Multiple sequence alignment - TraesCS2D01G477000

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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 TraesCS2D01G477000 chr2D 100.000 5401 0 0 1 5401 579190382 579184982 0.000000e+00 9974.0
1 TraesCS2D01G477000 chr2D 82.106 1738 283 18 2676 4403 579391517 579389798 0.000000e+00 1461.0
2 TraesCS2D01G477000 chr2D 80.184 1736 311 25 2703 4421 578931468 578929749 0.000000e+00 1269.0
3 TraesCS2D01G477000 chr2D 94.366 213 12 0 2437 2649 579187841 579187629 1.450000e-85 327.0
4 TraesCS2D01G477000 chr2D 94.366 213 12 0 2542 2754 579187946 579187734 1.450000e-85 327.0
5 TraesCS2D01G477000 chr2D 98.131 107 2 0 2438 2544 579187735 579187629 2.570000e-43 187.0
6 TraesCS2D01G477000 chr2D 98.131 107 2 0 2648 2754 579187945 579187839 2.570000e-43 187.0
7 TraesCS2D01G477000 chr2D 93.976 83 5 0 2442 2524 220628000 220627918 5.680000e-25 126.0
8 TraesCS2D01G477000 chr2B 93.841 4741 190 41 624 5317 696291815 696287130 0.000000e+00 7044.0
9 TraesCS2D01G477000 chr2B 82.397 1744 265 33 2676 4403 696675268 696673551 0.000000e+00 1482.0
10 TraesCS2D01G477000 chr2B 79.744 1797 325 28 2646 4420 695842921 695841142 0.000000e+00 1266.0
11 TraesCS2D01G477000 chr2B 90.358 643 54 5 4 639 696355462 696354821 0.000000e+00 837.0
12 TraesCS2D01G477000 chr2B 95.775 213 9 0 2437 2649 696289898 696289686 1.440000e-90 344.0
13 TraesCS2D01G477000 chr2B 94.836 213 11 0 2542 2754 696290003 696289791 3.120000e-87 333.0
14 TraesCS2D01G477000 chr2B 98.131 107 2 0 2648 2754 696290002 696289896 2.570000e-43 187.0
15 TraesCS2D01G477000 chr2B 97.196 107 3 0 2438 2544 696289792 696289686 1.200000e-41 182.0
16 TraesCS2D01G477000 chr2B 88.660 97 11 0 2442 2538 73977700 73977604 9.500000e-23 119.0
17 TraesCS2D01G477000 chr2B 88.406 69 7 1 327 395 579379072 579379005 1.250000e-11 82.4
18 TraesCS2D01G477000 chr2B 82.927 82 13 1 2571 2652 696675268 696675188 7.500000e-09 73.1
19 TraesCS2D01G477000 chr2A 96.057 2866 99 8 2542 5401 716897813 716894956 0.000000e+00 4654.0
20 TraesCS2D01G477000 chr2A 91.236 2727 125 25 1 2649 716900291 716897601 0.000000e+00 3607.0
21 TraesCS2D01G477000 chr2A 95.280 1483 62 7 3925 5401 716839959 716838479 0.000000e+00 2344.0
22 TraesCS2D01G477000 chr2A 82.604 1736 275 21 2676 4403 717142340 717140624 0.000000e+00 1507.0
23 TraesCS2D01G477000 chr2A 79.942 1735 317 23 2703 4421 716458617 716456898 0.000000e+00 1247.0
24 TraesCS2D01G477000 chr2A 92.925 212 15 0 3718 3929 716880557 716880346 5.250000e-80 309.0
25 TraesCS2D01G477000 chr2A 99.074 108 1 0 2437 2544 716897708 716897601 1.530000e-45 195.0
26 TraesCS2D01G477000 chr2A 94.393 107 6 0 2648 2754 716897812 716897706 1.200000e-36 165.0
27 TraesCS2D01G477000 chr3D 78.986 138 28 1 417 553 520711559 520711422 5.760000e-15 93.5
28 TraesCS2D01G477000 chr3A 82.292 96 16 1 315 410 352513204 352513110 1.250000e-11 82.4


