Multiple sequence alignment - TraesCS2B01G300100

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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 TraesCS2B01G300100 chr2B 100.000 5249 0 0 1 5249 421703769 421709017 0.000000e+00 9694.0
1 TraesCS2B01G300100 chr2B 97.297 37 1 0 383 419 111862022 111861986 4.390000e-06 63.9
2 TraesCS2B01G300100 chr2A 91.685 2297 111 35 3007 5249 474308960 474311230 0.000000e+00 3110.0
3 TraesCS2B01G300100 chr2A 93.799 1645 69 10 1274 2901 474307299 474308927 0.000000e+00 2442.0
4 TraesCS2B01G300100 chr2A 83.862 694 33 24 2 625 474283947 474284631 5.860000e-164 588.0
5 TraesCS2B01G300100 chr2A 95.161 248 7 3 383 625 474306485 474306732 2.290000e-103 387.0
6 TraesCS2B01G300100 chr2A 83.553 304 25 16 2 290 474303316 474303609 1.450000e-65 261.0
7 TraesCS2B01G300100 chr2A 92.308 52 3 1 3181 3231 444324872 444324821 7.290000e-09 73.1
8 TraesCS2B01G300100 chr2D 91.808 1770 115 18 1648 3394 354740953 354742715 0.000000e+00 2438.0
9 TraesCS2B01G300100 chr2D 93.723 1163 59 9 3414 4564 354742705 354743865 0.000000e+00 1731.0
10 TraesCS2B01G300100 chr2D 92.170 894 29 15 538 1418 354739804 354740669 0.000000e+00 1225.0
11 TraesCS2B01G300100 chr2D 90.612 490 35 6 4607 5095 354743863 354744342 1.590000e-179 640.0
12 TraesCS2B01G300100 chr2D 85.492 579 31 14 1 531 354682775 354683348 5.940000e-154 555.0
13 TraesCS2B01G300100 chr2D 92.073 164 12 1 5087 5249 354744361 354744524 4.090000e-56 230.0
14 TraesCS2B01G300100 chr2D 92.593 135 8 1 1403 1537 354740688 354740820 5.360000e-45 193.0
15 TraesCS2B01G300100 chr7D 85.965 114 11 4 311 419 94441228 94441115 3.320000e-22 117.0
16 TraesCS2B01G300100 chr7B 85.965 114 11 4 311 419 48465614 48465501 3.320000e-22 117.0
17 TraesCS2B01G300100 chr3A 85.321 109 8 4 311 419 36236238 36236338 7.190000e-19 106.0
18 TraesCS2B01G300100 chr1A 89.412 85 8 1 297 380 155857863 155857779 7.190000e-19 106.0
19 TraesCS2B01G300100 chr5B 86.735 98 8 4 284 379 290386484 290386578 2.590000e-18 104.0
20 TraesCS2B01G300100 chr3B 87.500 88 9 2 294 380 528176348 528176262 3.340000e-17 100.0
21 TraesCS2B01G300100 chr1B 87.952 83 7 2 3441 3520 49796783 49796865 1.560000e-15 95.3
22 TraesCS2B01G300100 chr1B 88.462 78 7 2 288 364 449987193 449987117 5.600000e-15 93.5
23 TraesCS2B01G300100 chr1B 91.667 48 2 2 373 419 491242120 491242166 1.220000e-06 65.8
24 TraesCS2B01G300100 chrUn 88.608 79 6 2 3444 3519 223708595 223708517 5.600000e-15 93.5
25 TraesCS2B01G300100 chrUn 88.608 79 6 2 3441 3516 246708883 246708961 5.600000e-15 93.5
26 TraesCS2B01G300100 chrUn 88.608 79 6 2 3444 3519 266189742 266189664 5.600000e-15 93.5
27 TraesCS2B01G300100 chr4B 88.608 79 6 2 3444 3519 495544425 495544347 5.600000e-15 93.5
28 TraesCS2B01G300100 chr3D 88.608 79 6 2 3444 3519 498433186 498433108 5.600000e-15 93.5
29 TraesCS2B01G300100 chr1D 88.608 79 6 2 3444 3519 350967061 350966983 5.600000e-15 93.5


