Multiple sequence alignment - TraesCS5D01G201900

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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 TraesCS5D01G201900 chr5D 100.000 4521 0 0 1 4521 306190518 306195038 0.000000e+00 8349
1 TraesCS5D01G201900 chr5A 92.649 4149 202 53 434 4521 391546857 391542751 0.000000e+00 5877
2 TraesCS5D01G201900 chr5A 86.861 548 33 12 17 536 391547928 391547392 1.090000e-160 577
3 TraesCS5D01G201900 chr5B 91.091 4187 225 65 432 4521 351473987 351478122 0.000000e+00 5529
4 TraesCS5D01G201900 chr5B 86.789 545 36 15 17 530 351473195 351473734 3.920000e-160 575
5 TraesCS5D01G201900 chr3D 84.190 253 29 4 3823 4074 443308463 443308705 7.560000e-58 235
6 TraesCS5D01G201900 chr1D 84.190 253 28 6 3823 4074 126870503 126870262 7.560000e-58 235
7 TraesCS5D01G201900 chr3A 87.255 204 22 4 3823 4024 562982041 562982242 3.520000e-56 230
8 TraesCS5D01G201900 chrUn 84.259 216 21 9 3823 4027 302550458 302550245 9.920000e-47 198
9 TraesCS5D01G201900 chr6A 83.568 213 22 10 3823 4024 561434044 561434254 2.150000e-43 187
10 TraesCS5D01G201900 chr6A 83.333 216 23 10 3823 4027 561619832 561619619 2.150000e-43 187
11 TraesCS5D01G201900 chr7B 88.571 140 15 1 3823 3961 44379273 44379134 7.780000e-38 169


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 TraesCS5D01G201900 chr5D 306190518 306195038 4520 False 8349 8349 100.000 1 4521 1 chr5D.!!$F1 4520
1 TraesCS5D01G201900 chr5A 391542751 391547928 5177 True 3227 5877 89.755 17 4521 2 chr5A.!!$R1 4504
2 TraesCS5D01G201900 chr5B 351473195 351478122 4927 False 3052 5529 88.940 17 4521 2 chr5B.!!$F1 4504

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
359 370 0.104934 AGATTCCGGGGTAGCTCCAT 60.105 55.000 0.00 0.0 38.11 3.41 F
570 1265 0.178975 ACCAAATGCAACTTCCCCGA 60.179 50.000 0.00 0.0 0.00 5.14 F
694 1391 1.139853 TGTGTTGGTCATTTTTGCCCC 59.860 47.619 0.00 0.0 0.00 5.80 F
780 1479 1.140312 AAGCAGTGACAGAAGGGGAA 58.860 50.000 0.00 0.0 0.00 3.97 F
2067 2800 1.763256 ATGGTGCCCATTCCCATGC 60.763 57.895 1.21 0.0 42.23 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 2305 1.618837 TCACAGTGGTAGCCAAGTCTC 59.381 52.381 0.00 0.0 34.18 3.36 R
2038 2771 2.257353 GGCACCATGTGACAAGACC 58.743 57.895 0.00 0.0 41.94 3.85 R
2341 3074 3.181429 ACCCAGCTCTTCATTTCCAAAGA 60.181 43.478 0.00 0.0 0.00 2.52 R
2716 3478 2.158385 ACCCAGCCTTTTGTAATCACCA 60.158 45.455 0.00 0.0 0.00 4.17 R
3911 4731 0.392998 AGGAAGGCACCATAGTTGCG 60.393 55.000 3.78 0.0 0.00 4.85 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
30 31 3.655211 CCCCCTGCCTTCAGTGCT 61.655 66.667 0.00 0.00 38.66 4.40
57 58 4.368808 CGCGCCGTGTTCCAGTTG 62.369 66.667 0.00 0.00 0.00 3.16
63 64 0.250124 CCGTGTTCCAGTTGTAGGCA 60.250 55.000 0.00 0.00 0.00 4.75
155 157 2.647158 GGAAGTCGCGTCCCCTCTT 61.647 63.158 5.77 2.77 0.00 2.85
300 311 2.000447 GCTGTGAGATTCCAACGGTAC 59.000 52.381 0.00 0.00 0.00 3.34
357 368 0.393448 GAAGATTCCGGGGTAGCTCC 59.607 60.000 0.00 0.00 0.00 4.70
359 370 0.104934 AGATTCCGGGGTAGCTCCAT 60.105 55.000 0.00 0.00 38.11 3.41
