Multiple sequence alignment - TraesCS7D01G231100

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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 TraesCS7D01G231100 chr7D 100.000 4858 0 0 1 4858 192162776 192157919 0.000000e+00 8972.0
1 TraesCS7D01G231100 chr7D 94.411 501 24 2 2596 3093 65433811 65433312 0.000000e+00 767.0
2 TraesCS7D01G231100 chr7D 100.000 53 0 0 2152 2204 506135751 506135803 1.110000e-16 99.0
3 TraesCS7D01G231100 chr7B 96.888 1864 39 5 700 2563 337642694 337640850 0.000000e+00 3103.0
4 TraesCS7D01G231100 chr7B 93.933 1780 81 15 3093 4858 337640857 337639091 0.000000e+00 2663.0
5 TraesCS7D01G231100 chr7B 93.781 611 27 4 42 649 337643291 337642689 0.000000e+00 907.0
6 TraesCS7D01G231100 chr7B 96.154 52 2 0 2153 2204 158926563 158926512 8.660000e-13 86.1
7 TraesCS7D01G231100 chr7A 92.370 2110 137 18 42 2144 201547814 201545722 0.000000e+00 2983.0
8 TraesCS7D01G231100 chr7A 93.787 1352 63 10 3406 4751 201543933 201542597 0.000000e+00 2012.0
9 TraesCS7D01G231100 chr7A 90.530 264 21 4 3093 3355 201544192 201543932 3.600000e-91 346.0
10 TraesCS7D01G231100 chr7A 84.211 361 38 9 2205 2563 201544528 201544185 2.800000e-87 333.0
11 TraesCS7D01G231100 chr7A 98.113 53 1 0 2152 2204 573671304 573671356 5.180000e-15 93.5
12 TraesCS7D01G231100 chr7A 92.727 55 4 0 2153 2207 501075758 501075704 4.030000e-11 80.5
13 TraesCS7D01G231100 chr5D 95.817 502 19 2 2596 3097 496320035 496320534 0.000000e+00 809.0
14 TraesCS7D01G231100 chr5D 92.157 51 4 0 2153 2203 55544553 55544503 6.740000e-09 73.1
15 TraesCS7D01G231100 chr1B 94.389 499 27 1 2596 3094 567473563 567474060 0.000000e+00 765.0
16 TraesCS7D01G231100 chr1B 93.988 499 29 1 2596 3094 251856274 251856771 0.000000e+00 754.0
17 TraesCS7D01G231100 chr1B 93.241 503 31 3 2596 3097 39386366 39386866 0.000000e+00 737.0
18 TraesCS7D01G231100 chr1B 92.727 55 4 0 2153 2207 415223912 415223858 4.030000e-11 80.5
19 TraesCS7D01G231100 chr1A 93.587 499 31 1 2596 3094 381813271 381813768 0.000000e+00 743.0
20 TraesCS7D01G231100 chr1A 97.222 36 1 0 2164 2199 485004532 485004497 1.460000e-05 62.1
21 TraesCS7D01G231100 chr5A 93.387 499 32 1 2596 3094 43492004 43492501 0.000000e+00 737.0
22 TraesCS7D01G231100 chr3D 93.587 499 23 5 2596 3093 435695193 435695683 0.000000e+00 736.0
23 TraesCS7D01G231100 chr3D 92.857 56 3 1 2153 2208 528814621 528814567 4.030000e-11 80.5
24 TraesCS7D01G231100 chr2B 92.857 504 35 1 2596 3099 408442983 408442481 0.000000e+00 730.0
25 TraesCS7D01G231100 chr1D 96.154 52 2 0 2153 2204 96067121 96067172 8.660000e-13 86.1
26 TraesCS7D01G231100 chr1D 92.000 50 3 1 2156 2204 439346865 439346816 8.720000e-08 69.4
27 TraesCS7D01G231100 chr1D 95.000 40 2 0 2163 2202 458139910 458139871 4.060000e-06 63.9
28 TraesCS7D01G231100 chr4B 90.476 63 5 1 2153 2214 212494747 212494809 1.120000e-11 82.4
