 54.545 17.98 15.12 44.01 2.94
7 8 2.553466 CCTCGTCTCCTATGGACCTAGG 60.553 59.091 7.41 7.41 39.81 3.02
8 9 2.785562 CCTCGTCTCCTATGGACCTAG 58.214 57.143 0.00 0.00 0.00 3.02
9 10 1.202903 GCCTCGTCTCCTATGGACCTA 60.203 57.143 0.00 0.00 0.00 3.08
10 11 0.468400 GCCTCGTCTCCTATGGACCT 60.468 60.000 0.00 0.00 0.00 3.85
11 12 0.755698 TGCCTCGTCTCCTATGGACC 60.756 60.000 0.00 0.00 0.00 4.46
12 13 0.671251 CTGCCTCGTCTCCTATGGAC 59.329 60.000 0.00 0.00 0.00 4.02
13 14 0.551396 TCTGCCTCGTCTCCTATGGA 59.449 55.000 0.00 0.00 0.00 3.41
30 74 2.651361 CTGCCGAACCGTCAGTCT 59.349 61.111 0.00 0.00 0.00 3.24
35 79 1.598685 TTTTCCCTGCCGAACCGTC 60.599 57.895 0.00 0.00 0.00 4.79
161 216 9.547753 GCATTAATCAGATCCAACTCTAGTAAA 57.452 33.333 0.00 0.00 0.00 2.01
181 236 1.707989 TCCAACACAGGAGGGCATTAA 59.292 47.619 0.00 0.00 32.77 1.40
295 350 5.050567 GGACAAAGTGAGTAGTGTTTTACGG 60.051 44.000 0.00 0.00 0.00 4.02
314 369 9.865321 GTAATAGCATCTTATATTACGGGACAA 57.135 33.333 0.00 0.00 35.98 3.18
498 582 1.136500 GACTTATTCCGGCCTTCGAGT 59.864 52.381 0.00 0.00 42.43 4.18
705 791 3.879892 GCACCTAAAACCTGATCATCCTC 59.120 47.826 0.00 0.00 0.00 3.71
732 818 7.671495 AGGTTTTATTGATTTCACAATTGGC 57.329 32.000 10.83 0.00 40.36 4.52
794 881 7.920160 ACCAAACTTGAAATTGTGAAATTGT 57.080 28.000 0.00 0.00 0.00 2.71
855 943 8.609176 TGTGTACAATTACAACTTTTGTCTCTC 58.391 33.333 0.00 0.00 44.12 3.20
919 1009 3.429085 GCTCAGTTTGTTATCGCCATTG 58.571 45.455 0.00 0.00 0.00 2.82
1098 1188 1.153989 CGCAGGAGGGGAGGAGATA 59.846 63.158 0.00 0.00 0.00 1.98
1114 1204 4.143333 TCTCCTGGTTAGGCGCGC 62.143 66.667 25.94 25.94 44.22 6.86
1209 1299 1.000618 ACTTCTTCCTCCGTTTCCGAC 59.999 52.381 0.00 0.00 35.63 4.79
1223 1313 0.116541 TTCTCCTCCCCCGACTTCTT 59.883 55.000 0.00 0.00 0.00 2.52
1312 1402 1.910580 CGTACCTTGGGCCATGAGGT 61.911 60.000 28.25 28.25 45.38 3.85
1352 1442 1.393883 GTCTTTACGCTAGGTTGCAGC 59.606 52.381 0.00 0.00 35.61 5.25
1406 1496 3.120786 CGAAGAACCTAACGCGTCAAAAT 60.121 43.478 14.44 0.00 0.00 1.82
1410 1500 0.592637 TCGAAGAACCTAACGCGTCA 59.407 50.000 14.44 0.00 0.00 4.35
1419 1509 0.698818 AGCCCCAATTCGAAGAACCT 59.301 50.000 3.35 0.00 45.90 3.50
1420 1510 1.095600 GAGCCCCAATTCGAAGAACC 58.904 55.000 3.35 0.00 45.90 3.62
1422 1512 1.628340 TCAGAGCCCCAATTCGAAGAA 59.372 47.619 3.35 0.00 45.90 2.52
1424 1514 2.113860 TTCAGAGCCCCAATTCGAAG 57.886 50.000 3.35 0.00 0.00 3.79
1426 1516 2.290896 ACAATTCAGAGCCCCAATTCGA 60.291 45.455 0.00 0.00 0.00 3.71
1427 1517 2.094675 ACAATTCAGAGCCCCAATTCG 58.905 47.619 0.00 0.00 0.00 3.34
1429 1519 2.564062 CACACAATTCAGAGCCCCAATT 59.436 45.455 0.00 0.00 0.00 2.32
1539 1629 1.593209 GCGAACAGGGTTGACGACA 60.593 57.895 0.00 0.00 32.78 4.35
