Multiple sequence alignment - TraesCS7D01G295800

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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 TraesCS7D01G295800 chr7D 100.000 2519 0 0 1 2519 371267062 371269580 0.000000e+00 4652.0
1 TraesCS7D01G295800 chr7D 78.254 607 62 28 1 583 417914597 417915157 2.420000e-85 326.0
2 TraesCS7D01G295800 chr7D 79.151 259 48 6 327 581 503976487 503976231 9.260000e-40 174.0
3 TraesCS7D01G295800 chr7D 92.188 64 2 1 2459 2519 154177159 154177222 1.240000e-13 87.9
4 TraesCS7D01G295800 chr7B 94.224 1887 58 16 600 2463 318840392 318842250 0.000000e+00 2833.0
5 TraesCS7D01G295800 chr7B 76.672 583 81 30 1 579 716989797 716990328 3.190000e-69 272.0
6 TraesCS7D01G295800 chr7B 82.007 289 38 10 1 278 524400653 524400368 1.510000e-57 233.0
7 TraesCS7D01G295800 chr7B 89.552 134 10 4 314 445 716684778 716684647 1.550000e-37 167.0
8 TraesCS7D01G295800 chr7A 93.545 1890 62 21 600 2463 414185670 414183815 0.000000e+00 2760.0
9 TraesCS7D01G295800 chr7A 75.203 617 100 34 1 606 418111822 418112396 2.500000e-60 243.0
10 TraesCS7D01G295800 chr3D 79.669 605 69 24 4 583 338301301 338300726 1.090000e-103 387.0
11 TraesCS7D01G295800 chr3D 76.771 607 72 33 1 583 5766693 5766132 2.470000e-70 276.0
12 TraesCS7D01G295800 chr3D 86.932 176 21 1 1 174 271485089 271484914 1.980000e-46 196.0
13 TraesCS7D01G295800 chr3D 89.706 68 4 1 2455 2519 8971802 8971869 1.610000e-12 84.2
14 TraesCS7D01G295800 chr5D 78.487 595 68 24 1 592 387959761 387960298 4.020000e-88 335.0
15 TraesCS7D01G295800 chr4D 77.924 607 69 23 1 583 66566819 66566254 4.040000e-83 318.0
16 TraesCS7D01G295800 chr4D 91.935 62 2 1 2461 2519 41411757 41411696 1.610000e-12 84.2
17 TraesCS7D01G295800 chr2B 79.226 491 60 21 2 486 45647030 45647484 1.130000e-78 303.0
18 TraesCS7D01G295800 chr2B 83.182 220 26 5 1 211 774737118 774736901 9.200000e-45 191.0
19 TraesCS7D01G295800 chr2B 91.176 68 3 1 2455 2519 106094850 106094917 3.450000e-14 89.8
20 TraesCS7D01G295800 chr2B 93.220 59 2 2 2461 2519 84143663 84143607 4.460000e-13 86.1
21 TraesCS7D01G295800 chr1A 83.451 284 33 6 1 276 319088187 319087910 4.160000e-63 252.0
22 TraesCS7D01G295800 chr5A 86.792 212 25 3 1 211 650032587 650032796 1.510000e-57 233.0
23 TraesCS7D01G295800 chr5A 88.542 192 21 1 1 191 679447131 679447322 5.420000e-57 231.0
24 TraesCS7D01G295800 chr6D 88.636 176 18 1 1 174 418532628 418532453 1.960000e-51 213.0
25 TraesCS7D01G295800 chr6D 76.611 419 47 22 200 592 140035974 140036367 1.540000e-42 183.0
26 TraesCS7D01G295800 chr6D 91.935 62 2 1 2461 2519 48662037 48662098 1.610000e-12 84.2
