Multiple sequence alignment - TraesCS5A01G365000

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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 TraesCS5A01G365000 chr5A 100.000 1894 0 0 1 1894 565392339 565394232 0.000000e+00 3498.0
1 TraesCS5A01G365000 chr5A 100.000 1883 0 0 2322 4204 565394660 565396542 0.000000e+00 3478.0
2 TraesCS5A01G365000 chr5A 90.793 391 32 3 3620 4010 565402977 565403363 1.730000e-143 520.0
3 TraesCS5A01G365000 chr5A 88.755 249 25 3 1647 1894 565393944 565394190 6.830000e-78 302.0
4 TraesCS5A01G365000 chr5A 88.755 249 25 3 1606 1852 565393985 565394232 6.830000e-78 302.0
5 TraesCS5A01G365000 chr5A 84.153 183 29 0 1628 1810 565394050 565394232 1.200000e-40 178.0
6 TraesCS5A01G365000 chr5B 85.167 1854 147 48 1 1776 545403172 545404975 0.000000e+00 1783.0
7 TraesCS5A01G365000 chr5B 90.138 1156 70 14 2367 3485 545405305 545406453 0.000000e+00 1463.0
8 TraesCS5A01G365000 chr5B 84.631 488 48 14 3516 3988 545406540 545407015 1.060000e-125 460.0
9 TraesCS5A01G365000 chr5B 87.980 391 41 4 3620 4010 545427800 545428184 1.380000e-124 457.0
10 TraesCS5A01G365000 chr5B 92.953 298 17 4 2362 2657 545405252 545405547 8.350000e-117 431.0
11 TraesCS5A01G365000 chr5D 87.377 1418 94 24 1 1361 447242561 447241172 0.000000e+00 1548.0
12 TraesCS5A01G365000 chr5D 94.267 907 34 6 2322 3210 447240699 447239793 0.000000e+00 1371.0
13 TraesCS5A01G365000 chr5D 92.505 507 26 8 3516 4016 447239381 447238881 0.000000e+00 715.0
14 TraesCS5A01G365000 chr5D 87.475 495 35 12 1387 1875 447241173 447240700 2.860000e-151 545.0
15 TraesCS5A01G365000 chr5D 90.281 391 32 5 3620 4010 447207289 447206905 1.350000e-139 507.0
16 TraesCS5A01G365000 chr5D 90.698 301 15 2 3214 3501 447239757 447239457 5.100000e-104 388.0
17 TraesCS5A01G365000 chr5D 98.137 161 3 0 4044 4204 447238895 447238735 8.900000e-72 281.0
18 TraesCS5A01G365000 chr5D 82.313 294 48 4 2415 2706 447240654 447240363 6.980000e-63 252.0
19 TraesCS5A01G365000 chr2D 83.665 251 37 4 2821 3069 536153400 536153648 2.530000e-57 233.0
20 TraesCS5A01G365000 chr2B 82.812 256 42 2 2817 3071 637576567 637576821 1.180000e-55 228.0
21 TraesCS5A01G365000 chr2A 83.200 250 40 2 2821 3069 678965364 678965612 1.180000e-55 228.0
22 TraesCS5A01G365000 chr4D 91.083 157 12 2 4050 4204 3465649 3465493 1.180000e-50 211.0
23 TraesCS5A01G365000 chr4D 87.719 57 7 0 3012 3068 506216839 506216783 2.710000e-07 67.6
24 TraesCS5A01G365000 chrUn 89.759 166 14 3 4042 4204 463872842 463873007 4.260000e-50 209.0
25 TraesCS5A01G365000 chrUn 89.222 167 14 4 4042 4204 262972361 262972527 5.510000e-49 206.0
26 TraesCS5A01G365000 chr6D 89.759 166 14 3 4042 4204 15843320 15843485 4.260000e-50 209.0
