Multiple sequence alignment - TraesCS5A01G043000

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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 TraesCS5A01G043000 chr5A 100.000 3109 0 0 1 3109 38795678 38798786 0.000000e+00 5742.0
1 TraesCS5A01G043000 chr5A 94.400 125 4 3 1586 1707 38797221 38797345 4.090000e-44 189.0
2 TraesCS5A01G043000 chr5A 94.400 125 4 3 1544 1668 38797263 38797384 4.090000e-44 189.0
3 TraesCS5A01G043000 chr5A 87.500 56 6 1 1228 1283 666949895 666949949 2.590000e-06 63.9
4 TraesCS5A01G043000 chr5A 92.105 38 3 0 1256 1293 528368670 528368707 2.000000e-03 54.7
5 TraesCS5A01G043000 chr5D 91.848 1742 78 22 743 2463 49305726 49307424 0.000000e+00 2372.0
6 TraesCS5A01G043000 chr5D 97.595 499 11 1 1 498 49303346 49303844 0.000000e+00 854.0
7 TraesCS5A01G043000 chr5D 89.506 648 60 6 2463 3109 49307470 49308110 0.000000e+00 813.0
8 TraesCS5A01G043000 chr5D 92.857 210 13 2 544 753 49303849 49304056 1.400000e-78 303.0
9 TraesCS5A01G043000 chr5D 91.489 47 1 3 1669 1712 49306525 49306571 9.310000e-06 62.1
10 TraesCS5A01G043000 chr5B 87.648 591 50 15 1623 2200 51975057 51975637 0.000000e+00 665.0
11 TraesCS5A01G043000 chr5B 83.228 632 68 12 2465 3078 51977978 51978589 2.110000e-151 545.0
12 TraesCS5A01G043000 chr5B 92.708 384 17 10 758 1130 51974369 51974752 7.580000e-151 544.0
13 TraesCS5A01G043000 chr5B 90.133 375 26 6 1282 1646 51974797 51975170 7.800000e-131 477.0
14 TraesCS5A01G043000 chr5B 87.651 413 28 5 9 411 51973817 51974216 2.830000e-125 459.0
15 TraesCS5A01G043000 chr5B 89.377 273 19 5 2194 2463 51975803 51976068 4.970000e-88 335.0
16 TraesCS5A01G043000 chr5B 96.000 50 1 1 1141 1189 321218097 321218048 2.570000e-11 80.5
17 TraesCS5A01G043000 chr5B 91.525 59 4 1 548 605 680607206 680607148 2.570000e-11 80.5
18 TraesCS5A01G043000 chr5B 86.301 73 7 1 1672 1741 51975064 51975136 3.320000e-10 76.8
19 TraesCS5A01G043000 chr5B 100.000 30 0 0 668 697 51974223 51974252 4.330000e-04 56.5
20 TraesCS5A01G043000 chr2D 92.958 71 3 2 545 614 618330178 618330247 5.490000e-18 102.0
21 TraesCS5A01G043000 chr2D 94.444 54 2 1 1141 1193 622871020 622871073 7.150000e-12 82.4
22 TraesCS5A01G043000 chr3B 93.939 66 2 2 550 614 599101330 599101394 7.100000e-17 99.0
23 TraesCS5A01G043000 chr7B 91.045 67 4 2 549 614 570439303 570439368 4.270000e-14 89.8
24 TraesCS5A01G043000 chr7B 92.308 39 3 0 1246 1284 131737155 131737193 4.330000e-04 56.5
25 TraesCS5A01G043000 chr7D 90.476 63 6 0 545 607 406363794 406363732 1.990000e-12 84.2
26 TraesCS5A01G043000 chr7D 97.872 47 1 0 1140 1186 535555476 535555522 7.150000e-12 82.4
