Multiple sequence alignment - TraesCS6A01G096000

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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 TraesCS6A01G096000 chr6A 100.000 5318 0 0 1 5318 63115736 63121053 0.000000e+00 9821.0
1 TraesCS6A01G096000 chr6A 92.308 39 3 0 4750 4788 63120380 63120342 7.440000e-04 56.5
2 TraesCS6A01G096000 chr6A 92.308 39 3 0 4607 4645 63120523 63120485 7.440000e-04 56.5
3 TraesCS6A01G096000 chr6D 96.501 3744 100 19 1589 5318 52337808 52341534 0.000000e+00 6159.0
4 TraesCS6A01G096000 chr6D 92.937 807 42 10 777 1570 52336330 52337134 0.000000e+00 1160.0
5 TraesCS6A01G096000 chr6D 95.714 70 3 0 705 774 52336216 52336285 4.350000e-21 113.0
6 TraesCS6A01G096000 chr6D 100.000 51 0 0 654 704 52336126 52336176 1.580000e-15 95.3
7 TraesCS6A01G096000 chr6D 94.872 39 2 0 4607 4645 52341006 52340968 1.600000e-05 62.1
8 TraesCS6A01G096000 chr6D 96.875 32 1 0 4757 4788 52340856 52340825 3.000000e-03 54.7
9 TraesCS6A01G096000 chr6B 95.547 3234 104 19 1590 4804 119126860 119130072 0.000000e+00 5138.0
10 TraesCS6A01G096000 chr6B 85.360 444 46 15 1 436 119124759 119125191 4.890000e-120 442.0
11 TraesCS6A01G096000 chr6B 91.212 330 15 7 948 1276 119125497 119125813 2.270000e-118 436.0
12 TraesCS6A01G096000 chr6B 91.531 307 17 8 1271 1570 119125894 119126198 1.070000e-111 414.0
13 TraesCS6A01G096000 chr6B 94.472 199 11 0 4840 5038 119130066 119130264 1.860000e-79 307.0
14 TraesCS6A01G096000 chr6B 82.845 239 16 13 476 689 119125192 119125430 1.950000e-44 191.0
15 TraesCS6A01G096000 chr1D 85.964 1318 135 29 3249 4548 245980876 245982161 0.000000e+00 1363.0
16 TraesCS6A01G096000 chr1D 88.605 860 54 16 1863 2683 245979356 245980210 0.000000e+00 1005.0
17 TraesCS6A01G096000 chr1D 86.070 603 58 19 964 1556 245973632 245974218 4.520000e-175 625.0
18 TraesCS6A01G096000 chr1D 92.171 281 22 0 2682 2962 245980181 245980461 1.070000e-106 398.0
19 TraesCS6A01G096000 chr1D 86.166 253 28 5 2976 3224 245980548 245980797 3.160000e-67 267.0
20 TraesCS6A01G096000 chr1D 90.909 110 9 1 1666 1775 245979207 245979315 4.290000e-31 147.0
21 TraesCS6A01G096000 chr1A 85.801 1317 137 28 3251 4548 306642596 306643881 0.000000e+00 1351.0
22 TraesCS6A01G096000 chr1A 88.099 1126 75 18 1863 2962 306641089 306642181 0.000000e+00 1282.0
23 TraesCS6A01G096000 chr1A 85.977 599 59 16 964 1556 306639429 306640008 7.570000e-173 617.0
24 TraesCS6A01G096000 chr1A 84.585 253 31 6 2976 3224 306642267 306642515 1.480000e-60 244.0
25 TraesCS6A01G096000 chr1A 91.892 111 7 2 1666 1775 306640939 306641048 2.560000e-33 154.0
