Multiple sequence alignment - TraesCS1B01G184900

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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 TraesCS1B01G184900 chr1B 100.000 2850 0 0 1 2850 332080009 332077160 0.000000e+00 5264.0
1 TraesCS1B01G184900 chr1D 94.229 1854 71 14 721 2553 246101714 246103552 0.000000e+00 2798.0
2 TraesCS1B01G184900 chr1D 91.017 423 18 8 676 1085 246100121 246100536 1.150000e-153 553.0
3 TraesCS1B01G184900 chr1D 80.565 566 72 23 144 682 246079967 246080521 4.420000e-108 401.0
4 TraesCS1B01G184900 chr1D 87.850 214 6 4 2542 2735 246103578 246103791 1.710000e-57 233.0
5 TraesCS1B01G184900 chr1D 94.737 114 6 0 2719 2832 246103804 246103917 8.110000e-41 178.0
6 TraesCS1B01G184900 chr1D 92.308 104 8 0 2747 2850 246103917 246104020 6.360000e-32 148.0
7 TraesCS1B01G184900 chr1D 88.288 111 11 2 1 110 246079866 246079975 6.410000e-27 132.0
8 TraesCS1B01G184900 chr1A 87.304 1654 144 32 138 1744 307042592 307044226 0.000000e+00 1831.0
9 TraesCS1B01G184900 chr1A 92.189 845 38 15 1716 2552 307044370 307045194 0.000000e+00 1170.0
10 TraesCS1B01G184900 chr1A 89.666 329 14 4 2542 2850 307045221 307045549 4.420000e-108 401.0
11 TraesCS1B01G184900 chr5A 82.906 117 19 1 378 494 690405473 690405588 1.400000e-18 104.0
12 TraesCS1B01G184900 chr5A 80.159 126 23 2 378 502 423141377 423141253 3.020000e-15 93.5
13 TraesCS1B01G184900 chr5A 81.905 105 18 1 392 496 503954893 503954996 1.410000e-13 87.9
14 TraesCS1B01G184900 chr5A 92.683 41 1 2 530 568 514184731 514184771 1.100000e-04 58.4
15 TraesCS1B01G184900 chr4D 79.577 142 24 4 355 494 417899144 417899006 2.340000e-16 97.1
16 TraesCS1B01G184900 chr2B 86.047 86 11 1 378 462 263811347 263811262 1.090000e-14 91.6
17 TraesCS1B01G184900 chr5D 84.270 89 12 2 369 455 276575432 276575344 5.060000e-13 86.1
18 TraesCS1B01G184900 chr7B 80.165 121 17 6 378 496 719159095 719158980 1.820000e-12 84.2
19 TraesCS1B01G184900 chr5B 82.558 86 15 0 376 461 586624100 586624015 3.040000e-10 76.8
20 TraesCS1B01G184900 chr4B 80.412 97 18 1 529 625 667353353 667353258 3.940000e-09 73.1
21 TraesCS1B01G184900 chr3D 97.143 35 1 0 758 792 93034473 93034439 3.070000e-05 60.2
22 TraesCS1B01G184900 chr3B 97.143 35 1 0 758 792 143256742 143256776 3.070000e-05 60.2
23 TraesCS1B01G184900 chr3A 97.143 35 1 0 758 792 547123095 547123129 3.070000e-05 60.2


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 TraesCS1B01G184900 chr1B 332077160 332080009 2849 True 5264.0 5264 100.000000 1 2850 1 chr1B.!!$R1 2849
1 TraesCS1B01G184900 chr1D 246100121 246104020 3899 False 782.0 2798 92.028200 676 2850 5 chr1D.!!$F2 2174
2 TraesCS1B01G184900 chr1D 246079866 246080521 655 False 266.5 401 84.426500 1 682 2 chr1D.!!$F1 681
3 TraesCS1B01G184900 chr1A 307042592 307045549 2957 False 1134.0 1831 89.719667 138 2850 3 chr1A.!!$F1 2712

