Multiple sequence alignment - TraesCS2B01G251800

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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 TraesCS2B01G251800 chr2B 100.000 2748 0 0 1 2748 265224011 265221264 0.000000e+00 5075.0
1 TraesCS2B01G251800 chr2B 99.438 178 0 1 2512 2689 675339942 675339766 3.410000e-84 322.0
2 TraesCS2B01G251800 chr2D 92.533 2558 103 24 2 2490 209515981 209513443 0.000000e+00 3585.0
3 TraesCS2B01G251800 chr2D 97.059 68 1 1 2682 2748 209512717 209512650 2.240000e-21 113.0
4 TraesCS2B01G251800 chr2A 92.439 2050 74 19 500 2490 262581668 262579641 0.000000e+00 2852.0
5 TraesCS2B01G251800 chr2A 87.564 587 59 11 240 824 262582806 262582232 0.000000e+00 667.0
6 TraesCS2B01G251800 chr2A 92.157 255 20 0 1 255 262583075 262582821 7.230000e-96 361.0
7 TraesCS2B01G251800 chr2A 97.059 68 1 1 2682 2748 262579135 262579068 2.240000e-21 113.0
8 TraesCS2B01G251800 chr2A 95.385 65 3 0 500 564 262582220 262582156 1.350000e-18 104.0
9 TraesCS2B01G251800 chr3B 98.907 183 1 1 2512 2693 473396919 473397101 2.640000e-85 326.0
10 TraesCS2B01G251800 chr4A 98.901 182 1 1 2512 2693 673448021 673447841 9.490000e-85 324.0
11 TraesCS2B01G251800 chr4A 81.091 275 38 9 517 785 618270257 618270523 9.970000e-50 207.0
12 TraesCS2B01G251800 chr1A 99.432 176 1 0 2512 2687 543931055 543930880 1.230000e-83 320.0
13 TraesCS2B01G251800 chr1A 98.883 179 0 2 2512 2689 515551304 515551481 4.420000e-83 318.0
14 TraesCS2B01G251800 chr7B 98.883 179 0 2 2512 2690 700410910 700410734 4.420000e-83 318.0
15 TraesCS2B01G251800 chr7B 97.814 183 2 2 2512 2694 282179691 282179871 5.710000e-82 315.0
16 TraesCS2B01G251800 chr7B 79.577 142 27 2 247 387 12950890 12951030 1.740000e-17 100.0
17 TraesCS2B01G251800 chr7A 97.826 184 1 3 2513 2695 438151645 438151464 5.710000e-82 315.0
18 TraesCS2B01G251800 chr7A 80.412 194 30 7 1 189 641489513 641489323 1.030000e-29 141.0
19 TraesCS2B01G251800 chr3D 99.412 170 0 1 2512 2680 153512232 153512401 9.560000e-80 307.0
20 TraesCS2B01G251800 chr5A 77.157 394 81 6 1 387 679371518 679371127 1.280000e-53 220.0
21 TraesCS2B01G251800 chr5A 78.723 282 48 10 510 785 357539041 357538766 7.820000e-41 178.0
22 TraesCS2B01G251800 chr5D 78.799 283 44 11 507 785 396918676 396918946 2.810000e-40 176.0
23 TraesCS2B01G251800 chr1B 80.973 226 39 4 1 224 686781974 686781751 2.810000e-40 176.0
24 TraesCS2B01G251800 chr1B 76.494 251 53 4 3 250 637517721 637517968 6.170000e-27 132.0
25 TraesCS2B01G251800 chr6D 79.221 231 48 0 1 231 53638051 53637821 7.880000e-36 161.0
26 TraesCS2B01G251800 chr7D 82.320 181 27 4 1 180 477071218 477071394 4.740000e-33 152.0
27 TraesCS2B01G251800 chr3A 81.921 177 32 0 1 177 502391024 502391200 1.700000e-32 150.0
28 TraesCS2B01G251800 chr1D 81.579 114 18 2 299 411 440402775 440402886 1.050000e-14 91.6


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 TraesCS2B01G251800 chr2B 265221264 265224011 2747 True 5075.0 5075 100.0000 1 2748 1 chr2B.!!$R1 2747
1 TraesCS2B01G251800 chr2D 209512650 209515981 3331 True 1849.0 3585 94.7960 2 2748 2 chr2D.!!$R1 2746
2 TraesCS2B01G251800 chr2A 262579068 262583075 4007 True 819.4 2852 92.9208 1 2748 5 chr2A.!!$R1 2747

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
698 1609 0.035439 AGGATCGGTTTTGGATGCGT 60.035 50.0 0.0 0.0 37.33 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2534 3505 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.0 0.0 0.0 44.78 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
61 62 1.134818 GGCCCGGATTTTTGGATCAAC 60.135 52.381 0.73 0.00 0.00 3.18
125 126 5.571784 ACGAGTCGAGAATAATGTTGGTA 57.428 39.130 21.50 0.00 0.00 3.25
