Multiple sequence alignment - TraesCS3A01G257300

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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 TraesCS3A01G257300 chr3A 100.000 2719 0 0 1 2719 479068824 479071542 0.000000e+00 5022.0
1 TraesCS3A01G257300 chr3B 91.127 1127 77 17 770 1888 465703969 465705080 0.000000e+00 1506.0
2 TraesCS3A01G257300 chr3B 90.345 725 56 11 1 713 465702846 465703568 0.000000e+00 939.0
3 TraesCS3A01G257300 chr3B 85.838 346 47 2 1908 2253 465705194 465705537 1.540000e-97 366.0
4 TraesCS3A01G257300 chr3B 80.402 199 35 4 2256 2452 243243576 243243772 6.070000e-32 148.0
5 TraesCS3A01G257300 chr3B 83.696 92 10 4 5 92 444137554 444137464 6.240000e-12 82.4
6 TraesCS3A01G257300 chr3D 95.337 772 27 8 770 1536 359603251 359604018 0.000000e+00 1218.0
7 TraesCS3A01G257300 chr3D 88.841 932 89 13 1791 2719 359618702 359619621 0.000000e+00 1131.0
8 TraesCS3A01G257300 chr3D 87.234 376 34 5 105 467 359602300 359602674 1.510000e-112 416.0
9 TraesCS3A01G257300 chr3D 76.637 672 118 26 1022 1671 359528146 359528800 4.340000e-88 335.0
10 TraesCS3A01G257300 chr3D 85.646 209 18 9 1598 1798 359604036 359604240 2.740000e-50 209.0
11 TraesCS3A01G257300 chr3D 94.495 109 6 0 1 109 359602053 359602161 4.660000e-38 169.0
12 TraesCS3A01G257300 chr3D 79.803 203 35 6 2256 2456 523191732 523191930 2.820000e-30 143.0
13 TraesCS3A01G257300 chr3D 78.537 205 35 9 2256 2456 498843309 498843508 2.840000e-25 126.0
14 TraesCS3A01G257300 chr3D 87.097 93 11 1 678 769 359603133 359603225 1.330000e-18 104.0
15 TraesCS3A01G257300 chr3D 86.517 89 7 4 517 604 359602677 359602761 2.880000e-15 93.5
16 TraesCS3A01G257300 chr4A 81.463 205 31 7 2255 2456 683610040 683610240 7.790000e-36 161.0
17 TraesCS3A01G257300 chr6B 80.905 199 28 8 2258 2454 34442421 34442611 6.070000e-32 148.0
18 TraesCS3A01G257300 chr5A 88.889 108 11 1 2 108 468882068 468881961 6.110000e-27 132.0
19 TraesCS3A01G257300 chr6A 81.879 149 19 8 2312 2456 535433601 535433457 4.760000e-23 119.0
20 TraesCS3A01G257300 chr1B 80.723 166 20 11 2289 2451 581108374 581108530 4.760000e-23 119.0
21 TraesCS3A01G257300 chr1B 97.222 36 1 0 2 37 40990962 40990997 8.130000e-06 62.1
22 TraesCS3A01G257300 chr2D 77.901 181 33 7 2278 2456 121373389 121373564 3.700000e-19 106.0
23 TraesCS3A01G257300 chr1D 82.407 108 14 4 2 105 25716339 25716445 3.730000e-14 89.8
24 TraesCS3A01G257300 chr4B 81.308 107 17 3 1 106 237140330 237140434 1.730000e-12 84.2
25 TraesCS3A01G257300 chr1A 97.222 36 1 0 2 37 26948973 26949008 8.130000e-06 62.1
26 TraesCS3A01G257300 chr2A 97.143 35 1 0 2 36 108519624 108519658 2.920000e-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 TraesCS3A01G257300 chr3A 479068824 479071542 2718 False 5022.00 5022 100.000000 1 2719 1 chr3A.!!$F1 2718
