Multiple sequence alignment - TraesCS7D01G315300

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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 TraesCS7D01G315300 chr7D 100.000 7347 0 0 1 7347 401154418 401147072 0.000000e+00 13568.0
1 TraesCS7D01G315300 chr7D 90.062 161 16 0 6721 6881 454079251 454079411 7.470000e-50 209.0
2 TraesCS7D01G315300 chr7B 98.052 2824 30 9 2558 5380 410848780 410845981 0.000000e+00 4887.0
3 TraesCS7D01G315300 chr7B 98.755 1847 18 3 654 2500 410850885 410849044 0.000000e+00 3278.0
4 TraesCS7D01G315300 chr7B 96.626 1986 26 6 5363 7347 410845795 410843850 0.000000e+00 3258.0
5 TraesCS7D01G315300 chr7B 83.932 473 51 7 21 492 410851660 410851212 5.270000e-116 429.0
6 TraesCS7D01G315300 chr7B 97.500 80 2 0 2481 2560 410848982 410848903 3.570000e-28 137.0
7 TraesCS7D01G315300 chr7A 88.530 4185 271 75 20 4121 459013348 459009290 0.000000e+00 4876.0
8 TraesCS7D01G315300 chr7A 92.501 2067 115 21 5237 7290 459007851 459005812 0.000000e+00 2922.0
9 TraesCS7D01G315300 chr7A 92.974 612 33 5 4588 5199 459008452 459007851 0.000000e+00 883.0
10 TraesCS7D01G315300 chr7A 91.515 165 13 1 4293 4457 459009267 459009104 7.420000e-55 226.0
11 TraesCS7D01G315300 chr7A 96.212 132 5 0 4442 4573 459008917 459008786 4.460000e-52 217.0
12 TraesCS7D01G315300 chr7A 88.024 167 18 1 6721 6887 253801833 253801669 5.820000e-46 196.0
13 TraesCS7D01G315300 chr5D 93.333 165 10 1 6721 6884 529218323 529218159 7.360000e-60 243.0
14 TraesCS7D01G315300 chr5D 85.057 174 25 1 6721 6893 83262595 83262768 7.580000e-40 176.0
15 TraesCS7D01G315300 chr2D 90.909 165 15 0 6721 6885 134301645 134301481 9.590000e-54 222.0
16 TraesCS7D01G315300 chr4D 91.304 161 14 0 6721 6881 34661684 34661524 3.450000e-53 220.0
17 TraesCS7D01G315300 chr5A 90.683 161 15 0 6721 6881 320214248 320214408 1.610000e-51 215.0
18 TraesCS7D01G315300 chr5A 92.806 139 10 0 6585 6723 439420898 439421036 1.250000e-47 202.0
19 TraesCS7D01G315300 chr2B 91.083 157 14 0 6722 6878 608226881 608226725 5.770000e-51 213.0
20 TraesCS7D01G315300 chr2B 93.333 135 9 0 6592 6726 118598305 118598171 4.500000e-47 200.0
21 TraesCS7D01G315300 chr2B 84.444 180 22 5 6716 6889 280474010 280474189 9.800000e-39 172.0
22 TraesCS7D01G315300 chr6D 88.202 178 16 4 6721 6894 67077713 67077537 2.690000e-49 207.0
23 TraesCS7D01G315300 chr3B 93.525 139 8 1 6585 6723 354011252 354011389 9.660000e-49 206.0
