Multiple sequence alignment - TraesCS2B01G624800

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 TraesCS2B01G624800 chr2B 100.000 2792 0 0 1 2792 797931322 797934113 0.000000e+00 5156.0
1 TraesCS2B01G624800 chr2B 90.374 1766 136 24 1 1761 797877710 797879446 0.000000e+00 2289.0
2 TraesCS2B01G624800 chr2B 80.629 604 97 14 1795 2390 797879513 797880104 1.530000e-122 449.0
3 TraesCS2B01G624800 chrUn 86.284 1655 188 22 935 2570 308430041 308428407 0.000000e+00 1762.0
4 TraesCS2B01G624800 chrUn 87.102 1287 151 13 1120 2398 275309086 275307807 0.000000e+00 1443.0
5 TraesCS2B01G624800 chrUn 86.350 674 84 6 1112 1781 15334952 15335621 0.000000e+00 728.0
6 TraesCS2B01G624800 chrUn 82.759 522 62 10 1878 2399 275307632 275307139 9.180000e-120 440.0
7 TraesCS2B01G624800 chrUn 88.732 284 24 7 87 365 15337568 15337848 9.580000e-90 340.0
8 TraesCS2B01G624800 chrUn 100.000 29 0 0 2591 2619 308428410 308428382 1.000000e-03 54.7


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 TraesCS2B01G624800 chr2B 797931322 797934113 2791 False 5156.00 5156 100.0000 1 2792 1 chr2B.!!$F1 2791
1 TraesCS2B01G624800 chr2B 797877710 797880104 2394 False 1369.00 2289 85.5015 1 2390 2 chr2B.!!$F2 2389
2 TraesCS2B01G624800 chrUn 275307139 275309086 1947 True 941.50 1443 84.9305 1120 2399 2 chrUn.!!$R1 1279
3 TraesCS2B01G624800 chrUn 308428382 308430041 1659 True 908.35 1762 93.1420 935 2619 2 chrUn.!!$R2 1684
4 TraesCS2B01G624800 chrUn 15334952 15337848 2896 False 534.00 728 87.5410 87 1781 2 chrUn.!!$F1 1694

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
855 856 0.328258 ACCCAAGAACGGATCCAAGG 59.672 55.0 13.41 3.51 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 2203 0.1023 AAAACACGAAAGCCTGCACC 59.898 50.0 0.0 0.0 0.0 5.01 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
28 29 1.462869 CGGCTACGTTGCGGTTTTTAG 60.463 52.381 18.61 0.00 34.81 1.85
29 30 1.598894 GCTACGTTGCGGTTTTTAGC 58.401 50.000 6.17 0.00 0.00 3.09
101 102 9.445878 AATTTAGGTAGTTACTGGAAGCTAAAC 57.554 33.333 15.67 0.00 41.79 2.01
242 243 9.956797 GGATTGAAACATCGAAATTTAATTGTG 57.043 29.630 0.00 0.00 0.00 3.33
370 371 9.599866 AACCTTCTAAAGTTTCAAAAGGAAATG 57.400 29.630 21.47 4.54 46.55 2.32
372 373 9.816354 CCTTCTAAAGTTTCAAAAGGAAATGAA 57.184 29.630 14.19 0.00 46.55 2.57
380 381 9.101655 AGTTTCAAAAGGAAATGAAAAGTGATG 57.898 29.630 2.82 0.00 46.55 3.07
386 387 7.543359 AAGGAAATGAAAAGTGATGGATTGA 57.457 32.000 0.00 0.00 0.00 2.57
388 389 8.827832 AGGAAATGAAAAGTGATGGATTGATA 57.172 30.769 0.00 0.00 0.00 2.15
399 400 6.013553 AGTGATGGATTGATATTGGGAGAGAG 60.014 42.308 0.00 0.00 0.00 3.20
400 401 6.013898 GTGATGGATTGATATTGGGAGAGAGA 60.014 42.308 0.00 0.00 0.00 3.10
402 403 5.720162 TGGATTGATATTGGGAGAGAGAGA 58.280 41.667 0.00 0.00 0.00 3.10
403 404 5.779260 TGGATTGATATTGGGAGAGAGAGAG 59.221 44.000 0.00 0.00 0.00 3.20
404 405 5.779771 GGATTGATATTGGGAGAGAGAGAGT 59.220 44.000 0.00 0.00 0.00 3.24
405 406 6.295236 GGATTGATATTGGGAGAGAGAGAGTG 60.295 46.154 0.00 0.00 0.00 3.51
406 407 4.478203 TGATATTGGGAGAGAGAGAGTGG 58.522 47.826 0.00 0.00 0.00 4.00