1 TraesCS3A01G257300 chr3B 465702846 465705537 2691 False 937.00 1506 89.103333 1 2253 3 chr3B.!!$F2 2252
2 TraesCS3A01G257300 chr3D 359618702 359619621 919 False 1131.00 1131 88.841000 1791 2719 1 chr3D.!!$F2 928
3 TraesCS3A01G257300 chr3D 359602053 359604240 2187 False 368.25 1218 89.387667 1 1798 6 chr3D.!!$F5 1797
4 TraesCS3A01G257300 chr3D 359528146 359528800 654 False 335.00 335 76.637000 1022 1671 1 chr3D.!!$F1 649

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
531 688 0.931005 CTCGAAGATTAAGCGGCACC 59.069 55.0 1.45 0.0 33.89 5.01 F
1569 2388 0.603975 GGCAGAGCCTTCAGAAACGT 60.604 55.0 0.00 0.0 46.69 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 2505 0.449388 GAAACGGCAAGAGGAGCATG 59.551 55.0 0.0 0.0 0.0 4.06 R
2673 3608 0.118346 TGGACTGACCCCCTATGTGT 59.882 55.0 0.0 0.0 38.0 3.72 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
98 99 5.485620 CTCTGGATCTCACATTCAAGAACA 58.514 41.667 0.00 0.00 0.00 3.18
122 266 9.277783 ACAATAGCAATTTACCTAGCTAGAATG 57.722 33.333 22.70 8.10 42.21 2.67
211 355 6.932960 GTGTTACCTAGTTGTCAACCTAACAT 59.067 38.462 18.95 4.50 0.00 2.71
300 455 7.208064 ACAGGAAGAAAATAGCTTATGGGTA 57.792 36.000 0.00 0.00 0.00 3.69
327 482 4.957684 TTTAAGGCCTAGGAGTAGATGC 57.042 45.455 14.75 0.00 0.00 3.91
390 547 1.968540 GCCTTGTTGAAGCTCCGCT 60.969 57.895 0.00 0.00 42.56 5.52
423 580 2.438021 ACACACTACCTGGTTGACACAT 59.562 45.455 15.16 0.00 0.00 3.21
460 617 1.226603 ACCACGATCGCTAACGCTC 60.227 57.895 16.60 0.00 39.84 5.03
476 633 1.134560 CGCTCCCACCACTACTTAGAC 59.865 57.143 0.00 0.00 0.00 2.59
478 635 2.816411 CTCCCACCACTACTTAGACCA 58.184 52.381 0.00 0.00 0.00 4.02
479 636 3.375699 CTCCCACCACTACTTAGACCAT 58.624 50.000 0.00 0.00 0.00 3.55
495 652 5.268131 AGACCATGCTATCTCTCCATAGA 57.732 43.478 0.00 0.00 0.00 1.98
526 683 5.289675 ACACAAGAATCTCGAAGATTAAGCG 59.710 40.000 9.23 0.00 44.41 4.68
527 684 4.806247 ACAAGAATCTCGAAGATTAAGCGG 59.194 41.667 9.23 3.23 44.41 5.52
531 688 0.931005 CTCGAAGATTAAGCGGCACC 59.069 55.000 1.45 0.00 33.89 5.01
544 701 2.281484 GCACCGTTGGAAGGAGCA 60.281 61.111 0.03 0.00 43.37 4.26
613 770 5.567138 AGCATTGTGACTACTATTTTGGC 57.433 39.130 0.00 0.00 0.00 4.52
615 772 4.399303 GCATTGTGACTACTATTTTGGCCT 59.601 41.667 3.32 0.00 0.00 5.19
616 773 5.677091 GCATTGTGACTACTATTTTGGCCTG 60.677 44.000 3.32 0.00 0.00 4.85
618 775 2.683362 GTGACTACTATTTTGGCCTGCC 59.317 50.000 3.32 0.00 0.00 4.85
634 810 2.439104 GCCCAGTCTGCCTCCCTAG 61.439 68.421 0.00 0.00 0.00 3.02
648 824 2.565645 CCTAGGCGATGGTCCCTCG 61.566 68.421 11.83 11.83 39.11 4.63
651 827 4.222847 GGCGATGGTCCCTCGTCC 62.223 72.222 16.61 14.02 38.37 4.79
653 829 3.900892 CGATGGTCCCTCGTCCCG 61.901 72.222 8.29 0.00 0.00 5.14
654 830 4.222847 GATGGTCCCTCGTCCCGC 62.223 72.222 0.00 0.00 0.00 6.13
661 837 4.824515 CCTCGTCCCGCCTCCTCT 62.825 72.222 0.00 0.00 0.00 3.69