26 TraesCS6A01G096000 chr1B 86.468 1175 115 27 3221 4379 332157799 332156653 0.000000e+00 1249.0
27 TraesCS6A01G096000 chr1B 88.019 1060 80 27 1666 2686 332159474 332158423 0.000000e+00 1210.0
28 TraesCS6A01G096000 chr1B 85.000 600 59 20 962 1549 332161103 332160523 9.930000e-162 580.0
29 TraesCS6A01G096000 chr1B 92.883 281 20 0 2682 2962 332158456 332158176 4.960000e-110 409.0
30 TraesCS6A01G096000 chr7D 72.792 283 59 14 203 481 565397344 565397612 4.420000e-11 80.5
31 TraesCS6A01G096000 chr7B 91.837 49 4 0 431 479 615790428 615790476 9.560000e-08 69.4


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 TraesCS6A01G096000 chr6A 63115736 63121053 5317 False 9821.000000 9821 100.000000 1 5318 1 chr6A.!!$F1 5317
1 TraesCS6A01G096000 chr6D 52336126 52341534 5408 False 1881.825000 6159 96.288000 654 5318 4 chr6D.!!$F1 4664
2 TraesCS6A01G096000 chr6B 119124759 119130264 5505 False 1154.666667 5138 90.161167 1 5038 6 chr6B.!!$F1 5037
3 TraesCS6A01G096000 chr1D 245979207 245982161 2954 False 636.000000 1363 88.763000 1666 4548 5 chr1D.!!$F2 2882
4 TraesCS6A01G096000 chr1D 245973632 245974218 586 False 625.000000 625 86.070000 964 1556 1 chr1D.!!$F1 592
5 TraesCS6A01G096000 chr1A 306639429 306643881 4452 False 729.600000 1351 87.270800 964 4548 5 chr1A.!!$F1 3584
6 TraesCS6A01G096000 chr1B 332156653 332161103 4450 True 862.000000 1249 88.092500 962 4379 4 chr1B.!!$R1 3417

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
451 458 0.035056 CGGCCCATCTGAAGGAGTTT 60.035 55.000 0.00 0.00 0.00 2.66 F
538 545 0.601311 AGTCAACGACCAGAAGCAGC 60.601 55.000 0.00 0.00 32.18 5.25 F
542 549 0.674895 AACGACCAGAAGCAGCCATC 60.675 55.000 0.00 0.00 0.00 3.51 F
1373 1603 1.103803 TTGTCTGCTCGCCTAGGTAG 58.896 55.000 11.31 9.65 0.00 3.18 F
2002 3277 1.142465 CATGCTGGCAGTCCTAATCCT 59.858 52.381 17.16 0.00 0.00 3.24 F
3758 5200 0.256464 TGCATCTGTGGATCATGGCA 59.744 50.000 0.00 0.00 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 3015 0.393448 TGCACTGTTAACGGCCTGTA 59.607 50.000 14.52 3.21 0.00 2.74 R
1782 3016 0.464735 TTGCACTGTTAACGGCCTGT 60.465 50.000 14.52 0.00 0.00 4.00 R
2174 3456 1.830477 TGAATGCCCAAAGTAATGCCC 59.170 47.619 0.00 0.00 0.00 5.36 R
3258 4687 2.158058 CAGCATTTGCCCATTGTTTTCG 59.842 45.455 0.00 0.00 43.38 3.46 R
3862 5304 1.693627 GACCTTCCTGGAGCGAGATA 58.306 55.000 0.00 0.00 39.71 1.98 R
4717 6187 0.178873 TGGGCTCTACTCCAACCCTT 60.179 55.000 0.00 0.00 41.44 3.95 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
266 270 8.414003 TGTCCACTGTATACTATAAAAGCTCAG 58.586 37.037 4.17 0.00 0.00 3.35