407 408 4.168871 TGATATTGGGAGAGAGAGAGTGGA 59.831 45.833 0.00 0.00 0.00 4.02
408 409 2.523325 TTGGGAGAGAGAGAGTGGAG 57.477 55.000 0.00 0.00 0.00 3.86
409 410 1.675007 TGGGAGAGAGAGAGTGGAGA 58.325 55.000 0.00 0.00 0.00 3.71
415 416 5.838521 GGGAGAGAGAGAGTGGAGAAATAAT 59.161 44.000 0.00 0.00 0.00 1.28
421 422 5.983540 AGAGAGTGGAGAAATAATGTGTCC 58.016 41.667 0.00 0.00 0.00 4.02
423 424 5.738909 AGAGTGGAGAAATAATGTGTCCTG 58.261 41.667 0.00 0.00 0.00 3.86
483 484 2.813172 TGCATGCGTCTTGATGAAGAAA 59.187 40.909 14.09 0.00 40.00 2.52
515 516 9.971922 ACACAAAAATCTAAAGAAGGAATCAAG 57.028 29.630 0.00 0.00 0.00 3.02
516 517 9.971922 CACAAAAATCTAAAGAAGGAATCAAGT 57.028 29.630 0.00 0.00 0.00 3.16
544 545 5.762179 ACAAGAGTGATTGGGATACTTGA 57.238 39.130 0.00 0.00 37.34 3.02
555 556 1.221414 GATACTTGATGAGGTGCCGC 58.779 55.000 0.00 0.00 0.00 6.53
560 561 1.830587 TTGATGAGGTGCCGCTCTGT 61.831 55.000 0.00 0.00 0.00 3.41
589 590 1.378911 TAGTTCACCGGCGGCTAGA 60.379 57.895 28.71 19.03 0.00 2.43
598 599 1.069258 GGCGGCTAGATACCACCAC 59.931 63.158 0.00 0.00 29.24 4.16
624 625 1.463444 GAATTACACCACACGAGCACC 59.537 52.381 0.00 0.00 0.00 5.01
629 630 0.813610 CACCACACGAGCACCTTTCA 60.814 55.000 0.00 0.00 0.00 2.69
689 690 1.598130 GCGTTGCTTCCTGGACACT 60.598 57.895 0.00 0.00 0.00 3.55
806 807 3.755378 CCATCCACACTCTTTCTCTTTGG 59.245 47.826 0.00 0.00 0.00 3.28
810 811 4.080582 TCCACACTCTTTCTCTTTGGTTGA 60.081 41.667 0.00 0.00 0.00 3.18
816 817 3.134081 TCTTTCTCTTTGGTTGACCTCGT 59.866 43.478 1.34 0.00 36.82 4.18
822 823 1.052124 TTGGTTGACCTCGTGACCCT 61.052 55.000 1.34 0.00 36.82 4.34
829 830 1.207329 GACCTCGTGACCCTGCTTAAT 59.793 52.381 0.00 0.00 0.00 1.40
831 832 2.039879 ACCTCGTGACCCTGCTTAATTT 59.960 45.455 0.00 0.00 0.00 1.82
855 856 0.328258 ACCCAAGAACGGATCCAAGG 59.672 55.000 13.41 3.51 0.00 3.61
905 906 6.038271 GGTGATCTTTCTCTCTCACTCTCTAC 59.962 46.154 0.00 0.00 38.41 2.59
906 907 6.038271 GTGATCTTTCTCTCTCACTCTCTACC 59.962 46.154 0.00 0.00 36.07 3.18
907 908 4.850680 TCTTTCTCTCTCACTCTCTACCC 58.149 47.826 0.00 0.00 0.00 3.69
913 914 5.849475 TCTCTCTCACTCTCTACCCATCTAT 59.151 44.000 0.00 0.00 0.00 1.98
914 915 6.331572 TCTCTCTCACTCTCTACCCATCTATT 59.668 42.308 0.00 0.00 0.00 1.73
915 916 7.514473 TCTCTCTCACTCTCTACCCATCTATTA 59.486 40.741 0.00 0.00 0.00 0.98
916 917 8.225863 TCTCTCACTCTCTACCCATCTATTAT 57.774 38.462 0.00 0.00 0.00 1.28
917 918 8.106462 TCTCTCACTCTCTACCCATCTATTATG 58.894 40.741 0.00 0.00 0.00 1.90
918 919 7.990055 TCTCACTCTCTACCCATCTATTATGA 58.010 38.462 0.00 0.00 0.00 2.15
919 920 8.448816 TCTCACTCTCTACCCATCTATTATGAA 58.551 37.037 0.00 0.00 0.00 2.57
920 921 9.253832 CTCACTCTCTACCCATCTATTATGAAT 57.746 37.037 0.00 0.00 0.00 2.57
948 949 2.658285 TCATGGGTTCATTGATCAGCC 58.342 47.619 0.00 0.50 0.00 4.85
958 959 5.767816 TCATTGATCAGCCAATCTCATTG 57.232 39.130 0.00 0.00 39.94 2.82
1206 1208 2.353803 GCTTCGCCTGAGGAAGAAACTA 60.354 50.000 0.65 0.00 42.74 2.24
1375 1377 2.412847 GGAAGATTTGAGCGGTTTGTCG 60.413 50.000 0.00 0.00 0.00 4.35
1442 1444 5.463724 CACTTTCTCACTACAGGTTTCTCAC 59.536 44.000 0.00 0.00 0.00 3.51
