Multiple sequence alignment - TraesCS2B01G432100

Loading Multiple Alignment...

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 TraesCS2B01G432100 chr2B 100.000 3076 0 0 1 3076 621220619 621217544 0.000000e+00 5681
1 TraesCS2B01G432100 chr2B 91.726 701 39 10 2390 3076 98589494 98588799 0.000000e+00 955
2 TraesCS2B01G432100 chr2B 90.732 205 7 7 2390 2582 621213317 621213113 2.350000e-66 263
3 TraesCS2B01G432100 chr2B 87.500 208 10 9 2390 2585 98582334 98582131 3.090000e-55 226
4 TraesCS2B01G432100 chr2B 86.555 119 16 0 1217 1335 621261878 621261760 6.920000e-27 132
5 TraesCS2B01G432100 chr2D 94.894 1645 71 8 751 2389 526123950 526125587 0.000000e+00 2560
6 TraesCS2B01G432100 chr2D 89.758 703 45 12 2389 3070 318587334 318588030 0.000000e+00 874
7 TraesCS2B01G432100 chr2D 72.148 894 178 56 1217 2067 526116566 526117431 4.020000e-49 206
8 TraesCS2B01G432100 chr2A 92.603 1798 87 20 619 2389 670666789 670665011 0.000000e+00 2542
9 TraesCS2B01G432100 chr2A 90.754 703 47 11 2390 3076 750364212 750363512 0.000000e+00 922
10 TraesCS2B01G432100 chr2A 85.714 126 18 0 1210 1335 670671508 670671383 1.920000e-27 134
11 TraesCS2B01G432100 chr7D 93.866 701 29 6 2389 3076 629606109 629605410 0.000000e+00 1044
12 TraesCS2B01G432100 chr7D 87.975 632 37 15 3 620 603600907 603601513 0.000000e+00 710
13 TraesCS2B01G432100 chr7D 91.262 206 5 8 2390 2582 629601180 629600975 5.060000e-68 268
14 TraesCS2B01G432100 chr3D 93.153 701 32 5 2390 3076 486061643 486062341 0.000000e+00 1014
15 TraesCS2B01G432100 chr3D 93.376 468 18 4 3 468 38412966 38413422 0.000000e+00 680
16 TraesCS2B01G432100 chr3D 92.647 136 10 0 485 620 42476368 42476233 2.420000e-46 196
17 TraesCS2B01G432100 chr3B 90.741 702 43 13 2390 3076 670209496 670208802 0.000000e+00 917
18 TraesCS2B01G432100 chr3B 87.296 614 49 10 1 611 766682806 766683393 0.000000e+00 675
19 TraesCS2B01G432100 chr3B 92.086 139 11 0 484 622 791768573 791768711 2.420000e-46 196
20 TraesCS2B01G432100 chr1B 90.057 704 49 14 2389 3076 595034320 595035018 0.000000e+00 893
21 TraesCS2B01G432100 chr1B 91.667 612 37 2 1 611 52614397 52613799 0.000000e+00 835
22 TraesCS2B01G432100 chr7A 89.700 699 52 14 2390 3076 15500419 15499729 0.000000e+00 874
23 TraesCS2B01G432100 chr4A 89.574 681 57 11 2400 3070 25488321 25488997 0.000000e+00 852
24 TraesCS2B01G432100 chr4A 91.176 136 11 1 485 619 140722998 140723133 1.880000e-42 183
25 TraesCS2B01G432100 chr4A 90.511 137 12 1 487 622 374638302 374638166 2.440000e-41 180