289 294 8.200792 TCAGTGTGTATTTTAAAAATGTTGGCT 58.799 29.630 4.44 0.00 0.00 4.75
413 420 6.041423 AGCAAATAAAAGACCCCAAATCAG 57.959 37.500 0.00 0.00 0.00 2.90
430 437 4.696479 ATCAGAATAGCTGTTACCTGGG 57.304 45.455 10.66 0.00 45.14 4.45
436 443 2.267961 CTGTTACCTGGGTCGGCC 59.732 66.667 0.00 0.00 0.00 6.13
446 453 2.190578 GGTCGGCCCATCTGAAGG 59.809 66.667 0.00 0.00 0.00 3.46
447 454 2.367202 GGTCGGCCCATCTGAAGGA 61.367 63.158 0.00 0.00 0.00 3.36
448 455 1.144936 GTCGGCCCATCTGAAGGAG 59.855 63.158 0.00 0.00 0.00 3.69
449 456 1.306141 TCGGCCCATCTGAAGGAGT 60.306 57.895 0.00 0.00 0.00 3.85
450 457 0.909610 TCGGCCCATCTGAAGGAGTT 60.910 55.000 0.00 0.00 0.00 3.01
451 458 0.035056 CGGCCCATCTGAAGGAGTTT 60.035 55.000 0.00 0.00 0.00 2.66
452 459 1.614317 CGGCCCATCTGAAGGAGTTTT 60.614 52.381 0.00 0.00 0.00 2.43
453 460 2.095461 GGCCCATCTGAAGGAGTTTTC 58.905 52.381 0.00 0.00 0.00 2.29
454 461 2.555227 GGCCCATCTGAAGGAGTTTTCA 60.555 50.000 0.00 0.00 35.83 2.69
460 467 3.802722 CTGAAGGAGTTTTCAGCGAAG 57.197 47.619 3.15 0.00 45.21 3.79
484 491 4.501400 CCTCAACTATATGATGCACGTGGA 60.501 45.833 18.88 16.39 0.00 4.02
499 506 3.269486 CGTGGACGTCATATAGGAGTG 57.731 52.381 18.91 0.00 34.11 3.51
504 511 5.184096 GTGGACGTCATATAGGAGTGATCAT 59.816 44.000 18.91 0.00 0.00 2.45
512 519 7.178274 GTCATATAGGAGTGATCATCTGGTTCT 59.822 40.741 0.00 0.00 0.00 3.01
538 545 0.601311 AGTCAACGACCAGAAGCAGC 60.601 55.000 0.00 0.00 32.18 5.25
541 548 0.957395 CAACGACCAGAAGCAGCCAT 60.957 55.000 0.00 0.00 0.00 4.40
542 549 0.674895 AACGACCAGAAGCAGCCATC 60.675 55.000 0.00 0.00 0.00 3.51
585 600 2.432628 CCCACTCGTCGTGCTTCC 60.433 66.667 0.00 0.00 42.42 3.46
617 632 2.097918 CTCGTTCTCCCGACGTCG 59.902 66.667 30.33 30.33 41.08 5.12
639 654 3.706373 GCCGTGCTTCCTCCCAGA 61.706 66.667 0.00 0.00 0.00 3.86
641 656 1.374947 CCGTGCTTCCTCCCAGAAA 59.625 57.895 0.00 0.00 0.00 2.52
712 793 3.669557 CGTGTAAAAACATAGCAGCCCAC 60.670 47.826 0.00 0.00 0.00 4.61
774 855 5.473796 AACTAAACGTCGATCTCTCTCTC 57.526 43.478 0.00 0.00 0.00 3.20
776 857 5.904941 ACTAAACGTCGATCTCTCTCTCTA 58.095 41.667 0.00 0.00 0.00 2.43
777 858 6.339730 ACTAAACGTCGATCTCTCTCTCTAA 58.660 40.000 0.00 0.00 0.00 2.10
778 859 6.817641 ACTAAACGTCGATCTCTCTCTCTAAA 59.182 38.462 0.00 0.00 0.00 1.85
989 1115 2.748058 AAATCCGTCGCCAAGCCACT 62.748 55.000 0.00 0.00 0.00 4.00
1024 1150 4.830765 CATTTCCGCCGCCTCCGA 62.831 66.667 0.00 0.00 36.29 4.55
1162 1300 1.850377 GATCACTCAGGACATGCTCG 58.150 55.000 0.00 0.00 0.00 5.03
1203 1341 2.361104 GCCACATCCTTTCGCCCA 60.361 61.111 0.00 0.00 0.00 5.36
