Multiple sequence alignment - TraesCS1D01G130200

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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 TraesCS1D01G130200 chr1D 100.000 3504 0 0 1 3504 143360857 143364360 0.000000e+00 6471.0
1 TraesCS1D01G130200 chr1D 84.000 75 9 3 1516 1588 413213142 413213215 6.280000e-08 69.4
2 TraesCS1D01G130200 chr1B 96.892 2381 59 11 1 2375 192533260 192535631 0.000000e+00 3973.0
3 TraesCS1D01G130200 chr1B 88.462 52 5 1 1525 1575 556989744 556989795 1.050000e-05 62.1
4 TraesCS1D01G130200 chr1A 97.067 2046 41 10 357 2394 146632239 146630205 0.000000e+00 3428.0
5 TraesCS1D01G130200 chr1A 91.209 364 17 4 1 362 146632972 146632622 6.800000e-132 481.0
6 TraesCS1D01G130200 chr1A 84.507 71 8 3 1516 1584 510281353 510281422 2.260000e-07 67.6
7 TraesCS1D01G130200 chr5D 96.807 971 15 10 2541 3501 524934944 524933980 0.000000e+00 1607.0
8 TraesCS1D01G130200 chr7D 94.250 1026 37 9 2484 3504 435413645 435414653 0.000000e+00 1548.0
9 TraesCS1D01G130200 chr7D 88.525 61 7 0 1516 1576 426644610 426644670 1.350000e-09 75.0
10 TraesCS1D01G130200 chr7B 92.288 778 49 9 2722 3491 7443814 7443040 0.000000e+00 1094.0
11 TraesCS1D01G130200 chr7B 93.897 213 10 2 2495 2706 7444008 7443798 5.640000e-83 318.0
12 TraesCS1D01G130200 chr7B 92.523 214 12 3 2495 2706 463534543 463534754 1.580000e-78 303.0
13 TraesCS1D01G130200 chr5B 91.871 775 55 5 2722 3491 540353656 540352885 0.000000e+00 1075.0
14 TraesCS1D01G130200 chr5B 92.166 217 9 7 2495 2706 540353853 540353640 2.040000e-77 300.0
15 TraesCS1D01G130200 chr7A 91.131 778 50 13 2717 3485 78436055 78436822 0.000000e+00 1037.0
16 TraesCS1D01G130200 chr3D 91.062 772 59 9 2722 3485 582522555 582523324 0.000000e+00 1035.0
17 TraesCS1D01G130200 chr3D 92.523 214 12 3 2495 2706 582522360 582522571 1.580000e-78 303.0
18 TraesCS1D01G130200 chr2A 90.641 780 53 15 2722 3491 38514911 38514142 0.000000e+00 1018.0
19 TraesCS1D01G130200 chr2A 79.281 584 114 5 1691 2269 768997959 768998540 5.450000e-108 401.0
20 TraesCS1D01G130200 chr4D 92.319 664 42 8 2830 3485 108907735 108908397 0.000000e+00 935.0
21 TraesCS1D01G130200 chr4D 93.711 159 8 2 2506 2662 108907573 108907731 1.630000e-58 237.0
22 TraesCS1D01G130200 chr4B 91.754 570 38 6 2929 3491 605928637 605928070 0.000000e+00 784.0
23 TraesCS1D01G130200 chr4B 92.784 194 10 3 2495 2686 605929115 605928924 9.580000e-71 278.0
24 TraesCS1D01G130200 chr6B 91.026 156 12 2 2510 2664 644835994 644835840 3.540000e-50 209.0
