Multiple sequence alignment - TraesCS4D01G166000

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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 TraesCS4D01G166000 chr4D 100.000 7829 0 0 1 7829 279298322 279290494 0.000000e+00 14458
1 TraesCS4D01G166000 chr4D 85.714 518 69 4 7308 7823 479623797 479624311 6.910000e-150 542
2 TraesCS4D01G166000 chr4B 95.211 5930 191 27 1560 7460 266080588 266086453 0.000000e+00 9291
3 TraesCS4D01G166000 chr4B 95.081 1667 38 14 1 1644 266078957 266080602 0.000000e+00 2584
4 TraesCS4D01G166000 chr4B 84.461 547 72 8 7281 7823 68848791 68849328 1.930000e-145 527
5 TraesCS4D01G166000 chr4A 95.611 2757 80 18 4540 7285 353873334 353870608 0.000000e+00 4383
6 TraesCS4D01G166000 chr4A 92.398 2907 121 19 1685 4556 353876560 353873719 0.000000e+00 4052
7 TraesCS4D01G166000 chr4A 94.051 1597 55 14 1 1561 353878137 353876545 0.000000e+00 2386
8 TraesCS4D01G166000 chr3D 86.306 555 62 9 7282 7829 590322592 590323139 6.770000e-165 592
9 TraesCS4D01G166000 chr3D 85.143 525 71 5 7311 7829 527215541 527215018 1.500000e-146 531
10 TraesCS4D01G166000 chr3D 96.739 92 2 1 1568 1658 263812289 263812198 1.360000e-32 152
11 TraesCS4D01G166000 chr3D 95.745 94 3 1 1566 1658 313292472 313292379 4.890000e-32 150
12 TraesCS4D01G166000 chr3D 95.745 94 2 2 1569 1660 538897858 538897765 4.890000e-32 150
13 TraesCS4D01G166000 chr7D 85.118 551 72 6 7284 7829 14686579 14687124 8.880000e-154 555
14 TraesCS4D01G166000 chr3B 85.333 525 66 6 7314 7829 666643329 666642807 4.160000e-147 532
15 TraesCS4D01G166000 chr7A 85.086 523 73 4 7311 7829 279205945 279205424 5.380000e-146 529
16 TraesCS4D01G166000 chr7A 84.704 523 75 4 7311 7829 279193425 279192904 1.160000e-142 518
17 TraesCS4D01G166000 chr3A 83.514 552 82 5 7282 7829 661937011 661936465 2.520000e-139 507
18 TraesCS4D01G166000 chr6D 86.957 184 24 0 3581 3764 332492913 332492730 2.860000e-49 207
19 TraesCS4D01G166000 chr6B 83.010 206 33 2 3557 3761 487843375 487843579 1.340000e-42 185
20 TraesCS4D01G166000 chr2B 84.393 173 22 4 3590 3758 473771548 473771719 1.750000e-36 165
21 TraesCS4D01G166000 chr5D 97.701 87 2 0 1572 1658 275416873 275416959 4.890000e-32 150
22 TraesCS4D01G166000 chr1D 95.652 92 3 1 1568 1658 53382958 53382867 6.330000e-31 147
23 TraesCS4D01G166000 chr1D 95.652 92 3 1 1568 1658 164444019 164443928 6.330000e-31 147
24 TraesCS4D01G166000 chr1D 93.000 100 5 2 1566 1663 297377100 297377199 2.280000e-30 145
25 TraesCS4D01G166000 chr1A 95.652 92 3 1 1568 1658 292770815 292770724 6.330000e-31 147


