Multiple sequence alignment - TraesCS2D01G473000

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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 TraesCS2D01G473000 chr2D 100.000 3092 0 0 1 3092 576579453 576582544 0.000000e+00 5710.0
1 TraesCS2D01G473000 chr2D 85.832 1581 159 40 788 2322 576294093 576295654 0.000000e+00 1618.0
2 TraesCS2D01G473000 chr2D 85.282 1454 150 32 897 2322 576460505 576461922 0.000000e+00 1441.0
3 TraesCS2D01G473000 chr2D 91.101 427 35 3 1 424 547776910 547776484 2.670000e-160 575.0
4 TraesCS2D01G473000 chr2D 89.336 422 40 5 3 421 484044570 484044989 2.730000e-145 525.0
5 TraesCS2D01G473000 chr2D 74.194 682 129 26 1366 2034 576291111 576291758 1.110000e-59 241.0
6 TraesCS2D01G473000 chr2A 91.397 1546 76 14 671 2192 714528678 714530190 0.000000e+00 2065.0
7 TraesCS2D01G473000 chr2A 84.621 1502 159 36 875 2322 714343949 714345432 0.000000e+00 1428.0
8 TraesCS2D01G473000 chr2A 89.766 684 41 8 1 681 714526565 714527222 0.000000e+00 848.0
9 TraesCS2D01G473000 chr2B 91.470 1313 83 20 422 1725 692614662 692615954 0.000000e+00 1777.0
10 TraesCS2D01G473000 chr2B 84.480 1424 153 39 812 2183 692489279 692490686 0.000000e+00 1343.0
11 TraesCS2D01G473000 chr2B 92.484 612 41 5 1805 2412 692616742 692617352 0.000000e+00 870.0
12 TraesCS2D01G473000 chr2B 88.485 330 30 5 2406 2728 692622404 692622732 2.890000e-105 392.0
13 TraesCS2D01G473000 chr2B 87.755 196 16 8 2900 3092 692625125 692625315 4.010000e-54 222.0
14 TraesCS2D01G473000 chr2B 98.361 61 1 0 2856 2916 692625046 692625106 1.170000e-19 108.0
15 TraesCS2D01G473000 chr2B 87.879 66 5 1 2208 2270 692524800 692524865 1.190000e-09 75.0
16 TraesCS2D01G473000 chrUn 84.480 1424 153 39 812 2183 328241970 328243377 0.000000e+00 1343.0
17 TraesCS2D01G473000 chrUn 89.074 421 40 6 1 419 32255884 32255468 4.570000e-143 518.0
18 TraesCS2D01G473000 chr1D 90.499 421 31 8 3 418 181630906 181630490 5.830000e-152 547.0
19 TraesCS2D01G473000 chr1D 90.000 410 34 7 2 408 426613725 426613320 9.820000e-145 523.0
20 TraesCS2D01G473000 chr4B 90.268 411 33 7 1 409 90464228 90463823 5.870000e-147 531.0
21 TraesCS2D01G473000 chr4B 90.625 96 8 1 2351 2445 574424678 574424773 3.240000e-25 126.0
22 TraesCS2D01G473000 chr3D 89.362 423 39 6 1 421 610421496 610421914 7.590000e-146 527.0
23 TraesCS2D01G473000 chr7B 89.074 421 41 4 1 419 725643598 725643181 4.570000e-143 518.0