27 TraesCS5A01G365000 chr6D 89.222 167 14 4 4042 4204 15834394 15834560 5.510000e-49 206.0
28 TraesCS5A01G365000 chr6D 89.222 167 14 4 4042 4204 15835610 15835776 5.510000e-49 206.0
29 TraesCS5A01G365000 chr6D 89.222 167 14 4 4042 4204 15836815 15836981 5.510000e-49 206.0
30 TraesCS5A01G365000 chr6D 89.222 167 14 4 4042 4204 15837423 15837589 5.510000e-49 206.0
31 TraesCS5A01G365000 chr3A 85.897 78 6 3 2970 3043 535727725 535727801 1.250000e-10 78.7
32 TraesCS5A01G365000 chr3D 83.333 78 8 3 2970 3043 414637651 414637575 2.710000e-07 67.6
33 TraesCS5A01G365000 chr3B 83.117 77 8 3 2971 3043 540476549 540476474 9.760000e-07 65.8


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 TraesCS5A01G365000 chr5A 565392339 565396542 4203 False 1551.600000 3498 92.33260 1 4204 5 chr5A.!!$F2 4203
1 TraesCS5A01G365000 chr5B 545403172 545407015 3843 False 1034.250000 1783 88.22225 1 3988 4 chr5B.!!$F2 3987
2 TraesCS5A01G365000 chr5D 447238735 447242561 3826 True 728.571429 1548 90.39600 1 4204 7 chr5D.!!$R2 4203
3 TraesCS5A01G365000 chr6D 15834394 15837589 3195 False 206.000000 206 89.22200 4042 4204 4 chr6D.!!$F2 162

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
685 716 0.250234 CCATGAAGTCGGCTGGAGAA 59.750 55.000 0.00 0.0 0.00 2.87 F
1216 1278 0.249953 TTTTGCTCGCACTTACCGGA 60.250 50.000 9.46 0.0 0.00 5.14 F
1670 1765 1.064946 CTGAGATCGTGCCGAGTCC 59.935 63.158 3.76 0.0 39.91 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1664 1759 1.064946 GTGATCTCAGGCGGACTCG 59.935 63.158 0.0 0.0 39.81 4.18 R
3082 3237 0.039618 GGCAATGGGGTTGAAGGAGA 59.960 55.000 0.0 0.0 40.37 3.71 R
3614 3898 0.242825 CTGAGCAAGGGCATGTGTTG 59.757 55.000 0.0 0.0 44.61 3.33 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 63 3.140895 CCTGGATCCCCCTGTTATTGATT 59.859 47.826 9.90 0.00 35.38 2.57
131 133 4.937620 TCTGACTTGGGAGATTTTGATTCG 59.062 41.667 0.00 0.00 0.00 3.34
202 210 5.584649 AGAAGTCATTTGTTCTGTTGTCGAA 59.415 36.000 0.00 0.00 31.63 3.71
264 274 6.372659 TGAGGATGAAATTAGCAGTGTCTTTC 59.627 38.462 0.00 0.00 0.00 2.62
275 285 2.047061 AGTGTCTTTCCACCAGCTGTA 58.953 47.619 13.81 0.00 35.93 2.74
308 319 6.423182 AGTACCATATGTTGTTAGCACCATT 58.577 36.000 1.24 0.00 30.29 3.16
319 330 6.842437 TGTTAGCACCATTATTTTGCCTTA 57.158 33.333 0.00 0.00 36.91 2.69
375 387 3.684305 GCAAAAGAGGTGTTGCTTGTTTT 59.316 39.130 1.26 0.00 45.34 2.43
400 426 1.673168 ATGCAATTCTTCTCTCCGGC 58.327 50.000 0.00 0.00 0.00 6.13
408 434 1.004394 TCTTCTCTCCGGCACTACTCA 59.996 52.381 0.00 0.00 0.00 3.41
495 521 1.593469 GAACTAATCTCGCGCCCTTTC 59.407 52.381 0.00 0.00 0.00 2.62
504 530 1.005156 GCGCCCTTTCAATTTGCCA 60.005 52.632 0.00 0.00 0.00 4.92
510 536 3.189080 GCCCTTTCAATTTGCCACAAATC 59.811 43.478 6.05 0.00 0.00 2.17
