Multiple sequence alignment - TraesCS2D01G278100

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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 TraesCS2D01G278100 chr2D 100.000 3457 0 0 1 3457 348726344 348722888 0.000000e+00 6384.0
1 TraesCS2D01G278100 chr2A 92.384 2232 90 25 436 2635 463932531 463930348 0.000000e+00 3107.0
2 TraesCS2D01G278100 chr2A 92.025 489 36 3 2971 3457 463930000 463929513 0.000000e+00 684.0
3 TraesCS2D01G278100 chr2A 88.806 268 14 1 2707 2974 463930312 463930061 7.200000e-82 315.0
4 TraesCS2D01G278100 chr2A 94.595 37 2 0 661 697 749548204 749548168 1.340000e-04 58.4
5 TraesCS2D01G278100 chr2B 95.021 1888 64 15 940 2806 414767002 414765124 0.000000e+00 2939.0
6 TraesCS2D01G278100 chr2B 89.112 845 62 15 4 823 414775185 414774346 0.000000e+00 1024.0
7 TraesCS2D01G278100 chr2B 94.091 220 13 0 3237 3456 414609395 414609176 5.530000e-88 335.0
8 TraesCS2D01G278100 chr2B 90.400 250 21 2 2971 3219 414609689 414609442 3.330000e-85 326.0
9 TraesCS2D01G278100 chr2B 95.775 142 6 0 813 954 414774386 414774245 2.680000e-56 230.0
10 TraesCS2D01G278100 chr2B 98.113 106 2 0 2869 2974 414765047 414764942 5.890000e-43 185.0
11 TraesCS2D01G278100 chr1B 72.997 337 70 13 3109 3427 278594056 278594389 7.900000e-17 99.0
12 TraesCS2D01G278100 chr4A 85.263 95 12 2 604 698 628087391 628087299 2.840000e-16 97.1
13 TraesCS2D01G278100 chr5D 81.905 105 19 0 595 699 462350573 462350469 4.750000e-14 89.8
14 TraesCS2D01G278100 chr7A 89.706 68 6 1 3136 3202 289296386 289296319 6.150000e-13 86.1


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 TraesCS2D01G278100 chr2D 348722888 348726344 3456 True 6384.000000 6384 100.000000 1 3457 1 chr2D.!!$R1 3456
1 TraesCS2D01G278100 chr2A 463929513 463932531 3018 True 1368.666667 3107 91.071667 436 3457 3 chr2A.!!$R2 3021
2 TraesCS2D01G278100 chr2B 414764942 414767002 2060 True 1562.000000 2939 96.567000 940 2974 2 chr2B.!!$R2 2034
3 TraesCS2D01G278100 chr2B 414774245 414775185 940 True 627.000000 1024 92.443500 4 954 2 chr2B.!!$R3 950
4 TraesCS2D01G278100 chr2B 414609176 414609689 513 True 330.500000 335 92.245500 2971 3456 2 chr2B.!!$R1 485

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
221 232 0.721718 GTCTTGTGGTGCTACGATGC 59.278 55.0 0.0 0.0 0.0 3.91 F
1064 1094 0.324285 CTCTCCCTTGCAGCTTCAGT 59.676 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 2166 1.888215 TGGAGTCGTCGTAGTTCACT 58.112 50.0 0.0 0.0 0.0 3.41 R
2745 2833 0.820226 TGGCTCTCATCCAACTCTCG 59.180 55.0 0.0 0.0 0.0 4.04 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