130 131 6.516718 AGTCGAGAATAATGTTGGTAGATGG 58.483 40.000 0.00 0.00 0.00 3.51
131 132 5.696724 GTCGAGAATAATGTTGGTAGATGGG 59.303 44.000 0.00 0.00 0.00 4.00
166 167 3.077359 CTGAAGGTAAGAAGTGGCTTGG 58.923 50.000 0.00 0.00 0.00 3.61
191 192 3.264450 GGAAGAAGAAGGAGATCAACCCA 59.736 47.826 0.00 0.00 0.00 4.51
231 232 0.458543 GAGAGCGACCATCGAAGCAA 60.459 55.000 1.69 0.00 43.74 3.91
265 296 0.821517 ATGGCGTCCGACAAGTGATA 59.178 50.000 0.00 0.00 36.35 2.15
266 297 0.821517 TGGCGTCCGACAAGTGATAT 59.178 50.000 0.00 0.00 0.00 1.63
280 311 3.021269 GTGATATATCACGCCGACCAA 57.979 47.619 25.89 0.00 46.46 3.67
310 341 9.473007 TGGTCCAGACATTTAATTTCATTATGA 57.527 29.630 0.00 0.00 0.00 2.15
337 368 7.757941 TGTCTGGATTGTTGAATTGTGATTA 57.242 32.000 0.00 0.00 0.00 1.75
394 425 8.701908 AAATTTGAGCTATATGATGGACATGT 57.298 30.769 0.00 0.00 39.77 3.21
396 427 4.572909 TGAGCTATATGATGGACATGTGC 58.427 43.478 10.90 10.90 39.77 4.57
463 494 4.012895 CGCTGTCCGTGGTTGTGC 62.013 66.667 0.00 0.00 0.00 4.57
465 496 2.111043 CTGTCCGTGGTTGTGCCT 59.889 61.111 0.00 0.00 38.35 4.75
467 498 2.110213 GTCCGTGGTTGTGCCTGA 59.890 61.111 0.00 0.00 38.35 3.86
469 500 0.889186 GTCCGTGGTTGTGCCTGAAT 60.889 55.000 0.00 0.00 38.35 2.57
489 522 1.270947 TGCGTTCACGGATTTTAGGGT 60.271 47.619 0.81 0.00 40.23 4.34
491 524 2.690786 CGTTCACGGATTTTAGGGTGA 58.309 47.619 0.00 0.00 37.61 4.02
494 527 1.894466 TCACGGATTTTAGGGTGACGA 59.106 47.619 0.00 0.00 34.71 4.20
575 1486 9.673454 GTTTAATTTCGGTTTGTATTGAACTCT 57.327 29.630 0.00 0.00 0.00 3.24
601 1512 8.253810 TCCTATGCTATGTAGTAGATGAATTGC 58.746 37.037 0.00 0.00 31.71 3.56
632 1543 3.073678 TGTTTGATGAACTCCGGTGATG 58.926 45.455 11.17 0.00 39.08 3.07
642 1553 2.569853 ACTCCGGTGATGTATGTTTCCA 59.430 45.455 11.17 0.00 0.00 3.53
666 1577 9.698309 CCATACGAACTAGAGATTTGAATATGT 57.302 33.333 0.00 0.00 0.00 2.29
685 1596 9.355215 GAATATGTGGTATTAGTTGTAGGATCG 57.645 37.037 0.00 0.00 33.16 3.69
698 1609 0.035439 AGGATCGGTTTTGGATGCGT 60.035 50.000 0.00 0.00 37.33 5.24
699 1610 0.377203 GGATCGGTTTTGGATGCGTC 59.623 55.000 0.00 0.00 0.00 5.19
708 1619 2.107041 TTGGATGCGTCTCCGGTGTT 62.107 55.000 5.77 0.00 38.21 3.32
739 1650 2.420722 TCATTTTCGGGATGCCGTAAAC 59.579 45.455 27.62 0.00 35.89 2.01
741 1652 1.637478 TTTCGGGATGCCGTAAACGC 61.637 55.000 25.75 0.00 38.18 4.84
742 1653 3.569690 CGGGATGCCGTAAACGCC 61.570 66.667 18.74 0.00 38.18 5.68
748 1660 1.198178 GATGCCGTAAACGCCTTTTGA 59.802 47.619 0.00 0.00 38.18 2.69
753 1665 3.000727 CCGTAAACGCCTTTTGAGAGAT 58.999 45.455 0.00 0.00 38.18 2.75
764 1676 1.841302 TTGAGAGATGGCGGGTTGCT 61.841 55.000 0.00 0.00 45.43 3.91
792 1704 4.456222 GTGCTAGAGATGCTCTTATACCGA 59.544 45.833 1.88 0.00 41.50 4.69
812 1724 5.710567 ACCGATAAAAAGAAGGAAAAGAGGG 59.289 40.000 0.00 0.00 0.00 4.30
857 1782 0.109597 GCACGAACTTGCTGGATTGG 60.110 55.000 0.00 0.00 39.59 3.16
951 1898 4.629523 GCCCGAACCCGAACCACA 62.630 66.667 0.00 0.00 38.22 4.17
1121 2068 0.698886 TTCCCATCCATCCCTCCCTG 60.699 60.000 0.00 0.00 0.00 4.45
1122 2069 2.838467 CCCATCCATCCCTCCCTGC 61.838 68.421 0.00 0.00 0.00 4.85
1217 2164 4.740695 CGGTTCCTTATTTCGTCTGATCTC 59.259 45.833 0.00 0.00 0.00 2.75
1366 2313 1.087501 GGCCTTGACAAGACCGAATC 58.912 55.000 16.99 0.00 0.00 2.52
1388 2335 8.705048 AATCGTAGGATTTTCTGTAGAAAGTC 57.295 34.615 16.85 16.85 44.77 3.01
1399 2346 5.727434 TCTGTAGAAAGTCCCCGTAATTTC 58.273 41.667 0.00 0.00 32.95 2.17
1400 2347 4.497300 TGTAGAAAGTCCCCGTAATTTCG 58.503 43.478 0.00 0.00 36.88 3.46
1609 2568 0.178858 TGGGAATGGGTCTGGGTGTA 60.179 55.000 0.00 0.00 0.00 2.90
1778 2737 4.302559 ACTCCCTCCTTCCATGTTTAAC 57.697 45.455 0.00 0.00 0.00 2.01
1789 2748 9.238368 TCCTTCCATGTTTAACTGTTTATAAGG 57.762 33.333 0.00 0.00 0.00 2.69