24 TraesCS7D01G315300 chr4A 91.275 149 11 2 6579 6726 658953947 658953800 1.250000e-47 202.0
25 TraesCS7D01G315300 chr5B 94.574 129 7 0 6595 6723 633962542 633962670 4.500000e-47 200.0
26 TraesCS7D01G315300 chr5B 94.595 37 1 1 2586 2622 619156840 619156875 1.000000e-03 56.5
27 TraesCS7D01G315300 chr5B 94.595 37 1 1 2586 2622 619210695 619210730 1.000000e-03 56.5
28 TraesCS7D01G315300 chr1B 93.939 132 8 0 6592 6723 47635563 47635694 4.500000e-47 200.0
29 TraesCS7D01G315300 chr6B 92.086 139 10 1 6586 6723 490650493 490650631 2.090000e-45 195.0
30 TraesCS7D01G315300 chr6B 92.857 56 3 1 6884 6939 199935469 199935415 6.110000e-11 80.5
31 TraesCS7D01G315300 chrUn 86.286 175 19 4 6721 6892 141680903 141680731 1.260000e-42 185.0
32 TraesCS7D01G315300 chrUn 94.595 37 1 1 2586 2622 334690248 334690213 1.000000e-03 56.5
33 TraesCS7D01G315300 chr3D 87.117 163 14 6 6721 6878 540545287 540545447 2.110000e-40 178.0
34 TraesCS7D01G315300 chr1D 85.882 170 21 2 6721 6887 286391227 286391058 2.110000e-40 178.0
35 TraesCS7D01G315300 chr6A 94.643 56 2 1 6884 6939 135448767 135448713 1.310000e-12 86.1


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 TraesCS7D01G315300 chr7D 401147072 401154418 7346 True 13568.0 13568 100.0000 1 7347 1 chr7D.!!$R1 7346
1 TraesCS7D01G315300 chr7B 410843850 410851660 7810 True 2397.8 4887 94.9730 21 7347 5 chr7B.!!$R1 7326
2 TraesCS7D01G315300 chr7A 459005812 459013348 7536 True 1824.8 4876 92.3464 20 7290 5 chr7A.!!$R2 7270

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
313 314 0.033504 CAACTAGACTGGTGCACGGT 59.966 55.000 11.45 12.21 42.79 4.83 F
398 419 0.388520 TGACACTGTCGGCGATTCAG 60.389 55.000 21.54 21.54 34.95 3.02 F
1358 1581 1.007336 GCGTCCGAGTACCAACTGTG 61.007 60.000 0.00 0.00 35.56 3.66 F
1888 2115 2.011947 TGCCTCTTCAAATCATGAGCG 58.988 47.619 0.09 0.00 39.77 5.03 F
2643 3102 9.959749 CCTTAGTAATTGAAAACTAGTGCAAAA 57.040 29.630 0.00 0.00 30.27 2.44 F
3571 4039 1.383525 CCGGCCCCCTAGAGGTTTA 60.384 63.158 0.00 0.00 0.00 2.01 F
3572 4040 1.408453 CCGGCCCCCTAGAGGTTTAG 61.408 65.000 0.00 0.00 0.00 1.85 F
3573 4041 1.408453 CGGCCCCCTAGAGGTTTAGG 61.408 65.000 0.00 0.00 39.99 2.69 F
5017 6019 1.871772 CTTGGGCTTGCACTTCTCG 59.128 57.895 0.00 0.00 0.00 4.04 F
5255 6257 3.963129 TGGATGTTTGTATTGGACTCCC 58.037 45.455 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1358 1581 2.294233 TGTCAGACAATTCAGCAAAGCC 59.706 45.455 0.00 0.00 0.00 4.35 R