29 TraesCS7D01G231100 chr6D 94.231 52 3 0 2153 2204 28282881 28282830 4.030000e-11 80.5
30 TraesCS7D01G231100 chr6D 94.231 52 3 0 2153 2204 348280412 348280463 4.030000e-11 80.5
31 TraesCS7D01G231100 chr6D 92.157 51 4 0 2153 2203 20026525 20026575 6.740000e-09 73.1
32 TraesCS7D01G231100 chr6D 92.308 39 3 0 2163 2201 211444642 211444680 6.790000e-04 56.5
33 TraesCS7D01G231100 chr4D 94.231 52 3 0 2153 2204 65536238 65536289 4.030000e-11 80.5
34 TraesCS7D01G231100 chr6A 91.379 58 4 1 2153 2209 115340000 115340057 1.450000e-10 78.7


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 TraesCS7D01G231100 chr7D 192157919 192162776 4857 True 8972.000000 8972 100.000000 1 4858 1 chr7D.!!$R2 4857
1 TraesCS7D01G231100 chr7B 337639091 337643291 4200 True 2224.333333 3103 94.867333 42 4858 3 chr7B.!!$R2 4816
2 TraesCS7D01G231100 chr7A 201542597 201547814 5217 True 1418.500000 2983 90.224500 42 4751 4 chr7A.!!$R2 4709
3 TraesCS7D01G231100 chr1B 39386366 39386866 500 False 737.000000 737 93.241000 2596 3097 1 chr1B.!!$F1 501
4 TraesCS7D01G231100 chr2B 408442481 408442983 502 True 730.000000 730 92.857000 2596 3099 1 chr2B.!!$R1 503


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
397 409 0.824109 TTACTCATCCTGGCGAGTGG 59.176 55.000 21.77 0.74 42.38 4.00 F
398 410 1.676678 TACTCATCCTGGCGAGTGGC 61.677 60.000 21.77 0.00 42.38 5.01 F
1287 1302 3.883489 GGAATACACATGCCCCTTTAGTC 59.117 47.826 0.00 0.00 0.00 2.59 F
2729 3881 0.179103 GTACCCGTACCCGTTGGATG 60.179 60.000 0.00 0.00 34.81 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1817 1.026718 ATTAGCTCCAACGCAGGTGC 61.027 55.000 11.53 11.53 45.93 5.01 R
2349 3500 1.354368 TCCCACATCCAAGTTTCTCCC 59.646 52.381 0.00 0.00 0.00 4.30 R
2913 4065 0.250727 TACCCTGCCTGCTTGTGAAC 60.251 55.000 0.00 0.00 0.00 3.18 R
4322 5477 0.403271 AGATCAAAGCACCTGCCTGT 59.597 50.000 0.00 0.00 43.38 4.00 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 3.827898 CCCACCCTCGCTCGAGTC 61.828 72.222 15.13 5.54 40.44 3.36
32 33 3.827898 CCACCCTCGCTCGAGTCC 61.828 72.222 15.13 0.00 40.44 3.85
33 34 3.062466 CACCCTCGCTCGAGTCCA 61.062 66.667 15.13 0.00 40.44 4.02
34 35 2.282958 ACCCTCGCTCGAGTCCAA 60.283 61.111 15.13 0.00 40.44 3.53
35 36 2.182030 CCCTCGCTCGAGTCCAAC 59.818 66.667 15.13 0.00 40.44 3.77
36 37 2.182030 CCTCGCTCGAGTCCAACC 59.818 66.667 15.13 0.00 40.44 3.77
37 38 2.182030 CTCGCTCGAGTCCAACCC 59.818 66.667 15.13 0.00 37.47 4.11
38 39 3.358076 CTCGCTCGAGTCCAACCCC 62.358 68.421 15.13 0.00 37.47 4.95
39 40 4.452733 CGCTCGAGTCCAACCCCC 62.453 72.222 15.13 0.00 0.00 5.40
40 41 3.319198 GCTCGAGTCCAACCCCCA 61.319 66.667 15.13 0.00 0.00 4.96
105 106 5.372373 CCATCTCCAACCTAATCTTTCTCC 58.628 45.833 0.00 0.00 0.00 3.71
111 112 4.116238 CAACCTAATCTTTCTCCTCTCGC 58.884 47.826 0.00 0.00 0.00 5.03
