Multiple sequence alignment - TraesCS4B01G272600

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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 TraesCS4B01G272600 chr4B 100.000 3004 0 0 1 3004 550434196 550431193 0.000000e+00 5548
1 TraesCS4B01G272600 chr4B 87.456 1435 138 19 727 2135 550502421 550503839 0.000000e+00 1615
2 TraesCS4B01G272600 chr4B 88.642 854 90 5 1285 2134 550487577 550486727 0.000000e+00 1033
3 TraesCS4B01G272600 chr4B 85.383 561 60 9 746 1290 550488312 550487758 2.020000e-156 562
4 TraesCS4B01G272600 chr4B 84.502 271 24 11 234 488 550501753 550502021 4.970000e-63 252
5 TraesCS4B01G272600 chr4D 89.963 2401 174 26 654 3004 442215842 442213459 0.000000e+00 3037
6 TraesCS4B01G272600 chr4D 88.966 1432 120 20 728 2138 442223410 442221996 0.000000e+00 1735
7 TraesCS4B01G272600 chr4D 88.252 1430 124 25 727 2135 442395694 442397100 0.000000e+00 1670
8 TraesCS4B01G272600 chr4D 88.039 1438 124 22 728 2138 442249210 442247794 0.000000e+00 1659
9 TraesCS4B01G272600 chr4D 84.416 924 129 11 1080 1998 441255867 441256780 0.000000e+00 894
10 TraesCS4B01G272600 chr4D 90.855 667 45 9 1 654 442216635 442215972 0.000000e+00 880
11 TraesCS4B01G272600 chr4D 86.607 224 20 6 440 654 442223865 442223643 3.870000e-59 239
12 TraesCS4B01G272600 chr4D 88.158 152 16 1 241 390 442389675 442389826 2.380000e-41 180
13 TraesCS4B01G272600 chr4A 87.678 2321 201 36 728 3004 24935182 24937461 0.000000e+00 2623
14 TraesCS4B01G272600 chr4A 87.006 1416 143 25 746 2135 24919828 24918428 0.000000e+00 1557
15 TraesCS4B01G272600 chr4A 82.720 1059 150 21 949 1998 26324385 26323351 0.000000e+00 911
16 TraesCS4B01G272600 chr5B 79.389 393 48 19 875 1237 687212530 687212919 2.310000e-61 246
17 TraesCS4B01G272600 chr1A 78.297 364 36 19 949 1287 569356150 569355805 8.500000e-46 195
18 TraesCS4B01G272600 chr5D 78.223 349 38 17 946 1273 544816695 544817026 3.950000e-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 TraesCS4B01G272600 chr4B 550431193 550434196 3003 True 5548.0 5548 100.0000 1 3004 1 chr4B.!!$R1 3003
1 TraesCS4B01G272600 chr4B 550501753 550503839 2086 False 933.5 1615 85.9790 234 2135 2 chr4B.!!$F1 1901
2 TraesCS4B01G272600 chr4B 550486727 550488312 1585 True 797.5 1033 87.0125 746 2134 2 chr4B.!!$R2 1388