26 27 4.205065 ACATGTACCATTGCCAATTTGG 57.795 40.909 11.27 11.27 41.55 3.28
61 62 1.774856 AGTAGGGTTGTGACCTTTGCT 59.225 47.619 0.00 0.00 45.75 3.91
72 73 3.062234 GTGACCTTTGCTCGCAAGTATAC 59.938 47.826 4.39 0.00 37.24 1.47
111 112 2.619177 GAGCCTCACTCGCTTATAGTCA 59.381 50.000 0.00 0.00 36.48 3.41
132 133 4.935205 TCAAAGCATAACATGTTACGAGCT 59.065 37.500 24.88 24.88 34.59 4.09
152 153 5.259632 AGCTTCCAATTGCAAACTAGAGAT 58.740 37.500 1.71 0.00 0.00 2.75
159 160 7.177216 TCCAATTGCAAACTAGAGATTGTGAAT 59.823 33.333 1.71 0.34 31.49 2.57
161 162 8.644619 CAATTGCAAACTAGAGATTGTGAATTG 58.355 33.333 1.71 15.95 35.81 2.32
190 191 7.094463 ACTGAAATTTTCATGAGATGTCACTCC 60.094 37.037 12.04 0.00 39.30 3.85
201 202 5.104235 TGAGATGTCACTCCATTGATTCCAT 60.104 40.000 0.00 0.00 36.22 3.41
221 232 0.721718 GTCTTGTGGTGCTACGATGC 59.278 55.000 0.00 0.00 0.00 3.91
224 235 1.806542 CTTGTGGTGCTACGATGCTTT 59.193 47.619 0.00 0.00 0.00 3.51
231 242 3.375299 GGTGCTACGATGCTTTCATCTTT 59.625 43.478 0.00 0.00 45.32 2.52
291 302 3.722147 TCAAAAGCGATCTAGCATCCTC 58.278 45.455 0.00 0.00 40.15 3.71
300 311 4.545610 GATCTAGCATCCTCGAACTTCTG 58.454 47.826 0.00 0.00 0.00 3.02
316 327 6.309251 CGAACTTCTGAAGATCTTAAGACACC 59.691 42.308 20.52 10.19 29.98 4.16
318 329 6.696411 ACTTCTGAAGATCTTAAGACACCAG 58.304 40.000 20.52 16.95 29.98 4.00
319 330 5.667539 TCTGAAGATCTTAAGACACCAGG 57.332 43.478 17.42 0.00 0.00 4.45
327 338 5.105567 TCTTAAGACACCAGGACAACAAA 57.894 39.130 0.00 0.00 0.00 2.83
329 340 6.126409 TCTTAAGACACCAGGACAACAAAAT 58.874 36.000 0.00 0.00 0.00 1.82
347 358 9.367717 CAACAAAATAAAATGAAAATCACGTGG 57.632 29.630 17.00 0.00 0.00 4.94
354 365 6.751514 AAATGAAAATCACGTGGCATAGTA 57.248 33.333 17.00 0.00 0.00 1.82
364 375 5.360429 TCACGTGGCATAGTAAATACACCTA 59.640 40.000 17.00 0.00 0.00 3.08
376 399 5.836024 AAATACACCTAACTGTCTCCCAA 57.164 39.130 0.00 0.00 0.00 4.12
395 418 5.078949 CCCAATATATGCCATTTGTCCAGA 58.921 41.667 0.00 0.00 0.00 3.86
396 419 5.539574 CCCAATATATGCCATTTGTCCAGAA 59.460 40.000 0.00 0.00 0.00 3.02
406 429 5.009631 CCATTTGTCCAGAAGACCATACAA 58.990 41.667 0.00 0.00 45.68 2.41
407 430 5.653769 CCATTTGTCCAGAAGACCATACAAT 59.346 40.000 0.00 0.00 45.68 2.71
408 431 6.153340 CCATTTGTCCAGAAGACCATACAATT 59.847 38.462 0.00 0.00 45.68 2.32
448 472 7.604549 TGATTGCTTATCACATGTGTCATTTT 58.395 30.769 24.63 5.36 38.35 1.82
467 491 8.287503 GTCATTTTAAGAACTACAACGGTGATT 58.712 33.333 7.88 0.00 0.00 2.57
526 550 5.163513 CAGTTGGTCTTGAACATAAATGGC 58.836 41.667 0.00 0.00 0.00 4.40
