Multiple sequence alignment - TraesCS3A01G364200

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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 TraesCS3A01G364200 chr3A 100.000 3812 0 0 1 3812 613166784 613170595 0.000000e+00 7040
1 TraesCS3A01G364200 chr3A 79.252 535 63 21 3285 3809 35434912 35435408 2.840000e-86 329
2 TraesCS3A01G364200 chr3D 93.352 1745 77 20 2077 3812 470886192 470887906 0.000000e+00 2543
3 TraesCS3A01G364200 chr3D 90.570 1718 89 31 406 2064 470884504 470886207 0.000000e+00 2207
4 TraesCS3A01G364200 chr3D 85.612 417 30 14 4 403 470884155 470884558 9.860000e-111 411
5 TraesCS3A01G364200 chr3B 91.825 1688 92 23 406 2064 625328747 625330417 0.000000e+00 2311
6 TraesCS3A01G364200 chr3B 91.818 1210 47 16 2077 3250 625330402 625331595 0.000000e+00 1639
7 TraesCS3A01G364200 chr3B 92.918 466 30 1 3229 3694 625331609 625332071 0.000000e+00 675
8 TraesCS3A01G364200 chr3B 89.409 406 32 7 2 405 625328407 625328803 5.690000e-138 501
9 TraesCS3A01G364200 chr7D 77.293 458 66 18 3360 3810 69089165 69088739 6.370000e-58 235


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 TraesCS3A01G364200 chr3A 613166784 613170595 3811 False 7040.000000 7040 100.000000 1 3812 1 chr3A.!!$F2 3811
1 TraesCS3A01G364200 chr3D 470884155 470887906 3751 False 1720.333333 2543 89.844667 4 3812 3 chr3D.!!$F1 3808
2 TraesCS3A01G364200 chr3B 625328407 625332071 3664 False 1281.500000 2311 91.492500 2 3694 4 chr3B.!!$F1 3692

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
322 340 0.325602 AAAGTAATCCCCCGAACGCA 59.674 50.0 0.0 0.0 0.00 5.24 F
351 369 0.479378 TTACACAGAACCCCCAACCC 59.521 55.0 0.0 0.0 0.00 4.11 F
478 496 0.892358 ACGTTCCGTCAGTCCAGCTA 60.892 55.0 0.0 0.0 33.69 3.32 F
1905 1992 0.899717 TTGATCAGCAAAGCCCACCC 60.900 55.0 0.0 0.0 32.46 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1963 0.745486 TGCTGATCAACTGATGCGGG 60.745 55.000 0.00 0.00 34.37 6.13 R
2222 2313 2.541556 CAGAGTTTAGCGCTTAGGGTC 58.458 52.381 18.68 6.81 0.00 4.46 R
2364 2455 8.553153 TGGGATTTACCATCTGTAAGACAAATA 58.447 33.333 0.00 0.00 40.13 1.40 R
2990 3113 0.322456 GTTGCTCAGGTGGGCATACA 60.322 55.000 5.12 0.00 38.30 2.29 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
48 52 8.751215 TTATTAATCCTATAGAGCCCCTTTCA 57.249 34.615 0.00 0.00 0.00 2.69
104 108 5.507985 CCCAAATCTCCCTCAAAATATTCGC 60.508 44.000 0.00 0.00 0.00 4.70
108 112 3.627577 TCTCCCTCAAAATATTCGCTTGC 59.372 43.478 0.00 0.00 0.00 4.01
181 185 6.935208 AGATCCAGTGAATATGACATGACATG 59.065 38.462 19.01 14.02 0.00 3.21