26 TraesCS2B01G432100 chr4A 89.781 137 14 0 485 621 485394899 485394763 3.150000e-40 176
27 TraesCS2B01G432100 chr7B 91.013 612 41 3 1 611 71378351 71377753 0.000000e+00 813
28 TraesCS2B01G432100 chr5B 91.028 613 40 4 1 611 524770515 524771114 0.000000e+00 813
29 TraesCS2B01G432100 chr4D 87.801 623 35 16 3 611 417846663 417847258 0.000000e+00 691
30 TraesCS2B01G432100 chr1D 86.901 626 39 16 3 610 26190519 26189919 0.000000e+00 662
31 TraesCS2B01G432100 chr1D 90.580 276 14 3 3 277 386402338 386402602 3.770000e-94 355
32 TraesCS2B01G432100 chr1D 90.336 238 11 3 38 274 7101016 7101242 4.980000e-78 302
33 TraesCS2B01G432100 chr5A 93.981 432 22 4 1 431 283112669 283112241 0.000000e+00 651
34 TraesCS2B01G432100 chr6B 91.852 135 10 1 485 618 560685439 560685305 1.460000e-43 187
35 TraesCS2B01G432100 chrUn 89.209 139 15 0 485 623 244859675 244859537 1.130000e-39 174
36 TraesCS2B01G432100 chrUn 89.209 139 15 0 485 623 338924524 338924662 1.130000e-39 174
37 TraesCS2B01G432100 chr6A 89.600 125 12 1 92 215 159943408 159943284 1.140000e-34 158


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 TraesCS2B01G432100 chr2B 621217544 621220619 3075 True 5681 5681 100.000 1 3076 1 chr2B.!!$R4 3075
1 TraesCS2B01G432100 chr2B 98588799 98589494 695 True 955 955 91.726 2390 3076 1 chr2B.!!$R2 686
2 TraesCS2B01G432100 chr2D 526123950 526125587 1637 False 2560 2560 94.894 751 2389 1 chr2D.!!$F3 1638
3 TraesCS2B01G432100 chr2D 318587334 318588030 696 False 874 874 89.758 2389 3070 1 chr2D.!!$F1 681
4 TraesCS2B01G432100 chr2D 526116566 526117431 865 False 206 206 72.148 1217 2067 1 chr2D.!!$F2 850
5 TraesCS2B01G432100 chr2A 670665011 670666789 1778 True 2542 2542 92.603 619 2389 1 chr2A.!!$R1 1770
6 TraesCS2B01G432100 chr2A 750363512 750364212 700 True 922 922 90.754 2390 3076 1 chr2A.!!$R3 686
7 TraesCS2B01G432100 chr7D 629605410 629606109 699 True 1044 1044 93.866 2389 3076 1 chr7D.!!$R2 687
8 TraesCS2B01G432100 chr7D 603600907 603601513 606 False 710 710 87.975 3 620 1 chr7D.!!$F1 617
9 TraesCS2B01G432100 chr3D 486061643 486062341 698 False 1014 1014 93.153 2390 3076 1 chr3D.!!$F2 686
10 TraesCS2B01G432100 chr3B 670208802 670209496 694 True 917 917 90.741 2390 3076 1 chr3B.!!$R1 686
11 TraesCS2B01G432100 chr3B 766682806 766683393 587 False 675 675 87.296 1 611 1 chr3B.!!$F1 610
12 TraesCS2B01G432100 chr1B 595034320 595035018 698 False 893 893 90.057 2389 3076 1 chr1B.!!$F1 687
13 TraesCS2B01G432100 chr1B 52613799 52614397 598 True 835 835 91.667 1 611 1 chr1B.!!$R1 610
14 TraesCS2B01G432100 chr7A 15499729 15500419 690 True 874 874 89.700 2390 3076 1 chr7A.!!$R1 686