533 557 4.766373 TCTTGAACATAAATGGCAGAGCAA 59.234 37.500 0.00 0.00 0.00 3.91
544 568 1.135859 GGCAGAGCAACATTTCTGACG 60.136 52.381 5.73 0.00 42.67 4.35
555 579 4.380531 ACATTTCTGACGCTCTCTCAAAA 58.619 39.130 0.00 0.00 0.00 2.44
568 592 6.147821 CGCTCTCTCAAAATTTCTTAGTTGGA 59.852 38.462 0.00 0.00 0.00 3.53
660 684 3.184178 CCGAAATGACAAATTGTGTTGCC 59.816 43.478 2.20 0.00 41.96 4.52
703 728 4.808077 AGCAAGCATGATAAATCTGTCG 57.192 40.909 0.00 0.00 0.00 4.35
717 744 9.113876 GATAAATCTGTCGTGTTTAGTTTTTGG 57.886 33.333 0.00 0.00 0.00 3.28
730 757 8.736244 TGTTTAGTTTTTGGCAGGATTATCTAC 58.264 33.333 0.00 0.00 0.00 2.59
749 776 4.868171 TCTACGCTCGCTAAATGAAATTGT 59.132 37.500 0.00 0.00 36.10 2.71
757 784 5.296780 TCGCTAAATGAAATTGTCATCTCCC 59.703 40.000 0.00 0.00 46.80 4.30
811 840 9.796120 TTTGATTTACTATTGCCTAAAAATCGG 57.204 29.630 0.00 0.00 36.56 4.18
977 1007 2.788786 GGTGACACAAAAACAATGCTCG 59.211 45.455 8.08 0.00 0.00 5.03
1018 1048 2.191908 TGGCACACACCACACTCC 59.808 61.111 0.00 0.00 33.75 3.85
1019 1049 2.374525 TGGCACACACCACACTCCT 61.375 57.895 0.00 0.00 33.75 3.69
1020 1050 1.598130 GGCACACACCACACTCCTC 60.598 63.158 0.00 0.00 0.00 3.71
1064 1094 0.324285 CTCTCCCTTGCAGCTTCAGT 59.676 55.000 0.00 0.00 0.00 3.41
1170 1200 3.441290 CTCTCGGCCCTCGACGTT 61.441 66.667 0.00 0.00 43.74 3.99
1182 1212 1.811359 CTCGACGTTTCCCTCTACACT 59.189 52.381 0.00 0.00 0.00 3.55
1536 1566 2.528797 CGACTTCGGGTTCCTTGTG 58.471 57.895 0.00 0.00 35.37 3.33
1648 1678 3.427598 GACTACCCTTCGGAGGCGC 62.428 68.421 3.32 0.00 42.09 6.53
2015 2045 1.722163 TGACGTCGTACGACAACGC 60.722 57.895 38.60 26.37 46.05 4.84
2152 2182 0.240411 GCCAGTGAACTACGACGACT 59.760 55.000 0.00 0.00 0.00 4.18
2492 2546 1.040339 CCTTCCCCGTCTCTCCTCTG 61.040 65.000 0.00 0.00 0.00 3.35
2704 2792 4.600692 TGACTTTGAGCTTACAGCACTA 57.399 40.909 0.00 0.00 45.56 2.74
2740 2828 2.158914 TGCTCTGCGGATGATGTACAAT 60.159 45.455 0.00 0.00 0.00 2.71
2745 2833 3.457234 TGCGGATGATGTACAATCTGAC 58.543 45.455 17.11 10.41 0.00 3.51
2748 2836 3.977579 CGGATGATGTACAATCTGACGAG 59.022 47.826 9.85 0.00 0.00 4.18
2772 2860 0.883814 GGATGAGAGCCATTCCAGCG 60.884 60.000 0.00 0.00 35.17 5.18
2804 2892 5.925397 GCACTTCGATCATATGAACTGATCT 59.075 40.000 9.99 0.00 44.42 2.75
2805 2893 7.087007 GCACTTCGATCATATGAACTGATCTA 58.913 38.462 9.99 0.00 44.42 1.98
2806 2894 7.758980 GCACTTCGATCATATGAACTGATCTAT 59.241 37.037 9.99 0.00 44.42 1.98
2807 2895 9.074443 CACTTCGATCATATGAACTGATCTATG 57.926 37.037 9.99 0.26 44.42 2.23