1888 2115 3.767278 CAAGCTGGAGCATCTTAAAAGC 58.233 45.455 0.65 0.00 45.16 3.51 R
2543 2877 1.625818 CTATTACCAGCTAGGGGGCAG 59.374 57.143 7.06 0.00 43.89 4.85 R
3256 3720 5.392595 CGCTAGCCTTGGTAAAAAGCATAAA 60.393 40.000 9.66 0.00 0.00 1.40 R
4417 4896 2.862541 TGCAGAATAAAGTGCACACCT 58.137 42.857 21.04 5.05 44.70 4.00 R
5017 6019 1.318158 CCAGCCAATTCCTGCCTGTC 61.318 60.000 0.00 0.00 0.00 3.51 R
5338 6340 3.883489 AGTGAACAAAAGTAAGGCAGGTC 59.117 43.478 0.00 0.00 0.00 3.85 R
5373 6579 5.295292 ACTCGGATTAAGATCACATTTGCAG 59.705 40.000 0.00 0.00 33.77 4.41 R
5905 7111 0.610232 ATCGGCCTTTGCAGCTTTCT 60.610 50.000 0.00 0.00 40.13 2.52 R
7243 8461 0.400213 TGGGCGGTCTGAGAACATTT 59.600 50.000 0.00 0.00 0.00 2.32 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
35 36 3.135895 CCCAATAGGTACGGTCCTTCATT 59.864 47.826 6.01 0.00 38.86 2.57
69 70 3.315191 GCTTCTGTGGTTTTGTAGCTTCA 59.685 43.478 0.00 0.00 0.00 3.02
118 119 1.374758 GCTGGTGTGGAAGTCGGAG 60.375 63.158 0.00 0.00 0.00 4.63
119 120 1.374758 CTGGTGTGGAAGTCGGAGC 60.375 63.158 0.00 0.00 0.00 4.70
120 121 2.432628 GGTGTGGAAGTCGGAGCG 60.433 66.667 0.00 0.00 0.00 5.03
141 142 2.718073 GGCGGCTCCGGAAGTCTAA 61.718 63.158 5.23 0.00 40.19 2.10
201 202 2.064581 GTCGGCTAGGTGGGTCCAT 61.065 63.158 0.00 0.00 39.02 3.41
254 255 1.930100 CGCCGAAGATCTCATGTGC 59.070 57.895 0.00 0.00 0.00 4.57
273 274 0.536460 CGTAGGGTGTTGGCTTTGGT 60.536 55.000 0.00 0.00 0.00 3.67
281 282 2.038557 GTGTTGGCTTTGGTCTCTAGGA 59.961 50.000 0.00 0.00 0.00 2.94
283 284 2.024176 TGGCTTTGGTCTCTAGGACA 57.976 50.000 11.82 0.00 46.16 4.02
289 290 4.389374 CTTTGGTCTCTAGGACAGCAAAA 58.611 43.478 11.82 6.94 46.16 2.44
312 313 0.317160 TCAACTAGACTGGTGCACGG 59.683 55.000 11.45 8.81 0.00 4.94
313 314 0.033504 CAACTAGACTGGTGCACGGT 59.966 55.000 11.45 12.21 42.79 4.83
364 365 2.541556 GCTCCGGATCTAAGTGTTGTC 58.458 52.381 3.57 0.00 0.00 3.18
398 419 0.388520 TGACACTGTCGGCGATTCAG 60.389 55.000 21.54 21.54 34.95 3.02
409 430 1.331756 GGCGATTCAGTTGGTGCATAG 59.668 52.381 0.00 0.00 0.00 2.23
410 431 2.009774 GCGATTCAGTTGGTGCATAGT 58.990 47.619 0.00 0.00 0.00 2.12
452 474 9.836076 TTATATCGTAGATGTATCGGTTTTCAG 57.164 33.333 0.00 0.00 45.12 3.02
453 475 5.571784 TCGTAGATGTATCGGTTTTCAGT 57.428 39.130 0.00 0.00 0.00 3.41
454 476 5.957798 TCGTAGATGTATCGGTTTTCAGTT 58.042 37.500 0.00 0.00 0.00 3.16
493 515 8.703378 AATTGGTCAATTCTCTCTTTTCTTCT 57.297 30.769 3.34 0.00 36.34 2.85
494 516 7.502120 TTGGTCAATTCTCTCTTTTCTTCTG 57.498 36.000 0.00 0.00 0.00 3.02