24 TraesCS2D01G473000 chr7A 80.159 126 24 1 2351 2475 652674660 652674785 3.280000e-15 93.5
25 TraesCS2D01G473000 chr5D 100.000 28 0 0 2353 2380 285249803 285249776 6.000000e-03 52.8


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 TraesCS2D01G473000 chr2D 576579453 576582544 3091 False 5710.000000 5710 100.000000 1 3092 1 chr2D.!!$F3 3091
1 TraesCS2D01G473000 chr2D 576460505 576461922 1417 False 1441.000000 1441 85.282000 897 2322 1 chr2D.!!$F2 1425
2 TraesCS2D01G473000 chr2D 576291111 576295654 4543 False 929.500000 1618 80.013000 788 2322 2 chr2D.!!$F4 1534
3 TraesCS2D01G473000 chr2A 714526565 714530190 3625 False 1456.500000 2065 90.581500 1 2192 2 chr2A.!!$F2 2191
4 TraesCS2D01G473000 chr2A 714343949 714345432 1483 False 1428.000000 1428 84.621000 875 2322 1 chr2A.!!$F1 1447
5 TraesCS2D01G473000 chr2B 692489279 692490686 1407 False 1343.000000 1343 84.480000 812 2183 1 chr2B.!!$F1 1371
6 TraesCS2D01G473000 chr2B 692614662 692617352 2690 False 1323.500000 1777 91.977000 422 2412 2 chr2B.!!$F3 1990
7 TraesCS2D01G473000 chr2B 692622404 692625315 2911 False 240.666667 392 91.533667 2406 3092 3 chr2B.!!$F4 686
8 TraesCS2D01G473000 chrUn 328241970 328243377 1407 False 1343.000000 1343 84.480000 812 2183 1 chrUn.!!$F1 1371

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
67 68 0.372679 GATCAGACTACGTCGTCGCA 59.627 55.0 13.82 5.72 41.18 5.10 F
275 277 0.680280 TCTGGAGGAGGTACTGTCGC 60.680 60.0 0.00 0.00 41.55 5.19 F
917 3159 0.957362 ATAAGACGCCTAGGTACGGC 59.043 55.0 11.31 8.71 44.11 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1013 3278 0.395862 GATCTCCGGTGAGGTCCAGA 60.396 60.0 12.42 0.0 42.04 3.86 R
1629 3907 0.913934 TGGGGCCATAGAACTGAGCA 60.914 55.0 4.39 0.0 0.00 4.26 R
2670 5738 0.250858 CAACCTGGGAGCACATGACA 60.251 55.0 0.00 0.0 0.00 3.58 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
67 68 0.372679 GATCAGACTACGTCGTCGCA 59.627 55.000 13.82 5.72 41.18 5.10
86 87 2.022129 CGCCTGTGTCGTGTCCTTC 61.022 63.158 0.00 0.00 0.00 3.46
130 131 1.063717 GGCTTTGGGGATGAGAATCCA 60.064 52.381 7.05 0.00 42.49 3.41
133 134 3.818180 CTTTGGGGATGAGAATCCAGAG 58.182 50.000 7.05 0.00 42.49 3.35
142 144 6.052360 GGATGAGAATCCAGAGTTAACCTTC 58.948 44.000 0.88 0.00 40.43 3.46
143 145 6.352222 GGATGAGAATCCAGAGTTAACCTTCA 60.352 42.308 0.88 0.19 40.43 3.02
145 147 5.046304 TGAGAATCCAGAGTTAACCTTCAGG 60.046 44.000 0.88 1.05 42.17 3.86