1581 1671 1.218875 CTGCGACAAACTGCGGTGTA 61.219 55.000 0.00 0.00 32.78 2.90
1599 1689 0.901124 CTGCCTGTAGAAGCCTGTCT 59.099 55.000 0.00 0.00 0.00 3.41
1633 1723 2.002586 CAAGTGTTCCGGCATCTACAG 58.997 52.381 0.00 0.00 0.00 2.74
1634 1724 1.943968 GCAAGTGTTCCGGCATCTACA 60.944 52.381 0.00 0.00 0.00 2.74
1635 1725 0.727398 GCAAGTGTTCCGGCATCTAC 59.273 55.000 0.00 0.00 0.00 2.59
1636 1726 0.392461 GGCAAGTGTTCCGGCATCTA 60.392 55.000 0.00 0.00 0.00 1.98
1637 1727 1.675641 GGCAAGTGTTCCGGCATCT 60.676 57.895 0.00 0.00 0.00 2.90
1638 1728 1.315257 ATGGCAAGTGTTCCGGCATC 61.315 55.000 0.00 0.00 41.60 3.91
1655 1756 6.624423 GCAATATAGTATGGAGCTGGCAAATG 60.624 42.308 0.00 0.00 0.00 2.32
1666 1767 8.719596 TCCAAAAAGGTAGCAATATAGTATGGA 58.280 33.333 0.00 0.00 39.02 3.41
1671 1772 9.309224 AGTTTTCCAAAAAGGTAGCAATATAGT 57.691 29.630 0.00 0.00 39.02 2.12
1679 1780 4.038042 AGCTCAGTTTTCCAAAAAGGTAGC 59.962 41.667 0.00 0.00 39.02 3.58
1680 1781 5.278512 GGAGCTCAGTTTTCCAAAAAGGTAG 60.279 44.000 17.19 0.00 39.02 3.18
1681 1782 4.583073 GGAGCTCAGTTTTCCAAAAAGGTA 59.417 41.667 17.19 0.00 39.02 3.08
1682 1783 3.384789 GGAGCTCAGTTTTCCAAAAAGGT 59.615 43.478 17.19 0.00 39.02 3.50
1683 1784 3.638627 AGGAGCTCAGTTTTCCAAAAAGG 59.361 43.478 17.19 0.00 39.47 3.11
1685 1786 4.956075 AGAAGGAGCTCAGTTTTCCAAAAA 59.044 37.500 17.19 0.00 33.32 1.94
1689 1790 2.439507 ACAGAAGGAGCTCAGTTTTCCA 59.560 45.455 17.19 0.00 33.32 3.53
1690 1791 3.133141 ACAGAAGGAGCTCAGTTTTCC 57.867 47.619 17.19 0.00 0.00 3.13
1718 1973 7.500227 ACTGAACCTTGATCACCATACATTATG 59.500 37.037 0.00 0.00 35.94 1.90
1725 1980 3.609853 GCACTGAACCTTGATCACCATA 58.390 45.455 0.00 0.00 0.00 2.74
1734 1989 1.331214 AATGTGGGCACTGAACCTTG 58.669 50.000 0.00 0.00 0.00 3.61
1758 2013 8.366671 ACAGACAATACTAACACTGAACTTTC 57.633 34.615 0.00 0.00 0.00 2.62
2086 2342 1.620819 AGACAGGGAGACACACATGAC 59.379 52.381 0.00 0.00 0.00 3.06
2558 2898 0.890683 GTTCCCCTGCATGGTTCAAG 59.109 55.000 7.30 0.00 0.00 3.02
2560 2900 0.251297 CAGTTCCCCTGCATGGTTCA 60.251 55.000 7.30 0.00 33.59 3.18
2612 2969 2.419990 CGGATGGCTTGTCTTGGTCATA 60.420 50.000 0.00 0.00 0.00 2.15
2847 3205 2.965147 CACACCAAAGAAGGAAACCCAT 59.035 45.455 0.00 0.00 0.00 4.00
2889 3247 1.059913 AGGAAACCCAGTCCTGACAG 58.940 55.000 0.00 0.00 44.14 3.51
2890 3248 1.420138 GAAGGAAACCCAGTCCTGACA 59.580 52.381 0.00 0.00 45.12 3.58
2891 3249 1.700186 AGAAGGAAACCCAGTCCTGAC 59.300 52.381 0.00 0.00 45.12 3.51
2892 3250 2.118403 AGAAGGAAACCCAGTCCTGA 57.882 50.000 0.00 0.00 45.12 3.86
2893 3251 2.887152 CAAAGAAGGAAACCCAGTCCTG 59.113 50.000 0.00 0.00 45.12 3.86
2895 3253 2.239400 CCAAAGAAGGAAACCCAGTCC 58.761 52.381 0.00 0.00 35.17 3.85
2896 3254 2.623416 CACCAAAGAAGGAAACCCAGTC 59.377 50.000 0.00 0.00 0.00 3.51