25 TraesCS1D01G130200 chr6D 94.828 58 3 0 2495 2552 9877201 9877144 1.340000e-14 91.6
26 TraesCS1D01G130200 chr6D 100.000 30 0 0 1531 1560 25827138 25827109 4.890000e-04 56.5


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 TraesCS1D01G130200 chr1D 143360857 143364360 3503 False 6471.0 6471 100.0000 1 3504 1 chr1D.!!$F1 3503
1 TraesCS1D01G130200 chr1B 192533260 192535631 2371 False 3973.0 3973 96.8920 1 2375 1 chr1B.!!$F1 2374
2 TraesCS1D01G130200 chr1A 146630205 146632972 2767 True 1954.5 3428 94.1380 1 2394 2 chr1A.!!$R1 2393
3 TraesCS1D01G130200 chr5D 524933980 524934944 964 True 1607.0 1607 96.8070 2541 3501 1 chr5D.!!$R1 960
4 TraesCS1D01G130200 chr7D 435413645 435414653 1008 False 1548.0 1548 94.2500 2484 3504 1 chr7D.!!$F2 1020
5 TraesCS1D01G130200 chr7B 7443040 7444008 968 True 706.0 1094 93.0925 2495 3491 2 chr7B.!!$R1 996
6 TraesCS1D01G130200 chr5B 540352885 540353853 968 True 687.5 1075 92.0185 2495 3491 2 chr5B.!!$R1 996
7 TraesCS1D01G130200 chr7A 78436055 78436822 767 False 1037.0 1037 91.1310 2717 3485 1 chr7A.!!$F1 768
8 TraesCS1D01G130200 chr3D 582522360 582523324 964 False 669.0 1035 91.7925 2495 3485 2 chr3D.!!$F1 990
9 TraesCS1D01G130200 chr2A 38514142 38514911 769 True 1018.0 1018 90.6410 2722 3491 1 chr2A.!!$R1 769
10 TraesCS1D01G130200 chr2A 768997959 768998540 581 False 401.0 401 79.2810 1691 2269 1 chr2A.!!$F1 578
11 TraesCS1D01G130200 chr4D 108907573 108908397 824 False 586.0 935 93.0150 2506 3485 2 chr4D.!!$F1 979
12 TraesCS1D01G130200 chr4B 605928070 605929115 1045 True 531.0 784 92.2690 2495 3491 2 chr4B.!!$R1 996

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
719 1115 1.675641 GACCACCAGCACCACCATC 60.676 63.158 0.0 0.0 0.0 3.51 F
2402 2807 0.466739 GGGGTTTGTTCACTCGGGTT 60.467 55.000 0.0 0.0 0.0 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2417 2822 0.387367 CGTAATCTCTCGATGGCCCG 60.387 60.000 0.00 0.00 0.0 6.13 R
3396 3903 1.070134 ACTTGCAACTCGAGGCTTGTA 59.930 47.619 18.41 9.81 0.0 2.41 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
31 32 8.159344 AGAAAGAAAAGAGAGGTTGTATGTTG 57.841 34.615 0.00 0.00 0.00 3.33
53 54 4.202101 TGGACAACCAGCAATAACAACAAG 60.202 41.667 0.00 0.00 41.77 3.16
56 57 5.827666 ACAACCAGCAATAACAACAAGTAC 58.172 37.500 0.00 0.00 0.00 2.73
89 90 3.935315 TCTTGCTCCTTCTCTCATTGTG 58.065 45.455 0.00 0.00 0.00 3.33
108 109 7.888021 TCATTGTGGGTGTTGTCTTAATAGAAT 59.112 33.333 0.00 0.00 30.65 2.40