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 TraesCS2D01G477000 chr2D 579184982 579190382 5400 True 2200.40 9974 96.9988 1 5401 5 chr2D.!!$R4 5400
1 TraesCS2D01G477000 chr2D 579389798 579391517 1719 True 1461.00 1461 82.1060 2676 4403 1 chr2D.!!$R3 1727
2 TraesCS2D01G477000 chr2D 578929749 578931468 1719 True 1269.00 1269 80.1840 2703 4421 1 chr2D.!!$R2 1718
3 TraesCS2D01G477000 chr2B 696287130 696291815 4685 True 1618.00 7044 95.9558 624 5317 5 chr2B.!!$R5 4693
4 TraesCS2D01G477000 chr2B 695841142 695842921 1779 True 1266.00 1266 79.7440 2646 4420 1 chr2B.!!$R3 1774
5 TraesCS2D01G477000 chr2B 696354821 696355462 641 True 837.00 837 90.3580 4 639 1 chr2B.!!$R4 635
6 TraesCS2D01G477000 chr2B 696673551 696675268 1717 True 777.55 1482 82.6620 2571 4403 2 chr2B.!!$R6 1832
7 TraesCS2D01G477000 chr2A 716838479 716839959 1480 True 2344.00 2344 95.2800 3925 5401 1 chr2A.!!$R2 1476
8 TraesCS2D01G477000 chr2A 716894956 716900291 5335 True 2155.25 4654 95.1900 1 5401 4 chr2A.!!$R5 5400
9 TraesCS2D01G477000 chr2A 717140624 717142340 1716 True 1507.00 1507 82.6040 2676 4403 1 chr2A.!!$R4 1727
10 TraesCS2D01G477000 chr2A 716456898 716458617 1719 True 1247.00 1247 79.9420 2703 4421 1 chr2A.!!$R1 1718

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
852 896 0.538287 AAGAAGCCACAGCCCAGTTC 60.538 55.000 0.0 0.0 41.25 3.01 F
1519 1601 0.179119 GCAGCATGAAGGCAATGGTC 60.179 55.000 0.0 0.0 39.69 4.02 F
2405 2492 1.216710 GAAGTCCAGGGTGCGAGAG 59.783 63.158 0.0 0.0 0.00 3.20 F
3986 4086 1.344763 ACAGACTCGCTTGGCTACTTT 59.655 47.619 0.0 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2235 0.170339 TCGTCGATCGTCACTGCAAT 59.830 50.0 15.94 0.0 40.80 3.56 R
3485 3584 0.899720 AAGATGCACATGCCCCAAAG 59.100 50.0 0.49 0.0 41.18 2.77 R
4068 4168 0.813210 GCATCCAGAGCTGCACTACC 60.813 60.0 1.02 0.0 38.28 3.18 R
5115 5229 0.476808 TGCCAGGTCCCCTTCCTAAA 60.477 55.0 0.00 0.0 33.54 1.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.859090 CCAGAAAATCATGCCCATAACTATTAA 58.141 33.333 0.00 0.00 0.00 1.40
163 169 3.225104 TCTCTGCAAGACTTTGGCAAAT 58.775 40.909 13.89 3.91 38.67 2.32
167 173 2.557924 TGCAAGACTTTGGCAAATCGAT 59.442 40.909 13.89 0.00 34.79 3.59
176 182 2.627945 TGGCAAATCGATACTGTCACC 58.372 47.619 9.90 3.97 0.00 4.02
232 238 5.360714 AGGTTTTTGAAAGCTCATTCAGTCA 59.639 36.000 1.35 0.00 40.21 3.41
271 277 6.469410 TGGAAAACCTTGAGTGATAACGTAT 58.531 36.000 0.00 0.00 0.00 3.06
308 316 2.425312 CCACCAAAGTGCACACTACAAA 59.575 45.455 21.04 0.00 43.09 2.83
318 326 5.067674 AGTGCACACTACAAATCACAATGTT 59.932 36.000 21.04 0.00 40.43 2.71
473 481 3.570926 TCACCACTAGATGTTGACGAC 57.429 47.619 0.00 0.00 0.00 4.34
517 525 1.610673 GACCCTCCACCTCTCAGCA 60.611 63.158 0.00 0.00 0.00 4.41
531 539 0.750546 TCAGCATCAAGATGGCAGCC 60.751 55.000 3.66 3.66 39.16 4.85
532 540 1.035385 CAGCATCAAGATGGCAGCCA 61.035 55.000 18.99 18.99 39.16 4.75
564 572 3.209812 GGAATTTCTCCGGCGGCC 61.210 66.667 23.83 9.54 33.37 6.13