1260 1402 3.004106 CACTCCTGCTTTCTTTGGTTCTG 59.996 47.826 0.00 0.00 0.00 3.02
1275 1503 5.135508 TGGTTCTGCTCTACTGTTAACTC 57.864 43.478 7.22 0.00 0.00 3.01
1280 1509 7.095565 GGTTCTGCTCTACTGTTAACTCTTTTC 60.096 40.741 7.22 0.00 0.00 2.29
1321 1550 9.863650 ACCTAGCAGAGTTCTTTATGTATACTA 57.136 33.333 4.17 0.00 0.00 1.82
1373 1603 1.103803 TTGTCTGCTCGCCTAGGTAG 58.896 55.000 11.31 9.65 0.00 3.18
1514 1749 3.689649 GGTTCATTTCCTCAAGCATACGT 59.310 43.478 0.00 0.00 0.00 3.57
1533 1768 7.412563 GCATACGTTCTGCTTGATTACTTGTAA 60.413 37.037 13.71 0.00 36.68 2.41
1551 1786 6.695713 ACTTGTAAATTTTCTTTGTTCGAGCC 59.304 34.615 0.00 0.00 0.00 4.70
1557 1792 2.831685 TCTTTGTTCGAGCCAGCTAA 57.168 45.000 0.00 0.00 0.00 3.09
1570 1805 7.847096 TCGAGCCAGCTAATAATTATGGATTA 58.153 34.615 6.28 0.00 34.82 1.75
1590 2402 1.426751 TCCCCACACGAGGTAGTTTT 58.573 50.000 0.00 0.00 0.00 2.43
1729 2962 7.370383 TCCTGTTTCAATAAAATGCTTGTCTC 58.630 34.615 0.00 0.00 0.00 3.36
1788 3027 8.107095 TGGATTTATGACCTTTATATACAGGCC 58.893 37.037 13.86 4.73 32.79 5.19
1931 3170 3.283751 ACTTCTGAGACTCCATACTCCG 58.716 50.000 0.00 0.00 32.84 4.63
2002 3277 1.142465 CATGCTGGCAGTCCTAATCCT 59.858 52.381 17.16 0.00 0.00 3.24
2174 3456 6.090763 TCGTGAACTACTGATACAATTTGCAG 59.909 38.462 0.00 0.00 34.65 4.41
2480 3763 4.022935 TCTCTGCCAAAAGTTTATGCACAG 60.023 41.667 7.64 7.67 0.00 3.66
2482 3765 4.824537 TCTGCCAAAAGTTTATGCACAGTA 59.175 37.500 7.64 0.00 0.00 2.74
2737 4022 9.466497 TGAATTACCTTTTCATTCTCTAATGCT 57.534 29.630 0.00 0.00 41.96 3.79
2892 4177 7.988904 AATAGAGAAAGAGAAATTACCGACG 57.011 36.000 0.00 0.00 0.00 5.12
3009 4376 7.608153 TGAACATCTCGAGGTTTTAGTGATAA 58.392 34.615 13.56 0.00 35.27 1.75
3010 4377 8.258007 TGAACATCTCGAGGTTTTAGTGATAAT 58.742 33.333 13.56 0.00 35.27 1.28
3011 4378 8.425577 AACATCTCGAGGTTTTAGTGATAATG 57.574 34.615 13.56 6.48 30.39 1.90
3012 4379 7.782049 ACATCTCGAGGTTTTAGTGATAATGA 58.218 34.615 13.56 0.00 0.00 2.57
3013 4380 8.424918 ACATCTCGAGGTTTTAGTGATAATGAT 58.575 33.333 13.56 0.00 0.00 2.45
3014 4381 9.914131 CATCTCGAGGTTTTAGTGATAATGATA 57.086 33.333 13.56 0.00 0.00 2.15
3057 4424 9.006839 AGATGATTATAACCAATGCACAGTATG 57.993 33.333 0.00 0.00 46.00 2.39
3095 4462 8.472683 TGTTGTTCACTTTATTTTGTCCTTTG 57.527 30.769 0.00 0.00 0.00 2.77
3231 4660 9.409312 GTCACTATGACAATGATCAGAATAGAG 57.591 37.037 0.09 3.49 46.22 2.43
3502 4937 2.066999 CCCAGGGAGGCTGAGTACC 61.067 68.421 0.00 0.00 35.39 3.34
3504 4939 2.760385 AGGGAGGCTGAGTACCGC 60.760 66.667 0.00 0.00 0.00 5.68
3694 5136 7.707464 TGCTTGTGCCATGATTATGATAAAAAG 59.293 33.333 0.00 0.00 38.71 2.27