362 373 4.256180 CCGGGGTAGCTCCATGGC 62.256 72.222 6.96 0.00 38.11 4.40
363 374 3.479203 CGGGGTAGCTCCATGGCA 61.479 66.667 6.96 0.00 38.11 4.92
364 375 2.512896 GGGGTAGCTCCATGGCAG 59.487 66.667 6.96 6.85 38.11 4.85
365 376 2.512896 GGGTAGCTCCATGGCAGG 59.487 66.667 6.96 0.56 38.11 4.85
375 386 1.774254 TCCATGGCAGGTATAACAGGG 59.226 52.381 6.96 0.00 36.21 4.45
380 391 2.849943 TGGCAGGTATAACAGGGATGTT 59.150 45.455 0.00 0.00 35.93 2.71
382 393 2.618709 GCAGGTATAACAGGGATGTTGC 59.381 50.000 3.95 0.00 33.59 4.17
383 394 2.872245 CAGGTATAACAGGGATGTTGCG 59.128 50.000 3.95 0.00 33.59 4.85
392 403 3.054655 ACAGGGATGTTGCGTTATTAGGT 60.055 43.478 0.00 0.00 0.00 3.08
402 413 8.638685 TGTTGCGTTATTAGGTTTAGATAGAC 57.361 34.615 0.00 0.00 0.00 2.59
403 414 7.433131 TGTTGCGTTATTAGGTTTAGATAGACG 59.567 37.037 0.00 0.00 0.00 4.18
430 441 5.840243 CCAGAAGATGGTTTGCATTATCA 57.160 39.130 0.00 0.00 44.91 2.15
433 469 4.951715 AGAAGATGGTTTGCATTATCAGCA 59.048 37.500 0.00 0.00 40.85 4.41
438 474 3.577848 TGGTTTGCATTATCAGCAGGTTT 59.422 39.130 0.00 0.00 43.75 3.27
463 499 1.254954 ACTCACTACTTGGACGTCCC 58.745 55.000 31.19 14.15 34.29 4.46
530 1225 7.014808 GCTAGGGATTATAGGAAGTAGGCTATG 59.985 44.444 0.00 0.00 0.00 2.23
533 1228 8.062536 AGGGATTATAGGAAGTAGGCTATGTAG 58.937 40.741 0.00 0.00 0.00 2.74
546 1241 4.543590 GCTATGTAGCTATCACCCATGT 57.456 45.455 0.00 0.00 45.62 3.21
561 1256 3.118112 ACCCATGTTTGAACCAAATGCAA 60.118 39.130 0.00 0.00 35.74 4.08
562 1257 3.250521 CCCATGTTTGAACCAAATGCAAC 59.749 43.478 0.00 0.00 35.74 4.17
563 1258 4.128643 CCATGTTTGAACCAAATGCAACT 58.871 39.130 0.00 0.00 35.74 3.16
565 1260 5.277442 CCATGTTTGAACCAAATGCAACTTC 60.277 40.000 0.00 0.00 35.74 3.01
569 1264 0.678950 AACCAAATGCAACTTCCCCG 59.321 50.000 0.00 0.00 0.00 5.73
570 1265 0.178975 ACCAAATGCAACTTCCCCGA 60.179 50.000 0.00 0.00 0.00 5.14
654 1350 4.145052 GGTGAATCTCACTTTCCTTTGGT 58.855 43.478 6.74 0.00 46.19 3.67
683 1380 3.550030 GCCACTAATGTGTTGTGTTGGTC 60.550 47.826 0.00 0.00 42.34 4.02
694 1391 1.139853 TGTGTTGGTCATTTTTGCCCC 59.860 47.619 0.00 0.00 0.00 5.80
769 1468 6.048732 TCAATCACCATACTTAAGCAGTGA 57.951 37.500 15.53 15.53 38.49 3.41
770 1469 5.874810 TCAATCACCATACTTAAGCAGTGAC 59.125 40.000 15.51 0.00 37.10 3.67
771 1470 4.882842 TCACCATACTTAAGCAGTGACA 57.117 40.909 1.29 0.00 35.97 3.58
773 1472 4.526650 TCACCATACTTAAGCAGTGACAGA 59.473 41.667 1.29 0.00 35.97 3.41
780 1479 1.140312 AAGCAGTGACAGAAGGGGAA 58.860 50.000 0.00 0.00 0.00 3.97
837 1545 7.992180 ATTTGCTACTTCAAACTTCAAAGTG 57.008 32.000 0.00 0.00 39.66 3.16
854 1562 7.517614 TCAAAGTGTTTTTATATGCTGACCA 57.482 32.000 0.00 0.00 0.00 4.02
871 1579 5.533903 GCTGACCATGGATTAAATGATCTGT 59.466 40.000 21.47 0.00 0.00 3.41
885 1616 6.446781 AATGATCTGTTGGACTATGCTTTG 57.553 37.500 0.00 0.00 0.00 2.77
892 1623 5.626142 TGTTGGACTATGCTTTGTTCCTTA 58.374 37.500 0.00 0.00 0.00 2.69
893 1624 6.065374 TGTTGGACTATGCTTTGTTCCTTAA 58.935 36.000 0.00 0.00 0.00 1.85
894 1625 6.206634 TGTTGGACTATGCTTTGTTCCTTAAG 59.793 38.462 0.00 0.00 0.00 1.85