581 612 2.396601 CTTGCGTGCATGAACACATTT 58.603 42.857 10.93 0.00 40.73 2.32
589 620 5.331458 CGTGCATGAACACATTTTACAACAC 60.331 40.000 4.29 0.00 40.73 3.32
590 621 5.046529 TGCATGAACACATTTTACAACACC 58.953 37.500 0.00 0.00 0.00 4.16
649 680 2.827921 GTTGAGTGGATCCCAAGCAAAT 59.172 45.455 9.90 0.00 34.18 2.32
671 702 1.995542 AGGAGGAAAAAGGAGCCATGA 59.004 47.619 0.00 0.00 0.00 3.07
673 704 2.757314 GGAGGAAAAAGGAGCCATGAAG 59.243 50.000 0.00 0.00 0.00 3.02
674 705 3.425659 GAGGAAAAAGGAGCCATGAAGT 58.574 45.455 0.00 0.00 0.00 3.01
675 706 3.425659 AGGAAAAAGGAGCCATGAAGTC 58.574 45.455 0.00 0.00 0.00 3.01
676 707 2.162408 GGAAAAAGGAGCCATGAAGTCG 59.838 50.000 0.00 0.00 0.00 4.18
677 708 1.826385 AAAAGGAGCCATGAAGTCGG 58.174 50.000 0.00 0.00 0.00 4.79
685 716 0.250234 CCATGAAGTCGGCTGGAGAA 59.750 55.000 0.00 0.00 0.00 2.87
689 720 1.229209 AAGTCGGCTGGAGAAGGGA 60.229 57.895 0.00 0.00 0.00 4.20
784 822 2.364972 AGAACCTCAAACCCACCAAG 57.635 50.000 0.00 0.00 0.00 3.61
830 873 1.338337 CCTCTGCCTCAGTGTATACCG 59.662 57.143 0.00 0.00 32.61 4.02
881 924 3.049708 TCACTTCACTGGATTCTGCTG 57.950 47.619 0.00 0.00 0.00 4.41
940 983 3.578688 CTTTAACCTTTGCACAGCCATC 58.421 45.455 0.00 0.00 0.00 3.51
945 988 1.651240 CTTTGCACAGCCATCCTCCG 61.651 60.000 0.00 0.00 0.00 4.63
1126 1186 7.175641 CCTTTCATCCATCTTACACACTTCTTT 59.824 37.037 0.00 0.00 0.00 2.52
1148 1208 0.380733 TAGCATGTGTAGAGGACGCG 59.619 55.000 3.53 3.53 41.82 6.01
1150 1210 0.867753 GCATGTGTAGAGGACGCGAG 60.868 60.000 15.93 0.00 41.82 5.03
1162 1222 1.126296 GGACGCGAGCTTGAGTTTAAC 59.874 52.381 15.93 0.00 0.00 2.01
1166 1226 3.218398 CGCGAGCTTGAGTTTAACTTTG 58.782 45.455 4.70 0.00 0.00 2.77
1204 1266 3.069443 TCACCCCTCACAAAATTTTGCTC 59.931 43.478 26.94 0.00 41.79 4.26
1213 1275 4.048504 ACAAAATTTTGCTCGCACTTACC 58.951 39.130 26.94 0.00 41.79 2.85
1215 1277 0.802494 ATTTTGCTCGCACTTACCGG 59.198 50.000 0.00 0.00 0.00 5.28
1216 1278 0.249953 TTTTGCTCGCACTTACCGGA 60.250 50.000 9.46 0.00 0.00 5.14
1258 1333 7.041107 TGCTGAAATTTATGCCAATTCTTACC 58.959 34.615 10.97 0.00 0.00 2.85
1275 1354 5.182487 TCTTACCGACAATTGTATGTGCAT 58.818 37.500 11.95 0.00 32.57 3.96
1276 1355 5.645929 TCTTACCGACAATTGTATGTGCATT 59.354 36.000 11.95 0.00 32.57 3.56
1289 1368 4.789012 ATGTGCATTTTCGGTTCATCTT 57.211 36.364 0.00 0.00 0.00 2.40
1290 1369 5.895636 ATGTGCATTTTCGGTTCATCTTA 57.104 34.783 0.00 0.00 0.00 2.10
1291 1370 5.295431 TGTGCATTTTCGGTTCATCTTAG 57.705 39.130 0.00 0.00 0.00 2.18
1361 1445 7.436673 TGCTGCGAAATTTGTACAAATTAAGTT 59.563 29.630 35.08 24.44 46.76 2.66
1575 1670 4.124351 TTCGCCTACCTGTCGCCG 62.124 66.667 0.00 0.00 0.00 6.46
1648 1743 1.302832 CCTGAGGTCACACCAAGCC 60.303 63.158 0.00 0.00 41.95 4.35
1649 1744 1.302832 CTGAGGTCACACCAAGCCC 60.303 63.158 0.00 0.00 41.95 5.19