495 517 5.471456 TGGTCAATTCTCTCTTTTCTTCTGC 59.529 40.000 0.00 0.00 0.00 4.26
496 518 5.390356 GGTCAATTCTCTCTTTTCTTCTGCG 60.390 44.000 0.00 0.00 0.00 5.18
497 519 5.406780 GTCAATTCTCTCTTTTCTTCTGCGA 59.593 40.000 0.00 0.00 0.00 5.10
498 520 5.991606 TCAATTCTCTCTTTTCTTCTGCGAA 59.008 36.000 0.00 0.00 0.00 4.70
499 521 6.652481 TCAATTCTCTCTTTTCTTCTGCGAAT 59.348 34.615 0.00 0.00 0.00 3.34
500 522 5.852738 TTCTCTCTTTTCTTCTGCGAATG 57.147 39.130 0.00 0.00 0.00 2.67
501 523 5.139435 TCTCTCTTTTCTTCTGCGAATGA 57.861 39.130 0.00 0.00 0.00 2.57
502 524 5.541845 TCTCTCTTTTCTTCTGCGAATGAA 58.458 37.500 0.00 0.00 0.00 2.57
503 525 6.169094 TCTCTCTTTTCTTCTGCGAATGAAT 58.831 36.000 0.00 0.00 0.00 2.57
504 526 6.652481 TCTCTCTTTTCTTCTGCGAATGAATT 59.348 34.615 0.00 0.00 0.00 2.17
505 527 6.835914 TCTCTTTTCTTCTGCGAATGAATTC 58.164 36.000 0.00 0.00 0.00 2.17
506 528 6.652481 TCTCTTTTCTTCTGCGAATGAATTCT 59.348 34.615 7.05 0.00 34.69 2.40
507 529 6.835914 TCTTTTCTTCTGCGAATGAATTCTC 58.164 36.000 7.05 0.00 34.69 2.87
536 558 7.701539 TCTTAATGATGAAAAGGCAAAGCTA 57.298 32.000 0.00 0.00 0.00 3.32
539 561 5.990120 ATGATGAAAAGGCAAAGCTACTT 57.010 34.783 0.00 0.00 0.00 2.24
547 569 2.158608 AGGCAAAGCTACTTCCTGTTGT 60.159 45.455 0.00 0.00 0.00 3.32
549 571 3.550842 GGCAAAGCTACTTCCTGTTGTTG 60.551 47.826 0.00 0.00 0.00 3.33
550 572 3.632189 CAAAGCTACTTCCTGTTGTTGC 58.368 45.455 0.00 0.00 35.73 4.17
551 573 2.938956 AGCTACTTCCTGTTGTTGCT 57.061 45.000 0.00 0.00 39.58 3.91
552 574 3.214696 AGCTACTTCCTGTTGTTGCTT 57.785 42.857 0.00 0.00 41.01 3.91
557 580 4.376340 ACTTCCTGTTGTTGCTTGAAAG 57.624 40.909 0.00 0.00 0.00 2.62
624 756 7.930217 TGTGAACTGTAAACTTAGTAGTACGT 58.070 34.615 0.00 0.00 33.17 3.57
625 757 9.051679 TGTGAACTGTAAACTTAGTAGTACGTA 57.948 33.333 0.00 0.00 33.17 3.57
717 931 9.309224 AGAATTAATAACTTTTTACCCAGCTGT 57.691 29.630 13.81 0.00 0.00 4.40
1358 1581 1.007336 GCGTCCGAGTACCAACTGTG 61.007 60.000 0.00 0.00 35.56 3.66
1888 2115 2.011947 TGCCTCTTCAAATCATGAGCG 58.988 47.619 0.09 0.00 39.77 5.03
2643 3102 9.959749 CCTTAGTAATTGAAAACTAGTGCAAAA 57.040 29.630 0.00 0.00 30.27 2.44
3571 4039 1.383525 CCGGCCCCCTAGAGGTTTA 60.384 63.158 0.00 0.00 0.00 2.01
3572 4040 1.408453 CCGGCCCCCTAGAGGTTTAG 61.408 65.000 0.00 0.00 0.00 1.85
3573 4041 1.408453 CGGCCCCCTAGAGGTTTAGG 61.408 65.000 0.00 0.00 39.99 2.69
3578 4046 2.541177 CCTAGAGGTTTAGGGGGCC 58.459 63.158 0.00 0.00 37.20 5.80