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 TraesCS2B01G300100 chr2B 421703769 421709017 5248 False 9694.000000 9694 100.000000 1 5249 1 chr2B.!!$F1 5248
1 TraesCS2B01G300100 chr2A 474303316 474311230 7914 False 1550.000000 3110 91.049500 2 5249 4 chr2A.!!$F2 5247
2 TraesCS2B01G300100 chr2A 474283947 474284631 684 False 588.000000 588 83.862000 2 625 1 chr2A.!!$F1 623
3 TraesCS2B01G300100 chr2D 354739804 354744524 4720 False 1076.166667 2438 92.163167 538 5249 6 chr2D.!!$F2 4711
4 TraesCS2B01G300100 chr2D 354682775 354683348 573 False 555.000000 555 85.492000 1 531 1 chr2D.!!$F1 530

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
794 3596 1.002430 TGGCACTCCAGAGTTGCTAAG 59.998 52.381 16.39 0.92 40.2 2.18 F
1375 4187 0.105039 CGGGGCTGATGGAACTAGAC 59.895 60.000 0.00 0.00 0.0 2.59 F
1900 4784 0.333312 TGGTTGAAGGGTGTGTGGTT 59.667 50.000 0.00 0.00 0.0 3.67 F
2923 5817 0.469144 GACAACTGGCCCCTGGAAAA 60.469 55.000 0.00 0.00 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 5019 0.817013 GCCCCAAATCGCTCAAATCA 59.183 50.0 0.00 0.00 0.00 2.57 R
3169 6064 0.687354 TCTTCCTCCAACAGGTCAGC 59.313 55.0 0.00 0.00 43.95 4.26 R
3312 6209 2.048444 ACACCTTATGGCATGAGCTG 57.952 50.0 13.43 12.51 41.70 4.24 R
4633 7562 0.250467 TTGGCAGCAGGACTCAAGAC 60.250 55.0 0.00 0.00 0.00 3.01 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
207 216 8.971321 CATTTTGGAAAGTGTGAACATTTCTAG 58.029 33.333 13.25 0.00 34.19 2.43
426 3219 7.229506 AGCATCTTATATTTGTGAAGTTAGGGC 59.770 37.037 0.00 0.00 0.00 5.19
513 3310 3.058160 CTCAAAGTGGGCTGGCCG 61.058 66.667 16.08 0.51 36.85 6.13
518 3315 1.774894 AAAGTGGGCTGGCCGAGTTA 61.775 55.000 16.08 0.00 36.63 2.24
537 3334 1.369091 ATCATCGCTTGGGTGTTCGC 61.369 55.000 0.00 0.00 0.00 4.70
658 3459 5.047519 GGGCCATCTTTATCATTCCATTGAG 60.048 44.000 4.39 0.00 0.00 3.02
794 3596 1.002430 TGGCACTCCAGAGTTGCTAAG 59.998 52.381 16.39 0.92 40.20 2.18
804 3606 5.538813 TCCAGAGTTGCTAAGTGACTTCTTA 59.461 40.000 0.00 0.00 0.00 2.10
1301 4111 1.660575 CGTCGTTTCGGTGCTCACT 60.661 57.895 0.00 0.00 0.00 3.41
1328 4138 0.462047 GATCGGAGTTGGAATGCCGT 60.462 55.000 0.00 0.00 43.92 5.68
1338 4148 1.271934 TGGAATGCCGTGGATTGTTTG 59.728 47.619 0.00 0.00 36.79 2.93
1370 4182 2.284515 ATTCCCGGGGCTGATGGAAC 62.285 60.000 23.50 0.00 39.54 3.62
1375 4187 0.105039 CGGGGCTGATGGAACTAGAC 59.895 60.000 0.00 0.00 0.00 2.59
1386 4198 1.202382 GGAACTAGACGACGATTGGGG 60.202 57.143 0.00 0.00 0.00 4.96
1418 4230 6.659745 TTGATGGAATTGGATGGATTCATC 57.340 37.500 5.30 5.30 46.78 2.92
1420 4232 6.008331 TGATGGAATTGGATGGATTCATCTC 58.992 40.000 13.81 3.40 46.70 2.75
1502 4350 8.692110 TTAATATTTACTTGCGACGAGAGAAA 57.308 30.769 0.00 0.00 0.00 2.52
1511 4359 1.318785 CGACGAGAGAAAACGAGCATG 59.681 52.381 0.00 0.00 0.00 4.06
1589 4437 6.889301 ATTTCGGATGCATTCTTGATACAT 57.111 33.333 0.00 0.00 0.00 2.29
1626 4475 1.154197 CCACCATGCGATGCAGATAG 58.846 55.000 0.00 0.00 43.65 2.08
1636 4485 5.154222 TGCGATGCAGATAGAGTTATAACG 58.846 41.667 9.91 0.00 33.32 3.18