1654 1749 4.641645 TCACACCAAGCCCGCCTG 62.642 66.667 0.00 0.00 0.00 4.85
1655 1750 4.641645 CACACCAAGCCCGCCTGA 62.642 66.667 0.00 0.00 0.00 3.86
1656 1751 4.335647 ACACCAAGCCCGCCTGAG 62.336 66.667 0.00 0.00 0.00 3.35
1657 1752 4.020617 CACCAAGCCCGCCTGAGA 62.021 66.667 0.00 0.00 0.00 3.27
1659 1754 2.203126 CCAAGCCCGCCTGAGATC 60.203 66.667 0.00 0.00 0.00 2.75
1660 1755 2.587194 CAAGCCCGCCTGAGATCG 60.587 66.667 0.00 0.00 0.00 3.69
1661 1756 3.077556 AAGCCCGCCTGAGATCGT 61.078 61.111 0.00 0.00 0.00 3.73
1662 1757 3.376935 AAGCCCGCCTGAGATCGTG 62.377 63.158 0.00 0.00 0.00 4.35
1664 1759 4.899239 CCCGCCTGAGATCGTGCC 62.899 72.222 0.00 0.00 0.00 5.01
1666 1761 4.193334 CGCCTGAGATCGTGCCGA 62.193 66.667 0.00 0.00 41.13 5.54
1667 1762 2.279120 GCCTGAGATCGTGCCGAG 60.279 66.667 3.76 0.00 39.91 4.63
1668 1763 3.069980 GCCTGAGATCGTGCCGAGT 62.070 63.158 3.76 0.00 39.91 4.18
1670 1765 1.064946 CTGAGATCGTGCCGAGTCC 59.935 63.158 3.76 0.00 39.91 3.85
1671 1766 2.024871 GAGATCGTGCCGAGTCCG 59.975 66.667 3.76 0.00 39.91 4.79
1672 1767 4.194720 AGATCGTGCCGAGTCCGC 62.195 66.667 3.76 0.00 39.91 5.54
1679 1774 3.532155 GCCGAGTCCGCCTGAGAT 61.532 66.667 0.00 0.00 0.00 2.75
1680 1775 2.725008 CCGAGTCCGCCTGAGATC 59.275 66.667 0.00 0.00 0.00 2.75
1682 1777 1.064946 CGAGTCCGCCTGAGATCAC 59.935 63.158 0.00 0.00 0.00 3.06
1683 1778 1.064946 GAGTCCGCCTGAGATCACG 59.935 63.158 0.00 0.00 0.00 4.35
1684 1779 2.583593 GTCCGCCTGAGATCACGC 60.584 66.667 0.00 0.00 0.00 5.34
1685 1780 3.838271 TCCGCCTGAGATCACGCC 61.838 66.667 0.00 0.00 0.00 5.68
1687 1782 4.193334 CGCCTGAGATCACGCCGA 62.193 66.667 0.00 0.00 0.00 5.54
1689 1784 2.279120 CCTGAGATCACGCCGAGC 60.279 66.667 0.00 0.00 0.00 5.03
1690 1785 2.279120 CTGAGATCACGCCGAGCC 60.279 66.667 0.00 0.00 0.00 4.70
1691 1786 3.781770 CTGAGATCACGCCGAGCCC 62.782 68.421 0.00 0.00 0.00 5.19
1692 1787 4.933064 GAGATCACGCCGAGCCCG 62.933 72.222 0.00 0.00 0.00 6.13
1702 1797 2.647875 CGAGCCCGCCTGAGATAG 59.352 66.667 0.00 0.00 0.00 2.08
1703 1798 2.341911 GAGCCCGCCTGAGATAGC 59.658 66.667 0.00 0.00 0.00 2.97
1708 1803 2.659897 CGCCTGAGATAGCGCCAC 60.660 66.667 2.29 0.00 46.50 5.01
1709 1804 2.818132 GCCTGAGATAGCGCCACT 59.182 61.111 2.29 0.00 0.00 4.00
1710 1805 1.593750 GCCTGAGATAGCGCCACTG 60.594 63.158 2.29 0.00 0.00 3.66
1785 1880 3.411517 CCCAGCCCACCGGAGATT 61.412 66.667 9.46 0.00 0.00 2.40
1881 1976 4.819761 GAGATCGCGCCACTGCCA 62.820 66.667 0.00 0.00 0.00 4.92
2557 2700 4.736896 GCCGGAAGTCGAGCCGTT 62.737 66.667 5.05 0.00 45.85 4.44
3081 3236 1.471676 CGAGTAAGCCACATCACCTCC 60.472 57.143 0.00 0.00 0.00 4.30
3082 3237 1.834263 GAGTAAGCCACATCACCTCCT 59.166 52.381 0.00 0.00 0.00 3.69
3164 3331 6.003326 TGCTGTAACCATTTCTTGATCTTCA 58.997 36.000 0.00 0.00 0.00 3.02