3720 4188 6.431234 AGCGTCTTAAAATTTCTCTTCATGGT 59.569 34.615 0.00 0.00 0.00 3.55
3725 4193 9.130661 TCTTAAAATTTCTCTTCATGGTGTCAA 57.869 29.630 0.00 0.00 0.00 3.18
4067 4546 5.559148 AAGGTGAGTTTGTCTCTTGAGAT 57.441 39.130 3.50 0.00 43.13 2.75
4068 4547 5.559148 AGGTGAGTTTGTCTCTTGAGATT 57.441 39.130 3.50 0.00 43.13 2.40
4150 4629 9.276590 TGCACATCATACTAAATAATTGAGAGG 57.723 33.333 0.00 0.00 0.00 3.69
4223 4702 6.284459 ACTCCCTCTGATCGAATGAATTAAC 58.716 40.000 0.00 0.00 0.00 2.01
4288 4767 4.202040 GCATCAATTCATTCGGATTGGACA 60.202 41.667 0.52 0.00 0.00 4.02
4399 4878 8.035394 CACTCTAGTTAAGTTAGGCTTCATTCA 58.965 37.037 0.00 0.00 38.57 2.57
4413 4892 4.820716 GCTTCATTCAGTATTGCAGGATCT 59.179 41.667 0.00 0.00 0.00 2.75
4417 4896 8.806429 TTCATTCAGTATTGCAGGATCTTTTA 57.194 30.769 0.00 0.00 0.00 1.52
4418 4897 8.442632 TCATTCAGTATTGCAGGATCTTTTAG 57.557 34.615 0.00 0.00 0.00 1.85
4815 5815 5.489792 AAGTAAGAGATGGTTGCTTCAGA 57.510 39.130 0.00 0.00 0.00 3.27
4833 5833 7.394077 TGCTTCAGATCTGGACATTTTGAAATA 59.606 33.333 22.42 0.00 0.00 1.40
4963 5965 7.482169 TTATTCTCCTGTCTGTAGTGACAAT 57.518 36.000 0.00 0.00 44.98 2.71
4964 5966 8.589701 TTATTCTCCTGTCTGTAGTGACAATA 57.410 34.615 0.00 0.00 44.98 1.90
4965 5967 7.667575 ATTCTCCTGTCTGTAGTGACAATAT 57.332 36.000 0.00 0.00 44.98 1.28
5017 6019 1.871772 CTTGGGCTTGCACTTCTCG 59.128 57.895 0.00 0.00 0.00 4.04
5255 6257 3.963129 TGGATGTTTGTATTGGACTCCC 58.037 45.455 0.00 0.00 0.00 4.30
5292 6294 6.038271 GTCATTCGTTAGATACCAATTTGGCT 59.962 38.462 15.49 7.25 42.67 4.75
5373 6579 8.871686 ACTTTTGTTCACTCATTTTGGTAATC 57.128 30.769 0.00 0.00 0.00 1.75
5725 6931 8.926710 GCATAAACTGAAGTGCGTATCTAATAT 58.073 33.333 0.00 0.00 0.00 1.28
5795 7001 7.093068 TGCAGTTCCTGTCTAACCTATCATTTA 60.093 37.037 0.00 0.00 33.43 1.40
5998 7206 6.530019 AGGCCTGGTTTAATAATCAAACAG 57.470 37.500 3.11 0.00 37.57 3.16
6113 7321 2.842496 TGAGAGGGCTGTGATTCTTGAT 59.158 45.455 0.00 0.00 0.00 2.57
6254 7462 1.374947 CCTGTGACCCGTGAACCAT 59.625 57.895 0.00 0.00 0.00 3.55
6402 7610 5.163581 CCTTGATTGGAAGTAAGATTGGCAG 60.164 44.000 0.00 0.00 0.00 4.85
6712 7921 7.291885 GGTAACACTAGGTTCCTATAATCCCTT 59.708 40.741 0.00 0.00 40.96 3.95
6738 7947 3.646637 AGACCCCTCCGTTCCTAAATATG 59.353 47.826 0.00 0.00 0.00 1.78
6739 7948 3.390311 GACCCCTCCGTTCCTAAATATGT 59.610 47.826 0.00 0.00 0.00 2.29
6969 8178 3.490800 TGTGATCAACAATCCATTGCG 57.509 42.857 0.00 0.00 41.38 4.85
7096 8307 1.620822 AAATCCAAGTCCAGTGTGCC 58.379 50.000 0.00 0.00 0.00 5.01