1673 4542 3.451141 TTTCCACAAACAAGGATGTGC 57.549 42.857 0.51 0.00 44.32 4.57
1686 4562 3.490348 AGGATGTGCCAATACCATAAGC 58.510 45.455 0.00 0.00 40.02 3.09
1814 4691 2.756907 ACAGATCAGTAGGAGGCACAT 58.243 47.619 0.00 0.00 0.00 3.21
1827 4704 3.558321 GGAGGCACATTGTTGGTGTACTA 60.558 47.826 0.00 0.00 38.51 1.82
1862 4746 3.064324 GGCAGTGGCATGACACCC 61.064 66.667 28.23 19.05 42.28 4.61
1900 4784 0.333312 TGGTTGAAGGGTGTGTGGTT 59.667 50.000 0.00 0.00 0.00 3.67
1920 4804 1.886777 GAGGAAGAGCGCTGCCATC 60.887 63.158 18.48 6.94 43.05 3.51
1938 4822 2.250939 CGGTTTGGCTTGAGTGCGA 61.251 57.895 0.00 0.00 0.00 5.10
2053 4937 1.446907 CATGCTTGAGTGTGGAGGAC 58.553 55.000 0.00 0.00 0.00 3.85
2135 5019 3.132111 GGATTGGGTTGTTTGTGTGTTCT 59.868 43.478 0.00 0.00 0.00 3.01
2144 5028 4.671377 TGTTTGTGTGTTCTGATTTGAGC 58.329 39.130 0.00 0.00 0.00 4.26
2180 5064 4.041567 TGAAGTTTCAAGGGTCTATCAGCA 59.958 41.667 0.00 0.00 33.55 4.41
2189 5073 1.542108 GGTCTATCAGCAGGGCATCAC 60.542 57.143 0.00 0.00 0.00 3.06
2377 5269 8.413229 CAAAAAGGAGGAAAACTTCATTAGTGA 58.587 33.333 0.00 0.00 37.12 3.41
2407 5299 3.253188 GCACTAGGAAAACTGCATGACAA 59.747 43.478 0.00 0.00 0.00 3.18
2412 5304 7.281774 CACTAGGAAAACTGCATGACAATCTAT 59.718 37.037 0.00 0.00 0.00 1.98
2485 5377 2.557924 TGGCTAGCACCAAAATCAAGTG 59.442 45.455 18.24 0.00 36.55 3.16
2488 5380 3.366374 GCTAGCACCAAAATCAAGTGGAC 60.366 47.826 10.63 0.00 38.36 4.02
2503 5395 3.393800 AGTGGACGAGTTCAAATGACAG 58.606 45.455 0.00 0.00 0.00 3.51
2514 5406 7.201393 CGAGTTCAAATGACAGTGTCTTCTATC 60.201 40.741 23.29 10.37 33.15 2.08
2593 5485 6.176183 GGCTACATTGCATAATAGGATCACT 58.824 40.000 0.00 0.00 34.04 3.41
2629 5521 2.298163 CCCTTGCTGTTTGCTTCTCAAT 59.702 45.455 0.00 0.00 43.37 2.57
2853 5747 9.778741 GGTATTCTCTTAATATCCAACATCACA 57.221 33.333 0.00 0.00 0.00 3.58
2923 5817 0.469144 GACAACTGGCCCCTGGAAAA 60.469 55.000 0.00 0.00 0.00 2.29
2928 5822 1.272704 ACTGGCCCCTGGAAAATTCTC 60.273 52.381 0.00 0.00 0.00 2.87
2936 5830 4.711355 CCCCTGGAAAATTCTCTGCAATTA 59.289 41.667 0.00 0.00 0.00 1.40
2969 5863 6.256975 CCGATATTTTGTTGAGATAACGTCCA 59.743 38.462 0.00 0.00 0.00 4.02
2970 5864 7.042051 CCGATATTTTGTTGAGATAACGTCCAT 60.042 37.037 0.00 0.00 0.00 3.41
2971 5865 8.974408 CGATATTTTGTTGAGATAACGTCCATA 58.026 33.333 0.00 0.00 0.00 2.74
2976 5870 8.786826 TTTGTTGAGATAACGTCCATAAATCT 57.213 30.769 0.00 0.00 0.00 2.40
3122 6017 4.678574 GCCATGCATTTTCTACATGAGCAA 60.679 41.667 0.00 0.00 43.04 3.91
3153 6048 2.464782 TGAGTGCTCCATCATGAGACT 58.535 47.619 0.09 0.00 34.11 3.24
3301 6198 4.212214 CCTTTTCGTCTCAACAGAGAAAGG 59.788 45.833 8.48 8.48 39.94 3.11
3312 6209 6.169094 TCAACAGAGAAAGGATCATCTTGTC 58.831 40.000 0.00 0.00 0.00 3.18
3313 6210 5.752036 ACAGAGAAAGGATCATCTTGTCA 57.248 39.130 0.00 0.00 0.00 3.58
3586 6483 6.205076 AGTCGATGCTAATTATGTAGAGACGT 59.795 38.462 0.00 0.00 0.00 4.34
3619 6516 4.372656 TGCTTTGGTTTATCGGTTTTTGG 58.627 39.130 0.00 0.00 0.00 3.28
