Multiple sequence alignment - TraesCS5A01G150100

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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 TraesCS5A01G150100 chr5A 100.000 3944 0 0 1 3944 327915683 327919626 0.000000e+00 7284
1 TraesCS5A01G150100 chr5A 83.654 1976 281 25 1002 2968 327907934 327909876 0.000000e+00 1821
2 TraesCS5A01G150100 chr5A 83.424 736 87 17 2249 2951 327910326 327911059 0.000000e+00 651
3 TraesCS5A01G150100 chr5B 97.153 2634 68 4 1313 3944 276906331 276908959 0.000000e+00 4442
4 TraesCS5A01G150100 chr5B 85.094 1959 274 18 1002 2951 276899463 276901412 0.000000e+00 1984
5 TraesCS5A01G150100 chr5B 80.952 840 98 30 1 804 276902184 276902997 3.370000e-170 608
6 TraesCS5A01G150100 chr5B 94.723 379 18 2 958 1336 276905801 276906177 4.390000e-164 588
7 TraesCS5A01G150100 chr5D 97.948 2144 43 1 967 3110 243807143 243809285 0.000000e+00 3714
8 TraesCS5A01G150100 chr5D 83.223 1955 294 20 1002 2951 228960441 228958516 0.000000e+00 1762
9 TraesCS5A01G150100 chr5D 96.067 534 18 2 3104 3635 243816202 243816734 0.000000e+00 867
10 TraesCS5A01G150100 chr5D 98.428 318 5 0 3627 3944 243817687 243818004 9.570000e-156 560
11 TraesCS5A01G150100 chr7B 91.304 299 17 3 24 313 54050884 54051182 2.210000e-107 399
12 TraesCS5A01G150100 chr6B 91.275 298 18 5 24 313 596602878 596603175 2.210000e-107 399
13 TraesCS5A01G150100 chr4D 91.275 298 17 6 24 313 134961991 134961695 7.940000e-107 398
14 TraesCS5A01G150100 chr1A 91.275 298 17 6 24 313 94579875 94579579 7.940000e-107 398
15 TraesCS5A01G150100 chr1A 90.604 298 19 6 24 313 94664956 94665252 1.720000e-103 387
16 TraesCS5A01G150100 chr4B 90.940 298 19 5 24 313 623346343 623346046 1.030000e-105 394
17 TraesCS5A01G150100 chr4B 90.940 298 18 6 24 313 495566946 495566650 3.690000e-105 392
18 TraesCS5A01G150100 chr1D 90.940 298 18 6 24 313 212446592 212446888 3.690000e-105 392
19 TraesCS5A01G150100 chr1D 91.429 245 21 0 3018 3262 351059202 351058958 1.760000e-88 337
20 TraesCS5A01G150100 chr6D 91.429 245 21 0 3018 3262 283196484 283196728 1.760000e-88 337
21 TraesCS5A01G150100 chr2A 91.429 245 21 0 3018 3262 444311982 444312226 1.760000e-88 337
22 TraesCS5A01G150100 chr2D 91.020 245 22 0 3018 3262 306156318 306156562 8.170000e-87 331
23 TraesCS5A01G150100 chr2D 91.102 236 21 0 3018 3253 291678547 291678782 1.770000e-83 320
24 TraesCS5A01G150100 chr2D 88.618 246 27 1 3018 3262 291775793 291775548 8.290000e-77 298
25 TraesCS5A01G150100 chr6A 90.612 245 23 0 3018 3262 375868028 375868272 3.800000e-85 326


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 TraesCS5A01G150100 chr5A 327915683 327919626 3943 False 7284.0 7284 100.0000 1 3944 1 chr5A.!!$F1 3943
1 TraesCS5A01G150100 chr5A 327907934 327911059 3125 False 1236.0 1821 83.5390 1002 2968 2 chr5A.!!$F2 1966
2 TraesCS5A01G150100 chr5B 276899463 276908959 9496 False 1905.5 4442 89.4805 1 3944 4 chr5B.!!$F1 3943
3 TraesCS5A01G150100 chr5D 243807143 243809285 2142 False 3714.0 3714 97.9480 967 3110 1 chr5D.!!$F1 2143
4 TraesCS5A01G150100 chr5D 228958516 228960441 1925 True 1762.0 1762 83.2230 1002 2951 1 chr5D.!!$R1 1949