662 838 3.213402 CTCGTCCCGCCTCCTCTC 61.213 72.222 0.00 0.00 0.00 3.20
663 839 4.816984 TCGTCCCGCCTCCTCTCC 62.817 72.222 0.00 0.00 0.00 3.71
664 840 4.824515 CGTCCCGCCTCCTCTCCT 62.825 72.222 0.00 0.00 0.00 3.69
665 841 2.601868 GTCCCGCCTCCTCTCCTA 59.398 66.667 0.00 0.00 0.00 2.94
666 842 1.529713 GTCCCGCCTCCTCTCCTAG 60.530 68.421 0.00 0.00 0.00 3.02
668 844 2.203567 CCGCCTCCTCTCCTAGGG 60.204 72.222 9.46 0.00 46.55 3.53
669 845 2.915137 CGCCTCCTCTCCTAGGGC 60.915 72.222 9.46 1.01 46.55 5.19
732 1505 4.927267 AACTGATGGTGGGATGAACTTA 57.073 40.909 0.00 0.00 0.00 2.24
837 1636 3.428862 GCATTTTTGGTCCCACCGATTAG 60.429 47.826 0.00 0.00 42.58 1.73
923 1725 4.948608 TTTTAGAAAGCACGTGTGACAA 57.051 36.364 18.38 1.60 0.00 3.18
927 1729 3.527533 AGAAAGCACGTGTGACAAGTTA 58.472 40.909 18.38 0.00 0.00 2.24
943 1745 3.887621 AGTTAAGCATAGCACTCGGAA 57.112 42.857 0.00 0.00 0.00 4.30
1474 2286 2.026905 GCCTCGTGAGATTCTCCCTCT 61.027 57.143 11.12 0.00 40.84 3.69
1485 2297 1.216710 CTCCCTCTTGACGCTGGAC 59.783 63.158 0.00 0.00 0.00 4.02
1536 2348 1.134610 CGTGGACGGGCTAGGTAAATT 60.135 52.381 0.00 0.00 35.37 1.82
1547 2366 5.066634 GGGCTAGGTAAATTTCTCAGAAAGC 59.933 44.000 5.94 0.51 0.00 3.51
1548 2367 5.220681 GGCTAGGTAAATTTCTCAGAAAGCG 60.221 44.000 5.94 0.00 0.00 4.68
1569 2388 0.603975 GGCAGAGCCTTCAGAAACGT 60.604 55.000 0.00 0.00 46.69 3.99
1570 2389 1.337823 GGCAGAGCCTTCAGAAACGTA 60.338 52.381 0.00 0.00 46.69 3.57
1571 2390 1.727335 GCAGAGCCTTCAGAAACGTAC 59.273 52.381 0.00 0.00 0.00 3.67
1572 2391 2.610727 GCAGAGCCTTCAGAAACGTACT 60.611 50.000 0.00 0.00 0.00 2.73
1577 2396 2.666994 GCCTTCAGAAACGTACTGTAGC 59.333 50.000 17.84 15.32 36.81 3.58
1581 2400 4.156664 TCAGAAACGTACTGTAGCTGAC 57.843 45.455 17.84 0.00 36.52 3.51
1592 2411 3.685756 ACTGTAGCTGACTTCGTCTAGTC 59.314 47.826 0.00 7.74 43.86 2.59
1605 2424 2.413239 CGTCTAGTCTGCCGTTTCGTTA 60.413 50.000 0.00 0.00 0.00 3.18
1616 2435 4.918583 TGCCGTTTCGTTAAATTTCATTCC 59.081 37.500 0.00 0.00 0.00 3.01
1698 2518 1.760192 AATGGTCATGCTCCTCTTGC 58.240 50.000 7.95 0.00 0.00 4.01
1703 2523 0.036732 TCATGCTCCTCTTGCCGTTT 59.963 50.000 0.00 0.00 0.00 3.60
1708 2528 0.035458 CTCCTCTTGCCGTTTCCTGT 59.965 55.000 0.00 0.00 0.00 4.00
1709 2529 0.472471 TCCTCTTGCCGTTTCCTGTT 59.528 50.000 0.00 0.00 0.00 3.16
1710 2530 0.875059 CCTCTTGCCGTTTCCTGTTC 59.125 55.000 0.00 0.00 0.00 3.18
1711 2531 1.543429 CCTCTTGCCGTTTCCTGTTCT 60.543 52.381 0.00 0.00 0.00 3.01
1712 2532 2.222027 CTCTTGCCGTTTCCTGTTCTT 58.778 47.619 0.00 0.00 0.00 2.52
1713 2533 2.618709 CTCTTGCCGTTTCCTGTTCTTT 59.381 45.455 0.00 0.00 0.00 2.52
1714 2534 3.020984 TCTTGCCGTTTCCTGTTCTTTT 58.979 40.909 0.00 0.00 0.00 2.27
1715 2535 3.066203 TCTTGCCGTTTCCTGTTCTTTTC 59.934 43.478 0.00 0.00 0.00 2.29
1716 2536 2.650322 TGCCGTTTCCTGTTCTTTTCT 58.350 42.857 0.00 0.00 0.00 2.52
1717 2537 2.357637 TGCCGTTTCCTGTTCTTTTCTG 59.642 45.455 0.00 0.00 0.00 3.02