3758 5200 0.256464 TGCATCTGTGGATCATGGCA 59.744 50.000 0.00 0.00 0.00 4.92
3862 5304 5.890334 TCGTGCTGTTTCTGAAATTTTCTT 58.110 33.333 6.06 0.00 0.00 2.52
3917 5359 3.251004 AGCTTTTGTGACGTTTCCATCTC 59.749 43.478 0.00 0.00 0.00 2.75
3996 5440 7.751732 TGTAGTATTGCACAAGAAAGCTAATG 58.248 34.615 0.00 0.00 0.00 1.90
4054 5499 2.161808 CAGATCAAAAGCTGCTCACTGG 59.838 50.000 1.00 0.00 31.11 4.00
4118 5565 7.669089 TTAAGACCAAAAGGGAAAACATCTT 57.331 32.000 0.00 0.00 41.15 2.40
4123 5571 4.261825 CCAAAAGGGAAAACATCTTACGCA 60.262 41.667 0.00 0.00 40.01 5.24
4443 5905 6.659745 TGTGGTATATAACGGCACTTATCT 57.340 37.500 0.00 0.00 0.00 1.98
4603 6073 9.106070 TCATGAAATCTCAGATCAATAACACTG 57.894 33.333 0.00 0.00 34.23 3.66
4604 6074 8.890718 CATGAAATCTCAGATCAATAACACTGT 58.109 33.333 0.00 0.00 34.23 3.55
4644 6114 2.242196 GGGGGAAATGAGGATGAGAACA 59.758 50.000 0.00 0.00 0.00 3.18
4717 6187 9.567776 TTAGAGTGACCTTTTTGACAAATATCA 57.432 29.630 0.50 1.32 0.00 2.15
4737 6207 0.178873 AGGGTTGGAGTAGAGCCCAA 60.179 55.000 0.00 0.00 41.67 4.12
4752 6222 4.721776 AGAGCCCAAATATTCAGGTCTGTA 59.278 41.667 11.20 0.00 34.24 2.74
4803 6273 0.693049 TTCCTTGGCAAGACTCCTCC 59.307 55.000 28.18 0.00 0.00 4.30
4879 6349 2.365105 GGTCCCTCGGTCCATCCA 60.365 66.667 0.00 0.00 35.57 3.41
4930 6400 3.220999 CTCTTCGCCGGTGTCCACA 62.221 63.158 16.01 0.00 0.00 4.17
5119 6589 4.146075 ATGCAATTTGGCGGCGGG 62.146 61.111 9.78 0.00 36.28 6.13
5183 6653 1.789464 CTTTACGGATCTGCGCTCATC 59.211 52.381 9.73 9.81 0.00 2.92
5192 6662 3.165058 TCTGCGCTCATCGATACTTTT 57.835 42.857 9.73 0.00 41.67 2.27
5237 6708 1.839354 TGATATTGGCTCTGTGCAGGA 59.161 47.619 3.96 0.00 45.15 3.86
5307 6778 2.028658 CGAGATGTGGGTGGATGATAGG 60.029 54.545 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 247 8.581057 CACTGAGCTTTTATAGTATACAGTGG 57.419 38.462 19.28 8.52 44.61 4.00
262 266 8.487176 GCCAACATTTTTAAAATACACACTGAG 58.513 33.333 0.55 0.00 0.00 3.35
266 270 8.137210 ACAGCCAACATTTTTAAAATACACAC 57.863 30.769 0.55 0.00 0.00 3.82
344 350 8.918961 TTAGTTTTTCTTTCGATTTCTTGCAA 57.081 26.923 0.00 0.00 0.00 4.08
388 394 6.836242 TGATTTGGGGTCTTTTATTTGCTTT 58.164 32.000 0.00 0.00 0.00 3.51
391 397 6.036577 TCTGATTTGGGGTCTTTTATTTGC 57.963 37.500 0.00 0.00 0.00 3.68
392 398 9.807649 CTATTCTGATTTGGGGTCTTTTATTTG 57.192 33.333 0.00 0.00 0.00 2.32
393 399 8.478066 GCTATTCTGATTTGGGGTCTTTTATTT 58.522 33.333 0.00 0.00 0.00 1.40
396 402 6.603201 CAGCTATTCTGATTTGGGGTCTTTTA 59.397 38.462 0.00 0.00 45.72 1.52
399 406 4.018050 ACAGCTATTCTGATTTGGGGTCTT 60.018 41.667 0.00 0.00 45.72 3.01