1447 1449 5.598830 TCTCACTACAGGTTTCTCACTTCTT 59.401 40.000 0.00 0.00 0.00 2.52
1449 1451 4.681942 CACTACAGGTTTCTCACTTCTTCG 59.318 45.833 0.00 0.00 0.00 3.79
1452 1454 4.310769 ACAGGTTTCTCACTTCTTCGATG 58.689 43.478 0.00 0.00 0.00 3.84
1555 1557 3.334583 TTGTGGAAGAGTATGGCAGAC 57.665 47.619 3.58 3.58 0.00 3.51
1568 1570 1.156645 GGCAGACTCGCATTGCTAGG 61.157 60.000 13.97 3.52 37.93 3.02
1609 1611 3.744238 AGGCGCCACTTAAAAATTGTT 57.256 38.095 31.54 0.00 0.00 2.83
1612 1614 4.038162 AGGCGCCACTTAAAAATTGTTACA 59.962 37.500 31.54 0.00 0.00 2.41
1614 1616 5.164002 GGCGCCACTTAAAAATTGTTACATG 60.164 40.000 24.80 0.00 0.00 3.21
1615 1617 5.667644 GCGCCACTTAAAAATTGTTACATGC 60.668 40.000 0.00 0.00 0.00 4.06
1616 1618 5.403766 CGCCACTTAAAAATTGTTACATGCA 59.596 36.000 0.00 0.00 0.00 3.96
1617 1619 6.074088 CGCCACTTAAAAATTGTTACATGCAA 60.074 34.615 0.00 0.00 0.00 4.08
1781 1786 9.533983 CATATTTCGATTCAATATGGTTCGAAG 57.466 33.333 15.87 6.00 45.88 3.79
1782 1787 7.786178 ATTTCGATTCAATATGGTTCGAAGA 57.214 32.000 15.33 10.27 45.88 2.87
1802 1837 4.822026 AGACATGGCTAAAGTGACTACAC 58.178 43.478 0.00 0.00 46.24 2.90
1917 1952 7.639113 TTCCACAAGAAGTTATTTCAGTTGT 57.361 32.000 0.00 0.00 35.65 3.32
1923 1958 9.072294 ACAAGAAGTTATTTCAGTTGTTTTTCG 57.928 29.630 0.00 0.00 38.31 3.46
1974 2009 2.611473 CGTGGAGCTCAACTGATGAAGT 60.611 50.000 19.09 0.00 42.60 3.01
1976 2011 2.634453 TGGAGCTCAACTGATGAAGTGA 59.366 45.455 17.19 0.00 39.81 3.41
2015 2050 0.467384 CTGGCCACCTCTACAGATGG 59.533 60.000 0.00 0.00 32.86 3.51
2037 2072 4.037923 GGAAGTTTTCTTTGCACCTCATGA 59.962 41.667 0.00 0.00 40.61 3.07
2038 2073 5.451798 GGAAGTTTTCTTTGCACCTCATGAA 60.452 40.000 0.00 0.00 40.61 2.57
2044 2079 7.465353 TTTCTTTGCACCTCATGAATCATTA 57.535 32.000 0.00 0.00 0.00 1.90
2045 2080 7.649533 TTCTTTGCACCTCATGAATCATTAT 57.350 32.000 0.00 0.00 0.00 1.28
2046 2081 7.649533 TCTTTGCACCTCATGAATCATTATT 57.350 32.000 0.00 0.00 0.00 1.40
2047 2082 7.709947 TCTTTGCACCTCATGAATCATTATTC 58.290 34.615 0.00 0.00 41.69 1.75
2093 2131 6.609616 ACAAAAGGAGGAGGAAATACAAACAA 59.390 34.615 0.00 0.00 0.00 2.83
2106 2144 9.213799 GGAAATACAAACAAAGGCAATTGATTA 57.786 29.630 10.34 0.00 34.38 1.75
2117 2155 8.533965 CAAAGGCAATTGATTATTTCATACGTG 58.466 33.333 10.34 0.00 33.34 4.49
2119 2157 7.642669 AGGCAATTGATTATTTCATACGTGAG 58.357 34.615 10.34 0.00 35.39 3.51
2122 2160 7.416817 CAATTGATTATTTCATACGTGAGCCA 58.583 34.615 0.00 0.00 35.39 4.75
2165 2203 0.888736 TTGGTTCTCGGCACATGGTG 60.889 55.000 0.00 0.00 36.51 4.17
2211 2249 3.264450 CAGATCACCAAAACTAGGAGGGT 59.736 47.826 0.00 0.00 0.00 4.34
2212 2250 3.916989 AGATCACCAAAACTAGGAGGGTT 59.083 43.478 0.00 0.00 0.00 4.11
2240 2278 2.494073 AGAAGGCGGTAGAAGTTCAGAG 59.506 50.000 5.50 0.00 0.00 3.35
2261 2300 2.554462 GTTGGGAGCAGAGAAAAGGTTC 59.446 50.000 0.00 0.00 0.00 3.62
2274 2313 7.222805 CAGAGAAAAGGTTCCTTTTTGCTTAAC 59.777 37.037 24.40 13.40 43.62 2.01
2300 2339 4.513318 GCCTCTATGAGATGGTTTGCTTAC 59.487 45.833 0.00 0.00 0.00 2.34
2304 2343 2.422597 TGAGATGGTTTGCTTACGTGG 58.577 47.619 0.00 0.00 0.00 4.94