15 TraesCS2B01G432100 chr4A 25488321 25488997 676 False 852 852 89.574 2400 3070 1 chr4A.!!$F1 670
16 TraesCS2B01G432100 chr7B 71377753 71378351 598 True 813 813 91.013 1 611 1 chr7B.!!$R1 610
17 TraesCS2B01G432100 chr5B 524770515 524771114 599 False 813 813 91.028 1 611 1 chr5B.!!$F1 610
18 TraesCS2B01G432100 chr4D 417846663 417847258 595 False 691 691 87.801 3 611 1 chr4D.!!$F1 608
19 TraesCS2B01G432100 chr1D 26189919 26190519 600 True 662 662 86.901 3 610 1 chr1D.!!$R1 607

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
474 485 0.042967 GCGATTCAAGTCGGCGATTC 60.043 55.0 14.79 0.0 41.72 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2149 0.605589 CGCTCCTCAAAGAGTCCTGT 59.394 55.0 0.0 0.0 36.2 4.0 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
58 60 2.125912 CTCCGACGCCTCTGTTGG 60.126 66.667 0.00 0.00 43.69 3.77
112 114 2.461637 CCCCCTCCTCCTTCCCTT 59.538 66.667 0.00 0.00 0.00 3.95
119 121 3.121030 CTCCTTCCCTTGTGCGCG 61.121 66.667 0.00 0.00 0.00 6.86
196 199 3.793144 CAAAGAGCTCGCACCGCC 61.793 66.667 8.37 0.00 0.00 6.13
250 255 1.526575 AAACCAATCCACGCAGCAGG 61.527 55.000 0.00 0.00 0.00 4.85
462 473 3.920446 TGTAGCACAAAGTAGCGATTCA 58.080 40.909 0.00 0.00 35.48 2.57
463 474 4.311606 TGTAGCACAAAGTAGCGATTCAA 58.688 39.130 0.00 0.00 35.48 2.69
464 475 4.388773 TGTAGCACAAAGTAGCGATTCAAG 59.611 41.667 0.00 0.00 35.48 3.02
465 476 3.403038 AGCACAAAGTAGCGATTCAAGT 58.597 40.909 0.00 0.00 35.48 3.16
466 477 3.433615 AGCACAAAGTAGCGATTCAAGTC 59.566 43.478 0.00 0.00 35.48 3.01
467 478 3.722082 GCACAAAGTAGCGATTCAAGTCG 60.722 47.826 0.00 0.00 44.14 4.18
468 479 2.993899 ACAAAGTAGCGATTCAAGTCGG 59.006 45.455 0.00 0.00 41.72 4.79
469 480 1.641577 AAGTAGCGATTCAAGTCGGC 58.358 50.000 0.00 0.00 41.72 5.54
470 481 0.525668 AGTAGCGATTCAAGTCGGCG 60.526 55.000 0.00 0.00 41.72 6.46
471 482 0.524816 GTAGCGATTCAAGTCGGCGA 60.525 55.000 4.99 4.99 41.72 5.54
472 483 0.384309 TAGCGATTCAAGTCGGCGAT 59.616 50.000 14.79 0.00 41.72 4.58
473 484 0.460284 AGCGATTCAAGTCGGCGATT 60.460 50.000 14.79 5.78 41.72 3.34
474 485 0.042967 GCGATTCAAGTCGGCGATTC 60.043 55.000 14.79 0.00 41.72 2.52
587 610 4.210537 CGTATTATGACGGTAAAGCCAAGG 59.789 45.833 0.00 0.00 39.19 3.61
615 638 7.227910 GTCAATCCGTGCTTTATTATTAGGGAA 59.772 37.037 0.00 0.00 0.00 3.97
620 643 7.996644 TCCGTGCTTTATTATTAGGGAAAGATT 59.003 33.333 0.00 0.00 31.83 2.40
621 644 9.280174 CCGTGCTTTATTATTAGGGAAAGATTA 57.720 33.333 0.00 0.00 31.83 1.75
630 653 8.777865 TTATTAGGGAAAGATTATCTGATGCG 57.222 34.615 0.00 0.00 0.00 4.73