334 340 8.437742 GTCATTCAAGGTTCAATAAAAATGCAG 58.562 33.333 0.00 0.00 0.00 4.41
345 351 3.375782 AAAAATGCAGAGTTGGAGCAC 57.624 42.857 0.00 0.00 41.60 4.40
402 797 2.717639 AGGGATGATACAACAGTGCC 57.282 50.000 0.00 0.00 0.00 5.01
411 806 2.071778 ACAACAGTGCCACTTTGGAT 57.928 45.000 17.81 2.74 40.96 3.41
521 917 9.574516 ACTTGGATTACAAAAGAACTAGAATGT 57.425 29.630 0.00 0.00 38.91 2.71
631 1027 3.506067 CCTTTTTGAGGGTCTTACGCATT 59.494 43.478 0.00 0.00 42.26 3.56
719 1115 1.675641 GACCACCAGCACCACCATC 60.676 63.158 0.00 0.00 0.00 3.51
1119 1521 2.671963 GTCCCCCGCCTTGTCAAC 60.672 66.667 0.00 0.00 0.00 3.18
1210 1612 4.641645 CACGCCAACTCCTGCCCA 62.642 66.667 0.00 0.00 0.00 5.36
1303 1705 2.623889 CCTCCGTATCTTCTTCCACGAT 59.376 50.000 0.00 0.00 36.53 3.73
1608 2010 2.126463 CACGTCGGTCGATGCTGT 60.126 61.111 11.89 0.00 42.86 4.40
2383 2788 1.577134 CACGTTTGAAACAGTTGCACG 59.423 47.619 8.93 0.00 0.00 5.34
2394 2799 0.681564 AGTTGCACGGGGTTTGTTCA 60.682 50.000 0.00 0.00 0.00 3.18
2395 2800 0.526739 GTTGCACGGGGTTTGTTCAC 60.527 55.000 0.00 0.00 0.00 3.18
2396 2801 0.681564 TTGCACGGGGTTTGTTCACT 60.682 50.000 0.00 0.00 0.00 3.41
2397 2802 1.098712 TGCACGGGGTTTGTTCACTC 61.099 55.000 0.00 0.00 0.00 3.51
2398 2803 1.938861 CACGGGGTTTGTTCACTCG 59.061 57.895 0.00 0.00 0.00 4.18
2399 2804 1.227734 ACGGGGTTTGTTCACTCGG 60.228 57.895 0.00 0.00 0.00 4.63
2400 2805 1.964373 CGGGGTTTGTTCACTCGGG 60.964 63.158 0.00 0.00 0.00 5.14
2401 2806 1.149854 GGGGTTTGTTCACTCGGGT 59.850 57.895 0.00 0.00 0.00 5.28
2402 2807 0.466739 GGGGTTTGTTCACTCGGGTT 60.467 55.000 0.00 0.00 0.00 4.11
2403 2808 1.395635 GGGTTTGTTCACTCGGGTTT 58.604 50.000 0.00 0.00 0.00 3.27
2404 2809 1.752498 GGGTTTGTTCACTCGGGTTTT 59.248 47.619 0.00 0.00 0.00 2.43
2405 2810 2.480587 GGGTTTGTTCACTCGGGTTTTG 60.481 50.000 0.00 0.00 0.00 2.44
2406 2811 2.164827 GGTTTGTTCACTCGGGTTTTGT 59.835 45.455 0.00 0.00 0.00 2.83
2407 2812 3.367600 GGTTTGTTCACTCGGGTTTTGTT 60.368 43.478 0.00 0.00 0.00 2.83
2408 2813 4.239304 GTTTGTTCACTCGGGTTTTGTTT 58.761 39.130 0.00 0.00 0.00 2.83
2409 2814 4.522722 TTGTTCACTCGGGTTTTGTTTT 57.477 36.364 0.00 0.00 0.00 2.43
2410 2815 4.522722 TGTTCACTCGGGTTTTGTTTTT 57.477 36.364 0.00 0.00 0.00 1.94
2411 2816 4.238514 TGTTCACTCGGGTTTTGTTTTTG 58.761 39.130 0.00 0.00 0.00 2.44
2412 2817 3.512033 TCACTCGGGTTTTGTTTTTGG 57.488 42.857 0.00 0.00 0.00 3.28
2413 2818 1.930503 CACTCGGGTTTTGTTTTTGGC 59.069 47.619 0.00 0.00 0.00 4.52