2308 2347 1.081442 GGTTTGCTTACGTGGCAGC 60.081 57.895 15.43 12.22 40.90 5.25
2362 2402 1.474330 CCACTTGTTTATCCCTGCCC 58.526 55.000 0.00 0.00 0.00 5.36
2395 2435 7.056006 TGTAGACATGGATGTGCTTGATATTT 58.944 34.615 0.00 0.00 41.95 1.40
2397 2437 9.224267 GTAGACATGGATGTGCTTGATATTTAT 57.776 33.333 0.00 0.00 41.95 1.40
2398 2438 8.332996 AGACATGGATGTGCTTGATATTTATC 57.667 34.615 0.00 0.00 41.95 1.75
2399 2439 7.940688 AGACATGGATGTGCTTGATATTTATCA 59.059 33.333 0.00 0.00 41.95 2.15
2400 2440 8.645814 ACATGGATGTGCTTGATATTTATCAT 57.354 30.769 0.00 0.00 39.79 2.45
2401 2441 9.085645 ACATGGATGTGCTTGATATTTATCATT 57.914 29.630 0.00 0.00 39.79 2.57
2493 2579 1.602311 AGTGCATAGCATTAGCAGGC 58.398 50.000 0.00 0.00 45.49 4.85
2547 2637 4.839668 TTTAACCACCGGTCTGAATTTG 57.160 40.909 2.59 0.00 33.12 2.32
2553 2643 1.953686 ACCGGTCTGAATTTGTTGGTG 59.046 47.619 0.00 0.00 0.00 4.17
2569 2659 1.811965 TGGTGGCATCGTCAAAATCTG 59.188 47.619 0.00 0.00 0.00 2.90
2574 2664 3.317711 TGGCATCGTCAAAATCTGTTTGT 59.682 39.130 0.00 0.00 0.00 2.83
2575 2665 4.517075 TGGCATCGTCAAAATCTGTTTGTA 59.483 37.500 0.00 0.00 0.00 2.41
2577 2667 5.334879 GGCATCGTCAAAATCTGTTTGTACT 60.335 40.000 0.00 0.00 0.00 2.73
2579 2669 6.303259 GCATCGTCAAAATCTGTTTGTACTTC 59.697 38.462 0.00 0.00 0.00 3.01
2580 2670 6.912203 TCGTCAAAATCTGTTTGTACTTCA 57.088 33.333 0.00 0.00 0.00 3.02
2581 2671 6.711579 TCGTCAAAATCTGTTTGTACTTCAC 58.288 36.000 0.00 0.00 0.00 3.18
2582 2672 6.314152 TCGTCAAAATCTGTTTGTACTTCACA 59.686 34.615 0.00 0.00 34.51 3.58
2589 2679 4.897224 CTGTTTGTACTTCACACACACAG 58.103 43.478 7.21 7.21 41.71 3.66
2622 2712 1.470632 GCTCTGCTCTTCACGCTGTAT 60.471 52.381 0.00 0.00 0.00 2.29
2631 2721 5.349817 GCTCTTCACGCTGTATATTGCATAT 59.650 40.000 0.00 0.00 0.00 1.78
2632 2722 6.454848 GCTCTTCACGCTGTATATTGCATATC 60.455 42.308 0.00 0.00 0.00 1.63
2640 2730 6.587608 CGCTGTATATTGCATATCTTCAGACA 59.412 38.462 0.00 0.00 0.00 3.41
2653 2743 8.607459 CATATCTTCAGACAGAAACATACAACC 58.393 37.037 0.00 0.00 35.40 3.77
2654 2744 6.174720 TCTTCAGACAGAAACATACAACCT 57.825 37.500 0.00 0.00 35.40 3.50
2655 2745 6.223852 TCTTCAGACAGAAACATACAACCTC 58.776 40.000 0.00 0.00 35.40 3.85
2656 2746 4.894784 TCAGACAGAAACATACAACCTCC 58.105 43.478 0.00 0.00 0.00 4.30
2657 2747 4.593206 TCAGACAGAAACATACAACCTCCT 59.407 41.667 0.00 0.00 0.00 3.69
2658 2748 5.778241 TCAGACAGAAACATACAACCTCCTA 59.222 40.000 0.00 0.00 0.00 2.94
2659 2749 6.440647 TCAGACAGAAACATACAACCTCCTAT 59.559 38.462 0.00 0.00 0.00 2.57
2660 2750 7.618117 TCAGACAGAAACATACAACCTCCTATA 59.382 37.037 0.00 0.00 0.00 1.31
2662 2752 7.620094 AGACAGAAACATACAACCTCCTATACT 59.380 37.037 0.00 0.00 0.00 2.12
2674 2764 7.520410 ACAACCTCCTATACTACCTCCTATACT 59.480 40.741 0.00 0.00 0.00 2.12
2677 2767 7.743139 ACCTCCTATACTACCTCCTATACTGAA 59.257 40.741 0.00 0.00 0.00 3.02
2679 2769 7.631933 TCCTATACTACCTCCTATACTGAAGC 58.368 42.308 0.00 0.00 0.00 3.86
2707 2828 5.240623 CAGAGAGATACGACAGAATTAGGCT 59.759 44.000 0.00 0.00 0.00 4.58
2710 2853 6.300703 AGAGATACGACAGAATTAGGCTACT 58.699 40.000 0.00 0.00 0.00 2.57