27 TraesCS7D01G295800 chr1D 79.853 273 30 8 308 556 432642809 432643080 2.580000e-40 176.0
28 TraesCS7D01G295800 chr1D 91.304 69 2 2 2454 2519 10407857 10407790 9.600000e-15 91.6
29 TraesCS7D01G295800 chr1D 92.188 64 2 1 2459 2519 242560266 242560329 1.240000e-13 87.9
30 TraesCS7D01G295800 chrUn 91.935 62 2 1 2461 2519 112721135 112721196 1.610000e-12 84.2


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 TraesCS7D01G295800 chr7D 371267062 371269580 2518 False 4652 4652 100.000 1 2519 1 chr7D.!!$F2 2518
1 TraesCS7D01G295800 chr7D 417914597 417915157 560 False 326 326 78.254 1 583 1 chr7D.!!$F3 582
2 TraesCS7D01G295800 chr7B 318840392 318842250 1858 False 2833 2833 94.224 600 2463 1 chr7B.!!$F1 1863
3 TraesCS7D01G295800 chr7B 716989797 716990328 531 False 272 272 76.672 1 579 1 chr7B.!!$F2 578
4 TraesCS7D01G295800 chr7A 414183815 414185670 1855 True 2760 2760 93.545 600 2463 1 chr7A.!!$R1 1863
5 TraesCS7D01G295800 chr7A 418111822 418112396 574 False 243 243 75.203 1 606 1 chr7A.!!$F1 605
6 TraesCS7D01G295800 chr3D 338300726 338301301 575 True 387 387 79.669 4 583 1 chr3D.!!$R3 579
7 TraesCS7D01G295800 chr3D 5766132 5766693 561 True 276 276 76.771 1 583 1 chr3D.!!$R1 582
8 TraesCS7D01G295800 chr5D 387959761 387960298 537 False 335 335 78.487 1 592 1 chr5D.!!$F1 591
9 TraesCS7D01G295800 chr4D 66566254 66566819 565 True 318 318 77.924 1 583 1 chr4D.!!$R2 582

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
421 497 0.10412 TGGGTATGTTCGATCGCCTG 59.896 55.0 11.09 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2323 2458 0.5312 GGAAGTGGCTAGTAGCACGT 59.469 55.0 23.24 16.22 44.75 4.49 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
26 27 1.519455 CGCCGCGAAGAAGAGGAAT 60.519 57.895 8.23 0.00 32.51 3.01
41 42 0.461135 GGAATACCGACCTGGCGTTA 59.539 55.000 9.11 1.09 43.94 3.18
44 45 2.521105 ATACCGACCTGGCGTTATTC 57.479 50.000 9.11 0.00 43.94 1.75
56 57 1.229428 CGTTATTCATGGCGGCAGAT 58.771 50.000 19.29 13.50 0.00 2.90
95 96 1.837439 CAGGTGAAGGCATGGTACCTA 59.163 52.381 14.36 0.00 39.63 3.08
128 129 0.389817 TCGTCTTGAACCAGATGCCG 60.390 55.000 0.00 0.00 30.77 5.69
208 227 2.633657 CTATGCCAACGCCGATGC 59.366 61.111 0.00 0.00 0.00 3.91
221 240 2.124983 GATGCCCAGCTCGAGCAA 60.125 61.111 36.87 18.00 45.16 3.91
227 246 0.392193 CCCAGCTCGAGCAATGAAGT 60.392 55.000 36.87 13.78 45.16 3.01
240 259 2.970324 GAAGTTGTGCCGACGCCA 60.970 61.111 0.00 0.00 0.00 5.69
294 325 0.739561 CGAGCCCGAGTACTAAAGCT 59.260 55.000 11.62 11.62 38.22 3.74
295 326 1.534175 CGAGCCCGAGTACTAAAGCTG 60.534 57.143 15.53 6.63 38.22 4.24