186 190 8.074370 CCAGTGAATATGACATGACATGAATTC 58.926 37.037 22.19 18.82 0.00 2.17
270 284 5.521906 TTAGATCTTCTCCATTCAGACGG 57.478 43.478 0.00 0.00 0.00 4.79
291 305 3.306710 GGTTCCATTTTCTTCCCGCAAAT 60.307 43.478 0.00 0.00 0.00 2.32
297 311 6.648725 TCCATTTTCTTCCCGCAAATAAAAAG 59.351 34.615 0.00 0.00 0.00 2.27
322 340 0.325602 AAAGTAATCCCCCGAACGCA 59.674 50.000 0.00 0.00 0.00 5.24
346 364 1.422402 TGGTCTTTACACAGAACCCCC 59.578 52.381 0.00 0.00 28.11 5.40
348 366 2.158579 GGTCTTTACACAGAACCCCCAA 60.159 50.000 0.00 0.00 0.00 4.12
350 368 2.158579 TCTTTACACAGAACCCCCAACC 60.159 50.000 0.00 0.00 0.00 3.77
351 369 0.479378 TTACACAGAACCCCCAACCC 59.521 55.000 0.00 0.00 0.00 4.11
352 370 1.428718 TACACAGAACCCCCAACCCC 61.429 60.000 0.00 0.00 0.00 4.95
353 371 3.190391 ACAGAACCCCCAACCCCC 61.190 66.667 0.00 0.00 0.00 5.40
354 372 4.360405 CAGAACCCCCAACCCCCG 62.360 72.222 0.00 0.00 0.00 5.73
355 373 4.932605 AGAACCCCCAACCCCCGT 62.933 66.667 0.00 0.00 0.00 5.28
356 374 4.355720 GAACCCCCAACCCCCGTC 62.356 72.222 0.00 0.00 0.00 4.79
360 378 3.576259 CCCCAACCCCCGTCAGTT 61.576 66.667 0.00 0.00 0.00 3.16
361 379 2.518933 CCCAACCCCCGTCAGTTT 59.481 61.111 0.00 0.00 0.00 2.66
362 380 1.602605 CCCAACCCCCGTCAGTTTC 60.603 63.158 0.00 0.00 0.00 2.78
363 381 1.964373 CCAACCCCCGTCAGTTTCG 60.964 63.158 0.00 0.00 0.00 3.46
364 382 1.070105 CAACCCCCGTCAGTTTCGA 59.930 57.895 0.00 0.00 0.00 3.71
365 383 1.070275 AACCCCCGTCAGTTTCGAC 59.930 57.895 0.00 0.00 0.00 4.20
398 416 4.077184 GGGCCCACGTGTCATCGA 62.077 66.667 19.95 0.00 34.70 3.59
399 417 2.813908 GGCCCACGTGTCATCGAC 60.814 66.667 15.65 0.00 34.70 4.20
400 418 2.048597 GCCCACGTGTCATCGACA 60.049 61.111 15.65 0.00 40.50 4.35
453 471 4.460683 GCGGGCCCACGTGTCATA 62.461 66.667 24.92 0.00 35.98 2.15
478 496 0.892358 ACGTTCCGTCAGTCCAGCTA 60.892 55.000 0.00 0.00 33.69 3.32
492 510 2.184579 GCTACCCGTCAGCACTCC 59.815 66.667 0.00 0.00 38.93 3.85
537 557 3.412879 GAGCTCGACCCGGTGTAGC 62.413 68.421 11.34 11.34 0.00 3.58
565 585 3.515286 GAGACGTCCGGCGATGGA 61.515 66.667 22.10 0.00 44.77 3.41
626 647 2.442272 CCATCGTCCCCTCCGACT 60.442 66.667 0.00 0.00 37.12 4.18
628 649 2.442272 ATCGTCCCCTCCGACTGG 60.442 66.667 0.00 0.00 37.12 4.00
629 650 3.298300 ATCGTCCCCTCCGACTGGT 62.298 63.158 0.00 0.00 37.12 4.00
814 835 1.815866 CCTGGGCCCTTTAAATGCG 59.184 57.895 25.70 0.00 0.00 4.73
840 861 4.559063 CATGGAGGCCGGAGCAGG 62.559 72.222 5.05 0.00 42.56 4.85
952 978 1.087771 CGTTCACGTGCCCTAATCCC 61.088 60.000 11.67 0.00 34.11 3.85
1199 1225 3.069016 TGTTCGGTGTTATGTCTCTGTGT 59.931 43.478 0.00 0.00 0.00 3.72