2414 2819 1.828595 ACTCGGGTTTTGTTTTTGGCT 59.171 42.857 0.00 0.00 0.00 4.75
2415 2820 2.200899 CTCGGGTTTTGTTTTTGGCTG 58.799 47.619 0.00 0.00 0.00 4.85
2416 2821 1.134670 TCGGGTTTTGTTTTTGGCTGG 60.135 47.619 0.00 0.00 0.00 4.85
2417 2822 1.021202 GGGTTTTGTTTTTGGCTGGC 58.979 50.000 0.00 0.00 0.00 4.85
2418 2823 0.655208 GGTTTTGTTTTTGGCTGGCG 59.345 50.000 0.00 0.00 0.00 5.69
2419 2824 0.655208 GTTTTGTTTTTGGCTGGCGG 59.345 50.000 0.00 0.00 0.00 6.13
2420 2825 0.462759 TTTTGTTTTTGGCTGGCGGG 60.463 50.000 0.00 0.00 0.00 6.13
2421 2826 2.932130 TTTGTTTTTGGCTGGCGGGC 62.932 55.000 13.82 13.82 41.27 6.13
2430 2835 4.598894 CTGGCGGGCCATCGAGAG 62.599 72.222 13.62 0.00 46.15 3.20
2445 2850 2.879026 TCGAGAGATTACGTGGATGAGG 59.121 50.000 0.00 0.00 33.31 3.86
2446 2851 2.619177 CGAGAGATTACGTGGATGAGGT 59.381 50.000 0.00 0.00 0.00 3.85
2447 2852 3.813724 CGAGAGATTACGTGGATGAGGTA 59.186 47.826 0.00 0.00 0.00 3.08
2448 2853 4.456222 CGAGAGATTACGTGGATGAGGTAT 59.544 45.833 0.00 0.00 0.00 2.73
2449 2854 5.617973 CGAGAGATTACGTGGATGAGGTATG 60.618 48.000 0.00 0.00 0.00 2.39
2450 2855 5.141182 AGAGATTACGTGGATGAGGTATGT 58.859 41.667 0.00 0.00 0.00 2.29
2451 2856 6.304624 AGAGATTACGTGGATGAGGTATGTA 58.695 40.000 0.00 0.00 0.00 2.29
2452 2857 6.776116 AGAGATTACGTGGATGAGGTATGTAA 59.224 38.462 0.00 0.00 32.32 2.41
2453 2858 7.451877 AGAGATTACGTGGATGAGGTATGTAAT 59.548 37.037 0.00 0.00 38.52 1.89
2454 2859 7.603651 AGATTACGTGGATGAGGTATGTAATC 58.396 38.462 15.51 15.51 45.14 1.75
2455 2860 6.971726 TTACGTGGATGAGGTATGTAATCT 57.028 37.500 0.00 0.00 0.00 2.40
2456 2861 5.871396 ACGTGGATGAGGTATGTAATCTT 57.129 39.130 0.00 0.00 0.00 2.40
2457 2862 6.971726 ACGTGGATGAGGTATGTAATCTTA 57.028 37.500 0.00 0.00 0.00 2.10
2458 2863 7.540474 ACGTGGATGAGGTATGTAATCTTAT 57.460 36.000 0.00 0.00 0.00 1.73
2459 2864 7.963532 ACGTGGATGAGGTATGTAATCTTATT 58.036 34.615 0.00 0.00 0.00 1.40
2460 2865 8.429641 ACGTGGATGAGGTATGTAATCTTATTT 58.570 33.333 0.00 0.00 0.00 1.40
2461 2866 8.926710 CGTGGATGAGGTATGTAATCTTATTTC 58.073 37.037 0.00 0.00 0.00 2.17
2462 2867 9.220767 GTGGATGAGGTATGTAATCTTATTTCC 57.779 37.037 0.00 0.00 0.00 3.13
2463 2868 8.094548 TGGATGAGGTATGTAATCTTATTTCCG 58.905 37.037 0.00 0.00 0.00 4.30
2464 2869 8.311836 GGATGAGGTATGTAATCTTATTTCCGA 58.688 37.037 0.00 0.00 0.00 4.55
2465 2870 9.141400 GATGAGGTATGTAATCTTATTTCCGAC 57.859 37.037 0.00 0.00 0.00 4.79
2466 2871 7.439381 TGAGGTATGTAATCTTATTTCCGACC 58.561 38.462 0.00 0.00 0.00 4.79