895 1626 6.121776 TGGACTATGCTTTGTTCCTTAAGA 57.878 37.500 3.36 0.00 0.00 2.10
896 1627 6.173339 TGGACTATGCTTTGTTCCTTAAGAG 58.827 40.000 3.36 0.00 0.00 2.85
897 1628 6.013725 TGGACTATGCTTTGTTCCTTAAGAGA 60.014 38.462 3.36 0.00 0.00 3.10
956 1689 9.090692 GCATGATGCAGTTTGAAGTATAATTTT 57.909 29.630 13.36 0.00 44.26 1.82
1146 1879 2.439507 TGATGGCCAAGTTCTCCCTATC 59.560 50.000 10.96 0.00 0.00 2.08
1281 2014 6.872628 TGGCTTTCACATGATCAGAATATC 57.127 37.500 0.00 0.00 0.00 1.63
1470 2203 6.818281 TTGGCTACATACCCTAGTACATTT 57.182 37.500 0.00 0.00 0.00 2.32
1572 2305 7.223971 TCTCATTTTTACCAATTCGTAGATCGG 59.776 37.037 0.00 0.00 40.32 4.18
1869 2602 7.701539 TGTTGCTAATATTTCTGGTGTCATT 57.298 32.000 0.00 0.00 0.00 2.57
1881 2614 5.316167 TCTGGTGTCATTGAAGCTTTATGT 58.684 37.500 17.13 0.00 0.00 2.29
1884 2617 7.611467 TCTGGTGTCATTGAAGCTTTATGTAAT 59.389 33.333 17.13 5.61 0.00 1.89
2049 2782 8.383175 AGAATTCTAATTTAGGGTCTTGTCACA 58.617 33.333 6.06 0.00 0.00 3.58
2067 2800 1.763256 ATGGTGCCCATTCCCATGC 60.763 57.895 1.21 0.00 42.23 4.06
2080 2813 5.163174 CCATTCCCATGCCCTAATTGAAATT 60.163 40.000 0.00 0.00 0.00 1.82
2123 2856 9.793252 TTGAATTGCTTGAGCTTTAAAGATATC 57.207 29.630 19.48 12.73 42.66 1.63
2130 2863 7.201565 GCTTGAGCTTTAAAGATATCGACAAGT 60.202 37.037 22.39 0.00 38.21 3.16
2148 2881 5.690865 ACAAGTATCTGTTGTTCCTTGGAA 58.309 37.500 0.00 0.00 34.37 3.53
2149 2882 6.126409 ACAAGTATCTGTTGTTCCTTGGAAA 58.874 36.000 3.39 0.00 34.37 3.13
2256 2989 8.721019 ATTTTGAGCTGACAATTTTTGAGAAA 57.279 26.923 0.00 0.00 0.00 2.52
2361 3094 5.656213 AATCTTTGGAAATGAAGAGCTGG 57.344 39.130 0.00 0.00 33.45 4.85
2442 3200 1.945394 GGGTGCTGCATCTATTGTCTG 59.055 52.381 13.32 0.00 0.00 3.51
2443 3201 2.636830 GGTGCTGCATCTATTGTCTGT 58.363 47.619 5.27 0.00 0.00 3.41
2444 3202 3.012518 GGTGCTGCATCTATTGTCTGTT 58.987 45.455 5.27 0.00 0.00 3.16
2445 3203 3.441572 GGTGCTGCATCTATTGTCTGTTT 59.558 43.478 5.27 0.00 0.00 2.83
2446 3204 4.635765 GGTGCTGCATCTATTGTCTGTTTA 59.364 41.667 5.27 0.00 0.00 2.01
2447 3205 5.123820 GGTGCTGCATCTATTGTCTGTTTAA 59.876 40.000 5.27 0.00 0.00 1.52
2448 3206 6.253746 GTGCTGCATCTATTGTCTGTTTAAG 58.746 40.000 5.27 0.00 0.00 1.85
2449 3207 5.163723 TGCTGCATCTATTGTCTGTTTAAGC 60.164 40.000 0.00 0.00 0.00 3.09
2450 3208 5.469373 TGCATCTATTGTCTGTTTAAGCG 57.531 39.130 0.00 0.00 0.00 4.68
2451 3209 4.332543 TGCATCTATTGTCTGTTTAAGCGG 59.667 41.667 0.00 0.00 0.00 5.52
2452 3210 4.332819 GCATCTATTGTCTGTTTAAGCGGT 59.667 41.667 0.00 0.00 0.00 5.68
2453 3211 5.522460 GCATCTATTGTCTGTTTAAGCGGTA 59.478 40.000 0.00 0.00 0.00 4.02
2454 3212 6.202954 GCATCTATTGTCTGTTTAAGCGGTAT 59.797 38.462 0.00 0.00 0.00 2.73
2455 3213 7.384115 GCATCTATTGTCTGTTTAAGCGGTATA 59.616 37.037 0.00 0.00 0.00 1.47
2456 3214 9.256477 CATCTATTGTCTGTTTAAGCGGTATAA 57.744 33.333 0.00 0.00 0.00 0.98
2457 3215 9.998106 ATCTATTGTCTGTTTAAGCGGTATAAT 57.002 29.630 0.00 1.65 0.00 1.28
2458 3216 9.256477 TCTATTGTCTGTTTAAGCGGTATAATG 57.744 33.333 0.00 0.00 0.00 1.90
2459 3217 9.256477 CTATTGTCTGTTTAAGCGGTATAATGA 57.744 33.333 0.00 0.00 0.00 2.57
