Multiple sequence alignment - TraesCS3D01G494700

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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 TraesCS3D01G494700 chr3D 100.000 3353 0 0 1 3353 587380900 587377548 0.000000e+00 6192
1 TraesCS3D01G494700 chr3D 85.604 2848 335 43 1 2823 603426795 603429592 0.000000e+00 2918
2 TraesCS3D01G494700 chr3D 76.302 768 146 31 1661 2409 585982693 585983443 8.780000e-101 377
3 TraesCS3D01G494700 chr3D 80.492 528 71 11 2854 3353 80910882 80911405 3.160000e-100 375
4 TraesCS3D01G494700 chr3D 77.745 337 50 10 2852 3166 358840323 358840656 2.050000e-42 183
5 TraesCS3D01G494700 chr3B 90.293 2905 235 30 2 2868 784433728 784430833 0.000000e+00 3759
6 TraesCS3D01G494700 chr3B 85.463 454 62 3 2900 3351 784430546 784430095 1.410000e-128 470
7 TraesCS3D01G494700 chr3B 80.000 525 74 16 2853 3353 269246431 269245914 3.180000e-95 359
8 TraesCS3D01G494700 chr3A 84.676 2793 341 46 55 2823 732641217 732638488 0.000000e+00 2706
9 TraesCS3D01G494700 chr2B 80.539 519 72 10 2852 3346 90381983 90382496 4.090000e-99 372
10 TraesCS3D01G494700 chr2B 79.190 543 83 10 2837 3353 229331201 229331739 1.910000e-92 350
11 TraesCS3D01G494700 chr2D 80.422 521 71 17 2854 3353 537719877 537720387 5.290000e-98 368
12 TraesCS3D01G494700 chr2D 79.661 531 69 23 2850 3353 365371940 365372458 2.480000e-91 346
13 TraesCS3D01G494700 chr7A 79.962 529 73 13 2853 3353 42033901 42033378 3.180000e-95 359
14 TraesCS3D01G494700 chr7A 77.148 512 76 13 2852 3324 729393301 729393810 3.320000e-65 259
15 TraesCS3D01G494700 chr7D 80.077 517 70 19 2850 3337 633691448 633691960 1.480000e-93 353
16 TraesCS3D01G494700 chr7D 77.947 526 87 14 2853 3353 600895645 600896166 5.440000e-78 302
17 TraesCS3D01G494700 chr1D 81.034 464 66 11 2911 3353 285434242 285433780 1.910000e-92 350
18 TraesCS3D01G494700 chr5D 79.304 517 77 22 2863 3353 531656714 531656202 5.360000e-88 335
19 TraesCS3D01G494700 chr5A 78.302 530 79 15 2851 3353 648358715 648359235 3.250000e-80 309
20 TraesCS3D01G494700 chr1B 77.083 336 51 12 2853 3166 176472465 176472796 1.600000e-38 171
21 TraesCS3D01G494700 chr4A 77.673 318 42 19 2853 3145 682002158 682001845 2.070000e-37 167


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 TraesCS3D01G494700 chr3D 587377548 587380900 3352 True 6192.0 6192 100.000 1 3353 1 chr3D.!!$R1 3352
1 TraesCS3D01G494700 chr3D 603426795 603429592 2797 False 2918.0 2918 85.604 1 2823 1 chr3D.!!$F4 2822