3637 6536 9.020731 GGTTTTTGGACTAGATTATTGAAGGAA 57.979 33.333 0.00 0.00 0.00 3.36
3824 6723 7.165485 TCTTCAAGAATCGATTCCAAAGGTTA 58.835 34.615 29.82 14.30 37.51 2.85
4036 6944 7.201741 GGCCAAGTAAGTCAGAAAATATCTTCC 60.202 40.741 0.00 0.00 35.73 3.46
4099 7007 1.461127 GCTTCAAGTGAGCAGGTAACG 59.539 52.381 0.00 0.00 46.39 3.18
4119 7027 2.874701 CGCCCTGTTTTCCTATGATCAG 59.125 50.000 0.09 0.00 0.00 2.90
4180 7088 9.708222 CAGATATTTTGTTTAATGAGACTTCGG 57.292 33.333 0.00 0.00 0.00 4.30
4209 7117 0.032416 AGGTCCAGGCTGTATACCGT 60.032 55.000 14.43 5.63 35.32 4.83
4309 7217 1.117150 ACACCGGCGTCCTGTTATAT 58.883 50.000 6.01 0.00 0.00 0.86
4356 7264 7.599998 GCTGTCTCAAATGGAAATATTGTGTTT 59.400 33.333 0.00 0.00 0.00 2.83
4365 7273 5.986135 TGGAAATATTGTGTTTGGTTTTCCG 59.014 36.000 0.00 0.00 42.13 4.30
4372 7280 3.181485 TGTGTTTGGTTTTCCGGTTCATC 60.181 43.478 0.00 0.00 44.36 2.92
4387 7295 1.596203 CATCGGCTCCATGCGACAT 60.596 57.895 0.00 0.00 44.05 3.06
4440 7362 5.471116 TGTGAACTGATGAGGAAGAACATTG 59.529 40.000 0.00 0.00 0.00 2.82
4515 7437 4.846779 ATGTAACAGCACGGTTTTCATT 57.153 36.364 0.00 0.00 32.29 2.57
4541 7463 8.936070 ACACTATAGCGAACATGTTTACATAA 57.064 30.769 13.36 0.00 34.26 1.90
4542 7464 8.814235 ACACTATAGCGAACATGTTTACATAAC 58.186 33.333 13.36 0.00 34.26 1.89
4565 7493 7.908193 ACGTTTAAAGATGCTTGTAGTTTTG 57.092 32.000 0.00 0.00 0.00 2.44
4567 7495 6.362283 CGTTTAAAGATGCTTGTAGTTTTGGG 59.638 38.462 0.00 0.00 0.00 4.12
4568 7496 7.430441 GTTTAAAGATGCTTGTAGTTTTGGGA 58.570 34.615 0.00 0.00 0.00 4.37
4572 7500 6.029346 AGATGCTTGTAGTTTTGGGATTTG 57.971 37.500 0.00 0.00 0.00 2.32
4575 7503 4.202202 TGCTTGTAGTTTTGGGATTTGTGG 60.202 41.667 0.00 0.00 0.00 4.17
4578 7506 6.546428 TTGTAGTTTTGGGATTTGTGGAAA 57.454 33.333 0.00 0.00 0.00 3.13
4579 7507 5.908341 TGTAGTTTTGGGATTTGTGGAAAC 58.092 37.500 0.00 0.00 0.00 2.78
4580 7508 4.053469 AGTTTTGGGATTTGTGGAAACG 57.947 40.909 0.00 0.00 33.52 3.60
4584 7512 3.773418 TGGGATTTGTGGAAACGTCTA 57.227 42.857 0.00 0.00 0.00 2.59
4622 7551 8.907222 ACATTTCAGTTTAATGCTCCAAAATT 57.093 26.923 0.00 0.00 36.65 1.82
4623 7552 8.776470 ACATTTCAGTTTAATGCTCCAAAATTG 58.224 29.630 0.00 0.00 36.65 2.32
4625 7554 5.237048 TCAGTTTAATGCTCCAAAATTGCC 58.763 37.500 0.00 0.00 0.00 4.52
4626 7555 4.091800 CAGTTTAATGCTCCAAAATTGCCG 59.908 41.667 0.00 0.00 0.00 5.69
4627 7556 4.021544 AGTTTAATGCTCCAAAATTGCCGA 60.022 37.500 0.00 0.00 0.00 5.54
4628 7557 4.734398 TTAATGCTCCAAAATTGCCGAT 57.266 36.364 0.00 0.00 0.00 4.18
4629 7558 2.589798 ATGCTCCAAAATTGCCGATG 57.410 45.000 0.00 0.00 0.00 3.84
4630 7559 0.108709 TGCTCCAAAATTGCCGATGC 60.109 50.000 0.00 0.00 38.26 3.91
4654 7583 1.074405 TCTTGAGTCCTGCTGCCAAAT 59.926 47.619 0.00 0.00 0.00 2.32
4740 7676 5.424121 ACATTTCTCAACAACTTCGAAGG 57.576 39.130 27.86 14.23 0.00 3.46
4756 7692 8.398878 ACTTCGAAGGTGGTTTATTTTATTGA 57.601 30.769 27.86 0.00 0.00 2.57
4757 7693 8.852135 ACTTCGAAGGTGGTTTATTTTATTGAA 58.148 29.630 27.86 0.00 0.00 2.69