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
194 196 0.586802 GGCTCGAGAAAAACTTGCGT 59.413 50.0 18.75 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 3812 0.596082 ATTCAACAAGAAACCGGGCG 59.404 50.0 6.32 0.0 40.22 6.13 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
67 69 1.466167 CCATGGCGTCACAGAAAGAAG 59.534 52.381 0.00 0.00 0.00 2.85
68 70 2.146342 CATGGCGTCACAGAAAGAAGT 58.854 47.619 0.00 0.00 0.00 3.01
78 80 4.765339 TCACAGAAAGAAGTCTCACCGATA 59.235 41.667 0.00 0.00 0.00 2.92
79 81 5.098893 CACAGAAAGAAGTCTCACCGATAG 58.901 45.833 0.00 0.00 0.00 2.08
96 98 3.499926 CGATAGGAGGTAGCCTAAGGGAA 60.500 52.174 0.00 0.00 43.39 3.97
97 99 2.480642 AGGAGGTAGCCTAAGGGAAG 57.519 55.000 0.00 0.00 36.22 3.46
98 100 1.062044 AGGAGGTAGCCTAAGGGAAGG 60.062 57.143 0.00 0.00 36.22 3.46
100 102 2.321719 GAGGTAGCCTAAGGGAAGGAG 58.678 57.143 0.00 0.00 39.15 3.69
101 103 1.938069 AGGTAGCCTAAGGGAAGGAGA 59.062 52.381 0.00 0.00 39.15 3.71
102 104 2.090999 AGGTAGCCTAAGGGAAGGAGAG 60.091 54.545 0.00 0.00 39.15 3.20
103 105 2.091222 GGTAGCCTAAGGGAAGGAGAGA 60.091 54.545 0.00 0.00 39.15 3.10
104 106 2.470057 AGCCTAAGGGAAGGAGAGAG 57.530 55.000 0.00 0.00 39.15 3.20
105 107 1.933765 AGCCTAAGGGAAGGAGAGAGA 59.066 52.381 0.00 0.00 39.15 3.10
106 108 2.091333 AGCCTAAGGGAAGGAGAGAGAG 60.091 54.545 0.00 0.00 39.15 3.20
107 109 2.091555 GCCTAAGGGAAGGAGAGAGAGA 60.092 54.545 0.00 0.00 39.15 3.10
108 110 3.832527 CCTAAGGGAAGGAGAGAGAGAG 58.167 54.545 0.00 0.00 39.15 3.20
109 111 3.461831 CCTAAGGGAAGGAGAGAGAGAGA 59.538 52.174 0.00 0.00 39.15 3.10
110 112 3.669939 AAGGGAAGGAGAGAGAGAGAG 57.330 52.381 0.00 0.00 0.00 3.20
111 113 2.858644 AGGGAAGGAGAGAGAGAGAGA 58.141 52.381 0.00 0.00 0.00 3.10
112 114 2.780010 AGGGAAGGAGAGAGAGAGAGAG 59.220 54.545 0.00 0.00 0.00 3.20
113 115 2.777692 GGGAAGGAGAGAGAGAGAGAGA 59.222 54.545 0.00 0.00 0.00 3.10
114 116 3.181450 GGGAAGGAGAGAGAGAGAGAGAG 60.181 56.522 0.00 0.00 0.00 3.20
115 117 3.711704 GGAAGGAGAGAGAGAGAGAGAGA 59.288 52.174 0.00 0.00 0.00 3.10
116 118 4.202305 GGAAGGAGAGAGAGAGAGAGAGAG 60.202 54.167 0.00 0.00 0.00 3.20
117 119 4.271807 AGGAGAGAGAGAGAGAGAGAGA 57.728 50.000 0.00 0.00 0.00 3.10
118 120 4.222336 AGGAGAGAGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
119 121 4.078922 AGGAGAGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
120 122 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
121 123 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
122 124 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
123 125 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
124 126 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
125 127 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
126 128 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
127 129 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