2808 2896 8.801299 ACTTCGATCATATGAACTGATCTATGT 58.199 33.333 9.99 0.83 44.42 2.29
2809 2897 9.636879 CTTCGATCATATGAACTGATCTATGTT 57.363 33.333 9.99 0.00 44.42 2.71
2810 2898 8.976986 TCGATCATATGAACTGATCTATGTTG 57.023 34.615 9.99 0.00 44.42 3.33
2811 2899 8.796475 TCGATCATATGAACTGATCTATGTTGA 58.204 33.333 9.99 0.00 44.42 3.18
2812 2900 8.858186 CGATCATATGAACTGATCTATGTTGAC 58.142 37.037 9.99 0.00 44.42 3.18
2813 2901 8.754230 ATCATATGAACTGATCTATGTTGACG 57.246 34.615 9.99 0.00 0.00 4.35
2834 2922 3.560481 CGTGTAGTGTAGAGATCGTCCAT 59.440 47.826 0.00 0.00 0.00 3.41
3007 3190 1.079073 CCCTCATTGGTGGCCCTTT 59.921 57.895 0.00 0.00 0.00 3.11
3008 3191 0.545071 CCCTCATTGGTGGCCCTTTT 60.545 55.000 0.00 0.00 0.00 2.27
3050 3233 3.309296 GACATCCCAGATCTAGGGTTCA 58.691 50.000 22.26 9.95 46.82 3.18
3069 3252 1.548719 CATCTCCGTGTGGGTACAAGA 59.451 52.381 0.00 0.00 38.37 3.02
3185 3368 1.080354 TGAAGGTGGATCCCCTCGT 59.920 57.895 18.86 7.50 36.75 4.18
3186 3369 0.976073 TGAAGGTGGATCCCCTCGTC 60.976 60.000 18.86 14.75 36.75 4.20
3188 3371 4.222847 GGTGGATCCCCTCGTCGC 62.223 72.222 9.90 0.00 0.00 5.19
3229 3414 3.503363 GCACGGCAGCATCACTCC 61.503 66.667 0.00 0.00 0.00 3.85
3263 3477 4.069232 CTGCCTCGACCGCTTGGA 62.069 66.667 1.75 0.00 36.26 3.53
3295 3509 1.746615 CACTTGGGAGGCGTCCATG 60.747 63.158 25.86 16.61 46.07 3.66
3364 3578 1.228644 TCCTTTCCTCGGTCGACCA 60.229 57.895 32.80 19.01 35.14 4.02
3393 3607 0.988145 GACCTGGATGATGGGGGTCA 60.988 60.000 0.00 0.00 43.98 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.239714 ACCAAATTGGCAATGGTACATGTAAA 60.240 34.615 20.99 0.00 45.37 2.01
26 27 3.269178 CCCTACTACCCGATCGAGATAC 58.731 54.545 18.66 0.00 0.00 2.24
61 62 4.895224 AGACTTCGATGTATACTTGCGA 57.105 40.909 3.63 7.67 0.00 5.10
72 73 3.993081 GGCTCAATGGATAGACTTCGATG 59.007 47.826 0.00 0.00 0.00 3.84
101 102 9.651718 GTAACATGTTATGCTTTGACTATAAGC 57.348 33.333 20.72 0.00 46.33 3.09
109 110 4.935205 AGCTCGTAACATGTTATGCTTTGA 59.065 37.500 26.42 12.57 33.31 2.69
111 112 5.163754 GGAAGCTCGTAACATGTTATGCTTT 60.164 40.000 32.29 24.49 38.13 3.51
117 118 5.391523 GCAATTGGAAGCTCGTAACATGTTA 60.392 40.000 14.35 14.35 0.00 2.41
132 133 6.489700 TCACAATCTCTAGTTTGCAATTGGAA 59.510 34.615 8.47 8.47 0.00 3.53
159 160 9.467258 GACATCTCATGAAAATTTCAGTTTCAA 57.533 29.630 14.10 0.00 45.43 2.69
161 162 8.909671 GTGACATCTCATGAAAATTTCAGTTTC 58.090 33.333 14.10 4.51 43.98 2.78
190 191 4.740268 CACCACAAGACATGGAATCAATG 58.260 43.478 0.00 0.00 39.87 2.82
201 202 1.939381 GCATCGTAGCACCACAAGACA 60.939 52.381 0.00 0.00 0.00 3.41