196 198 3.956199 TCCCAATCTCATCCATTTCTTGC 59.044 43.478 0.00 0.00 0.00 4.01
252 256 2.027625 GAACCCTCACTCCGTTGCG 61.028 63.158 0.00 0.00 0.00 4.85
290 295 2.266554 GTCTGGCTCTCGTTCTTGATG 58.733 52.381 0.00 0.00 0.00 3.07
293 298 1.895798 TGGCTCTCGTTCTTGATGACT 59.104 47.619 0.00 0.00 0.00 3.41
311 316 1.740025 ACTGCTCCTAAAAGAATGCGC 59.260 47.619 0.00 0.00 0.00 6.09
330 335 3.431572 GCGCTCATCTGATTCTGATAACC 59.568 47.826 0.00 0.00 0.00 2.85
331 336 4.625028 CGCTCATCTGATTCTGATAACCA 58.375 43.478 5.81 0.00 0.00 3.67
392 404 5.527214 TGTTGATTAATTACTCATCCTGGCG 59.473 40.000 6.37 0.00 0.00 5.69
393 405 5.545063 TGATTAATTACTCATCCTGGCGA 57.455 39.130 1.60 0.00 0.00 5.54
394 406 5.541845 TGATTAATTACTCATCCTGGCGAG 58.458 41.667 10.38 10.38 35.30 5.03
395 407 5.070446 TGATTAATTACTCATCCTGGCGAGT 59.930 40.000 18.59 18.59 44.51 4.18
396 408 2.898729 ATTACTCATCCTGGCGAGTG 57.101 50.000 21.77 5.65 42.38 3.51
397 409 0.824109 TTACTCATCCTGGCGAGTGG 59.176 55.000 21.77 0.74 42.38 4.00
398 410 1.676678 TACTCATCCTGGCGAGTGGC 61.677 60.000 21.77 0.00 42.38 5.01
484 496 5.674525 TGGAGCTGGTCAGAATAAACTATG 58.325 41.667 9.30 0.00 0.00 2.23
663 675 7.806690 TGTGAGTTTTGATAGCTTGATGTTAC 58.193 34.615 0.00 0.00 0.00 2.50
665 677 8.454106 GTGAGTTTTGATAGCTTGATGTTACAT 58.546 33.333 0.00 0.00 0.00 2.29
666 678 9.013229 TGAGTTTTGATAGCTTGATGTTACATT 57.987 29.630 0.00 0.00 0.00 2.71
733 746 4.030753 GCTCTCGAGTAATTGTCGACAAAG 59.969 45.833 32.69 22.81 41.41 2.77
1223 1236 7.425224 AATATACTCTGCTAATAATCGGCCT 57.575 36.000 0.00 0.00 0.00 5.19
1287 1302 3.883489 GGAATACACATGCCCCTTTAGTC 59.117 47.826 0.00 0.00 0.00 2.59
1320 1336 6.060788 ACAATTCTTTTGCTTAAATTGGCCA 58.939 32.000 0.00 0.00 41.29 5.36
1496 1512 9.917129 CATGCTTCATATTCTAAATATTTGGCA 57.083 29.630 11.05 0.00 0.00 4.92
1535 1551 9.302345 CGTGATAGACAGTGTTCTTAATATTGT 57.698 33.333 0.00 0.00 0.00 2.71
1801 1817 8.970859 ACAAATATGTATTTCCCTCTTCAGAG 57.029 34.615 0.00 0.00 38.24 3.35
1892 1908 7.071069 TCTTACTCCATGCATGATGTATTCT 57.929 36.000 28.31 6.28 0.00 2.40
1993 2010 7.787725 AAATATATTCTTTGTGTCTCGGGTC 57.212 36.000 0.00 0.00 0.00 4.46
2349 3500 4.104776 AGAAAAACACACACGATTGCTTG 58.895 39.130 0.00 0.00 0.00 4.01
2380 3531 1.616994 GGATGTGGGAAAGGGTTCAGG 60.617 57.143 0.00 0.00 35.25 3.86
2411 3562 9.989869 GGAATTTTAGTGAAGCTAAATGTCTAC 57.010 33.333 0.00 0.00 45.77 2.59
2423 3574 5.514204 GCTAAATGTCTACGTCGTGTGTAAT 59.486 40.000 8.47 0.00 0.00 1.89
2494 3645 7.710907 TCGCTTAGTGTAGCAATCATTTCTTAT 59.289 33.333 0.00 0.00 41.28 1.73
2558 3710 9.860898 ATGCCTTTATCAAATTTTCTTACACTC 57.139 29.630 0.00 0.00 0.00 3.51
2559 3711 8.303876 TGCCTTTATCAAATTTTCTTACACTCC 58.696 33.333 0.00 0.00 0.00 3.85
2560 3712 8.523658 GCCTTTATCAAATTTTCTTACACTCCT 58.476 33.333 0.00 0.00 0.00 3.69
2561 3713 9.846248 CCTTTATCAAATTTTCTTACACTCCTG 57.154 33.333 0.00 0.00 0.00 3.86