296 327 0.175989 AGCCCGAGTACTAAAGCTGC 59.824 55.000 11.15 0.00 0.00 5.25
297 328 1.146358 GCCCGAGTACTAAAGCTGCG 61.146 60.000 0.00 0.00 0.00 5.18
298 329 1.146358 CCCGAGTACTAAAGCTGCGC 61.146 60.000 0.00 0.00 0.00 6.09
299 330 0.179134 CCGAGTACTAAAGCTGCGCT 60.179 55.000 9.73 0.00 42.56 5.92
300 331 0.917259 CGAGTACTAAAGCTGCGCTG 59.083 55.000 9.73 10.04 39.62 5.18
391 422 9.565090 CATGTCTATGATTCCTTCCTTTTGATA 57.435 33.333 0.00 0.00 36.36 2.15
395 426 5.191727 TGATTCCTTCCTTTTGATAGCCA 57.808 39.130 0.00 0.00 0.00 4.75
396 427 5.195940 TGATTCCTTCCTTTTGATAGCCAG 58.804 41.667 0.00 0.00 0.00 4.85
412 466 3.421844 AGCCAGACTTTTGGGTATGTTC 58.578 45.455 0.00 0.00 46.57 3.18
420 496 0.828022 TTGGGTATGTTCGATCGCCT 59.172 50.000 11.09 0.00 0.00 5.52
421 497 0.104120 TGGGTATGTTCGATCGCCTG 59.896 55.000 11.09 0.00 0.00 4.85
512 616 0.545787 TCTTGGGGCCGAAACCTAGA 60.546 55.000 1.68 5.95 36.51 2.43
513 617 0.326927 CTTGGGGCCGAAACCTAGAA 59.673 55.000 1.68 0.00 32.37 2.10
527 631 2.567615 ACCTAGAAGCACGACTGGAAAT 59.432 45.455 0.00 0.00 0.00 2.17
545 649 0.318762 ATTCGATCGCTCCTAAGGCC 59.681 55.000 11.09 0.00 0.00 5.19
583 688 1.169661 ACGCCAAAAGACATTCGCCA 61.170 50.000 0.00 0.00 0.00 5.69
586 691 1.474077 GCCAAAAGACATTCGCCAGAT 59.526 47.619 0.00 0.00 0.00 2.90
587 692 2.733227 GCCAAAAGACATTCGCCAGATG 60.733 50.000 0.00 0.00 0.00 2.90
588 693 2.489329 CCAAAAGACATTCGCCAGATGT 59.511 45.455 0.00 0.00 0.00 3.06
589 694 3.495193 CAAAAGACATTCGCCAGATGTG 58.505 45.455 0.00 0.00 0.00 3.21
590 695 1.089920 AAGACATTCGCCAGATGTGC 58.910 50.000 0.00 0.00 0.00 4.57
591 696 0.251354 AGACATTCGCCAGATGTGCT 59.749 50.000 0.00 0.00 0.00 4.40
592 697 1.482182 AGACATTCGCCAGATGTGCTA 59.518 47.619 0.00 0.00 0.00 3.49
593 698 1.863454 GACATTCGCCAGATGTGCTAG 59.137 52.381 0.00 0.00 0.00 3.42
594 699 1.208052 ACATTCGCCAGATGTGCTAGT 59.792 47.619 0.00 0.00 0.00 2.57
595 700 1.596260 CATTCGCCAGATGTGCTAGTG 59.404 52.381 0.00 0.00 0.00 2.74
596 701 0.740868 TTCGCCAGATGTGCTAGTGC 60.741 55.000 0.00 0.00 40.20 4.40
597 702 1.153489 CGCCAGATGTGCTAGTGCT 60.153 57.895 0.00 0.00 40.48 4.40
598 703 1.150567 CGCCAGATGTGCTAGTGCTC 61.151 60.000 0.00 0.00 40.48 4.26
640 745 2.510874 CACGTCTTCTCGAGCTAACTG 58.489 52.381 7.81 4.78 34.70 3.16
1218 1349 0.830648 CGTCCTCTTTATCCCTGGCA 59.169 55.000 0.00 0.00 0.00 4.92
1293 1424 2.125350 GCTGACCTCAAGAGCCGG 60.125 66.667 0.00 0.00 0.00 6.13
1443 1574 2.584391 GGTCGACAAGGGTCAGGCT 61.584 63.158 18.91 0.00 44.54 4.58
1676 1807 5.370875 AATCAAAAGGGGATGAGAGAGAG 57.629 43.478 0.00 0.00 0.00 3.20
1677 1808 4.066578 TCAAAAGGGGATGAGAGAGAGA 57.933 45.455 0.00 0.00 0.00 3.10