581 589 3.184683 CGCTGCAGTTCTCCGAGC 61.185 66.667 16.64 0.00 0.00 5.03
621 629 6.605119 ACTTACTCCATCCATCCCAAAATAG 58.395 40.000 0.00 0.00 0.00 1.73
627 635 4.535781 CATCCATCCCAAAATAGGTGACA 58.464 43.478 0.00 0.00 0.00 3.58
734 773 5.253330 AGGACAGAATAAAAGCCGAAATCA 58.747 37.500 0.00 0.00 0.00 2.57
735 774 5.710099 AGGACAGAATAAAAGCCGAAATCAA 59.290 36.000 0.00 0.00 0.00 2.57
764 805 6.590068 AGACAGAATGAGATTGACCCAATAG 58.410 40.000 0.00 0.00 39.69 1.73
807 851 4.841813 TCCAGGCCGAACCAATAGATTATA 59.158 41.667 0.00 0.00 43.14 0.98
841 885 2.429930 CGACCCACCAAGAAGCCA 59.570 61.111 0.00 0.00 0.00 4.75
842 886 1.966451 CGACCCACCAAGAAGCCAC 60.966 63.158 0.00 0.00 0.00 5.01
843 887 1.150536 GACCCACCAAGAAGCCACA 59.849 57.895 0.00 0.00 0.00 4.17
844 888 0.890996 GACCCACCAAGAAGCCACAG 60.891 60.000 0.00 0.00 0.00 3.66
847 891 2.116125 ACCAAGAAGCCACAGCCC 59.884 61.111 0.00 0.00 41.25 5.19
848 892 2.115910 CCAAGAAGCCACAGCCCA 59.884 61.111 0.00 0.00 41.25 5.36
849 893 1.975407 CCAAGAAGCCACAGCCCAG 60.975 63.158 0.00 0.00 41.25 4.45
850 894 1.228367 CAAGAAGCCACAGCCCAGT 60.228 57.895 0.00 0.00 41.25 4.00
851 895 0.825010 CAAGAAGCCACAGCCCAGTT 60.825 55.000 0.00 0.00 41.25 3.16
852 896 0.538287 AAGAAGCCACAGCCCAGTTC 60.538 55.000 0.00 0.00 41.25 3.01
853 897 1.973812 GAAGCCACAGCCCAGTTCC 60.974 63.158 0.00 0.00 41.25 3.62
919 963 1.078143 GAAGCCCATTCTCGCCACT 60.078 57.895 0.00 0.00 34.86 4.00
927 971 1.205655 CATTCTCGCCACTGAAGGAGA 59.794 52.381 0.00 0.00 36.05 3.71
1102 1168 0.528466 GCGCTGTGCTCTGCTACATA 60.528 55.000 14.45 0.00 41.73 2.29
1103 1169 1.203928 CGCTGTGCTCTGCTACATAC 58.796 55.000 14.45 0.00 36.58 2.39
1104 1170 1.202348 CGCTGTGCTCTGCTACATACT 60.202 52.381 14.45 0.00 36.58 2.12
1105 1171 2.200067 GCTGTGCTCTGCTACATACTG 58.800 52.381 10.03 0.00 35.98 2.74
1106 1172 2.200067 CTGTGCTCTGCTACATACTGC 58.800 52.381 0.00 0.00 0.00 4.40
1107 1173 1.203928 GTGCTCTGCTACATACTGCG 58.796 55.000 0.00 0.00 0.00 5.18
1108 1174 1.102978 TGCTCTGCTACATACTGCGA 58.897 50.000 0.00 0.00 0.00 5.10
1109 1175 1.476488 TGCTCTGCTACATACTGCGAA 59.524 47.619 0.00 0.00 0.00 4.70
1204 1272 1.834188 GGATTGTGGTAGTGTTGGGG 58.166 55.000 0.00 0.00 0.00 4.96
1250 1318 2.066999 GGCCGGGAGACTGAATCCT 61.067 63.158 2.18 0.00 39.98 3.24
1290 1361 4.699522 GGCGGACGGGCAAGAAGT 62.700 66.667 1.39 0.00 41.77 3.01
1303 1374 5.405571 CGGGCAAGAAGTATATGTATGTGTC 59.594 44.000 0.00 0.00 0.00 3.67
1304 1375 5.701290 GGGCAAGAAGTATATGTATGTGTCC 59.299 44.000 0.00 0.00 0.00 4.02
1307 1378 6.647067 GCAAGAAGTATATGTATGTGTCCCTC 59.353 42.308 0.00 0.00 0.00 4.30
1331 1412 4.889409 TGGTCTTGAAATTATGGAGGATGC 59.111 41.667 0.00 0.00 0.00 3.91
1361 1442 5.665459 CTCAGATCGATGTAGGGTTTCTTT 58.335 41.667 0.54 0.00 0.00 2.52
1412 1494 8.209584 ACATACTTCTGAGATTATGTGATGCTT 58.790 33.333 13.50 0.00 34.56 3.91
1433 1515 5.877012 GCTTTCTTCTTGGACTGATATGTGA 59.123 40.000 0.00 0.00 0.00 3.58
1458 1540 9.548208 GATTTCTTTTCATACTTAACTGAGTGC 57.452 33.333 0.00 0.00 0.00 4.40