2467 2872 6.453092 AGGTATGTAATCTTATTTCCGACCG 58.547 40.000 0.00 0.00 0.00 4.79
2468 2873 6.266103 AGGTATGTAATCTTATTTCCGACCGA 59.734 38.462 0.00 0.00 0.00 4.69
2469 2874 6.585322 GGTATGTAATCTTATTTCCGACCGAG 59.415 42.308 0.00 0.00 0.00 4.63
2470 2875 5.840243 TGTAATCTTATTTCCGACCGAGA 57.160 39.130 0.00 0.00 0.00 4.04
2471 2876 6.401047 TGTAATCTTATTTCCGACCGAGAT 57.599 37.500 0.00 0.00 0.00 2.75
2472 2877 7.514784 TGTAATCTTATTTCCGACCGAGATA 57.485 36.000 0.00 0.00 0.00 1.98
2473 2878 8.118976 TGTAATCTTATTTCCGACCGAGATAT 57.881 34.615 0.00 0.00 0.00 1.63
2474 2879 8.242053 TGTAATCTTATTTCCGACCGAGATATC 58.758 37.037 0.00 0.00 0.00 1.63
2475 2880 5.640189 TCTTATTTCCGACCGAGATATCC 57.360 43.478 0.00 0.00 0.00 2.59
2476 2881 5.322754 TCTTATTTCCGACCGAGATATCCT 58.677 41.667 0.00 0.00 0.00 3.24
2477 2882 6.479006 TCTTATTTCCGACCGAGATATCCTA 58.521 40.000 0.00 0.00 0.00 2.94
2478 2883 7.117397 TCTTATTTCCGACCGAGATATCCTAT 58.883 38.462 0.00 0.00 0.00 2.57
2479 2884 7.614583 TCTTATTTCCGACCGAGATATCCTATT 59.385 37.037 0.00 0.00 0.00 1.73
2480 2885 6.607004 ATTTCCGACCGAGATATCCTATTT 57.393 37.500 0.00 0.00 0.00 1.40
2481 2886 6.415206 TTTCCGACCGAGATATCCTATTTT 57.585 37.500 0.00 0.00 0.00 1.82
2482 2887 5.386958 TCCGACCGAGATATCCTATTTTG 57.613 43.478 0.00 0.00 0.00 2.44
2485 2890 6.888088 TCCGACCGAGATATCCTATTTTGATA 59.112 38.462 0.00 0.00 0.00 2.15
2578 2985 6.998968 TTTGTTTGTGGCTTTTTCATTGAT 57.001 29.167 0.00 0.00 0.00 2.57
2694 3104 1.618837 CCGGTATACACAGCTAGGCAT 59.381 52.381 5.01 0.00 0.00 4.40
2708 3118 2.191128 AGGCATCGAAGCTTGTTTCT 57.809 45.000 12.92 0.00 34.17 2.52
2799 3213 5.526111 TGTTTCGTCTTAGAAAAGGACAAGG 59.474 40.000 0.00 0.00 41.18 3.61
3216 3723 7.069826 TGTCACATCTAAGTATGACATCATCCA 59.930 37.037 0.00 0.00 44.88 3.41
3279 3786 4.415150 ATGAGTGTGCCTGGGCCG 62.415 66.667 9.28 0.00 41.09 6.13
3389 3896 0.471591 TTGACTTGCAATTGGGCCCT 60.472 50.000 25.70 0.00 0.00 5.19
3390 3897 0.407528 TGACTTGCAATTGGGCCCTA 59.592 50.000 25.70 17.71 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.202111 ACTTGTTGTTATTGCTGGTTGTCC 60.202 41.667 0.00 0.00 0.00 4.02
68 69 3.307269 CCACAATGAGAGAAGGAGCAAGA 60.307 47.826 0.00 0.00 0.00 3.02
177 182 9.513906 TCTTGATGTGAAACTCCATTAATTACA 57.486 29.630 0.00 0.00 38.04 2.41
193 198 4.592942 AGCTAGCCATTTTCTTGATGTGA 58.407 39.130 12.13 0.00 0.00 3.58
292 298 6.166984 TGAATGACAGTGAGAGAAAACTCT 57.833 37.500 0.00 0.00 37.73 3.24
334 340 1.528129 CCTTCCAAGTGCTCCAACTC 58.472 55.000 0.00 0.00 0.00 3.01