2714 2857 2.693591 CGACAGAATTAGGCTACTGGGA 59.306 50.000 13.32 0.00 35.08 4.37
2717 2860 2.771943 CAGAATTAGGCTACTGGGACCA 59.228 50.000 0.00 0.00 0.00 4.02
2720 2863 0.974010 TTAGGCTACTGGGACCACGG 60.974 60.000 0.00 0.00 0.00 4.94
2739 2882 1.965754 GCTCGGAGTGCCTTGAGGAT 61.966 60.000 6.90 0.00 41.67 3.24
2743 2886 0.467804 GGAGTGCCTTGAGGATCTCC 59.532 60.000 18.23 18.23 43.53 3.71
2764 2907 1.144936 GGCCAGGACGATGAGGAAG 59.855 63.158 0.00 0.00 0.00 3.46
2765 2908 1.617947 GGCCAGGACGATGAGGAAGT 61.618 60.000 0.00 0.00 0.00 3.01
2782 2926 4.720902 TGGTCCTGCCATGCCGTG 62.721 66.667 0.00 0.00 43.61 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.030274 GTGTTACCACTCCACCATTTGC 60.030 50.000 0.00 0.00 38.61 3.68
29 30 3.004315 GTGTGTTACCACTCCACCATTTG 59.996 47.826 0.00 0.00 42.34 2.32
91 92 8.188139 TCATTTATTTCAATCCGTTTAGCTTCC 58.812 33.333 0.00 0.00 0.00 3.46
266 267 3.025262 ACGCCCAGACCTTTAAAACAAA 58.975 40.909 0.00 0.00 0.00 2.83
355 356 8.337532 CCATCACTTTTCATTTCCTTTTGAAAC 58.662 33.333 0.00 0.00 45.38 2.78
370 371 7.503566 TCTCCCAATATCAATCCATCACTTTTC 59.496 37.037 0.00 0.00 0.00 2.29
372 373 6.914665 TCTCCCAATATCAATCCATCACTTT 58.085 36.000 0.00 0.00 0.00 2.66
375 376 6.013898 TCTCTCTCCCAATATCAATCCATCAC 60.014 42.308 0.00 0.00 0.00 3.06
380 381 5.779771 ACTCTCTCTCTCCCAATATCAATCC 59.220 44.000 0.00 0.00 0.00 3.01
386 387 4.418526 TCTCCACTCTCTCTCTCCCAATAT 59.581 45.833 0.00 0.00 0.00 1.28
388 389 2.584965 TCTCCACTCTCTCTCTCCCAAT 59.415 50.000 0.00 0.00 0.00 3.16
399 400 5.814705 CAGGACACATTATTTCTCCACTCTC 59.185 44.000 0.00 0.00 0.00 3.20
400 401 5.249393 ACAGGACACATTATTTCTCCACTCT 59.751 40.000 0.00 0.00 0.00 3.24
402 403 5.221925 ACACAGGACACATTATTTCTCCACT 60.222 40.000 0.00 0.00 0.00 4.00
403 404 5.003804 ACACAGGACACATTATTTCTCCAC 58.996 41.667 0.00 0.00 0.00 4.02
404 405 5.003160 CACACAGGACACATTATTTCTCCA 58.997 41.667 0.00 0.00 0.00 3.86
405 406 5.003804 ACACACAGGACACATTATTTCTCC 58.996 41.667 0.00 0.00 0.00 3.71
406 407 6.874134 AGTACACACAGGACACATTATTTCTC 59.126 38.462 0.00 0.00 0.00 2.87
407 408 6.769512 AGTACACACAGGACACATTATTTCT 58.230 36.000 0.00 0.00 0.00 2.52
408 409 8.604035 CATAGTACACACAGGACACATTATTTC 58.396 37.037 0.00 0.00 0.00 2.17
409 410 8.100791 ACATAGTACACACAGGACACATTATTT 58.899 33.333 0.00 0.00 0.00 1.40
415 416 3.554129 GCACATAGTACACACAGGACACA 60.554 47.826 0.00 0.00 0.00 3.72
421 422 3.592898 TCCTGCACATAGTACACACAG 57.407 47.619 0.00 0.00 0.00 3.66
423 424 4.994852 TCTTTTCCTGCACATAGTACACAC 59.005 41.667 0.00 0.00 0.00 3.82
515 516 5.401531 TCCCAATCACTCTTGTGTAGTAC 57.598 43.478 0.00 0.00 44.14 2.73
516 517 6.895756 AGTATCCCAATCACTCTTGTGTAGTA 59.104 38.462 0.00 0.00 44.14 1.82
517 518 5.721960 AGTATCCCAATCACTCTTGTGTAGT 59.278 40.000 0.00 0.00 44.14 2.73
518 519 6.227298 AGTATCCCAATCACTCTTGTGTAG 57.773 41.667 0.00 0.00 44.14 2.74
535 536 1.871080 CGGCACCTCATCAAGTATCC 58.129 55.000 0.00 0.00 0.00 2.59
544 545 2.267006 CACAGAGCGGCACCTCAT 59.733 61.111 1.45 0.00 34.26 2.90
555 556 0.687354 ACTACCAGCCAACCACAGAG 59.313 55.000 0.00 0.00 0.00 3.35
560 561 3.717842 GTGAACTACCAGCCAACCA 57.282 52.632 0.00 0.00 0.00 3.67