1513 1595 1.755395 GGATGGCAGCATGAAGGCA 60.755 57.895 14.68 14.68 44.70 4.75
1519 1601 0.179119 GCAGCATGAAGGCAATGGTC 60.179 55.000 0.00 0.00 39.69 4.02
1535 1617 3.663995 TGGTCAAATTTGATGGTGCTG 57.336 42.857 23.05 0.00 39.73 4.41
1543 1625 3.421919 TTTGATGGTGCTGACATCTCA 57.578 42.857 14.00 2.57 43.88 3.27
1545 1627 1.904537 TGATGGTGCTGACATCTCACT 59.095 47.619 14.00 0.00 43.88 3.41
1552 1634 3.679025 GTGCTGACATCTCACTCAGAAAG 59.321 47.826 0.00 0.00 36.75 2.62
1554 1636 4.039609 TGCTGACATCTCACTCAGAAAGAA 59.960 41.667 0.00 0.00 36.75 2.52
1598 1680 4.069232 CGGAGGAGTTGCAGCCGA 62.069 66.667 0.00 0.00 44.43 5.54
1599 1681 2.586792 GGAGGAGTTGCAGCCGAT 59.413 61.111 0.00 0.00 0.00 4.18
1600 1682 1.522580 GGAGGAGTTGCAGCCGATC 60.523 63.158 0.00 0.00 0.00 3.69
1601 1683 1.522580 GAGGAGTTGCAGCCGATCC 60.523 63.158 0.00 0.00 0.00 3.36
1602 1684 2.892425 GGAGTTGCAGCCGATCCG 60.892 66.667 0.00 0.00 0.00 4.18
1649 1731 1.967066 AGTTCCAGCCGATCTATCTGG 59.033 52.381 14.84 14.84 46.60 3.86
1868 1950 3.809905 CCATTACCTTCTACTTGGCTCC 58.190 50.000 0.00 0.00 0.00 4.70
2032 2119 8.590204 TGTGTAGTTTAAGATCTGGATACACAA 58.410 33.333 23.41 14.36 45.04 3.33
2073 2160 5.695851 AATTGAACTCTGGCACAAAGTAG 57.304 39.130 0.00 0.00 38.70 2.57
2106 2193 9.086336 GTATTGTATTCATGGTTTTGGTGAATG 57.914 33.333 9.40 0.00 41.31 2.67
2107 2194 6.035368 TGTATTCATGGTTTTGGTGAATGG 57.965 37.500 9.40 0.00 41.31 3.16
2131 2218 7.515957 GAATTAATCCAGTTTTCAGCACATG 57.484 36.000 0.00 0.00 0.00 3.21
2135 2222 4.044336 TCCAGTTTTCAGCACATGTTTG 57.956 40.909 0.00 0.00 0.00 2.93
2148 2235 6.645827 CAGCACATGTTTGGTTGATGAAATTA 59.354 34.615 0.00 0.00 0.00 1.40
2172 2259 2.630090 CAGTGACGATCGACGACATAG 58.370 52.381 24.34 8.76 46.07 2.23
2193 2280 3.263681 AGGCTCAGTAAGTCCCCTAAAAC 59.736 47.826 0.00 0.00 0.00 2.43
2194 2281 3.263681 GGCTCAGTAAGTCCCCTAAAACT 59.736 47.826 0.00 0.00 0.00 2.66
2207 2294 5.538433 TCCCCTAAAACTGAGGTCAAAAATG 59.462 40.000 0.00 0.00 31.52 2.32
2347 2434 1.305219 AAACGACATGGGCATGACCG 61.305 55.000 14.43 1.17 41.20 4.79
2405 2492 1.216710 GAAGTCCAGGGTGCGAGAG 59.783 63.158 0.00 0.00 0.00 3.20
2585 2672 2.362369 GGCTAGCAGCTCCAGTGGA 61.362 63.158 18.24 12.40 41.99 4.02
2706 2799 2.032681 GCATCACCTATCGGCCCC 59.967 66.667 0.00 0.00 0.00 5.80
3368 3467 5.396213 GGAGATGCTCATAAAGAAGAGGTGT 60.396 44.000 0.00 0.00 32.54 4.16
3452 3551 8.438513 GTTGTTTCTGATGGACGATCATATATG 58.561 37.037 6.36 6.36 40.46 1.78
3485 3584 6.228258 TGTTGGTGACATAGTAAAGGACTTC 58.772 40.000 0.00 0.00 42.32 3.01
3911 4011 3.058224 GGCTGTCAATACCTGTTGTGTTC 60.058 47.826 0.00 0.00 0.00 3.18
3938 4038 6.892485 TCCAAGATTCAAGATGAGCTTCATA 58.108 36.000 0.00 0.00 37.20 2.15
3939 4039 7.341030 TCCAAGATTCAAGATGAGCTTCATAA 58.659 34.615 0.00 0.00 37.20 1.90
3977 4077 1.937108 GCTTACAGCACAGACTCGCTT 60.937 52.381 0.00 0.00 41.89 4.68
3986 4086 1.344763 ACAGACTCGCTTGGCTACTTT 59.655 47.619 0.00 0.00 0.00 2.66