3244 3443 1.619654 TTGGAAGCTGGACACCATTG 58.380 50.000 0.00 0.00 30.82 2.82
3270 3469 5.077564 TGCTCAAGTTCAGAGGAAGTAGTA 58.922 41.667 0.00 0.00 35.63 1.82
3325 3530 5.283294 TGTTTTGAATGTGAGCATGTTCAG 58.717 37.500 13.02 0.00 35.15 3.02
3432 3646 7.288158 TCCATCTTCATGAATTTCATAATGGCA 59.712 33.333 22.40 15.17 34.28 4.92
3451 3665 1.005347 CAACCACGTTCGTCAGTTGAC 60.005 52.381 22.20 2.16 40.12 3.18
3471 3685 2.103263 ACAAGTCTCTGACGAAGGCTTT 59.897 45.455 0.00 0.00 37.67 3.51
3507 3728 3.158676 AGTGACCACTGAGAACTACTCC 58.841 50.000 1.31 0.00 44.34 3.85
3508 3729 2.231721 GTGACCACTGAGAACTACTCCC 59.768 54.545 0.00 0.00 44.34 4.30
3512 3733 2.291930 CCACTGAGAACTACTCCCTCCT 60.292 54.545 0.00 0.00 44.34 3.69
3513 3734 3.020984 CACTGAGAACTACTCCCTCCTC 58.979 54.545 0.00 0.00 44.34 3.71
3514 3735 2.024751 ACTGAGAACTACTCCCTCCTCC 60.025 54.545 0.00 0.00 44.34 4.30
3574 3856 1.268285 CGTGCACAAAATCAACCGACA 60.268 47.619 18.64 0.00 0.00 4.35
3606 3890 4.909696 TCAACACACACATAAAACAGGG 57.090 40.909 0.00 0.00 0.00 4.45
3607 3891 4.274147 TCAACACACACATAAAACAGGGT 58.726 39.130 0.00 0.00 0.00 4.34
3608 3892 5.437946 TCAACACACACATAAAACAGGGTA 58.562 37.500 0.00 0.00 0.00 3.69
3609 3893 6.065374 TCAACACACACATAAAACAGGGTAT 58.935 36.000 0.00 0.00 0.00 2.73
3610 3894 7.225011 TCAACACACACATAAAACAGGGTATA 58.775 34.615 0.00 0.00 0.00 1.47
3611 3895 7.720074 TCAACACACACATAAAACAGGGTATAA 59.280 33.333 0.00 0.00 0.00 0.98
3613 3897 8.466617 ACACACACATAAAACAGGGTATAAAA 57.533 30.769 0.00 0.00 0.00 1.52
3614 3898 8.354426 ACACACACATAAAACAGGGTATAAAAC 58.646 33.333 0.00 0.00 0.00 2.43
3615 3899 8.353684 CACACACATAAAACAGGGTATAAAACA 58.646 33.333 0.00 0.00 0.00 2.83
3616 3900 8.915036 ACACACATAAAACAGGGTATAAAACAA 58.085 29.630 0.00 0.00 0.00 2.83
3618 3902 8.915036 ACACATAAAACAGGGTATAAAACAACA 58.085 29.630 0.00 0.00 0.00 3.33
3645 3931 0.473755 TTGCTCAGGCTGGAACTTCA 59.526 50.000 15.73 1.28 39.59 3.02
3674 3960 1.066858 AGGGTATGTCTGCAGAACGTG 60.067 52.381 20.19 0.00 0.00 4.49
3784 4070 4.259017 GCAAAACGAGATAAAAATGCGAGC 60.259 41.667 0.00 0.00 0.00 5.03
3865 4162 5.140454 ACCTTCTGTTTATTCTTGTGGCTT 58.860 37.500 0.00 0.00 0.00 4.35
3922 4219 1.440938 TTTCTGTTGGTTCGGTGCCG 61.441 55.000 3.94 3.94 41.35 5.69
3923 4220 4.025401 CTGTTGGTTCGGTGCCGC 62.025 66.667 5.64 0.00 39.59 6.53
3965 4262 2.332063 AATGGTAGGCACCTGAATCG 57.668 50.000 0.00 0.00 45.98 3.34
3993 4290 9.593134 CAAACAGAGAAACTAAGCATAGAGTAT 57.407 33.333 2.38 0.00 33.15 2.12
4170 4469 5.888161 AGCTTTATAAGAACTGTCCCCATTG 59.112 40.000 0.00 0.00 0.00 2.82
4175 4474 3.814504 AGAACTGTCCCCATTGTTCAT 57.185 42.857 0.00 0.00 40.62 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 63 8.512956 CAGTAGCTCAAGTCACTAACTAAGTAA 58.487 37.037 0.00 0.00 37.17 2.24