214 216 5.007385 CGTAGCCTAGGAGTTGTGTATTT 57.993 43.478 14.75 0.00 0.00 1.40
225 227 8.161699 AGGAGTTGTGTATTTTTCGTTTATGT 57.838 30.769 0.00 0.00 0.00 2.29
241 243 8.317891 TCGTTTATGTTGTGTCTTGTATCATT 57.682 30.769 0.00 0.00 0.00 2.57
244 246 5.902613 ATGTTGTGTCTTGTATCATTGGG 57.097 39.130 0.00 0.00 0.00 4.12
245 247 4.078537 TGTTGTGTCTTGTATCATTGGGG 58.921 43.478 0.00 0.00 0.00 4.96
275 277 0.680280 TCTGGAGGAGGTACTGTCGC 60.680 60.000 0.00 0.00 41.55 5.19
293 295 1.399855 CGCGAGGTATACGACATCAGG 60.400 57.143 0.00 0.00 38.85 3.86
303 306 3.208747 ACGACATCAGGGTTTGTTTCT 57.791 42.857 0.00 0.00 0.00 2.52
392 395 1.078918 CGTTCTGATGCAGAGGCCA 60.079 57.895 5.01 0.00 41.75 5.36
402 405 1.635817 GCAGAGGCCAGGGGTTATCA 61.636 60.000 5.01 0.00 0.00 2.15
410 413 3.374764 GCCAGGGGTTATCATCCTTTTT 58.625 45.455 0.00 0.00 0.00 1.94
434 441 1.813192 AAAAAGGTGGTGCGTGGTG 59.187 52.632 0.00 0.00 0.00 4.17
446 453 1.954146 CGTGGTGTGTGGTCGAAGG 60.954 63.158 0.00 0.00 0.00 3.46
449 456 1.338890 TGGTGTGTGGTCGAAGGGAA 61.339 55.000 0.00 0.00 0.00 3.97
452 459 2.289819 GGTGTGTGGTCGAAGGGAAATA 60.290 50.000 0.00 0.00 0.00 1.40
455 462 3.816523 TGTGTGGTCGAAGGGAAATAAAC 59.183 43.478 0.00 0.00 0.00 2.01
456 463 3.189910 GTGTGGTCGAAGGGAAATAAACC 59.810 47.826 0.00 0.00 0.00 3.27
548 555 7.179338 TGCTATAGTTTTTATTGGCAAGGGAAA 59.821 33.333 5.96 3.46 0.00 3.13
762 2239 2.356313 AAGTCGAGCACACAGGCG 60.356 61.111 0.00 0.00 39.27 5.52
880 3085 9.286170 GGGACTACTTGATTAACTCTTTTCTTT 57.714 33.333 0.00 0.00 0.00 2.52
917 3159 0.957362 ATAAGACGCCTAGGTACGGC 59.043 55.000 11.31 8.71 44.11 5.68
950 3197 6.612306 GGGTGCAAATTCTGTTCTAGTTTAG 58.388 40.000 0.00 0.00 0.00 1.85
975 3240 5.584551 AGTTCAAGACCAATTAACTCCCT 57.415 39.130 0.00 0.00 0.00 4.20
1013 3278 1.825191 CGGCCATGGCTAACAGCAT 60.825 57.895 34.70 0.00 44.75 3.79
1144 3413 1.140375 ATTAGTTCGCCCGTCGTCC 59.860 57.895 0.00 0.00 39.67 4.79
1159 3428 3.766691 TCCAAGTCGGCGGCTACC 61.767 66.667 17.05 0.00 33.14 3.18
1200 3469 1.077930 AGACGGGATCGACGAGGAA 60.078 57.895 14.27 0.00 40.11 3.36
1255 3527 1.982395 AGCCAAGACACGGATCCGA 60.982 57.895 39.55 0.00 42.83 4.55
1274 3546 1.606668 GAATGTGACCGCCAAGTTCAA 59.393 47.619 0.00 0.00 0.00 2.69
1308 3580 4.936685 AGAGAAAAGGAGCCAGGTAAAT 57.063 40.909 0.00 0.00 0.00 1.40
1312 3584 6.069381 AGAGAAAAGGAGCCAGGTAAATGTAT 60.069 38.462 0.00 0.00 0.00 2.29