4004 4104 9.331282 GGCTACTTTTCTGAAATACATGATACT 57.669 33.333 0.00 0.00 0.00 2.12
4037 4137 5.986135 ACTCTTCGATGAATACTACAATGCC 59.014 40.000 2.36 0.00 0.00 4.40
4068 4168 1.336517 TGAGTGGCGTCCGTCTTTTAG 60.337 52.381 0.00 0.00 0.00 1.85
4095 4195 2.147150 CAGCTCTGGATGCAGATGATG 58.853 52.381 18.00 15.57 0.00 3.07
4121 4221 3.968265 TCCTTTGGAAGATTGGGATGAC 58.032 45.455 0.00 0.00 0.00 3.06
4135 4247 1.605710 GGATGACCATCTCAATTGCCG 59.394 52.381 9.56 0.00 37.92 5.69
4417 4529 7.246674 TGAGATAAATTTGCAACGTCCTATC 57.753 36.000 0.00 2.20 0.00 2.08
4431 4543 3.487042 CGTCCTATCACTAACACACCTCG 60.487 52.174 0.00 0.00 0.00 4.63
4434 4546 0.973632 ATCACTAACACACCTCGCCA 59.026 50.000 0.00 0.00 0.00 5.69
4637 4749 6.696583 TGTTAGAACTTTGCATGTTCATGTTG 59.303 34.615 25.03 5.29 44.30 3.33
4672 4784 5.945155 GCTGCTAGTAGCTTCGATAGTTAT 58.055 41.667 23.83 0.00 42.97 1.89
4841 4953 8.397906 ACTTTCATTATCACATCGTTGGTTATG 58.602 33.333 0.00 0.00 0.00 1.90
4848 4960 4.020573 TCACATCGTTGGTTATGGACTTCT 60.021 41.667 0.00 0.00 0.00 2.85
5110 5224 3.122613 CGTCAAGCTCTGAAGATGAACAC 59.877 47.826 6.14 0.00 35.73 3.32
5115 5229 6.263842 TCAAGCTCTGAAGATGAACACAAAAT 59.736 34.615 0.00 0.00 0.00 1.82
5117 5231 7.047460 AGCTCTGAAGATGAACACAAAATTT 57.953 32.000 0.00 0.00 0.00 1.82
5120 5234 7.540055 GCTCTGAAGATGAACACAAAATTTAGG 59.460 37.037 0.00 0.00 0.00 2.69
5239 5353 1.142748 CTGAGCGAGGGTTGCTAGG 59.857 63.158 0.00 0.00 44.18 3.02
5282 5398 3.791245 TGCCATGTTCTGTTTTTGGTTC 58.209 40.909 0.00 0.00 0.00 3.62
5283 5399 3.196469 TGCCATGTTCTGTTTTTGGTTCA 59.804 39.130 0.00 0.00 0.00 3.18
5332 5451 2.033424 GCTGGTTGTGTTGTTCTTCTCC 59.967 50.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 165 4.935205 TGAAAGGGTGACAGTATCGATTTG 59.065 41.667 1.71 5.62 0.00 2.32
163 169 3.132289 GGATGAAAGGGTGACAGTATCGA 59.868 47.826 0.00 0.00 0.00 3.59
167 173 2.976185 TGTGGATGAAAGGGTGACAGTA 59.024 45.455 0.00 0.00 0.00 2.74
249 255 7.749126 CCAAATACGTTATCACTCAAGGTTTTC 59.251 37.037 0.00 0.00 0.00 2.29
271 277 0.036388 GTGGATCGTCTCTGGCCAAA 60.036 55.000 7.01 0.00 0.00 3.28
308 316 7.943079 TGGAATCTTACATCAACATTGTGAT 57.057 32.000 0.00 0.00 38.84 3.06
318 326 7.815840 TTTGTGAAGTTGGAATCTTACATCA 57.184 32.000 0.00 0.00 0.00 3.07
439 447 7.004555 TCTAGTGGTGATCATAGTTTTGTGT 57.995 36.000 0.00 0.00 0.00 3.72
517 525 1.481871 CCTTTGGCTGCCATCTTGAT 58.518 50.000 24.03 0.00 31.53 2.57
531 539 2.741486 TTCCGGTCCCTTCGCCTTTG 62.741 60.000 0.00 0.00 0.00 2.77
532 540 1.848886 ATTCCGGTCCCTTCGCCTTT 61.849 55.000 0.00 0.00 0.00 3.11
564 572 3.184683 GCTCGGAGAACTGCAGCG 61.185 66.667 15.27 9.11 34.09 5.18
577 585 0.999406 CGTATGTCAGGGTTTGCTCG 59.001 55.000 0.00 0.00 0.00 5.03
581 589 4.817517 AGTAAGTCGTATGTCAGGGTTTG 58.182 43.478 0.00 0.00 0.00 2.93
649 657 8.670490 ACAGGTCCTTCTACATCACTATCTATA 58.330 37.037 0.00 0.00 0.00 1.31
650 658 7.450014 CACAGGTCCTTCTACATCACTATCTAT 59.550 40.741 0.00 0.00 0.00 1.98