638 661 7.377928 GGAAAGATTATCTGATGCGTTCAAATG 59.622 37.037 0.00 0.00 32.78 2.32
640 663 6.722301 AGATTATCTGATGCGTTCAAATGTG 58.278 36.000 0.00 0.00 32.78 3.21
651 674 4.841841 GCGTTCAAATGTGCATCAAATTTG 59.158 37.500 12.15 12.15 45.36 2.32
654 677 6.906143 CGTTCAAATGTGCATCAAATTTGTTT 59.094 30.769 17.47 6.48 44.71 2.83
693 718 7.809546 TTTGAAATATAACGGGACATATGCA 57.190 32.000 1.58 0.00 0.00 3.96
707 732 3.630769 ACATATGCAGACAGCTTTGGATG 59.369 43.478 1.58 0.00 45.94 3.51
708 733 2.502142 ATGCAGACAGCTTTGGATGA 57.498 45.000 0.00 0.00 45.94 2.92
709 734 1.527034 TGCAGACAGCTTTGGATGAC 58.473 50.000 0.00 0.00 45.94 3.06
712 737 0.976641 AGACAGCTTTGGATGACCGA 59.023 50.000 0.00 0.00 39.42 4.69
713 738 1.079503 GACAGCTTTGGATGACCGAC 58.920 55.000 0.00 0.00 39.42 4.79
732 757 1.651987 CGCATCCGTATTTGTGGACT 58.348 50.000 0.00 0.00 37.02 3.85
733 758 1.327460 CGCATCCGTATTTGTGGACTG 59.673 52.381 0.00 0.00 37.02 3.51
734 759 1.670811 GCATCCGTATTTGTGGACTGG 59.329 52.381 0.00 0.00 37.02 4.00
735 760 2.939640 GCATCCGTATTTGTGGACTGGT 60.940 50.000 0.00 0.00 37.02 4.00
736 761 2.754946 TCCGTATTTGTGGACTGGTC 57.245 50.000 0.00 0.00 0.00 4.02
745 770 3.479979 GGACTGGTCCTTTCCCGT 58.520 61.111 12.09 0.00 46.16 5.28
746 771 1.295746 GGACTGGTCCTTTCCCGTC 59.704 63.158 12.09 0.00 46.16 4.79
747 772 1.192803 GGACTGGTCCTTTCCCGTCT 61.193 60.000 12.09 0.00 46.16 4.18
748 773 0.685660 GACTGGTCCTTTCCCGTCTT 59.314 55.000 0.00 0.00 38.23 3.01
749 774 0.685660 ACTGGTCCTTTCCCGTCTTC 59.314 55.000 0.00 0.00 0.00 2.87
785 810 0.643820 CGATTTAGTGGACGGCGTTC 59.356 55.000 16.19 14.22 0.00 3.95
789 814 1.236616 TTAGTGGACGGCGTTCGAGA 61.237 55.000 16.19 0.00 42.43 4.04
806 831 2.342651 CGAGATGCACTTAGACACAACG 59.657 50.000 0.00 0.00 0.00 4.10
818 843 8.810427 CACTTAGACACAACGAAAAACTAACTA 58.190 33.333 0.00 0.00 0.00 2.24
831 856 3.880047 ACTAACTATAGTTGCGCCACA 57.120 42.857 25.27 5.26 39.36 4.17
843 868 1.206849 TGCGCCACATTCTCATGTCTA 59.793 47.619 4.18 0.00 42.14 2.59
849 874 5.233988 GCCACATTCTCATGTCTATAGTCC 58.766 45.833 0.00 0.00 42.14 3.85
1011 1036 1.891150 AGAGAAACAATGGCTTGCAGG 59.109 47.619 0.00 0.00 35.69 4.85
1028 1053 2.616510 GCAGGCGAGGCATATTCCTATT 60.617 50.000 0.00 0.00 36.38 1.73
1154 1179 6.464322 AGCGAAGGTACATTCATGGATATGAA 60.464 38.462 19.31 5.31 46.76 2.57
1171 1197 6.073765 GGATATGAATTTGACGCACGATAACT 60.074 38.462 0.00 0.00 0.00 2.24
1416 1447 7.013274 GTGCTAATTAATCAAATGGCCTACAGA 59.987 37.037 3.32 0.00 0.00 3.41
1457 1488 2.422165 TGCTCCGGCAAACACGTA 59.578 55.556 0.00 0.00 46.36 3.57