27 TraesCS5A01G043000 chr7D 94.231 52 2 1 1143 1194 549121433 549121483 9.240000e-11 78.7
28 TraesCS5A01G043000 chr7D 89.655 58 6 0 1129 1186 25821460 25821403 1.200000e-09 75.0
29 TraesCS5A01G043000 chr2B 97.872 47 1 0 1140 1186 57036466 57036420 7.150000e-12 82.4
30 TraesCS5A01G043000 chr4B 91.525 59 3 2 1144 1201 34029088 34029145 2.570000e-11 80.5
31 TraesCS5A01G043000 chr4B 100.000 30 0 0 1254 1283 652003493 652003464 4.330000e-04 56.5
32 TraesCS5A01G043000 chr3A 97.826 46 1 0 1141 1186 18825548 18825593 2.570000e-11 80.5
33 TraesCS5A01G043000 chr7A 90.164 61 4 2 555 614 237383755 237383696 9.240000e-11 78.7
34 TraesCS5A01G043000 chr7A 92.453 53 4 0 555 607 596311359 596311307 3.320000e-10 76.8
35 TraesCS5A01G043000 chr1B 85.294 68 7 3 549 614 649310754 649310688 2.000000e-07 67.6
36 TraesCS5A01G043000 chr4D 94.286 35 2 0 1256 1290 6207683 6207649 2.000000e-03 54.7
37 TraesCS5A01G043000 chr3D 100.000 29 0 0 1256 1284 462811531 462811559 2.000000e-03 54.7
38 TraesCS5A01G043000 chr3D 100.000 29 0 0 1256 1284 525535647 525535675 2.000000e-03 54.7
39 TraesCS5A01G043000 chr3D 100.000 29 0 0 1256 1284 593227289 593227317 2.000000e-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 TraesCS5A01G043000 chr5A 38795678 38798786 3108 False 2040.0000 5742 96.266667 1 3109 3 chr5A.!!$F3 3108
1 TraesCS5A01G043000 chr5D 49303346 49308110 4764 False 880.8200 2372 92.659000 1 3109 5 chr5D.!!$F1 3108
2 TraesCS5A01G043000 chr5B 51973817 51978589 4772 False 394.7875 665 89.630750 9 3078 8 chr5B.!!$F1 3069

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
769 2460 0.035739 TCTTGGAACCCACTTACGGC 59.964 55.0 0.00 0.0 30.78 5.68 F
1784 3505 0.603707 CAGAGAACAAAGAGGCGCCA 60.604 55.0 31.54 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 3691 0.313987 TGGCCGTACTCTGATATGCG 59.686 55.0 0.0 0.0 0.00 4.73 R
2913 6767 0.676184 GAGCTATCTCCATCACGCCA 59.324 55.0 0.0 0.0 33.19 5.69 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
36 37 3.629398 CCATGGCTAGAGTGCTAAAAAGG 59.371 47.826 0.00 0.00 0.00 3.11
246 257 2.684374 CACTCCAATCGATGAATGCCAA 59.316 45.455 0.00 0.00 0.00 4.52
446 457 6.128063 ACTGCCGAGTTCCGTTCTATATATAC 60.128 42.308 0.00 0.00 36.31 1.47
483 494 6.254281 ACCAGGTCGATTTTTAACTCATTG 57.746 37.500 0.00 0.00 0.00 2.82
498 509 1.063642 TCATTGGGGTTGTGGTGTTCA 60.064 47.619 0.00 0.00 0.00 3.18
499 510 1.759445 CATTGGGGTTGTGGTGTTCAA 59.241 47.619 0.00 0.00 0.00 2.69
501 512 0.396417 TGGGGTTGTGGTGTTCAAGG 60.396 55.000 0.00 0.00 0.00 3.61