128 130 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
129 131 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
130 132 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
131 133 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
132 134 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
133 135 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
134 136 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
135 137 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
136 138 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
152 154 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
192 194 1.873591 TCTGGCTCGAGAAAAACTTGC 59.126 47.619 18.75 0.00 0.00 4.01
194 196 0.586802 GGCTCGAGAAAAACTTGCGT 59.413 50.000 18.75 0.00 0.00 5.24
197 199 0.856641 TCGAGAAAAACTTGCGTCCG 59.143 50.000 0.00 0.00 0.00 4.79
200 202 2.219216 CGAGAAAAACTTGCGTCCGTTA 59.781 45.455 0.00 0.00 0.00 3.18
202 204 2.937799 AGAAAAACTTGCGTCCGTTACA 59.062 40.909 0.00 0.00 0.00 2.41
224 226 7.721286 ACAAAGATAATGATAAGAGAAGCGG 57.279 36.000 0.00 0.00 0.00 5.52
225 227 6.203723 ACAAAGATAATGATAAGAGAAGCGGC 59.796 38.462 0.00 0.00 0.00 6.53
232 238 2.238847 TAAGAGAAGCGGCGCATGGT 62.239 55.000 35.02 16.00 0.00 3.55
257 264 2.660064 GGAGCACGTGGAGGTGGAT 61.660 63.158 18.88 0.00 38.36 3.41
263 270 0.898789 ACGTGGAGGTGGATCGAGTT 60.899 55.000 0.00 0.00 0.00 3.01
265 272 1.065701 CGTGGAGGTGGATCGAGTTAG 59.934 57.143 0.00 0.00 0.00 2.34
278 285 6.127054 TGGATCGAGTTAGGAAAATCAGTCAT 60.127 38.462 0.00 0.00 30.10 3.06
290 297 9.265901 AGGAAAATCAGTCATGTAGATTATTCG 57.734 33.333 9.32 0.00 32.11 3.34
291 298 9.046296 GGAAAATCAGTCATGTAGATTATTCGT 57.954 33.333 9.32 0.00 32.11 3.85
355 365 3.338249 ACAAGCAAAGTCGCTCACATAT 58.662 40.909 0.00 0.00 42.89 1.78
358 368 4.123497 AGCAAAGTCGCTCACATATACA 57.877 40.909 0.00 0.00 37.91 2.29
367 383 2.285220 GCTCACATATACAAGCACACCG 59.715 50.000 0.00 0.00 34.86 4.94
408 428 4.100189 CCCTATCCTTATAAGCATCTCCGG 59.900 50.000 6.99 0.00 0.00 5.14
430 450 3.759086 GGAGACTGAGCCGACATATCATA 59.241 47.826 0.00 0.00 0.00 2.15
433 453 5.718146 AGACTGAGCCGACATATCATATTG 58.282 41.667 0.00 0.00 0.00 1.90
441 461 7.040494 AGCCGACATATCATATTGAGATTGAG 58.960 38.462 0.00 0.00 0.00 3.02
448 468 9.939802 CATATCATATTGAGATTGAGGAAGTCA 57.060 33.333 0.00 0.00 0.00 3.41
452 472 8.657712 TCATATTGAGATTGAGGAAGTCATCAT 58.342 33.333 0.00 0.00 36.49 2.45
457 477 6.608808 TGAGATTGAGGAAGTCATCATAGACA 59.391 38.462 0.00 0.00 40.98 3.41
463 483 5.026121 AGGAAGTCATCATAGACACCTTCA 58.974 41.667 0.00 0.00 41.33 3.02
473 493 3.685139 AGACACCTTCATTGTCGACAT 57.315 42.857 20.80 6.88 46.73 3.06
483 503 3.057526 TCATTGTCGACATGAACGTCTCT 60.058 43.478 20.80 0.00 33.54 3.10
498 518 1.993370 GTCTCTTCCCATTGAACGACG 59.007 52.381 0.00 0.00 0.00 5.12
502 522 0.668096 TTCCCATTGAACGACGTCGG 60.668 55.000 37.89 21.83 44.95 4.79