1288 1352 4.922719 AGTAGATCGGATTCGTCTTGTTC 58.077 43.478 4.22 0.00 37.69 3.18
1330 1394 6.349426 GCGCGATGATTTTAGTTTTCGTATA 58.651 36.000 12.10 0.00 0.00 1.47
1331 1395 7.007697 GCGCGATGATTTTAGTTTTCGTATAT 58.992 34.615 12.10 0.00 0.00 0.86
1333 1397 8.211838 CGCGATGATTTTAGTTTTCGTATATGA 58.788 33.333 0.00 0.00 0.00 2.15
1334 1398 9.517361 GCGATGATTTTAGTTTTCGTATATGAG 57.483 33.333 0.00 0.00 0.00 2.90
1337 1401 7.847487 TGATTTTAGTTTTCGTATATGAGCCG 58.153 34.615 0.00 0.00 0.00 5.52
1410 1475 1.592223 CCCGTCTCTCCAAGTGGAC 59.408 63.158 0.00 0.00 39.78 4.02
1424 1489 4.809426 CCAAGTGGACACCGATTATCTTAC 59.191 45.833 0.00 0.00 37.39 2.34
1433 1498 5.245526 ACACCGATTATCTTACAGTATCCCC 59.754 44.000 0.00 0.00 0.00 4.81
1434 1499 4.461781 ACCGATTATCTTACAGTATCCCCG 59.538 45.833 0.00 0.00 0.00 5.73
1435 1500 4.421948 CGATTATCTTACAGTATCCCCGC 58.578 47.826 0.00 0.00 0.00 6.13
1480 1546 2.855963 GGATTCATGCTGCGATGTTTTG 59.144 45.455 10.40 0.00 0.00 2.44
1753 1840 8.759641 GTCACACATCTATATCAATGAACTGTC 58.240 37.037 4.67 0.00 0.00 3.51
1854 1941 6.238184 CCCTCAAAAGAAAATCACAAAAGCAC 60.238 38.462 0.00 0.00 0.00 4.40
1876 1963 6.688813 GCACTTAAAGCATGTATAACTCTTGC 59.311 38.462 0.00 0.00 36.61 4.01
1905 1992 0.899717 TTGATCAGCAAAGCCCACCC 60.900 55.000 0.00 0.00 32.46 4.61
1918 2005 1.203013 GCCCACCCACCTTTACTTTCT 60.203 52.381 0.00 0.00 0.00 2.52
1945 2034 7.013823 AGGAGAAGAGATGAAATTTCACTGA 57.986 36.000 22.71 0.43 40.49 3.41
1947 2036 6.093357 GGAGAAGAGATGAAATTTCACTGACC 59.907 42.308 22.71 14.31 40.49 4.02
1986 2075 3.565307 TGGAGCTTTGATCTTTGGTTGT 58.435 40.909 0.00 0.00 0.00 3.32
2001 2090 8.810652 TCTTTGGTTGTAATTTTCATACTTGC 57.189 30.769 0.00 0.00 0.00 4.01
2009 2098 7.721402 TGTAATTTTCATACTTGCACAAGGTT 58.279 30.769 14.51 0.00 42.53 3.50
2042 2131 5.294306 CGTGTACATGTTGGCTATCTTCAAT 59.706 40.000 2.30 0.00 0.00 2.57
2048 2137 4.661222 TGTTGGCTATCTTCAATCAACCA 58.339 39.130 0.00 0.00 35.13 3.67
2049 2138 4.701651 TGTTGGCTATCTTCAATCAACCAG 59.298 41.667 0.00 0.00 35.13 4.00
2050 2139 4.842531 TGGCTATCTTCAATCAACCAGA 57.157 40.909 0.00 0.00 0.00 3.86
2051 2140 5.178096 TGGCTATCTTCAATCAACCAGAA 57.822 39.130 0.00 0.00 0.00 3.02
2052 2141 5.569355 TGGCTATCTTCAATCAACCAGAAA 58.431 37.500 0.00 0.00 0.00 2.52
2053 2142 6.009589 TGGCTATCTTCAATCAACCAGAAAA 58.990 36.000 0.00 0.00 0.00 2.29
2054 2143 6.664816 TGGCTATCTTCAATCAACCAGAAAAT 59.335 34.615 0.00 0.00 0.00 1.82
2055 2144 7.178983 TGGCTATCTTCAATCAACCAGAAAATT 59.821 33.333 0.00 0.00 0.00 1.82
2056 2145 7.704047 GGCTATCTTCAATCAACCAGAAAATTC 59.296 37.037 0.00 0.00 0.00 2.17