502 513 0.396556 GGGGTTGTGGTGTTCAAGGT 60.397 55.000 0.00 0.00 0.00 3.50
503 514 1.133730 GGGGTTGTGGTGTTCAAGGTA 60.134 52.381 0.00 0.00 0.00 3.08
504 515 2.657143 GGGTTGTGGTGTTCAAGGTAA 58.343 47.619 0.00 0.00 0.00 2.85
505 516 3.025262 GGGTTGTGGTGTTCAAGGTAAA 58.975 45.455 0.00 0.00 0.00 2.01
506 517 3.639561 GGGTTGTGGTGTTCAAGGTAAAT 59.360 43.478 0.00 0.00 0.00 1.40
507 518 4.828387 GGGTTGTGGTGTTCAAGGTAAATA 59.172 41.667 0.00 0.00 0.00 1.40
508 519 5.302313 GGGTTGTGGTGTTCAAGGTAAATAA 59.698 40.000 0.00 0.00 0.00 1.40
509 520 6.443792 GGTTGTGGTGTTCAAGGTAAATAAG 58.556 40.000 0.00 0.00 0.00 1.73
510 521 6.443792 GTTGTGGTGTTCAAGGTAAATAAGG 58.556 40.000 0.00 0.00 0.00 2.69
511 522 4.521256 TGTGGTGTTCAAGGTAAATAAGGC 59.479 41.667 0.00 0.00 0.00 4.35
512 523 4.521256 GTGGTGTTCAAGGTAAATAAGGCA 59.479 41.667 0.00 0.00 0.00 4.75
513 524 4.764823 TGGTGTTCAAGGTAAATAAGGCAG 59.235 41.667 0.00 0.00 0.00 4.85
514 525 4.380550 GGTGTTCAAGGTAAATAAGGCAGC 60.381 45.833 0.00 0.00 0.00 5.25
515 526 4.217550 GTGTTCAAGGTAAATAAGGCAGCA 59.782 41.667 0.00 0.00 0.00 4.41
516 527 4.458989 TGTTCAAGGTAAATAAGGCAGCAG 59.541 41.667 0.00 0.00 0.00 4.24
517 528 3.016736 TCAAGGTAAATAAGGCAGCAGC 58.983 45.455 0.00 0.00 41.10 5.25
518 529 3.019564 CAAGGTAAATAAGGCAGCAGCT 58.980 45.455 0.00 0.00 41.70 4.24
519 530 2.648059 AGGTAAATAAGGCAGCAGCTG 58.352 47.619 18.93 18.93 41.70 4.24
528 539 4.400109 CAGCAGCTGCACCGCTTG 62.400 66.667 38.24 23.38 45.16 4.01
567 578 4.650131 ACAACCTACTCCTATAAGCACCTC 59.350 45.833 0.00 0.00 0.00 3.85
583 594 1.166129 CCTCCGAAAGACTGAGTCGA 58.834 55.000 6.99 0.00 37.67 4.20
584 595 1.746220 CCTCCGAAAGACTGAGTCGAT 59.254 52.381 6.99 0.00 37.67 3.59
588 599 5.413213 CCTCCGAAAGACTGAGTCGATATAT 59.587 44.000 6.99 0.00 37.67 0.86
616 627 5.459110 TGAAATTTACGAATGTACCGCTC 57.541 39.130 0.00 0.00 0.00 5.03
653 664 7.857885 GGTAAAATGATGTTCCATCTCGAAATC 59.142 37.037 5.87 0.00 0.00 2.17
661 672 6.226052 TGTTCCATCTCGAAATCCATGATAG 58.774 40.000 0.00 0.00 0.00 2.08
718 729 7.798071 ACAATTACCGGTTGGATTATTCTAGA 58.202 34.615 15.04 0.00 39.21 2.43
769 2460 0.035739 TCTTGGAACCCACTTACGGC 59.964 55.000 0.00 0.00 30.78 5.68
1008 2707 3.013219 GGAGGCTTCAAGAATGACTTCC 58.987 50.000 0.00 0.00 36.61 3.46
1086 2786 4.214971 TCTCTTCTCATGCTTGTGCTTTTC 59.785 41.667 0.00 0.00 40.48 2.29
1090 2790 6.262944 TCTTCTCATGCTTGTGCTTTTCTTTA 59.737 34.615 0.00 0.00 40.48 1.85
1210 2916 9.476928 AGATTCTATGTAACTAACCACACTAGT 57.523 33.333 0.00 0.00 0.00 2.57
1442 3148 2.282555 CGAGGTACATGTTGATCAAGCG 59.717 50.000 8.80 2.76 0.00 4.68