503 523 1.373748 CCCATTGAACGACGTCGGT 60.374 57.895 37.89 35.07 44.92 4.69
505 525 1.623081 CCATTGAACGACGTCGGTGG 61.623 60.000 37.89 29.52 40.66 4.61
512 532 2.911484 CGACGTCGGTGGAAGGTCA 61.911 63.158 29.70 0.00 35.37 4.02
516 536 1.202722 ACGTCGGTGGAAGGTCAAAAT 60.203 47.619 0.00 0.00 0.00 1.82
517 537 2.037511 ACGTCGGTGGAAGGTCAAAATA 59.962 45.455 0.00 0.00 0.00 1.40
518 538 3.267483 CGTCGGTGGAAGGTCAAAATAT 58.733 45.455 0.00 0.00 0.00 1.28
519 539 3.687698 CGTCGGTGGAAGGTCAAAATATT 59.312 43.478 0.00 0.00 0.00 1.28
520 540 4.155280 CGTCGGTGGAAGGTCAAAATATTT 59.845 41.667 0.00 0.00 0.00 1.40
521 541 5.335348 CGTCGGTGGAAGGTCAAAATATTTT 60.335 40.000 7.64 7.64 0.00 1.82
522 542 6.452242 GTCGGTGGAAGGTCAAAATATTTTT 58.548 36.000 10.77 0.00 0.00 1.94
552 572 1.246649 ATGCGAGCACCAATGTCAAA 58.753 45.000 0.00 0.00 0.00 2.69
558 578 3.369147 CGAGCACCAATGTCAAAGTCTAG 59.631 47.826 0.00 0.00 0.00 2.43
561 581 3.437049 GCACCAATGTCAAAGTCTAGGAC 59.563 47.826 0.00 0.00 0.00 3.85
575 595 6.742559 AGTCTAGGACTTAAACTTTGGTGA 57.257 37.500 0.00 0.00 40.28 4.02
576 596 7.133133 AGTCTAGGACTTAAACTTTGGTGAA 57.867 36.000 0.00 0.00 40.28 3.18
578 598 6.764560 GTCTAGGACTTAAACTTTGGTGAACA 59.235 38.462 0.00 0.00 0.00 3.18
582 602 3.383505 ACTTAAACTTTGGTGAACAGGGC 59.616 43.478 0.00 0.00 0.00 5.19
583 603 0.744281 AAACTTTGGTGAACAGGGCG 59.256 50.000 0.00 0.00 0.00 6.13
588 608 2.433664 GGTGAACAGGGCGTACCG 60.434 66.667 0.00 0.00 46.96 4.02
589 609 2.341176 GTGAACAGGGCGTACCGT 59.659 61.111 0.00 0.00 46.96 4.83
602 622 3.052036 GCGTACCGTTGTTCTTCTAACA 58.948 45.455 0.00 0.00 0.00 2.41
609 629 5.238650 ACCGTTGTTCTTCTAACAATCCAAG 59.761 40.000 6.59 0.00 41.51 3.61
612 632 5.689383 TGTTCTTCTAACAATCCAAGCAC 57.311 39.130 0.00 0.00 0.00 4.40
623 643 7.506590 AACAATCCAAGCACAGATTGGTTCG 62.507 44.000 20.08 6.02 45.81 3.95
641 673 6.724263 TGGTTCGCATGTTGATGATTTATAC 58.276 36.000 0.00 0.00 0.00 1.47
642 674 6.542005 TGGTTCGCATGTTGATGATTTATACT 59.458 34.615 0.00 0.00 0.00 2.12
643 675 7.713073 TGGTTCGCATGTTGATGATTTATACTA 59.287 33.333 0.00 0.00 0.00 1.82
670 709 6.334202 TGTGGAAACAGAATAAACACCAAAC 58.666 36.000 0.00 0.00 44.46 2.93
730 773 1.145571 AACTAGCCTGTGGGTTTGGA 58.854 50.000 0.00 0.00 34.28 3.53
876 920 1.792367 TCAAAATCGCTGTCAGTGACG 59.208 47.619 18.14 13.51 37.59 4.35
1009 1063 6.055588 CCCGTCTTATTCTACATCCACATTT 58.944 40.000 0.00 0.00 0.00 2.32
1015 1069 8.274322 TCTTATTCTACATCCACATTTCCACAT 58.726 33.333 0.00 0.00 0.00 3.21
1122 2721 2.665185 GGTGTCGCAAGCCTTCGT 60.665 61.111 0.00 0.00 37.18 3.85
1178 2780 3.254024 AACCTCGCCATCGCCAAGT 62.254 57.895 0.00 0.00 35.26 3.16
1640 3242 0.396435 CATGATGGGGCTAGCCGTTA 59.604 55.000 27.24 15.93 36.85 3.18
1655 3257 1.078143 GTTAGTCAGCAGGCCTGGG 60.078 63.158 33.46 10.63 42.05 4.45
1712 3314 0.673644 CGGCGGAGGAATCAACAACT 60.674 55.000 0.00 0.00 0.00 3.16