1678 1809 4.029520 TCAAAAGGGGATGAGAGAGAGAG 58.970 47.826 0.00 0.00 0.00 3.20
1679 1810 4.029520 CAAAAGGGGATGAGAGAGAGAGA 58.970 47.826 0.00 0.00 0.00 3.10
1680 1811 3.600448 AAGGGGATGAGAGAGAGAGAG 57.400 52.381 0.00 0.00 0.00 3.20
1681 1812 2.787956 AGGGGATGAGAGAGAGAGAGA 58.212 52.381 0.00 0.00 0.00 3.10
1682 1813 2.713167 AGGGGATGAGAGAGAGAGAGAG 59.287 54.545 0.00 0.00 0.00 3.20
1683 1814 2.711009 GGGGATGAGAGAGAGAGAGAGA 59.289 54.545 0.00 0.00 0.00 3.10
1684 1815 3.244700 GGGGATGAGAGAGAGAGAGAGAG 60.245 56.522 0.00 0.00 0.00 3.20
1685 1816 3.648067 GGGATGAGAGAGAGAGAGAGAGA 59.352 52.174 0.00 0.00 0.00 3.10
1686 1817 4.262808 GGGATGAGAGAGAGAGAGAGAGAG 60.263 54.167 0.00 0.00 0.00 3.20
1687 1818 4.590647 GGATGAGAGAGAGAGAGAGAGAGA 59.409 50.000 0.00 0.00 0.00 3.10
1688 1819 5.279406 GGATGAGAGAGAGAGAGAGAGAGAG 60.279 52.000 0.00 0.00 0.00 3.20
1689 1820 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
1690 1821 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
1691 1822 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1692 1823 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1693 1824 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1694 1825 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1695 1826 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1696 1827 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1996 2129 7.847711 TTATGAGGGGAATTAAGAGAGAGAG 57.152 40.000 0.00 0.00 0.00 3.20
2092 2225 9.713740 CATCACTCAACTTATCTTATTCTTTGC 57.286 33.333 0.00 0.00 0.00 3.68
2097 2230 5.485662 ACTTATCTTATTCTTTGCCGTGC 57.514 39.130 0.00 0.00 0.00 5.34
2259 2393 0.606604 GAGGGTAAGCCTCACGTCAA 59.393 55.000 0.00 0.00 34.72 3.18
2269 2404 1.137086 CCTCACGTCAATGTAGAGGGG 59.863 57.143 7.74 0.00 41.65 4.79
2318 2453 4.201676 CGTGCACAGTGCTTAATTAATCGA 60.202 41.667 25.83 0.00 45.31 3.59
2323 2458 6.035650 GCACAGTGCTTAATTAATCGACACTA 59.964 38.462 18.92 0.00 40.96 2.74
2354 2492 5.724854 ACTAGCCACTTCCCTCAAATACTTA 59.275 40.000 0.00 0.00 0.00 2.24
2357 2495 4.566907 GCCACTTCCCTCAAATACTTACCA 60.567 45.833 0.00 0.00 0.00 3.25
2380 2518 1.660607 CACTAGTAATGGTGCACGCAG 59.339 52.381 11.45 2.43 0.00 5.18
2381 2519 0.652592 CTAGTAATGGTGCACGCAGC 59.347 55.000 14.07 14.07 43.90 5.25
2450 2588 9.921637 ATTTTCTTTGTTTGTCAGACAACTAAA 57.078 25.926 15.93 16.71 37.90 1.85
2465 2603 9.522804 CAGACAACTAAACTAATCATCTACTCC 57.477 37.037 0.00 0.00 0.00 3.85
2466 2604 8.697292 AGACAACTAAACTAATCATCTACTCCC 58.303 37.037 0.00 0.00 0.00 4.30
2467 2605 8.611051 ACAACTAAACTAATCATCTACTCCCT 57.389 34.615 0.00 0.00 0.00 4.20