1718 2538 2.357952 GCCGTTTCCTGTTCTTTTCTGT 59.642 45.455 0.00 0.00 0.00 3.41
1723 2543 5.163754 CGTTTCCTGTTCTTTTCTGTGTTCT 60.164 40.000 0.00 0.00 0.00 3.01
1748 2586 1.352017 TGTGTGATCTGTTCCTGGCAT 59.648 47.619 0.00 0.00 0.00 4.40
1758 2596 1.667724 GTTCCTGGCATTGATGAGTCG 59.332 52.381 0.00 0.00 0.00 4.18
1767 2605 3.796717 GCATTGATGAGTCGTGATTCGTA 59.203 43.478 0.00 0.00 40.80 3.43
1768 2606 4.317418 GCATTGATGAGTCGTGATTCGTAC 60.317 45.833 0.00 0.00 40.80 3.67
1778 2616 3.366724 TCGTGATTCGTACATTTGCAGTC 59.633 43.478 0.00 0.00 40.80 3.51
1823 2661 9.442047 TTGGTGTTTGTCAAGTTCATTTTTATT 57.558 25.926 0.00 0.00 0.00 1.40
1828 2666 9.900264 GTTTGTCAAGTTCATTTTTATTGTCAC 57.100 29.630 0.00 0.00 0.00 3.67
1850 2688 2.391616 TACTTGCTCTGCTGACATGG 57.608 50.000 0.00 0.00 0.00 3.66
1899 2737 3.701205 TGCTAACTCCTGAATGCTGAA 57.299 42.857 0.00 0.00 0.00 3.02
1937 2869 2.713895 TTGCTCAGACTTCAGAGACG 57.286 50.000 2.99 0.00 32.00 4.18
1950 2883 0.533032 AGAGACGCTTAAGGTGAGCC 59.467 55.000 4.29 0.00 36.81 4.70
2019 2952 1.396301 GAGCAGAGCACTCCAAATTCG 59.604 52.381 0.00 0.00 0.00 3.34
2027 2960 6.147164 CAGAGCACTCCAAATTCGTAAGTTTA 59.853 38.462 0.00 0.00 39.48 2.01
2061 2994 6.064846 ACTGCTATATAACATTGCTTGTGC 57.935 37.500 0.00 0.00 38.99 4.57
2071 3004 1.742761 TTGCTTGTGCTGCTATCCTC 58.257 50.000 0.00 0.00 40.48 3.71
2076 3009 1.995376 TGTGCTGCTATCCTCGGATA 58.005 50.000 0.00 5.60 36.17 2.59
2131 3064 2.494073 CAGATATTCTACCTCCCCGCTC 59.506 54.545 0.00 0.00 0.00 5.03
2153 3086 7.329499 GCTCCAATCTGATGATATATGTCTGT 58.671 38.462 0.89 0.00 31.70 3.41
2204 3137 8.457238 AGAGAATTTAAACTTCAGTTCTGCTT 57.543 30.769 4.61 0.00 37.25 3.91
2229 3162 3.996921 AGAGCCACAAGATCTGTCAAT 57.003 42.857 0.00 0.00 35.47 2.57
2282 3215 3.493272 CTTATACGATGCTAGGTGCTCG 58.507 50.000 0.00 0.00 43.06 5.03
2283 3216 0.598562 ATACGATGCTAGGTGCTCGG 59.401 55.000 0.00 0.00 42.34 4.63
2301 3234 1.810755 CGGGGAGGTGCTTAGAAAAAC 59.189 52.381 0.00 0.00 0.00 2.43
2303 3236 2.820197 GGGGAGGTGCTTAGAAAAACAG 59.180 50.000 0.00 0.00 0.00 3.16
2304 3237 2.229062 GGGAGGTGCTTAGAAAAACAGC 59.771 50.000 0.00 0.00 30.96 4.40
2306 3239 3.149981 GAGGTGCTTAGAAAAACAGCCT 58.850 45.455 0.00 0.00 31.11 4.58
2307 3240 2.887152 AGGTGCTTAGAAAAACAGCCTG 59.113 45.455 0.00 0.00 31.11 4.85
2309 3242 3.057946 GGTGCTTAGAAAAACAGCCTGAG 60.058 47.826 0.00 0.00 32.11 3.35
2323 3256 3.255149 CAGCCTGAGTTTTTCTGAAGCAT 59.745 43.478 0.00 0.00 0.00 3.79
2325 3258 3.254166 GCCTGAGTTTTTCTGAAGCATCA 59.746 43.478 0.00 0.00 0.00 3.07
2341 3274 9.409312 CTGAAGCATCAGTGTCTATTTCTATAG 57.591 37.037 10.80 0.00 46.60 1.31
2342 3275 9.136323 TGAAGCATCAGTGTCTATTTCTATAGA 57.864 33.333 0.00 0.00 40.30 1.98
2461 3395 5.712446 TGCATTGTACAAGGCCTTACAATTA 59.288 36.000 34.56 23.45 46.35 1.40
2490 3424 1.467035 GGTAGTAAGACACAGACGCCG 60.467 57.143 0.00 0.00 0.00 6.46