2460 3218 8.677148 ATTGTCTGTTTAAGCGGTATAATGAT 57.323 30.769 0.00 0.00 0.00 2.45
2461 3219 8.500753 TTGTCTGTTTAAGCGGTATAATGATT 57.499 30.769 0.00 0.00 0.00 2.57
2462 3220 8.500753 TGTCTGTTTAAGCGGTATAATGATTT 57.499 30.769 0.00 0.00 0.00 2.17
2463 3221 8.609176 TGTCTGTTTAAGCGGTATAATGATTTC 58.391 33.333 0.00 0.00 0.00 2.17
2464 3222 8.609176 GTCTGTTTAAGCGGTATAATGATTTCA 58.391 33.333 0.00 0.00 0.00 2.69
2465 3223 9.168451 TCTGTTTAAGCGGTATAATGATTTCAA 57.832 29.630 0.00 0.00 0.00 2.69
2466 3224 9.221775 CTGTTTAAGCGGTATAATGATTTCAAC 57.778 33.333 0.00 0.00 0.00 3.18
2467 3225 8.952278 TGTTTAAGCGGTATAATGATTTCAACT 58.048 29.630 0.00 0.00 0.00 3.16
2471 3229 8.500753 AAGCGGTATAATGATTTCAACTGTTA 57.499 30.769 0.00 0.00 0.00 2.41
2496 3254 4.266029 GCATTTCAGATATTGTTTGGTGCG 59.734 41.667 0.00 0.00 0.00 5.34
2543 3305 6.992063 AATGCTAGTTCAGAATGGTTACTG 57.008 37.500 0.00 0.00 36.16 2.74
2559 3321 4.941873 GGTTACTGTTGCTGGTTATTAGCT 59.058 41.667 0.00 0.00 41.66 3.32
2560 3322 6.110707 GGTTACTGTTGCTGGTTATTAGCTA 58.889 40.000 0.00 0.00 41.66 3.32
2604 3366 3.631453 TCCTGTCTGGATGCAACAC 57.369 52.632 0.00 0.00 40.56 3.32
2618 3380 6.765036 TGGATGCAACACATAATTGTTTGTTT 59.235 30.769 4.20 0.00 39.84 2.83
2701 3463 3.069586 CCCCGACACTGATAGATTTAGCA 59.930 47.826 0.00 0.00 0.00 3.49
2830 3592 6.860023 GTCACACCAAAGAAGAAATTGATGAG 59.140 38.462 0.00 0.00 0.00 2.90
2875 3637 5.168526 TGAAATCGGAAAAGAATATGCCG 57.831 39.130 0.00 0.00 43.11 5.69
3103 3865 2.167219 CAGTGATGCTACCCGTGCG 61.167 63.158 0.00 0.00 0.00 5.34
3184 3946 5.644644 GCATATGATATGCTTGGTTTAGCC 58.355 41.667 25.76 0.00 41.52 3.93
3397 4159 1.135721 GATGCATTTGGTCAAGAGGCC 59.864 52.381 0.00 0.00 0.00 5.19
3439 4201 2.143122 GTGAGTGAAAGCGATGGTGAA 58.857 47.619 0.00 0.00 0.00 3.18
3543 4305 5.170748 AGAAACAGGTTTGCAGACAAAAAG 58.829 37.500 9.87 0.00 46.94 2.27
3548 4310 2.604462 GGTTTGCAGACAAAAAGTGCTG 59.396 45.455 9.87 0.00 46.94 4.41
3562 4330 8.088365 ACAAAAAGTGCTGTCCCTTTATTTATC 58.912 33.333 0.00 0.00 30.95 1.75
3568 4336 9.700831 AGTGCTGTCCCTTTATTTATCTATTTT 57.299 29.630 0.00 0.00 0.00 1.82
3621 4390 8.742777 AGTGTAATGCATGTAAGAACATTTGAT 58.257 29.630 0.00 0.00 44.07 2.57
3713 4504 1.235724 GAGTGGTGTAGTGGGCAAAC 58.764 55.000 0.00 0.00 0.00 2.93
3719 4510 1.602377 GTGTAGTGGGCAAACAGTGAC 59.398 52.381 0.00 0.00 0.00 3.67
3721 4512 1.873591 GTAGTGGGCAAACAGTGACAG 59.126 52.381 0.00 0.00 36.72 3.51
3722 4513 0.466189 AGTGGGCAAACAGTGACAGG 60.466 55.000 0.00 0.00 36.72 4.00
3772 4590 4.337264 AGCCACCCCAAGATATTCTTTT 57.663 40.909 0.00 0.00 33.78 2.27
3774 4592 5.837829 AGCCACCCCAAGATATTCTTTTAA 58.162 37.500 0.00 0.00 33.78 1.52
3775 4593 5.893824 AGCCACCCCAAGATATTCTTTTAAG 59.106 40.000 0.00 0.00 33.78 1.85
3819 4638 3.683822 GCCTCAGTGCTCAATCTATATGC 59.316 47.826 0.00 0.00 0.00 3.14
3820 4639 4.252073 CCTCAGTGCTCAATCTATATGCC 58.748 47.826 0.00 0.00 0.00 4.40
3883 4703 6.017026 CCTTTTCCTGACTTTAGAAAGGTGAC 60.017 42.308 6.94 0.00 40.31 3.67
3898 4718 4.481368 AGGTGACGTTTCATTATGGCTA 57.519 40.909 0.00 0.00 33.11 3.93