2468 2606 8.697292 ACAACTAAACTAATCATCTACTCCCTC 58.303 37.037 0.00 0.00 0.00 4.30
2469 2607 7.842887 ACTAAACTAATCATCTACTCCCTCC 57.157 40.000 0.00 0.00 0.00 4.30
2470 2608 5.793030 AAACTAATCATCTACTCCCTCCG 57.207 43.478 0.00 0.00 0.00 4.63
2471 2609 4.456662 ACTAATCATCTACTCCCTCCGT 57.543 45.455 0.00 0.00 0.00 4.69
2472 2610 4.805744 ACTAATCATCTACTCCCTCCGTT 58.194 43.478 0.00 0.00 0.00 4.44
2473 2611 4.828387 ACTAATCATCTACTCCCTCCGTTC 59.172 45.833 0.00 0.00 0.00 3.95
2474 2612 2.068834 TCATCTACTCCCTCCGTTCC 57.931 55.000 0.00 0.00 0.00 3.62
2475 2613 1.041437 CATCTACTCCCTCCGTTCCC 58.959 60.000 0.00 0.00 0.00 3.97
2476 2614 0.635009 ATCTACTCCCTCCGTTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
2477 2615 0.410663 TCTACTCCCTCCGTTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
2478 2616 1.203212 TCTACTCCCTCCGTTCCCAAA 60.203 52.381 0.00 0.00 0.00 3.28
2479 2617 1.838077 CTACTCCCTCCGTTCCCAAAT 59.162 52.381 0.00 0.00 0.00 2.32
2480 2618 0.328258 ACTCCCTCCGTTCCCAAATG 59.672 55.000 0.00 0.00 0.00 2.32
2481 2619 0.328258 CTCCCTCCGTTCCCAAATGT 59.672 55.000 0.00 0.00 0.00 2.71
2482 2620 1.557832 CTCCCTCCGTTCCCAAATGTA 59.442 52.381 0.00 0.00 0.00 2.29
2483 2621 1.279846 TCCCTCCGTTCCCAAATGTAC 59.720 52.381 0.00 0.00 0.00 2.90
2484 2622 1.280998 CCCTCCGTTCCCAAATGTACT 59.719 52.381 0.00 0.00 0.00 2.73
2485 2623 2.290705 CCCTCCGTTCCCAAATGTACTT 60.291 50.000 0.00 0.00 0.00 2.24
2486 2624 3.418047 CCTCCGTTCCCAAATGTACTTT 58.582 45.455 0.00 0.00 0.00 2.66
2487 2625 3.439129 CCTCCGTTCCCAAATGTACTTTC 59.561 47.826 0.00 0.00 0.00 2.62
2488 2626 4.324267 CTCCGTTCCCAAATGTACTTTCT 58.676 43.478 0.00 0.00 0.00 2.52
2489 2627 5.484715 CTCCGTTCCCAAATGTACTTTCTA 58.515 41.667 0.00 0.00 0.00 2.10
2490 2628 6.057321 TCCGTTCCCAAATGTACTTTCTAT 57.943 37.500 0.00 0.00 0.00 1.98
2491 2629 7.185318 TCCGTTCCCAAATGTACTTTCTATA 57.815 36.000 0.00 0.00 0.00 1.31
2492 2630 7.270047 TCCGTTCCCAAATGTACTTTCTATAG 58.730 38.462 0.00 0.00 0.00 1.31
2493 2631 7.124599 TCCGTTCCCAAATGTACTTTCTATAGA 59.875 37.037 0.00 0.00 0.00 1.98
2494 2632 7.931948 CCGTTCCCAAATGTACTTTCTATAGAT 59.068 37.037 2.58 0.00 0.00 1.98
2495 2633 9.326413 CGTTCCCAAATGTACTTTCTATAGATT 57.674 33.333 2.58 0.00 0.00 2.40
2505 2643 9.653287 TGTACTTTCTATAGATTTCAACAGGTG 57.347 33.333 2.58 0.00 0.00 4.00
2506 2644 9.871238 GTACTTTCTATAGATTTCAACAGGTGA 57.129 33.333 2.58 0.00 0.00 4.02
2507 2645 8.779354 ACTTTCTATAGATTTCAACAGGTGAC 57.221 34.615 2.58 0.00 35.39 3.67
2508 2646 8.598041 ACTTTCTATAGATTTCAACAGGTGACT 58.402 33.333 2.58 0.00 46.44 3.41