221 232 6.147864 TCAAAAGGACACCAAAGATGAAAG 57.852 37.500 0.00 0.00 0.00 2.62
224 235 5.139727 ACATCAAAAGGACACCAAAGATGA 58.860 37.500 0.00 0.00 36.16 2.92
231 242 5.830457 TGTTCATAACATCAAAAGGACACCA 59.170 36.000 0.00 0.00 36.25 4.17
269 280 4.314121 GAGGATGCTAGATCGCTTTTGAT 58.686 43.478 0.00 0.00 0.00 2.57
273 284 1.957177 TCGAGGATGCTAGATCGCTTT 59.043 47.619 0.00 0.00 35.23 3.51
277 288 3.252215 AGAAGTTCGAGGATGCTAGATCG 59.748 47.826 0.00 0.00 36.54 3.69
291 302 6.309251 GGTGTCTTAAGATCTTCAGAAGTTCG 59.691 42.308 18.66 0.00 33.47 3.95
300 311 5.407407 TGTCCTGGTGTCTTAAGATCTTC 57.593 43.478 12.24 0.00 0.00 2.87
318 329 9.579610 CGTGATTTTCATTTTATTTTGTTGTCC 57.420 29.630 0.00 0.00 0.00 4.02
327 338 8.250332 ACTATGCCACGTGATTTTCATTTTATT 58.750 29.630 19.30 0.00 0.00 1.40
329 340 7.151999 ACTATGCCACGTGATTTTCATTTTA 57.848 32.000 19.30 0.00 0.00 1.52
347 358 7.652507 GGAGACAGTTAGGTGTATTTACTATGC 59.347 40.741 0.00 0.00 0.00 3.14
354 365 5.836024 TTGGGAGACAGTTAGGTGTATTT 57.164 39.130 0.00 0.00 0.00 1.40
364 375 5.589367 ATGGCATATATTGGGAGACAGTT 57.411 39.130 0.00 0.00 0.00 3.16
376 399 6.006449 GGTCTTCTGGACAAATGGCATATAT 58.994 40.000 0.00 0.00 46.16 0.86
433 457 8.669946 TGTAGTTCTTAAAATGACACATGTGA 57.330 30.769 31.94 11.45 0.00 3.58
467 491 5.441500 TGAAGGATTGTTTGTGTGAGGTTA 58.558 37.500 0.00 0.00 0.00 2.85
512 536 4.280425 TGTTGCTCTGCCATTTATGTTCAA 59.720 37.500 0.00 0.00 0.00 2.69
526 550 1.802960 AGCGTCAGAAATGTTGCTCTG 59.197 47.619 0.00 0.00 40.42 3.35
533 557 3.667497 TTGAGAGAGCGTCAGAAATGT 57.333 42.857 0.00 0.00 0.00 2.71
544 568 7.440523 TCCAACTAAGAAATTTTGAGAGAGC 57.559 36.000 0.00 0.00 0.00 4.09
653 677 2.309528 TATCATCCTCACGGCAACAC 57.690 50.000 0.00 0.00 0.00 3.32
660 684 7.919690 TGCTAAAGAAAATTATCATCCTCACG 58.080 34.615 0.00 0.00 0.00 4.35
698 723 4.022464 TGCCAAAAACTAAACACGACAG 57.978 40.909 0.00 0.00 0.00 3.51
703 728 7.602753 AGATAATCCTGCCAAAAACTAAACAC 58.397 34.615 0.00 0.00 0.00 3.32
717 744 1.068194 AGCGAGCGTAGATAATCCTGC 60.068 52.381 0.00 0.00 0.00 4.85
730 757 4.002267 TGACAATTTCATTTAGCGAGCG 57.998 40.909 0.00 0.00 0.00 5.03
749 776 5.705441 GCAAAATATATTGTCGGGGAGATGA 59.295 40.000 0.00 0.00 32.80 2.92
785 814 9.796120 CCGATTTTTAGGCAATAGTAAATCAAA 57.204 29.630 0.00 0.00 33.69 2.69
786 815 9.179909 TCCGATTTTTAGGCAATAGTAAATCAA 57.820 29.630 0.00 0.00 33.69 2.57
787 816 8.617809 GTCCGATTTTTAGGCAATAGTAAATCA 58.382 33.333 0.00 0.00 33.69 2.57
788 817 7.797123 CGTCCGATTTTTAGGCAATAGTAAATC 59.203 37.037 0.00 0.00 0.00 2.17