3911 4731 7.843490 TCATTATGGCTAGTACAAACAACTC 57.157 36.000 0.00 0.00 0.00 3.01
3922 4742 3.211045 ACAAACAACTCGCAACTATGGT 58.789 40.909 0.00 0.00 0.00 3.55
3937 4757 3.785887 ACTATGGTGCCTTCCTAATCCAA 59.214 43.478 0.00 0.00 0.00 3.53
3969 4789 4.518970 TGTCTTTCAGGTTTTGGTGCTATC 59.481 41.667 0.00 0.00 0.00 2.08
3970 4790 4.762251 GTCTTTCAGGTTTTGGTGCTATCT 59.238 41.667 0.00 0.00 0.00 1.98
3979 4799 8.345565 CAGGTTTTGGTGCTATCTATTGTTATC 58.654 37.037 0.00 0.00 0.00 1.75
3981 4801 9.555727 GGTTTTGGTGCTATCTATTGTTATCTA 57.444 33.333 0.00 0.00 0.00 1.98
4220 5040 3.133901 TCTTTGGTCTGTGTGAGTTGCTA 59.866 43.478 0.00 0.00 0.00 3.49
4459 5281 9.627395 TTTACTCTAGATATCTTTGCGCTATTC 57.373 33.333 11.25 0.00 0.00 1.75
4481 5304 2.160417 GCAGTGCAGTGGAATAGTTGAC 59.840 50.000 22.71 0.00 0.00 3.18
4491 5314 2.671396 GGAATAGTTGACGAACGTGCAT 59.329 45.455 4.19 0.00 37.15 3.96
4498 5321 0.163788 GACGAACGTGCATGAACAGG 59.836 55.000 14.17 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.621082 CAGGGGGAAGGGAAGAGAAC 59.379 60.000 0.00 0.00 0.00 3.01
1 2 1.208165 GCAGGGGGAAGGGAAGAGAA 61.208 60.000 0.00 0.00 0.00 2.87
2 3 1.616628 GCAGGGGGAAGGGAAGAGA 60.617 63.158 0.00 0.00 0.00 3.10
3 4 2.684499 GGCAGGGGGAAGGGAAGAG 61.684 68.421 0.00 0.00 0.00 2.85
4 5 2.614013 GGCAGGGGGAAGGGAAGA 60.614 66.667 0.00 0.00 0.00 2.87
5 6 2.216782 GAAGGCAGGGGGAAGGGAAG 62.217 65.000 0.00 0.00 0.00 3.46
6 7 2.121042 AAGGCAGGGGGAAGGGAA 60.121 61.111 0.00 0.00 0.00 3.97
7 8 2.614013 GAAGGCAGGGGGAAGGGA 60.614 66.667 0.00 0.00 0.00 4.20
8 9 2.941025 TGAAGGCAGGGGGAAGGG 60.941 66.667 0.00 0.00 0.00 3.95
9 10 2.234296 ACTGAAGGCAGGGGGAAGG 61.234 63.158 0.00 0.00 46.60 3.46
10 11 1.001641 CACTGAAGGCAGGGGGAAG 60.002 63.158 0.00 0.00 46.60 3.46
11 12 3.170362 CACTGAAGGCAGGGGGAA 58.830 61.111 0.00 0.00 46.60 3.97
12 13 3.650950 GCACTGAAGGCAGGGGGA 61.651 66.667 0.00 0.00 45.91 4.81
13 14 3.655211 AGCACTGAAGGCAGGGGG 61.655 66.667 0.00 0.00 45.91 5.40
14 15 2.360852 CAGCACTGAAGGCAGGGG 60.361 66.667 0.00 0.00 45.91 4.79
57 58 2.203209 CGCCCCAGGAATGCCTAC 60.203 66.667 0.00 0.00 44.80 3.18
63 64 3.017581 AAGGAGCGCCCCAGGAAT 61.018 61.111 11.77 0.00 34.66 3.01
119 121 2.298661 CGGAGCCCAAACCCTACCT 61.299 63.158 0.00 0.00 0.00 3.08
159 161 3.400054 CCAAGGACCGAGACCCCC 61.400 72.222 0.00 0.00 0.00 5.40
300 311 1.883275 CACTAGATGCGAGGACCTAGG 59.117 57.143 7.41 7.41 34.46 3.02
349 360 1.059913 ATACCTGCCATGGAGCTACC 58.940 55.000 18.40 0.00 39.54 3.18
357 368 3.181440 ACATCCCTGTTATACCTGCCATG 60.181 47.826 0.00 0.00 28.70 3.66
359 370 2.487775 ACATCCCTGTTATACCTGCCA 58.512 47.619 0.00 0.00 28.70 4.92
362 373 2.872245 CGCAACATCCCTGTTATACCTG 59.128 50.000 0.00 0.00 43.76 4.00
363 374 2.504175 ACGCAACATCCCTGTTATACCT 59.496 45.455 0.00 0.00 43.76 3.08
364 375 2.914059 ACGCAACATCCCTGTTATACC 58.086 47.619 0.00 0.00 43.76 2.73
365 376 6.613755 AATAACGCAACATCCCTGTTATAC 57.386 37.500 0.00 0.00 43.76 1.47
375 386 9.472361 TCTATCTAAACCTAATAACGCAACATC 57.528 33.333 0.00 0.00 0.00 3.06