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 TraesCS4D01G166000 chr4D 279290494 279298322 7828 True 14458.0 14458 100.000 1 7829 1 chr4D.!!$R1 7828
1 TraesCS4D01G166000 chr4D 479623797 479624311 514 False 542.0 542 85.714 7308 7823 1 chr4D.!!$F1 515
2 TraesCS4D01G166000 chr4B 266078957 266086453 7496 False 5937.5 9291 95.146 1 7460 2 chr4B.!!$F2 7459
3 TraesCS4D01G166000 chr4B 68848791 68849328 537 False 527.0 527 84.461 7281 7823 1 chr4B.!!$F1 542
4 TraesCS4D01G166000 chr4A 353870608 353878137 7529 True 3607.0 4383 94.020 1 7285 3 chr4A.!!$R1 7284
5 TraesCS4D01G166000 chr3D 590322592 590323139 547 False 592.0 592 86.306 7282 7829 1 chr3D.!!$F1 547
6 TraesCS4D01G166000 chr3D 527215018 527215541 523 True 531.0 531 85.143 7311 7829 1 chr3D.!!$R3 518
7 TraesCS4D01G166000 chr7D 14686579 14687124 545 False 555.0 555 85.118 7284 7829 1 chr7D.!!$F1 545
8 TraesCS4D01G166000 chr3B 666642807 666643329 522 True 532.0 532 85.333 7314 7829 1 chr3B.!!$R1 515
9 TraesCS4D01G166000 chr7A 279205424 279205945 521 True 529.0 529 85.086 7311 7829 1 chr7A.!!$R2 518
10 TraesCS4D01G166000 chr7A 279192904 279193425 521 True 518.0 518 84.704 7311 7829 1 chr7A.!!$R1 518
11 TraesCS4D01G166000 chr3A 661936465 661937011 546 True 507.0 507 83.514 7282 7829 1 chr3A.!!$R1 547

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
668 686 1.404843 GGGGTGTTTGGTTGCAAGTA 58.595 50.000 0.00 0.00 0.00 2.24 F
1525 1582 0.886490 CAGCCATCTATTGCCGACCC 60.886 60.000 0.00 0.00 0.00 4.46 F
2417 2547 1.603802 ACAATCACAGTGTTCCGCAAG 59.396 47.619 0.00 0.00 0.00 4.01 F
3984 4148 0.028902 GTGGGACTTTGACAACGTGC 59.971 55.000 7.66 7.66 0.00 5.34 F
4367 4541 0.253020 TAGGGTTTGGGGGTCTCCTC 60.253 60.000 0.00 0.00 35.33 3.71 F
4819 5403 1.208293 GGAGGTGAGTCTTGGGCTAAG 59.792 57.143 3.92 3.92 37.76 2.18 F
5889 6473 1.482593 ACCTCCAGCCATAGTTCTTCG 59.517 52.381 0.00 0.00 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1653 0.674534 ACCCATAAGATCTCGCGACC 59.325 55.000 3.71 0.0 0.00 4.79 R
3469 3612 1.236628 GTCGGATCTAGAGGCGCTAA 58.763 55.000 7.64 0.0 0.00 3.09 R
4306 4480 0.253894 CAGATCCAGCCACCACATCA 59.746 55.000 0.00 0.0 0.00 3.07 R
4819 5403 1.145119 ACCCTTCTCCCTTTTGGTGTC 59.855 52.381 0.00 0.0 38.10 3.67 R
5572 6156 1.200948 GAGCTGTCCTGGTTGCAAATC 59.799 52.381 0.00 0.0 0.00 2.17 R
6165 6749 2.619840 TTTTGCGCGCTTCTTGCCAA 62.620 50.000 33.29 12.7 38.78 4.52 R
7734 8345 0.821517 CACCGCTGGAGTACACCATA 59.178 55.000 12.75 0.0 39.34 2.74 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