401 408 3.891049 ACAGCTATTCTGATTTGGGGTC 58.109 45.455 0.00 0.00 45.72 4.46
405 412 5.297776 CCAGGTAACAGCTATTCTGATTTGG 59.702 44.000 0.00 0.00 45.72 3.28
413 420 2.483188 CCGACCCAGGTAACAGCTATTC 60.483 54.545 0.00 0.00 41.41 1.75
430 437 1.144936 CTCCTTCAGATGGGCCGAC 59.855 63.158 0.00 0.00 0.00 4.79
441 448 1.873591 GCTTCGCTGAAAACTCCTTCA 59.126 47.619 0.00 0.00 34.22 3.02
442 449 1.197949 GGCTTCGCTGAAAACTCCTTC 59.802 52.381 0.00 0.00 0.00 3.46
443 450 1.202818 AGGCTTCGCTGAAAACTCCTT 60.203 47.619 0.00 0.00 0.00 3.36
444 451 0.398318 AGGCTTCGCTGAAAACTCCT 59.602 50.000 0.00 0.00 0.00 3.69
445 452 0.799393 GAGGCTTCGCTGAAAACTCC 59.201 55.000 0.00 0.00 0.00 3.85
446 453 1.512926 TGAGGCTTCGCTGAAAACTC 58.487 50.000 0.00 11.39 0.00 3.01
447 454 1.604278 GTTGAGGCTTCGCTGAAAACT 59.396 47.619 0.00 0.00 0.00 2.66
448 455 1.604278 AGTTGAGGCTTCGCTGAAAAC 59.396 47.619 0.00 0.00 0.00 2.43
449 456 1.967319 AGTTGAGGCTTCGCTGAAAA 58.033 45.000 0.00 0.00 0.00 2.29
450 457 2.831685 TAGTTGAGGCTTCGCTGAAA 57.168 45.000 0.00 0.00 0.00 2.69
451 458 4.099419 TCATATAGTTGAGGCTTCGCTGAA 59.901 41.667 0.00 0.00 0.00 3.02
452 459 3.636764 TCATATAGTTGAGGCTTCGCTGA 59.363 43.478 0.00 0.00 0.00 4.26
453 460 3.982475 TCATATAGTTGAGGCTTCGCTG 58.018 45.455 0.00 0.00 0.00 5.18
454 461 4.564041 CATCATATAGTTGAGGCTTCGCT 58.436 43.478 0.00 0.00 0.00 4.93
455 462 3.124297 GCATCATATAGTTGAGGCTTCGC 59.876 47.826 5.87 0.00 46.81 4.70
456 463 4.917887 GCATCATATAGTTGAGGCTTCG 57.082 45.455 5.87 0.00 46.81 3.79
461 468 3.742882 CCACGTGCATCATATAGTTGAGG 59.257 47.826 10.91 0.00 0.00 3.86
462 469 4.445718 GTCCACGTGCATCATATAGTTGAG 59.554 45.833 10.91 0.00 0.00 3.02
463 470 4.368315 GTCCACGTGCATCATATAGTTGA 58.632 43.478 10.91 0.00 0.00 3.18
464 471 3.182372 CGTCCACGTGCATCATATAGTTG 59.818 47.826 10.91 0.00 34.11 3.16
465 472 3.381045 CGTCCACGTGCATCATATAGTT 58.619 45.455 10.91 0.00 34.11 2.24
466 473 3.013276 CGTCCACGTGCATCATATAGT 57.987 47.619 10.91 0.00 34.11 2.12
484 491 5.417266 CCAGATGATCACTCCTATATGACGT 59.583 44.000 0.00 0.00 0.00 4.34
491 498 6.376864 CGATAGAACCAGATGATCACTCCTAT 59.623 42.308 0.00 0.00 39.76 2.57
492 499 5.707764 CGATAGAACCAGATGATCACTCCTA 59.292 44.000 0.00 0.00 39.76 2.94
512 519 4.482386 CTTCTGGTCGTTGACTTTCGATA 58.518 43.478 0.00 0.00 38.32 2.92
538 545 1.608590 AGCGTTGTTCTGGTTTGATGG 59.391 47.619 0.00 0.00 0.00 3.51
541 548 1.673920 GGAAGCGTTGTTCTGGTTTGA 59.326 47.619 0.00 0.00 0.00 2.69
542 549 1.403679 TGGAAGCGTTGTTCTGGTTTG 59.596 47.619 0.00 0.00 0.00 2.93