3 TraesCS4B01G272600 chr4D 442213459 442216635 3176 True 1958.5 3037 90.4090 1 3004 2 chr4D.!!$R2 3003
4 TraesCS4B01G272600 chr4D 442395694 442397100 1406 False 1670.0 1670 88.2520 727 2135 1 chr4D.!!$F3 1408
5 TraesCS4B01G272600 chr4D 442247794 442249210 1416 True 1659.0 1659 88.0390 728 2138 1 chr4D.!!$R1 1410
6 TraesCS4B01G272600 chr4D 442221996 442223865 1869 True 987.0 1735 87.7865 440 2138 2 chr4D.!!$R3 1698
7 TraesCS4B01G272600 chr4D 441255867 441256780 913 False 894.0 894 84.4160 1080 1998 1 chr4D.!!$F1 918
8 TraesCS4B01G272600 chr4A 24935182 24937461 2279 False 2623.0 2623 87.6780 728 3004 1 chr4A.!!$F1 2276
9 TraesCS4B01G272600 chr4A 24918428 24919828 1400 True 1557.0 1557 87.0060 746 2135 1 chr4A.!!$R1 1389
10 TraesCS4B01G272600 chr4A 26323351 26324385 1034 True 911.0 911 82.7200 949 1998 1 chr4A.!!$R2 1049

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
79 82 1.093972 TAGCATGGACATTGTTGGCG 58.906 50.000 0.00 0.0 0.00 5.69 F
438 454 1.135333 GTTTGGTCGTTTGGCCTCAAA 59.865 47.619 3.32 0.0 40.23 2.69 F
1078 1409 0.322008 CTCCCTGTTTCTGGCACTCC 60.322 60.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1073 1404 0.891373 TTTCTGCTCGAGAGGGAGTG 59.109 55.0 18.75 0.0 36.41 3.51 R
1490 2035 0.948623 TGCACATACGCGACTTGCTT 60.949 50.0 15.93 0.0 43.27 3.91 R
2441 3002 0.532862 CCCCATTGATTCCTCCGACG 60.533 60.0 0.00 0.0 0.00 5.12 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
76 79 8.586570 TTTTTAAGTTAGCATGGACATTGTTG 57.413 30.769 0.00 0.00 0.00 3.33
79 82 1.093972 TAGCATGGACATTGTTGGCG 58.906 50.000 0.00 0.00 0.00 5.69
118 121 9.816354 AATTGTATTCATATAACAAAACCAGCC 57.184 29.630 0.00 0.00 0.00 4.85
130 133 3.584733 AAACCAGCCTGAAGAGTTTCT 57.415 42.857 0.00 0.00 34.31 2.52
135 138 3.261897 CCAGCCTGAAGAGTTTCTCCTAA 59.738 47.826 0.00 0.00 34.31 2.69
174 177 6.828502 ACATAACTGTCGTATAGTTGCATG 57.171 37.500 10.43 9.52 38.70 4.06
181 184 7.039270 ACTGTCGTATAGTTGCATGATTGTAA 58.961 34.615 0.00 0.00 0.00 2.41
182 185 7.010183 ACTGTCGTATAGTTGCATGATTGTAAC 59.990 37.037 0.00 0.00 45.55 2.50
208 211 4.109766 TCATACGGCTTATTCAGTTGACG 58.890 43.478 0.00 0.00 0.00 4.35
221 224 9.932207 TTATTCAGTTGACGAGGATTAAGTAAA 57.068 29.630 0.00 0.00 0.00 2.01
267 271 2.368439 TGCCTTGGTGTGCTTATCATC 58.632 47.619 0.00 0.00 0.00 2.92
305 309 4.312443 TCCGAGTGTAATTCAAACAGGAC 58.688 43.478 0.00 0.00 0.00 3.85