1792 2751 7.179269 TCCATGTTTAACTGTTTATAAGGCCT 58.821 34.615 0.00 0.00 0.00 5.19
1942 2901 7.611467 TCTGTCACGGAAACCTTATACTAGTAA 59.389 37.037 6.70 0.00 0.00 2.24
2272 3243 3.068165 ACTCTTGCCCTTGTTTAAACTGC 59.932 43.478 18.72 15.15 0.00 4.40
2290 3261 7.566760 AAACTGCGAATGGTATATGAATTCA 57.433 32.000 11.26 11.26 31.88 2.57
2358 3329 4.278975 AGGTTGAACTAGCTTTCTGAGG 57.721 45.455 0.00 0.00 0.00 3.86
2380 3351 3.922171 ACATCCAGATCACTTTCCCTC 57.078 47.619 0.00 0.00 0.00 4.30
2414 3385 4.095483 CCTCCTCTGTCGAAATCCAATTTG 59.905 45.833 0.00 0.00 31.47 2.32
2458 3429 9.384764 GTTTTCACCTGAATTTAGTAGATAGCT 57.615 33.333 0.00 0.00 33.54 3.32
2490 3461 0.753867 GGGCGAGGGTTTTTGGAAAA 59.246 50.000 0.00 0.00 0.00 2.29
2491 3462 1.270094 GGGCGAGGGTTTTTGGAAAAG 60.270 52.381 0.00 0.00 0.00 2.27
2493 3464 2.159014 GGCGAGGGTTTTTGGAAAAGTT 60.159 45.455 0.00 0.00 0.00 2.66
2494 3465 3.120792 GCGAGGGTTTTTGGAAAAGTTC 58.879 45.455 0.00 0.00 0.00 3.01
2495 3466 3.429684 GCGAGGGTTTTTGGAAAAGTTCA 60.430 43.478 0.00 0.00 0.00 3.18
2496 3467 4.749976 CGAGGGTTTTTGGAAAAGTTCAA 58.250 39.130 0.00 0.00 0.00 2.69
2497 3468 5.356426 CGAGGGTTTTTGGAAAAGTTCAAT 58.644 37.500 0.00 0.00 0.00 2.57
2498 3469 5.815222 CGAGGGTTTTTGGAAAAGTTCAATT 59.185 36.000 0.00 0.00 0.00 2.32
2500 3471 7.492994 CGAGGGTTTTTGGAAAAGTTCAATTAA 59.507 33.333 0.00 0.00 0.00 1.40
2501 3472 9.168451 GAGGGTTTTTGGAAAAGTTCAATTAAA 57.832 29.630 0.00 0.00 0.00 1.52
2502 3473 9.521841 AGGGTTTTTGGAAAAGTTCAATTAAAA 57.478 25.926 0.00 0.00 0.00 1.52
2520 3491 1.389555 AAAACTATAGGCCTTGGCGC 58.610 50.000 12.58 0.00 0.00 6.53
2522 3493 0.179045 AACTATAGGCCTTGGCGCAG 60.179 55.000 12.58 0.00 0.00 5.18
2523 3494 1.338136 ACTATAGGCCTTGGCGCAGT 61.338 55.000 12.58 2.51 0.00 4.40
2524 3495 0.882042 CTATAGGCCTTGGCGCAGTG 60.882 60.000 12.58 0.00 0.00 3.66
2525 3496 2.324014 TATAGGCCTTGGCGCAGTGG 62.324 60.000 12.58 8.70 0.00 4.00
2527 3498 4.715523 GGCCTTGGCGCAGTGGTA 62.716 66.667 10.83 0.00 0.00 3.25
2530 3501 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
2531 3502 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
2533 3504 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
2541 3512 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2545 3516 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2546 3517 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2547 3518 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2548 3519 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2551 3522 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2552 3523 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2562 3533 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
2563 3534 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
2564 3535 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
2565 3536 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
2566 3537 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
2568 3539 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
2571 3542 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
2573 3544 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
2575 3546 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
2576 3547 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
2591 3562 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
2592 3563 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
2593 3564 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
2594 3565 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
2595 3566 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
2596 3567 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