1754 3531 1.470098 CTGTTTCCATTCCTTCCTGCG 59.530 52.381 0.00 0.00 0.00 5.18
1802 3580 3.645884 GCAAGAGTTTCTGTACGGTGTA 58.354 45.455 0.64 0.00 0.00 2.90
1873 3651 2.937799 CGTCTCCGCTTCTTCTAGTACT 59.062 50.000 0.00 0.00 0.00 2.73
1874 3652 4.118410 CGTCTCCGCTTCTTCTAGTACTA 58.882 47.826 1.89 1.89 0.00 1.82
1883 3661 8.591312 CCGCTTCTTCTAGTACTATATACGTAC 58.409 40.741 2.33 11.50 37.96 3.67
2034 3812 4.364415 TGTGTACTTTGAAACTGTTGCC 57.636 40.909 0.00 0.00 0.00 4.52
2037 3815 0.102300 ACTTTGAAACTGTTGCCGCC 59.898 50.000 0.00 0.00 0.00 6.13
2066 3844 3.848272 TGTTGAATCTCGAATTTGGGC 57.152 42.857 0.00 0.00 0.00 5.36
2081 3859 2.541120 GGGCGATCATCTGCTGTGC 61.541 63.158 0.00 0.00 0.00 4.57
2087 3865 1.030488 ATCATCTGCTGTGCTGCACC 61.030 55.000 28.17 15.25 38.12 5.01
2092 3870 0.953727 CTGCTGTGCTGCACCTTTTA 59.046 50.000 28.17 9.78 38.12 1.52
2259 4041 5.479375 AGATATGCAAATTCTGGCCATTAGG 59.521 40.000 5.51 0.00 38.23 2.69
2406 4191 4.187694 GGAAGTTCTCTGCTGATAACCAG 58.812 47.826 15.29 0.00 45.67 4.00
2451 4236 2.670148 GGAGATTGCCACCGGGTCT 61.670 63.158 6.32 0.00 36.17 3.85
2464 4249 4.080975 CCACCGGGTCTTTTTGGTACTATA 60.081 45.833 6.32 0.00 32.29 1.31
2465 4250 5.397109 CCACCGGGTCTTTTTGGTACTATAT 60.397 44.000 6.32 0.00 32.29 0.86
2466 4251 6.183360 CCACCGGGTCTTTTTGGTACTATATA 60.183 42.308 6.32 0.00 32.29 0.86
2507 4292 5.369685 AAAAACATCATATGCACGTGACA 57.630 34.783 22.23 17.15 0.00 3.58
2617 4441 7.174253 TCCCTTAACTTAGCAATTGTACAACAG 59.826 37.037 11.22 7.58 0.00 3.16
2685 4527 1.524621 CGCTTGAGTATGCAGGGGG 60.525 63.158 0.00 0.00 0.00 5.40
2691 4533 1.490490 TGAGTATGCAGGGGGAACATC 59.510 52.381 0.00 0.00 0.00 3.06
2750 4621 4.776308 TCCCTGTTAGTTAGAAGGAAGTCC 59.224 45.833 0.00 0.00 30.92 3.85
2775 4646 2.344500 CCCCGTAACAAGTCCGCA 59.656 61.111 0.00 0.00 0.00 5.69
2781 4652 1.987770 CGTAACAAGTCCGCACGTTAT 59.012 47.619 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.304134 GACGCCATGGTTCCCCTTT 60.304 57.895 14.67 0.00 0.00 3.11
58 60 4.399618 TCCTATCGGTGAGACTTCTTTCTG 59.600 45.833 0.00 0.00 0.00 3.02
67 69 1.881324 GCTACCTCCTATCGGTGAGAC 59.119 57.143 0.00 0.00 35.98 3.36
68 70 1.202903 GGCTACCTCCTATCGGTGAGA 60.203 57.143 0.00 0.00 35.98 3.27
78 80 1.062044 CCTTCCCTTAGGCTACCTCCT 60.062 57.143 0.00 0.00 40.21 3.69
79 81 1.062352 TCCTTCCCTTAGGCTACCTCC 60.062 57.143 0.00 0.00 34.61 4.30
92 94 2.777692 TCTCTCTCTCTCTCTCCTTCCC 59.222 54.545 0.00 0.00 0.00 3.97
96 98 4.078922 TCTCTCTCTCTCTCTCTCTCTCCT 60.079 50.000 0.00 0.00 0.00 3.69
97 99 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
98 100 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
100 102 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
101 103 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
102 104 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