1328 3600 1.300931 TATCCAGCTTCGATGCGCC 60.301 57.895 16.59 0.00 38.13 6.53
1587 3865 2.270986 GGGCAGCCACAAGTTCCTG 61.271 63.158 15.19 0.00 0.00 3.86
1608 3886 3.716006 CACAGGTGCGTTCTGGCG 61.716 66.667 5.89 0.00 36.62 5.69
1629 3907 4.657824 CGGTCGCCGGTGTTCAGT 62.658 66.667 16.01 0.00 44.15 3.41
1725 4006 2.735663 CCAGATGATGCTTCGCTACATC 59.264 50.000 13.40 13.40 42.46 3.06
1736 4750 5.049336 TGCTTCGCTACATCTATACAGACTC 60.049 44.000 0.00 0.00 32.25 3.36
1737 4751 5.049336 GCTTCGCTACATCTATACAGACTCA 60.049 44.000 0.00 0.00 32.25 3.41
1738 4752 6.513556 GCTTCGCTACATCTATACAGACTCAA 60.514 42.308 0.00 0.00 32.25 3.02
1739 4753 7.511959 TTCGCTACATCTATACAGACTCAAT 57.488 36.000 0.00 0.00 32.25 2.57
1740 4754 6.903419 TCGCTACATCTATACAGACTCAATG 58.097 40.000 0.00 0.00 32.25 2.82
1741 4755 5.570973 CGCTACATCTATACAGACTCAATGC 59.429 44.000 0.00 0.00 32.25 3.56
1745 4759 2.035961 TCTATACAGACTCAATGCCGCC 59.964 50.000 0.00 0.00 0.00 6.13
1746 4760 0.541392 ATACAGACTCAATGCCGCCA 59.459 50.000 0.00 0.00 0.00 5.69
1792 4815 4.377708 TCGCGGTGATGCAGCACT 62.378 61.111 31.82 0.00 38.20 4.40
1988 5014 2.415010 CGCCATCCTCGAGACCAG 59.585 66.667 15.71 0.80 0.00 4.00
2002 5034 1.975363 GACCAGTGAGCGCTTCATGC 61.975 60.000 13.26 0.00 38.29 4.06
2058 5090 6.772605 TCATGAAGAGGAAGAAGTTGATCAA 58.227 36.000 3.38 3.38 0.00 2.57
2059 5091 7.400439 TCATGAAGAGGAAGAAGTTGATCAAT 58.600 34.615 12.12 0.00 0.00 2.57
2063 5095 5.319453 AGAGGAAGAAGTTGATCAATGCAA 58.681 37.500 12.12 0.00 0.00 4.08
2135 5189 1.534729 ACATTTCGGAAAGTGCCTCC 58.465 50.000 9.30 0.00 0.00 4.30
2185 5239 7.687941 AGATTGATGTACTAAAACCTTGGTG 57.312 36.000 0.00 0.00 0.00 4.17
2192 5246 6.622549 TGTACTAAAACCTTGGTGTTTGTTG 58.377 36.000 13.31 1.01 38.41 3.33
2197 5252 3.586100 ACCTTGGTGTTTGTTGACAAC 57.414 42.857 11.54 11.54 37.74 3.32
2283 5342 0.856982 TTGGATCCCTTGGGTGTTGT 59.143 50.000 9.90 0.00 0.00 3.32
2332 5392 1.236616 CCCTTGTGCACGAATGAGCA 61.237 55.000 13.13 0.00 39.47 4.26
2357 5417 5.635417 TCTCAGATAGCGAACCTCATATG 57.365 43.478 0.00 0.00 0.00 1.78
2382 5442 4.513406 AGGTTCTTTGTGGTGGAACTAA 57.487 40.909 0.00 0.00 39.20 2.24
2394 5455 3.284617 GTGGAACTAACACACAGGGTTT 58.715 45.455 0.00 0.00 38.67 3.27
2401 5462 3.655615 AACACACAGGGTTTAAGTCCA 57.344 42.857 2.11 0.00 0.00 4.02
2412 5473 3.335579 GTTTAAGTCCAAGACTCGGCAT 58.664 45.455 0.00 0.00 42.59 4.40