2 TraesCS3D01G494700 chr3D 585982693 585983443 750 False 377.0 377 76.302 1661 2409 1 chr3D.!!$F3 748
3 TraesCS3D01G494700 chr3D 80910882 80911405 523 False 375.0 375 80.492 2854 3353 1 chr3D.!!$F1 499
4 TraesCS3D01G494700 chr3B 784430095 784433728 3633 True 2114.5 3759 87.878 2 3351 2 chr3B.!!$R2 3349
5 TraesCS3D01G494700 chr3B 269245914 269246431 517 True 359.0 359 80.000 2853 3353 1 chr3B.!!$R1 500
6 TraesCS3D01G494700 chr3A 732638488 732641217 2729 True 2706.0 2706 84.676 55 2823 1 chr3A.!!$R1 2768
7 TraesCS3D01G494700 chr2B 90381983 90382496 513 False 372.0 372 80.539 2852 3346 1 chr2B.!!$F1 494
8 TraesCS3D01G494700 chr2B 229331201 229331739 538 False 350.0 350 79.190 2837 3353 1 chr2B.!!$F2 516
9 TraesCS3D01G494700 chr2D 537719877 537720387 510 False 368.0 368 80.422 2854 3353 1 chr2D.!!$F2 499
10 TraesCS3D01G494700 chr2D 365371940 365372458 518 False 346.0 346 79.661 2850 3353 1 chr2D.!!$F1 503
11 TraesCS3D01G494700 chr7A 42033378 42033901 523 True 359.0 359 79.962 2853 3353 1 chr7A.!!$R1 500
12 TraesCS3D01G494700 chr7A 729393301 729393810 509 False 259.0 259 77.148 2852 3324 1 chr7A.!!$F1 472
13 TraesCS3D01G494700 chr7D 633691448 633691960 512 False 353.0 353 80.077 2850 3337 1 chr7D.!!$F2 487
14 TraesCS3D01G494700 chr7D 600895645 600896166 521 False 302.0 302 77.947 2853 3353 1 chr7D.!!$F1 500
15 TraesCS3D01G494700 chr5D 531656202 531656714 512 True 335.0 335 79.304 2863 3353 1 chr5D.!!$R1 490
16 TraesCS3D01G494700 chr5A 648358715 648359235 520 False 309.0 309 78.302 2851 3353 1 chr5A.!!$F1 502

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
801 843 0.958822 GGGTTGCCCTAAGTTGTGTG 59.041 55.0 0.0 0.0 41.34 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2468 2527 0.040058 TGCTCATTGCCTTGATGGGT 59.96 50.0 0.0 0.0 42.0 4.51 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
57 60 2.224744 TGCCAAGTTGCTCTACATTGGA 60.225 45.455 6.45 0.00 42.46 3.53
110 113 8.956533 TTGTATACACTATGTGCATGTGTAAT 57.043 30.769 20.34 14.35 46.01 1.89
159 162 1.691434 GGGCCAAACTTTCCATGTTGA 59.309 47.619 4.39 0.00 0.00 3.18
165 168 5.447144 GCCAAACTTTCCATGTTGACAAAAC 60.447 40.000 0.00 0.00 0.00 2.43
181 184 3.393278 ACAAAACACCTAGCCCAGAGTTA 59.607 43.478 0.00 0.00 0.00 2.24
182 185 3.697619 AAACACCTAGCCCAGAGTTAC 57.302 47.619 0.00 0.00 0.00 2.50
183 186 2.320681 ACACCTAGCCCAGAGTTACA 57.679 50.000 0.00 0.00 0.00 2.41
184 187 2.616524 ACACCTAGCCCAGAGTTACAA 58.383 47.619 0.00 0.00 0.00 2.41
382 399 7.523219 TGTGGAACATCATACGAAATAAACAC 58.477 34.615 0.00 0.00 45.67 3.32