380 391 7.263100 TCGTCTATCTAAACCTAATAACGCA 57.737 36.000 0.00 0.00 0.00 5.24
382 393 6.800892 GGCTCGTCTATCTAAACCTAATAACG 59.199 42.308 0.00 0.00 0.00 3.18
383 394 7.089538 GGGCTCGTCTATCTAAACCTAATAAC 58.910 42.308 0.00 0.00 0.00 1.89
392 403 3.308035 TCTGGGGCTCGTCTATCTAAA 57.692 47.619 0.00 0.00 0.00 1.85
418 429 7.832503 AATTAAACCTGCTGATAATGCAAAC 57.167 32.000 0.00 0.00 40.13 2.93
422 433 8.405531 TGAGTAAATTAAACCTGCTGATAATGC 58.594 33.333 0.00 0.00 0.00 3.56
429 440 7.907214 AGTAGTGAGTAAATTAAACCTGCTG 57.093 36.000 0.00 0.00 0.00 4.41
430 441 7.390718 CCAAGTAGTGAGTAAATTAAACCTGCT 59.609 37.037 0.00 0.00 0.00 4.24
433 469 7.601508 CGTCCAAGTAGTGAGTAAATTAAACCT 59.398 37.037 0.00 0.00 0.00 3.50
438 474 6.350445 GGGACGTCCAAGTAGTGAGTAAATTA 60.350 42.308 34.40 0.00 37.91 1.40
463 499 7.061210 CGAGAGAAATGTACAGTAAACTGACAG 59.939 40.741 16.74 0.00 46.59 3.51
530 1225 4.335594 GGTTCAAACATGGGTGATAGCTAC 59.664 45.833 0.00 0.00 0.00 3.58
533 1228 3.088532 TGGTTCAAACATGGGTGATAGC 58.911 45.455 0.00 2.41 0.00 2.97
546 1241 3.432890 GGGGAAGTTGCATTTGGTTCAAA 60.433 43.478 0.00 0.00 37.75 2.69
561 1256 0.977395 CAAAGAGGACTCGGGGAAGT 59.023 55.000 0.00 0.00 34.09 3.01
562 1257 0.391793 GCAAAGAGGACTCGGGGAAG 60.392 60.000 0.00 0.00 34.09 3.46
563 1258 0.836400 AGCAAAGAGGACTCGGGGAA 60.836 55.000 0.00 0.00 34.09 3.97
565 1260 0.461961 CTAGCAAAGAGGACTCGGGG 59.538 60.000 0.00 0.00 34.09 5.73
618 1314 6.206634 GTGAGATTCACCCAAACTTGTTGATA 59.793 38.462 0.00 0.00 41.37 2.15
744 1443 7.066284 GTCACTGCTTAAGTATGGTGATTGAAT 59.934 37.037 15.36 0.00 36.83 2.57
752 1451 5.482908 CTTCTGTCACTGCTTAAGTATGGT 58.517 41.667 4.02 0.00 36.83 3.55
756 1455 3.260884 CCCCTTCTGTCACTGCTTAAGTA 59.739 47.826 4.02 0.00 36.83 2.24
769 1468 7.414266 AGCTTATCTTTTATTTCCCCTTCTGT 58.586 34.615 0.00 0.00 0.00 3.41
770 1469 7.888250 AGCTTATCTTTTATTTCCCCTTCTG 57.112 36.000 0.00 0.00 0.00 3.02
771 1470 9.800572 GATAGCTTATCTTTTATTTCCCCTTCT 57.199 33.333 0.00 0.00 32.44 2.85
773 1472 9.936329 TTGATAGCTTATCTTTTATTTCCCCTT 57.064 29.630 0.00 0.00 36.17 3.95
828 1536 8.081633 TGGTCAGCATATAAAAACACTTTGAAG 58.918 33.333 0.00 0.00 0.00 3.02
830 1538 7.517614 TGGTCAGCATATAAAAACACTTTGA 57.482 32.000 0.00 0.00 0.00 2.69
831 1539 7.276218 CCATGGTCAGCATATAAAAACACTTTG 59.724 37.037 2.57 0.00 0.00 2.77
832 1540 7.178274 TCCATGGTCAGCATATAAAAACACTTT 59.822 33.333 12.58 0.00 0.00 2.66
833 1541 6.663093 TCCATGGTCAGCATATAAAAACACTT 59.337 34.615 12.58 0.00 0.00 3.16
834 1542 6.186957 TCCATGGTCAGCATATAAAAACACT 58.813 36.000 12.58 0.00 0.00 3.55
835 1543 6.449635 TCCATGGTCAGCATATAAAAACAC 57.550 37.500 12.58 0.00 0.00 3.32
836 1544 7.658525 AATCCATGGTCAGCATATAAAAACA 57.341 32.000 12.58 0.00 0.00 2.83
854 1562 9.293404 CATAGTCCAACAGATCATTTAATCCAT 57.707 33.333 0.00 0.00 0.00 3.41
871 1579 6.539173 TCTTAAGGAACAAAGCATAGTCCAA 58.461 36.000 1.85 0.00 0.00 3.53
956 1689 3.034635 GCTTCCTTAGTCAGATCCTCCA 58.965 50.000 0.00 0.00 0.00 3.86
1146 1879 0.670162 CAGTGTTCCAAAGGCCACTG 59.330 55.000 5.01 16.01 41.82 3.66
1281 2014 5.247862 TGTGCTGCATAATATGGGATGTAG 58.752 41.667 5.27 6.36 38.42 2.74