62 63 1.749033 GCTCCCAGCCGCTAGTTAT 59.251 57.895 0.00 0.00 34.48 1.89
134 135 9.634021 AATCTTCCCTGATTTACTCTATTTTCC 57.366 33.333 0.00 0.00 33.33 3.13
162 163 5.305128 TCCTGCCAATTTGTTTCTCATTCTT 59.695 36.000 0.00 0.00 0.00 2.52
510 524 9.950680 GTTGATTCTCAGATTTGTTTCTTTGTA 57.049 29.630 0.00 0.00 0.00 2.41
521 535 5.888691 TGTTTCTTTGTATGTGTGTGTGT 57.111 34.783 0.00 0.00 0.00 3.72
544 562 1.412606 GCGCGCGCTTACATATCTC 59.587 57.895 44.38 13.88 38.26 2.75
668 686 1.404843 GGGGTGTTTGGTTGCAAGTA 58.595 50.000 0.00 0.00 0.00 2.24
1162 1181 7.598759 TTTAGAGGTACAAGTTCTTCTGACT 57.401 36.000 0.00 0.00 0.00 3.41
1227 1246 7.719778 TTGATATGTCATCAAAATCGAGGAG 57.280 36.000 0.00 0.00 35.35 3.69
1230 1249 7.439356 TGATATGTCATCAAAATCGAGGAGTTC 59.561 37.037 0.00 0.00 0.00 3.01
1346 1379 5.909610 CCTCAAGCTTTCTTTTTACTGTTCG 59.090 40.000 0.00 0.00 0.00 3.95
1380 1413 8.264347 TGAATCACATGTTAGACCTGCTTATTA 58.736 33.333 0.00 0.00 0.00 0.98
1418 1475 4.853743 GCGAAAAAGACCTGCTTATCTTTG 59.146 41.667 9.45 1.61 35.24 2.77
1420 1477 4.790765 AAAAGACCTGCTTATCTTTGGC 57.209 40.909 9.45 0.00 35.24 4.52
1525 1582 0.886490 CAGCCATCTATTGCCGACCC 60.886 60.000 0.00 0.00 0.00 4.46
1581 1638 2.038659 CCCCAACTTGTTTCCATGTGT 58.961 47.619 0.00 0.00 0.00 3.72
1596 1653 3.189910 CCATGTGTCAGAACCATGAGTTG 59.810 47.826 10.76 0.00 39.40 3.16
1633 1760 2.468915 GGTTTCACCTCTAGCCTACCT 58.531 52.381 0.00 0.00 34.73 3.08
1658 1785 3.636764 ACTTGTTTGGGACTAAAGGCTTG 59.363 43.478 0.00 0.00 0.00 4.01
1659 1786 3.306472 TGTTTGGGACTAAAGGCTTGT 57.694 42.857 0.00 0.00 0.00 3.16
1660 1787 4.440826 TGTTTGGGACTAAAGGCTTGTA 57.559 40.909 0.00 0.00 0.00 2.41
1661 1788 4.794334 TGTTTGGGACTAAAGGCTTGTAA 58.206 39.130 0.00 0.00 0.00 2.41
1662 1789 5.202004 TGTTTGGGACTAAAGGCTTGTAAA 58.798 37.500 0.00 0.00 0.00 2.01
1663 1790 5.068067 TGTTTGGGACTAAAGGCTTGTAAAC 59.932 40.000 0.00 4.37 0.00 2.01
1664 1791 4.440826 TGGGACTAAAGGCTTGTAAACA 57.559 40.909 0.00 0.00 0.00 2.83
1665 1792 4.794334 TGGGACTAAAGGCTTGTAAACAA 58.206 39.130 0.00 0.00 0.00 2.83
1666 1793 5.390387 TGGGACTAAAGGCTTGTAAACAAT 58.610 37.500 0.00 0.00 35.02 2.71
1667 1794 6.544650 TGGGACTAAAGGCTTGTAAACAATA 58.455 36.000 0.00 0.00 35.02 1.90
1668 1795 6.431852 TGGGACTAAAGGCTTGTAAACAATAC 59.568 38.462 0.00 0.00 35.02 1.89
1669 1796 6.431852 GGGACTAAAGGCTTGTAAACAATACA 59.568 38.462 0.00 0.00 35.02 2.29
1670 1797 7.122204 GGGACTAAAGGCTTGTAAACAATACAT 59.878 37.037 0.00 0.00 35.02 2.29
1671 1798 7.968405 GGACTAAAGGCTTGTAAACAATACATG 59.032 37.037 0.00 0.00 35.02 3.21