2566 3718 8.740123 TCAAATTTTCTTACACTCCTGTTACA 57.260 30.769 0.00 0.00 0.00 2.41
2567 3719 8.836413 TCAAATTTTCTTACACTCCTGTTACAG 58.164 33.333 5.22 5.22 0.00 2.74
2568 3720 8.836413 CAAATTTTCTTACACTCCTGTTACAGA 58.164 33.333 14.66 0.00 32.44 3.41
2569 3721 8.974060 AATTTTCTTACACTCCTGTTACAGAA 57.026 30.769 14.66 0.00 32.44 3.02
2570 3722 8.608844 ATTTTCTTACACTCCTGTTACAGAAG 57.391 34.615 14.66 5.32 32.44 2.85
2571 3723 6.726490 TTCTTACACTCCTGTTACAGAAGT 57.274 37.500 14.66 6.11 32.44 3.01
2572 3724 7.828508 TTCTTACACTCCTGTTACAGAAGTA 57.171 36.000 14.66 7.80 32.44 2.24
2573 3725 8.418597 TTCTTACACTCCTGTTACAGAAGTAT 57.581 34.615 14.66 0.00 32.44 2.12
2574 3726 9.524496 TTCTTACACTCCTGTTACAGAAGTATA 57.476 33.333 14.66 0.00 32.44 1.47
2575 3727 9.175312 TCTTACACTCCTGTTACAGAAGTATAG 57.825 37.037 14.66 7.18 32.44 1.31
2576 3728 8.874744 TTACACTCCTGTTACAGAAGTATAGT 57.125 34.615 14.66 6.21 32.44 2.12
2577 3729 9.964354 TTACACTCCTGTTACAGAAGTATAGTA 57.036 33.333 14.66 5.22 32.44 1.82
2578 3730 8.874744 ACACTCCTGTTACAGAAGTATAGTAA 57.125 34.615 14.66 0.00 32.44 2.24
2579 3731 9.476928 ACACTCCTGTTACAGAAGTATAGTAAT 57.523 33.333 14.66 0.00 32.44 1.89
2583 3735 9.925545 TCCTGTTACAGAAGTATAGTAATACCA 57.074 33.333 14.66 0.00 35.05 3.25
2590 3742 9.839185 ACAGAAGTATAGTAATACCATACCCAT 57.161 33.333 5.58 0.00 39.08 4.00
2594 3746 9.498039 AAGTATAGTAATACCATACCCATACCC 57.502 37.037 5.58 0.00 39.08 3.69
2595 3747 7.781693 AGTATAGTAATACCATACCCATACCCG 59.218 40.741 5.58 0.00 39.08 5.28
2596 3748 4.755437 AGTAATACCATACCCATACCCGT 58.245 43.478 0.00 0.00 0.00 5.28
2597 3749 5.902760 AGTAATACCATACCCATACCCGTA 58.097 41.667 0.00 0.00 0.00 4.02
2598 3750 6.505754 AGTAATACCATACCCATACCCGTAT 58.494 40.000 0.00 0.00 0.00 3.06
2599 3751 5.687166 AATACCATACCCATACCCGTATG 57.313 43.478 7.72 7.72 40.92 2.39
2667 3819 5.757988 GGTACAAAATTCTACCCATACCCA 58.242 41.667 0.00 0.00 0.00 4.51
2729 3881 0.179103 GTACCCGTACCCGTTGGATG 60.179 60.000 0.00 0.00 34.81 3.51
2747 3899 0.402504 TGCCCAACGGGTAGAACAAT 59.597 50.000 0.06 0.00 46.51 2.71
2756 3908 3.244284 ACGGGTAGAACAATTAGCACACA 60.244 43.478 0.00 0.00 0.00 3.72
2789 3941 9.891828 TCACATTTTTACACTCATTGATAACAC 57.108 29.630 0.00 0.00 0.00 3.32
2840 3992 8.812329 GCTCAATAACAAGTAGATGAGTACAAG 58.188 37.037 0.00 0.00 34.39 3.16
2859 4011 8.470805 AGTACAAGATACTCATAAGTCAACAGG 58.529 37.037 0.00 0.00 36.92 4.00
2923 4075 7.066404 TGACAACTTAACATTAGTTCACAAGCA 59.934 33.333 0.00 0.00 39.15 3.91
2962 4114 4.950205 CCCGTGGGTACAAGATTATACT 57.050 45.455 0.00 0.00 0.00 2.12
2977 4129 6.559429 AGATTATACTCGTACCCTACCCATT 58.441 40.000 0.00 0.00 0.00 3.16
3004 4156 2.158460 ACGGGTAGGGTATGGGTACTAC 60.158 54.545 0.00 0.00 36.07 2.73
3033 4185 2.116827 TAAAAGTGTGCCCATACCCG 57.883 50.000 0.00 0.00 0.00 5.28
3158 4311 7.179966 TGTTCCACTACTAGGACTTCTTGATA 58.820 38.462 0.00 0.00 34.19 2.15