789 818 7.281549 ACGTCCGATTTTTAGGCAATAGTAAAT 59.718 33.333 0.00 0.00 0.00 1.40
790 819 6.594937 ACGTCCGATTTTTAGGCAATAGTAAA 59.405 34.615 0.00 0.00 0.00 2.01
791 820 6.108015 ACGTCCGATTTTTAGGCAATAGTAA 58.892 36.000 0.00 0.00 0.00 2.24
792 821 5.663456 ACGTCCGATTTTTAGGCAATAGTA 58.337 37.500 0.00 0.00 0.00 1.82
793 822 4.510571 ACGTCCGATTTTTAGGCAATAGT 58.489 39.130 0.00 0.00 0.00 2.12
794 823 5.479716 AACGTCCGATTTTTAGGCAATAG 57.520 39.130 0.00 0.00 0.00 1.73
795 824 5.411977 TCAAACGTCCGATTTTTAGGCAATA 59.588 36.000 0.00 0.00 0.00 1.90
796 825 4.216687 TCAAACGTCCGATTTTTAGGCAAT 59.783 37.500 0.00 0.00 0.00 3.56
797 826 3.564644 TCAAACGTCCGATTTTTAGGCAA 59.435 39.130 0.00 0.00 0.00 4.52
798 827 3.139850 TCAAACGTCCGATTTTTAGGCA 58.860 40.909 0.00 0.00 0.00 4.75
799 828 3.817148 TCAAACGTCCGATTTTTAGGC 57.183 42.857 0.00 0.00 0.00 3.93
800 829 7.524065 AGTAAATCAAACGTCCGATTTTTAGG 58.476 34.615 22.65 0.00 41.08 2.69
803 832 9.337091 CAATAGTAAATCAAACGTCCGATTTTT 57.663 29.630 22.65 16.21 41.08 1.94
804 833 7.483691 GCAATAGTAAATCAAACGTCCGATTTT 59.516 33.333 22.65 12.98 41.08 1.82
805 834 6.964934 GCAATAGTAAATCAAACGTCCGATTT 59.035 34.615 21.70 21.70 42.79 2.17
806 835 6.457799 GGCAATAGTAAATCAAACGTCCGATT 60.458 38.462 6.59 6.59 33.27 3.34
807 836 5.007332 GGCAATAGTAAATCAAACGTCCGAT 59.993 40.000 0.00 0.00 0.00 4.18
808 837 4.330620 GGCAATAGTAAATCAAACGTCCGA 59.669 41.667 0.00 0.00 0.00 4.55
809 838 4.331717 AGGCAATAGTAAATCAAACGTCCG 59.668 41.667 0.00 0.00 0.00 4.79
810 839 5.813080 AGGCAATAGTAAATCAAACGTCC 57.187 39.130 0.00 0.00 0.00 4.79
811 840 9.615295 TTTTTAGGCAATAGTAAATCAAACGTC 57.385 29.630 0.00 0.00 0.00 4.34
1018 1048 4.269183 AGTGAGATGACAGTGTAGAGGAG 58.731 47.826 0.00 0.00 0.00 3.69
1019 1049 4.018870 AGAGTGAGATGACAGTGTAGAGGA 60.019 45.833 0.00 0.00 0.00 3.71
1020 1050 4.269183 AGAGTGAGATGACAGTGTAGAGG 58.731 47.826 0.00 0.00 0.00 3.69
1113 1143 2.279318 GCGAAGTAGTAGCCGGCC 60.279 66.667 26.15 9.10 0.00 6.13
1169 1199 3.544698 AGAGGTGAGTGTAGAGGGAAA 57.455 47.619 0.00 0.00 0.00 3.13
1170 1200 3.592427 AGTAGAGGTGAGTGTAGAGGGAA 59.408 47.826 0.00 0.00 0.00 3.97
1182 1212 4.627015 AGAGAGAGGAGTAGTAGAGGTGA 58.373 47.826 0.00 0.00 0.00 4.02
1363 1393 3.717294 GTCCCCAGATGCCGTGGT 61.717 66.667 0.00 0.00 32.62 4.16
2015 2045 2.037136 AGGTACGACGACACGGAGG 61.037 63.158 0.00 0.00 37.61 4.30
2136 2166 1.888215 TGGAGTCGTCGTAGTTCACT 58.112 50.000 0.00 0.00 0.00 3.41
2459 2513 3.071892 CGGGGAAGGCACCAGTTAATATA 59.928 47.826 3.41 0.00 37.48 0.86
2463 2517 1.377229 CGGGGAAGGCACCAGTTAA 59.623 57.895 3.41 0.00 37.48 2.01