582 583 1.362717 CGGTGGTGGTATCTAGCCG 59.637 63.158 0.00 0.00 0.00 5.52
589 590 0.539986 AATTCTCGCGGTGGTGGTAT 59.460 50.000 6.13 0.00 0.00 2.73
598 599 0.719465 GTGTGGTGTAATTCTCGCGG 59.281 55.000 6.13 0.00 0.00 6.46
624 625 4.334759 CAGCCAGGAATGTCACTATGAAAG 59.665 45.833 0.00 0.00 0.00 2.62
629 630 1.842562 AGCAGCCAGGAATGTCACTAT 59.157 47.619 0.00 0.00 0.00 2.12
689 690 0.104144 TGTGGAGAGGGAAGGGGAAA 60.104 55.000 0.00 0.00 0.00 3.13
777 778 4.971282 AGAAAGAGTGTGGATGGATGGATA 59.029 41.667 0.00 0.00 0.00 2.59
806 807 1.668151 GCAGGGTCACGAGGTCAAC 60.668 63.158 0.00 0.00 0.00 3.18
810 811 1.276622 ATTAAGCAGGGTCACGAGGT 58.723 50.000 0.00 0.00 0.00 3.85
816 817 3.761752 GGTAGCAAAATTAAGCAGGGTCA 59.238 43.478 5.04 0.00 0.00 4.02
822 823 5.563867 CGTTCTTGGGTAGCAAAATTAAGCA 60.564 40.000 5.04 0.00 0.00 3.91
829 830 2.642154 TCCGTTCTTGGGTAGCAAAA 57.358 45.000 0.00 0.00 0.00 2.44
831 832 1.065709 GGATCCGTTCTTGGGTAGCAA 60.066 52.381 0.00 0.00 0.00 3.91
915 916 9.772973 CAATGAACCCATGAATCATAAATTCAT 57.227 29.630 16.06 16.06 46.29 2.57
916 917 8.979534 TCAATGAACCCATGAATCATAAATTCA 58.020 29.630 13.82 13.82 41.59 2.57
917 918 9.991906 ATCAATGAACCCATGAATCATAAATTC 57.008 29.630 0.00 0.99 33.60 2.17
918 919 9.991906 GATCAATGAACCCATGAATCATAAATT 57.008 29.630 0.00 0.00 33.60 1.82
919 920 9.150028 TGATCAATGAACCCATGAATCATAAAT 57.850 29.630 0.00 0.00 33.35 1.40
920 921 8.536340 TGATCAATGAACCCATGAATCATAAA 57.464 30.769 0.00 0.00 33.35 1.40
925 926 4.261909 GGCTGATCAATGAACCCATGAATC 60.262 45.833 0.00 0.00 32.36 2.52
948 949 6.488006 AGAACCGGGAAATATCAATGAGATTG 59.512 38.462 6.32 0.00 41.57 2.67
958 959 7.660208 TGCTAAGAAATAGAACCGGGAAATATC 59.340 37.037 6.32 0.00 33.04 1.63
1206 1208 3.416156 GCACTCCTTGAAGACATCCTTT 58.584 45.455 0.00 0.00 34.68 3.11
1375 1377 1.535896 GACAAACCTTTCGGCTTCCTC 59.464 52.381 0.00 0.00 0.00 3.71
1442 1444 4.057406 AGAAGATGCCTCATCGAAGAAG 57.943 45.455 0.00 0.00 44.67 2.85
1447 1449 3.431346 CCTTCAAGAAGATGCCTCATCGA 60.431 47.826 11.25 0.00 44.67 3.59
1449 1451 2.617774 GCCTTCAAGAAGATGCCTCATC 59.382 50.000 11.25 0.00 40.79 2.92
1452 1454 2.119801 TGCCTTCAAGAAGATGCCTC 57.880 50.000 11.25 0.00 40.79 4.70
1555 1557 1.737838 TCAAACCCTAGCAATGCGAG 58.262 50.000 8.41 8.41 0.00 5.03
1568 1570 5.863935 GCCTTGTGATCTTTGTAATCAAACC 59.136 40.000 0.00 0.00 38.44 3.27
1630 1632 9.237187 TCCAACTATGTTTGTGCTTTCATATAA 57.763 29.630 0.00 0.00 0.00 0.98
1689 1691 6.773976 TCTTCAACCAAAGACTTGAATTGT 57.226 33.333 0.00 0.00 36.15 2.71
1777 1782 3.589988 AGTCACTTTAGCCATGTCTTCG 58.410 45.455 0.00 0.00 0.00 3.79
1781 1786 4.566004 TGTGTAGTCACTTTAGCCATGTC 58.434 43.478 0.00 0.00 44.14 3.06
1782 1787 4.617253 TGTGTAGTCACTTTAGCCATGT 57.383 40.909 0.00 0.00 44.14 3.21
1802 1837 4.708421 ACAAAATGGATCTGGACTCCAATG 59.292 41.667 0.00 0.04 45.57 2.82
1816 1851 5.163426 CCCATTAGCTATGCAACAAAATGGA 60.163 40.000 22.62 0.00 42.83 3.41
1917 1952 2.602660 GCTGAAAAACTGCAGCGAAAAA 59.397 40.909 15.27 0.00 46.66 1.94
2015 2050 5.186996 TCATGAGGTGCAAAGAAAACTTC 57.813 39.130 0.00 0.00 0.00 3.01