383 400 7.389330 TGTGGAACATCATACGAAATAAACACT 59.611 33.333 0.00 0.00 45.67 3.55
384 401 7.903431 GTGGAACATCATACGAAATAAACACTC 59.097 37.037 0.00 0.00 44.52 3.51
415 432 4.581824 GTCACCATATGCATCACTCCAAAT 59.418 41.667 0.19 0.00 0.00 2.32
422 439 2.170166 GCATCACTCCAAATCCAACCA 58.830 47.619 0.00 0.00 0.00 3.67
450 469 5.304614 CGAGGGAGGGAATTTCATCTACTTA 59.695 44.000 0.00 0.00 0.00 2.24
465 484 8.472007 TCATCTACTTATTCCTCTCTCTTTCC 57.528 38.462 0.00 0.00 0.00 3.13
468 487 7.064229 TCTACTTATTCCTCTCTCTTTCCCTC 58.936 42.308 0.00 0.00 0.00 4.30
469 488 5.849140 ACTTATTCCTCTCTCTTTCCCTCT 58.151 41.667 0.00 0.00 0.00 3.69
470 489 5.897250 ACTTATTCCTCTCTCTTTCCCTCTC 59.103 44.000 0.00 0.00 0.00 3.20
471 490 4.625225 ATTCCTCTCTCTTTCCCTCTCT 57.375 45.455 0.00 0.00 0.00 3.10
472 491 4.412060 TTCCTCTCTCTTTCCCTCTCTT 57.588 45.455 0.00 0.00 0.00 2.85
473 492 4.412060 TCCTCTCTCTTTCCCTCTCTTT 57.588 45.455 0.00 0.00 0.00 2.52
474 493 4.757692 TCCTCTCTCTTTCCCTCTCTTTT 58.242 43.478 0.00 0.00 0.00 2.27
475 494 4.530161 TCCTCTCTCTTTCCCTCTCTTTTG 59.470 45.833 0.00 0.00 0.00 2.44
476 495 4.285775 CCTCTCTCTTTCCCTCTCTTTTGT 59.714 45.833 0.00 0.00 0.00 2.83
477 496 5.220710 TCTCTCTTTCCCTCTCTTTTGTG 57.779 43.478 0.00 0.00 0.00 3.33
483 502 2.274542 TCCCTCTCTTTTGTGCCCATA 58.725 47.619 0.00 0.00 0.00 2.74
485 504 2.290896 CCCTCTCTTTTGTGCCCATACA 60.291 50.000 0.00 0.00 0.00 2.29
489 508 5.652014 CCTCTCTTTTGTGCCCATACAAATA 59.348 40.000 5.08 0.00 46.43 1.40
491 530 6.245408 TCTCTTTTGTGCCCATACAAATAGT 58.755 36.000 5.08 0.00 46.43 2.12
499 538 5.049405 GTGCCCATACAAATAGTACATCAGC 60.049 44.000 0.00 0.00 35.05 4.26
500 539 5.063204 GCCCATACAAATAGTACATCAGCA 58.937 41.667 0.00 0.00 35.05 4.41
517 556 1.006998 AGCATGCCCCATTAGGAAACA 59.993 47.619 15.66 0.00 38.24 2.83
658 699 6.967199 ACTTGTCGACAAAATCAAGAAAGAAC 59.033 34.615 29.32 0.00 39.39 3.01
674 715 7.980742 AGAAAGAACAAAAACAATTACGGAC 57.019 32.000 0.00 0.00 0.00 4.79
675 716 6.976349 AGAAAGAACAAAAACAATTACGGACC 59.024 34.615 0.00 0.00 0.00 4.46
679 720 5.523438 ACAAAAACAATTACGGACCACAT 57.477 34.783 0.00 0.00 0.00 3.21
781 823 7.556275 GGGACCACAAATATGTTGAATCTTCTA 59.444 37.037 0.00 0.00 37.82 2.10
783 825 8.511604 ACCACAAATATGTTGAATCTTCTAGG 57.488 34.615 0.00 0.00 37.82 3.02
789 831 3.686016 TGTTGAATCTTCTAGGGTTGCC 58.314 45.455 0.00 0.00 0.00 4.52
801 843 0.958822 GGGTTGCCCTAAGTTGTGTG 59.041 55.000 0.00 0.00 41.34 3.82
1055 1099 3.064931 GGGTACGAGCTACCATAAATGC 58.935 50.000 6.49 0.00 46.53 3.56