4758 7694 9.685828 CTTCGAAGGTGGTTTATTTTATTGAAA 57.314 29.630 17.70 0.00 0.00 2.69
4800 7736 1.067516 CCAGGTTTGCTGACACCAAAG 59.932 52.381 0.00 0.00 35.25 2.77
4801 7737 0.746659 AGGTTTGCTGACACCAAAGC 59.253 50.000 14.72 14.72 45.82 3.51
4809 7745 2.153645 CTGACACCAAAGCAGCATACA 58.846 47.619 0.00 0.00 0.00 2.29
4823 7759 8.606040 AAGCAGCATACATTTACAAACATTTT 57.394 26.923 0.00 0.00 0.00 1.82
4829 7765 7.944120 GCATACATTTACAAACATTTTGTCACG 59.056 33.333 7.54 0.00 34.11 4.35
4845 7781 0.096976 CACGCCGCCTCATTTACAAG 59.903 55.000 0.00 0.00 0.00 3.16
4898 7834 2.044650 GCTCTGCCTCATTGCCCA 60.045 61.111 0.00 0.00 0.00 5.36
4974 7910 4.084287 CACCTGGATCCCATTTCCATATG 58.916 47.826 9.90 0.00 42.26 1.78
4975 7911 3.094572 CCTGGATCCCATTTCCATATGC 58.905 50.000 9.90 0.00 42.26 3.14
5111 8075 4.007659 CCACTTGGGGTTAACATGTCTAC 58.992 47.826 8.10 0.00 0.00 2.59
5113 8077 4.454504 CACTTGGGGTTAACATGTCTACAC 59.545 45.833 8.10 0.97 0.00 2.90
5124 8088 3.904339 ACATGTCTACACTGAAGAGGGTT 59.096 43.478 0.00 0.00 37.01 4.11
5172 8136 5.122869 CCAAGTCATGTCTACATTGAACAGG 59.877 44.000 0.00 0.00 33.61 4.00
5173 8137 5.745312 AGTCATGTCTACATTGAACAGGA 57.255 39.130 0.00 0.00 33.61 3.86
5210 8174 1.303561 TGGCTCACCACTTGGCATC 60.304 57.895 0.00 0.00 42.67 3.91
5211 8175 1.303561 GGCTCACCACTTGGCATCA 60.304 57.895 0.00 0.00 39.32 3.07
5216 8180 1.203038 TCACCACTTGGCATCAATGGT 60.203 47.619 6.65 6.65 44.58 3.55
5218 8182 1.619827 ACCACTTGGCATCAATGGTTG 59.380 47.619 6.65 0.00 40.86 3.77
5225 8189 0.896923 GCATCAATGGTTGGGCTTGA 59.103 50.000 0.00 0.00 33.75 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 183 6.030548 TGTTCACACTTTCCAAAATGTTCA 57.969 33.333 0.00 0.00 0.00 3.18
178 184 7.538303 AATGTTCACACTTTCCAAAATGTTC 57.462 32.000 0.00 0.00 0.00 3.18
513 3310 2.906354 ACACCCAAGCGATGATAACTC 58.094 47.619 0.00 0.00 0.00 3.01
518 3315 1.369091 GCGAACACCCAAGCGATGAT 61.369 55.000 0.00 0.00 0.00 2.45
663 3465 9.626045 GGATCGAAAAATGAGAAACTATGTTTT 57.374 29.630 0.00 0.00 0.00 2.43
766 3568 4.164843 ACTCTGGAGTGCCAACTAAAAA 57.835 40.909 2.15 0.00 45.41 1.94
767 3569 3.857157 ACTCTGGAGTGCCAACTAAAA 57.143 42.857 2.15 0.00 45.41 1.52
768 3570 3.476552 CAACTCTGGAGTGCCAACTAAA 58.523 45.455 3.88 0.00 45.41 1.85
769 3571 2.810400 GCAACTCTGGAGTGCCAACTAA 60.810 50.000 3.88 0.00 45.41 2.24
770 3572 1.270839 GCAACTCTGGAGTGCCAACTA 60.271 52.381 3.88 0.00 45.41 2.24
771 3573 0.536006 GCAACTCTGGAGTGCCAACT 60.536 55.000 3.88 0.00 45.41 3.16
1203 4007 2.614001 GGGGGAGCTCTCACTTGAT 58.386 57.895 17.22 0.00 32.48 2.57
1226 4030 1.069358 GATAGAGGAACAGAAGGGCGG 59.931 57.143 0.00 0.00 0.00 6.13
1228 4032 4.495690 AAAGATAGAGGAACAGAAGGGC 57.504 45.455 0.00 0.00 0.00 5.19
1301 4111 1.974957 TCCAACTCCGATCTTGAACCA 59.025 47.619 0.00 0.00 0.00 3.67
1328 4138 9.853555 GAATATAACAATCACACAAACAATCCA 57.146 29.630 0.00 0.00 0.00 3.41
1338 4148 3.818773 CCCCGGGAATATAACAATCACAC 59.181 47.826 26.32 0.00 0.00 3.82