345 351 2.027385 GCATTCTAAGGCCCTTCCAAG 58.973 52.381 0.00 0.00 37.29 3.61
402 797 2.554032 AGGAACGAGCAAATCCAAAGTG 59.446 45.455 0.00 0.00 35.62 3.16
411 806 1.967319 AGCAGAAAGGAACGAGCAAA 58.033 45.000 0.00 0.00 0.00 3.68
521 917 9.981114 ATTACATCGTTCATCTGATATTGTACA 57.019 29.630 0.00 0.00 0.00 2.90
719 1115 2.311701 TGCGTGGTAACTTTCGCCG 61.312 57.895 11.46 0.00 45.44 6.46
1119 1521 0.852777 CATGGAGATAAACGACCGCG 59.147 55.000 0.00 0.00 44.79 6.46
1210 1612 0.250038 ACACGATGTCTTGCAGCTGT 60.250 50.000 16.64 0.00 0.00 4.40
1608 2010 7.279313 GGAGAAGTTTCTGTTGTACAGTACAAA 59.721 37.037 24.75 14.99 46.03 2.83
1624 2026 3.119424 CGAGTGAGGTAGGGAGAAGTTTC 60.119 52.174 0.00 0.00 0.00 2.78
1629 2031 1.030488 CGCGAGTGAGGTAGGGAGAA 61.030 60.000 0.00 0.00 0.00 2.87
2283 2688 7.381678 ACTCTTACTACAAGCAAACTAAACGAG 59.618 37.037 0.00 0.00 0.00 4.18
2383 2788 0.466739 AACCCGAGTGAACAAACCCC 60.467 55.000 0.00 0.00 0.00 4.95
2394 2799 1.828595 AGCCAAAAACAAAACCCGAGT 59.171 42.857 0.00 0.00 0.00 4.18
2395 2800 2.200899 CAGCCAAAAACAAAACCCGAG 58.799 47.619 0.00 0.00 0.00 4.63
2396 2801 1.134670 CCAGCCAAAAACAAAACCCGA 60.135 47.619 0.00 0.00 0.00 5.14
2397 2802 1.294857 CCAGCCAAAAACAAAACCCG 58.705 50.000 0.00 0.00 0.00 5.28
2398 2803 1.021202 GCCAGCCAAAAACAAAACCC 58.979 50.000 0.00 0.00 0.00 4.11
2399 2804 0.655208 CGCCAGCCAAAAACAAAACC 59.345 50.000 0.00 0.00 0.00 3.27
2400 2805 0.655208 CCGCCAGCCAAAAACAAAAC 59.345 50.000 0.00 0.00 0.00 2.43
2401 2806 0.462759 CCCGCCAGCCAAAAACAAAA 60.463 50.000 0.00 0.00 0.00 2.44
2402 2807 1.144936 CCCGCCAGCCAAAAACAAA 59.855 52.632 0.00 0.00 0.00 2.83
2403 2808 2.818132 CCCGCCAGCCAAAAACAA 59.182 55.556 0.00 0.00 0.00 2.83
2404 2809 3.922640 GCCCGCCAGCCAAAAACA 61.923 61.111 0.00 0.00 0.00 2.83
2415 2820 1.816863 TAATCTCTCGATGGCCCGCC 61.817 60.000 0.00 0.00 0.00 6.13
2416 2821 0.667792 GTAATCTCTCGATGGCCCGC 60.668 60.000 0.00 0.00 0.00 6.13
2417 2822 0.387367 CGTAATCTCTCGATGGCCCG 60.387 60.000 0.00 0.00 0.00 6.13
2418 2823 0.674534 ACGTAATCTCTCGATGGCCC 59.325 55.000 0.00 0.00 0.00 5.80
2419 2824 1.603172 CCACGTAATCTCTCGATGGCC 60.603 57.143 0.00 0.00 0.00 5.36
2420 2825 1.337071 TCCACGTAATCTCTCGATGGC 59.663 52.381 0.00 0.00 32.65 4.40
2421 2826 3.253432 TCATCCACGTAATCTCTCGATGG 59.747 47.826 0.00 0.00 33.29 3.51
2422 2827 4.471373 CTCATCCACGTAATCTCTCGATG 58.529 47.826 0.00 0.00 0.00 3.84
2423 2828 3.504134 CCTCATCCACGTAATCTCTCGAT 59.496 47.826 0.00 0.00 0.00 3.59