1079 1123 2.586425 TGAGCCAAAGGTGAAGAAAGG 58.414 47.619 0.00 0.00 0.00 3.11
1129 1173 9.391006 GTGTACTAATTGATAATGGACCAAAGA 57.609 33.333 0.00 0.00 0.00 2.52
1134 1178 9.177608 CTAATTGATAATGGACCAAAGAGTCAA 57.822 33.333 0.00 5.99 38.59 3.18
1142 1186 3.500299 GGACCAAAGAGTCAAGAAGAAGC 59.500 47.826 0.00 0.00 38.59 3.86
1152 1196 1.728971 CAAGAAGAAGCTGTAGGTGCG 59.271 52.381 0.00 0.00 35.28 5.34
1182 1226 0.324943 TAGCTCCAAACTCCACTGGC 59.675 55.000 0.00 0.00 32.33 4.85
1187 1231 1.066430 TCCAAACTCCACTGGCGATAC 60.066 52.381 0.00 0.00 32.33 2.24
1320 1364 9.902196 ATATACTTTGTTTTTACCTTTGAACGG 57.098 29.630 0.00 0.00 0.00 4.44
1340 1384 3.004419 CGGACTTGGATAACAGCGAGATA 59.996 47.826 0.00 0.00 0.00 1.98
1344 1388 3.650070 TGGATAACAGCGAGATAGCAG 57.350 47.619 0.00 0.00 40.15 4.24
1363 1407 2.169352 CAGACTACACAAGCCCTGCTAT 59.831 50.000 0.00 0.00 38.25 2.97
1369 1413 2.174210 ACACAAGCCCTGCTATGATCAT 59.826 45.455 13.81 13.81 38.25 2.45
1483 1527 9.559958 GTGATAGACATTTACATTTTCAAGGTG 57.440 33.333 0.00 0.00 0.00 4.00
1486 1530 6.449698 AGACATTTACATTTTCAAGGTGCTG 58.550 36.000 0.00 0.00 0.00 4.41
1487 1531 6.265196 AGACATTTACATTTTCAAGGTGCTGA 59.735 34.615 0.00 0.00 0.00 4.26
1504 1548 5.335897 GGTGCTGACTTGCTCAATGAAATTA 60.336 40.000 0.00 0.00 32.46 1.40
1508 1552 7.031372 GCTGACTTGCTCAATGAAATTATTGA 58.969 34.615 4.08 4.08 42.93 2.57
1545 1592 6.849085 AACAGGTGGTGCATATGAAAATTA 57.151 33.333 6.97 0.00 0.00 1.40
1632 1679 6.420604 GTGTAATTCTGGAACACCAACATTTG 59.579 38.462 0.00 0.00 38.02 2.32
1667 1714 5.128827 AGTCATTCGACACCCACATACTATT 59.871 40.000 0.00 0.00 45.23 1.73
1668 1715 5.815740 GTCATTCGACACCCACATACTATTT 59.184 40.000 0.00 0.00 42.13 1.40
1713 1760 9.603921 AAATTATCAAGAACATGGCCTAAAATG 57.396 29.630 3.32 0.97 0.00 2.32
1714 1761 5.603170 ATCAAGAACATGGCCTAAAATGG 57.397 39.130 3.32 0.00 0.00 3.16
1721 1768 5.514274 ACATGGCCTAAAATGGAATTACG 57.486 39.130 3.32 0.00 33.67 3.18
1723 1770 5.833131 ACATGGCCTAAAATGGAATTACGAT 59.167 36.000 3.32 0.00 33.67 3.73
1913 1971 5.467735 TGCATGCACACTAGATATTAGCAAG 59.532 40.000 18.46 0.00 33.91 4.01
1949 2007 5.794687 TTTTATGTCCTTGTATGTGCTCG 57.205 39.130 0.00 0.00 0.00 5.03
2155 2214 2.094078 CCACAAATTGGTAGTGGGCATG 60.094 50.000 10.26 0.00 46.98 4.06
2157 2216 2.562298 ACAAATTGGTAGTGGGCATGTG 59.438 45.455 0.00 0.00 0.00 3.21
2193 2252 4.789012 TGGAAAAGCAGCTTTTATGAGG 57.211 40.909 29.18 0.00 42.72 3.86
2199 2258 3.973425 AGCAGCTTTTATGAGGGACATT 58.027 40.909 0.00 0.00 40.07 2.71
2260 2319 4.170468 AGACACAAAGACCTTGTTGGAT 57.830 40.909 0.00 0.00 46.49 3.41