7197 8415 3.191371 AGGGCAAAATAGCACGAAAAGAG 59.809 43.478 0.00 0.00 44.43 2.85
7272 8490 1.003718 GACCGCCCAGCAGTACTTT 60.004 57.895 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.980397 CGTACCTATTGGGAAACGTAGTAATT 59.020 38.462 0.00 0.00 40.40 1.40
1 2 6.461509 CCGTACCTATTGGGAAACGTAGTAAT 60.462 42.308 14.04 0.00 42.15 1.89
2 3 5.163561 CCGTACCTATTGGGAAACGTAGTAA 60.164 44.000 14.04 0.00 42.15 2.24
3 4 4.338118 CCGTACCTATTGGGAAACGTAGTA 59.662 45.833 14.04 0.00 42.15 1.82
4 5 3.131046 CCGTACCTATTGGGAAACGTAGT 59.869 47.826 14.04 0.00 42.15 2.73
5 6 3.131046 ACCGTACCTATTGGGAAACGTAG 59.869 47.826 14.04 6.01 42.15 3.51
6 7 3.096092 ACCGTACCTATTGGGAAACGTA 58.904 45.455 14.04 0.00 42.15 3.57
7 8 1.901833 ACCGTACCTATTGGGAAACGT 59.098 47.619 14.04 0.00 42.15 3.99
8 9 2.543641 GACCGTACCTATTGGGAAACG 58.456 52.381 10.23 10.23 42.78 3.60
9 10 2.502947 AGGACCGTACCTATTGGGAAAC 59.497 50.000 0.00 0.00 38.65 2.78
10 11 2.836667 AGGACCGTACCTATTGGGAAA 58.163 47.619 0.00 0.00 38.65 3.13
11 12 2.555732 AGGACCGTACCTATTGGGAA 57.444 50.000 0.00 0.00 38.65 3.97
12 13 2.292389 TGAAGGACCGTACCTATTGGGA 60.292 50.000 0.00 0.00 39.62 4.37
13 14 2.112998 TGAAGGACCGTACCTATTGGG 58.887 52.381 0.00 0.00 39.62 4.12
14 15 4.377897 GAATGAAGGACCGTACCTATTGG 58.622 47.826 0.00 0.00 39.62 3.16
15 16 4.049186 CGAATGAAGGACCGTACCTATTG 58.951 47.826 0.00 0.00 39.62 1.90
16 17 3.703052 ACGAATGAAGGACCGTACCTATT 59.297 43.478 0.00 0.00 39.62 1.73
17 18 3.294214 ACGAATGAAGGACCGTACCTAT 58.706 45.455 0.00 0.00 39.62 2.57
18 19 2.726821 ACGAATGAAGGACCGTACCTA 58.273 47.619 0.00 0.00 39.62 3.08
23 24 0.953960 GCCAACGAATGAAGGACCGT 60.954 55.000 0.00 0.00 36.77 4.83
35 36 3.936203 AGAAGCCACCGCCAACGA 61.936 61.111 0.00 0.00 43.93 3.85
69 70 0.312416 GCACTCGCCTAGACGATGAT 59.688 55.000 0.32 0.00 42.02 2.45
103 104 2.432628 CGCTCCGACTTCCACACC 60.433 66.667 0.00 0.00 0.00 4.16
141 142 1.484038 AAGCCAAACACCACACACAT 58.516 45.000 0.00 0.00 0.00 3.21
254 255 0.536460 ACCAAAGCCAACACCCTACG 60.536 55.000 0.00 0.00 0.00 3.51
273 274 3.582647 TGATGGTTTTGCTGTCCTAGAGA 59.417 43.478 0.00 0.00 0.00 3.10
281 282 4.516698 CAGTCTAGTTGATGGTTTTGCTGT 59.483 41.667 0.00 0.00 0.00 4.40
283 284 4.074970 CCAGTCTAGTTGATGGTTTTGCT 58.925 43.478 0.00 0.00 0.00 3.91
289 290 1.977854 TGCACCAGTCTAGTTGATGGT 59.022 47.619 5.48 5.48 46.91 3.55
349 350 4.174762 GACCGAAGACAACACTTAGATCC 58.825 47.826 0.00 0.00 0.00 3.36