2037 2072 3.641906 ACTCCCGTCCGAGAATAATGATT 59.358 43.478 0.00 0.00 33.83 2.57
2038 2073 3.231818 ACTCCCGTCCGAGAATAATGAT 58.768 45.455 0.00 0.00 33.83 2.45
2044 2079 0.106619 AGCTACTCCCGTCCGAGAAT 60.107 55.000 0.00 0.00 33.83 2.40
2045 2080 0.323178 AAGCTACTCCCGTCCGAGAA 60.323 55.000 0.00 0.00 33.83 2.87
2046 2081 0.543277 TAAGCTACTCCCGTCCGAGA 59.457 55.000 0.00 0.00 33.83 4.04
2047 2082 0.662085 GTAAGCTACTCCCGTCCGAG 59.338 60.000 0.00 0.00 35.88 4.63
2093 2131 7.995289 TCACGTATGAAATAATCAATTGCCTT 58.005 30.769 0.00 0.00 42.54 4.35
2106 2144 4.100963 TCATACCTGGCTCACGTATGAAAT 59.899 41.667 16.74 0.00 43.19 2.17
2113 2151 1.511305 CGTCATACCTGGCTCACGT 59.489 57.895 0.00 0.00 0.00 4.49
2117 2155 2.288886 GGTATTCCGTCATACCTGGCTC 60.289 54.545 11.40 0.00 43.91 4.70
2119 2157 2.165319 GGTATTCCGTCATACCTGGC 57.835 55.000 11.40 0.00 43.91 4.85
2144 2182 0.452987 CCATGTGCCGAGAACCAATG 59.547 55.000 0.00 0.00 0.00 2.82
2151 2189 2.347114 CACCACCATGTGCCGAGA 59.653 61.111 0.00 0.00 31.34 4.04
2165 2203 0.102300 AAAACACGAAAGCCTGCACC 59.898 50.000 0.00 0.00 0.00 5.01
2211 2249 4.202326 ACTTCTACCGCCTTCTCTTTGAAA 60.202 41.667 0.00 0.00 33.79 2.69
2212 2250 3.323979 ACTTCTACCGCCTTCTCTTTGAA 59.676 43.478 0.00 0.00 0.00 2.69
2240 2278 2.278332 ACCTTTTCTCTGCTCCCAAC 57.722 50.000 0.00 0.00 0.00 3.77
2274 2313 4.040217 AGCAAACCATCTCATAGAGGCTAG 59.960 45.833 0.00 0.00 0.00 3.42
2300 2339 1.677576 ACCATGATAAATGCTGCCACG 59.322 47.619 0.00 0.00 0.00 4.94
2304 2343 7.306983 GCATAAAAAGACCATGATAAATGCTGC 60.307 37.037 0.00 0.00 34.61 5.25
2308 2347 7.924412 AGCTGCATAAAAAGACCATGATAAATG 59.076 33.333 1.02 0.00 0.00 2.32
2362 2402 2.768253 TCCATGTCTACAAGCCACAG 57.232 50.000 0.00 0.00 0.00 3.66
2374 2414 8.102800 TGATAAATATCAAGCACATCCATGTC 57.897 34.615 0.67 0.00 39.58 3.06
2395 2435 9.866655 AGTGCCTCCTTCAATTAATAAATGATA 57.133 29.630 0.00 0.00 0.00 2.15
2397 2437 7.833682 TGAGTGCCTCCTTCAATTAATAAATGA 59.166 33.333 0.00 0.00 0.00 2.57
2398 2438 7.999679 TGAGTGCCTCCTTCAATTAATAAATG 58.000 34.615 0.00 0.00 0.00 2.32
2399 2439 8.773033 ATGAGTGCCTCCTTCAATTAATAAAT 57.227 30.769 0.00 0.00 0.00 1.40
2400 2440 9.866655 ATATGAGTGCCTCCTTCAATTAATAAA 57.133 29.630 0.00 0.00 0.00 1.40
2401 2441 9.866655 AATATGAGTGCCTCCTTCAATTAATAA 57.133 29.630 0.00 0.00 0.00 1.40
2406 2482 6.894103 AGAAAATATGAGTGCCTCCTTCAATT 59.106 34.615 0.50 0.00 0.00 2.32
2440 2519 0.536233 AGCCATGCACAACCGTGTTA 60.536 50.000 0.00 0.00 45.50 2.41
2441 2520 1.391157 AAGCCATGCACAACCGTGTT 61.391 50.000 0.00 0.00 45.50 3.32
2443 2522 1.372004 CAAGCCATGCACAACCGTG 60.372 57.895 0.00 0.00 46.56 4.94
2444 2523 3.041701 CAAGCCATGCACAACCGT 58.958 55.556 0.00 0.00 0.00 4.83
2471 2550 2.551459 CCTGCTAATGCTATGCACTTCC 59.449 50.000 0.00 0.00 43.04 3.46
2493 2579 3.196007 ACTTCACACAACACAACAACG 57.804 42.857 0.00 0.00 0.00 4.10
2531 2620 1.269448 CCAACAAATTCAGACCGGTGG 59.731 52.381 14.63 3.59 0.00 4.61
2547 2637 2.228822 AGATTTTGACGATGCCACCAAC 59.771 45.455 0.00 0.00 0.00 3.77
2553 2643 3.900941 ACAAACAGATTTTGACGATGCC 58.099 40.909 3.81 0.00 33.83 4.40