5 TraesCS5A01G150100 chr5D 243816202 243818004 1802 False 713.5 867 97.2475 3104 3944 2 chr5D.!!$F2 840

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
564 3345 0.034896 AGTCAAGTGGCGGGTAGTTG 59.965 55.0 0.00 0.0 0.00 3.16 F
583 3364 0.108041 GCCCCTGCCAATGTCAATTG 60.108 55.0 0.00 0.0 42.49 2.32 F
1734 7359 0.111253 ATGCTATAGCTTGGGGTGCC 59.889 55.0 24.61 0.0 42.66 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2413 8038 0.398318 GAATTCCGGGGCTCTAGCAT 59.602 55.000 0.0 0.0 44.36 3.79 R
2521 8146 2.058675 CACGGACCTTCTCAACCCT 58.941 57.895 0.0 0.0 0.00 4.34 R
3245 10046 0.461961 GCGTTCAGATAGGGCACTCT 59.538 55.000 0.0 0.0 0.00 3.24 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
66 2788 0.107654 GACCCCATTGAAGACGGGAG 60.108 60.000 0.00 0.00 43.21 4.30
90 2812 3.551846 AGGTATAACAAGGCCATTTCCG 58.448 45.455 5.01 0.00 0.00 4.30
93 2815 2.871096 TAACAAGGCCATTTCCGTCT 57.129 45.000 5.01 0.00 0.00 4.18
96 2818 1.339727 ACAAGGCCATTTCCGTCTACC 60.340 52.381 5.01 0.00 0.00 3.18
97 2819 1.065418 CAAGGCCATTTCCGTCTACCT 60.065 52.381 5.01 0.00 0.00 3.08
98 2820 1.286248 AGGCCATTTCCGTCTACCTT 58.714 50.000 5.01 0.00 0.00 3.50
109 2831 1.465794 GTCTACCTTCTCACGGAGCT 58.534 55.000 0.00 0.00 0.00 4.09
113 2835 1.853963 ACCTTCTCACGGAGCTGTAT 58.146 50.000 0.00 0.00 0.00 2.29
116 2838 2.534298 CTTCTCACGGAGCTGTATGTG 58.466 52.381 0.00 0.00 0.00 3.21
125 2847 2.165845 GGAGCTGTATGTGGACGTTACT 59.834 50.000 0.00 0.00 0.00 2.24
135 2857 3.006003 TGTGGACGTTACTGCTCATACAA 59.994 43.478 0.00 0.00 0.00 2.41
138 2860 3.858238 GGACGTTACTGCTCATACAACTC 59.142 47.826 0.00 0.00 0.00 3.01
144 2866 1.209019 CTGCTCATACAACTCCCAGCT 59.791 52.381 0.00 0.00 0.00 4.24
148 2870 2.432146 CTCATACAACTCCCAGCTAGCA 59.568 50.000 18.83 0.00 0.00 3.49
192 2914 7.177878 AGAAGTCATGGAAGTGTGGATAAATT 58.822 34.615 0.00 0.00 0.00 1.82
194 2916 6.484288 AGTCATGGAAGTGTGGATAAATTGA 58.516 36.000 0.00 0.00 0.00 2.57
195 2917 6.375455 AGTCATGGAAGTGTGGATAAATTGAC 59.625 38.462 0.00 0.00 0.00 3.18
255 2977 7.270779 GTCCTAAATATGGACGGTCTTAAGTT 58.729 38.462 8.23 2.25 43.55 2.66
258 2980 8.953313 CCTAAATATGGACGGTCTTAAGTTTTT 58.047 33.333 8.23 3.02 0.00 1.94
259 2981 9.983804 CTAAATATGGACGGTCTTAAGTTTTTC 57.016 33.333 8.23 0.00 0.00 2.29
294 3023 7.504924 AGATCTCATTTTAGGTCGAGTAGAG 57.495 40.000 0.00 0.00 31.53 2.43
298 3027 4.940046 TCATTTTAGGTCGAGTAGAGACGT 59.060 41.667 0.00 0.00 39.38 4.34
314 3043 1.313812 ACGTTAGGGAGTCTCTGGCG 61.314 60.000 1.61 9.50 0.00 5.69
319 3048 2.581354 GGAGTCTCTGGCGTGCAT 59.419 61.111 0.00 0.00 0.00 3.96
333 3062 0.523072 GTGCATGAAGACGCCAACAT 59.477 50.000 0.00 0.00 0.00 2.71
338 3067 2.010145 TGAAGACGCCAACATAGCTC 57.990 50.000 0.00 0.00 0.00 4.09
366 3095 2.668212 CGGCGTGGTGACCAACAT 60.668 61.111 5.57 0.00 34.18 2.71
368 3097 2.677003 GGCGTGGTGACCAACATCG 61.677 63.158 5.57 6.97 34.18 3.84
449 3190 1.228552 GGCAGTGGTGTGGGTGATT 60.229 57.895 0.00 0.00 0.00 2.57
452 3193 1.887956 GCAGTGGTGTGGGTGATTGAT 60.888 52.381 0.00 0.00 0.00 2.57
492 3273 4.814294 GGTAGAGGTGGTGCGGCG 62.814 72.222 0.51 0.51 0.00 6.46
539 3320 4.758251 TGGTGCGGCGGTCATCAG 62.758 66.667 9.78 0.00 0.00 2.90