1521 3227 3.507377 AAGGCCAACAGGGTTCCCG 62.507 63.158 5.01 0.73 39.65 5.14
1532 3238 2.892425 GTTCCCGCCATCTGCTCG 60.892 66.667 0.00 0.00 38.05 5.03
1717 3426 3.210012 AAGCCCCGGTTGCTGATGT 62.210 57.895 15.66 0.00 39.48 3.06
1784 3505 0.603707 CAGAGAACAAAGAGGCGCCA 60.604 55.000 31.54 0.00 0.00 5.69
1786 3507 1.578206 GAGAACAAAGAGGCGCCACC 61.578 60.000 31.54 20.10 39.61 4.61
1787 3508 1.896660 GAACAAAGAGGCGCCACCA 60.897 57.895 31.54 0.00 43.14 4.17
1788 3509 1.228552 AACAAAGAGGCGCCACCAT 60.229 52.632 31.54 11.92 43.14 3.55
1865 3586 1.134699 CACCATGCGTACAGAGGTCAT 60.135 52.381 0.00 0.00 36.34 3.06
1873 3594 2.084546 GTACAGAGGTCATTGGGCAAC 58.915 52.381 0.00 0.00 0.00 4.17
1915 3636 6.284891 TGGCGTCAGATATGAATATGATGA 57.715 37.500 6.43 0.00 41.06 2.92
1959 3688 4.024725 CACATAGTCGTAGCTACAGTCCTC 60.025 50.000 23.21 6.74 0.00 3.71
1960 3689 2.041251 AGTCGTAGCTACAGTCCTCC 57.959 55.000 23.21 3.05 0.00 4.30
1961 3690 1.560611 AGTCGTAGCTACAGTCCTCCT 59.439 52.381 23.21 5.15 0.00 3.69
1962 3691 1.941975 GTCGTAGCTACAGTCCTCCTC 59.058 57.143 23.21 0.00 0.00 3.71
1979 3708 1.401670 CCTCGCATATCAGAGTACGGC 60.402 57.143 0.00 0.00 32.88 5.68
1984 3713 2.289072 GCATATCAGAGTACGGCCATGT 60.289 50.000 2.24 0.00 0.00 3.21
2084 3813 1.135373 TCGATGTTCAGCGAGGAGAAC 60.135 52.381 9.03 0.00 43.31 3.01
2162 3892 2.467566 TCTGTAAACTCTTTCGGCCC 57.532 50.000 0.00 0.00 0.00 5.80
2252 4156 6.041069 TGTGGTTTAGTTTTTCATAAGGTGGG 59.959 38.462 0.00 0.00 0.00 4.61
2287 4191 2.094762 AGAGGTAACGCATGTGGAAC 57.905 50.000 11.65 7.88 46.39 3.62
2310 4238 7.369803 ACAATAAGATGCTTGACTTGTAGTG 57.630 36.000 0.00 0.00 0.00 2.74
2311 4239 6.372659 ACAATAAGATGCTTGACTTGTAGTGG 59.627 38.462 0.00 0.00 0.00 4.00
2312 4240 4.357918 AAGATGCTTGACTTGTAGTGGT 57.642 40.909 0.00 0.00 0.00 4.16
2313 4241 3.931578 AGATGCTTGACTTGTAGTGGTC 58.068 45.455 0.00 0.00 0.00 4.02
2324 4252 6.038382 TGACTTGTAGTGGTCGAGAGATAATC 59.962 42.308 0.00 0.00 45.19 1.75
2370 4298 2.325583 TGCCGTCCATCCAATAGAAC 57.674 50.000 0.00 0.00 0.00 3.01
2371 4299 1.837439 TGCCGTCCATCCAATAGAACT 59.163 47.619 0.00 0.00 0.00 3.01
2394 4322 3.569049 AAAGCCGTGGTCCTCGACG 62.569 63.158 14.81 4.09 43.44 5.12
2425 4353 1.507141 CGAGCGGGCATGGAAATACC 61.507 60.000 0.00 0.00 39.54 2.73
2431 4359 3.815809 CGGGCATGGAAATACCTTTCTA 58.184 45.455 0.00 0.00 40.55 2.10
2463 4391 4.437121 CGTAGTCCTAGAAAACTCTGACGG 60.437 50.000 0.00 0.00 0.00 4.79
2464 4392 2.231721 AGTCCTAGAAAACTCTGACGGC 59.768 50.000 0.00 0.00 0.00 5.68
2465 4393 2.231721 GTCCTAGAAAACTCTGACGGCT 59.768 50.000 0.00 0.00 0.00 5.52
2481 6318 2.158726 ACGGCTAAGGGTTGTTTTCTGA 60.159 45.455 0.00 0.00 0.00 3.27