2421 5482 0.456221 AGACTCGGCATTGGTACTCG 59.544 55.000 0.00 0.00 0.00 4.18
2462 5523 8.953368 ATTTTAGGTTTTACGACGATATTCCT 57.047 30.769 0.00 6.39 0.00 3.36
2465 5526 5.969423 AGGTTTTACGACGATATTCCTTCA 58.031 37.500 0.00 0.00 0.00 3.02
2469 5530 5.823209 TTACGACGATATTCCTTCAGTGA 57.177 39.130 0.00 0.00 0.00 3.41
2472 5533 4.035792 ACGACGATATTCCTTCAGTGAGAG 59.964 45.833 0.00 0.00 0.00 3.20
2473 5534 4.555708 CGACGATATTCCTTCAGTGAGAGG 60.556 50.000 12.59 12.59 0.00 3.69
2491 5552 6.590292 GTGAGAGGAATCTTCAAATAACGACA 59.410 38.462 0.00 0.00 0.00 4.35
2582 5649 9.848710 AGATTTGATATGTCACAGATCTGAATT 57.151 29.630 29.27 3.89 33.78 2.17
2592 5659 7.068341 GTCACAGATCTGAATTAATGATTCGC 58.932 38.462 29.27 5.68 45.85 4.70
2597 5664 5.403897 TCTGAATTAATGATTCGCGGAAC 57.596 39.130 6.13 0.00 45.85 3.62
2602 5669 6.704050 TGAATTAATGATTCGCGGAACTATGA 59.296 34.615 6.13 0.00 45.85 2.15
2607 5674 5.403897 TGATTCGCGGAACTATGATTTTC 57.596 39.130 6.13 0.00 0.00 2.29
2637 5705 6.037098 TGAAAAAGTACAATGGGTGAAAACG 58.963 36.000 0.00 0.00 0.00 3.60
2654 5722 6.691388 GTGAAAACGAAGCAAACTATGAAAGT 59.309 34.615 0.00 0.00 41.49 2.66
2670 5738 4.204012 TGAAAGTTCTGTTTTGGATCGGT 58.796 39.130 0.00 0.00 0.00 4.69
2792 5860 0.105408 AAGTGTTAGTGTCCGCGGTT 59.895 50.000 27.15 11.99 0.00 4.44
2794 5862 0.877213 GTGTTAGTGTCCGCGGTTGT 60.877 55.000 27.15 11.08 0.00 3.32
2795 5863 0.876777 TGTTAGTGTCCGCGGTTGTG 60.877 55.000 27.15 0.00 0.00 3.33
2809 5877 2.384382 GGTTGTGAACACTTTCATGCG 58.616 47.619 6.51 0.00 43.72 4.73
2814 5882 4.930963 TGTGAACACTTTCATGCGAAAAT 58.069 34.783 6.51 0.00 43.72 1.82
2827 5895 2.253603 GCGAAAATGAACACTCATGCC 58.746 47.619 0.00 0.00 41.66 4.40
2828 5896 2.867429 CGAAAATGAACACTCATGCCC 58.133 47.619 0.00 0.00 41.66 5.36
2829 5897 2.228582 CGAAAATGAACACTCATGCCCA 59.771 45.455 0.00 0.00 41.66 5.36
2832 7420 3.880047 AATGAACACTCATGCCCAATG 57.120 42.857 0.00 0.00 41.66 2.82
2838 7426 4.032960 ACACTCATGCCCAATGTTCTAA 57.967 40.909 0.00 0.00 37.56 2.10
2987 8304 6.490040 GCACCTATAATCTATTTCCAGGCAAA 59.510 38.462 0.00 0.00 0.00 3.68
2994 8311 4.595986 TCTATTTCCAGGCAAACTAACCC 58.404 43.478 0.00 0.00 0.00 4.11
3004 8321 6.296026 CAGGCAAACTAACCCATAGCTATTA 58.704 40.000 2.64 0.00 34.78 0.98
3005 8322 6.942576 CAGGCAAACTAACCCATAGCTATTAT 59.057 38.462 2.64 0.00 34.78 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.645868 GGAGTGCATAAACTCGTCGC 59.354 55.000 0.00 0.00 46.31 5.19