1672 1799 8.630054 ACTAAAGGCTTGTAAACAATACATGA 57.370 30.769 0.00 0.00 35.02 3.07
1675 1802 8.630054 AAAGGCTTGTAAACAATACATGAGTA 57.370 30.769 0.00 0.00 35.02 2.59
1740 1870 4.314961 CTGATATGGCAGCGTACCAATAA 58.685 43.478 0.00 0.00 41.49 1.40
1775 1905 6.273071 ACAATTACCTTTGAAGCAAGTTGAC 58.727 36.000 7.16 0.00 0.00 3.18
2048 2178 5.120830 CCTGTGACTAAGCATGTAGTGTTTC 59.879 44.000 0.96 0.00 34.40 2.78
2213 2343 7.877612 TGTCTACAGCAACTATTTCAGATTCAA 59.122 33.333 0.00 0.00 0.00 2.69
2373 2503 1.866601 GAACAATTGCCAGTTTGCACC 59.133 47.619 5.05 0.00 41.88 5.01
2417 2547 1.603802 ACAATCACAGTGTTCCGCAAG 59.396 47.619 0.00 0.00 0.00 4.01
2543 2673 6.815641 CACTTGCTGACTGTGTAAGATCTTAT 59.184 38.462 17.95 1.86 32.73 1.73
2790 2920 5.066505 GTGCACAAGATAAATCCCTACCAAG 59.933 44.000 13.17 0.00 0.00 3.61
2798 2928 2.254152 ATCCCTACCAAGAGCTGACA 57.746 50.000 0.00 0.00 0.00 3.58
3164 3303 5.746990 ATGGTAGCCTTGATATGGTAGTC 57.253 43.478 0.00 0.00 0.00 2.59
3466 3609 2.029649 CCTTCCTGTCATTTGTGGCAAG 60.030 50.000 0.00 0.00 0.00 4.01
3469 3612 3.030291 TCCTGTCATTTGTGGCAAGTTT 58.970 40.909 0.00 0.00 0.00 2.66
3479 3622 0.250727 TGGCAAGTTTTAGCGCCTCT 60.251 50.000 2.29 0.00 45.13 3.69
3609 3766 6.543465 TCACAACACAAGTCATGAAAGAATCT 59.457 34.615 0.00 0.00 0.00 2.40
3769 3926 2.097825 AGAAGGCTTCAACATGGCATC 58.902 47.619 27.70 0.00 0.00 3.91
3921 4085 7.531857 TGCACCCTAAACATGATTTTAGAAA 57.468 32.000 14.38 0.00 40.24 2.52
3984 4148 0.028902 GTGGGACTTTGACAACGTGC 59.971 55.000 7.66 7.66 0.00 5.34
4022 4186 4.011517 GCCGTCGTTGGGGAGGAA 62.012 66.667 0.00 0.00 0.00 3.36
4031 4205 3.157949 GGGGAGGAAGAGGAGGCG 61.158 72.222 0.00 0.00 0.00 5.52
4192 4366 1.408822 GGTGGTGGTGAATGATCTCCC 60.409 57.143 0.00 0.00 38.25 4.30
4194 4368 0.918983 GGTGGTGAATGATCTCCCCA 59.081 55.000 0.00 0.00 38.25 4.96
4248 4422 2.572284 GCTACGGGCTCGAGTGTT 59.428 61.111 15.95 0.00 40.11 3.32
4301 4475 3.912907 GGATCCGGATCCGCACGT 61.913 66.667 40.59 8.88 46.84 4.49
4306 4480 1.105167 TCCGGATCCGCACGTATCTT 61.105 55.000 29.12 0.00 38.24 2.40
4367 4541 0.253020 TAGGGTTTGGGGGTCTCCTC 60.253 60.000 0.00 0.00 35.33 3.71
4426 4600 4.335647 CCTTGCTGGGCCGACTGT 62.336 66.667 0.00 0.00 0.00 3.55
4499 4673 2.153898 TTAGGCTGGCCCACTGCAAT 62.154 55.000 8.11 0.00 44.93 3.56
4631 5208 5.715070 CCTCTCTAGATTATAACAAGGCCG 58.285 45.833 0.00 0.00 0.00 6.13
4719 5300 9.896263 TTAAATAAATGGGTTTTGAACTACGAC 57.104 29.630 0.00 0.00 0.00 4.34
4819 5403 1.208293 GGAGGTGAGTCTTGGGCTAAG 59.792 57.143 3.92 3.92 37.76 2.18
5572 6156 2.604462 GCAGTTCAAAAACAAGTGGCTG 59.396 45.455 0.00 0.00 37.88 4.85