3245 4398 4.900635 AATCACTTGGTTGTGTGAGTTC 57.099 40.909 0.00 0.00 44.85 3.01
3403 4558 7.275341 GTGCTCCTATCTCATATTTGATCGAAG 59.725 40.741 1.10 0.00 0.00 3.79
3592 4747 0.683504 ATCGCGACCCACCTCTTACT 60.684 55.000 12.93 0.00 0.00 2.24
3624 4779 3.894759 AGTAATCTGTAGCCTGTCGGTA 58.105 45.455 0.00 0.00 0.00 4.02
3735 4890 1.541620 AAGTTCAGACCCCTCCCCC 60.542 63.158 0.00 0.00 0.00 5.40
3893 5048 6.292061 GCTAAAGATCAGCACTACGATGAAAG 60.292 42.308 0.00 0.00 38.93 2.62
3920 5075 3.133464 ACGGAATGCGTGCATGGG 61.133 61.111 8.30 3.56 36.68 4.00
4060 5215 4.200092 GGAAGGACAGGCTAAATCGATTT 58.800 43.478 25.48 25.48 0.00 2.17
4211 5366 6.207417 ACATAATAGGAAATGCTACACATGCC 59.793 38.462 0.00 0.00 39.60 4.40
4265 5420 4.142491 CGCAGGATGGCAAATGTTTAGTTA 60.142 41.667 0.00 0.00 35.86 2.24
4267 5422 6.340522 GCAGGATGGCAAATGTTTAGTTAAT 58.659 36.000 0.00 0.00 35.86 1.40
4268 5423 7.488322 GCAGGATGGCAAATGTTTAGTTAATA 58.512 34.615 0.00 0.00 35.86 0.98
4269 5424 7.435192 GCAGGATGGCAAATGTTTAGTTAATAC 59.565 37.037 0.00 0.00 35.86 1.89
4270 5425 8.686334 CAGGATGGCAAATGTTTAGTTAATACT 58.314 33.333 0.00 0.00 38.44 2.12
4271 5426 8.903820 AGGATGGCAAATGTTTAGTTAATACTC 58.096 33.333 0.00 0.00 35.78 2.59
4272 5427 8.135529 GGATGGCAAATGTTTAGTTAATACTCC 58.864 37.037 0.00 0.00 35.78 3.85
4273 5428 7.079182 TGGCAAATGTTTAGTTAATACTCCG 57.921 36.000 0.00 0.00 35.78 4.63
4357 5512 0.815734 ATCTGCATTCTGCTGTTGCC 59.184 50.000 14.84 3.08 45.31 4.52
4419 5574 2.517959 CATGGCCCTGAAAGAAGTTCA 58.482 47.619 0.97 0.00 44.20 3.18
4422 5577 2.108075 TGGCCCTGAAAGAAGTTCATCA 59.892 45.455 0.00 8.25 45.27 3.07
4435 5590 9.741647 AAAGAAGTTCATCACATCTTTCTTTTC 57.258 29.630 5.50 0.00 46.00 2.29
4588 5745 2.287608 GGAACTGGAAGAAAACCAAGCG 60.288 50.000 0.00 0.00 36.95 4.68
4610 5767 5.390991 GCGTTCTCTTTCCCTTCAATAGTTG 60.391 44.000 0.00 0.00 0.00 3.16
4619 5776 4.518970 TCCCTTCAATAGTTGTGCAGTTTC 59.481 41.667 0.00 0.00 0.00 2.78
4637 5794 4.037923 AGTTTCGTTGATGCAGGTGAAAAT 59.962 37.500 0.00 0.00 0.00 1.82
4809 5984 5.321102 ACACTGATTATGCCACAGGTTTAA 58.679 37.500 0.00 0.00 36.17 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.827898 GACTCGAGCGAGGGTGGG 61.828 72.222 22.11 0.00 45.88 4.61
15 16 3.827898 GGACTCGAGCGAGGGTGG 61.828 72.222 22.11 0.06 45.88 4.61
16 17 2.636412 TTGGACTCGAGCGAGGGTG 61.636 63.158 22.11 0.42 45.88 4.61
17 18 2.282958 TTGGACTCGAGCGAGGGT 60.283 61.111 22.11 4.76 45.88 4.34
18 19 2.182030 GTTGGACTCGAGCGAGGG 59.818 66.667 22.11 1.48 45.88 4.30
19 20 2.182030 GGTTGGACTCGAGCGAGG 59.818 66.667 22.11 6.37 45.88 4.63
20 21 2.182030 GGGTTGGACTCGAGCGAG 59.818 66.667 13.61 17.46 46.91 5.03
21 22 3.379445 GGGGTTGGACTCGAGCGA 61.379 66.667 13.61 0.00 0.00 4.93
22 23 4.452733 GGGGGTTGGACTCGAGCG 62.453 72.222 13.61 0.00 0.00 5.03
23 24 3.316573 CTGGGGGTTGGACTCGAGC 62.317 68.421 13.61 5.26 0.00 5.03