78 80 3.751479 TCTTTCAACTGCAGTAGCTCA 57.249 42.857 22.01 2.60 42.74 4.26
193 201 2.785713 TCGTCAGTCATTCGACAACA 57.214 45.000 0.00 0.00 45.23 3.33
202 210 7.751768 TGAAGATACTCATATCGTCAGTCAT 57.248 36.000 8.32 0.00 45.59 3.06
282 292 6.342906 TGGTGCTAACAACATATGGTACTAC 58.657 40.000 7.80 0.00 39.04 2.73
308 319 2.161410 CACGCTGCTGTAAGGCAAAATA 59.839 45.455 0.00 0.00 41.94 1.40
319 330 0.173481 ATACACGATCACGCTGCTGT 59.827 50.000 0.00 0.00 43.96 4.40
375 387 4.333649 CGGAGAGAAGAATTGCATTTGCTA 59.666 41.667 3.94 0.00 42.66 3.49
400 426 9.495572 AAAGGTAAAGAGAAAAGATGAGTAGTG 57.504 33.333 0.00 0.00 0.00 2.74
408 434 6.565999 CGTTGCGAAAGGTAAAGAGAAAAGAT 60.566 38.462 0.00 0.00 0.00 2.40
495 521 6.480981 AGAAAGTTCAGATTTGTGGCAAATTG 59.519 34.615 8.27 8.59 0.00 2.32
504 530 6.489361 AGCATTCTCAGAAAGTTCAGATTTGT 59.511 34.615 0.00 0.00 0.00 2.83
510 536 6.252441 CGTACTAGCATTCTCAGAAAGTTCAG 59.748 42.308 0.00 0.00 0.00 3.02
581 612 2.877786 CAGCATCTGTGTGGTGTTGTAA 59.122 45.455 6.77 0.00 41.41 2.41
589 620 1.534163 CACAAGTCAGCATCTGTGTGG 59.466 52.381 7.67 0.00 32.61 4.17
590 621 2.032290 CACACAAGTCAGCATCTGTGTG 60.032 50.000 16.91 16.91 46.74 3.82
649 680 1.444933 TGGCTCCTTTTTCCTCCTCA 58.555 50.000 0.00 0.00 0.00 3.86
671 702 1.229209 TCCCTTCTCCAGCCGACTT 60.229 57.895 0.00 0.00 0.00 3.01
673 704 2.726351 CCTCCCTTCTCCAGCCGAC 61.726 68.421 0.00 0.00 0.00 4.79
674 705 2.364317 CCTCCCTTCTCCAGCCGA 60.364 66.667 0.00 0.00 0.00 5.54
675 706 2.364317 TCCTCCCTTCTCCAGCCG 60.364 66.667 0.00 0.00 0.00 5.52
676 707 2.069430 CCTCCTCCCTTCTCCAGCC 61.069 68.421 0.00 0.00 0.00 4.85
677 708 0.399806 ATCCTCCTCCCTTCTCCAGC 60.400 60.000 0.00 0.00 0.00 4.85
678 709 1.715785 GATCCTCCTCCCTTCTCCAG 58.284 60.000 0.00 0.00 0.00 3.86
680 711 0.565674 AGGATCCTCCTCCCTTCTCC 59.434 60.000 9.02 0.00 45.66 3.71
704 735 0.394080 GCTGCTGCCCAGAGAGAAAT 60.394 55.000 3.85 0.00 44.64 2.17
705 736 1.002868 GCTGCTGCCCAGAGAGAAA 60.003 57.895 3.85 0.00 44.64 2.52
784 822 3.644738 AGGCATGGAAATGATTGGATTCC 59.355 43.478 0.00 0.00 42.39 3.01
830 873 3.371285 GGGACGATTGAGCTTTAGTGTTC 59.629 47.826 0.00 0.00 0.00 3.18
881 924 1.353076 GCAAATGCAGCAAAGCTACC 58.647 50.000 0.00 0.00 36.40 3.18
940 983 2.868044 GCTGTTGATATAGCCACGGAGG 60.868 54.545 5.28 0.00 41.84 4.30
1126 1186 2.298610 CGTCCTCTACACATGCTAGGA 58.701 52.381 0.00 0.00 33.97 2.94
1148 1208 5.163652 ACACACCAAAGTTAAACTCAAGCTC 60.164 40.000 0.00 0.00 0.00 4.09
1150 1210 4.993905 ACACACCAAAGTTAAACTCAAGC 58.006 39.130 0.00 0.00 0.00 4.01
1204 1266 2.785342 GCGTAAAATTCCGGTAAGTGCG 60.785 50.000 0.00 1.15 0.00 5.34
1213 1275 4.151512 AGCAAAATTTGGCGTAAAATTCCG 59.848 37.500 11.90 6.40 38.49 4.30
1215 1277 6.221858 TCAGCAAAATTTGGCGTAAAATTC 57.778 33.333 11.90 0.97 38.49 2.17