5889 6473 1.482593 ACCTCCAGCCATAGTTCTTCG 59.517 52.381 0.00 0.00 0.00 3.79
5999 6583 8.930846 ATTTCCTTAGATGGTCATAATCTTGG 57.069 34.615 0.00 0.00 35.92 3.61
6075 6659 5.630680 GCTTCATTGGACATTAAAGTGTGTG 59.369 40.000 0.00 0.00 31.16 3.82
6076 6660 6.707440 TTCATTGGACATTAAAGTGTGTGT 57.293 33.333 0.00 0.00 31.16 3.72
6243 6827 2.348411 AAGCCGGGATGTAAAGGATG 57.652 50.000 2.18 0.00 0.00 3.51
6367 6951 9.689976 CCAGTAACATTTGAATAATGTTTGTCA 57.310 29.630 17.78 1.59 45.52 3.58
6399 6983 7.044798 GTCTACTTTATCTCTGGCACAATCTT 58.955 38.462 0.00 0.00 38.70 2.40
6412 6996 8.826710 TCTGGCACAATCTTTTATCTTATAACG 58.173 33.333 0.00 0.00 38.70 3.18
6494 7078 7.271511 AGAAGATAAGCTGTGTAGATCAAAGG 58.728 38.462 0.00 0.00 32.27 3.11
6571 7155 7.390440 TGTTGCAGTTGTATAGCTGATTTAGTT 59.610 33.333 7.52 0.00 37.32 2.24
6999 7583 1.326213 ACTGGAGATGGCTCGTGGAG 61.326 60.000 0.00 0.00 42.25 3.86
7015 7599 2.365617 GTGGAGATTCAAGGATCGCCTA 59.634 50.000 11.67 0.00 46.28 3.93
7017 7601 3.648067 TGGAGATTCAAGGATCGCCTATT 59.352 43.478 11.67 0.00 46.28 1.73
7018 7602 4.249661 GGAGATTCAAGGATCGCCTATTC 58.750 47.826 4.08 0.00 46.28 1.75
7019 7603 4.262635 GGAGATTCAAGGATCGCCTATTCA 60.263 45.833 4.08 0.00 46.28 2.57
7020 7604 5.486526 GAGATTCAAGGATCGCCTATTCAT 58.513 41.667 0.00 0.00 46.28 2.57
7024 7608 8.932610 AGATTCAAGGATCGCCTATTCATATAT 58.067 33.333 0.00 0.00 46.28 0.86
7117 7709 1.359848 AATCGTTAGTCGGCTGCAAG 58.640 50.000 0.00 0.00 40.32 4.01
7150 7742 0.250901 CACCAGTTAACCAGCCAGCT 60.251 55.000 0.88 0.00 0.00 4.24
7166 7759 1.128200 AGCTGTGACTGTTGGTACCA 58.872 50.000 11.60 11.60 0.00 3.25
7330 7924 3.214045 CCAATTGTTGGCATTGCGT 57.786 47.368 4.43 0.00 45.17 5.24
7381 7976 9.035607 CGTAGCCATATGATTCTCAATATAACC 57.964 37.037 3.65 0.00 0.00 2.85
7385 7980 9.113838 GCCATATGATTCTCAATATAACCGAAT 57.886 33.333 3.65 0.00 0.00 3.34
7405 8000 8.507249 ACCGAATTAGACTGAATTCTTTTTGAG 58.493 33.333 7.05 0.00 41.65 3.02
7526 8136 5.470098 ACCGTTCATTGGCTGATATATTCAC 59.530 40.000 0.00 0.00 32.72 3.18
7528 8138 5.389830 CGTTCATTGGCTGATATATTCACGG 60.390 44.000 0.00 0.00 32.72 4.94
7535 8146 5.187772 TGGCTGATATATTCACGGCTTAGAT 59.812 40.000 0.00 0.00 36.35 1.98
7536 8147 6.379988 TGGCTGATATATTCACGGCTTAGATA 59.620 38.462 0.00 0.00 36.35 1.98
7537 8148 7.069950 TGGCTGATATATTCACGGCTTAGATAT 59.930 37.037 0.00 0.00 36.35 1.63
7570 8181 2.857483 TGGTCAACGACAACCATCATT 58.143 42.857 0.00 0.00 40.60 2.57
7594 8205 4.402155 TGAAAGTCATTGTGGTTGCTCTTT 59.598 37.500 0.00 0.00 0.00 2.52