1470 2203 1.680860 CCATGATCAGCAACAGCAGGA 60.681 52.381 0.09 0.00 0.00 3.86
1572 2305 1.618837 TCACAGTGGTAGCCAAGTCTC 59.381 52.381 0.00 0.00 34.18 3.36
1869 2602 7.786178 ACGAGCAATATTACATAAAGCTTCA 57.214 32.000 0.00 0.00 31.74 3.02
1881 2614 7.436376 CAGTCATCTGAAGAACGAGCAATATTA 59.564 37.037 0.00 0.00 43.76 0.98
1884 2617 5.105063 CAGTCATCTGAAGAACGAGCAATA 58.895 41.667 0.00 0.00 43.76 1.90
1984 2717 4.138290 TCCCTTCGAGCATTGTGTAAAAA 58.862 39.130 0.00 0.00 0.00 1.94
1999 2732 4.576053 TGATCATGTTTAAGCATCCCTTCG 59.424 41.667 1.27 0.00 34.95 3.79
2038 2771 2.257353 GGCACCATGTGACAAGACC 58.743 57.895 0.00 0.00 41.94 3.85
2067 2800 5.619132 AATCCAGGCAATTTCAATTAGGG 57.381 39.130 0.00 0.00 0.00 3.53
2080 2813 6.985645 GCAATTCAACAAATATAATCCAGGCA 59.014 34.615 0.00 0.00 0.00 4.75
2123 2856 4.152402 CCAAGGAACAACAGATACTTGTCG 59.848 45.833 0.00 0.00 34.94 4.35
2130 2863 8.956426 GTTATCATTTCCAAGGAACAACAGATA 58.044 33.333 0.00 3.23 33.41 1.98
2219 2952 7.438564 TGTCAGCTCAAAATACTAGTACAACA 58.561 34.615 4.31 0.00 0.00 3.33
2341 3074 3.181429 ACCCAGCTCTTCATTTCCAAAGA 60.181 43.478 0.00 0.00 0.00 2.52
2361 3094 7.391148 TCAGAAATTGGTAGCTCAAAATACC 57.609 36.000 0.00 0.00 41.60 2.73
2401 3135 8.683615 GCACCCTAAGCTTAACAATAGTATTTT 58.316 33.333 7.74 0.00 0.00 1.82
2424 3158 4.691860 AAACAGACAATAGATGCAGCAC 57.308 40.909 4.07 0.00 0.00 4.40
2442 3200 9.221775 CAGTTGAAATCATTATACCGCTTAAAC 57.778 33.333 0.00 0.00 0.00 2.01
2443 3201 8.952278 ACAGTTGAAATCATTATACCGCTTAAA 58.048 29.630 0.00 0.00 0.00 1.52
2444 3202 8.500753 ACAGTTGAAATCATTATACCGCTTAA 57.499 30.769 0.00 0.00 0.00 1.85
2445 3203 8.500753 AACAGTTGAAATCATTATACCGCTTA 57.499 30.769 0.00 0.00 0.00 3.09
2446 3204 7.391148 AACAGTTGAAATCATTATACCGCTT 57.609 32.000 0.00 0.00 0.00 4.68
2447 3205 8.500753 TTAACAGTTGAAATCATTATACCGCT 57.499 30.769 0.00 0.00 0.00 5.52
2448 3206 7.376072 GCTTAACAGTTGAAATCATTATACCGC 59.624 37.037 0.00 0.00 0.00 5.68
2449 3207 8.394877 TGCTTAACAGTTGAAATCATTATACCG 58.605 33.333 0.00 0.00 0.00 4.02
2455 3213 9.199982 CTGAAATGCTTAACAGTTGAAATCATT 57.800 29.630 0.00 0.00 36.53 2.57
2456 3214 8.579006 TCTGAAATGCTTAACAGTTGAAATCAT 58.421 29.630 0.00 0.00 36.53 2.45
2457 3215 7.939782 TCTGAAATGCTTAACAGTTGAAATCA 58.060 30.769 0.00 0.00 36.53 2.57
2458 3216 8.976986 ATCTGAAATGCTTAACAGTTGAAATC 57.023 30.769 0.00 0.00 36.53 2.17
2461 3219 9.844790 CAATATCTGAAATGCTTAACAGTTGAA 57.155 29.630 0.00 0.00 36.53 2.69
2462 3220 9.013229 ACAATATCTGAAATGCTTAACAGTTGA 57.987 29.630 0.00 0.00 36.53 3.18
2463 3221 9.630098 AACAATATCTGAAATGCTTAACAGTTG 57.370 29.630 0.00 0.00 36.53 3.16
2465 3223 9.630098 CAAACAATATCTGAAATGCTTAACAGT 57.370 29.630 0.00 0.00 0.00 3.55
2466 3224 9.079833 CCAAACAATATCTGAAATGCTTAACAG 57.920 33.333 0.00 0.00 0.00 3.16
2467 3225 8.584157 ACCAAACAATATCTGAAATGCTTAACA 58.416 29.630 0.00 0.00 0.00 2.41
2471 3229 5.870978 GCACCAAACAATATCTGAAATGCTT 59.129 36.000 0.00 0.00 0.00 3.91
2496 3254 4.676546 ACAAAAAGAAAGCAGACAAGCTC 58.323 39.130 0.00 0.00 45.89 4.09