2273 2332 8.383175 AGACCTTGTTGGATCTAGTGATAAAAA 58.617 33.333 0.00 0.00 39.71 1.94
2325 2384 9.177608 GTTGATAACCATGGTATGCATATGTAT 57.822 33.333 20.12 8.75 0.00 2.29
2425 2484 8.177119 TGGACATTTACATAATTATTGGGAGC 57.823 34.615 0.00 0.00 0.00 4.70
2438 2497 0.752658 TGGGAGCTGTCATACATCCG 59.247 55.000 0.00 0.00 29.98 4.18
2451 2510 6.046593 GTCATACATCCGAGTGTTTATTCCA 58.953 40.000 0.00 0.00 33.62 3.53
2464 2523 9.141400 GAGTGTTTATTCCAGTGAGTAGTTTAG 57.859 37.037 0.00 0.00 0.00 1.85
2468 2527 8.780249 GTTTATTCCAGTGAGTAGTTTAGCAAA 58.220 33.333 0.00 0.00 0.00 3.68
2527 2588 7.831691 TGAATAGAAATTTTGAGGGACACAA 57.168 32.000 0.00 0.00 37.09 3.33
2530 2591 4.886579 AGAAATTTTGAGGGACACAATGC 58.113 39.130 0.00 0.00 38.93 3.56
2538 2599 5.327616 TGAGGGACACAATGCAATATTTG 57.672 39.130 0.00 0.00 0.00 2.32
2565 2632 6.602410 TGGATAATTGCTTGGATTTGTTCA 57.398 33.333 0.00 0.00 0.00 3.18
2588 2655 6.855914 TCACGCAAAACAAATTCTCATACTTC 59.144 34.615 0.00 0.00 0.00 3.01
2590 2657 6.148948 CGCAAAACAAATTCTCATACTTCCA 58.851 36.000 0.00 0.00 0.00 3.53
2621 2688 7.108841 TGATATGTTCCTAGTGGTACAGTTC 57.891 40.000 0.00 0.00 44.77 3.01
2654 2722 3.692257 AGTCCTCACATGAGAAACAGG 57.308 47.619 10.55 0.00 44.74 4.00
2733 2802 7.887381 TGACCTTGTAAACTTTGTTCTTCAAA 58.113 30.769 0.00 0.00 42.79 2.69
2737 2806 9.203421 CCTTGTAAACTTTGTTCTTCAAAAGTT 57.797 29.630 7.52 7.52 44.08 2.66
2829 2898 9.101655 GTTCAAATTCAAAATATCCTCCCAATG 57.898 33.333 0.00 0.00 0.00 2.82
2830 2899 8.606754 TCAAATTCAAAATATCCTCCCAATGA 57.393 30.769 0.00 0.00 0.00 2.57
2833 2902 4.473444 TCAAAATATCCTCCCAATGAGCC 58.527 43.478 0.00 0.00 39.98 4.70
2883 2952 0.179156 GTCCGTGCATTGCAATGAGG 60.179 55.000 37.36 32.09 41.47 3.86
2885 2954 1.140161 CGTGCATTGCAATGAGGGG 59.860 57.895 37.36 20.70 41.47 4.79
2886 2955 1.314534 CGTGCATTGCAATGAGGGGA 61.315 55.000 37.36 13.61 41.47 4.81
2978 3308 2.037251 GACAGAGCAAGGAGTTGTGGTA 59.963 50.000 0.00 0.00 35.92 3.25
3040 3390 1.745489 GGATCACCCAACTCGTGCC 60.745 63.158 0.00 0.00 34.14 5.01
3041 3391 1.296715 GATCACCCAACTCGTGCCT 59.703 57.895 0.00 0.00 0.00 4.75
3075 3426 4.458829 ACCGCCTCCATCTCGGGA 62.459 66.667 4.89 0.00 46.78 5.14
3138 3489 3.049674 CACGGTTGCTGCGACCAT 61.050 61.111 32.46 20.01 37.77 3.55
3174 3529 3.572584 GCGTAACCGGATGGATTACTAG 58.427 50.000 9.46 0.00 39.21 2.57
3302 3675 5.545658 TTTCTAATTAGAGCCAAACTGCG 57.454 39.130 14.63 0.00 36.02 5.18
3308 3682 2.191128 AGAGCCAAACTGCGATTCTT 57.809 45.000 0.00 0.00 36.02 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 60 7.480760 ACAACAACCTATAATGCTGGAATTT 57.519 32.000 0.00 0.00 0.00 1.82