2424 2829 2.879026 CCTCATCCACGTAATCTCTCGA 59.121 50.000 0.00 0.00 0.00 4.04
2425 2830 2.619177 ACCTCATCCACGTAATCTCTCG 59.381 50.000 0.00 0.00 0.00 4.04
2426 2831 5.241949 ACATACCTCATCCACGTAATCTCTC 59.758 44.000 0.00 0.00 0.00 3.20
2427 2832 5.141182 ACATACCTCATCCACGTAATCTCT 58.859 41.667 0.00 0.00 0.00 3.10
2428 2833 5.455056 ACATACCTCATCCACGTAATCTC 57.545 43.478 0.00 0.00 0.00 2.75
2429 2834 6.971726 TTACATACCTCATCCACGTAATCT 57.028 37.500 0.00 0.00 0.00 2.40
2430 2835 7.603651 AGATTACATACCTCATCCACGTAATC 58.396 38.462 0.00 0.00 41.70 1.75
2431 2836 7.540474 AGATTACATACCTCATCCACGTAAT 57.460 36.000 0.00 0.00 32.36 1.89
2432 2837 6.971726 AGATTACATACCTCATCCACGTAA 57.028 37.500 0.00 0.00 0.00 3.18
2433 2838 6.971726 AAGATTACATACCTCATCCACGTA 57.028 37.500 0.00 0.00 0.00 3.57
2434 2839 5.871396 AAGATTACATACCTCATCCACGT 57.129 39.130 0.00 0.00 0.00 4.49
2435 2840 8.833231 AAATAAGATTACATACCTCATCCACG 57.167 34.615 0.00 0.00 0.00 4.94
2436 2841 9.220767 GGAAATAAGATTACATACCTCATCCAC 57.779 37.037 0.00 0.00 0.00 4.02
2437 2842 8.094548 CGGAAATAAGATTACATACCTCATCCA 58.905 37.037 0.00 0.00 0.00 3.41
2438 2843 8.311836 TCGGAAATAAGATTACATACCTCATCC 58.688 37.037 0.00 0.00 0.00 3.51
2439 2844 9.141400 GTCGGAAATAAGATTACATACCTCATC 57.859 37.037 0.00 0.00 0.00 2.92
2440 2845 8.095169 GGTCGGAAATAAGATTACATACCTCAT 58.905 37.037 0.00 0.00 0.00 2.90
2441 2846 7.439381 GGTCGGAAATAAGATTACATACCTCA 58.561 38.462 0.00 0.00 0.00 3.86
2442 2847 6.585322 CGGTCGGAAATAAGATTACATACCTC 59.415 42.308 0.00 0.00 0.00 3.85
2443 2848 6.266103 TCGGTCGGAAATAAGATTACATACCT 59.734 38.462 0.00 0.00 0.00 3.08
2444 2849 6.449698 TCGGTCGGAAATAAGATTACATACC 58.550 40.000 0.00 0.00 0.00 2.73
2445 2850 7.365741 TCTCGGTCGGAAATAAGATTACATAC 58.634 38.462 0.00 0.00 0.00 2.39
2446 2851 7.514784 TCTCGGTCGGAAATAAGATTACATA 57.485 36.000 0.00 0.00 0.00 2.29
2447 2852 6.401047 TCTCGGTCGGAAATAAGATTACAT 57.599 37.500 0.00 0.00 0.00 2.29
2448 2853 5.840243 TCTCGGTCGGAAATAAGATTACA 57.160 39.130 0.00 0.00 0.00 2.41
2449 2854 7.701501 GGATATCTCGGTCGGAAATAAGATTAC 59.298 40.741 2.05 0.00 0.00 1.89
2450 2855 7.614583 AGGATATCTCGGTCGGAAATAAGATTA 59.385 37.037 2.05 0.00 0.00 1.75
2451 2856 6.437793 AGGATATCTCGGTCGGAAATAAGATT 59.562 38.462 2.05 0.00 0.00 2.40
2452 2857 5.952947 AGGATATCTCGGTCGGAAATAAGAT 59.047 40.000 2.05 0.00 0.00 2.40
2453 2858 5.322754 AGGATATCTCGGTCGGAAATAAGA 58.677 41.667 2.05 0.00 0.00 2.10
2454 2859 5.646577 AGGATATCTCGGTCGGAAATAAG 57.353 43.478 2.05 0.00 0.00 1.73