547 3328 4.498520 CGGTCATCAGCGGCGAGT 62.499 66.667 12.98 0.00 39.95 4.18
548 3329 2.583593 GGTCATCAGCGGCGAGTC 60.584 66.667 12.98 0.00 0.00 3.36
549 3330 2.181777 GTCATCAGCGGCGAGTCA 59.818 61.111 12.98 0.00 0.00 3.41
550 3331 1.446099 GTCATCAGCGGCGAGTCAA 60.446 57.895 12.98 0.00 0.00 3.18
551 3332 1.153765 TCATCAGCGGCGAGTCAAG 60.154 57.895 12.98 0.00 0.00 3.02
552 3333 1.446792 CATCAGCGGCGAGTCAAGT 60.447 57.895 12.98 0.00 0.00 3.16
553 3334 1.446792 ATCAGCGGCGAGTCAAGTG 60.447 57.895 12.98 0.00 0.00 3.16
554 3335 2.842394 ATCAGCGGCGAGTCAAGTGG 62.842 60.000 12.98 0.00 0.00 4.00
559 3340 4.681978 GCGAGTCAAGTGGCGGGT 62.682 66.667 0.00 0.00 0.00 5.28
560 3341 2.967397 CGAGTCAAGTGGCGGGTA 59.033 61.111 0.00 0.00 0.00 3.69
561 3342 1.153823 CGAGTCAAGTGGCGGGTAG 60.154 63.158 0.00 0.00 0.00 3.18
562 3343 1.874345 CGAGTCAAGTGGCGGGTAGT 61.874 60.000 0.00 0.00 0.00 2.73
563 3344 0.320697 GAGTCAAGTGGCGGGTAGTT 59.679 55.000 0.00 0.00 0.00 2.24
564 3345 0.034896 AGTCAAGTGGCGGGTAGTTG 59.965 55.000 0.00 0.00 0.00 3.16
565 3346 1.302192 TCAAGTGGCGGGTAGTTGC 60.302 57.895 0.00 0.00 0.00 4.17
570 3351 4.796495 GGCGGGTAGTTGCCCCTG 62.796 72.222 0.00 0.00 45.91 4.45
572 3353 4.796495 CGGGTAGTTGCCCCTGCC 62.796 72.222 0.00 0.00 45.91 4.85
573 3354 3.657350 GGGTAGTTGCCCCTGCCA 61.657 66.667 8.69 0.00 42.89 4.92
574 3355 2.438795 GGTAGTTGCCCCTGCCAA 59.561 61.111 2.56 0.00 37.20 4.52
575 3356 1.000359 GGTAGTTGCCCCTGCCAAT 60.000 57.895 2.56 0.00 37.20 3.16
576 3357 1.322538 GGTAGTTGCCCCTGCCAATG 61.323 60.000 2.56 0.00 37.20 2.82
577 3358 0.611896 GTAGTTGCCCCTGCCAATGT 60.612 55.000 0.00 0.00 36.33 2.71
578 3359 0.323360 TAGTTGCCCCTGCCAATGTC 60.323 55.000 0.00 0.00 36.33 3.06
579 3360 1.907807 GTTGCCCCTGCCAATGTCA 60.908 57.895 0.00 0.00 36.33 3.58
580 3361 1.152376 TTGCCCCTGCCAATGTCAA 60.152 52.632 0.00 0.00 36.33 3.18
581 3362 0.544833 TTGCCCCTGCCAATGTCAAT 60.545 50.000 0.00 0.00 36.33 2.57
582 3363 0.544833 TGCCCCTGCCAATGTCAATT 60.545 50.000 0.00 0.00 36.33 2.32
583 3364 0.108041 GCCCCTGCCAATGTCAATTG 60.108 55.000 0.00 0.00 42.49 2.32
595 3376 6.514947 CCAATGTCAATTGTGTTATATGGGG 58.485 40.000 5.13 0.00 41.46 4.96
607 3388 4.225942 TGTTATATGGGGAGATGCATCCTC 59.774 45.833 23.06 17.89 40.62 3.71
611 3392 4.328208 GGAGATGCATCCTCCCCT 57.672 61.111 23.06 3.07 43.37 4.79
612 3393 2.065483 GGAGATGCATCCTCCCCTC 58.935 63.158 23.06 12.42 43.37 4.30
613 3394 0.765903 GGAGATGCATCCTCCCCTCA 60.766 60.000 23.06 0.00 43.37 3.86
614 3395 1.135094 GAGATGCATCCTCCCCTCAA 58.865 55.000 23.06 0.00 0.00 3.02
615 3396 1.704070 GAGATGCATCCTCCCCTCAAT 59.296 52.381 23.06 0.00 0.00 2.57
616 3397 2.909006 GAGATGCATCCTCCCCTCAATA 59.091 50.000 23.06 0.00 0.00 1.90
617 3398 3.522750 GAGATGCATCCTCCCCTCAATAT 59.477 47.826 23.06 0.00 0.00 1.28
618 3399 3.921486 AGATGCATCCTCCCCTCAATATT 59.079 43.478 23.06 0.00 0.00 1.28
619 3400 3.513909 TGCATCCTCCCCTCAATATTG 57.486 47.619 9.29 9.29 0.00 1.90
622 3403 3.560882 GCATCCTCCCCTCAATATTGGAG 60.561 52.174 15.36 12.94 43.29 3.86
628 3409 5.509498 CTCCCCTCAATATTGGAGAAAACA 58.491 41.667 15.36 0.00 45.93 2.83
631 3412 5.394553 CCCCTCAATATTGGAGAAAACAAGC 60.395 44.000 15.36 0.00 34.24 4.01