67 68 2.694829 GAAGGACACGACACAGGCGT 62.695 60.000 0.00 0.00 43.67 5.68
86 87 0.764890 TTCAGTCCACCACCTTCAGG 59.235 55.000 0.00 0.00 42.17 3.86
214 216 8.144155 TGATACAAGACACAACATAAACGAAA 57.856 30.769 0.00 0.00 0.00 3.46
225 227 4.380843 ACCCCAATGATACAAGACACAA 57.619 40.909 0.00 0.00 0.00 3.33
241 243 1.009060 TCCAGATAGCCACTAACCCCA 59.991 52.381 0.00 0.00 0.00 4.96
244 246 2.630580 CTCCTCCAGATAGCCACTAACC 59.369 54.545 0.00 0.00 0.00 2.85
245 247 2.630580 CCTCCTCCAGATAGCCACTAAC 59.369 54.545 0.00 0.00 0.00 2.34
275 277 2.228059 ACCCTGATGTCGTATACCTCG 58.772 52.381 0.00 0.00 0.00 4.63
293 295 6.512297 TCTGGAAATAAAGCAGAAACAAACC 58.488 36.000 0.00 0.00 0.00 3.27
303 306 4.576053 CACCATCGATCTGGAAATAAAGCA 59.424 41.667 12.02 0.00 39.73 3.91
428 435 1.954146 CCTTCGACCACACACCACG 60.954 63.158 0.00 0.00 0.00 4.94
434 441 3.189910 GGTTTATTTCCCTTCGACCACAC 59.810 47.826 0.00 0.00 0.00 3.82
446 453 9.507329 TGCTATATCAGATCTTGGTTTATTTCC 57.493 33.333 0.00 0.00 0.00 3.13
449 456 9.007901 GCTTGCTATATCAGATCTTGGTTTATT 57.992 33.333 0.00 0.00 0.00 1.40
452 459 6.359804 TGCTTGCTATATCAGATCTTGGTTT 58.640 36.000 0.00 0.00 0.00 3.27
455 462 7.450124 AAATGCTTGCTATATCAGATCTTGG 57.550 36.000 0.00 0.00 0.00 3.61
456 463 9.823098 GTAAAATGCTTGCTATATCAGATCTTG 57.177 33.333 0.00 0.00 0.00 3.02
548 555 0.685097 AGATGTGCTACACCGTTGGT 59.315 50.000 0.00 0.00 35.62 3.67
762 2239 1.059549 CGTTGTTATCGGTTACGTGGC 59.940 52.381 0.00 0.00 41.85 5.01
870 3068 4.053009 AGGGGGAATCCAAAGAAAAGAG 57.947 45.455 0.09 0.00 37.22 2.85
880 3085 7.365295 GCGTCTTATATATAAAGGGGGAATCCA 60.365 40.741 0.09 0.00 37.22 3.41
917 3159 0.170116 AATTTGCACCCGCGTATGTG 59.830 50.000 4.92 10.78 42.97 3.21
950 3197 5.461526 GGAGTTAATTGGTCTTGAACTTGC 58.538 41.667 0.00 0.00 30.66 4.01
975 3240 2.741092 GGCGGTGGAGAACAGACA 59.259 61.111 0.00 0.00 31.22 3.41
1013 3278 0.395862 GATCTCCGGTGAGGTCCAGA 60.396 60.000 12.42 0.00 42.04 3.86
1144 3413 2.509336 CTGGTAGCCGCCGACTTG 60.509 66.667 0.00 0.00 0.00 3.16
1159 3428 5.500234 TGGGTAGAATTTGATCTTCCACTG 58.500 41.667 0.00 0.00 38.31 3.66
1255 3527 1.608590 CTTGAACTTGGCGGTCACATT 59.391 47.619 0.00 0.00 0.00 2.71
1274 3546 3.134442 CCTTTTCTCTAGGATGCTCAGCT 59.866 47.826 0.00 0.00 34.56 4.24
1328 3600 1.202348 ACGGAGAGAAGATGCACATCG 60.202 52.381 5.04 0.00 42.48 3.84
1369 3641 4.232221 GACTTGTCGACGAATTTCTGGTA 58.768 43.478 11.62 0.00 0.00 3.25