572 587 2.182030 GGGAGGAAGCACGACGAG 59.818 66.667 0.00 0.00 0.00 4.18
581 596 4.410400 GGCACACCGGGGAGGAAG 62.410 72.222 12.96 0.00 45.00 3.46
639 654 2.586914 GCTATACGGGCGGCGTTT 60.587 61.111 9.37 6.90 0.00 3.60
641 656 4.280494 CAGCTATACGGGCGGCGT 62.280 66.667 9.37 7.30 34.52 5.68
742 823 2.215196 GACGTTTAGTTTGTGGGCTGA 58.785 47.619 0.00 0.00 0.00 4.26
751 832 5.644636 AGAGAGAGAGATCGACGTTTAGTTT 59.355 40.000 0.00 0.00 0.00 2.66
790 913 0.972134 CAGGTGTCTCCTTCAGCTCA 59.028 55.000 0.00 0.00 45.67 4.26
795 918 2.583441 CGGGCAGGTGTCTCCTTCA 61.583 63.158 0.00 0.00 45.67 3.02
799 922 2.997897 AGTCGGGCAGGTGTCTCC 60.998 66.667 0.00 0.00 0.00 3.71
1069 1207 3.570638 CTGATGCAGAAGCGGCGG 61.571 66.667 9.78 0.00 46.23 6.13
1070 1208 4.233635 GCTGATGCAGAAGCGGCG 62.234 66.667 0.51 0.51 46.23 6.46
1071 1209 3.129502 TGCTGATGCAGAAGCGGC 61.130 61.111 16.19 11.00 45.31 6.53
1203 1341 1.338769 GGTGAGTACTTTCCACCGCAT 60.339 52.381 14.51 0.00 40.61 4.73
1260 1402 9.425577 ACTTATGAAAAGAGTTAACAGTAGAGC 57.574 33.333 8.61 0.00 0.00 4.09
1275 1503 9.774742 GCTAGGTAAATCACAACTTATGAAAAG 57.225 33.333 0.00 0.00 0.00 2.27
1280 1509 7.766278 ACTCTGCTAGGTAAATCACAACTTATG 59.234 37.037 0.00 0.00 0.00 1.90
1323 1552 9.014297 CAGTATACCCAAAGAACTTTTGAGATT 57.986 33.333 0.00 0.00 0.00 2.40
1324 1553 8.383175 TCAGTATACCCAAAGAACTTTTGAGAT 58.617 33.333 0.00 0.00 0.00 2.75
1327 1556 7.741785 TCTCAGTATACCCAAAGAACTTTTGA 58.258 34.615 0.00 0.00 0.00 2.69
1328 1557 7.979444 TCTCAGTATACCCAAAGAACTTTTG 57.021 36.000 0.00 0.00 0.00 2.44
1533 1768 3.319122 AGCTGGCTCGAACAAAGAAAATT 59.681 39.130 0.00 0.00 0.00 1.82
1551 1786 9.125026 GTGGGGATAATCCATAATTATTAGCTG 57.875 37.037 0.00 0.00 40.03 4.24
1557 1792 7.265599 TCGTGTGGGGATAATCCATAATTAT 57.734 36.000 0.00 0.00 42.15 1.28
1570 1805 1.652947 AAACTACCTCGTGTGGGGAT 58.347 50.000 0.00 0.00 0.00 3.85
1781 3015 0.393448 TGCACTGTTAACGGCCTGTA 59.607 50.000 14.52 3.21 0.00 2.74
1782 3016 0.464735 TTGCACTGTTAACGGCCTGT 60.465 50.000 14.52 0.00 0.00 4.00
1788 3027 4.909305 CCATAAACACTTGCACTGTTAACG 59.091 41.667 8.94 0.00 31.43 3.18
1931 3170 9.118236 GAAAACTATGAAACATTGCAGAACTAC 57.882 33.333 0.00 0.00 0.00 2.73
2002 3277 5.497464 TCCACATTGTCAAGTAAGATGGA 57.503 39.130 0.00 0.00 0.00 3.41
2174 3456 1.830477 TGAATGCCCAAAGTAATGCCC 59.170 47.619 0.00 0.00 0.00 5.36
2460 3743 3.981211 ACTGTGCATAAACTTTTGGCAG 58.019 40.909 0.00 0.00 34.18 4.85
2892 4177 2.357257 GGGAAGGGACAAAATCTCCTCC 60.357 54.545 0.00 0.00 30.14 4.30
3010 4377 9.241919 TCATCTTGAAGTTAAAAGGCAATATCA 57.758 29.630 0.00 0.00 0.00 2.15