647 3428 6.387041 AAACAAGCTGTTTCTTAGGGTTAC 57.613 37.500 8.03 0.00 46.61 2.50
736 3521 3.739589 TATTGGCGAAAGGGACCTGCC 62.740 57.143 10.42 10.42 45.91 4.85
746 3531 2.586792 GACCTGCCGGAGATGCTT 59.413 61.111 5.05 0.00 0.00 3.91
761 3546 5.163612 GGAGATGCTTTAATTTGTGTCTCCC 60.164 44.000 6.79 0.00 42.85 4.30
766 3551 6.303839 TGCTTTAATTTGTGTCTCCCTACTT 58.696 36.000 0.00 0.00 0.00 2.24
783 3576 6.664816 TCCCTACTTTTAGTCCGAGTGATTTA 59.335 38.462 0.00 0.00 0.00 1.40
793 3586 6.159988 AGTCCGAGTGATTTAAGAGTGAAAG 58.840 40.000 0.00 0.00 0.00 2.62
900 5664 7.710896 AGTTTTAAAGGATCTGCTATTGATGC 58.289 34.615 0.00 0.00 33.36 3.91
904 5668 1.002430 GGATCTGCTATTGATGCCCGA 59.998 52.381 0.00 0.00 0.00 5.14
917 6366 2.418368 TGCCCGAGAGCAAACATAAT 57.582 45.000 0.00 0.00 40.56 1.28
919 6368 1.261619 GCCCGAGAGCAAACATAATCG 59.738 52.381 0.00 0.00 0.00 3.34
922 6371 2.930040 CCGAGAGCAAACATAATCGTGT 59.070 45.455 0.00 0.00 0.00 4.49
926 6375 3.055094 AGAGCAAACATAATCGTGTCCCT 60.055 43.478 0.00 0.00 0.00 4.20
934 6383 4.162320 ACATAATCGTGTCCCTGAGAACAT 59.838 41.667 0.00 0.00 0.00 2.71
938 6387 3.138304 TCGTGTCCCTGAGAACATTTTG 58.862 45.455 0.00 0.00 0.00 2.44
940 6389 3.187227 CGTGTCCCTGAGAACATTTTGAG 59.813 47.826 0.00 0.00 0.00 3.02
941 6390 4.137543 GTGTCCCTGAGAACATTTTGAGT 58.862 43.478 0.00 0.00 0.00 3.41
943 6392 5.763204 GTGTCCCTGAGAACATTTTGAGTTA 59.237 40.000 0.00 0.00 0.00 2.24
944 6393 6.262273 GTGTCCCTGAGAACATTTTGAGTTAA 59.738 38.462 0.00 0.00 0.00 2.01
945 6394 7.004086 TGTCCCTGAGAACATTTTGAGTTAAT 58.996 34.615 0.00 0.00 0.00 1.40
946 6395 8.160765 TGTCCCTGAGAACATTTTGAGTTAATA 58.839 33.333 0.00 0.00 0.00 0.98
948 6397 9.581289 TCCCTGAGAACATTTTGAGTTAATAAA 57.419 29.630 0.00 0.00 0.00 1.40
960 6409 7.908827 TTGAGTTAATAAATTCCGTACAGCA 57.091 32.000 0.00 0.00 0.00 4.41
961 6410 7.534085 TGAGTTAATAAATTCCGTACAGCAG 57.466 36.000 0.00 0.00 0.00 4.24
962 6411 7.324935 TGAGTTAATAAATTCCGTACAGCAGA 58.675 34.615 0.00 0.00 0.00 4.26
963 6412 7.277098 TGAGTTAATAAATTCCGTACAGCAGAC 59.723 37.037 0.00 0.00 0.00 3.51
964 6413 6.255020 AGTTAATAAATTCCGTACAGCAGACG 59.745 38.462 0.00 0.00 40.02 4.18
969 6418 4.957266 CGTACAGCAGACGGACAA 57.043 55.556 0.00 0.00 36.66 3.18
970 6419 3.188773 CGTACAGCAGACGGACAAA 57.811 52.632 0.00 0.00 36.66 2.83
971 6420 1.060713 CGTACAGCAGACGGACAAAG 58.939 55.000 0.00 0.00 36.66 2.77
972 6421 0.790814 GTACAGCAGACGGACAAAGC 59.209 55.000 0.00 0.00 0.00 3.51
973 6422 0.320421 TACAGCAGACGGACAAAGCC 60.320 55.000 0.00 0.00 0.00 4.35
974 6423 1.302033 CAGCAGACGGACAAAGCCT 60.302 57.895 0.00 0.00 0.00 4.58
981 6430 1.673920 GACGGACAAAGCCTTTCAACA 59.326 47.619 0.00 0.00 0.00 3.33
983 6432 1.676006 CGGACAAAGCCTTTCAACACT 59.324 47.619 0.00 0.00 0.00 3.55
1119 6568 2.192443 CTCCGGCTCGACCTCCTA 59.808 66.667 0.00 0.00 35.61 2.94
1121 6570 2.907917 CCGGCTCGACCTCCTAGG 60.908 72.222 0.82 0.82 42.49 3.02
1344 6969 1.305381 CGTCCTCACCTCCCTCCTT 60.305 63.158 0.00 0.00 0.00 3.36
1529 7154 4.003788 CCCGGACAGCTTCACGGT 62.004 66.667 0.73 0.00 44.57 4.83
1720 7345 0.681733 GATGCCGGAGAAGGATGCTA 59.318 55.000 5.05 0.00 0.00 3.49