1629 3907 0.913934 TGGGGCCATAGAACTGAGCA 60.914 55.000 4.39 0.00 0.00 4.26
1725 4006 2.224042 TGGCGGCATTGAGTCTGTATAG 60.224 50.000 7.97 0.00 0.00 1.31
1767 4790 1.588932 CATCACCGCGACGCTGTAT 60.589 57.895 16.64 8.22 0.00 2.29
1792 4815 2.434185 GTCTGCCGCGACCATCAA 60.434 61.111 8.23 0.00 0.00 2.57
2058 5090 5.010012 ACGAGTCCTTTTGAATTTCTTGCAT 59.990 36.000 0.00 0.00 0.00 3.96
2059 5091 4.338118 ACGAGTCCTTTTGAATTTCTTGCA 59.662 37.500 0.00 0.00 0.00 4.08
2063 5095 7.562454 TTTGTACGAGTCCTTTTGAATTTCT 57.438 32.000 0.00 0.00 0.00 2.52
2135 5189 3.623863 ACATTTTCGGCTTACAAACGTG 58.376 40.909 0.00 0.00 0.00 4.49
2192 5246 6.593770 ACCTTCCATTTTTCAAGTTTGTTGTC 59.406 34.615 0.00 0.00 0.00 3.18
2197 5252 9.108284 ACATAAACCTTCCATTTTTCAAGTTTG 57.892 29.630 0.00 0.00 0.00 2.93
2209 5265 6.667414 TCATAAGGCAAACATAAACCTTCCAT 59.333 34.615 0.00 0.00 41.57 3.41
2299 5358 3.877508 GCACAAGGGTTCTGTATATGGTC 59.122 47.826 0.00 0.00 0.00 4.02
2332 5392 7.014134 CCATATGAGGTTCGCTATCTGAGATAT 59.986 40.741 3.65 0.00 0.00 1.63
2357 5417 3.217681 TCCACCACAAAGAACCTAACC 57.782 47.619 0.00 0.00 0.00 2.85
2363 5423 4.396790 TGTGTTAGTTCCACCACAAAGAAC 59.603 41.667 0.00 0.00 40.14 3.01
2382 5442 3.201266 TCTTGGACTTAAACCCTGTGTGT 59.799 43.478 0.00 0.00 0.00 3.72
2394 5455 2.354704 CCAATGCCGAGTCTTGGACTTA 60.355 50.000 10.67 0.00 43.53 2.24
2401 5462 1.135083 CGAGTACCAATGCCGAGTCTT 60.135 52.381 0.00 0.00 0.00 3.01
2441 5502 7.099266 TGAAGGAATATCGTCGTAAAACCTA 57.901 36.000 0.00 0.00 0.00 3.08
2453 5514 5.521906 TTCCTCTCACTGAAGGAATATCG 57.478 43.478 14.11 0.00 35.73 2.92
2462 5523 7.331934 CGTTATTTGAAGATTCCTCTCACTGAA 59.668 37.037 0.00 0.00 0.00 3.02
2465 5526 6.814146 GTCGTTATTTGAAGATTCCTCTCACT 59.186 38.462 0.00 0.00 0.00 3.41
2469 5530 9.099454 GTAATGTCGTTATTTGAAGATTCCTCT 57.901 33.333 0.00 0.00 0.00 3.69
2507 5568 3.793559 AGACACAACTTGCGTTTCTACT 58.206 40.909 0.00 0.00 0.00 2.57
2515 5576 1.800805 ATCTGGAGACACAACTTGCG 58.199 50.000 0.00 0.00 35.60 4.85
2532 5596 8.296713 TCTATACTTGAAGGTGCAAACAAAATC 58.703 33.333 0.00 0.00 0.00 2.17
2571 5638 5.406477 TCCGCGAATCATTAATTCAGATCTG 59.594 40.000 17.07 17.07 43.44 2.90
2573 5640 5.845985 TCCGCGAATCATTAATTCAGATC 57.154 39.130 8.23 0.00 43.44 2.75
2577 5644 6.704050 TCATAGTTCCGCGAATCATTAATTCA 59.296 34.615 8.23 0.00 43.44 2.57
2582 5649 7.225734 TGAAAATCATAGTTCCGCGAATCATTA 59.774 33.333 8.23 0.00 0.00 1.90