2569 2659 4.630069 AGACTGTGTGTGTGAAGTACAAAC 59.370 41.667 0.00 0.00 45.97 2.93
2574 2664 2.483013 GGCAGACTGTGTGTGTGAAGTA 60.483 50.000 6.81 0.00 41.88 2.24
2575 2665 1.656652 GCAGACTGTGTGTGTGAAGT 58.343 50.000 6.81 0.00 41.88 3.01
2577 2667 0.251634 TGGCAGACTGTGTGTGTGAA 59.748 50.000 6.81 0.00 41.88 3.18
2579 2669 1.779025 GCTGGCAGACTGTGTGTGTG 61.779 60.000 20.86 0.00 42.18 3.82
2580 2670 1.524621 GCTGGCAGACTGTGTGTGT 60.525 57.895 20.86 0.00 0.00 3.72
2581 2671 1.226686 GAGCTGGCAGACTGTGTGTG 61.227 60.000 20.86 0.00 0.00 3.82
2582 2672 1.070445 GAGCTGGCAGACTGTGTGT 59.930 57.895 20.86 0.00 0.00 3.72
2589 2679 1.448189 CAGAGCAGAGCTGGCAGAC 60.448 63.158 20.86 11.32 39.88 3.51
2622 2712 8.969260 ATGTTTCTGTCTGAAGATATGCAATA 57.031 30.769 0.00 0.00 35.89 1.90
2631 2721 6.174720 AGGTTGTATGTTTCTGTCTGAAGA 57.825 37.500 0.00 0.00 35.89 2.87
2632 2722 5.409826 GGAGGTTGTATGTTTCTGTCTGAAG 59.590 44.000 0.00 0.00 35.89 3.02
2640 2730 8.066247 AGGTAGTATAGGAGGTTGTATGTTTCT 58.934 37.037 0.00 0.00 0.00 2.52
2644 2734 6.104392 AGGAGGTAGTATAGGAGGTTGTATGT 59.896 42.308 0.00 0.00 0.00 2.29
2653 2743 7.771826 GCTTCAGTATAGGAGGTAGTATAGGAG 59.228 44.444 0.00 0.00 0.00 3.69
2654 2744 7.239143 TGCTTCAGTATAGGAGGTAGTATAGGA 59.761 40.741 0.00 0.00 0.00 2.94
2655 2745 7.403671 TGCTTCAGTATAGGAGGTAGTATAGG 58.596 42.308 0.00 0.00 0.00 2.57
2656 2746 9.469097 AATGCTTCAGTATAGGAGGTAGTATAG 57.531 37.037 0.00 0.00 0.00 1.31
2657 2747 9.463902 GAATGCTTCAGTATAGGAGGTAGTATA 57.536 37.037 0.00 0.00 0.00 1.47
2658 2748 7.950684 TGAATGCTTCAGTATAGGAGGTAGTAT 59.049 37.037 0.00 0.00 34.08 2.12
2659 2749 7.295340 TGAATGCTTCAGTATAGGAGGTAGTA 58.705 38.462 0.00 0.00 34.08 1.82
2660 2750 6.136857 TGAATGCTTCAGTATAGGAGGTAGT 58.863 40.000 0.00 0.00 34.08 2.73
2674 2764 4.399303 TGTCGTATCTCTCTGAATGCTTCA 59.601 41.667 0.00 0.00 38.17 3.02
2677 2767 4.203226 TCTGTCGTATCTCTCTGAATGCT 58.797 43.478 0.00 0.00 0.00 3.79
2679 2769 7.807433 CCTAATTCTGTCGTATCTCTCTGAATG 59.193 40.741 0.00 0.00 32.09 2.67
2686 2807 6.205853 CAGTAGCCTAATTCTGTCGTATCTCT 59.794 42.308 0.00 0.00 0.00 3.10
2687 2808 6.375377 CAGTAGCCTAATTCTGTCGTATCTC 58.625 44.000 0.00 0.00 0.00 2.75
2695 2816 2.772515 GGTCCCAGTAGCCTAATTCTGT 59.227 50.000 0.00 0.00 0.00 3.41
2696 2817 2.771943 TGGTCCCAGTAGCCTAATTCTG 59.228 50.000 0.00 0.00 0.00 3.02
2707 2828 3.066190 CGAGCCGTGGTCCCAGTA 61.066 66.667 0.00 0.00 0.00 2.74
2720 2863 1.965754 ATCCTCAAGGCACTCCGAGC 61.966 60.000 0.00 0.00 38.49 5.03
2728 2871 0.984961 CCCAGGAGATCCTCAAGGCA 60.985 60.000 0.00 0.00 46.65 4.75
2733 2876 1.383664 CTGGCCCAGGAGATCCTCA 60.384 63.158 1.63 0.00 46.65 3.86
2734 2877 3.560989 CTGGCCCAGGAGATCCTC 58.439 66.667 1.63 0.00 46.65 3.71
2743 2886 2.503061 CTCATCGTCCTGGCCCAG 59.497 66.667 2.91 2.91 0.00 4.45
2746 2889 1.144936 CTTCCTCATCGTCCTGGCC 59.855 63.158 0.00 0.00 0.00 5.36
2751 2894 0.175989 GGACCACTTCCTCATCGTCC 59.824 60.000 0.00 0.00 41.95 4.79
2770 2913 4.789075 GCTTGCACGGCATGGCAG 62.789 66.667 20.37 14.05 41.68 4.85


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

AutoCloner maintained by Alex Coulton.