2491 3425 1.466167 GTAGTAAGACACAGACGCCGA 59.534 52.381 0.00 0.00 0.00 5.54
2497 3431 1.291877 GACACAGACGCCGAGCATTT 61.292 55.000 0.00 0.00 0.00 2.32
2521 3455 2.567615 AGCCATGAAACCGACTCTAACT 59.432 45.455 0.00 0.00 0.00 2.24
2530 3464 1.269831 CCGACTCTAACTGCCTATGCC 60.270 57.143 0.00 0.00 36.33 4.40
2532 3466 2.101582 CGACTCTAACTGCCTATGCCTT 59.898 50.000 0.00 0.00 36.33 4.35
2533 3467 3.430929 CGACTCTAACTGCCTATGCCTTT 60.431 47.826 0.00 0.00 36.33 3.11
2534 3468 4.518249 GACTCTAACTGCCTATGCCTTTT 58.482 43.478 0.00 0.00 36.33 2.27
2535 3469 4.518249 ACTCTAACTGCCTATGCCTTTTC 58.482 43.478 0.00 0.00 36.33 2.29
2540 3474 4.790765 ACTGCCTATGCCTTTTCTTTTC 57.209 40.909 0.00 0.00 36.33 2.29
2541 3475 4.151883 ACTGCCTATGCCTTTTCTTTTCA 58.848 39.130 0.00 0.00 36.33 2.69
2570 3505 1.411930 GGTTACCCCGCCCCATTTTAT 60.412 52.381 0.00 0.00 0.00 1.40
2579 3514 3.520569 CGCCCCATTTTATTGAAACAGG 58.479 45.455 0.00 0.00 0.00 4.00
2589 3524 2.957491 TTGAAACAGGGCACAACAAG 57.043 45.000 0.00 0.00 0.00 3.16
2605 3540 0.031857 CAAGCCACGAATGTTTGCCA 59.968 50.000 0.00 0.00 0.00 4.92
2620 3555 5.619220 TGTTTGCCAAGCCAGAAAATAAAT 58.381 33.333 0.00 0.00 0.00 1.40
2629 3564 6.983906 AGCCAGAAAATAAATCCATTAGGG 57.016 37.500 0.00 0.00 34.83 3.53
2641 3576 0.947244 CATTAGGGCATCTCCAACGC 59.053 55.000 0.00 0.00 36.21 4.84
2643 3578 0.107703 TTAGGGCATCTCCAACGCTG 60.108 55.000 0.00 0.00 36.21 5.18
2646 3581 2.437359 GCATCTCCAACGCTGGCT 60.437 61.111 0.00 0.00 43.17 4.75
2650 3585 4.020617 CTCCAACGCTGGCTCCCA 62.021 66.667 0.00 0.00 43.17 4.37
2656 3591 1.047801 AACGCTGGCTCCCAAATTTT 58.952 45.000 0.00 0.00 30.80 1.82
2660 3595 2.174360 GCTGGCTCCCAAATTTTCTCT 58.826 47.619 0.00 0.00 30.80 3.10
2671 3606 4.168760 CAAATTTTCTCTTGCATCCGTCC 58.831 43.478 0.00 0.00 0.00 4.79
2672 3607 2.859165 TTTTCTCTTGCATCCGTCCT 57.141 45.000 0.00 0.00 0.00 3.85
2673 3608 3.973206 TTTTCTCTTGCATCCGTCCTA 57.027 42.857 0.00 0.00 0.00 2.94
2674 3609 2.961526 TTCTCTTGCATCCGTCCTAC 57.038 50.000 0.00 0.00 0.00 3.18
2675 3610 1.847328 TCTCTTGCATCCGTCCTACA 58.153 50.000 0.00 0.00 0.00 2.74
2676 3611 1.476891 TCTCTTGCATCCGTCCTACAC 59.523 52.381 0.00 0.00 0.00 2.90
2677 3612 1.204704 CTCTTGCATCCGTCCTACACA 59.795 52.381 0.00 0.00 0.00 3.72
2678 3613 1.831106 TCTTGCATCCGTCCTACACAT 59.169 47.619 0.00 0.00 0.00 3.21
2692 3627 0.118346 ACACATAGGGGGTCAGTCCA 59.882 55.000 0.00 0.00 38.11 4.02
2693 3628 0.541863 CACATAGGGGGTCAGTCCAC 59.458 60.000 0.00 0.00 39.32 4.02
2702 3637 2.203379 TCAGTCCACGGACACGGA 60.203 61.111 18.21 9.57 46.76 4.69
2704 3639 0.322726 TCAGTCCACGGACACGGATA 60.323 55.000 18.21 0.00 46.76 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 266 3.762288 GGATTTGGGTCCTAACCTTGTTC 59.238 47.826 0.00 0.00 45.66 3.18
211 355 5.643348 CCATGCTTATTTGTATGATCGGCTA 59.357 40.000 0.00 0.00 32.93 3.93