2510 2648 9.871238 TTTCTATAGATTTCAACAGGTGACTAC 57.129 33.333 2.58 0.00 40.21 2.73
2511 2649 8.589701 TCTATAGATTTCAACAGGTGACTACA 57.410 34.615 0.00 0.00 40.21 2.74
2512 2650 9.201989 TCTATAGATTTCAACAGGTGACTACAT 57.798 33.333 0.00 0.00 40.21 2.29
2515 2653 6.100004 AGATTTCAACAGGTGACTACATACG 58.900 40.000 0.00 0.00 40.21 3.06
2516 2654 3.861276 TCAACAGGTGACTACATACGG 57.139 47.619 0.00 0.00 40.21 4.02
2517 2655 3.423749 TCAACAGGTGACTACATACGGA 58.576 45.455 0.00 0.00 40.21 4.69
2518 2656 3.442625 TCAACAGGTGACTACATACGGAG 59.557 47.826 0.00 0.00 40.21 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.184431 TGAATAACGCCAGGTCGGTA 58.816 50.000 3.88 3.88 35.97 4.02
41 42 2.430465 GACATATCTGCCGCCATGAAT 58.570 47.619 0.00 0.00 0.00 2.57
44 45 0.319813 TCGACATATCTGCCGCCATG 60.320 55.000 0.00 0.00 0.00 3.66
56 57 0.306840 GCTCGTCCATCGTCGACATA 59.693 55.000 17.16 2.88 40.80 2.29
105 106 1.066573 CATCTGGTTCAAGACGAGGCT 60.067 52.381 0.00 0.00 35.08 4.58
111 112 1.026718 CCCGGCATCTGGTTCAAGAC 61.027 60.000 0.00 0.00 0.00 3.01
208 227 0.392193 ACTTCATTGCTCGAGCTGGG 60.392 55.000 35.27 23.78 42.66 4.45
214 233 0.874390 GGCACAACTTCATTGCTCGA 59.126 50.000 0.00 0.00 42.62 4.04
221 240 2.325082 GGCGTCGGCACAACTTCAT 61.325 57.895 14.73 0.00 42.47 2.57
240 259 3.276846 GTGCTCGGGTTGTGCGTT 61.277 61.111 0.00 0.00 39.94 4.84
245 264 1.598130 GCTTCAGTGCTCGGGTTGT 60.598 57.895 0.00 0.00 0.00 3.32
248 267 2.345244 CAGCTTCAGTGCTCGGGT 59.655 61.111 0.00 0.00 41.98 5.28
391 422 3.421844 GAACATACCCAAAAGTCTGGCT 58.578 45.455 0.00 0.00 34.88 4.75
395 426 4.181578 CGATCGAACATACCCAAAAGTCT 58.818 43.478 10.26 0.00 0.00 3.24
396 427 3.242316 GCGATCGAACATACCCAAAAGTC 60.242 47.826 21.57 0.00 0.00 3.01
492 596 0.546598 CTAGGTTTCGGCCCCAAGAT 59.453 55.000 0.00 0.00 0.00 2.40
512 616 2.163818 TCGAATTTCCAGTCGTGCTT 57.836 45.000 0.00 0.00 41.31 3.91
513 617 2.271800 GATCGAATTTCCAGTCGTGCT 58.728 47.619 0.00 0.00 41.31 4.40
527 631 1.040893 TGGCCTTAGGAGCGATCGAA 61.041 55.000 21.57 2.28 0.00 3.71
556 661 0.102300 GTCTTTTGGCGTTTGCACCT 59.898 50.000 0.00 0.00 45.35 4.00
574 679 1.208052 ACTAGCACATCTGGCGAATGT 59.792 47.619 0.00 0.00 36.08 2.71
583 688 4.808414 TTGTTAGAGCACTAGCACATCT 57.192 40.909 7.20 0.00 45.49 2.90
586 691 3.067106 GCTTTGTTAGAGCACTAGCACA 58.933 45.455 7.20 0.91 45.49 4.57
587 692 2.416893 GGCTTTGTTAGAGCACTAGCAC 59.583 50.000 7.20 0.00 45.49 4.40
588 693 2.038426 TGGCTTTGTTAGAGCACTAGCA 59.962 45.455 3.68 3.68 45.49 3.49
589 694 2.416893 GTGGCTTTGTTAGAGCACTAGC 59.583 50.000 0.00 0.00 41.89 3.42
590 695 3.433615 GTGTGGCTTTGTTAGAGCACTAG 59.566 47.826 0.00 0.00 41.89 2.57