1734 7359 0.111253 ATGCTATAGCTTGGGGTGCC 59.889 55.000 24.61 0.00 42.66 5.01
1758 7383 1.002087 GTCGGGGGATATGCTTCGAAT 59.998 52.381 12.05 0.00 0.00 3.34
1857 7482 3.797546 GCGCTCTCAGCTTGCACC 61.798 66.667 0.00 0.00 39.60 5.01
2050 7675 1.477558 GGAATGCGATGATCTTGGGGT 60.478 52.381 0.00 0.00 0.00 4.95
2091 7716 4.222810 GGTAAGATTGGATTTGCCCTTGTT 59.777 41.667 0.00 0.00 34.97 2.83
2294 7919 2.747855 GTTGCTCCAGGAAGCCCG 60.748 66.667 8.05 0.00 41.77 6.13
2413 8038 1.669115 GCCTTGAAGCAGCTCGTCA 60.669 57.895 0.00 0.00 0.00 4.35
2521 8146 4.286297 AGATCGGACATGAAGGTGAAAA 57.714 40.909 0.00 0.00 0.00 2.29
3102 9903 2.555664 AGAATGAGAGCAAGAAGGGGA 58.444 47.619 0.00 0.00 0.00 4.81
3303 10104 7.189693 TCTTGTGTGTAGCTTCAAGTTATTG 57.810 36.000 0.00 0.00 38.53 1.90
3311 10112 8.450964 GTGTAGCTTCAAGTTATTGCAGAAATA 58.549 33.333 0.00 0.00 32.08 1.40
3312 10113 9.008965 TGTAGCTTCAAGTTATTGCAGAAATAA 57.991 29.630 0.00 0.00 38.21 1.40
3358 10162 4.574599 AAATTGTGCCTCTCTTTGTGTC 57.425 40.909 0.00 0.00 0.00 3.67
3457 10261 5.163426 TGCATCACTGTTCTTCCACAAATTT 60.163 36.000 0.00 0.00 0.00 1.82
3478 10282 4.517952 TTTGCCATACACCATTGAGTTG 57.482 40.909 0.00 0.00 0.00 3.16
3496 10300 3.064931 GTTGACTGTAGGTTGTGCTACC 58.935 50.000 0.00 0.00 38.53 3.18
3553 10357 3.855689 CCTGAACTGGCACAAATTAGG 57.144 47.619 0.00 0.00 38.70 2.69
3758 11523 4.759693 GGTACACAATGTCACCTGAATTGA 59.240 41.667 6.46 0.00 35.67 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.493278 GTGAAACACATATGCCAGGCTT 59.507 45.455 14.15 9.31 36.32 4.35
1 2 2.094675 GTGAAACACATATGCCAGGCT 58.905 47.619 14.15 0.35 36.32 4.58
2 3 1.818060 TGTGAAACACATATGCCAGGC 59.182 47.619 3.66 3.66 45.67 4.85
40 2762 1.988107 TCTTCAATGGGGTCTGCTCTT 59.012 47.619 0.00 0.00 0.00 2.85
43 2765 0.036010 CGTCTTCAATGGGGTCTGCT 60.036 55.000 0.00 0.00 0.00 4.24
44 2766 1.026718 CCGTCTTCAATGGGGTCTGC 61.027 60.000 0.00 0.00 0.00 4.26
45 2767 3.159298 CCGTCTTCAATGGGGTCTG 57.841 57.895 0.00 0.00 0.00 3.51
66 2788 4.338400 GGAAATGGCCTTGTTATACCTCAC 59.662 45.833 3.32 0.00 0.00 3.51
74 2796 2.871096 AGACGGAAATGGCCTTGTTA 57.129 45.000 3.32 0.00 0.00 2.41
90 2812 1.133407 CAGCTCCGTGAGAAGGTAGAC 59.867 57.143 5.24 0.00 0.00 2.59
93 2815 2.502142 TACAGCTCCGTGAGAAGGTA 57.498 50.000 5.24 1.97 0.00 3.08
96 2818 2.534298 CACATACAGCTCCGTGAGAAG 58.466 52.381 5.24 0.00 0.00 2.85
97 2819 1.204704 CCACATACAGCTCCGTGAGAA 59.795 52.381 5.24 0.00 0.00 2.87
98 2820 0.817654 CCACATACAGCTCCGTGAGA 59.182 55.000 5.24 0.00 0.00 3.27
109 2831 2.559231 TGAGCAGTAACGTCCACATACA 59.441 45.455 0.00 0.00 0.00 2.29
113 2835 2.559231 TGTATGAGCAGTAACGTCCACA 59.441 45.455 0.00 0.00 0.00 4.17
116 2838 3.846360 AGTTGTATGAGCAGTAACGTCC 58.154 45.455 0.00 0.00 0.00 4.79
125 2847 1.279496 AGCTGGGAGTTGTATGAGCA 58.721 50.000 0.00 0.00 0.00 4.26
135 2857 2.239681 ACTACTTGCTAGCTGGGAGT 57.760 50.000 17.23 16.55 0.00 3.85
138 2860 2.432510 AGCTAACTACTTGCTAGCTGGG 59.567 50.000 17.23 8.32 45.72 4.45
144 2866 7.117397 TCTAGAGGAAAGCTAACTACTTGCTA 58.883 38.462 0.00 0.00 35.85 3.49
148 2870 7.670559 TGACTTCTAGAGGAAAGCTAACTACTT 59.329 37.037 9.14 0.00 33.07 2.24
218 2940 5.425539 CCATATTTAGGACGGATAGGGTGAT 59.574 44.000 0.00 0.00 0.00 3.06