2597 3568 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
2598 3569 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
2599 3570 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
2600 3571 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
2601 3572 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
2602 3573 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
2603 3574 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2604 3575 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2605 3576 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2606 3577 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2607 3578 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2608 3579 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2610 3581 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2611 3582 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
2612 3583 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
2614 3585 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
2615 3586 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
2616 3587 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
2617 3588 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
2618 3589 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
2635 3730 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2636 3731 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2637 3732 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2638 3733 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2673 3768 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
2674 3769 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
2675 3770 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
2676 3771 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
2677 3772 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
2678 3773 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 2.178580 ACCTCTCCTTCTCAAGCTCTG 58.821 52.381 0.00 0.00 0.00 3.35
125 126 1.767681 GCATCCAAGAGACTCCCATCT 59.232 52.381 0.00 0.00 0.00 2.90
130 131 2.419851 CCTTCAGCATCCAAGAGACTCC 60.420 54.545 0.00 0.00 0.00 3.85
131 132 2.235898 ACCTTCAGCATCCAAGAGACTC 59.764 50.000 0.00 0.00 0.00 3.36
166 167 2.482494 TGATCTCCTTCTTCTTCCCCC 58.518 52.381 0.00 0.00 0.00 5.40
170 171 4.257731 GTGGGTTGATCTCCTTCTTCTTC 58.742 47.826 0.00 0.00 0.00 2.87
219 220 0.250124 TTGTCCGTTGCTTCGATGGT 60.250 50.000 0.00 0.00 0.00 3.55
231 232 0.392998 GCCATCCATGTCTTGTCCGT 60.393 55.000 0.00 0.00 0.00 4.69
265 296 1.227147 CGGTTGGTCGGCGTGATAT 60.227 57.895 6.85 0.00 0.00 1.63
266 297 2.182284 CGGTTGGTCGGCGTGATA 59.818 61.111 6.85 0.00 0.00 2.15
280 311 3.713826 ATTAAATGTCTGGACCACGGT 57.286 42.857 0.00 0.00 0.00 4.83
310 341 5.535783 TCACAATTCAACAATCCAGACATGT 59.464 36.000 0.00 0.00 0.00 3.21
394 425 5.051816 CGTATCTAAACCCTTAAATCCGCA 58.948 41.667 0.00 0.00 0.00 5.69
396 427 5.924825 CCTCGTATCTAAACCCTTAAATCCG 59.075 44.000 0.00 0.00 0.00 4.18
463 494 1.086696 AATCCGTGAACGCATTCAGG 58.913 50.000 8.17 8.17 45.58 3.86
465 496 3.126171 CCTAAAATCCGTGAACGCATTCA 59.874 43.478 0.00 0.00 42.73 2.57
467 498 2.422127 CCCTAAAATCCGTGAACGCATT 59.578 45.455 0.00 0.00 38.18 3.56
469 500 1.270947 ACCCTAAAATCCGTGAACGCA 60.271 47.619 0.00 0.00 38.18 5.24
485 516 1.698506 TTTGGCAAATTCGTCACCCT 58.301 45.000 8.93 0.00 0.00 4.34
489 522 2.625314 TCCACATTTGGCAAATTCGTCA 59.375 40.909 22.26 5.36 43.56 4.35
491 524 3.006752 ACATCCACATTTGGCAAATTCGT 59.993 39.130 22.26 15.25 43.56 3.85
494 527 5.999205 TCTACATCCACATTTGGCAAATT 57.001 34.783 22.26 11.42 43.56 1.82
575 1486 8.253810 GCAATTCATCTACTACATAGCATAGGA 58.746 37.037 0.00 0.00 0.00 2.94