1469 1500 2.138596 AACACGTAACCGTCGTCATT 57.861 45.000 0.00 0.00 46.28 2.57
1571 1602 1.682451 CCGGGATGGCGGAGAAACTA 61.682 60.000 0.00 0.00 0.00 2.24
1622 1653 2.813754 CGAGAGGTGAAAAAGGCATTCA 59.186 45.455 0.00 0.00 34.56 2.57
1668 1699 2.063266 TCCGATTAACGTTCTGCACAC 58.937 47.619 2.82 0.00 40.78 3.82
1690 1725 0.179073 ACGGATGTGCTGTGATAGGC 60.179 55.000 0.00 0.00 33.94 3.93
1736 1774 2.673775 TTTCTTTCATCAGGGTGCCA 57.326 45.000 0.00 0.00 0.00 4.92
2096 2149 4.020617 CCTGCTTGGTGGCGGAGA 62.021 66.667 0.00 0.00 40.74 3.71
2122 2175 0.318441 TCTTTGAGGAGCGTGGACAG 59.682 55.000 0.00 0.00 0.00 3.51
2192 2258 2.073816 GGTGAACAATTCGTGATCCGT 58.926 47.619 3.97 0.00 37.94 4.69
2198 2264 2.538449 ACAATTCGTGATCCGTAATCGC 59.462 45.455 3.97 0.00 40.79 4.58
2253 2320 8.028938 AGGTACAAAATTTGAAATTGGAGATCG 58.971 33.333 13.19 0.00 0.00 3.69
2296 2363 9.814507 CACTTAACGTAAAAACTGCATGTATAA 57.185 29.630 0.00 0.00 0.00 0.98
2396 2466 4.349342 AGGAAATGGCCCTAGATGTTAGAG 59.651 45.833 0.00 0.00 30.92 2.43
2491 2592 3.593442 ACTCTCCCTGAGATCGATCTT 57.407 47.619 27.90 12.68 45.39 2.40
2512 2617 4.237976 TCCCGATCTCTTCTTGTACTCT 57.762 45.455 0.00 0.00 0.00 3.24
2684 2795 0.824109 CCTATCTTCCACCACGAGCA 59.176 55.000 0.00 0.00 0.00 4.26
2759 2873 3.461773 CTCTCGGACCGCCACCAT 61.462 66.667 9.66 0.00 0.00 3.55
2809 2923 1.038681 TATGGAAGGCCGTCGTGCTA 61.039 55.000 12.79 0.00 36.79 3.49
2812 2926 3.291101 GAAGGCCGTCGTGCTACCA 62.291 63.158 1.94 0.00 0.00 3.25
2959 3073 0.740149 CACAGCAGCAACAACTCCAA 59.260 50.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 3.991536 GAGGCGTCGGAGTTGGAGC 62.992 68.421 0.00 0.00 0.00 4.70
58 60 1.000771 GGAAGTGGAGGAAAGGGGC 60.001 63.158 0.00 0.00 0.00 5.80
222 226 2.275380 GGATTGGTTTGGGCGCACT 61.275 57.895 12.74 0.00 0.00 4.40
359 370 3.185188 CAGGCTTCATTGGATTACGATCG 59.815 47.826 14.88 14.88 32.84 3.69
462 473 0.038526 ACGACTTGAATCGCCGACTT 60.039 50.000 0.00 0.00 46.22 3.01
463 474 0.038526 AACGACTTGAATCGCCGACT 60.039 50.000 0.00 0.00 46.22 4.18
464 475 0.788391 AAACGACTTGAATCGCCGAC 59.212 50.000 0.00 0.00 46.22 4.79
465 476 1.458064 GAAAACGACTTGAATCGCCGA 59.542 47.619 0.00 0.00 46.22 5.54
466 477 1.459592 AGAAAACGACTTGAATCGCCG 59.540 47.619 0.00 0.00 46.22 6.46
467 478 4.859629 ATAGAAAACGACTTGAATCGCC 57.140 40.909 0.00 0.00 46.22 5.54
468 479 5.553952 CGGTATAGAAAACGACTTGAATCGC 60.554 44.000 0.00 0.00 46.22 4.58
470 481 7.306632 CCATCGGTATAGAAAACGACTTGAATC 60.307 40.741 0.00 0.00 38.24 2.52
471 482 6.479001 CCATCGGTATAGAAAACGACTTGAAT 59.521 38.462 0.00 0.00 38.24 2.57