2057 2146 8.465201 GCTATCTTCAATCAACCAGAAAATTCT 58.535 33.333 0.00 0.00 38.25 2.40
2222 2313 1.262950 TCAATCAGAACAAACGCCACG 59.737 47.619 0.00 0.00 0.00 4.94
2267 2358 6.017934 GCCGATAGTCATGTCAACACATTATT 60.018 38.462 0.00 0.00 40.66 1.40
2281 2372 8.253810 TCAACACATTATTGGTTGTTTCTTTCA 58.746 29.630 13.69 0.00 41.87 2.69
2506 2597 2.290323 GGTGGCCGAGAATATTATGGCT 60.290 50.000 18.99 0.49 45.06 4.75
2517 2608 0.466922 ATTATGGCTGCTCTGCACCC 60.467 55.000 0.00 0.00 35.08 4.61
2526 2617 1.602888 CTCTGCACCCAAGCAAGCT 60.603 57.895 0.00 0.00 45.13 3.74
2636 2727 4.202172 GCACTTTAGGCAACCAAGGTTTTA 60.202 41.667 0.79 0.00 36.00 1.52
2734 2826 8.557029 GGCAAGGTATAGTGTTGTTGTATATTC 58.443 37.037 0.00 0.00 0.00 1.75
2838 2957 1.628846 GCTTGGTGTCCTCTCCCTTTA 59.371 52.381 0.00 0.00 0.00 1.85
2855 2974 5.007528 TCCCTTTACGAACAAGGTAAAAACG 59.992 40.000 9.98 0.00 39.50 3.60
2856 2975 5.007528 CCCTTTACGAACAAGGTAAAAACGA 59.992 40.000 9.98 0.00 39.50 3.85
2857 2976 5.903530 CCTTTACGAACAAGGTAAAAACGAC 59.096 40.000 0.00 0.00 38.84 4.34
2858 2977 6.238184 CCTTTACGAACAAGGTAAAAACGACT 60.238 38.462 0.00 0.00 38.84 4.18
2859 2978 7.042791 CCTTTACGAACAAGGTAAAAACGACTA 60.043 37.037 0.00 0.00 38.84 2.59
2860 2979 7.763172 TTACGAACAAGGTAAAAACGACTAA 57.237 32.000 0.00 0.00 0.00 2.24
2861 2980 6.660887 ACGAACAAGGTAAAAACGACTAAA 57.339 33.333 0.00 0.00 0.00 1.85
2862 2981 6.477742 ACGAACAAGGTAAAAACGACTAAAC 58.522 36.000 0.00 0.00 0.00 2.01
2923 3046 1.067565 TGGTCTTGCTCTCTGCTTACG 60.068 52.381 0.00 0.00 43.37 3.18
2990 3113 0.326238 TCTGGAAAGCGATAGGGGGT 60.326 55.000 0.00 0.00 0.00 4.95
3259 3420 2.222227 ACCCAAATTCTTCTCCCAGC 57.778 50.000 0.00 0.00 0.00 4.85
3263 3424 3.563043 CCCAAATTCTTCTCCCAGCTCTT 60.563 47.826 0.00 0.00 0.00 2.85
3288 3449 9.480861 TTCAGAGAGTATATTTCTTCTCTTCCA 57.519 33.333 0.38 0.00 37.39 3.53
3340 3501 9.410556 CGATGAAGAAATTTTGTTTATTCACCT 57.589 29.630 11.34 0.00 40.81 4.00
3462 3623 7.065923 GGTTGAGATAAGATAACAAAGGTCACC 59.934 40.741 0.00 0.00 0.00 4.02
3520 3681 6.470278 AGTTAACGCCCTACTTTTTATGTCT 58.530 36.000 0.00 0.00 0.00 3.41
3604 3765 3.187700 CCTAGCGTTGTATCCAGTTCAC 58.812 50.000 0.00 0.00 0.00 3.18
3610 3771 3.813166 CGTTGTATCCAGTTCACTTTGGT 59.187 43.478 0.00 0.00 35.89 3.67
3615 3776 2.930950 TCCAGTTCACTTTGGTTGAGG 58.069 47.619 0.00 0.00 35.89 3.86
3627 3788 3.853623 GTTGAGGAAGCAACAGCAC 57.146 52.632 0.00 0.00 45.65 4.40
3646 3807 2.907910 CAAGTATGCTCACCACTTGC 57.092 50.000 11.05 0.00 41.75 4.01
3650 3811 2.499756 TATGCTCACCACTTGCGCGA 62.500 55.000 12.10 0.00 38.92 5.87
3658 3819 1.573932 CACTTGCGCGAATGTTCCA 59.426 52.632 12.10 0.00 0.00 3.53