123 126 6.890268 AGTTTGGCCCTTATAACTTCCTAAAG 59.110 38.462 0.00 0.00 38.54 1.85
159 162 1.774856 ACTCTGGGCTAGGTGTTTTGT 59.225 47.619 0.00 0.00 0.00 2.83
165 168 3.914426 ATTGTAACTCTGGGCTAGGTG 57.086 47.619 0.00 0.00 0.00 4.00
181 184 1.805120 CGACGGAGCCGGAATTATTGT 60.805 52.381 5.05 0.00 44.69 2.71
182 185 0.859232 CGACGGAGCCGGAATTATTG 59.141 55.000 5.05 0.00 44.69 1.90
183 186 0.878961 GCGACGGAGCCGGAATTATT 60.879 55.000 5.05 0.00 44.69 1.40
184 187 1.300697 GCGACGGAGCCGGAATTAT 60.301 57.895 5.05 0.00 44.69 1.28
206 210 3.379688 TGTTTGTGTGTATGTGTGCATGT 59.620 39.130 0.00 0.00 36.58 3.21
217 221 8.749026 TTTTAGGACCTTTATGTTTGTGTGTA 57.251 30.769 0.00 0.00 0.00 2.90
253 269 7.704578 TGCTGAATTCAGTACTAACTACTCT 57.295 36.000 30.88 0.00 45.45 3.24
368 385 6.430000 ACTTTGCTGGAGTGTTTATTTCGTAT 59.570 34.615 0.00 0.00 0.00 3.06
372 389 5.915196 GTGACTTTGCTGGAGTGTTTATTTC 59.085 40.000 0.00 0.00 0.00 2.17
379 396 0.546122 TGGTGACTTTGCTGGAGTGT 59.454 50.000 0.00 0.00 0.00 3.55
380 397 1.901591 ATGGTGACTTTGCTGGAGTG 58.098 50.000 0.00 0.00 0.00 3.51
382 399 2.357009 GCATATGGTGACTTTGCTGGAG 59.643 50.000 4.56 0.00 0.00 3.86
383 400 2.290832 TGCATATGGTGACTTTGCTGGA 60.291 45.455 4.56 0.00 34.47 3.86
384 401 2.093890 TGCATATGGTGACTTTGCTGG 58.906 47.619 4.56 0.00 34.47 4.85
415 432 1.299648 CTCCCTCGCAATGGTTGGA 59.700 57.895 0.00 0.00 0.00 3.53
422 439 1.284785 TGAAATTCCCTCCCTCGCAAT 59.715 47.619 0.00 0.00 0.00 3.56
450 469 4.625225 AGAGAGGGAAAGAGAGAGGAAT 57.375 45.455 0.00 0.00 0.00 3.01
463 482 1.075601 ATGGGCACAAAAGAGAGGGA 58.924 50.000 0.00 0.00 0.00 4.20
465 484 3.071874 TGTATGGGCACAAAAGAGAGG 57.928 47.619 0.00 0.00 0.00 3.69
473 492 6.418946 TGATGTACTATTTGTATGGGCACAA 58.581 36.000 0.00 0.00 36.65 3.33
474 493 5.995446 TGATGTACTATTTGTATGGGCACA 58.005 37.500 0.00 0.00 33.23 4.57
475 494 5.049405 GCTGATGTACTATTTGTATGGGCAC 60.049 44.000 0.00 0.00 33.23 5.01
476 495 5.063204 GCTGATGTACTATTTGTATGGGCA 58.937 41.667 0.00 0.00 33.23 5.36
477 496 5.063204 TGCTGATGTACTATTTGTATGGGC 58.937 41.667 0.00 0.00 33.23 5.36
483 502 3.885297 GGGCATGCTGATGTACTATTTGT 59.115 43.478 18.92 0.00 31.50 2.83
485 504 3.117550 TGGGGCATGCTGATGTACTATTT 60.118 43.478 18.92 0.00 31.50 1.40
489 508 0.848735 ATGGGGCATGCTGATGTACT 59.151 50.000 18.92 0.00 31.50 2.73
491 530 2.224843 CCTAATGGGGCATGCTGATGTA 60.225 50.000 18.92 4.37 31.50 2.29
499 538 2.224113 GCATGTTTCCTAATGGGGCATG 60.224 50.000 9.78 9.78 39.99 4.06