103 105 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
104 106 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
105 107 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
106 108 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
107 109 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
108 110 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
109 111 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
110 112 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
111 113 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
112 114 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
113 115 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
114 116 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
115 117 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
116 118 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
117 119 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
118 120 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
119 121 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
120 122 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
121 123 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
122 124 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
123 125 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
124 126 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
125 127 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
126 128 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
127 129 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
128 130 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
129 131 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
130 132 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
131 133 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
132 134 3.386078 TGCTCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
133 135 3.378512 TGCTCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
134 136 3.827008 TGCTCTCTCTCTCTCTCTCTC 57.173 52.381 0.00 0.00 0.00 3.20
135 137 3.713248 TCATGCTCTCTCTCTCTCTCTCT 59.287 47.826 0.00 0.00 0.00 3.10
136 138 4.063689 CTCATGCTCTCTCTCTCTCTCTC 58.936 52.174 0.00 0.00 0.00 3.20
152 154 0.743097 GCAAACCCATCTCCTCATGC 59.257 55.000 0.00 0.00 0.00 4.06
192 194 8.570096 TCTTATCATTATCTTTGTAACGGACG 57.430 34.615 0.00 0.00 0.00 4.79
200 202 6.203723 GCCGCTTCTCTTATCATTATCTTTGT 59.796 38.462 0.00 0.00 0.00 2.83
202 204 5.406780 CGCCGCTTCTCTTATCATTATCTTT 59.593 40.000 0.00 0.00 0.00 2.52
225 227 4.838152 CTCCCGTGGGACCATGCG 62.838 72.222 2.72 0.00 39.76 4.73
241 248 2.982130 GATCCACCTCCACGTGCT 59.018 61.111 10.91 0.00 32.10 4.40
250 257 4.469945 TGATTTTCCTAACTCGATCCACCT 59.530 41.667 0.00 0.00 0.00 4.00
253 260 5.186992 TGACTGATTTTCCTAACTCGATCCA 59.813 40.000 0.00 0.00 0.00 3.41