3660 3821 0.447801 ACTTGCGCGAATGTTCCATC 59.552 50.000 12.10 0.00 0.00 3.51
3697 3858 7.201617 GCTTGCTATACCATTACTTTCGTCTTT 60.202 37.037 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 76 8.909423 TTTTGAGGGAGATTTGGGTATTTATT 57.091 30.769 0.00 0.00 0.00 1.40
78 82 6.770785 CGAATATTTTGAGGGAGATTTGGGTA 59.229 38.462 0.00 0.00 0.00 3.69
104 108 3.329231 TTGCACCGAACGAGCAAG 58.671 55.556 17.42 0.00 42.71 4.01
108 112 1.278637 GTTGGTTGCACCGAACGAG 59.721 57.895 0.00 0.00 42.58 4.18
186 190 9.061435 GGGAAACATTAAATAGAGAAGATCCAG 57.939 37.037 0.00 0.00 0.00 3.86
207 211 2.903784 TCTTGACAGAGGATTCGGGAAA 59.096 45.455 0.00 0.00 0.00 3.13
268 282 0.170339 GCGGGAAGAAAATGGAACCG 59.830 55.000 0.00 0.00 42.47 4.44
270 284 3.378911 TTTGCGGGAAGAAAATGGAAC 57.621 42.857 0.00 0.00 0.00 3.62
306 320 0.392060 AACTGCGTTCGGGGGATTAC 60.392 55.000 0.00 0.00 0.00 1.89
307 321 0.325602 AAACTGCGTTCGGGGGATTA 59.674 50.000 0.00 0.00 0.00 1.75
322 340 4.204799 GGGTTCTGTGTAAAGACCAAACT 58.795 43.478 0.00 0.00 0.00 2.66
334 352 2.774633 GGGGTTGGGGGTTCTGTGT 61.775 63.158 0.00 0.00 0.00 3.72
346 364 1.070105 TCGAAACTGACGGGGGTTG 59.930 57.895 0.00 0.00 0.00 3.77
348 366 2.739132 GTCGAAACTGACGGGGGT 59.261 61.111 0.00 0.00 0.00 4.95
381 399 4.077184 TCGATGACACGTGGGCCC 62.077 66.667 21.57 17.59 34.70 5.80
382 400 2.813908 GTCGATGACACGTGGGCC 60.814 66.667 21.57 9.12 32.09 5.80
383 401 2.048597 TGTCGATGACACGTGGGC 60.049 61.111 21.57 12.05 37.67 5.36
403 421 0.733909 GTCGAAACTAACGGGGGTCG 60.734 60.000 0.00 0.00 45.88 4.79
404 422 0.733909 CGTCGAAACTAACGGGGGTC 60.734 60.000 0.00 0.00 35.32 4.46
405 423 1.290009 CGTCGAAACTAACGGGGGT 59.710 57.895 0.00 0.00 35.32 4.95
406 424 4.173971 CGTCGAAACTAACGGGGG 57.826 61.111 0.00 0.00 35.32 5.40
534 554 0.386352 CGTCTCCGTTCGTTGTGCTA 60.386 55.000 0.00 0.00 0.00 3.49
565 585 1.299468 GATGCGCGACGGAAGAGAT 60.299 57.895 12.10 0.00 0.00 2.75
611 632 2.442272 CCAGTCGGAGGGGACGAT 60.442 66.667 0.00 0.00 42.82 3.73
623 644 3.660111 GTGTGCCGCCAACCAGTC 61.660 66.667 0.00 0.00 0.00 3.51
700 721 1.513586 CTCGGTAGTGAACGCGTCC 60.514 63.158 14.44 7.37 0.00 4.79
798 819 1.684049 CCCGCATTTAAAGGGCCCA 60.684 57.895 27.56 1.75 38.51 5.36
840 861 3.736482 CTACTCGACTCGTGGCGCC 62.736 68.421 22.73 22.73 0.00 6.53
1242 1279 4.838152 TCTGCTCCGCCGCAATCC 62.838 66.667 0.00 0.00 39.80 3.01
1254 1291 1.448922 GATCTACTCCGGCGTCTGCT 61.449 60.000 0.00 0.00 42.25 4.24
1262 1299 1.197264 GACGAATCCGATCTACTCCGG 59.803 57.143 0.00 0.00 46.57 5.14
1264 1301 3.315749 ACAAGACGAATCCGATCTACTCC 59.684 47.826 0.00 0.00 39.50 3.85