2566 3328 3.565902 GGACTACAGCAATGATAAAGGCC 59.434 47.826 0.00 0.00 0.00 5.19
2567 3329 4.274459 CAGGACTACAGCAATGATAAAGGC 59.726 45.833 0.00 0.00 0.00 4.35
2568 3330 5.431765 ACAGGACTACAGCAATGATAAAGG 58.568 41.667 0.00 0.00 0.00 3.11
2603 3365 8.956533 AACCAAAGCTAAACAAACAATTATGT 57.043 26.923 0.00 0.00 43.14 2.29
2716 3478 2.158385 ACCCAGCCTTTTGTAATCACCA 60.158 45.455 0.00 0.00 0.00 4.17
2875 3637 8.563732 GCTTGTTTTATATGAAGATCCTCCTTC 58.436 37.037 0.00 0.00 42.09 3.46
2971 3733 2.817844 TGCGAGTGCTTCAGAGTACTTA 59.182 45.455 0.00 0.00 46.96 2.24
3103 3865 2.094762 ACGGACTATGAAGGCACAAC 57.905 50.000 0.00 0.00 29.10 3.32
3184 3946 1.380524 CATCCAGCAGGCTCTCTTTG 58.619 55.000 0.00 0.00 33.74 2.77
3397 4159 1.403679 GTCTCCCACTCAGAGTCATCG 59.596 57.143 0.00 0.00 32.93 3.84
3439 4201 4.715792 TCTGCTTCTCTCCTTTCATCATCT 59.284 41.667 0.00 0.00 0.00 2.90
3568 4336 8.434392 ACACTTATTAGAAGGAAACCACAGTTA 58.566 33.333 0.00 0.00 34.19 2.24
3672 4463 6.906901 ACTCCTGTTTGTAGGATAATTAGGGA 59.093 38.462 0.00 0.00 45.44 4.20
3713 4504 8.154649 ACTTTTAGTTACAATTCCTGTCACTG 57.845 34.615 2.71 0.00 41.57 3.66
3736 4553 2.167075 GGTGGCTACGGTACATACAACT 59.833 50.000 0.00 0.00 0.00 3.16
3779 4597 7.874528 CACTGAGGCAGGAAATTTTCTAATTTT 59.125 33.333 8.93 0.00 38.13 1.82
3790 4608 0.694771 TGAGCACTGAGGCAGGAAAT 59.305 50.000 0.00 0.00 35.51 2.17
3819 4638 6.597262 TTGCTAATGATTATGTGTGTACGG 57.403 37.500 0.00 0.00 0.00 4.02
3820 4639 8.006027 CAGATTGCTAATGATTATGTGTGTACG 58.994 37.037 0.00 0.00 0.00 3.67
3883 4703 7.067532 TGTTTGTACTAGCCATAATGAAACG 57.932 36.000 0.00 0.00 0.00 3.60
3898 4718 4.451096 CCATAGTTGCGAGTTGTTTGTACT 59.549 41.667 0.00 0.00 0.00 2.73
3911 4731 0.392998 AGGAAGGCACCATAGTTGCG 60.393 55.000 3.78 0.00 0.00 4.85
3922 4742 2.511218 AGATGCTTGGATTAGGAAGGCA 59.489 45.455 0.00 0.00 0.00 4.75
3937 4757 3.498774 ACCTGAAAGACAACAGATGCT 57.501 42.857 0.00 0.00 36.38 3.79
3979 4799 6.047870 AGCACAATGAGAGCAATCTTACTAG 58.952 40.000 0.00 0.00 36.17 2.57
3981 4801 4.841422 AGCACAATGAGAGCAATCTTACT 58.159 39.130 0.00 0.00 36.17 2.24
3987 4807 2.161012 CGACAAGCACAATGAGAGCAAT 59.839 45.455 0.00 0.00 36.17 3.56
4194 5014 3.270877 ACTCACACAGACCAAAGAACAC 58.729 45.455 0.00 0.00 0.00 3.32
4220 5040 7.619050 AGACAACATTCTCAATAGTCTGTCAT 58.381 34.615 0.00 0.00 33.96 3.06
4428 5248 7.385205 GCGCAAAGATATCTAGAGTAAATTGGA 59.615 37.037 5.46 0.00 0.00 3.53
4430 5250 8.304202 AGCGCAAAGATATCTAGAGTAAATTG 57.696 34.615 11.47 5.49 0.00 2.32
4435 5255 7.465173 CGAATAGCGCAAAGATATCTAGAGTA 58.535 38.462 11.47 1.06 29.98 2.59
4436 5256 6.318628 CGAATAGCGCAAAGATATCTAGAGT 58.681 40.000 11.47 0.00 29.98 3.24
4437 5257 6.788766 CGAATAGCGCAAAGATATCTAGAG 57.211 41.667 11.47 5.17 29.98 2.43
4459 5281 1.129251 CAACTATTCCACTGCACTGCG 59.871 52.381 0.00 0.00 0.00 5.18
4481 5304 0.110688 CACCTGTTCATGCACGTTCG 60.111 55.000 0.00 0.00 0.00 3.95
4491 5314 1.357137 TGCCCTGTATCACCTGTTCA 58.643 50.000 0.00 0.00 0.00 3.18
4498 5321 3.509575 TCATGGTTTTTGCCCTGTATCAC 59.490 43.478 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.