419 433 9.695155 AATTAGGCTACCAAGTAATAATGTTGT 57.305 29.630 0.00 0.00 0.00 3.32
422 436 7.826690 AGGCTACCAAGTAATAATGTTGTTTG 58.173 34.615 0.00 0.00 0.00 2.93
438 454 1.135333 GTTTGGTCGTTTGGCCTCAAA 59.865 47.619 3.32 0.00 40.23 2.69
448 464 3.457610 TTGGCCTCAAAAAGAAGCAAG 57.542 42.857 3.32 0.00 35.31 4.01
488 508 8.562052 TGCATGCATATTATTTGACTACTTCAG 58.438 33.333 18.46 0.00 34.94 3.02
504 524 5.759506 ACTTCAGTGATTAGATCGATCGT 57.240 39.130 19.33 9.93 0.00 3.73
507 527 5.751243 TCAGTGATTAGATCGATCGTCAA 57.249 39.130 23.34 17.60 0.00 3.18
512 532 7.480229 CAGTGATTAGATCGATCGTCAATAGTC 59.520 40.741 23.34 15.44 0.00 2.59
659 921 1.448540 CTCTGGCTTTCGCGTGGAT 60.449 57.895 5.77 0.00 36.88 3.41
670 932 5.277345 GCTTTCGCGTGGATACTTTTCATAT 60.277 40.000 5.77 0.00 37.61 1.78
694 959 4.212214 CAGTTCAGTAGAAACCTCTTGCAC 59.788 45.833 0.00 0.00 35.08 4.57
744 1037 5.106078 GCGAGCTAGCTATAGACTTGGTTAT 60.106 44.000 19.38 0.00 0.00 1.89
773 1066 8.573035 TCTGGAACCATTTCAAATTAGTTGTAC 58.427 33.333 0.85 0.00 38.47 2.90
854 1162 1.202256 ACGTTCGATGATTAGAGCGCA 60.202 47.619 11.47 0.00 43.20 6.09
855 1163 1.852280 CGTTCGATGATTAGAGCGCAA 59.148 47.619 11.47 0.00 34.69 4.85
856 1164 2.097685 CGTTCGATGATTAGAGCGCAAG 60.098 50.000 11.47 0.00 34.69 4.01
863 1171 3.925379 TGATTAGAGCGCAAGAGTCAAA 58.075 40.909 11.47 0.00 43.02 2.69
919 1227 6.509656 ACCGCGATCTCATATGTTAGTTAAA 58.490 36.000 8.23 0.00 0.00 1.52
945 1255 5.171476 ACACGACAATCATTCTTCTCGATT 58.829 37.500 0.00 0.00 0.00 3.34
947 1257 6.811665 ACACGACAATCATTCTTCTCGATTTA 59.188 34.615 0.00 0.00 0.00 1.40
951 1261 9.784824 CGACAATCATTCTTCTCGATTTAATAC 57.215 33.333 0.00 0.00 0.00 1.89
1005 1316 1.833630 TCGCAATCATTCCTCACCTCT 59.166 47.619 0.00 0.00 0.00 3.69
1020 1331 3.948473 TCACCTCTAAATCCACTCTCGAG 59.052 47.826 5.93 5.93 0.00 4.04
1023 1346 5.533154 CACCTCTAAATCCACTCTCGAGTAT 59.467 44.000 13.13 0.00 40.20 2.12
1073 1404 1.407989 CCATCTCTCCCTGTTTCTGGC 60.408 57.143 0.00 0.00 0.00 4.85
1078 1409 0.322008 CTCCCTGTTTCTGGCACTCC 60.322 60.000 0.00 0.00 0.00 3.85
1303 1834 7.436970 CACAATACTACTACGGTTTATGCATGA 59.563 37.037 10.16 0.00 0.00 3.07
1335 1871 0.801872 GCAATCCATGTGTGCGTGTA 59.198 50.000 0.00 0.00 0.00 2.90
1378 1923 1.965930 GTGAAGGTGGCGCATGTGA 60.966 57.895 10.83 0.00 0.00 3.58