591 696 3.399330 GTGTGGCTTTGTTAGAGCACTA 58.601 45.455 0.00 0.00 41.89 2.74
592 697 2.222027 GTGTGGCTTTGTTAGAGCACT 58.778 47.619 0.00 0.00 41.89 4.40
593 698 1.266989 GGTGTGGCTTTGTTAGAGCAC 59.733 52.381 0.00 0.00 41.89 4.40
594 699 1.604604 GGTGTGGCTTTGTTAGAGCA 58.395 50.000 0.00 0.00 41.89 4.26
595 700 0.881796 GGGTGTGGCTTTGTTAGAGC 59.118 55.000 0.00 0.00 39.41 4.09
596 701 1.880027 GTGGGTGTGGCTTTGTTAGAG 59.120 52.381 0.00 0.00 0.00 2.43
597 702 1.213182 TGTGGGTGTGGCTTTGTTAGA 59.787 47.619 0.00 0.00 0.00 2.10
598 703 1.336755 GTGTGGGTGTGGCTTTGTTAG 59.663 52.381 0.00 0.00 0.00 2.34
838 963 2.492599 TTTGGAGGGGAGGAGAGGGG 62.493 65.000 0.00 0.00 0.00 4.79
842 967 2.764269 CTATGTTTGGAGGGGAGGAGA 58.236 52.381 0.00 0.00 0.00 3.71
844 969 1.213296 GCTATGTTTGGAGGGGAGGA 58.787 55.000 0.00 0.00 0.00 3.71
849 980 0.753111 GGCAGGCTATGTTTGGAGGG 60.753 60.000 0.00 0.00 0.00 4.30
1194 1325 1.574339 AGGGATAAAGAGGACGAGGGA 59.426 52.381 0.00 0.00 0.00 4.20
1275 1406 2.659016 CGGCTCTTGAGGTCAGCA 59.341 61.111 0.00 0.00 0.00 4.41
1278 1409 4.069232 CGCCGGCTCTTGAGGTCA 62.069 66.667 26.68 0.00 0.00 4.02
1443 1574 3.399181 CGGCAGAGGGGGCAAGTA 61.399 66.667 0.00 0.00 0.00 2.24
1676 1807 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1677 1808 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1678 1809 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
1679 1810 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
1680 1811 4.646945 TGTCTCTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
1681 1812 4.614475 TGTCTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
1682 1813 4.646945 TCTGTCTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
1683 1814 4.614475 TCTGTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
1684 1815 4.739137 GCTCTGTCTCTCTCTCTCTCTCTC 60.739 54.167 0.00 0.00 0.00 3.20
1685 1816 3.133721 GCTCTGTCTCTCTCTCTCTCTCT 59.866 52.174 0.00 0.00 0.00 3.10
1686 1817 3.462021 GCTCTGTCTCTCTCTCTCTCTC 58.538 54.545 0.00 0.00 0.00 3.20
1687 1818 2.159043 CGCTCTGTCTCTCTCTCTCTCT 60.159 54.545 0.00 0.00 0.00 3.10
1688 1819 2.159099 TCGCTCTGTCTCTCTCTCTCTC 60.159 54.545 0.00 0.00 0.00 3.20
1689 1820 1.831106 TCGCTCTGTCTCTCTCTCTCT 59.169 52.381 0.00 0.00 0.00 3.10
1690 1821 2.159099 TCTCGCTCTGTCTCTCTCTCTC 60.159 54.545 0.00 0.00 0.00 3.20
1691 1822 1.831106 TCTCGCTCTGTCTCTCTCTCT 59.169 52.381 0.00 0.00 0.00 3.10
1692 1823 2.309528 TCTCGCTCTGTCTCTCTCTC 57.690 55.000 0.00 0.00 0.00 3.20
1693 1824 2.236146 TCTTCTCGCTCTGTCTCTCTCT 59.764 50.000 0.00 0.00 0.00 3.10
1694 1825 2.627945 TCTTCTCGCTCTGTCTCTCTC 58.372 52.381 0.00 0.00 0.00 3.20