300 455 4.995624 ACTCCTAGGCCTTAAAACAACT 57.004 40.909 12.58 0.00 0.00 3.16
342 497 1.379044 GGGTCACCCTGCCAATGAG 60.379 63.158 5.22 0.00 41.34 2.90
423 580 0.906066 TGCTGGGCAGATTACGGTTA 59.094 50.000 0.00 0.00 33.32 2.85
460 617 2.420129 GCATGGTCTAAGTAGTGGTGGG 60.420 54.545 0.00 0.00 0.00 4.61
476 633 5.012458 TGGTTTCTATGGAGAGATAGCATGG 59.988 44.000 0.00 0.00 32.33 3.66
478 635 5.604231 TGTGGTTTCTATGGAGAGATAGCAT 59.396 40.000 0.00 0.00 37.29 3.79
479 636 4.962362 TGTGGTTTCTATGGAGAGATAGCA 59.038 41.667 0.00 0.00 34.07 3.49
495 652 3.804036 TCGAGATTCTTGTGTGTGGTTT 58.196 40.909 0.82 0.00 0.00 3.27
526 683 3.056328 GCTCCTTCCAACGGTGCC 61.056 66.667 0.00 0.00 35.56 5.01
527 684 2.281484 TGCTCCTTCCAACGGTGC 60.281 61.111 0.00 0.00 40.48 5.01
531 688 1.884235 AAAGACTGCTCCTTCCAACG 58.116 50.000 0.00 0.00 0.00 4.10
566 723 7.073342 ACAAAACGATAAGATAGTCCTTTGC 57.927 36.000 0.00 0.00 0.00 3.68
613 770 4.106925 GGAGGCAGACTGGGCAGG 62.107 72.222 4.26 0.00 35.46 4.85
615 772 3.252585 TAGGGAGGCAGACTGGGCA 62.253 63.158 4.26 0.00 35.46 5.36
616 773 2.365635 TAGGGAGGCAGACTGGGC 60.366 66.667 4.26 0.00 0.00 5.36
618 775 3.962557 CCTAGGGAGGCAGACTGG 58.037 66.667 0.00 0.00 35.54 4.00
634 810 4.222847 GGACGAGGGACCATCGCC 62.223 72.222 27.27 23.44 43.91 5.54
648 824 1.529713 CTAGGAGAGGAGGCGGGAC 60.530 68.421 0.00 0.00 0.00 4.46
657 833 2.846754 GCCTGGCCCTAGGAGAGG 60.847 72.222 11.48 12.91 46.25 3.69
658 834 2.846754 GGCCTGGCCCTAGGAGAG 60.847 72.222 27.77 2.41 44.06 3.20
668 844 2.883386 CTCTTTATTGATCAGGCCTGGC 59.117 50.000 32.23 23.59 0.00 4.85
669 845 2.883386 GCTCTTTATTGATCAGGCCTGG 59.117 50.000 32.23 14.13 0.00 4.45
718 1491 3.375699 TCTCTCCTAAGTTCATCCCACC 58.624 50.000 0.00 0.00 0.00 4.61
732 1505 0.882474 CCGTTCACGTTCTCTCTCCT 59.118 55.000 0.00 0.00 37.74 3.69
755 1529 2.315794 CCCCATCCCCACCACATCA 61.316 63.158 0.00 0.00 0.00 3.07
796 1595 4.827087 CTCGCAGCGGCATCACCT 62.827 66.667 16.42 0.00 41.24 4.00
811 1610 0.388520 GTGGGACCAAAAATGCGCTC 60.389 55.000 9.73 0.00 0.00 5.03
815 1614 0.894835 ATCGGTGGGACCAAAAATGC 59.105 50.000 0.00 0.00 38.47 3.56
817 1616 4.042271 ACTAATCGGTGGGACCAAAAAT 57.958 40.909 0.00 0.00 38.47 1.82
819 1618 4.847990 ATACTAATCGGTGGGACCAAAA 57.152 40.909 0.00 0.00 38.47 2.44
923 1725 3.887621 TTCCGAGTGCTATGCTTAACT 57.112 42.857 0.00 0.00 0.00 2.24
927 1729 1.337823 ACGTTTCCGAGTGCTATGCTT 60.338 47.619 0.00 0.00 37.88 3.91
943 1745 2.203153 GCCCAGGTGTCACACGTT 60.203 61.111 0.00 0.00 34.83 3.99
1474 2286 1.000955 GAAGAGGAAGTCCAGCGTCAA 59.999 52.381 0.00 0.00 38.89 3.18
1485 2297 2.370647 GATCGGGGGCGAAGAGGAAG 62.371 65.000 0.00 0.00 0.00 3.46
1524 2336 5.220681 CGCTTTCTGAGAAATTTACCTAGCC 60.221 44.000 8.23 0.00 0.00 3.93
1528 2340 4.938226 CCTCGCTTTCTGAGAAATTTACCT 59.062 41.667 8.23 0.00 35.43 3.08