221 2943 4.776308 GTCCATATTTAGGACGGATAGGGT 59.224 45.833 0.00 0.00 45.35 4.34
247 2969 3.555586 CGAGGACCCCGAAAAACTTAAGA 60.556 47.826 10.09 0.00 0.00 2.10
248 2970 2.740447 CGAGGACCCCGAAAAACTTAAG 59.260 50.000 0.00 0.00 0.00 1.85
249 2971 2.368221 TCGAGGACCCCGAAAAACTTAA 59.632 45.455 0.00 0.00 32.64 1.85
250 2972 1.969923 TCGAGGACCCCGAAAAACTTA 59.030 47.619 0.00 0.00 32.64 2.24
251 2973 0.760572 TCGAGGACCCCGAAAAACTT 59.239 50.000 0.00 0.00 32.64 2.66
255 2977 0.822164 GATCTCGAGGACCCCGAAAA 59.178 55.000 13.56 0.00 35.48 2.29
258 2980 1.148723 GAGATCTCGAGGACCCCGA 59.851 63.158 13.56 0.00 34.61 5.14
259 2981 0.538516 ATGAGATCTCGAGGACCCCG 60.539 60.000 17.76 0.00 0.00 5.73
294 3023 0.456628 GCCAGAGACTCCCTAACGTC 59.543 60.000 0.00 0.00 0.00 4.34
298 3027 1.605058 GCACGCCAGAGACTCCCTAA 61.605 60.000 0.00 0.00 0.00 2.69
314 3043 0.523072 ATGTTGGCGTCTTCATGCAC 59.477 50.000 0.00 0.00 36.08 4.57
319 3048 1.405526 GGAGCTATGTTGGCGTCTTCA 60.406 52.381 0.00 0.00 34.52 3.02
349 3078 2.668212 ATGTTGGTCACCACGCCG 60.668 61.111 0.00 0.00 30.78 6.46
354 3083 0.533978 CCACACGATGTTGGTCACCA 60.534 55.000 0.00 0.00 0.00 4.17
432 3173 0.537143 TCAATCACCCACACCACTGC 60.537 55.000 0.00 0.00 0.00 4.40
441 3182 0.959867 CGCACACCATCAATCACCCA 60.960 55.000 0.00 0.00 0.00 4.51
444 3185 1.802636 CCCGCACACCATCAATCAC 59.197 57.895 0.00 0.00 0.00 3.06
473 3254 2.955881 GCCGCACCACCTCTACCTT 61.956 63.158 0.00 0.00 0.00 3.50
474 3255 3.391382 GCCGCACCACCTCTACCT 61.391 66.667 0.00 0.00 0.00 3.08
542 3323 3.291101 TACCCGCCACTTGACTCGC 62.291 63.158 0.00 0.00 0.00 5.03
543 3324 1.153823 CTACCCGCCACTTGACTCG 60.154 63.158 0.00 0.00 0.00 4.18
544 3325 0.320697 AACTACCCGCCACTTGACTC 59.679 55.000 0.00 0.00 0.00 3.36
545 3326 0.034896 CAACTACCCGCCACTTGACT 59.965 55.000 0.00 0.00 0.00 3.41
546 3327 1.574702 GCAACTACCCGCCACTTGAC 61.575 60.000 0.00 0.00 0.00 3.18
547 3328 1.302192 GCAACTACCCGCCACTTGA 60.302 57.895 0.00 0.00 0.00 3.02
548 3329 3.263941 GCAACTACCCGCCACTTG 58.736 61.111 0.00 0.00 0.00 3.16
557 3338 2.438795 TTGGCAGGGGCAACTACC 59.561 61.111 0.70 0.00 42.98 3.18
563 3344 0.544833 AATTGACATTGGCAGGGGCA 60.545 50.000 0.00 0.00 43.71 5.36
564 3345 0.108041 CAATTGACATTGGCAGGGGC 60.108 55.000 0.00 0.00 36.82 5.80
565 3346 1.066716 CACAATTGACATTGGCAGGGG 60.067 52.381 13.59 0.00 43.82 4.79
566 3347 1.619827 ACACAATTGACATTGGCAGGG 59.380 47.619 13.59 0.00 43.82 4.45
567 3348 3.389925 AACACAATTGACATTGGCAGG 57.610 42.857 13.59 0.00 43.82 4.85
568 3349 6.698329 CCATATAACACAATTGACATTGGCAG 59.302 38.462 13.59 0.00 43.82 4.85
569 3350 6.406737 CCCATATAACACAATTGACATTGGCA 60.407 38.462 13.59 0.00 43.82 4.92
570 3351 5.984926 CCCATATAACACAATTGACATTGGC 59.015 40.000 13.59 0.00 43.82 4.52
571 3352 6.323482 TCCCCATATAACACAATTGACATTGG 59.677 38.462 13.59 9.02 43.82 3.16
572 3353 7.285172 TCTCCCCATATAACACAATTGACATTG 59.715 37.037 13.59 2.05 44.90 2.82
573 3354 7.353525 TCTCCCCATATAACACAATTGACATT 58.646 34.615 13.59 5.70 0.00 2.71
574 3355 6.910191 TCTCCCCATATAACACAATTGACAT 58.090 36.000 13.59 2.13 0.00 3.06
575 3356 6.320434 TCTCCCCATATAACACAATTGACA 57.680 37.500 13.59 0.00 0.00 3.58