2483 6320 2.225727 GGCTAAGGGTTGTTTTCTGACG 59.774 50.000 0.00 0.00 0.00 4.35
2521 6358 4.562789 GCAAAAGGCGGATTTTATCACTTC 59.437 41.667 0.00 0.00 31.29 3.01
2528 6365 5.763204 GGCGGATTTTATCACTTCTATGGAA 59.237 40.000 0.00 0.00 0.00 3.53
2543 6380 1.209621 TGGAAACCGCTAGGCCTAAT 58.790 50.000 14.85 0.00 42.76 1.73
2581 6418 1.280421 CTTGACTGCTAGGCCTTCCTT 59.720 52.381 12.58 0.00 40.66 3.36
2623 6477 6.704493 TGTATTTTGCTAGGAGTTAATAGGCG 59.296 38.462 0.00 0.00 0.00 5.52
2636 6490 5.938125 AGTTAATAGGCGTTCACTTGATGTT 59.062 36.000 0.00 0.00 0.00 2.71
2639 6493 3.678056 AGGCGTTCACTTGATGTTAGA 57.322 42.857 0.00 0.00 0.00 2.10
2640 6494 4.002906 AGGCGTTCACTTGATGTTAGAA 57.997 40.909 0.00 0.00 0.00 2.10
2665 6519 6.796785 AAATGGAAATGGAGGATTAGGTTG 57.203 37.500 0.00 0.00 0.00 3.77
2711 6565 3.695830 AACTTGACGGCTTTGATAGGA 57.304 42.857 0.00 0.00 0.00 2.94
2728 6582 5.995282 TGATAGGACTGTTGTTGTGGTTAAG 59.005 40.000 0.00 0.00 0.00 1.85
2743 6597 2.092375 GGTTAAGAGGGCTGCATAACCT 60.092 50.000 13.50 9.25 41.34 3.50
2777 6631 3.303395 CGCTTTCTTGACTGAGTTGGTTC 60.303 47.826 0.00 0.00 0.00 3.62
2798 6652 6.072673 GGTTCGTACTTGTGGAGATGAAAATT 60.073 38.462 0.00 0.00 0.00 1.82
2819 6673 4.879295 TTATTCATGGTTGTGGGAGGAT 57.121 40.909 0.00 0.00 0.00 3.24
2820 6674 2.512692 TTCATGGTTGTGGGAGGATG 57.487 50.000 0.00 0.00 0.00 3.51
2878 6732 6.441093 AATGAAAATTTCAGCGCTAGATGA 57.559 33.333 10.99 0.00 43.98 2.92
2917 6771 7.935338 ATGCTATAATTGAAAATCTTTGGCG 57.065 32.000 0.00 0.00 0.00 5.69
2918 6772 6.862209 TGCTATAATTGAAAATCTTTGGCGT 58.138 32.000 0.00 0.00 0.00 5.68
2919 6773 6.751425 TGCTATAATTGAAAATCTTTGGCGTG 59.249 34.615 0.00 0.00 0.00 5.34
2920 6774 6.972328 GCTATAATTGAAAATCTTTGGCGTGA 59.028 34.615 0.00 0.00 0.00 4.35
2921 6775 7.649306 GCTATAATTGAAAATCTTTGGCGTGAT 59.351 33.333 0.00 0.00 0.00 3.06
2923 6777 3.574284 TGAAAATCTTTGGCGTGATGG 57.426 42.857 0.00 0.00 0.00 3.51
2924 6778 3.153130 TGAAAATCTTTGGCGTGATGGA 58.847 40.909 0.00 0.00 0.00 3.41
2939 6793 3.507233 GTGATGGAGATAGCTCTCTCAGG 59.493 52.174 25.39 0.00 46.11 3.86
2956 6810 2.821378 TCAGGACGTCGATTTACTTGGA 59.179 45.455 9.92 0.00 0.00 3.53
2958 6812 4.081862 TCAGGACGTCGATTTACTTGGAAT 60.082 41.667 9.92 0.00 0.00 3.01
2990 6844 8.780249 TCTTGCTACACCAACTTATTAAAAGTC 58.220 33.333 4.29 0.00 0.00 3.01
2996 6850 5.470777 CACCAACTTATTAAAAGTCGGGTCA 59.529 40.000 15.67 0.00 36.39 4.02
2998 6852 5.106436 CCAACTTATTAAAAGTCGGGTCACC 60.106 44.000 0.00 0.00 0.00 4.02
3005 6859 1.117142 AAGTCGGGTCACCTTTCGGA 61.117 55.000 0.00 0.00 33.28 4.55