1216 1278 6.610741 TTCAGCAAAATTTGGCGTAAAATT 57.389 29.167 11.90 4.86 40.60 1.82
1258 1333 4.262743 CCGAAAATGCACATACAATTGTCG 59.737 41.667 15.85 10.29 0.00 4.35
1275 1354 5.064707 GCATGCTACTAAGATGAACCGAAAA 59.935 40.000 11.37 0.00 0.00 2.29
1276 1355 4.570772 GCATGCTACTAAGATGAACCGAAA 59.429 41.667 11.37 0.00 0.00 3.46
1290 1369 9.877178 GTAATATCAACCTATTAGCATGCTACT 57.123 33.333 26.87 23.08 0.00 2.57
1291 1370 9.877178 AGTAATATCAACCTATTAGCATGCTAC 57.123 33.333 26.87 12.02 0.00 3.58
1361 1445 8.977505 ACGTTAGTGTTTTCTTACGCTAATTTA 58.022 29.630 11.51 0.00 46.66 1.40
1368 1452 4.026640 TGTGACGTTAGTGTTTTCTTACGC 60.027 41.667 0.00 0.00 41.87 4.42
1370 1454 6.254157 TCAGTGTGACGTTAGTGTTTTCTTAC 59.746 38.462 0.00 0.00 0.00 2.34
1372 1456 5.172934 TCAGTGTGACGTTAGTGTTTTCTT 58.827 37.500 0.00 0.00 0.00 2.52
1374 1458 5.652744 ATCAGTGTGACGTTAGTGTTTTC 57.347 39.130 0.00 0.00 0.00 2.29
1641 1736 3.011517 ATCTCAGGCGGGCTTGGT 61.012 61.111 0.00 0.00 0.00 3.67
1663 1758 2.121538 TGATCTCAGGCGGACTCGG 61.122 63.158 0.00 0.00 36.79 4.63
1664 1759 1.064946 GTGATCTCAGGCGGACTCG 59.935 63.158 0.00 0.00 39.81 4.18
1665 1760 1.064946 CGTGATCTCAGGCGGACTC 59.935 63.158 0.00 0.00 0.00 3.36
1666 1761 3.069980 GCGTGATCTCAGGCGGACT 62.070 63.158 8.88 0.00 45.78 3.85
1667 1762 2.583593 GCGTGATCTCAGGCGGAC 60.584 66.667 8.88 0.00 45.78 4.79
1672 1767 2.279120 GCTCGGCGTGATCTCAGG 60.279 66.667 13.77 0.00 35.07 3.86
1673 1768 2.279120 GGCTCGGCGTGATCTCAG 60.279 66.667 13.77 0.00 0.00 3.35
1684 1779 2.912542 TATCTCAGGCGGGCTCGG 60.913 66.667 8.71 0.00 36.79 4.63
1685 1780 2.647875 CTATCTCAGGCGGGCTCG 59.352 66.667 0.00 0.00 39.81 5.03
1686 1781 2.341911 GCTATCTCAGGCGGGCTC 59.658 66.667 0.00 0.00 0.00 4.70
1687 1782 3.610669 CGCTATCTCAGGCGGGCT 61.611 66.667 0.00 0.00 46.42 5.19
1692 1787 1.593750 CAGTGGCGCTATCTCAGGC 60.594 63.158 7.64 0.00 0.00 4.85
1693 1788 1.593750 GCAGTGGCGCTATCTCAGG 60.594 63.158 7.64 0.00 0.00 3.86
1694 1789 1.593750 GGCAGTGGCGCTATCTCAG 60.594 63.158 7.64 0.00 42.47 3.35
1695 1790 2.501128 GGCAGTGGCGCTATCTCA 59.499 61.111 7.64 0.00 42.47 3.27
1696 1791 2.659897 CGGCAGTGGCGCTATCTC 60.660 66.667 26.78 0.00 45.68 2.75
1770 1865 2.825836 GCAATCTCCGGTGGGCTG 60.826 66.667 0.00 0.00 0.00 4.85
2351 2446 2.732658 GGGTACACTATCGGCGGG 59.267 66.667 7.21 0.00 0.00 6.13
2459 2554 2.204291 TCTGGTGGCCCTGGGAAT 60.204 61.111 19.27 0.00 0.00 3.01
2619 2762 3.775654 CGGGCTGGGAGTCACCTC 61.776 72.222 0.00 0.00 38.98 3.85
3081 3236 1.467920 GCAATGGGGTTGAAGGAGAG 58.532 55.000 0.00 0.00 40.37 3.20
3082 3237 0.039618 GGCAATGGGGTTGAAGGAGA 59.960 55.000 0.00 0.00 40.37 3.71
3164 3331 4.401925 GGCAGTTATCATAGCCTGGAAAT 58.598 43.478 0.00 0.00 43.70 2.17