576 3357 6.294176 GCATCTCCCCATATAACACAATTGAC 60.294 42.308 13.59 0.00 0.00 3.18
577 3358 5.769662 GCATCTCCCCATATAACACAATTGA 59.230 40.000 13.59 0.00 0.00 2.57
578 3359 5.535783 TGCATCTCCCCATATAACACAATTG 59.464 40.000 3.24 3.24 0.00 2.32
579 3360 5.704354 TGCATCTCCCCATATAACACAATT 58.296 37.500 0.00 0.00 0.00 2.32
580 3361 5.323382 TGCATCTCCCCATATAACACAAT 57.677 39.130 0.00 0.00 0.00 2.71
581 3362 4.787135 TGCATCTCCCCATATAACACAA 57.213 40.909 0.00 0.00 0.00 3.33
582 3363 4.263462 GGATGCATCTCCCCATATAACACA 60.263 45.833 25.28 0.00 0.00 3.72
583 3364 4.018960 AGGATGCATCTCCCCATATAACAC 60.019 45.833 25.28 4.35 35.79 3.32
595 3376 1.135094 TTGAGGGGAGGATGCATCTC 58.865 55.000 25.28 19.00 0.00 2.75
607 3388 5.394553 GCTTGTTTTCTCCAATATTGAGGGG 60.395 44.000 17.23 0.91 0.00 4.79
608 3389 5.420104 AGCTTGTTTTCTCCAATATTGAGGG 59.580 40.000 17.23 7.19 0.00 4.30
609 3390 6.071728 ACAGCTTGTTTTCTCCAATATTGAGG 60.072 38.462 17.23 8.83 0.00 3.86
610 3391 6.917533 ACAGCTTGTTTTCTCCAATATTGAG 58.082 36.000 17.23 11.76 0.00 3.02
611 3392 6.899393 ACAGCTTGTTTTCTCCAATATTGA 57.101 33.333 17.23 2.58 0.00 2.57
628 3409 7.228590 TGTAATGTAACCCTAAGAAACAGCTT 58.771 34.615 0.00 0.00 0.00 3.74
658 3439 5.044476 TCCAACAGCTCCCCTAAAATCAATA 60.044 40.000 0.00 0.00 0.00 1.90
660 3441 3.075283 TCCAACAGCTCCCCTAAAATCAA 59.925 43.478 0.00 0.00 0.00 2.57
661 3442 2.647299 TCCAACAGCTCCCCTAAAATCA 59.353 45.455 0.00 0.00 0.00 2.57
662 3443 3.282885 CTCCAACAGCTCCCCTAAAATC 58.717 50.000 0.00 0.00 0.00 2.17
663 3444 2.649816 ACTCCAACAGCTCCCCTAAAAT 59.350 45.455 0.00 0.00 0.00 1.82
701 3485 6.249035 TCGCCAATAAAAACCAACTAGAAG 57.751 37.500 0.00 0.00 0.00 2.85
704 3488 5.861787 CCTTTCGCCAATAAAAACCAACTAG 59.138 40.000 0.00 0.00 0.00 2.57
715 3499 1.953311 GCAGGTCCCTTTCGCCAATAA 60.953 52.381 0.00 0.00 0.00 1.40
736 3521 5.447818 GGAGACACAAATTAAAGCATCTCCG 60.448 44.000 0.00 0.00 41.08 4.63
737 3522 5.163612 GGGAGACACAAATTAAAGCATCTCC 60.164 44.000 8.19 8.19 46.85 3.71
746 3531 9.498176 GACTAAAAGTAGGGAGACACAAATTAA 57.502 33.333 0.00 0.00 0.00 1.40
761 3546 9.291664 CTCTTAAATCACTCGGACTAAAAGTAG 57.708 37.037 0.00 0.00 0.00 2.57
766 3551 7.223260 TCACTCTTAAATCACTCGGACTAAA 57.777 36.000 0.00 0.00 0.00 1.85
820 5584 9.081204 GGTCAAAAAGAATAAACTACCCCTAAA 57.919 33.333 0.00 0.00 0.00 1.85
884 5648 1.002430 TCGGGCATCAATAGCAGATCC 59.998 52.381 0.00 0.00 0.00 3.36
894 5658 0.250684 TGTTTGCTCTCGGGCATCAA 60.251 50.000 0.00 0.00 42.09 2.57
895 5659 0.035152 ATGTTTGCTCTCGGGCATCA 60.035 50.000 0.00 0.00 42.09 3.07
900 5664 2.285220 CACGATTATGTTTGCTCTCGGG 59.715 50.000 0.00 0.00 0.00 5.14
904 5668 3.055094 AGGGACACGATTATGTTTGCTCT 60.055 43.478 0.00 0.00 31.24 4.09
917 6366 3.138304 CAAAATGTTCTCAGGGACACGA 58.862 45.455 0.00 0.00 0.00 4.35
919 6368 4.137543 ACTCAAAATGTTCTCAGGGACAC 58.862 43.478 0.00 0.00 0.00 3.67
922 6371 9.581289 TTTATTAACTCAAAATGTTCTCAGGGA 57.419 29.630 0.00 0.00 0.00 4.20
934 6383 8.784994 TGCTGTACGGAATTTATTAACTCAAAA 58.215 29.630 5.68 0.00 0.00 2.44
938 6387 7.514747 CGTCTGCTGTACGGAATTTATTAACTC 60.515 40.741 5.68 0.00 34.69 3.01
940 6389 6.408428 CGTCTGCTGTACGGAATTTATTAAC 58.592 40.000 5.68 0.00 34.69 2.01