500 539 2.041701 GCATGTTTCCTAATGGGGCAT 58.958 47.619 0.00 0.00 35.33 4.40
658 699 8.527567 AAATATGTGGTCCGTAATTGTTTTTG 57.472 30.769 0.00 0.00 0.00 2.44
670 711 1.202245 CCGCCAAAAATATGTGGTCCG 60.202 52.381 3.11 0.11 37.23 4.79
674 715 1.204467 ACAGCCGCCAAAAATATGTGG 59.796 47.619 0.00 0.00 38.00 4.17
675 716 2.261345 CACAGCCGCCAAAAATATGTG 58.739 47.619 0.00 0.00 0.00 3.21
679 720 1.323412 ACACACAGCCGCCAAAAATA 58.677 45.000 0.00 0.00 0.00 1.40
761 803 8.960591 CAACCCTAGAAGATTCAACATATTTGT 58.039 33.333 0.00 0.00 37.82 2.83
789 831 7.026631 TGAAAGAACATTCACACAACTTAGG 57.973 36.000 0.00 0.00 34.50 2.69
869 911 5.768662 AGAGAGACCAATGCATATCAAATGG 59.231 40.000 10.64 10.64 39.96 3.16
871 913 8.216423 AGTTAGAGAGACCAATGCATATCAAAT 58.784 33.333 0.00 0.00 0.00 2.32
1055 1099 2.972625 TCTTCACCTTTGGCTCATACG 58.027 47.619 0.00 0.00 0.00 3.06
1079 1123 7.386299 CACCTGATTGACTAATATCCTTGCTAC 59.614 40.741 0.00 0.00 0.00 3.58
1129 1173 3.556004 GCACCTACAGCTTCTTCTTGACT 60.556 47.826 0.00 0.00 0.00 3.41
1134 1178 0.969894 ACGCACCTACAGCTTCTTCT 59.030 50.000 0.00 0.00 0.00 2.85
1142 1186 1.924524 CCGAATAACACGCACCTACAG 59.075 52.381 0.00 0.00 0.00 2.74
1152 1196 4.251268 AGTTTGGAGCTACCGAATAACAC 58.749 43.478 0.00 0.00 43.17 3.32
1307 1351 3.842007 TCCAAGTCCGTTCAAAGGTAA 57.158 42.857 0.00 0.00 0.00 2.85
1320 1364 3.984633 GCTATCTCGCTGTTATCCAAGTC 59.015 47.826 0.00 0.00 0.00 3.01
1340 1384 0.322975 CAGGGCTTGTGTAGTCTGCT 59.677 55.000 0.00 0.00 0.00 4.24
1344 1388 2.168521 TCATAGCAGGGCTTGTGTAGTC 59.831 50.000 0.00 0.00 40.44 2.59
1363 1407 5.415389 CACAAAACCAGGACATACATGATCA 59.585 40.000 0.00 0.00 31.40 2.92
1369 1413 2.937519 TGCACAAAACCAGGACATACA 58.062 42.857 0.00 0.00 0.00 2.29
1430 1474 3.070446 TGTGGTCCGTTGTAGACTGAAAT 59.930 43.478 0.00 0.00 34.56 2.17
1483 1527 7.031372 TCAATAATTTCATTGAGCAAGTCAGC 58.969 34.615 0.38 0.00 39.43 4.26
1508 1552 7.613801 TGCACCACCTGTTTATATGTAGAAAAT 59.386 33.333 0.00 0.00 0.00 1.82
1632 1679 7.118680 TGGGTGTCGAATGACTAGAAATAAAAC 59.881 37.037 0.00 0.00 45.70 2.43
1746 1795 7.936496 TGATTGGAAGTGTTTGCTGAATATA 57.064 32.000 0.00 0.00 0.00 0.86
1855 1910 9.809096 CTGTTCCGCTGAAGATATATATTATGT 57.191 33.333 0.00 0.00 0.00 2.29
1874 1930 2.409378 GCATGCAATTGTTTCTGTTCCG 59.591 45.455 14.21 0.00 0.00 4.30
2084 2143 0.611896 AAAACCGCCCCAGAATGAGG 60.612 55.000 0.00 0.00 39.69 3.86
2155 2214 0.181350 CCATACCCTTCAGAGGCCAC 59.819 60.000 5.01 0.00 42.09 5.01
2157 2216 1.213296 TTCCATACCCTTCAGAGGCC 58.787 55.000 0.00 0.00 42.09 5.19