24 25 2.982130 CTGGGGGTTGGACTCGAG 59.018 66.667 11.84 11.84 0.00 4.04
25 26 3.319198 GCTGGGGGTTGGACTCGA 61.319 66.667 0.00 0.00 0.00 4.04
26 27 3.612247 CTGCTGGGGGTTGGACTCG 62.612 68.421 0.00 0.00 0.00 4.18
27 28 2.352805 CTGCTGGGGGTTGGACTC 59.647 66.667 0.00 0.00 0.00 3.36
28 29 3.971702 GCTGCTGGGGGTTGGACT 61.972 66.667 0.00 0.00 0.00 3.85
31 32 4.748144 GAGGCTGCTGGGGGTTGG 62.748 72.222 0.00 0.00 0.00 3.77
32 33 4.748144 GGAGGCTGCTGGGGGTTG 62.748 72.222 0.00 0.00 0.00 3.77
35 36 4.120755 GAAGGAGGCTGCTGGGGG 62.121 72.222 10.05 0.00 0.00 5.40
36 37 4.120755 GGAAGGAGGCTGCTGGGG 62.121 72.222 10.05 0.00 0.00 4.96
37 38 3.013932 AGGAAGGAGGCTGCTGGG 61.014 66.667 10.05 0.00 0.00 4.45
38 39 0.689080 TAGAGGAAGGAGGCTGCTGG 60.689 60.000 10.05 0.00 0.00 4.85
39 40 0.752054 CTAGAGGAAGGAGGCTGCTG 59.248 60.000 10.05 0.00 0.00 4.41
40 41 0.338120 ACTAGAGGAAGGAGGCTGCT 59.662 55.000 1.28 1.28 0.00 4.24
252 256 4.878397 CCAGACACCAAAATCCATCTCTAC 59.122 45.833 0.00 0.00 0.00 2.59
290 295 2.223135 GCGCATTCTTTTAGGAGCAGTC 60.223 50.000 0.30 0.00 0.00 3.51
293 298 2.009774 GAGCGCATTCTTTTAGGAGCA 58.990 47.619 11.47 0.00 0.00 4.26
311 316 6.580788 ACTGTGGTTATCAGAATCAGATGAG 58.419 40.000 0.00 0.00 36.81 2.90
397 409 0.750850 TACAGATTAGGGGCAGTCGC 59.249 55.000 0.00 0.00 37.44 5.19
398 410 1.068741 GGTACAGATTAGGGGCAGTCG 59.931 57.143 0.00 0.00 0.00 4.18
695 707 0.947244 AGAGCAGAACCAAAACGCTG 59.053 50.000 0.00 0.00 31.86 5.18
699 711 2.484889 ACTCGAGAGCAGAACCAAAAC 58.515 47.619 21.68 0.00 0.00 2.43
733 746 6.931840 AGAAGTTCAGAACCAAGAGAATACAC 59.068 38.462 9.85 0.00 0.00 2.90
986 999 2.607750 ACATGGAGCCCCGACAGT 60.608 61.111 0.00 0.00 34.29 3.55
1223 1236 5.719085 ACAGACATTGGCCAAATATTACCAA 59.281 36.000 24.71 15.84 45.68 3.67
1287 1302 2.580589 CAAAAGAATTGTACCACGGCG 58.419 47.619 4.80 4.80 0.00 6.46
1320 1336 5.728637 AAGAATTTTCTTGCTCGGGATTT 57.271 34.783 4.80 0.00 45.27 2.17
1442 1458 7.201617 GCTTTTGCATCCCTATTACGGATATAC 60.202 40.741 0.00 0.00 46.58 1.47
1509 1525 9.302345 ACAATATTAAGAACACTGTCTATCACG 57.698 33.333 0.00 0.00 0.00 4.35
1535 1551 7.223584 TGTCTCTCACTCCACAATATTTTTGA 58.776 34.615 0.00 0.00 0.00 2.69
1542 1558 5.080337 AGAACTGTCTCTCACTCCACAATA 58.920 41.667 0.00 0.00 0.00 1.90
1630 1646 5.009911 CACAGGACACCAAATCATTGAGAAA 59.990 40.000 0.00 0.00 38.94 2.52
1801 1817 1.026718 ATTAGCTCCAACGCAGGTGC 61.027 55.000 11.53 11.53 45.93 5.01
1925 1942 5.590663 TGATGACCTCAGACAGATACAGTAC 59.409 44.000 0.00 0.00 0.00 2.73
1988 2005 3.670627 GCAATGCAGAAAGTAAAGACCCG 60.671 47.826 0.00 0.00 0.00 5.28
1993 2010 6.672147 ACTTACAGCAATGCAGAAAGTAAAG 58.328 36.000 8.35 2.26 29.11 1.85
2328 3479 3.242712 CCAAGCAATCGTGTGTGTTTTTC 59.757 43.478 0.00 0.00 0.00 2.29
2349 3500 1.354368 TCCCACATCCAAGTTTCTCCC 59.646 52.381 0.00 0.00 0.00 4.30