1490 2035 3.431912 GCTACGTCATCATTTGTGACACA 59.568 43.478 3.56 3.56 44.77 3.72
1500 2045 0.376852 TTGTGACACAAGCAAGTCGC 59.623 50.000 17.02 0.00 43.59 5.19
1869 2414 3.474570 GGCACTGCCTCTCGGGAT 61.475 66.667 13.28 0.00 46.69 3.85
2069 2616 7.486647 ACAACTATTATTATCGACGAGGTGTT 58.513 34.615 3.01 0.00 29.24 3.32
2113 2661 5.927030 TCTGCACGTATGATTGTTTCTTTC 58.073 37.500 0.00 0.00 0.00 2.62
2147 2696 1.201424 ACTGTTCGGTTCCCCTATCC 58.799 55.000 0.00 0.00 0.00 2.59
2149 2698 1.768870 CTGTTCGGTTCCCCTATCCAT 59.231 52.381 0.00 0.00 0.00 3.41
2166 2715 6.147821 CCTATCCATTGTAAATTGTAGCCTCG 59.852 42.308 0.00 0.00 0.00 4.63
2167 2716 4.839121 TCCATTGTAAATTGTAGCCTCGT 58.161 39.130 0.00 0.00 0.00 4.18
2244 2803 5.034852 TCACTGATGGTTTGTCTTGAAGA 57.965 39.130 0.00 0.00 0.00 2.87
2272 2831 9.574516 AATCATCAGACCTTTACAAACTTTACT 57.425 29.630 0.00 0.00 0.00 2.24
2283 2842 1.878953 AACTTTACTGGAGCACACCG 58.121 50.000 0.00 0.00 0.00 4.94
2292 2851 2.281692 AGCACACCGCATGCAAGA 60.282 55.556 19.57 0.00 45.92 3.02
2314 2873 7.093289 CAAGAATACTTCCAGGAAAGACTCCTA 60.093 40.741 2.72 0.00 42.80 2.94
2335 2894 5.069251 CCTACAGTCCTACCACCTAAGATTG 59.931 48.000 0.00 0.00 0.00 2.67
2337 2896 3.197766 CAGTCCTACCACCTAAGATTGCA 59.802 47.826 0.00 0.00 0.00 4.08
2372 2931 5.650703 GGGTAACAAGTTTGGTATAGCACAT 59.349 40.000 3.60 0.00 32.20 3.21
2374 2933 5.643379 AACAAGTTTGGTATAGCACATGG 57.357 39.130 3.60 0.00 0.00 3.66
2386 2945 0.543277 GCACATGGAGGAGGATCACA 59.457 55.000 0.00 0.00 36.25 3.58
2405 2966 7.255801 GGATCACAATTTTCTTTGGTGGAACTA 60.256 37.037 0.00 0.00 36.74 2.24
2420 2981 6.125860 TGGTGGAACTATAGATCTAGGGTTCT 60.126 42.308 29.22 11.44 36.74 3.01
2441 3002 8.982685 GGTTCTTCTTTGAATCCTCAATTTTTC 58.017 33.333 0.00 0.00 41.22 2.29
2472 3033 6.325804 AGGAATCAATGGGGAATGAGATTTTC 59.674 38.462 0.00 0.00 28.94 2.29
2487 3051 5.832595 TGAGATTTTCCAGTTCAACAATGGA 59.167 36.000 0.00 0.00 41.33 3.41
2511 3078 1.305201 GGCGGCAATTTCGAGGATTA 58.695 50.000 3.07 0.00 0.00 1.75
2521 3088 6.239064 GCAATTTCGAGGATTAGGTCTAGAGA 60.239 42.308 0.00 0.00 0.00 3.10
2526 3093 7.556416 TCGAGGATTAGGTCTAGAGATAGAA 57.444 40.000 0.00 0.00 0.00 2.10
2616 3190 3.483869 GCCGGAGCCCTGGAGATT 61.484 66.667 5.05 0.00 41.53 2.40
2626 3200 1.638529 CCTGGAGATTCGCCCTATCT 58.361 55.000 3.83 0.00 35.12 1.98