1695 1826 2.779755 TCTTCTCGCTCTGTCTCTCT 57.220 50.000 0.00 0.00 0.00 3.10
1696 1827 3.006940 TCTTCTTCTCGCTCTGTCTCTC 58.993 50.000 0.00 0.00 0.00 3.20
1974 2107 6.036926 TCTCTCTCTCTTAATTCCCCTCAT 57.963 41.667 0.00 0.00 0.00 2.90
1996 2129 8.359642 AGCTATGTACATCTCTCTTTCTTGATC 58.640 37.037 12.68 0.00 0.00 2.92
2259 2393 4.827789 TGCTTATCCTAACCCCTCTACAT 58.172 43.478 0.00 0.00 0.00 2.29
2323 2458 0.531200 GGAAGTGGCTAGTAGCACGT 59.469 55.000 23.24 16.22 44.75 4.49
2354 2492 2.903784 TGCACCATTACTAGTGTCTGGT 59.096 45.455 16.02 16.02 40.68 4.00
2357 2495 2.674177 GCGTGCACCATTACTAGTGTCT 60.674 50.000 12.15 0.00 36.35 3.41
2450 2588 4.456662 ACGGAGGGAGTAGATGATTAGT 57.543 45.455 0.00 0.00 0.00 2.24
2463 2601 1.279846 GTACATTTGGGAACGGAGGGA 59.720 52.381 0.00 0.00 0.00 4.20
2464 2602 1.280998 AGTACATTTGGGAACGGAGGG 59.719 52.381 0.00 0.00 0.00 4.30
2465 2603 2.781681 AGTACATTTGGGAACGGAGG 57.218 50.000 0.00 0.00 0.00 4.30
2466 2604 4.324267 AGAAAGTACATTTGGGAACGGAG 58.676 43.478 0.00 0.00 0.00 4.63
2467 2605 4.360951 AGAAAGTACATTTGGGAACGGA 57.639 40.909 0.00 0.00 0.00 4.69
2468 2606 7.270047 TCTATAGAAAGTACATTTGGGAACGG 58.730 38.462 0.00 0.00 0.00 4.44
2469 2607 8.888579 ATCTATAGAAAGTACATTTGGGAACG 57.111 34.615 6.52 0.00 0.00 3.95
2479 2617 9.653287 CACCTGTTGAAATCTATAGAAAGTACA 57.347 33.333 6.52 7.11 0.00 2.90
2480 2618 9.871238 TCACCTGTTGAAATCTATAGAAAGTAC 57.129 33.333 6.52 2.98 0.00 2.73
2481 2619 9.871238 GTCACCTGTTGAAATCTATAGAAAGTA 57.129 33.333 6.52 0.00 35.39 2.24
2482 2620 8.598041 AGTCACCTGTTGAAATCTATAGAAAGT 58.402 33.333 6.52 0.00 35.39 2.66
2484 2622 9.871238 GTAGTCACCTGTTGAAATCTATAGAAA 57.129 33.333 6.52 0.00 35.39 2.52
2485 2623 9.031537 TGTAGTCACCTGTTGAAATCTATAGAA 57.968 33.333 6.52 0.00 35.39 2.10
2486 2624 8.589701 TGTAGTCACCTGTTGAAATCTATAGA 57.410 34.615 4.57 4.57 35.39 1.98
2489 2627 7.921214 CGTATGTAGTCACCTGTTGAAATCTAT 59.079 37.037 0.00 0.00 35.39 1.98
2490 2628 7.255569 CGTATGTAGTCACCTGTTGAAATCTA 58.744 38.462 0.00 0.00 35.39 1.98
2491 2629 6.100004 CGTATGTAGTCACCTGTTGAAATCT 58.900 40.000 0.00 0.00 35.39 2.40
2492 2630 5.291128 CCGTATGTAGTCACCTGTTGAAATC 59.709 44.000 0.00 0.00 35.39 2.17
2493 2631 5.046878 TCCGTATGTAGTCACCTGTTGAAAT 60.047 40.000 0.00 0.00 35.39 2.17
2494 2632 4.281435 TCCGTATGTAGTCACCTGTTGAAA 59.719 41.667 0.00 0.00 35.39 2.69
2495 2633 3.827876 TCCGTATGTAGTCACCTGTTGAA 59.172 43.478 0.00 0.00 35.39 2.69
2496 2634 3.423749 TCCGTATGTAGTCACCTGTTGA 58.576 45.455 0.00 0.00 0.00 3.18
2497 2635 3.770666 CTCCGTATGTAGTCACCTGTTG 58.229 50.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.