3011 6865 1.202545 GGGTCACCTTTCGGATAGCTC 60.203 57.143 0.00 0.00 0.00 4.09
3056 6910 4.805192 CCCTAATTATGTTGTGTGCATTGC 59.195 41.667 0.46 0.46 0.00 3.56
3080 6934 4.703379 AGGGGACTTTCTGATCATGATC 57.297 45.455 25.91 25.91 37.44 2.92
3088 6942 1.973515 TCTGATCATGATCCCCTTCCG 59.026 52.381 28.61 11.12 37.02 4.30
3096 6950 1.278127 TGATCCCCTTCCGTTTGACTC 59.722 52.381 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 7.496263 CCCTCAACTAAAGAAAGGTATAGCTTC 59.504 40.741 17.11 10.80 0.00 3.86
246 257 0.249826 CGGCCACCAGTTTGCATTTT 60.250 50.000 2.24 0.00 0.00 1.82
423 434 5.942236 AGTATATATAGAACGGAACTCGGCA 59.058 40.000 0.00 0.00 44.45 5.69
446 457 3.665190 GACCTGGTTTCCTACAAGACAG 58.335 50.000 0.00 0.00 28.09 3.51
483 494 0.396556 ACCTTGAACACCACAACCCC 60.397 55.000 0.00 0.00 0.00 4.95
498 509 3.019564 CAGCTGCTGCCTTATTTACCTT 58.980 45.455 17.73 0.00 40.80 3.50
499 510 2.648059 CAGCTGCTGCCTTATTTACCT 58.352 47.619 17.73 0.00 40.80 3.08
536 547 9.662947 GCTTATAGGAGTAGGTTGTTAAAAGAA 57.337 33.333 0.00 0.00 0.00 2.52
537 548 8.818860 TGCTTATAGGAGTAGGTTGTTAAAAGA 58.181 33.333 0.00 0.00 0.00 2.52
538 549 8.880750 GTGCTTATAGGAGTAGGTTGTTAAAAG 58.119 37.037 0.00 0.00 0.00 2.27
539 550 7.825761 GGTGCTTATAGGAGTAGGTTGTTAAAA 59.174 37.037 0.00 0.00 0.00 1.52
540 551 7.181485 AGGTGCTTATAGGAGTAGGTTGTTAAA 59.819 37.037 0.00 0.00 0.00 1.52
541 552 6.670902 AGGTGCTTATAGGAGTAGGTTGTTAA 59.329 38.462 0.00 0.00 0.00 2.01
542 553 6.200114 AGGTGCTTATAGGAGTAGGTTGTTA 58.800 40.000 0.00 0.00 0.00 2.41
547 558 3.751245 CGGAGGTGCTTATAGGAGTAGGT 60.751 52.174 0.00 0.00 0.00 3.08
552 563 3.637229 TCTTTCGGAGGTGCTTATAGGAG 59.363 47.826 0.00 0.00 0.00 3.69
559 570 1.001406 CTCAGTCTTTCGGAGGTGCTT 59.999 52.381 0.00 0.00 35.32 3.91
567 578 6.242508 TGATATATCGACTCAGTCTTTCGG 57.757 41.667 2.61 0.00 33.50 4.30
588 599 7.675403 GCGGTACATTCGTAAATTTCAAGATGA 60.675 37.037 0.00 0.00 0.00 2.92
616 627 5.401550 ACATCATTTTACCATTCAACAGCG 58.598 37.500 0.00 0.00 0.00 5.18
653 664 7.448469 CCTAAATAACTTGAACCCCTATCATGG 59.552 40.741 0.00 0.00 0.00 3.66
661 672 7.284820 TGCTATACCTAAATAACTTGAACCCC 58.715 38.462 0.00 0.00 0.00 4.95
718 729 2.578021 ACTGGCCACAACCATTCTAGAT 59.422 45.455 0.00 0.00 39.54 1.98
1008 2707 0.868406 GCTCACAAACCTCTGGTTCG 59.132 55.000 2.22 0.00 46.20 3.95
1066 2766 4.500603 AGAAAAGCACAAGCATGAGAAG 57.499 40.909 0.00 0.00 45.49 2.85
1136 2838 7.007697 GCGTTTTTGACATTACACTAGTACAG 58.992 38.462 0.00 0.00 0.00 2.74
1210 2916 4.202121 GGAGTAGGACATAAGCGTCAATGA 60.202 45.833 0.00 0.00 37.66 2.57