2411 3562 2.219903 TGCAGAACAATTACACACGACG 59.780 45.455 0.00 0.00 0.00 5.12
2423 3574 3.554934 AGAAACTGTCCATGCAGAACAA 58.445 40.909 7.27 0.00 39.62 2.83
2494 3645 5.290493 AGTGTTCAGAAGTTATGTGACCA 57.710 39.130 0.00 0.00 29.71 4.02
2557 3709 9.925545 TGGTATTACTATACTTCTGTAACAGGA 57.074 33.333 0.00 0.00 37.39 3.86
2564 3716 9.839185 ATGGGTATGGTATTACTATACTTCTGT 57.161 33.333 22.18 10.62 40.86 3.41
2568 3720 9.498039 GGGTATGGGTATGGTATTACTATACTT 57.502 37.037 22.18 13.74 40.86 2.24
2569 3721 7.781693 CGGGTATGGGTATGGTATTACTATACT 59.218 40.741 22.18 10.95 40.86 2.12
2570 3722 7.561356 ACGGGTATGGGTATGGTATTACTATAC 59.439 40.741 17.50 17.50 40.49 1.47
2571 3723 7.651607 ACGGGTATGGGTATGGTATTACTATA 58.348 38.462 0.00 0.00 0.00 1.31
2572 3724 6.505754 ACGGGTATGGGTATGGTATTACTAT 58.494 40.000 0.00 0.00 0.00 2.12
2573 3725 5.902760 ACGGGTATGGGTATGGTATTACTA 58.097 41.667 0.00 0.00 0.00 1.82
2574 3726 4.755437 ACGGGTATGGGTATGGTATTACT 58.245 43.478 0.00 0.00 0.00 2.24
2575 3727 6.576185 CATACGGGTATGGGTATGGTATTAC 58.424 44.000 10.32 0.00 41.31 1.89
2576 3728 6.795144 CATACGGGTATGGGTATGGTATTA 57.205 41.667 10.32 0.00 41.31 0.98
2577 3729 5.687166 CATACGGGTATGGGTATGGTATT 57.313 43.478 10.32 0.00 41.31 1.89
2588 3740 1.533625 CCCATTGCCATACGGGTATG 58.466 55.000 11.07 11.07 41.86 2.39
2592 3744 0.762418 TCTACCCATTGCCATACGGG 59.238 55.000 0.00 0.00 44.88 5.28
2593 3745 1.878102 GCTCTACCCATTGCCATACGG 60.878 57.143 0.00 0.00 0.00 4.02
2594 3746 1.202639 TGCTCTACCCATTGCCATACG 60.203 52.381 0.00 0.00 0.00 3.06
2595 3747 2.638480 TGCTCTACCCATTGCCATAC 57.362 50.000 0.00 0.00 0.00 2.39
2596 3748 3.882102 ATTGCTCTACCCATTGCCATA 57.118 42.857 0.00 0.00 0.00 2.74
2597 3749 2.761786 ATTGCTCTACCCATTGCCAT 57.238 45.000 0.00 0.00 0.00 4.40
2598 3750 2.422803 GGTATTGCTCTACCCATTGCCA 60.423 50.000 4.46 0.00 36.00 4.92
2599 3751 2.230660 GGTATTGCTCTACCCATTGCC 58.769 52.381 4.46 0.00 36.00 4.52
2600 3752 2.930950 TGGTATTGCTCTACCCATTGC 58.069 47.619 11.32 0.00 40.47 3.56
2601 3753 5.003804 GGTATGGTATTGCTCTACCCATTG 58.996 45.833 11.32 0.00 40.47 2.82
2602 3754 5.242795 GGTATGGTATTGCTCTACCCATT 57.757 43.478 11.32 2.11 40.47 3.16
2603 3755 4.910458 GGTATGGTATTGCTCTACCCAT 57.090 45.455 11.32 6.74 40.47 4.00
2734 3886 3.244284 TGTGTGCTAATTGTTCTACCCGT 60.244 43.478 0.00 0.00 0.00 5.28
2747 3899 5.574891 AATGTGAACAACTTGTGTGCTAA 57.425 34.783 0.00 0.00 40.60 3.09
2756 3908 9.086336 CAATGAGTGTAAAAATGTGAACAACTT 57.914 29.630 0.00 0.00 0.00 2.66
2840 3992 8.453238 TCTACTCCTGTTGACTTATGAGTATC 57.547 38.462 0.00 0.00 35.47 2.24
2856 4008 7.496529 TTTTCATGTGACTTTTCTACTCCTG 57.503 36.000 0.00 0.00 0.00 3.86
2913 4065 0.250727 TACCCTGCCTGCTTGTGAAC 60.251 55.000 0.00 0.00 0.00 3.18
2962 4114 4.338118 CGTTAAGTAATGGGTAGGGTACGA 59.662 45.833 0.00 0.00 0.00 3.43
2977 4129 3.052186 ACCCATACCCTACCCGTTAAGTA 60.052 47.826 0.00 0.00 0.00 2.24