2897 3255 2.024369 ACACCAAAGAAGGAAACCCAGT 60.024 45.455 0.00 0.00 0.00 4.00
2898 3256 2.362077 CACACCAAAGAAGGAAACCCAG 59.638 50.000 0.00 0.00 0.00 4.45
2899 3257 2.383855 CACACCAAAGAAGGAAACCCA 58.616 47.619 0.00 0.00 0.00 4.51
2900 3258 1.068588 GCACACCAAAGAAGGAAACCC 59.931 52.381 0.00 0.00 0.00 4.11
2901 3259 2.031870 AGCACACCAAAGAAGGAAACC 58.968 47.619 0.00 0.00 0.00 3.27
2902 3260 2.952310 AGAGCACACCAAAGAAGGAAAC 59.048 45.455 0.00 0.00 0.00 2.78
2903 3261 3.214328 GAGAGCACACCAAAGAAGGAAA 58.786 45.455 0.00 0.00 0.00 3.13
2904 3262 2.172505 TGAGAGCACACCAAAGAAGGAA 59.827 45.455 0.00 0.00 0.00 3.36
2905 3263 1.768275 TGAGAGCACACCAAAGAAGGA 59.232 47.619 0.00 0.00 0.00 3.36
2906 3264 2.260844 TGAGAGCACACCAAAGAAGG 57.739 50.000 0.00 0.00 0.00 3.46
2907 3265 3.629398 AGTTTGAGAGCACACCAAAGAAG 59.371 43.478 2.93 0.00 31.40 2.85
2908 3266 3.378112 CAGTTTGAGAGCACACCAAAGAA 59.622 43.478 2.93 0.00 31.40 2.52
2909 3267 2.945008 CAGTTTGAGAGCACACCAAAGA 59.055 45.455 2.93 0.00 31.40 2.52
2910 3268 2.684881 ACAGTTTGAGAGCACACCAAAG 59.315 45.455 2.93 0.00 31.40 2.77
2911 3269 2.722094 ACAGTTTGAGAGCACACCAAA 58.278 42.857 0.00 0.00 0.00 3.28
2912 3270 2.418368 ACAGTTTGAGAGCACACCAA 57.582 45.000 0.00 0.00 0.00 3.67
2913 3271 2.418368 AACAGTTTGAGAGCACACCA 57.582 45.000 0.00 0.00 0.00 4.17
2914 3272 3.782889 AAAACAGTTTGAGAGCACACC 57.217 42.857 0.00 0.00 0.00 4.16
2915 3273 5.880341 ACTAAAAACAGTTTGAGAGCACAC 58.120 37.500 12.98 0.00 30.49 3.82
2916 3274 5.065988 GGACTAAAAACAGTTTGAGAGCACA 59.934 40.000 12.98 0.00 30.49 4.57
2917 3275 5.297029 AGGACTAAAAACAGTTTGAGAGCAC 59.703 40.000 12.98 3.32 30.49 4.40
2918 3276 5.296780 CAGGACTAAAAACAGTTTGAGAGCA 59.703 40.000 12.98 0.00 30.49 4.26
2919 3277 5.752712 CAGGACTAAAAACAGTTTGAGAGC 58.247 41.667 12.98 6.37 30.49 4.09
2920 3278 5.296780 TGCAGGACTAAAAACAGTTTGAGAG 59.703 40.000 12.98 7.55 30.49 3.20
2921 3279 5.189928 TGCAGGACTAAAAACAGTTTGAGA 58.810 37.500 12.98 0.00 30.49 3.27
2922 3280 5.499139 TGCAGGACTAAAAACAGTTTGAG 57.501 39.130 0.00 3.16 32.03 3.02
2923 3281 5.163561 CCTTGCAGGACTAAAAACAGTTTGA 60.164 40.000 0.00 0.00 37.67 2.69
2924 3282 5.043248 CCTTGCAGGACTAAAAACAGTTTG 58.957 41.667 0.00 0.00 37.67 2.93
2925 3283 4.953579 TCCTTGCAGGACTAAAAACAGTTT 59.046 37.500 0.00 0.00 40.06 2.66
2926 3284 4.532834 TCCTTGCAGGACTAAAAACAGTT 58.467 39.130 0.00 0.00 40.06 3.16
2927 3285 4.164843 TCCTTGCAGGACTAAAAACAGT 57.835 40.909 0.00 0.00 40.06 3.55
2939 3297 6.357367 ACTTTACTTATGGTATCCTTGCAGG 58.643 40.000 0.00 0.00 36.46 4.85
3001 3359 9.258826 CCTTGAAATAATGTTGATTCAAACACA 57.741 29.630 0.00 0.00 42.56 3.72


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

AutoCloner maintained by Alex Coulton.