3129 4496 8.877779 CATCTAAAATCTGCTAATAGGAATCGG 58.122 37.037 0.00 0.00 0.00 4.18
3231 4660 2.557920 AAGAAGGGCGGATGATGATC 57.442 50.000 0.00 0.00 0.00 2.92
3258 4687 2.158058 CAGCATTTGCCCATTGTTTTCG 59.842 45.455 0.00 0.00 43.38 3.46
3259 4688 3.401182 TCAGCATTTGCCCATTGTTTTC 58.599 40.909 0.00 0.00 43.38 2.29
3342 4777 6.698008 CCAGTGAGGCATCAAAACATAATA 57.302 37.500 0.92 0.00 37.14 0.98
3502 4937 9.697250 TCTTATATAAACATTTCAAGAAACGCG 57.303 29.630 3.53 3.53 32.51 6.01
3758 5200 6.992063 ATGTCAGCTTTCTCGATAATGTTT 57.008 33.333 0.00 0.00 0.00 2.83
3843 5285 7.007815 GCGAGATAAGAAAATTTCAGAAACAGC 59.992 37.037 8.55 2.79 0.00 4.40
3862 5304 1.693627 GACCTTCCTGGAGCGAGATA 58.306 55.000 0.00 0.00 39.71 1.98
3996 5440 6.114767 TGGGGTTTCTACCGTATTTCAATAC 58.885 40.000 0.23 0.23 46.04 1.89
4054 5499 0.610687 AAGTCTGCTAGTGCTGGGTC 59.389 55.000 0.00 0.00 40.48 4.46
4085 5532 8.541899 TTCCCTTTTGGTCTTAATAACTTTGT 57.458 30.769 0.00 0.00 38.10 2.83
4118 5565 4.948608 TTTCTTGACAACAAACTGCGTA 57.051 36.364 0.00 0.00 35.49 4.42
4254 5708 1.838112 TCATCGGCTTGCCTTTGAAT 58.162 45.000 10.12 0.00 0.00 2.57
4311 5768 3.636153 AAGAATGCAACCTCCTAGGAC 57.364 47.619 7.62 0.00 37.67 3.85
4425 5887 7.214381 AGCAACAAGATAAGTGCCGTTATATA 58.786 34.615 0.00 0.00 0.00 0.86
4443 5905 7.753309 TGCTTACCTAAAATTCTAGCAACAA 57.247 32.000 0.00 0.00 34.55 2.83
4603 6073 0.902531 TCTCCTCCAAATCGTCCCAC 59.097 55.000 0.00 0.00 0.00 4.61
4604 6074 1.195115 CTCTCCTCCAAATCGTCCCA 58.805 55.000 0.00 0.00 0.00 4.37
4644 6114 1.756538 CCATAAAGGGCGCTCCAAATT 59.243 47.619 2.00 4.92 38.24 1.82
4706 6176 5.255397 ACTCCAACCCTTGATATTTGTCA 57.745 39.130 0.00 0.00 0.00 3.58
4717 6187 0.178873 TGGGCTCTACTCCAACCCTT 60.179 55.000 0.00 0.00 41.44 3.95
4737 6207 8.783660 TGAGGATAAGTACAGACCTGAATATT 57.216 34.615 3.76 0.00 0.00 1.28
4752 6222 3.977326 GAGAGGGGGAAATGAGGATAAGT 59.023 47.826 0.00 0.00 0.00 2.24
4803 6273 1.011242 CGCGTGTGTTGGACAGTTG 60.011 57.895 0.00 0.00 34.28 3.16
4893 6363 3.635191 TGGCTGTCATCACCGGCA 61.635 61.111 0.00 0.00 39.56 5.69
4923 6393 1.114627 CGATGAGGAGGATGTGGACA 58.885 55.000 0.00 0.00 0.00 4.02
4930 6400 1.409427 GTCGAAACCGATGAGGAGGAT 59.591 52.381 0.00 0.00 45.00 3.24
5119 6589 1.736645 CACGACGATGTGGGTCCAC 60.737 63.158 12.89 12.89 46.33 4.02
5150 6620 1.200716 CCGTAAAGCCAGACTCACGTA 59.799 52.381 0.00 0.00 0.00 3.57
5183 6653 3.914364 GCAAGAAAGCACCAAAAGTATCG 59.086 43.478 0.00 0.00 0.00 2.92
5192 6662 2.016318 CATATCCGCAAGAAAGCACCA 58.984 47.619 0.00 0.00 43.02 4.17


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

AutoCloner maintained by Alex Coulton.