2634 3208 4.421131 AGATTCGCCCTATCTAGAACCAT 58.579 43.478 0.00 0.00 30.74 3.55
2653 3227 3.231818 CATAACCTGAGGGTCGGTATCT 58.768 50.000 2.38 0.00 46.67 1.98
2689 3263 1.531739 GGAGCCCTAGAGATCCAGCG 61.532 65.000 3.29 0.00 0.00 5.18
2696 3270 3.157881 CCTAGAGATCCAGCGTATCCAA 58.842 50.000 0.00 0.00 0.00 3.53
2705 3279 1.398390 CAGCGTATCCAAAGAAGGTGC 59.602 52.381 0.00 0.00 0.00 5.01
2737 3311 0.179000 CGAAGATCCAAGGGTCAGGG 59.821 60.000 1.65 0.00 0.00 4.45
2747 3321 0.701310 AGGGTCAGGGGTTGGAGTTT 60.701 55.000 0.00 0.00 0.00 2.66
2775 3349 0.523072 CAAAGGCGATGTCAACTGGG 59.477 55.000 0.00 0.00 0.00 4.45
2776 3350 0.110486 AAAGGCGATGTCAACTGGGT 59.890 50.000 0.00 0.00 0.00 4.51
2779 3353 1.745489 GCGATGTCAACTGGGTCCC 60.745 63.158 0.00 0.00 0.00 4.46
2781 3355 1.553690 CGATGTCAACTGGGTCCCCT 61.554 60.000 5.13 0.00 36.94 4.79
2787 3361 0.753262 CAACTGGGTCCCCTAGATCG 59.247 60.000 5.13 0.00 36.94 3.69
2812 3386 1.674057 CTTGGACCGCTGGAGTTCT 59.326 57.895 1.50 0.00 0.00 3.01
2821 3395 2.693591 CCGCTGGAGTTCTGAGGTATAA 59.306 50.000 0.00 0.00 31.50 0.98
2854 3428 1.780309 AGTGTTGGGTTTGAGATGGGA 59.220 47.619 0.00 0.00 0.00 4.37
2887 3461 3.193267 TGGCTTTGTGTATGGATCTTTGC 59.807 43.478 0.00 0.00 0.00 3.68
2891 3465 5.375417 TTTGTGTATGGATCTTTGCTGTG 57.625 39.130 0.00 0.00 0.00 3.66
2898 3472 2.627699 TGGATCTTTGCTGTGGGTTTTC 59.372 45.455 0.00 0.00 0.00 2.29
2926 3500 3.862877 TGGTGTATCATGATCCCCAAG 57.137 47.619 12.53 0.00 0.00 3.61
2947 3521 6.177610 CAAGCTTATACAAGACCTAAACCCA 58.822 40.000 0.00 0.00 33.20 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.923733 TTGTGGTGAAAACCAATTAGTGT 57.076 34.783 0.00 0.00 42.10 3.55
66 69 0.387239 GCTTCACGCCAACAATGTCC 60.387 55.000 0.00 0.00 0.00 4.02
74 77 5.053145 ACAATTAAATTTGCTTCACGCCAA 58.947 33.333 0.00 0.00 38.05 4.52
75 78 4.626042 ACAATTAAATTTGCTTCACGCCA 58.374 34.783 0.00 0.00 38.05 5.69
76 79 6.885735 ATACAATTAAATTTGCTTCACGCC 57.114 33.333 0.00 0.00 38.05 5.68
95 98 7.831690 TCAGGCTGGTTTTGTTATATGAATACA 59.168 33.333 15.73 0.00 0.00 2.29
174 177 7.891183 ATAAGCCGTATGATCAGTTACAATC 57.109 36.000 0.09 0.00 0.00 2.67
181 184 5.537300 ACTGAATAAGCCGTATGATCAGT 57.463 39.130 0.09 0.00 36.25 3.41
182 185 5.985530 TCAACTGAATAAGCCGTATGATCAG 59.014 40.000 0.09 0.00 34.89 2.90
191 194 1.927174 CCTCGTCAACTGAATAAGCCG 59.073 52.381 0.00 0.00 0.00 5.52