472 483 5.808540 CCATCGGTATAGAAAACGACTTGAA 59.191 40.000 0.00 0.00 38.24 2.69
473 484 5.345702 CCATCGGTATAGAAAACGACTTGA 58.654 41.667 0.00 0.00 38.24 3.02
474 485 4.025979 GCCATCGGTATAGAAAACGACTTG 60.026 45.833 0.00 0.00 38.24 3.16
570 592 1.628846 ACTCCTTGGCTTTACCGTCAT 59.371 47.619 0.00 0.00 43.94 3.06
578 600 1.073923 ACGGATTGACTCCTTGGCTTT 59.926 47.619 0.00 0.00 42.47 3.51
581 603 1.648467 GCACGGATTGACTCCTTGGC 61.648 60.000 0.00 0.00 42.28 4.52
587 610 7.095187 CCCTAATAATAAAGCACGGATTGACTC 60.095 40.741 0.00 0.00 0.00 3.36
615 638 7.191551 CACATTTGAACGCATCAGATAATCTT 58.808 34.615 0.00 0.00 39.77 2.40
620 643 3.688673 TGCACATTTGAACGCATCAGATA 59.311 39.130 0.00 0.00 39.77 1.98
621 644 2.488937 TGCACATTTGAACGCATCAGAT 59.511 40.909 0.00 0.00 39.77 2.90
630 653 9.881529 ATAAACAAATTTGATGCACATTTGAAC 57.118 25.926 24.64 0.00 41.31 3.18
670 693 7.172532 GTCTGCATATGTCCCGTTATATTTCAA 59.827 37.037 4.29 0.00 0.00 2.69
672 695 6.649141 TGTCTGCATATGTCCCGTTATATTTC 59.351 38.462 4.29 0.00 0.00 2.17
677 702 3.803715 GCTGTCTGCATATGTCCCGTTAT 60.804 47.826 4.29 0.00 42.31 1.89
687 712 3.881688 GTCATCCAAAGCTGTCTGCATAT 59.118 43.478 4.39 0.00 45.94 1.78
688 713 3.273434 GTCATCCAAAGCTGTCTGCATA 58.727 45.455 4.39 0.00 45.94 3.14
693 718 0.976641 TCGGTCATCCAAAGCTGTCT 59.023 50.000 0.00 0.00 0.00 3.41
707 732 0.575390 CAAATACGGATGCGTCGGTC 59.425 55.000 17.88 0.00 38.63 4.79
708 733 0.108520 ACAAATACGGATGCGTCGGT 60.109 50.000 17.88 21.12 40.51 4.69
709 734 0.300491 CACAAATACGGATGCGTCGG 59.700 55.000 17.88 11.63 0.00 4.79
712 737 1.066430 AGTCCACAAATACGGATGCGT 60.066 47.619 18.47 18.47 32.83 5.24
713 738 1.327460 CAGTCCACAAATACGGATGCG 59.673 52.381 4.58 4.58 32.83 4.73
730 755 0.685660 GAAGACGGGAAAGGACCAGT 59.314 55.000 0.00 0.00 40.68 4.00
731 756 0.389948 CGAAGACGGGAAAGGACCAG 60.390 60.000 0.00 0.00 35.72 4.00
732 757 1.669440 CGAAGACGGGAAAGGACCA 59.331 57.895 0.00 0.00 35.72 4.02
733 758 4.592426 CGAAGACGGGAAAGGACC 57.408 61.111 0.00 0.00 35.72 4.46
743 768 1.289109 ACCGCATTTGTCCGAAGACG 61.289 55.000 0.00 0.00 46.74 4.18
744 769 0.165944 CACCGCATTTGTCCGAAGAC 59.834 55.000 0.00 0.00 43.83 3.01
745 770 0.250124 ACACCGCATTTGTCCGAAGA 60.250 50.000 0.00 0.00 0.00 2.87
746 771 0.165944 GACACCGCATTTGTCCGAAG 59.834 55.000 0.00 0.00 37.93 3.79
747 772 2.240230 GACACCGCATTTGTCCGAA 58.760 52.632 0.00 0.00 37.93 4.30
748 773 3.960237 GACACCGCATTTGTCCGA 58.040 55.556 0.00 0.00 37.93 4.55
768 793 0.244450 TCGAACGCCGTCCACTAAAT 59.756 50.000 0.00 0.00 39.75 1.40