3244 3443 3.244044 ACTTCCTCTGAACTTGAGCAGAC 60.244 47.826 0.00 0.00 36.31 3.51
3325 3530 7.448748 AAGTTAGATGGGTACATTCACAAAC 57.551 36.000 0.00 0.00 37.47 2.93
3393 3600 7.864686 TCATGAAGATGGAAAATTACATAGCG 58.135 34.615 0.00 0.00 30.10 4.26
3426 3640 0.816018 TGACGAACGTGGTTGCCATT 60.816 50.000 4.19 0.00 35.28 3.16
3432 3646 1.283736 GTCAACTGACGAACGTGGTT 58.716 50.000 4.19 6.97 35.12 3.67
3451 3665 2.447244 AAGCCTTCGTCAGAGACTTG 57.553 50.000 0.00 0.00 0.00 3.16
3504 3725 2.197324 CGAGGAGGGAGGAGGGAG 59.803 72.222 0.00 0.00 0.00 4.30
3506 3727 2.197324 CTCGAGGAGGGAGGAGGG 59.803 72.222 3.91 0.00 0.00 4.30
3507 3728 2.520741 GCTCGAGGAGGGAGGAGG 60.521 72.222 15.58 0.00 32.10 4.30
3508 3729 0.686112 AAAGCTCGAGGAGGGAGGAG 60.686 60.000 15.58 0.00 32.10 3.69
3512 3733 2.420129 GCAATAAAAGCTCGAGGAGGGA 60.420 50.000 15.58 0.00 0.00 4.20
3513 3734 1.943340 GCAATAAAAGCTCGAGGAGGG 59.057 52.381 15.58 0.00 0.00 4.30
3514 3735 2.911484 AGCAATAAAAGCTCGAGGAGG 58.089 47.619 15.58 0.00 38.01 4.30
3547 3829 3.632855 TGATTTTGTGCACGCATTACA 57.367 38.095 13.13 5.42 0.00 2.41
3574 3856 1.754803 TGTGTGTTGAAGAGACGACCT 59.245 47.619 0.00 0.00 0.00 3.85
3587 3869 8.466617 TTTATACCCTGTTTTATGTGTGTGTT 57.533 30.769 0.00 0.00 0.00 3.32
3606 3890 4.625311 GCAAGGGCATGTGTTGTTTTATAC 59.375 41.667 0.00 0.00 40.72 1.47
3607 3891 4.526262 AGCAAGGGCATGTGTTGTTTTATA 59.474 37.500 0.00 0.00 44.61 0.98
3608 3892 3.324556 AGCAAGGGCATGTGTTGTTTTAT 59.675 39.130 0.00 0.00 44.61 1.40
3609 3893 2.697751 AGCAAGGGCATGTGTTGTTTTA 59.302 40.909 0.00 0.00 44.61 1.52
3610 3894 1.485895 AGCAAGGGCATGTGTTGTTTT 59.514 42.857 0.00 0.00 44.61 2.43
3611 3895 1.069049 GAGCAAGGGCATGTGTTGTTT 59.931 47.619 0.00 0.00 44.61 2.83
3613 3897 0.467844 TGAGCAAGGGCATGTGTTGT 60.468 50.000 0.00 0.00 44.61 3.32
3614 3898 0.242825 CTGAGCAAGGGCATGTGTTG 59.757 55.000 0.00 0.00 44.61 3.33
3615 3899 0.896940 CCTGAGCAAGGGCATGTGTT 60.897 55.000 0.00 0.00 43.15 3.32
3616 3900 1.303888 CCTGAGCAAGGGCATGTGT 60.304 57.895 0.00 0.00 43.15 3.72
3645 3931 2.103263 GCAGACATACCCTTCTTCCGAT 59.897 50.000 0.00 0.00 0.00 4.18
3784 4070 0.788391 GTAGAACAAGCCGTTGACCG 59.212 55.000 0.00 0.00 38.19 4.79
3865 4162 1.589630 CGGTGAAGTGATCCGTCCA 59.410 57.895 0.00 0.00 39.51 4.02
3922 4219 2.093658 TCAAGAGAACGGAATACCTGGC 60.094 50.000 0.00 0.00 0.00 4.85
3923 4220 3.887621 TCAAGAGAACGGAATACCTGG 57.112 47.619 0.00 0.00 0.00 4.45
3924 4221 7.041780 CCATTAATCAAGAGAACGGAATACCTG 60.042 40.741 0.00 0.00 0.00 4.00
3965 4262 4.773323 ATGCTTAGTTTCTCTGTTTGCC 57.227 40.909 0.00 0.00 0.00 4.52
4170 4469 3.889196 TGCAAGTAACAACGGATGAAC 57.111 42.857 0.00 0.00 0.00 3.18
4175 4474 0.878416 GGCATGCAAGTAACAACGGA 59.122 50.000 21.36 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.