2584 5651 5.527214 TGAAAATCATAGTTCCGCGAATCAT 59.473 36.000 8.23 0.00 0.00 2.45
2590 5657 4.794248 TCATGAAAATCATAGTTCCGCG 57.206 40.909 0.00 0.00 34.28 6.46
2607 5674 7.377398 TCACCCATTGTACTTTTTCATTCATG 58.623 34.615 0.00 0.00 0.00 3.07
2637 5705 8.534778 CAAAACAGAACTTTCATAGTTTGCTTC 58.465 33.333 0.00 0.00 47.00 3.86
2654 5722 3.201353 TGACACCGATCCAAAACAGAA 57.799 42.857 0.00 0.00 0.00 3.02
2656 5724 2.813754 ACATGACACCGATCCAAAACAG 59.186 45.455 0.00 0.00 0.00 3.16
2665 5733 1.221840 GGGAGCACATGACACCGAT 59.778 57.895 0.00 0.00 0.00 4.18
2670 5738 0.250858 CAACCTGGGAGCACATGACA 60.251 55.000 0.00 0.00 0.00 3.58
2764 5832 5.579511 GCGGACACTAACACTTAACATGTAT 59.420 40.000 0.00 0.00 0.00 2.29
2775 5843 0.877213 ACAACCGCGGACACTAACAC 60.877 55.000 35.90 0.00 0.00 3.32
2783 5851 1.433837 AAGTGTTCACAACCGCGGAC 61.434 55.000 35.90 19.30 0.00 4.79
2784 5852 0.745128 AAAGTGTTCACAACCGCGGA 60.745 50.000 35.90 5.52 0.00 5.54
2785 5853 0.316689 GAAAGTGTTCACAACCGCGG 60.317 55.000 26.86 26.86 33.61 6.46
2792 5860 4.362932 TTTTCGCATGAAAGTGTTCACA 57.637 36.364 0.00 0.00 46.40 3.58
2794 5862 5.180367 TCATTTTCGCATGAAAGTGTTCA 57.820 34.783 11.37 0.00 46.27 3.18
2795 5863 5.458452 TGTTCATTTTCGCATGAAAGTGTTC 59.542 36.000 11.37 7.70 46.27 3.18
2809 5877 3.940209 TGGGCATGAGTGTTCATTTTC 57.060 42.857 0.00 0.00 42.12 2.29
2814 5882 2.291209 ACATTGGGCATGAGTGTTCA 57.709 45.000 0.00 0.00 36.24 3.18
2845 7433 2.368439 TGCTATTGGGCATGAGTGTTC 58.632 47.619 0.00 0.00 37.29 3.18
2848 7436 3.549423 CGATTTGCTATTGGGCATGAGTG 60.549 47.826 0.00 0.00 42.09 3.51
2849 7437 2.620115 CGATTTGCTATTGGGCATGAGT 59.380 45.455 0.00 0.00 42.09 3.41
2850 7438 2.880268 TCGATTTGCTATTGGGCATGAG 59.120 45.455 0.00 0.00 42.09 2.90
2851 7439 2.618241 GTCGATTTGCTATTGGGCATGA 59.382 45.455 0.00 0.00 42.09 3.07
2852 7440 2.620115 AGTCGATTTGCTATTGGGCATG 59.380 45.455 0.00 0.00 42.09 4.06
2853 7441 2.936202 AGTCGATTTGCTATTGGGCAT 58.064 42.857 0.00 0.00 42.09 4.40
2854 7442 2.418368 AGTCGATTTGCTATTGGGCA 57.582 45.000 0.00 0.00 40.74 5.36
2909 8191 7.591795 TGATTTTTGTTTTAAGATTCGCGCTTA 59.408 29.630 5.56 0.09 0.00 3.09
2956 8273 8.597662 TGGAAATAGATTATAGGTGCGTTTAC 57.402 34.615 0.00 0.00 0.00 2.01
2962 8279 5.560724 TGCCTGGAAATAGATTATAGGTGC 58.439 41.667 0.00 0.00 30.54 5.01
2987 8304 4.775780 TGCGGATAATAGCTATGGGTTAGT 59.224 41.667 7.09 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.