1536 2348 0.969149 TCTGCCTCGCTTTCTGAGAA 59.031 50.000 0.00 0.00 35.43 2.87
1561 2380 4.162096 AGTCAGCTACAGTACGTTTCTG 57.838 45.455 15.55 15.55 38.68 3.02
1581 2400 2.251893 GAAACGGCAGACTAGACGAAG 58.748 52.381 0.00 0.00 44.57 3.79
1592 2411 5.060446 GGAATGAAATTTAACGAAACGGCAG 59.940 40.000 0.00 0.00 36.07 4.85
1605 2424 7.484975 TGTAACAAGACAACGGAATGAAATTT 58.515 30.769 0.00 0.00 36.07 1.82
1685 2505 0.449388 GAAACGGCAAGAGGAGCATG 59.551 55.000 0.00 0.00 0.00 4.06
1698 2518 3.377172 ACACAGAAAAGAACAGGAAACGG 59.623 43.478 0.00 0.00 0.00 4.44
1703 2523 6.659242 AGAAAAGAACACAGAAAAGAACAGGA 59.341 34.615 0.00 0.00 0.00 3.86
1708 2528 7.040755 TCACACAGAAAAGAACACAGAAAAGAA 60.041 33.333 0.00 0.00 0.00 2.52
1709 2529 6.429692 TCACACAGAAAAGAACACAGAAAAGA 59.570 34.615 0.00 0.00 0.00 2.52
1710 2530 6.611381 TCACACAGAAAAGAACACAGAAAAG 58.389 36.000 0.00 0.00 0.00 2.27
1711 2531 6.567687 TCACACAGAAAAGAACACAGAAAA 57.432 33.333 0.00 0.00 0.00 2.29
1712 2532 6.599244 AGATCACACAGAAAAGAACACAGAAA 59.401 34.615 0.00 0.00 0.00 2.52
1713 2533 6.037500 CAGATCACACAGAAAAGAACACAGAA 59.962 38.462 0.00 0.00 0.00 3.02
1714 2534 5.525012 CAGATCACACAGAAAAGAACACAGA 59.475 40.000 0.00 0.00 0.00 3.41
1715 2535 5.295292 ACAGATCACACAGAAAAGAACACAG 59.705 40.000 0.00 0.00 0.00 3.66
1716 2536 5.185454 ACAGATCACACAGAAAAGAACACA 58.815 37.500 0.00 0.00 0.00 3.72
1717 2537 5.741388 ACAGATCACACAGAAAAGAACAC 57.259 39.130 0.00 0.00 0.00 3.32
1718 2538 5.296780 GGAACAGATCACACAGAAAAGAACA 59.703 40.000 0.00 0.00 0.00 3.18
1723 2543 4.136796 CCAGGAACAGATCACACAGAAAA 58.863 43.478 0.00 0.00 0.00 2.29
1748 2586 4.428615 TGTACGAATCACGACTCATCAA 57.571 40.909 0.00 0.00 45.77 2.57
1758 2596 4.436050 CCAGACTGCAAATGTACGAATCAC 60.436 45.833 0.00 0.00 0.00 3.06
1778 2616 3.680937 CCAATTAAACAATGTGCAGCCAG 59.319 43.478 0.00 0.00 0.00 4.85
1823 2661 1.068588 AGCAGAGCAAGTAACGTGACA 59.931 47.619 5.68 0.00 0.00 3.58
1828 2666 1.783284 TGTCAGCAGAGCAAGTAACG 58.217 50.000 0.00 0.00 0.00 3.18
1850 2688 5.127845 TCAGGATATCAGACCTCTTTGTCAC 59.872 44.000 4.83 0.00 37.73 3.67
1856 2694 5.136068 TGTCTCAGGATATCAGACCTCTT 57.864 43.478 15.45 0.00 36.49 2.85
1899 2737 9.597170 CTGAGCAATATATGTAGTATCAGCAAT 57.403 33.333 0.00 0.00 0.00 3.56
1950 2883 3.454082 GGGCAGGATCATAGGAATAGGAG 59.546 52.174 0.00 0.00 0.00 3.69
2061 2994 3.761218 AGTCACATATCCGAGGATAGCAG 59.239 47.826 16.01 11.13 40.01 4.24
2071 3004 7.515215 CGACAAGTTTCATTAGTCACATATCCG 60.515 40.741 0.00 0.00 0.00 4.18
2076 3009 5.547465 TCCGACAAGTTTCATTAGTCACAT 58.453 37.500 0.00 0.00 0.00 3.21
2131 3064 9.152595 CAAGACAGACATATATCATCAGATTGG 57.847 37.037 0.00 0.00 35.67 3.16
2153 3086 4.922206 ACCATCCAAAAGATAGCACAAGA 58.078 39.130 0.00 0.00 32.37 3.02
2215 3148 4.897509 TGTCCAGATTGACAGATCTTGT 57.102 40.909 0.00 0.00 44.55 3.16
2229 3162 2.683968 GTTCTTGCACGTATGTCCAGA 58.316 47.619 0.00 0.00 0.00 3.86