1388 3094 3.020237 GCCGGTCAGGGTCTTCCTC 62.020 68.421 1.90 0.00 46.12 3.71
1442 3148 1.156736 CCACCGTGATCTTGTGGTTC 58.843 55.000 16.18 0.00 43.62 3.62
1521 3227 3.503363 GGTGTGCGAGCAGATGGC 61.503 66.667 0.00 0.00 45.30 4.40
1708 3417 2.747460 GCGGAGGCACATCAGCAA 60.747 61.111 2.62 0.00 39.77 3.91
1795 3516 2.976490 ATGGAGGTGGCTGGTGCTC 61.976 63.158 0.00 0.00 39.59 4.26
1797 3518 2.563013 ATCATGGAGGTGGCTGGTGC 62.563 60.000 0.00 0.00 38.76 5.01
1799 3520 1.825105 ATATCATGGAGGTGGCTGGT 58.175 50.000 0.00 0.00 0.00 4.00
1873 3594 1.335810 CATGAATGTTGCTCGGATGGG 59.664 52.381 0.00 0.00 0.00 4.00
1915 3636 1.875514 CTGCGTAATATGGTGCAGCAT 59.124 47.619 31.85 31.85 46.97 3.79
1959 3688 1.401670 GCCGTACTCTGATATGCGAGG 60.402 57.143 0.00 0.00 0.00 4.63
1960 3689 1.401670 GGCCGTACTCTGATATGCGAG 60.402 57.143 0.00 0.00 0.00 5.03
1961 3690 0.596577 GGCCGTACTCTGATATGCGA 59.403 55.000 0.00 0.00 0.00 5.10
1962 3691 0.313987 TGGCCGTACTCTGATATGCG 59.686 55.000 0.00 0.00 0.00 4.73
1979 3708 3.915575 GCTGAAGAGCCCACATGG 58.084 61.111 0.00 0.00 39.57 3.66
2084 3813 2.067091 CTATGCTGCATGCGTTGGGG 62.067 60.000 24.59 0.00 46.63 4.96
2162 3892 3.526931 TCTATCTCACTTGCCCTTTCG 57.473 47.619 0.00 0.00 0.00 3.46
2207 4109 6.321181 ACCACATATCCATTTTACACCACATC 59.679 38.462 0.00 0.00 0.00 3.06
2208 4110 6.194235 ACCACATATCCATTTTACACCACAT 58.806 36.000 0.00 0.00 0.00 3.21
2209 4111 5.575157 ACCACATATCCATTTTACACCACA 58.425 37.500 0.00 0.00 0.00 4.17
2210 4112 6.524101 AACCACATATCCATTTTACACCAC 57.476 37.500 0.00 0.00 0.00 4.16
2228 4130 6.452242 CCCACCTTATGAAAAACTAAACCAC 58.548 40.000 0.00 0.00 0.00 4.16
2242 4146 1.994885 ATCCCACGCCCCACCTTATG 61.995 60.000 0.00 0.00 0.00 1.90
2252 4156 1.369625 CTCTACACAAATCCCACGCC 58.630 55.000 0.00 0.00 0.00 5.68
2287 4191 6.372659 ACCACTACAAGTCAAGCATCTTATTG 59.627 38.462 0.00 0.00 0.00 1.90
2310 4238 4.202161 TGCCAGAAAGATTATCTCTCGACC 60.202 45.833 0.00 0.00 31.03 4.79
2311 4239 4.938080 TGCCAGAAAGATTATCTCTCGAC 58.062 43.478 0.00 0.00 31.03 4.20
2312 4240 5.598416 TTGCCAGAAAGATTATCTCTCGA 57.402 39.130 0.00 0.00 31.03 4.04
2313 4241 7.151308 ACTATTGCCAGAAAGATTATCTCTCG 58.849 38.462 0.00 0.00 31.03 4.04
2324 4252 5.741388 AAATAGCGACTATTGCCAGAAAG 57.259 39.130 11.25 0.00 36.85 2.62
2370 4298 0.535102 AGGACCACGGCTTTGTGAAG 60.535 55.000 0.00 0.00 42.55 3.02
2371 4299 0.534203 GAGGACCACGGCTTTGTGAA 60.534 55.000 0.00 0.00 42.55 3.18
2394 4322 1.345176 CCGCTCGCGAATGACTTTC 59.655 57.895 11.33 0.00 42.83 2.62
2425 4353 3.546670 GGACTACGTCGCAACATAGAAAG 59.453 47.826 0.00 0.00 32.65 2.62
2431 4359 2.362736 TCTAGGACTACGTCGCAACAT 58.637 47.619 0.00 0.00 32.65 2.71