1370 4182 0.822164 AACCCCCAATCGTCGTCTAG 59.178 55.000 0.00 0.00 0.00 2.43
1375 4187 0.321298 AGAACAACCCCCAATCGTCG 60.321 55.000 0.00 0.00 0.00 5.12
1386 4198 5.467035 TCCAATTCCATCAAAGAACAACC 57.533 39.130 0.00 0.00 0.00 3.77
1418 4230 4.940046 AGCATATCAAACCAAGTCACTGAG 59.060 41.667 0.00 0.00 0.00 3.35
1420 4232 6.149308 TGTTAGCATATCAAACCAAGTCACTG 59.851 38.462 0.00 0.00 0.00 3.66
1502 4350 2.028112 TGTTCTAGAAGGCATGCTCGTT 60.028 45.455 18.92 8.90 0.00 3.85
1547 4395 5.061311 CGAAATTATCACAGCAAAAGCCAAG 59.939 40.000 0.00 0.00 0.00 3.61
1556 4404 3.277715 TGCATCCGAAATTATCACAGCA 58.722 40.909 0.00 0.00 0.00 4.41
1589 4437 5.343715 TGGTGGGGTAACTTAGACTATCAA 58.656 41.667 0.00 0.00 0.00 2.57
1733 4609 1.556911 CACTGTCCAGGCATAGGTCTT 59.443 52.381 0.00 0.00 0.00 3.01
1814 4691 7.691213 TCCTGGAATAAATAGTACACCAACAA 58.309 34.615 0.00 0.00 0.00 2.83
1827 4704 1.202818 GCCGCCTCTCCTGGAATAAAT 60.203 52.381 0.00 0.00 0.00 1.40
1862 4746 2.332104 CAGGACGCCGATGAATATGAG 58.668 52.381 0.00 0.00 0.00 2.90
1900 4784 4.087892 GGCAGCGCTCTTCCTCCA 62.088 66.667 7.13 0.00 0.00 3.86
1920 4804 1.781025 TTCGCACTCAAGCCAAACCG 61.781 55.000 0.00 0.00 0.00 4.44
1938 4822 3.612247 CTGCTACTGCCGCCACCTT 62.612 63.158 0.00 0.00 38.71 3.50
2053 4937 1.599606 CTCCACCAGGTGTCTCCTCG 61.600 65.000 18.82 1.08 46.24 4.63
2135 5019 0.817013 GCCCCAAATCGCTCAAATCA 59.183 50.000 0.00 0.00 0.00 2.57
2144 5028 1.256812 AACTTCAAGGCCCCAAATCG 58.743 50.000 0.00 0.00 0.00 3.34
2180 5064 3.323403 GCTGATACTCTTAGTGATGCCCT 59.677 47.826 0.00 0.00 0.00 5.19
2189 5073 8.354711 TCATAATACCCTGCTGATACTCTTAG 57.645 38.462 0.00 0.00 0.00 2.18
2346 5237 6.764379 TGAAGTTTTCCTCCTTTTTGTGTTT 58.236 32.000 0.00 0.00 0.00 2.83
2363 5255 7.448469 AGTGCCACTATTTCACTAATGAAGTTT 59.552 33.333 0.00 0.00 45.54 2.66
2377 5269 4.459337 GCAGTTTTCCTAGTGCCACTATTT 59.541 41.667 4.77 0.00 38.30 1.40
2485 5377 3.131396 ACACTGTCATTTGAACTCGTCC 58.869 45.455 0.00 0.00 0.00 4.79
2488 5380 4.747108 AGAAGACACTGTCATTTGAACTCG 59.253 41.667 11.80 0.00 34.60 4.18
2514 5406 7.953158 ATGTGACCATTCATAGACTTAATCG 57.047 36.000 0.00 0.00 33.11 3.34
2593 5485 3.328931 AGCAAGGGAAAAGACTGATCTCA 59.671 43.478 0.00 0.00 32.34 3.27
2601 5493 2.473816 GCAAACAGCAAGGGAAAAGAC 58.526 47.619 0.00 0.00 44.79 3.01
2629 5521 1.202989 TGGGCTCACTGCAAATTACCA 60.203 47.619 0.00 0.00 45.15 3.25
2699 5593 7.485810 TCTGCTTAAAAGGGAAAGTTTTGTAC 58.514 34.615 0.00 0.00 0.00 2.90
2853 5747 7.139896 TGCACTGAACGATAACACAAAATAT 57.860 32.000 0.00 0.00 0.00 1.28
2859 5753 2.036604 TCCTGCACTGAACGATAACACA 59.963 45.455 0.00 0.00 0.00 3.72
2868 5762 3.664107 TGTAAGTCATCCTGCACTGAAC 58.336 45.455 0.00 0.00 0.00 3.18
2923 5817 8.682936 ATCGGTAGAAAATAATTGCAGAGAAT 57.317 30.769 0.00 0.00 0.00 2.40
2943 5837 6.257193 GGACGTTATCTCAACAAAATATCGGT 59.743 38.462 0.00 0.00 0.00 4.69
2990 5884 7.451255 ACCTAGAATCCAACATTGACATCAAAA 59.549 33.333 0.00 0.00 39.55 2.44
3169 6064 0.687354 TCTTCCTCCAACAGGTCAGC 59.313 55.000 0.00 0.00 43.95 4.26