239 242 1.001181 GCACACCAAGGCATCAATGTT 59.999 47.619 0.00 0.00 0.00 2.71
419 433 1.475403 TTTGAGGCCAAACGACCAAA 58.525 45.000 5.01 0.70 37.36 3.28
422 436 1.679153 TCTTTTTGAGGCCAAACGACC 59.321 47.619 5.01 0.00 41.54 4.79
438 454 2.230750 GCATCCTCTTGCTTGCTTCTTT 59.769 45.455 0.00 0.00 39.57 2.52
474 494 8.687242 TCGATCTAATCACTGAAGTAGTCAAAT 58.313 33.333 0.00 0.00 37.60 2.32
488 508 7.298854 TGACTATTGACGATCGATCTAATCAC 58.701 38.462 24.34 11.14 0.00 3.06
496 516 7.260558 TCTAAACTGACTATTGACGATCGAT 57.739 36.000 24.34 7.62 0.00 3.59
504 524 6.452242 TGTCGCTTTCTAAACTGACTATTGA 58.548 36.000 0.00 0.00 0.00 2.57
507 527 6.026947 ACTGTCGCTTTCTAAACTGACTAT 57.973 37.500 0.00 0.00 0.00 2.12
512 532 2.408704 CCGACTGTCGCTTTCTAAACTG 59.591 50.000 23.87 2.70 38.82 3.16
537 557 0.677731 TCCAAATCCTTGCAGCTCCG 60.678 55.000 0.00 0.00 0.00 4.63
670 932 4.100963 TGCAAGAGGTTTCTACTGAACTGA 59.899 41.667 0.00 0.00 31.96 3.41
684 949 4.685169 CACAAATATTCGTGCAAGAGGT 57.315 40.909 1.81 0.00 0.00 3.85
694 959 0.026156 TCAGCGCGCACAAATATTCG 59.974 50.000 35.10 7.73 0.00 3.34
739 1024 7.696992 TTTGAAATGGTTCCAGAGTATAACC 57.303 36.000 0.00 0.00 42.49 2.85
744 1037 8.792633 CAACTAATTTGAAATGGTTCCAGAGTA 58.207 33.333 6.57 0.00 37.39 2.59
758 1051 9.841295 AGGTTAACTGAGTACAACTAATTTGAA 57.159 29.630 5.42 0.00 38.73 2.69
802 1098 7.390440 TGATCAATGGATGTCGTTTCTTAACTT 59.610 33.333 0.00 0.00 32.67 2.66
823 1121 3.275999 TCATCGAACGTAGGTCTGATCA 58.724 45.455 0.00 0.00 0.00 2.92
854 1162 1.129058 ACCTCCACCGTTTGACTCTT 58.871 50.000 0.00 0.00 0.00 2.85
855 1163 1.129058 AACCTCCACCGTTTGACTCT 58.871 50.000 0.00 0.00 0.00 3.24
856 1164 1.226746 CAACCTCCACCGTTTGACTC 58.773 55.000 0.00 0.00 0.00 3.36
863 1171 1.852157 ATGGATGCAACCTCCACCGT 61.852 55.000 14.77 0.00 45.27 4.83
919 1227 6.330278 TCGAGAAGAATGATTGTCGTGTTAT 58.670 36.000 8.82 0.00 43.95 1.89
937 1247 6.962686 TGTAGCTAGCGTATTAAATCGAGAA 58.037 36.000 9.55 0.00 0.00 2.87
947 1257 9.640963 CTTAAATAGGAATGTAGCTAGCGTATT 57.359 33.333 9.55 11.07 0.00 1.89
951 1261 5.926542 TGCTTAAATAGGAATGTAGCTAGCG 59.073 40.000 9.55 0.00 0.00 4.26
1005 1316 5.594725 AGCTTGATACTCGAGAGTGGATTTA 59.405 40.000 21.68 0.00 42.52 1.40
1053 1376 1.407989 GCCAGAAACAGGGAGAGATGG 60.408 57.143 0.00 0.00 0.00 3.51
1073 1404 0.891373 TTTCTGCTCGAGAGGGAGTG 59.109 55.000 18.75 0.00 36.41 3.51