707 715 4.647611 TCGGCTTTTATTCTGTCCTTCAA 58.352 39.130 0.00 0.00 0.00 2.69
723 762 4.821805 TCTGTCTTCTTTTGATTTCGGCTT 59.178 37.500 0.00 0.00 0.00 4.35
727 766 7.800767 TCTCATTCTGTCTTCTTTTGATTTCG 58.199 34.615 0.00 0.00 0.00 3.46
734 773 6.432472 GGGTCAATCTCATTCTGTCTTCTTTT 59.568 38.462 0.00 0.00 0.00 2.27
735 774 5.942826 GGGTCAATCTCATTCTGTCTTCTTT 59.057 40.000 0.00 0.00 0.00 2.52
807 851 0.406361 TCGGCCCTGTTAAAACCCAT 59.594 50.000 0.00 0.00 0.00 4.00
848 892 1.446792 CGAGATGCGTGCAGGAACT 60.447 57.895 11.29 5.42 34.63 3.01
849 893 3.084579 CGAGATGCGTGCAGGAAC 58.915 61.111 11.29 0.32 34.64 3.62
919 963 3.521126 CCAATCTTTCCCTCTCTCCTTCA 59.479 47.826 0.00 0.00 0.00 3.02
1053 1097 0.185901 ACAGAGCAAGGGGAAAGCAA 59.814 50.000 0.00 0.00 0.00 3.91
1111 1177 2.543430 CGACCAAAAATGGCACCTTTTG 59.457 45.455 21.33 21.33 38.81 2.44
1112 1178 2.432510 TCGACCAAAAATGGCACCTTTT 59.567 40.909 0.00 0.00 0.00 2.27
1267 1335 1.303398 TTGCCCGTCCGCCAAAATA 60.303 52.632 0.00 0.00 0.00 1.40
1268 1336 2.598985 TTGCCCGTCCGCCAAAAT 60.599 55.556 0.00 0.00 0.00 1.82
1272 1340 4.697756 CTTCTTGCCCGTCCGCCA 62.698 66.667 0.00 0.00 0.00 5.69
1274 1342 0.103572 TATACTTCTTGCCCGTCCGC 59.896 55.000 0.00 0.00 0.00 5.54
1278 1349 5.163343 ACACATACATATACTTCTTGCCCGT 60.163 40.000 0.00 0.00 0.00 5.28
1290 1361 5.965486 AGACCAGAGGGACACATACATATA 58.035 41.667 0.00 0.00 38.05 0.86
1303 1374 5.116084 TCCATAATTTCAAGACCAGAGGG 57.884 43.478 0.00 0.00 41.29 4.30
1304 1375 5.104360 TCCTCCATAATTTCAAGACCAGAGG 60.104 44.000 0.00 0.00 38.81 3.69
1307 1378 5.009410 GCATCCTCCATAATTTCAAGACCAG 59.991 44.000 0.00 0.00 0.00 4.00
1331 1412 2.235845 ACATCGATCTGAGCACATGG 57.764 50.000 0.00 0.00 0.00 3.66
1337 1418 3.068873 AGAAACCCTACATCGATCTGAGC 59.931 47.826 0.00 0.00 0.00 4.26
1408 1490 5.645067 CACATATCAGTCCAAGAAGAAAGCA 59.355 40.000 0.00 0.00 0.00 3.91
1412 1494 8.324306 AGAAATCACATATCAGTCCAAGAAGAA 58.676 33.333 0.00 0.00 0.00 2.52
1433 1515 8.515414 GGCACTCAGTTAAGTATGAAAAGAAAT 58.485 33.333 0.00 0.00 0.00 2.17
1449 1531 0.471617 AGCTTCACAGGCACTCAGTT 59.528 50.000 0.00 0.00 34.60 3.16
1457 1539 0.255890 TTCCCCATAGCTTCACAGGC 59.744 55.000 0.00 0.00 0.00 4.85
1458 1540 2.487986 GGATTCCCCATAGCTTCACAGG 60.488 54.545 0.00 0.00 34.14 4.00
1513 1595 4.283978 TCAGCACCATCAAATTTGACCATT 59.716 37.500 22.71 4.59 40.49 3.16
1519 1601 5.068234 AGATGTCAGCACCATCAAATTTG 57.932 39.130 12.15 12.15 40.93 2.32
1535 1617 4.819769 AGCTTCTTTCTGAGTGAGATGTC 58.180 43.478 0.00 0.00 0.00 3.06
1543 1625 5.862845 TGATTCTTGAGCTTCTTTCTGAGT 58.137 37.500 0.00 0.00 0.00 3.41
1545 1627 5.862845 ACTGATTCTTGAGCTTCTTTCTGA 58.137 37.500 0.00 0.00 0.00 3.27
1552 1634 3.688673 CCTTGGACTGATTCTTGAGCTTC 59.311 47.826 0.00 0.00 0.00 3.86
1554 1636 2.641815 ACCTTGGACTGATTCTTGAGCT 59.358 45.455 0.00 0.00 0.00 4.09
1597 1679 1.144936 CTGCAACTCCTCCCGGATC 59.855 63.158 0.73 0.00 39.01 3.36
1598 1680 3.036429 GCTGCAACTCCTCCCGGAT 62.036 63.158 0.73 0.00 39.01 4.18