3265 6162 6.070767 TGAGACGAAAAGGACCTATGATTTCT 60.071 38.462 12.45 3.80 0.00 2.52
3301 6198 2.548904 GGCATGAGCTGACAAGATGATC 59.451 50.000 0.00 0.00 41.70 2.92
3312 6209 2.048444 ACACCTTATGGCATGAGCTG 57.952 50.000 13.43 12.51 41.70 4.24
3313 6210 2.372264 CAACACCTTATGGCATGAGCT 58.628 47.619 13.43 0.00 41.70 4.09
3417 6314 6.038997 ACCTTCAGTTCTGTCCACTATTAC 57.961 41.667 0.00 0.00 0.00 1.89
3586 6483 4.399004 AAACCAAAGCAATGCACTTGTA 57.601 36.364 8.35 0.00 37.18 2.41
3637 6536 5.675684 CAAGGTTTTGGGCCTTATATTGT 57.324 39.130 4.53 0.00 43.87 2.71
3824 6723 5.362263 ACGTGTGAACCAGTTTAATACACT 58.638 37.500 0.00 0.00 35.92 3.55
4036 6944 9.942850 ATTTTTACAGAAACATATTTTCCCCTG 57.057 29.630 0.00 0.00 0.00 4.45
4099 7007 4.156455 TCTGATCATAGGAAAACAGGGC 57.844 45.455 0.00 0.00 0.00 5.19
4119 7027 7.278461 TCTAGGTTGCAGACTAGAATACATC 57.722 40.000 20.63 0.00 41.84 3.06
4180 7088 0.668535 GCCTGGACCTGAACAACAAC 59.331 55.000 0.00 0.00 0.00 3.32
4209 7117 4.033009 TCCTGTTATCTCTTCTCATGGCA 58.967 43.478 0.00 0.00 0.00 4.92
4309 7217 4.638421 AGCACTTACAAGTACAGCAAAACA 59.362 37.500 0.00 0.00 37.08 2.83
4330 7238 6.624423 ACACAATATTTCCATTTGAGACAGC 58.376 36.000 0.00 0.00 0.00 4.40
4365 7273 2.537560 CGCATGGAGCCGATGAACC 61.538 63.158 0.00 0.00 41.38 3.62
4372 7280 0.583438 CTTTATGTCGCATGGAGCCG 59.417 55.000 0.00 0.00 41.38 5.52
4440 7362 3.744238 ATTTGGGCCAAAGTAACACAC 57.256 42.857 32.84 0.00 36.76 3.82
4541 7463 6.915843 CCAAAACTACAAGCATCTTTAAACGT 59.084 34.615 0.00 0.00 0.00 3.99
4542 7464 6.362283 CCCAAAACTACAAGCATCTTTAAACG 59.638 38.462 0.00 0.00 0.00 3.60
4564 7492 2.649531 AGACGTTTCCACAAATCCCA 57.350 45.000 0.00 0.00 0.00 4.37
4565 7493 4.258543 TCATAGACGTTTCCACAAATCCC 58.741 43.478 0.00 0.00 0.00 3.85
4567 7495 7.693951 CAGATTTCATAGACGTTTCCACAAATC 59.306 37.037 0.00 0.88 0.00 2.17
4568 7496 7.174946 ACAGATTTCATAGACGTTTCCACAAAT 59.825 33.333 0.00 0.00 0.00 2.32
4572 7500 7.772332 ATACAGATTTCATAGACGTTTCCAC 57.228 36.000 0.00 0.00 0.00 4.02
4623 7552 0.723981 GACTCAAGACTTGCATCGGC 59.276 55.000 10.50 0.00 41.68 5.54
4625 7554 1.998315 CAGGACTCAAGACTTGCATCG 59.002 52.381 10.50 1.86 0.00 3.84
4626 7555 1.736681 GCAGGACTCAAGACTTGCATC 59.263 52.381 10.50 9.65 40.95 3.91
4627 7556 1.350351 AGCAGGACTCAAGACTTGCAT 59.650 47.619 16.09 0.52 42.89 3.96
4628 7557 0.761187 AGCAGGACTCAAGACTTGCA 59.239 50.000 16.09 0.00 42.89 4.08
4629 7558 1.155042 CAGCAGGACTCAAGACTTGC 58.845 55.000 10.50 8.16 41.40 4.01
4630 7559 1.155042 GCAGCAGGACTCAAGACTTG 58.845 55.000 9.03 9.03 0.00 3.16
4633 7562 0.250467 TTGGCAGCAGGACTCAAGAC 60.250 55.000 0.00 0.00 0.00 3.01
4634 7563 0.473755 TTTGGCAGCAGGACTCAAGA 59.526 50.000 0.00 0.00 0.00 3.02
4635 7564 1.542492 ATTTGGCAGCAGGACTCAAG 58.458 50.000 0.00 0.00 0.00 3.02
4636 7565 2.877097 TATTTGGCAGCAGGACTCAA 57.123 45.000 0.00 0.00 0.00 3.02
4637 7566 2.877097 TTATTTGGCAGCAGGACTCA 57.123 45.000 0.00 0.00 0.00 3.41
4688 7617 7.121611 TCACCAATGTATGTAGTAAGTCGAAGA 59.878 37.037 0.00 0.00 0.00 2.87