7601 8212 6.003326 TCATTGTGGTTGCTCTTTCTTATGA 58.997 36.000 0.00 0.00 0.00 2.15
7646 8257 5.183522 ACCCTTAGTTCTCTCTTTACTGTCG 59.816 44.000 0.00 0.00 0.00 4.35
7649 8260 6.294065 CCTTAGTTCTCTCTTTACTGTCGTGT 60.294 42.308 0.00 0.00 0.00 4.49
7672 8283 1.987855 CCACCAGCCGGACTCCTAA 60.988 63.158 5.05 0.00 35.59 2.69
7699 8310 1.445582 GCGTCCGTCTGATTCCGTT 60.446 57.895 0.00 0.00 0.00 4.44
7706 8317 2.414138 CCGTCTGATTCCGTTTTGTACC 59.586 50.000 0.00 0.00 0.00 3.34
7725 8336 1.227999 CGAATGTTGGTGACACGCCT 61.228 55.000 0.00 0.00 42.04 5.52
7734 8345 0.814010 GTGACACGCCTTGTTGGTCT 60.814 55.000 0.00 0.00 39.17 3.85
7818 8429 4.664688 ACTTCTGAACTCCCCATCATTT 57.335 40.909 0.00 0.00 0.00 2.32
7825 8436 3.567478 ACTCCCCATCATTTAGAGCAC 57.433 47.619 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 6.271488 TGAGAAACAAATTGGCAGGAATAG 57.729 37.500 0.00 0.00 0.00 1.73
510 524 4.312231 GCGCGCACACACACACAT 62.312 61.111 29.10 0.00 0.00 3.21
544 562 1.892209 AACAGCTAACCAAACCGGAG 58.108 50.000 9.46 0.00 38.63 4.63
1227 1246 5.886960 AGACATGACAGGCTAATTTGAAC 57.113 39.130 0.00 0.00 0.00 3.18
1230 1249 7.714377 AGAATCTAGACATGACAGGCTAATTTG 59.286 37.037 0.00 0.00 0.00 2.32
1346 1379 9.167311 AGGTCTAACATGTGATTCAAGTTAATC 57.833 33.333 0.00 0.00 38.92 1.75
1385 1418 6.705825 AGCAGGTCTTTTTCGCAAAATAAAAT 59.294 30.769 0.00 0.00 31.28 1.82
1390 1423 3.733443 AGCAGGTCTTTTTCGCAAAAT 57.267 38.095 0.00 0.00 31.28 1.82
1420 1477 2.198827 TGGTTCACATGCTTACCCAG 57.801 50.000 7.90 0.00 0.00 4.45
1550 1607 5.514500 AACAAGTTGGGGTACTCATGTAT 57.486 39.130 7.96 0.00 0.00 2.29
1554 1611 3.139397 TGGAAACAAGTTGGGGTACTCAT 59.861 43.478 7.96 0.00 37.44 2.90
1596 1653 0.674534 ACCCATAAGATCTCGCGACC 59.325 55.000 3.71 0.00 0.00 4.79
1633 1760 3.634910 GCCTTTAGTCCCAAACAAGTTGA 59.365 43.478 10.54 0.00 39.87 3.18
1662 1789 9.332502 TGTTTACAACAACTACTCATGTATTGT 57.667 29.630 0.00 0.00 38.72 2.71
1740 1870 5.491078 TCAAAGGTAATTGTCCCCAGTAGAT 59.509 40.000 0.00 0.00 0.00 1.98
1775 1905 5.939883 TGATCATAGAATTTCTTATGCCGGG 59.060 40.000 2.18 0.00 0.00 5.73
1892 2022 9.778741 ATAGACTTGACAAATAACAGAGTTCAA 57.221 29.630 0.00 0.00 0.00 2.69
2009 2139 1.002868 CAGGTGAACAGCAGGGGAG 60.003 63.158 6.76 0.00 0.00 4.30
2048 2178 6.940298 TCCTTGAATTTACCCTCAAACTGTAG 59.060 38.462 0.00 0.00 31.41 2.74
2185 2315 6.096673 TCTGAAATAGTTGCTGTAGACACA 57.903 37.500 0.00 0.00 0.00 3.72
2202 2332 9.701098 CTGAATCAAATTTCCTTGAATCTGAAA 57.299 29.630 0.00 0.00 38.75 2.69
2213 2343 5.950549 AGATGTGCTCTGAATCAAATTTCCT 59.049 36.000 0.00 0.00 31.12 3.36