257 264 6.037786 ACATGACTGATTTTCCTAACTCGA 57.962 37.500 0.00 0.00 0.00 4.04
265 272 9.046296 ACGAATAATCTACATGACTGATTTTCC 57.954 33.333 0.00 0.00 33.24 3.13
278 285 6.640518 AGGAGAAAAGCACGAATAATCTACA 58.359 36.000 0.00 0.00 0.00 2.74
286 293 8.837389 GGTTATAAATAGGAGAAAAGCACGAAT 58.163 33.333 0.00 0.00 0.00 3.34
287 294 8.044908 AGGTTATAAATAGGAGAAAAGCACGAA 58.955 33.333 0.00 0.00 0.00 3.85
288 295 7.562135 AGGTTATAAATAGGAGAAAAGCACGA 58.438 34.615 0.00 0.00 0.00 4.35
289 296 7.787725 AGGTTATAAATAGGAGAAAAGCACG 57.212 36.000 0.00 0.00 0.00 5.34
326 336 4.062293 AGCGACTTTGCTTGTATTGTGTA 58.938 39.130 0.00 0.00 44.46 2.90
338 348 4.783450 GCTTGTATATGTGAGCGACTTTGC 60.783 45.833 0.00 0.00 0.00 3.68
367 383 0.247537 GGTGTGCGTGCGTTTATAGC 60.248 55.000 0.00 0.00 0.00 2.97
376 392 0.177141 TAAGGATAGGGTGTGCGTGC 59.823 55.000 0.00 0.00 0.00 5.34
408 428 1.957177 TGATATGTCGGCTCAGTCTCC 59.043 52.381 0.00 0.00 0.00 3.71
430 450 8.149647 GTCTATGATGACTTCCTCAATCTCAAT 58.850 37.037 0.00 0.00 34.39 2.57
433 453 6.922957 GTGTCTATGATGACTTCCTCAATCTC 59.077 42.308 0.00 0.00 37.79 2.75
441 461 5.344743 TGAAGGTGTCTATGATGACTTCC 57.655 43.478 0.00 0.00 37.79 3.46
448 468 5.105351 TGTCGACAATGAAGGTGTCTATGAT 60.105 40.000 17.62 0.00 42.68 2.45
452 472 4.219725 TCATGTCGACAATGAAGGTGTCTA 59.780 41.667 24.13 0.00 42.68 2.59
457 477 2.736721 CGTTCATGTCGACAATGAAGGT 59.263 45.455 29.97 14.13 36.21 3.50
463 483 3.577649 AGAGACGTTCATGTCGACAAT 57.422 42.857 24.13 8.50 43.70 2.71
473 493 3.399330 GTTCAATGGGAAGAGACGTTCA 58.601 45.455 0.00 0.00 35.82 3.18
483 503 0.668096 CCGACGTCGTTCAATGGGAA 60.668 55.000 33.49 0.00 37.74 3.97
498 518 5.638596 AAATATTTTGACCTTCCACCGAC 57.361 39.130 0.00 0.00 0.00 4.79
521 541 5.352284 TGGTGCTCGCATTTTTCTTAAAAA 58.648 33.333 0.00 0.47 43.76 1.94
522 542 4.938080 TGGTGCTCGCATTTTTCTTAAAA 58.062 34.783 0.00 0.00 37.62 1.52
523 543 4.576216 TGGTGCTCGCATTTTTCTTAAA 57.424 36.364 0.00 0.00 0.00 1.52
526 546 3.243839 ACATTGGTGCTCGCATTTTTCTT 60.244 39.130 0.00 0.00 0.00 2.52
552 572 6.742559 TCACCAAAGTTTAAGTCCTAGACT 57.257 37.500 0.00 0.00 45.64 3.24
558 578 4.037565 CCCTGTTCACCAAAGTTTAAGTCC 59.962 45.833 0.00 0.00 0.00 3.85
561 581 3.550030 CGCCCTGTTCACCAAAGTTTAAG 60.550 47.826 0.00 0.00 0.00 1.85
569 589 1.071814 GGTACGCCCTGTTCACCAA 59.928 57.895 0.00 0.00 30.73 3.67
583 603 5.697633 TGGATTGTTAGAAGAACAACGGTAC 59.302 40.000 5.08 0.00 42.18 3.34
588 608 5.915196 GTGCTTGGATTGTTAGAAGAACAAC 59.085 40.000 5.08 1.02 42.18 3.32
589 609 5.592282 TGTGCTTGGATTGTTAGAAGAACAA 59.408 36.000 5.41 5.41 43.33 2.83
602 622 2.489329 CGAACCAATCTGTGCTTGGATT 59.511 45.455 8.55 1.46 44.95 3.01
609 629 0.523072 ACATGCGAACCAATCTGTGC 59.477 50.000 0.00 0.00 0.00 4.57
612 632 3.127376 TCATCAACATGCGAACCAATCTG 59.873 43.478 0.00 0.00 0.00 2.90
623 643 9.603298 CACATGTAGTATAAATCATCAACATGC 57.397 33.333 0.00 0.00 44.16 4.06