777 802 2.765250 AAGTGCATCTCGAACGCCGT 62.765 55.000 0.00 0.00 39.75 5.68
785 810 2.342651 CGTTGTGTCTAAGTGCATCTCG 59.657 50.000 0.00 0.00 0.00 4.04
789 814 5.065988 AGTTTTTCGTTGTGTCTAAGTGCAT 59.934 36.000 0.00 0.00 0.00 3.96
806 831 6.019762 GTGGCGCAACTATAGTTAGTTTTTC 58.980 40.000 17.62 5.45 44.48 2.29
818 843 2.401583 TGAGAATGTGGCGCAACTAT 57.598 45.000 17.46 4.44 0.00 2.12
972 997 4.065088 CTCTTGGTTGACGGAATGAAGAA 58.935 43.478 0.00 0.00 0.00 2.52
1011 1036 3.477899 GCAAATAGGAATATGCCTCGC 57.522 47.619 5.15 1.46 39.50 5.03
1154 1179 1.396996 GCCAGTTATCGTGCGTCAAAT 59.603 47.619 0.00 0.00 0.00 2.32
1416 1447 1.611673 CGGGTTCTCTTTGCACCTGAT 60.612 52.381 0.00 0.00 39.06 2.90
1469 1500 4.682334 TCGGGGCACTGGTCGGTA 62.682 66.667 0.00 0.00 0.00 4.02
1562 1593 1.262882 CGGCGTTACGTAGTTTCTCC 58.737 55.000 6.63 0.00 37.78 3.71
1565 1596 1.262882 CTCCGGCGTTACGTAGTTTC 58.737 55.000 6.01 0.00 37.78 2.78
1571 1602 2.674380 AGGACTCCGGCGTTACGT 60.674 61.111 6.01 0.00 0.00 3.57
1615 1646 6.072112 TCTGTAAGACAAAACTTGAATGCC 57.928 37.500 0.00 0.00 38.67 4.40
1622 1653 7.788375 ACGAGATCGATCTGTAAGACAAAACTT 60.788 37.037 31.88 4.25 44.97 2.66
1668 1699 2.385315 CTATCACAGCACATCCGTACG 58.615 52.381 8.69 8.69 0.00 3.67
1670 1701 1.068588 GCCTATCACAGCACATCCGTA 59.931 52.381 0.00 0.00 0.00 4.02
1690 1725 1.742761 AACCAACATCTGATGCTCGG 58.257 50.000 17.24 16.09 0.00 4.63
1736 1774 2.512692 TCTTGCCATGGTACTTGCAT 57.487 45.000 14.67 0.00 33.08 3.96
2096 2149 0.605589 CGCTCCTCAAAGAGTCCTGT 59.394 55.000 0.00 0.00 36.20 4.00
2122 2175 2.831526 ACCATTTATTTGACCTGTGGCC 59.168 45.455 0.00 0.00 0.00 5.36
2228 2294 7.275560 CCGATCTCCAATTTCAAATTTTGTACC 59.724 37.037 8.89 0.00 0.00 3.34
2244 2310 3.945285 GCTAATTTCCAACCGATCTCCAA 59.055 43.478 0.00 0.00 0.00 3.53
2253 2320 6.379386 GTTAAGTGAGTGCTAATTTCCAACC 58.621 40.000 0.00 0.00 0.00 3.77
2333 2400 5.067273 ACATTTCTTCCACGTTATCCAACA 58.933 37.500 0.00 0.00 34.05 3.33
2491 2592 4.237976 AGAGTACAAGAAGAGATCGGGA 57.762 45.455 0.00 0.00 0.00 5.14
2556 2664 1.028905 TTGGGTTGGAAGCGTTGAAG 58.971 50.000 0.00 0.00 0.00 3.02
2641 2752 1.410517 GCGGAGGAAGACATGATCTCA 59.589 52.381 0.00 0.00 36.27 3.27
2684 2795 0.321653 GACATGGAGGTGGAAAGCGT 60.322 55.000 0.00 0.00 0.00 5.07
2759 2873 3.484953 TCCCCTTGTTAGCTTCTCCTA 57.515 47.619 0.00 0.00 0.00 2.94
2809 2923 2.125912 GCGCGTCTGATCTGTGGT 60.126 61.111 8.43 0.00 0.00 4.16
2812 2926 1.445066 CTGTGCGCGTCTGATCTGT 60.445 57.895 8.43 0.00 0.00 3.41
2959 3073 3.143741 ACAGAGATCCCATCAGATACCCT 59.856 47.826 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.