1078 1409 1.805871 GCCATCTTTCTGCTCGAGAGG 60.806 57.143 18.75 7.70 30.18 3.69
1263 1600 5.902613 AGTATTGTGACAATTGATGGTGG 57.097 39.130 16.75 0.00 0.00 4.61
1335 1871 3.581755 GCACATGCAAACACATTCAGAT 58.418 40.909 0.00 0.00 41.59 2.90
1378 1923 3.242543 CGCAACGTATAGGTTCTCGTACT 60.243 47.826 7.83 0.00 35.49 2.73
1490 2035 0.948623 TGCACATACGCGACTTGCTT 60.949 50.000 15.93 0.00 43.27 3.91
1500 2045 1.743623 TTCCGGGCTTGCACATACG 60.744 57.895 0.00 0.00 0.00 3.06
1501 2046 1.654023 GGTTCCGGGCTTGCACATAC 61.654 60.000 0.00 0.00 0.00 2.39
1893 2438 2.203938 ACCGGTGGAGGTGATGGT 60.204 61.111 6.12 0.00 44.07 3.55
2046 2592 7.486647 ACAACACCTCGTCGATAATAATAGTT 58.513 34.615 0.00 0.00 0.00 2.24
2069 2616 7.390162 TGCAGATGAGAAATTACATGTACAACA 59.610 33.333 4.68 1.51 0.00 3.33
2147 2696 5.351465 ACAGACGAGGCTACAATTTACAATG 59.649 40.000 0.00 0.00 0.00 2.82
2149 2698 4.890088 ACAGACGAGGCTACAATTTACAA 58.110 39.130 0.00 0.00 0.00 2.41
2166 2715 6.472163 CCACGCCAAATAATATTTGAACAGAC 59.528 38.462 23.09 7.62 0.00 3.51
2167 2716 6.405286 CCCACGCCAAATAATATTTGAACAGA 60.405 38.462 23.09 0.00 0.00 3.41
2215 2774 5.624159 AGACAAACCATCAGTGATTTGAGA 58.376 37.500 19.63 0.00 35.93 3.27
2244 2803 7.823745 AAGTTTGTAAAGGTCTGATGATTGT 57.176 32.000 0.00 0.00 0.00 2.71
2272 2831 4.639906 TGCATGCGGTGTGCTCCA 62.640 61.111 14.09 0.00 46.63 3.86
2314 2873 3.197983 GCAATCTTAGGTGGTAGGACTGT 59.802 47.826 0.00 0.00 0.00 3.55
2315 2874 3.197766 TGCAATCTTAGGTGGTAGGACTG 59.802 47.826 0.00 0.00 0.00 3.51
2316 2875 3.450904 TGCAATCTTAGGTGGTAGGACT 58.549 45.455 0.00 0.00 0.00 3.85
2317 2876 3.906720 TGCAATCTTAGGTGGTAGGAC 57.093 47.619 0.00 0.00 0.00 3.85
2318 2877 4.919774 TTTGCAATCTTAGGTGGTAGGA 57.080 40.909 0.00 0.00 0.00 2.94
2319 2878 5.476945 AGTTTTTGCAATCTTAGGTGGTAGG 59.523 40.000 0.00 0.00 0.00 3.18
2320 2879 6.431234 AGAGTTTTTGCAATCTTAGGTGGTAG 59.569 38.462 0.00 0.00 0.00 3.18
2321 2880 6.303839 AGAGTTTTTGCAATCTTAGGTGGTA 58.696 36.000 0.00 0.00 0.00 3.25
2322 2881 5.140454 AGAGTTTTTGCAATCTTAGGTGGT 58.860 37.500 0.00 0.00 0.00 4.16
2335 2894 6.387041 ACTTGTTACCCTTAGAGTTTTTGC 57.613 37.500 0.00 0.00 0.00 3.68
2337 2896 7.398047 ACCAAACTTGTTACCCTTAGAGTTTTT 59.602 33.333 0.00 0.00 35.75 1.94
2372 2931 4.934797 AGAAAATTGTGATCCTCCTCCA 57.065 40.909 0.00 0.00 0.00 3.86