601 1512 6.293081 CGGAGTTCATCAAACATAGCATAAGG 60.293 42.308 0.00 0.00 40.56 2.69
642 1553 9.698309 CCACATATTCAAATCTCTAGTTCGTAT 57.302 33.333 0.00 0.00 0.00 3.06
666 1577 6.549433 AAACCGATCCTACAACTAATACCA 57.451 37.500 0.00 0.00 0.00 3.25
698 1609 4.963373 TGATTTTTGTAGAACACCGGAGA 58.037 39.130 9.46 0.00 0.00 3.71
699 1610 5.880054 ATGATTTTTGTAGAACACCGGAG 57.120 39.130 9.46 1.26 0.00 4.63
708 1619 6.329496 GCATCCCGAAAATGATTTTTGTAGA 58.671 36.000 14.85 11.78 35.20 2.59
741 1652 0.035056 ACCCGCCATCTCTCAAAAGG 60.035 55.000 0.00 0.00 0.00 3.11
742 1653 1.470098 CAACCCGCCATCTCTCAAAAG 59.530 52.381 0.00 0.00 0.00 2.27
748 1660 2.270205 CAGCAACCCGCCATCTCT 59.730 61.111 0.00 0.00 44.04 3.10
753 1665 3.965258 ACATCCAGCAACCCGCCA 61.965 61.111 0.00 0.00 44.04 5.69
983 1930 3.907260 ATGTCGCTGTGGCCTGTGG 62.907 63.158 3.32 0.00 34.44 4.17
984 1931 2.359107 ATGTCGCTGTGGCCTGTG 60.359 61.111 3.32 0.87 34.44 3.66
985 1932 2.359107 CATGTCGCTGTGGCCTGT 60.359 61.111 3.32 0.00 34.44 4.00
986 1933 3.807538 GCATGTCGCTGTGGCCTG 61.808 66.667 3.32 0.00 37.77 4.85
1122 2069 2.441035 AAAGGAAAGGGGAAGGCGGG 62.441 60.000 0.00 0.00 0.00 6.13
1217 2164 5.133221 ACTTGCAGGCATATAAAGGGTTAG 58.867 41.667 0.00 0.00 0.00 2.34
1399 2346 2.695359 ACACTGTAATACTGCAACCCG 58.305 47.619 0.00 0.00 0.00 5.28
1400 2347 5.704053 AGTAAACACTGTAATACTGCAACCC 59.296 40.000 6.73 0.00 0.00 4.11
1663 2622 0.108851 TCGCACGCTCAAGCATCTTA 60.109 50.000 2.50 0.00 42.21 2.10
1792 2751 2.069465 AAAATTGTGTGCGCGCCTCA 62.069 50.000 30.77 24.15 0.00 3.86
1802 2761 8.478877 TGGTCAAAGTTTACCATAAAATTGTGT 58.521 29.630 10.90 0.00 40.84 3.72
1942 2901 2.831526 GCCCCTTGACCAACAACAATAT 59.168 45.455 0.00 0.00 34.56 1.28
2082 3052 3.191162 TGGTTGAATCAATAGTGCACAGC 59.809 43.478 21.04 4.15 0.00 4.40
2148 3118 8.261522 TGTTTAAGTAGTGATATGTGTATGCCA 58.738 33.333 0.00 0.00 0.00 4.92
2272 3243 7.510549 ACCCTTTGAATTCATATACCATTCG 57.489 36.000 9.40 0.00 30.69 3.34
2290 3261 3.989056 TCCCAGAGTTTTGAAACCCTTT 58.011 40.909 3.14 0.00 39.71 3.11
2358 3329 4.195416 GAGGGAAAGTGATCTGGATGTTC 58.805 47.826 0.00 0.00 0.00 3.18
2380 3351 3.243569 CGACAGAGGAGGCCTATAGTTTG 60.244 52.174 4.42 2.31 31.76 2.93
2414 3385 0.396811 ACAGTGTAGCAGGTTGGGTC 59.603 55.000 0.00 0.00 0.00 4.46
2458 3429 4.680237 CGCCCTCTGTGGTTCGCA 62.680 66.667 0.00 0.00 0.00 5.10
2500 3471 1.749063 GCGCCAAGGCCTATAGTTTTT 59.251 47.619 5.16 0.00 37.98 1.94
2501 3472 1.340600 TGCGCCAAGGCCTATAGTTTT 60.341 47.619 5.16 0.00 37.98 2.43
2502 3473 0.254747 TGCGCCAAGGCCTATAGTTT 59.745 50.000 5.16 0.00 37.98 2.66
2504 3475 1.338136 ACTGCGCCAAGGCCTATAGT 61.338 55.000 5.16 1.44 37.98 2.12
2506 3477 1.146041 CACTGCGCCAAGGCCTATA 59.854 57.895 5.16 0.00 37.98 1.31
2507 3478 2.124570 CACTGCGCCAAGGCCTAT 60.125 61.111 5.16 0.00 37.98 2.57
2508 3479 4.408821 CCACTGCGCCAAGGCCTA 62.409 66.667 5.16 0.00 37.98 3.93
2510 3481 4.715523 TACCACTGCGCCAAGGCC 62.716 66.667 4.18 0.00 37.98 5.19
2513 3484 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
2516 3487 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
2520 3491 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2522 3493 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2523 3494 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2524 3495 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2525 3496 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2526 3497 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2527 3498 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2530 3501 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2531 3502 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2533 3504 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2534 3505 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2546 3517 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