1599 1681 3.706373 GCTGCAACTCCTCCCGGA 61.706 66.667 0.73 0.00 37.82 5.14
1600 1682 4.785453 GGCTGCAACTCCTCCCGG 62.785 72.222 0.50 0.00 0.00 5.73
1602 1684 2.543067 AATCGGCTGCAACTCCTCCC 62.543 60.000 0.50 0.00 0.00 4.30
1603 1685 0.678048 AAATCGGCTGCAACTCCTCC 60.678 55.000 0.50 0.00 0.00 4.30
1604 1686 0.449388 CAAATCGGCTGCAACTCCTC 59.551 55.000 0.50 0.00 0.00 3.71
1605 1687 0.962356 CCAAATCGGCTGCAACTCCT 60.962 55.000 0.50 0.00 0.00 3.69
1606 1688 1.508088 CCAAATCGGCTGCAACTCC 59.492 57.895 0.50 0.00 0.00 3.85
1607 1689 0.960364 TCCCAAATCGGCTGCAACTC 60.960 55.000 0.50 0.00 0.00 3.01
1608 1690 0.962356 CTCCCAAATCGGCTGCAACT 60.962 55.000 0.50 0.00 0.00 3.16
1609 1691 1.508088 CTCCCAAATCGGCTGCAAC 59.492 57.895 0.50 0.00 0.00 4.17
1610 1692 1.678635 CCTCCCAAATCGGCTGCAA 60.679 57.895 0.50 0.00 0.00 4.08
1611 1693 2.045045 CCTCCCAAATCGGCTGCA 60.045 61.111 0.50 0.00 0.00 4.41
1612 1694 1.821332 CTCCTCCCAAATCGGCTGC 60.821 63.158 0.00 0.00 0.00 5.25
1613 1695 0.035056 AACTCCTCCCAAATCGGCTG 60.035 55.000 0.00 0.00 0.00 4.85
1614 1696 0.253327 GAACTCCTCCCAAATCGGCT 59.747 55.000 0.00 0.00 0.00 5.52
1615 1697 0.748367 GGAACTCCTCCCAAATCGGC 60.748 60.000 0.00 0.00 38.44 5.54
1616 1698 0.618458 TGGAACTCCTCCCAAATCGG 59.382 55.000 0.00 0.00 44.69 4.18
1617 1699 2.014068 GCTGGAACTCCTCCCAAATCG 61.014 57.143 0.00 0.00 44.69 3.34
1649 1731 2.229784 CTGCAAACTGAACCTTCCCATC 59.770 50.000 0.00 0.00 0.00 3.51
1769 1851 1.714794 GACATCCACTCCGTCACTTG 58.285 55.000 0.00 0.00 0.00 3.16
2073 2160 9.169468 CAAAACCATGAATACAATACGAATAGC 57.831 33.333 0.00 0.00 0.00 2.97
2092 2179 6.706295 GGATTAATTCCATTCACCAAAACCA 58.294 36.000 0.00 0.00 44.74 3.67
2106 2193 6.024552 TGTGCTGAAAACTGGATTAATTCC 57.975 37.500 0.00 0.00 45.69 3.01
2107 2194 7.092716 ACATGTGCTGAAAACTGGATTAATTC 58.907 34.615 0.00 0.00 0.00 2.17
2122 2209 3.220940 TCATCAACCAAACATGTGCTGA 58.779 40.909 0.00 0.00 0.00 4.26
2123 2210 3.646611 TCATCAACCAAACATGTGCTG 57.353 42.857 0.00 0.00 0.00 4.41
2124 2211 4.669206 TTTCATCAACCAAACATGTGCT 57.331 36.364 0.00 0.00 0.00 4.40
2125 2212 5.927954 AATTTCATCAACCAAACATGTGC 57.072 34.783 0.00 0.00 0.00 4.57
2126 2213 7.958567 GCAATAATTTCATCAACCAAACATGTG 59.041 33.333 0.00 0.00 0.00 3.21
2127 2214 7.660617 TGCAATAATTTCATCAACCAAACATGT 59.339 29.630 0.00 0.00 0.00 3.21
2128 2215 8.030744 TGCAATAATTTCATCAACCAAACATG 57.969 30.769 0.00 0.00 0.00 3.21
2129 2216 7.879160 ACTGCAATAATTTCATCAACCAAACAT 59.121 29.630 0.00 0.00 0.00 2.71
2130 2217 7.171167 CACTGCAATAATTTCATCAACCAAACA 59.829 33.333 0.00 0.00 0.00 2.83
2131 2218 7.384660 TCACTGCAATAATTTCATCAACCAAAC 59.615 33.333 0.00 0.00 0.00 2.93
2135 2222 5.512788 CGTCACTGCAATAATTTCATCAACC 59.487 40.000 0.00 0.00 0.00 3.77
2148 2235 0.170339 TCGTCGATCGTCACTGCAAT 59.830 50.000 15.94 0.00 40.80 3.56
2172 2259 3.263681 AGTTTTAGGGGACTTACTGAGCC 59.736 47.826 0.00 0.00 43.67 4.70
2193 2280 2.821969 CCTCCCACATTTTTGACCTCAG 59.178 50.000 0.00 0.00 0.00 3.35