2374 2933 5.478332 ACCAAAGAAAATTGTGATCCTCCTC 59.522 40.000 0.00 0.00 0.00 3.71
2386 2945 9.981460 AGATCTATAGTTCCACCAAAGAAAATT 57.019 29.630 7.12 0.00 0.00 1.82
2405 2966 8.655901 GGATTCAAAGAAGAACCCTAGATCTAT 58.344 37.037 2.11 0.00 27.82 1.98
2420 2981 6.855914 CGACGAAAAATTGAGGATTCAAAGAA 59.144 34.615 0.00 0.00 45.82 2.52
2436 2997 3.438781 CCATTGATTCCTCCGACGAAAAA 59.561 43.478 0.00 0.00 0.00 1.94
2441 3002 0.532862 CCCCATTGATTCCTCCGACG 60.533 60.000 0.00 0.00 0.00 5.12
2472 3033 2.440409 CCTCCTCCATTGTTGAACTGG 58.560 52.381 0.00 0.00 0.00 4.00
2487 3051 2.438434 CGAAATTGCCGCCCTCCT 60.438 61.111 0.00 0.00 0.00 3.69
2511 3078 5.399727 CCACCCTTCTTCTATCTCTAGACCT 60.400 48.000 0.00 0.00 33.66 3.85
2521 3088 7.189079 GCTATATAAGCCACCCTTCTTCTAT 57.811 40.000 0.00 0.00 46.25 1.98
2610 3184 3.193903 GGTTCTAGATAGGGCGAATCTCC 59.806 52.174 3.75 0.00 35.36 3.71
2616 3190 3.830755 GGTTATGGTTCTAGATAGGGCGA 59.169 47.826 0.00 0.00 0.00 5.54
2653 3227 0.857675 TCCATACCCAGGATCTCCGA 59.142 55.000 0.00 0.00 42.08 4.55
2689 3263 3.131046 CCAATGGCACCTTCTTTGGATAC 59.869 47.826 9.20 0.00 40.03 2.24
2696 3270 1.272480 GGTACCCAATGGCACCTTCTT 60.272 52.381 12.43 0.00 43.88 2.52
2728 3302 0.701310 AAACTCCAACCCCTGACCCT 60.701 55.000 0.00 0.00 0.00 4.34
2737 3311 0.887836 GGACACCCGAAACTCCAACC 60.888 60.000 0.00 0.00 0.00 3.77
2747 3321 2.589157 ATCGCCTTTGGACACCCGA 61.589 57.895 0.00 0.00 34.29 5.14
2802 3376 5.361285 TCTCTTTATACCTCAGAACTCCAGC 59.639 44.000 0.00 0.00 0.00 4.85
2803 3377 6.040391 CCTCTCTTTATACCTCAGAACTCCAG 59.960 46.154 0.00 0.00 0.00 3.86
2812 3386 4.556697 TGGCATCCTCTCTTTATACCTCA 58.443 43.478 0.00 0.00 0.00 3.86
2821 3395 1.004044 CCAACACTGGCATCCTCTCTT 59.996 52.381 0.00 0.00 35.39 2.85
2854 3428 7.178274 TCCATACACAAAGCCATGTTAGAAAAT 59.822 33.333 0.00 0.00 0.00 1.82
2887 3461 4.751098 CACCATTTTCATGAAAACCCACAG 59.249 41.667 30.64 18.77 42.32 3.66
2891 3465 6.696411 TGATACACCATTTTCATGAAAACCC 58.304 36.000 30.64 15.65 42.32 4.11
2898 3472 6.294899 GGGGATCATGATACACCATTTTCATG 60.295 42.308 19.71 5.60 44.29 3.07
2926 3500 4.575236 GCTGGGTTTAGGTCTTGTATAAGC 59.425 45.833 0.00 0.00 33.82 3.09
2947 3521 6.327626 TCATAGGAAGGCTGAACTATTAAGCT 59.672 38.462 0.00 0.00 37.12 3.74


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

AutoCloner maintained by Alex Coulton.