2222 2352 5.534654 AGGTAGAGTAGATGTGCTCTGAATC 59.465 44.000 18.90 2.24 44.71 2.52
2373 2503 1.929836 GAACAGCTGAGCCATTACTCG 59.070 52.381 23.35 0.00 39.68 4.18
2417 2547 9.902684 ATCATTATCTCCATAATTGAGATCACC 57.097 33.333 9.41 0.00 44.30 4.02
2543 2673 9.256228 ACCAGAGTCTGTTTCACTATCTTTATA 57.744 33.333 18.74 0.00 0.00 0.98
2549 2679 4.464597 AGGACCAGAGTCTGTTTCACTATC 59.535 45.833 18.74 2.63 43.05 2.08
2591 2721 2.352561 TCACACCCCCTTAGATGGAA 57.647 50.000 0.00 0.00 0.00 3.53
2798 2928 9.321562 GAATGGATAATTGTCATTGAATTGCTT 57.678 29.630 4.48 0.00 32.05 3.91
3062 3192 5.423931 TCATAGAATAGCACACCCACTGTAA 59.576 40.000 0.00 0.00 0.00 2.41
3403 3546 6.464222 TGCAAGTTACTTACATTAGAGCAGT 58.536 36.000 0.00 0.00 0.00 4.40
3466 3609 2.034305 TCGGATCTAGAGGCGCTAAAAC 59.966 50.000 7.64 0.00 0.00 2.43
3469 3612 1.236628 GTCGGATCTAGAGGCGCTAA 58.763 55.000 7.64 0.00 0.00 3.09
3689 3846 4.323417 TCGCTTCCATTGTATGAGTTGTT 58.677 39.130 0.00 0.00 0.00 2.83
3921 4085 3.871006 ACGACGTGCATCATGTTAATCAT 59.129 39.130 0.00 0.00 33.38 2.45
4054 4228 2.972713 GGACCAAGCCATCTCTACCATA 59.027 50.000 0.00 0.00 0.00 2.74
4130 4304 3.781307 CCCATCCTTCCGCCGTCA 61.781 66.667 0.00 0.00 0.00 4.35
4295 4469 1.324435 CACCACATCAAGATACGTGCG 59.676 52.381 0.00 0.00 0.00 5.34
4301 4475 2.195727 TCCAGCCACCACATCAAGATA 58.804 47.619 0.00 0.00 0.00 1.98
4306 4480 0.253894 CAGATCCAGCCACCACATCA 59.746 55.000 0.00 0.00 0.00 3.07
4426 4600 2.736721 GAGCTTAACATGAGACGCAACA 59.263 45.455 0.00 0.00 0.00 3.33
4558 4733 6.438425 AGAGTTCATTTGATGCCCTAAACATT 59.562 34.615 0.00 0.00 0.00 2.71
4565 5142 3.726557 TCAGAGTTCATTTGATGCCCT 57.273 42.857 0.00 0.00 0.00 5.19
4631 5208 7.846644 TCCAAATGGATTGTATTTTTCATGC 57.153 32.000 0.00 0.00 39.78 4.06
4719 5300 9.220767 CAATTTTAGCCTAAGCCTACCTATTAG 57.779 37.037 0.00 0.00 41.25 1.73
4819 5403 1.145119 ACCCTTCTCCCTTTTGGTGTC 59.855 52.381 0.00 0.00 38.10 3.67
4866 5450 8.539117 AGACCCCAAGATCTATTTTATTTTGG 57.461 34.615 0.00 0.00 37.99 3.28
5016 5600 8.635765 ACTGTGGTTGTCAATTCAACTATTAT 57.364 30.769 9.21 0.00 44.66 1.28
5234 5818 1.969103 TCTGATGAATATCGCTCGCG 58.031 50.000 0.00 0.00 36.04 5.87
5572 6156 1.200948 GAGCTGTCCTGGTTGCAAATC 59.799 52.381 0.00 0.00 0.00 2.17
5637 6221 4.775236 AGTTCTCACAAGGATATGAAGCC 58.225 43.478 0.00 0.00 0.00 4.35
5916 6500 3.323403 AGTGAAGAAGCTGCTACAAGTCT 59.677 43.478 0.90 0.00 0.00 3.24
6075 6659 9.788960 CAAAGAAGGTAAGCTCCAAAATATAAC 57.211 33.333 0.00 0.00 0.00 1.89
6076 6660 8.466798 GCAAAGAAGGTAAGCTCCAAAATATAA 58.533 33.333 0.00 0.00 0.00 0.98