354 355 4.116961 CAAGTGACCGAAGACAACACTTA 58.883 43.478 0.00 0.00 45.70 2.24
386 407 1.787847 CACCAACTGAATCGCCGAC 59.212 57.895 0.00 0.00 0.00 4.79
398 419 2.611292 GCTGATGAGACTATGCACCAAC 59.389 50.000 0.00 0.00 0.00 3.77
426 448 9.836076 CTGAAAACCGATACATCTACGATATAA 57.164 33.333 0.00 0.00 0.00 0.98
473 495 5.406780 TCGCAGAAGAAAAGAGAGAATTGAC 59.593 40.000 0.00 0.00 0.00 3.18
482 504 6.840075 AGAATTCATTCGCAGAAGAAAAGAG 58.160 36.000 8.44 0.00 45.90 2.85
484 506 6.840075 AGAGAATTCATTCGCAGAAGAAAAG 58.160 36.000 8.44 0.00 45.90 2.27
486 508 6.808008 AAGAGAATTCATTCGCAGAAGAAA 57.192 33.333 8.44 0.00 45.90 2.52
487 509 6.808008 AAAGAGAATTCATTCGCAGAAGAA 57.192 33.333 8.44 0.00 45.90 2.52
488 510 6.808008 AAAAGAGAATTCATTCGCAGAAGA 57.192 33.333 8.44 0.00 45.90 2.87
489 511 7.303998 AGAAAAAGAGAATTCATTCGCAGAAG 58.696 34.615 8.44 0.00 45.90 2.85
490 512 7.206981 AGAAAAAGAGAATTCATTCGCAGAA 57.793 32.000 8.44 0.00 45.90 3.02
491 513 6.808008 AGAAAAAGAGAATTCATTCGCAGA 57.192 33.333 8.44 0.00 41.56 4.26
492 514 8.955061 TTAAGAAAAAGAGAATTCATTCGCAG 57.045 30.769 8.44 0.00 41.56 5.18
493 515 9.345517 CATTAAGAAAAAGAGAATTCATTCGCA 57.654 29.630 8.44 0.00 41.56 5.10
494 516 9.559958 TCATTAAGAAAAAGAGAATTCATTCGC 57.440 29.630 8.44 0.00 41.56 4.70
503 525 9.696917 GCCTTTTCATCATTAAGAAAAAGAGAA 57.303 29.630 7.30 0.00 41.55 2.87
504 526 8.859090 TGCCTTTTCATCATTAAGAAAAAGAGA 58.141 29.630 7.30 0.00 41.55 3.10
505 527 9.480053 TTGCCTTTTCATCATTAAGAAAAAGAG 57.520 29.630 7.30 0.81 41.55 2.85
506 528 9.829507 TTTGCCTTTTCATCATTAAGAAAAAGA 57.170 25.926 7.30 0.00 41.55 2.52
536 558 4.016444 TCTTTCAAGCAACAACAGGAAGT 58.984 39.130 0.00 0.00 0.00 3.01
539 561 5.398603 TTTTCTTTCAAGCAACAACAGGA 57.601 34.783 0.00 0.00 0.00 3.86
591 614 9.530633 ACTAAGTTTACAGTTCACAAAGTAGAG 57.469 33.333 0.00 0.00 0.00 2.43
700 914 9.705290 CAAATATTTACAGCTGGGTAAAAAGTT 57.295 29.630 19.93 8.29 43.97 2.66
701 915 8.311109 CCAAATATTTACAGCTGGGTAAAAAGT 58.689 33.333 19.93 3.10 43.97 2.66
711 925 8.776376 AAAATTGGACCAAATATTTACAGCTG 57.224 30.769 13.48 13.48 0.00 4.24
717 931 9.982651 TCGTTGAAAAATTGGACCAAATATTTA 57.017 25.926 11.82 0.70 0.00 1.40
754 968 1.665679 CAGACGTTATGGCTCGCATTT 59.334 47.619 0.00 0.00 0.00 2.32
1358 1581 2.294233 TGTCAGACAATTCAGCAAAGCC 59.706 45.455 0.00 0.00 0.00 4.35
1888 2115 3.767278 CAAGCTGGAGCATCTTAAAAGC 58.233 45.455 0.65 0.00 45.16 3.51
2543 2877 1.625818 CTATTACCAGCTAGGGGGCAG 59.374 57.143 7.06 0.00 43.89 4.85