3004 4156 2.693074 GGCACACTTTTATACCCATGGG 59.307 50.000 30.23 30.23 42.03 4.00
3158 4311 1.698506 TTCCACACGCCCAAAGAAAT 58.301 45.000 0.00 0.00 0.00 2.17
3245 4398 0.749091 ATGTGGTGGGATCGTGCATG 60.749 55.000 0.00 0.00 0.00 4.06
3316 4469 4.348168 GGGAAGATGTTAGAGAAGCCCATA 59.652 45.833 0.00 0.00 33.28 2.74
3317 4470 3.137360 GGGAAGATGTTAGAGAAGCCCAT 59.863 47.826 0.00 0.00 33.28 4.00
3337 4492 7.280652 CAGCCATGATTTTTATTTTGGTAAGGG 59.719 37.037 0.00 0.00 0.00 3.95
3385 4540 7.215789 AGAGTTGCTTCGATCAAATATGAGAT 58.784 34.615 2.70 0.00 39.39 2.75
3403 4558 5.407502 AGTGTTTTTGTACCAAAGAGTTGC 58.592 37.500 0.00 0.00 33.01 4.17
3592 4747 5.470368 GCTACAGATTACTATTGGATGCGA 58.530 41.667 0.00 0.00 0.00 5.10
3624 4779 8.153550 GGATCAGACTAGTTGGATTTATCATGT 58.846 37.037 10.46 0.00 0.00 3.21
3735 4890 1.880027 GTACACAGTGCTTGGGAAAGG 59.120 52.381 0.00 0.00 33.14 3.11
3920 5075 2.216898 GGGATATCACAAGACAGCAGC 58.783 52.381 4.83 0.00 0.00 5.25
4164 5319 2.066262 ACACAATTCCGCTGTTACTCG 58.934 47.619 0.00 0.00 0.00 4.18
4211 5366 3.743521 TCAGGTGAACAGGAAATCAGTG 58.256 45.455 0.00 0.00 0.00 3.66
4269 5424 8.815189 CATGATATAGCAGAAAATGATACGGAG 58.185 37.037 0.00 0.00 31.30 4.63
4270 5425 7.765819 CCATGATATAGCAGAAAATGATACGGA 59.234 37.037 0.00 0.00 31.30 4.69
4271 5426 7.550551 ACCATGATATAGCAGAAAATGATACGG 59.449 37.037 0.00 0.00 31.30 4.02
4272 5427 8.484641 ACCATGATATAGCAGAAAATGATACG 57.515 34.615 0.00 0.00 31.30 3.06
4273 5428 9.440773 TGACCATGATATAGCAGAAAATGATAC 57.559 33.333 0.00 0.00 31.30 2.24
4322 5477 0.403271 AGATCAAAGCACCTGCCTGT 59.597 50.000 0.00 0.00 43.38 4.00
4346 5501 2.974148 CACAGCGGCAACAGCAGA 60.974 61.111 1.45 0.00 38.34 4.26
4357 5512 3.584250 CTGCGCCTGAAACACAGCG 62.584 63.158 4.18 0.00 44.52 5.18
4419 5574 5.350914 CAGCGAGAGAAAAGAAAGATGTGAT 59.649 40.000 0.00 0.00 0.00 3.06
4422 5577 3.434984 GCAGCGAGAGAAAAGAAAGATGT 59.565 43.478 0.00 0.00 0.00 3.06
4528 5683 1.657751 GCCGATGCAGGAAAACTCCC 61.658 60.000 0.00 0.00 37.47 4.30
4588 5745 6.568653 GCACAACTATTGAAGGGAAAGAGAAC 60.569 42.308 0.00 0.00 0.00 3.01
4610 5767 1.664016 CCTGCATCAACGAAACTGCAC 60.664 52.381 0.00 0.00 39.54 4.57
4619 5776 5.046910 ACTAATTTTCACCTGCATCAACG 57.953 39.130 0.00 0.00 0.00 4.10
4727 5885 9.314133 TGCTAGTATATATCCACTGTTTCAGAT 57.686 33.333 3.70 0.00 35.18 2.90
4785 5950 4.568072 AACCTGTGGCATAATCAGTGTA 57.432 40.909 0.00 0.00 0.00 2.90
4789 5954 5.895636 TGTTAAACCTGTGGCATAATCAG 57.104 39.130 0.00 0.00 0.00 2.90
4790 5955 6.656632 TTTGTTAAACCTGTGGCATAATCA 57.343 33.333 0.00 0.00 0.00 2.57
4831 6006 5.778750 AGCTTAGGACTCCTTGTGTACTAAA 59.221 40.000 1.94 0.00 39.49 1.85
4833 6008 4.705507 CAGCTTAGGACTCCTTGTGTACTA 59.294 45.833 1.94 0.00 34.61 1.82



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

AutoCloner maintained by Alex Coulton.