2455 2860 7.713734 AATAGGATATCTCGGTCGGAAATAA 57.286 36.000 2.05 0.00 0.00 1.40
2456 2861 7.713734 AAATAGGATATCTCGGTCGGAAATA 57.286 36.000 2.05 0.00 0.00 1.40
2457 2862 6.607004 AAATAGGATATCTCGGTCGGAAAT 57.393 37.500 2.05 0.00 0.00 2.17
2458 2863 6.041182 TCAAAATAGGATATCTCGGTCGGAAA 59.959 38.462 2.05 0.00 0.00 3.13
2459 2864 5.537295 TCAAAATAGGATATCTCGGTCGGAA 59.463 40.000 2.05 0.00 0.00 4.30
2460 2865 5.074804 TCAAAATAGGATATCTCGGTCGGA 58.925 41.667 2.05 0.00 0.00 4.55
2461 2866 5.386958 TCAAAATAGGATATCTCGGTCGG 57.613 43.478 2.05 0.00 0.00 4.79
2472 2877 8.990163 ACCCAACGTTTATATCAAAATAGGAT 57.010 30.769 0.00 0.00 0.00 3.24
2473 2878 8.810990 AACCCAACGTTTATATCAAAATAGGA 57.189 30.769 0.00 0.00 0.00 2.94
2474 2879 9.296400 CAAACCCAACGTTTATATCAAAATAGG 57.704 33.333 0.00 0.00 42.98 2.57
2475 2880 9.849166 ACAAACCCAACGTTTATATCAAAATAG 57.151 29.630 0.00 0.00 42.98 1.73
2476 2881 9.843334 GACAAACCCAACGTTTATATCAAAATA 57.157 29.630 0.00 0.00 42.98 1.40
2477 2882 7.815549 GGACAAACCCAACGTTTATATCAAAAT 59.184 33.333 0.00 0.00 42.98 1.82
2478 2883 7.146648 GGACAAACCCAACGTTTATATCAAAA 58.853 34.615 0.00 0.00 42.98 2.44
2479 2884 6.264744 TGGACAAACCCAACGTTTATATCAAA 59.735 34.615 0.00 0.00 42.98 2.69
2480 2885 5.768662 TGGACAAACCCAACGTTTATATCAA 59.231 36.000 0.00 0.00 42.98 2.57
2481 2886 5.314529 TGGACAAACCCAACGTTTATATCA 58.685 37.500 0.00 0.00 42.98 2.15
2482 2887 5.883503 TGGACAAACCCAACGTTTATATC 57.116 39.130 0.00 0.00 42.98 1.63
2485 2890 3.892588 ACATGGACAAACCCAACGTTTAT 59.107 39.130 0.00 0.00 42.98 1.40
2490 2895 1.001815 GTGACATGGACAAACCCAACG 60.002 52.381 0.00 0.00 40.04 4.10
2491 2896 2.028130 TGTGACATGGACAAACCCAAC 58.972 47.619 0.00 0.00 40.04 3.77
2568 2975 9.474920 CCAGCTGTAAAAAGTTATCAATGAAAA 57.525 29.630 13.81 0.00 0.00 2.29
2578 2985 6.439675 AAACGAACCAGCTGTAAAAAGTTA 57.560 33.333 13.81 0.00 0.00 2.24
2665 3075 0.828677 GTGTATACCGGCCCAGTCTT 59.171 55.000 0.00 0.00 0.00 3.01
2799 3213 5.163774 TGTGGCTTTTGTCTTGCAATTTTTC 60.164 36.000 0.00 0.00 36.89 2.29
3126 3628 9.829507 TGTTGGTGTTTCAGAAAATATTCAATT 57.170 25.926 0.00 0.00 38.06 2.32
3216 3723 7.042254 GGACAAACAAACAAGAGACTATACGTT 60.042 37.037 0.00 0.00 0.00 3.99
3259 3766 2.976490 GCCCAGGCACACTCATCCT 61.976 63.158 3.12 0.00 41.49 3.24
3396 3903 1.070134 ACTTGCAACTCGAGGCTTGTA 59.930 47.619 18.41 9.81 0.00 2.41


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

AutoCloner maintained by Alex Coulton.