6165 6749 2.619840 TTTTGCGCGCTTCTTGCCAA 62.620 50.000 33.29 12.70 38.78 4.52
6243 6827 4.173256 CCCGAAGTTTCCATATTTTGTGC 58.827 43.478 0.00 0.00 0.00 4.57
6338 6922 8.849490 CAAACATTATTCAAATGTTACTGGACG 58.151 33.333 14.52 0.00 46.62 4.79
6367 6951 7.119846 GTGCCAGAGATAAAGTAGACACATTTT 59.880 37.037 0.00 0.00 0.00 1.82
6477 7061 4.040952 ACAAGTCCTTTGATCTACACAGCT 59.959 41.667 0.00 0.00 39.21 4.24
6494 7078 9.846248 AGTTGCTCATCATAAAATAAACAAGTC 57.154 29.630 0.00 0.00 0.00 3.01
6571 7155 7.116075 ACCAGCTATTACCGATTAAGTTACA 57.884 36.000 0.00 0.00 0.00 2.41
6581 7165 8.205512 TGTTCAATAATTACCAGCTATTACCGA 58.794 33.333 0.00 0.00 0.00 4.69
6613 7197 6.058553 AGTGACCATTCTCAATCAAGATCA 57.941 37.500 0.00 0.00 0.00 2.92
6999 7583 9.553064 AATATATGAATAGGCGATCCTTGAATC 57.447 33.333 0.00 0.00 40.66 2.52
7017 7601 9.807649 CACGGAGATGATGATTACAATATATGA 57.192 33.333 0.00 0.00 0.00 2.15
7018 7602 9.807649 TCACGGAGATGATGATTACAATATATG 57.192 33.333 0.00 0.00 0.00 1.78
7024 7608 5.237127 GCATTCACGGAGATGATGATTACAA 59.763 40.000 0.00 0.00 0.00 2.41
7150 7742 5.000591 CACAATATGGTACCAACAGTCACA 58.999 41.667 20.76 0.00 0.00 3.58
7166 7759 5.175859 ACCTCACGAACGAATTCACAATAT 58.824 37.500 6.22 0.00 34.14 1.28
7330 7924 5.530915 CCTTTTGGAGTAATGTGTCTGAACA 59.469 40.000 0.00 0.00 44.07 3.18
7511 8121 3.769739 AAGCCGTGAATATATCAGCCA 57.230 42.857 0.00 0.00 39.19 4.75
7535 8146 9.438228 TGTCGTTGACCATGTTTAGAAATAATA 57.562 29.630 0.00 0.00 0.00 0.98
7536 8147 8.330466 TGTCGTTGACCATGTTTAGAAATAAT 57.670 30.769 0.00 0.00 0.00 1.28
7537 8148 7.731882 TGTCGTTGACCATGTTTAGAAATAA 57.268 32.000 0.00 0.00 0.00 1.40
7570 8181 3.953612 AGAGCAACCACAATGACTTTCAA 59.046 39.130 0.00 0.00 0.00 2.69
7601 8212 5.431765 GGTGGACACTCTTGTGATAATCAT 58.568 41.667 3.03 0.00 46.55 2.45
7615 8226 3.166679 GAGAGAACTAAGGGTGGACACT 58.833 50.000 2.13 0.00 0.00 3.55
7646 8257 2.264794 CGGCTGGTGGGAGTACAC 59.735 66.667 0.00 0.00 40.60 2.90
7649 8260 2.682494 GTCCGGCTGGTGGGAGTA 60.682 66.667 12.43 0.00 36.30 2.59
7669 8280 3.736252 CAGACGGACGCATATCCTTTTAG 59.264 47.826 0.00 0.00 36.52 1.85
7672 8283 1.754803 TCAGACGGACGCATATCCTTT 59.245 47.619 0.00 0.00 36.52 3.11
7699 8310 3.312973 GTGTCACCAACATTCGGTACAAA 59.687 43.478 0.00 0.00 40.80 2.83
7706 8317 1.206578 GGCGTGTCACCAACATTCG 59.793 57.895 0.00 0.00 40.80 3.34
7725 8336 3.904965 TGGAGTACACCATAGACCAACAA 59.095 43.478 8.07 0.00 34.77 2.83
7734 8345 0.821517 CACCGCTGGAGTACACCATA 59.178 55.000 12.75 0.00 39.34 2.74


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

AutoCloner maintained by Alex Coulton.