4693 7622 8.870879 GTTTCTCACCAATGTATGTAGTAAGTC 58.129 37.037 0.00 0.00 0.00 3.01
4730 7666 8.852135 TCAATAAAATAAACCACCTTCGAAGTT 58.148 29.630 23.03 12.89 0.00 2.66
4756 7692 7.992033 TGGATTCCTTGTGTCAATTTTCAATTT 59.008 29.630 3.95 0.00 0.00 1.82
4757 7693 7.507829 TGGATTCCTTGTGTCAATTTTCAATT 58.492 30.769 3.95 0.00 0.00 2.32
4758 7694 7.065120 TGGATTCCTTGTGTCAATTTTCAAT 57.935 32.000 3.95 0.00 0.00 2.57
4759 7695 6.462768 CCTGGATTCCTTGTGTCAATTTTCAA 60.463 38.462 3.95 0.00 0.00 2.69
4760 7696 5.010922 CCTGGATTCCTTGTGTCAATTTTCA 59.989 40.000 3.95 0.00 0.00 2.69
4761 7697 5.011023 ACCTGGATTCCTTGTGTCAATTTTC 59.989 40.000 0.00 0.00 0.00 2.29
4762 7698 4.901250 ACCTGGATTCCTTGTGTCAATTTT 59.099 37.500 0.00 0.00 0.00 1.82
4766 7702 3.593442 AACCTGGATTCCTTGTGTCAA 57.407 42.857 0.00 0.00 0.00 3.18
4773 7709 2.158475 TGTCAGCAAACCTGGATTCCTT 60.158 45.455 0.00 0.00 42.05 3.36
4800 7736 7.795859 ACAAAATGTTTGTAAATGTATGCTGC 58.204 30.769 4.59 0.00 0.00 5.25
4801 7737 8.976471 TGACAAAATGTTTGTAAATGTATGCTG 58.024 29.630 6.36 0.00 31.96 4.41
4802 7738 8.977505 GTGACAAAATGTTTGTAAATGTATGCT 58.022 29.630 6.36 0.00 31.96 3.79
4803 7739 7.944120 CGTGACAAAATGTTTGTAAATGTATGC 59.056 33.333 6.36 0.00 31.96 3.14
4804 7740 7.944120 GCGTGACAAAATGTTTGTAAATGTATG 59.056 33.333 6.36 0.00 31.96 2.39
4805 7741 7.115663 GGCGTGACAAAATGTTTGTAAATGTAT 59.884 33.333 6.36 0.00 31.96 2.29
4806 7742 6.418226 GGCGTGACAAAATGTTTGTAAATGTA 59.582 34.615 6.36 0.00 31.96 2.29
4807 7743 5.233263 GGCGTGACAAAATGTTTGTAAATGT 59.767 36.000 6.36 0.00 31.96 2.71
4809 7745 4.442733 CGGCGTGACAAAATGTTTGTAAAT 59.557 37.500 6.36 0.00 31.96 1.40
4823 7759 1.017177 GTAAATGAGGCGGCGTGACA 61.017 55.000 9.37 6.63 0.00 3.58
4829 7765 1.732405 GCAACTTGTAAATGAGGCGGC 60.732 52.381 0.00 0.00 0.00 6.53
4845 7781 2.742053 TGAGGCAGACGATTTTAGCAAC 59.258 45.455 0.00 0.00 0.00 4.17
4898 7834 6.936279 TCGAGAATTTGAGATTTGTACCTCT 58.064 36.000 0.00 0.00 0.00 3.69
4903 7839 7.433708 TGCTTTCGAGAATTTGAGATTTGTA 57.566 32.000 0.00 0.00 0.00 2.41
4996 7932 0.819582 TAACCCGTAGAAAGGAGCGG 59.180 55.000 0.00 0.00 43.40 5.52
5055 7991 5.360649 TGGACATGGAAATACGTTATCCA 57.639 39.130 16.03 16.03 46.60 3.41
5111 8075 6.318900 GGTTTATTCCATAACCCTCTTCAGTG 59.681 42.308 0.00 0.00 0.00 3.66
5113 8077 6.423182 TGGTTTATTCCATAACCCTCTTCAG 58.577 40.000 0.00 0.00 29.52 3.02
5124 8088 5.139727 CAAGCCCTGATGGTTTATTCCATA 58.860 41.667 0.00 0.00 46.72 2.74
5172 8136 7.609146 TGAGCCATGATGATTTCTACCATTATC 59.391 37.037 0.00 0.00 0.00 1.75
5173 8137 7.392673 GTGAGCCATGATGATTTCTACCATTAT 59.607 37.037 0.00 0.00 0.00 1.28
5210 8174 0.251742 TCCCTCAAGCCCAACCATTG 60.252 55.000 0.00 0.00 0.00 2.82
5211 8175 0.251787 GTCCCTCAAGCCCAACCATT 60.252 55.000 0.00 0.00 0.00 3.16
5216 8180 1.352622 ACACTGTCCCTCAAGCCCAA 61.353 55.000 0.00 0.00 0.00 4.12
5218 8182 0.036294 GTACACTGTCCCTCAAGCCC 60.036 60.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.