2464 2518 1.833787 GACGGGGAAGGCACCAGTTA 61.834 60.000 3.41 0.00 37.48 2.24
2465 2519 3.175710 ACGGGGAAGGCACCAGTT 61.176 61.111 3.41 0.00 37.48 3.16
2492 2546 1.275291 TCCCTCGATGTTGGAGTGAAC 59.725 52.381 0.00 0.00 0.00 3.18
2704 2792 5.501715 CGCAGAGCAATTTCGTTTATACAT 58.498 37.500 0.00 0.00 0.00 2.29
2740 2828 3.013219 CTCTCATCCAACTCTCGTCAGA 58.987 50.000 0.00 0.00 0.00 3.27
2745 2833 0.820226 TGGCTCTCATCCAACTCTCG 59.180 55.000 0.00 0.00 0.00 4.04
2748 2836 2.092753 TGGAATGGCTCTCATCCAACTC 60.093 50.000 0.00 0.00 37.13 3.01
2772 2860 2.941453 TGATCGAAGTGCAGTAGACC 57.059 50.000 0.00 0.00 0.00 3.85
2804 2892 6.238022 CGATCTCTACACTACACGTCAACATA 60.238 42.308 0.00 0.00 0.00 2.29
2805 2893 5.447413 CGATCTCTACACTACACGTCAACAT 60.447 44.000 0.00 0.00 0.00 2.71
2806 2894 4.142966 CGATCTCTACACTACACGTCAACA 60.143 45.833 0.00 0.00 0.00 3.33
2807 2895 4.142945 ACGATCTCTACACTACACGTCAAC 60.143 45.833 0.00 0.00 0.00 3.18
2808 2896 3.999001 ACGATCTCTACACTACACGTCAA 59.001 43.478 0.00 0.00 0.00 3.18
2809 2897 3.593096 ACGATCTCTACACTACACGTCA 58.407 45.455 0.00 0.00 0.00 4.35
2810 2898 3.001127 GGACGATCTCTACACTACACGTC 59.999 52.174 0.00 0.00 44.81 4.34
2811 2899 2.935201 GGACGATCTCTACACTACACGT 59.065 50.000 0.00 0.00 35.53 4.49
2812 2900 2.934553 TGGACGATCTCTACACTACACG 59.065 50.000 0.00 0.00 0.00 4.49
2813 2901 6.615264 TTATGGACGATCTCTACACTACAC 57.385 41.667 0.00 0.00 0.00 2.90
2834 2922 6.986904 TTATGGTATGCACACGATGTTTTA 57.013 33.333 2.54 0.00 0.00 1.52
2954 3073 1.152963 GAACCCCATCCATGACCGG 60.153 63.158 0.00 0.00 0.00 5.28
3007 3190 0.823356 GTGCCCAGAGAAGCAACCAA 60.823 55.000 0.00 0.00 41.48 3.67
3008 3191 1.228245 GTGCCCAGAGAAGCAACCA 60.228 57.895 0.00 0.00 41.48 3.67
3050 3233 1.933021 TCTTGTACCCACACGGAGAT 58.067 50.000 0.00 0.00 33.30 2.75
3069 3252 3.511146 CCACTGCATCCCAAAGTTTACAT 59.489 43.478 0.00 0.00 0.00 2.29
3125 3308 0.530650 ATCGCAAGCATACAGTCGGG 60.531 55.000 0.00 0.00 37.18 5.14
3195 3380 3.077556 CCACCTACCAGAGCCGCT 61.078 66.667 0.00 0.00 0.00 5.52
3263 3477 2.283529 AAGTGATCCACCTCGCCGT 61.284 57.895 0.00 0.00 34.49 5.68
3295 3509 3.134127 GAAGCCCACACCCGCATC 61.134 66.667 0.00 0.00 0.00 3.91
3322 3536 2.125106 GACTCCCGGACCATGTGC 60.125 66.667 0.73 0.00 0.00 4.57
3326 3540 2.052690 CAGACGACTCCCGGACCAT 61.053 63.158 0.73 0.00 43.93 3.55
3364 3578 0.761187 CATCCAGGTCCATCGGTCAT 59.239 55.000 0.00 0.00 0.00 3.06
3434 3648 3.179830 GACACACAAGAGCGTCGATATT 58.820 45.455 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.