641 673 7.040755 TGGTGTTTATTCTGTTTCCACATGTAG 60.041 37.037 0.00 0.00 30.39 2.74
642 674 6.773200 TGGTGTTTATTCTGTTTCCACATGTA 59.227 34.615 0.00 0.00 30.39 2.29
643 675 5.596361 TGGTGTTTATTCTGTTTCCACATGT 59.404 36.000 0.00 0.00 30.39 3.21
701 744 7.223260 ACCCACAGGCTAGTTTTATTTTAAC 57.777 36.000 0.00 0.00 36.11 2.01
719 762 0.336737 ACCCAAGTTCCAAACCCACA 59.663 50.000 0.00 0.00 0.00 4.17
730 773 4.590850 GAAGCATTCAGAAACCCAAGTT 57.409 40.909 0.00 0.00 46.62 2.66
785 828 3.426525 GCGAGGTAAATAATCGGTTACGG 59.573 47.826 0.00 0.00 41.39 4.02
821 865 3.088532 TCGTCATTTTCCCCATCCTTTG 58.911 45.455 0.00 0.00 0.00 2.77
876 920 1.145803 GGAATCGGCCGTATTACTGC 58.854 55.000 27.15 10.79 0.00 4.40
1009 1063 1.519234 GCGAGCGTGATGATGTGGA 60.519 57.895 0.00 0.00 0.00 4.02
1015 1069 2.880879 GCTTCGCGAGCGTGATGA 60.881 61.111 17.24 1.43 42.46 2.92
1072 2671 4.657824 CACCACCGGTTCGCGTCT 62.658 66.667 2.97 0.00 31.02 4.18
1387 2989 2.838748 ATCTCTGGGTCGTCTCCGCA 62.839 60.000 0.00 0.00 0.00 5.69
1477 3079 4.452733 ACGGCCGCCTTGTAGAGC 62.453 66.667 28.58 0.00 0.00 4.09
1478 3080 2.509336 CACGGCCGCCTTGTAGAG 60.509 66.667 28.58 0.00 0.00 2.43
1569 3171 4.749310 CGGCAAGCCTCGTGAGCT 62.749 66.667 9.73 0.00 44.19 4.09
1619 3221 1.130054 ACGGCTAGCCCCATCATGAT 61.130 55.000 28.09 1.18 0.00 2.45
1640 3242 3.325753 GACCCAGGCCTGCTGACT 61.326 66.667 28.39 6.40 0.00 3.41
1655 3257 2.484062 CCATCATGGCCTTGGCGAC 61.484 63.158 17.95 0.00 0.00 5.19
1712 3314 3.450904 AGGCTTACTGGTGATGGACTTA 58.549 45.455 0.00 0.00 0.00 2.24
1788 3566 1.680735 ACACCGTACACCGTACAGAAA 59.319 47.619 5.24 0.00 33.66 2.52
1802 3580 1.678598 TTTCGAGTCCCACACACCGT 61.679 55.000 0.00 0.00 0.00 4.83
1874 3652 9.748708 ATTAACAACCAATGTACGTACGTATAT 57.251 29.630 29.05 27.47 42.99 0.86
2034 3812 0.596082 ATTCAACAAGAAACCGGGCG 59.404 50.000 6.32 0.00 40.22 6.13
2037 3815 3.064207 TCGAGATTCAACAAGAAACCGG 58.936 45.455 0.00 0.00 40.22 5.28
2066 3844 1.087771 TGCAGCACAGCAGATGATCG 61.088 55.000 0.00 0.00 40.11 3.69
2081 3859 3.399440 TTGGCCAAATAAAAGGTGCAG 57.601 42.857 17.98 0.00 0.00 4.41
2092 3870 5.122082 CGCATTTACATTTCTTTGGCCAAAT 59.878 36.000 30.46 17.24 0.00 2.32
2259 4041 4.517285 TCAACTCAACTTATCATGGAGGC 58.483 43.478 0.00 0.00 0.00 4.70
2296 4078 7.875554 GGATCTATCCCAACAGAAGAGAATAAC 59.124 40.741 0.00 0.00 41.20 1.89
2406 4191 4.698780 ACCAGAGGAGGTTAATAAAAACGC 59.301 41.667 0.00 0.00 39.34 4.84
2486 4271 5.048782 AGTTGTCACGTGCATATGATGTTTT 60.049 36.000 11.67 0.00 0.00 2.43
2507 4292 3.595190 ACTTCCCAGTAAGCCAAAGTT 57.405 42.857 0.00 0.00 0.00 2.66
2617 4441 5.449588 CCACTGTAATCCTGCACAAATGATC 60.450 44.000 0.00 0.00 0.00 2.92
2691 4533 5.360591 AGTACACCTTGTGAACAGAAGAAG 58.639 41.667 12.21 7.30 36.96 2.85
2750 4621 2.145536 ACTTGTTACGGGGCTTTTACG 58.854 47.619 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.