2463 4391 2.225727 CCGTCAGAAAACAACCCTTAGC 59.774 50.000 0.00 0.00 0.00 3.09
2464 4392 3.735591 TCCGTCAGAAAACAACCCTTAG 58.264 45.455 0.00 0.00 0.00 2.18
2465 4393 3.388676 TCTCCGTCAGAAAACAACCCTTA 59.611 43.478 0.00 0.00 0.00 2.69
2481 6318 0.917533 TGCTCCCTAGTAGTCTCCGT 59.082 55.000 0.00 0.00 0.00 4.69
2483 6320 3.133183 CCTTTTGCTCCCTAGTAGTCTCC 59.867 52.174 0.00 0.00 0.00 3.71
2517 6354 2.158943 GCCTAGCGGTTTCCATAGAAGT 60.159 50.000 0.00 0.00 32.35 3.01
2521 6358 0.759346 AGGCCTAGCGGTTTCCATAG 59.241 55.000 1.29 0.00 0.00 2.23
2528 6365 4.498894 AGTAAAATTAGGCCTAGCGGTT 57.501 40.909 13.36 8.67 0.00 4.44
2567 6404 2.672098 CTAGAGAAGGAAGGCCTAGCA 58.328 52.381 5.16 0.00 46.28 3.49
2595 6432 9.614792 CCTATTAACTCCTAGCAAAATACACTT 57.385 33.333 0.00 0.00 0.00 3.16
2640 6494 7.457535 TCAACCTAATCCTCCATTTCCATTTTT 59.542 33.333 0.00 0.00 0.00 1.94
2665 6519 6.997222 AGACCGCACGTAAAACTTAATAATC 58.003 36.000 0.00 0.00 0.00 1.75
2711 6565 3.551846 CCCTCTTAACCACAACAACAGT 58.448 45.455 0.00 0.00 0.00 3.55
2728 6582 0.817229 GCTCAGGTTATGCAGCCCTC 60.817 60.000 0.00 0.00 0.00 4.30
2743 6597 0.685097 AGAAAGCGGGTTAGTGCTCA 59.315 50.000 0.00 0.00 41.46 4.26
2777 6631 9.490663 GAATAAATTTTCATCTCCACAAGTACG 57.509 33.333 0.00 0.00 0.00 3.67
2798 6652 4.017591 ACATCCTCCCACAACCATGAATAA 60.018 41.667 0.00 0.00 0.00 1.40
2868 6722 8.889849 TTAAACATAAAAAGTTCATCTAGCGC 57.110 30.769 0.00 0.00 0.00 5.92
2913 6767 0.676184 GAGCTATCTCCATCACGCCA 59.324 55.000 0.00 0.00 33.19 5.69
2914 6768 0.965439 AGAGCTATCTCCATCACGCC 59.035 55.000 0.00 0.00 40.22 5.68
2915 6769 2.346099 GAGAGCTATCTCCATCACGC 57.654 55.000 0.00 0.00 45.41 5.34
2924 6778 2.805295 CGACGTCCTGAGAGAGCTATCT 60.805 54.545 11.45 11.45 38.98 1.98
2939 6793 8.571461 ACTATTATTCCAAGTAAATCGACGTC 57.429 34.615 5.18 5.18 0.00 4.34
3005 6859 3.767309 ATTATCCCCTCTCGGAGCTAT 57.233 47.619 0.00 0.00 34.69 2.97
3011 6865 4.822350 GGAAAAGAAATTATCCCCTCTCGG 59.178 45.833 0.00 0.00 0.00 4.63
3026 6880 7.014711 TGCACACAACATAATTAGGGAAAAGAA 59.985 33.333 1.74 0.00 0.00 2.52
3028 6882 6.686630 TGCACACAACATAATTAGGGAAAAG 58.313 36.000 1.74 0.00 0.00 2.27
3044 6898 1.659233 CCCTTCGCAATGCACACAA 59.341 52.632 5.91 0.00 0.00 3.33
3056 6910 3.118629 TCATGATCAGAAAGTCCCCTTCG 60.119 47.826 0.09 0.00 0.00 3.79
3068 6922 1.973515 CGGAAGGGGATCATGATCAGA 59.026 52.381 31.49 0.00 39.54 3.27
3073 6927 1.912731 TCAAACGGAAGGGGATCATGA 59.087 47.619 0.00 0.00 0.00 3.07
3080 6934 1.900486 ACTAGAGTCAAACGGAAGGGG 59.100 52.381 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.