941 6390 6.578020 CGTCTGCTGTACGGAATTTATTAA 57.422 37.500 5.68 0.00 34.69 1.40
952 6401 1.060713 CTTTGTCCGTCTGCTGTACG 58.939 55.000 8.03 8.03 40.01 3.67
954 6403 0.320421 GGCTTTGTCCGTCTGCTGTA 60.320 55.000 0.00 0.00 0.00 2.74
956 6405 0.886490 AAGGCTTTGTCCGTCTGCTG 60.886 55.000 0.00 0.00 0.00 4.41
957 6406 0.179018 AAAGGCTTTGTCCGTCTGCT 60.179 50.000 12.53 0.00 0.00 4.24
958 6407 0.238553 GAAAGGCTTTGTCCGTCTGC 59.761 55.000 18.79 0.00 0.00 4.26
960 6409 1.947456 GTTGAAAGGCTTTGTCCGTCT 59.053 47.619 18.79 0.00 0.00 4.18
961 6410 1.673920 TGTTGAAAGGCTTTGTCCGTC 59.326 47.619 18.79 1.98 0.00 4.79
962 6411 1.404035 GTGTTGAAAGGCTTTGTCCGT 59.596 47.619 18.79 0.00 0.00 4.69
963 6412 1.676006 AGTGTTGAAAGGCTTTGTCCG 59.324 47.619 18.79 0.00 0.00 4.79
964 6413 2.223805 CCAGTGTTGAAAGGCTTTGTCC 60.224 50.000 18.79 3.57 0.00 4.02
965 6414 2.687935 TCCAGTGTTGAAAGGCTTTGTC 59.312 45.455 18.79 4.43 0.00 3.18
966 6415 2.689983 CTCCAGTGTTGAAAGGCTTTGT 59.310 45.455 18.79 0.00 0.00 2.83
969 6418 1.133668 AGCTCCAGTGTTGAAAGGCTT 60.134 47.619 0.00 0.00 0.00 4.35
970 6419 0.475906 AGCTCCAGTGTTGAAAGGCT 59.524 50.000 0.00 0.00 0.00 4.58
971 6420 1.000938 CAAGCTCCAGTGTTGAAAGGC 60.001 52.381 0.00 0.00 0.00 4.35
972 6421 1.610522 CCAAGCTCCAGTGTTGAAAGG 59.389 52.381 0.00 0.00 0.00 3.11
973 6422 1.000938 GCCAAGCTCCAGTGTTGAAAG 60.001 52.381 0.00 0.00 0.00 2.62
974 6423 1.032014 GCCAAGCTCCAGTGTTGAAA 58.968 50.000 0.00 0.00 0.00 2.69
981 6430 1.999648 TGAAATTGCCAAGCTCCAGT 58.000 45.000 0.00 0.00 0.00 4.00
983 6432 2.231964 GACATGAAATTGCCAAGCTCCA 59.768 45.455 0.00 0.00 0.00 3.86
1065 6514 1.766864 TTTGACGGTGAGGGGTGGA 60.767 57.895 0.00 0.00 0.00 4.02
1720 7345 1.231068 CCATGGCACCCCAAGCTAT 59.769 57.895 0.00 0.00 46.14 2.97
1734 7359 0.401738 AAGCATATCCCCCGACCATG 59.598 55.000 0.00 0.00 0.00 3.66
1857 7482 2.535485 TATCAAGTGCACCCAGCCGG 62.535 60.000 14.63 0.00 44.83 6.13
2091 7716 0.907486 CTGACTTCTCCATCTGGCCA 59.093 55.000 4.71 4.71 34.44 5.36
2294 7919 6.564709 TTGGCATATCATCAATAAGCTGAC 57.435 37.500 0.00 0.00 35.39 3.51
2410 8035 1.686325 TTCCGGGGCTCTAGCATGAC 61.686 60.000 0.00 0.00 44.36 3.06
2413 8038 0.398318 GAATTCCGGGGCTCTAGCAT 59.602 55.000 0.00 0.00 44.36 3.79
2521 8146 2.058675 CACGGACCTTCTCAACCCT 58.941 57.895 0.00 0.00 0.00 4.34
3102 9903 2.421529 GCCGGTCCCTTCACAAAGATAT 60.422 50.000 1.90 0.00 34.14 1.63
3245 10046 0.461961 GCGTTCAGATAGGGCACTCT 59.538 55.000 0.00 0.00 0.00 3.24
3323 10125 7.820872 AGAGGCACAATTTTTCAGAAATATTGG 59.179 33.333 28.39 21.62 33.03 3.16
3339 10141 3.144506 CTGACACAAAGAGAGGCACAAT 58.855 45.455 0.00 0.00 0.00 2.71
3358 10162 1.238439 AACGCTCAACCATCAACCTG 58.762 50.000 0.00 0.00 0.00 4.00
3457 10261 4.022416 GTCAACTCAATGGTGTATGGCAAA 60.022 41.667 0.00 0.00 34.34 3.68
3496 10300 1.470098 CCCAAACGCCAGAATCTGAAG 59.530 52.381 12.53 7.55 32.44 3.02
3571 10375 4.871513 TGAACTGTGATGAGTACTGTGTC 58.128 43.478 0.00 0.00 31.77 3.67
3758 11523 0.546122 TGCAAGACACCAGAACACCT 59.454 50.000 0.00 0.00 0.00 4.00
3785 11550 2.242196 ACATGGGAATGGAGACGGAAAT 59.758 45.455 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.