3256 3720 5.392595 CGCTAGCCTTGGTAAAAAGCATAAA 60.393 40.000 9.66 0.00 0.00 1.40
3725 4193 9.760077 AGTCGACGGAATAAATATTTCTACAAT 57.240 29.630 10.46 0.00 0.00 2.71
4150 4629 7.860872 CCTGAAAAACAGTAAAGTGGATTACAC 59.139 37.037 0.00 0.00 46.11 2.90
4155 4634 5.701224 TCCCTGAAAAACAGTAAAGTGGAT 58.299 37.500 0.00 0.00 44.40 3.41
4223 4702 4.022762 AGAGTACATTGTATAGAGGCTGCG 60.023 45.833 0.00 0.00 0.00 5.18
4288 4767 4.215613 GGTCAAAACGGAAAATGCTACTCT 59.784 41.667 0.00 0.00 0.00 3.24
4399 4878 5.882557 CACACCTAAAAGATCCTGCAATACT 59.117 40.000 0.00 0.00 0.00 2.12
4413 4892 5.300539 TGCAGAATAAAGTGCACACCTAAAA 59.699 36.000 21.04 0.00 44.70 1.52
4417 4896 2.862541 TGCAGAATAAAGTGCACACCT 58.137 42.857 21.04 5.05 44.70 4.00
4771 5771 7.283329 ACTTTCTCTCTTTGAAAAGGAAGCTA 58.717 34.615 3.08 0.00 36.67 3.32
4815 5815 6.664816 TCAAGCCTATTTCAAAATGTCCAGAT 59.335 34.615 0.00 0.00 0.00 2.90
4902 5902 8.995027 TTGCAAGGTAAATATTAGGATGATGT 57.005 30.769 0.00 0.00 0.00 3.06
4919 5919 9.243105 AGAATAAACATACTAACATTGCAAGGT 57.757 29.630 11.64 11.64 0.00 3.50
5017 6019 1.318158 CCAGCCAATTCCTGCCTGTC 61.318 60.000 0.00 0.00 0.00 3.51
5255 6257 6.771076 TCTAACGAATGACAAATCCAATTCG 58.229 36.000 13.36 13.36 44.17 3.34
5292 6294 8.306038 CCCAATCAATATTGTGTCTCTGAAAAA 58.694 33.333 14.97 0.00 40.84 1.94
5338 6340 3.883489 AGTGAACAAAAGTAAGGCAGGTC 59.117 43.478 0.00 0.00 0.00 3.85
5373 6579 5.295292 ACTCGGATTAAGATCACATTTGCAG 59.705 40.000 0.00 0.00 33.77 4.41
5732 6938 4.931661 ATGAATTAAGCAATGCAGGGAG 57.068 40.909 8.35 0.00 32.99 4.30
5905 7111 0.610232 ATCGGCCTTTGCAGCTTTCT 60.610 50.000 0.00 0.00 40.13 2.52
6113 7321 5.155278 TCTCGCTTACCCTGTTTAAATGA 57.845 39.130 0.00 0.00 0.00 2.57
6402 7610 7.223971 TGTCAACAGAACAACAGAACTATGTAC 59.776 37.037 0.00 0.00 31.70 2.90
6691 7900 6.085416 AGGAAGGGATTATAGGAACCTAGTG 58.915 44.000 6.72 0.00 31.45 2.74
6712 7921 1.219824 AGGAACGGAGGGGTCTAGGA 61.220 60.000 0.00 0.00 0.00 2.94
6738 7947 6.913170 TGCATTGGAATCTCTAAAAAGACAC 58.087 36.000 0.00 0.00 0.00 3.67
6739 7948 6.942005 TCTGCATTGGAATCTCTAAAAAGACA 59.058 34.615 0.00 0.00 0.00 3.41
6969 8178 2.869233 TTTGTCTCAAGCCAAACAGC 57.131 45.000 0.00 0.00 0.00 4.40
7197 8415 5.156355 ACAGAACAATTTCATCATGCGTTC 58.844 37.500 0.00 0.00 33.72 3.95
7243 8461 0.400213 TGGGCGGTCTGAGAACATTT 59.600 50.000 0.00 0.00 0.00 2.32
7272 8490 2.733858 GCTGAACTGTTTTTCGCAACCA 60.734 45.455 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.