2193 2252 5.437289 TGTTGTCAACAATCTGAATGTCC 57.563 39.130 16.05 0.00 38.72 4.02
2325 2384 4.044825 ACCAAATTACCTGGTCCACCATAA 59.955 41.667 0.63 0.00 44.05 1.90
2385 2444 8.673711 TGTAAATGTCCAACTCAATAAGTATGC 58.326 33.333 0.00 0.00 37.17 3.14
2425 2484 6.201044 GGAATAAACACTCGGATGTATGACAG 59.799 42.308 0.00 0.00 30.75 3.51
2438 2497 7.964604 AAACTACTCACTGGAATAAACACTC 57.035 36.000 0.00 0.00 0.00 3.51
2451 2510 4.699925 TGGGTTTGCTAAACTACTCACT 57.300 40.909 10.28 0.00 41.14 3.41
2464 2523 1.275856 TCATTGCCTTGATGGGTTTGC 59.724 47.619 0.00 0.00 36.00 3.68
2468 2527 0.040058 TGCTCATTGCCTTGATGGGT 59.960 50.000 0.00 0.00 42.00 4.51
2527 2588 8.372459 AGCAATTATCCATGACAAATATTGCAT 58.628 29.630 21.10 11.03 41.91 3.96
2530 2591 8.984764 CCAAGCAATTATCCATGACAAATATTG 58.015 33.333 0.00 0.00 0.00 1.90
2538 2599 6.576185 ACAAATCCAAGCAATTATCCATGAC 58.424 36.000 0.00 0.00 0.00 3.06
2565 2632 6.149633 GGAAGTATGAGAATTTGTTTTGCGT 58.850 36.000 0.00 0.00 0.00 5.24
2588 2655 7.939039 ACCACTAGGAACATATCAATACATTGG 59.061 37.037 2.26 0.00 37.05 3.16
2590 2657 9.998106 GTACCACTAGGAACATATCAATACATT 57.002 33.333 0.00 0.00 38.69 2.71
2601 2668 3.194968 CCGAACTGTACCACTAGGAACAT 59.805 47.826 0.00 0.00 38.69 2.71
2606 2673 0.175073 GCCCGAACTGTACCACTAGG 59.825 60.000 0.00 0.00 42.21 3.02
2621 2688 2.435410 GGACTTTGTACCCGCCCG 60.435 66.667 0.00 0.00 0.00 6.13
2702 2771 6.220726 ACAAAGTTTACAAGGTCAATGCTT 57.779 33.333 0.00 0.00 0.00 3.91
2784 2853 4.979197 TGAACCGTTTCATTTTGGAATTCG 59.021 37.500 0.00 0.00 36.79 3.34
2790 2859 6.595772 TGAATTTGAACCGTTTCATTTTGG 57.404 33.333 0.00 0.00 41.50 3.28
2791 2860 8.886816 TTTTGAATTTGAACCGTTTCATTTTG 57.113 26.923 0.00 0.00 41.50 2.44
2818 2887 2.358615 GGAAAAGGCTCATTGGGAGGAT 60.359 50.000 0.00 0.00 44.22 3.24
2829 2898 7.265673 AGTAAAGAAAAACAAGGAAAAGGCTC 58.734 34.615 0.00 0.00 0.00 4.70
2830 2899 7.182817 AGTAAAGAAAAACAAGGAAAAGGCT 57.817 32.000 0.00 0.00 0.00 4.58
2833 2902 9.020813 GTGCTAGTAAAGAAAAACAAGGAAAAG 57.979 33.333 0.00 0.00 0.00 2.27
2978 3308 2.821969 GCCAAACATGTCCTGTGAGAAT 59.178 45.455 0.00 0.00 38.39 2.40
3058 3409 3.758133 ATCCCGAGATGGAGGCGGT 62.758 63.158 0.00 0.00 43.35 5.68
3075 3426 0.333993 AATGAGGAGGCAGCCACAAT 59.666 50.000 15.80 0.00 32.29 2.71
3119 3470 4.012895 GGTCGCAGCAACCGTGTG 62.013 66.667 0.00 0.00 0.00 3.82
3174 3529 3.855689 ACAGGATTTATGCACTGCAAC 57.144 42.857 8.03 0.00 43.62 4.17


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

AutoCloner maintained by Alex Coulton.