2253 3186 3.299340 AGCATCGTATAAGGCCTAACG 57.701 47.619 22.60 22.60 36.71 3.18
2282 3215 2.820197 CTGTTTTTCTAAGCACCTCCCC 59.180 50.000 0.00 0.00 0.00 4.81
2283 3216 2.229062 GCTGTTTTTCTAAGCACCTCCC 59.771 50.000 0.00 0.00 36.91 4.30
2301 3234 2.620115 TGCTTCAGAAAAACTCAGGCTG 59.380 45.455 8.58 8.58 0.00 4.85
2303 3236 3.254166 TGATGCTTCAGAAAAACTCAGGC 59.746 43.478 0.00 0.00 0.00 4.85
2317 3250 9.973450 TTCTATAGAAATAGACACTGATGCTTC 57.027 33.333 12.87 0.00 43.03 3.86
2361 3294 4.030977 CGGTGCTTATTTGTACACGTAGAC 59.969 45.833 0.00 0.00 33.81 2.59
2362 3295 4.082841 TCGGTGCTTATTTGTACACGTAGA 60.083 41.667 0.00 0.00 33.81 2.59
2423 3357 3.505386 ACAATGCAAGGTGTTTATGGGA 58.495 40.909 0.00 0.00 0.00 4.37
2461 3395 3.080319 GTGTCTTACTACCTCTCCGTGT 58.920 50.000 0.00 0.00 0.00 4.49
2490 3424 3.256558 GGTTTCATGGCTTCAAATGCTC 58.743 45.455 0.00 0.00 0.00 4.26
2491 3425 2.353011 CGGTTTCATGGCTTCAAATGCT 60.353 45.455 0.00 0.00 0.00 3.79
2497 3431 1.347707 AGAGTCGGTTTCATGGCTTCA 59.652 47.619 0.00 0.00 0.00 3.02
2521 3455 5.304101 TCTTTGAAAAGAAAAGGCATAGGCA 59.696 36.000 0.15 0.00 41.75 4.75
2570 3505 1.134848 GCTTGTTGTGCCCTGTTTCAA 60.135 47.619 0.00 0.00 0.00 2.69
2589 3524 1.284297 GCTTGGCAAACATTCGTGGC 61.284 55.000 0.00 0.00 40.55 5.01
2594 3529 2.818130 TTCTGGCTTGGCAAACATTC 57.182 45.000 0.00 0.00 0.00 2.67
2605 3540 6.183361 GCCCTAATGGATTTATTTTCTGGCTT 60.183 38.462 0.00 0.00 35.39 4.35
2620 3555 1.140852 CGTTGGAGATGCCCTAATGGA 59.859 52.381 0.00 0.00 35.39 3.41
2641 3576 3.615834 GCAAGAGAAAATTTGGGAGCCAG 60.616 47.826 0.00 0.00 33.81 4.85
2643 3578 2.299867 TGCAAGAGAAAATTTGGGAGCC 59.700 45.455 0.00 0.00 0.00 4.70
2646 3581 3.193267 CGGATGCAAGAGAAAATTTGGGA 59.807 43.478 0.00 0.00 0.00 4.37
2650 3585 4.082125 AGGACGGATGCAAGAGAAAATTT 58.918 39.130 0.00 0.00 0.00 1.82
2656 3591 1.476891 GTGTAGGACGGATGCAAGAGA 59.523 52.381 0.00 0.00 0.00 3.10
2660 3595 3.452755 CTATGTGTAGGACGGATGCAA 57.547 47.619 0.00 0.00 0.00 4.08
2671 3606 2.040178 GGACTGACCCCCTATGTGTAG 58.960 57.143 0.00 0.00 0.00 2.74
2672 3607 1.363280 TGGACTGACCCCCTATGTGTA 59.637 52.381 0.00 0.00 38.00 2.90
2673 3608 0.118346 TGGACTGACCCCCTATGTGT 59.882 55.000 0.00 0.00 38.00 3.72
2674 3609 0.541863 GTGGACTGACCCCCTATGTG 59.458 60.000 0.00 0.00 38.00 3.21
2675 3610 0.976073 CGTGGACTGACCCCCTATGT 60.976 60.000 0.00 0.00 38.00 2.29
2676 3611 1.686325 CCGTGGACTGACCCCCTATG 61.686 65.000 0.00 0.00 38.00 2.23
2677 3612 1.382695 CCGTGGACTGACCCCCTAT 60.383 63.158 0.00 0.00 38.00 2.57
2678 3613 2.038329 CCGTGGACTGACCCCCTA 59.962 66.667 0.00 0.00 38.00 3.53
2687 3622 1.651240 CGTATCCGTGTCCGTGGACT 61.651 60.000 19.17 2.08 44.80 3.85
2692 3627 1.678635 TTCCCGTATCCGTGTCCGT 60.679 57.895 0.00 0.00 0.00 4.69
2693 3628 1.226773 GTTCCCGTATCCGTGTCCG 60.227 63.158 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.