2194 2281 2.490718 CCCTCCCACATTTTTGACCTCA 60.491 50.000 0.00 0.00 0.00 3.86
2207 2294 4.494515 GGTGTGAAACCCTCCCAC 57.505 61.111 0.00 0.00 44.02 4.61
2347 2434 2.633488 GGTTACCCTTCTGATGACTGC 58.367 52.381 0.00 0.00 0.00 4.40
2585 2672 1.341877 TGAATGGGCCGATTGGTGATT 60.342 47.619 18.68 0.00 37.67 2.57
2613 2700 3.118811 GCTGGTAGGGATAGATGATCTGC 60.119 52.174 4.96 0.00 34.66 4.26
2706 2799 2.189594 TGATCTGCCACCACTTGAAG 57.810 50.000 0.00 0.00 0.00 3.02
2948 3047 7.912250 GCAAGTAAATGTTCTTCCATATCACTG 59.088 37.037 0.00 0.00 0.00 3.66
3452 3551 3.733443 ATGTCACCAACAAGGAAAAGC 57.267 42.857 0.00 0.00 42.37 3.51
3485 3584 0.899720 AAGATGCACATGCCCCAAAG 59.100 50.000 0.49 0.00 41.18 2.77
3832 3932 1.420514 CCTGCATCTCCATGACCAGAT 59.579 52.381 0.00 0.00 32.39 2.90
3860 3960 4.350368 TGAGTTTTGCCAGTACTCATCA 57.650 40.909 6.82 0.00 42.31 3.07
3911 4011 4.378774 AGCTCATCTTGAATCTTGGATCG 58.621 43.478 0.00 0.00 0.00 3.69
3938 4038 2.153366 CCTGTTGCAGGCGAAATTTT 57.847 45.000 1.93 0.00 45.13 1.82
3939 4039 3.892200 CCTGTTGCAGGCGAAATTT 57.108 47.368 1.93 0.00 45.13 1.82
3977 4077 9.109393 GTATCATGTATTTCAGAAAAGTAGCCA 57.891 33.333 0.00 0.00 0.00 4.75
3986 4086 7.125659 TCCTGGACAGTATCATGTATTTCAGAA 59.874 37.037 0.00 0.00 32.25 3.02
4004 4104 2.525368 TCATCGAAGAGTTCCTGGACA 58.475 47.619 0.00 0.00 43.63 4.02
4037 4137 1.812922 GCCACTCAGCTGATCCGTG 60.813 63.158 18.63 20.54 0.00 4.94
4068 4168 0.813210 GCATCCAGAGCTGCACTACC 60.813 60.000 1.02 0.00 38.28 3.18
4095 4195 4.796606 TCCCAATCTTCCAAAGGATCATC 58.203 43.478 0.00 0.00 0.00 2.92
4121 4221 1.605710 GACATCCGGCAATTGAGATGG 59.394 52.381 25.00 14.90 40.33 3.51
4135 4247 3.914312 TCGTCAAGTTCTGAAGACATCC 58.086 45.455 8.42 0.00 37.59 3.51
4226 4338 2.028876 GCAAGTGTGGGGTACTTTGTT 58.971 47.619 0.00 0.00 36.29 2.83
4417 4529 1.359848 GATGGCGAGGTGTGTTAGTG 58.640 55.000 0.00 0.00 0.00 2.74
4431 4543 2.508526 GGTTGGTGATCATAGGATGGC 58.491 52.381 0.00 0.00 32.67 4.40
4434 4546 3.397527 ACTGGGTTGGTGATCATAGGAT 58.602 45.455 0.00 0.00 36.13 3.24
4672 4784 3.506844 TGCAAACATGAGATTAAGCAGCA 59.493 39.130 0.00 0.00 0.00 4.41
4927 5040 2.356741 GGAACGAATCCCCTTCCATTCA 60.357 50.000 0.00 0.00 43.00 2.57
5110 5224 3.769300 CCAGGTCCCCTTCCTAAATTTTG 59.231 47.826 0.00 0.00 33.54 2.44
5115 5229 0.476808 TGCCAGGTCCCCTTCCTAAA 60.477 55.000 0.00 0.00 33.54 1.85
5117 5231 1.306997 CTGCCAGGTCCCCTTCCTA 60.307 63.158 0.00 0.00 33.54 2.94
5120 5234 4.785453 CGCTGCCAGGTCCCCTTC 62.785 72.222 0.00 0.00 0.00 3.46
5239 5353 4.982701 ACAGCAGCAGCCCCCAAC 62.983 66.667 0.00 0.00 43.56 3.77
5271 5385 3.634910 GGCTAGAACCTGAACCAAAAACA 59.365 43.478 0.00 0.00 0.00 2.83
5282 5398 2.162681 CACCCAAAAGGCTAGAACCTG 58.837 52.381 0.00 0.00 39.93 4.00
5283 5399 1.547901 GCACCCAAAAGGCTAGAACCT 60.548 52.381 0.00 0.00 43.91 3.50
5332 5451 3.966543 GGGTGGTGTGGGGGTGAG 61.967 72.222 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.