2547 3518 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
2548 3519 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
2551 3522 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
2552 3523 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
2554 3525 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
2555 3526 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
2557 3528 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2558 3529 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2559 3530 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2560 3531 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2562 3533 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2563 3534 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2564 3535 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
2565 3536 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
2566 3537 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
2568 3539 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
2581 3552 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2582 3553 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
2584 3555 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
2586 3557 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2587 3558 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2589 3560 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2591 3562 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2592 3563 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
2593 3564 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
2594 3565 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
2595 3566 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
2596 3567 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
2597 3568 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
2598 3569 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
2599 3570 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
2600 3571 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
2601 3572 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
2602 3573 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
2603 3574 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
2604 3575 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
2605 3576 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
2606 3577 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
2616 3587 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2617 3588 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2618 3589 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2629 3724 4.735599 AGGGTCGGGGAAGGGTCC 62.736 72.222 0.00 0.00 44.10 4.46
2648 3743 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2649 3744 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2651 3746 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2657 3752 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
2658 3753 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
2659 3754 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
2660 3755 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
2661 3756 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
2667 3762 4.994756 AAAAGGGGCAGCCCGGTG 62.995 66.667 25.18 0.00 46.66 4.94
2668 3763 4.233558 AAAAAGGGGCAGCCCGGT 62.234 61.111 25.18 11.58 46.66 5.28


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

AutoCloner maintained by Alex Coulton.