1265 1302 4.555348 ACAAGACGAATCCGATCTACTC 57.445 45.455 0.00 0.00 39.50 2.59
1266 1303 4.641094 AGAACAAGACGAATCCGATCTACT 59.359 41.667 0.00 0.00 39.50 2.57
1267 1304 4.922719 AGAACAAGACGAATCCGATCTAC 58.077 43.478 0.00 0.00 39.50 2.59
1288 1352 1.852895 CGCGAACGAGGAAGGATTAAG 59.147 52.381 0.00 0.00 43.93 1.85
1330 1394 2.434884 CAACAGACGGCGGCTCAT 60.435 61.111 15.04 0.00 0.00 2.90
1331 1395 4.680237 CCAACAGACGGCGGCTCA 62.680 66.667 15.04 0.00 0.00 4.26
1333 1397 4.681978 GTCCAACAGACGGCGGCT 62.682 66.667 10.88 10.88 35.30 5.52
1410 1475 5.621555 CGGGGATACTGTAAGATAATCGGTG 60.622 48.000 0.00 0.00 37.43 4.94
1424 1489 2.929592 GCTTATTACGGCGGGGATACTG 60.930 54.545 13.24 3.62 0.00 2.74
1433 1498 6.799925 CCAAATTAATAAGGCTTATTACGGCG 59.200 38.462 30.03 20.86 37.70 6.46
1434 1499 7.088272 CCCAAATTAATAAGGCTTATTACGGC 58.912 38.462 30.03 0.00 37.70 5.68
1435 1500 7.449086 TCCCCAAATTAATAAGGCTTATTACGG 59.551 37.037 30.03 25.62 37.70 4.02
1480 1546 1.949465 ATGAATCCTTCGCCCGTAAC 58.051 50.000 0.00 0.00 0.00 2.50
1753 1840 4.578105 ACCTGCTGTTTCTTGAAAGAGAAG 59.422 41.667 19.87 18.30 37.01 2.85
1854 1941 6.511767 CGGGCAAGAGTTATACATGCTTTAAG 60.512 42.308 0.00 0.00 37.20 1.85
1876 1963 0.745486 TGCTGATCAACTGATGCGGG 60.745 55.000 0.00 0.00 34.37 6.13
1918 2005 9.224267 CAGTGAAATTTCATCTCTTCTCCTTTA 57.776 33.333 23.05 0.00 39.73 1.85
1933 2022 8.073768 TCAAAACTTATCGGTCAGTGAAATTTC 58.926 33.333 11.41 11.41 0.00 2.17
1986 2075 9.906660 CTTAACCTTGTGCAAGTATGAAAATTA 57.093 29.630 10.56 0.00 36.72 1.40
2001 2090 3.128349 ACACGCTGTACTTAACCTTGTG 58.872 45.455 0.00 0.00 0.00 3.33
2196 2287 4.497340 GGCGTTTGTTCTGATTGAAACTGA 60.497 41.667 0.00 0.00 36.30 3.41
2222 2313 2.541556 CAGAGTTTAGCGCTTAGGGTC 58.458 52.381 18.68 6.81 0.00 4.46
2364 2455 8.553153 TGGGATTTACCATCTGTAAGACAAATA 58.447 33.333 0.00 0.00 40.13 1.40
2506 2597 1.900016 CTTGCTTGGGTGCAGAGCA 60.900 57.895 9.23 9.23 44.27 4.26
2517 2608 0.804364 TGTATTCCGCAGCTTGCTTG 59.196 50.000 6.58 0.00 42.25 4.01
2526 2617 4.729227 TCTTACATCACTGTATTCCGCA 57.271 40.909 0.00 0.00 37.68 5.69
2607 2698 4.027674 TGGTTGCCTAAAGTGCTGATTA 57.972 40.909 0.00 0.00 0.00 1.75
2790 2909 4.381292 GCTTAGTAGTAAAACGAGCCTGGA 60.381 45.833 0.00 0.00 31.42 3.86
2838 2957 6.091986 TGTTTAGTCGTTTTTACCTTGTTCGT 59.908 34.615 0.00 0.00 0.00 3.85
2855 2974 7.548427 GTCCAATAGTAAGGTCCTTGTTTAGTC 59.452 40.741 14.84 0.00 0.00 2.59
2856 2975 7.016858 TGTCCAATAGTAAGGTCCTTGTTTAGT 59.983 37.037 14.84 0.00 0.00 2.24
2857 2976 7.391620 TGTCCAATAGTAAGGTCCTTGTTTAG 58.608 38.462 14.84 0.20 0.00 1.85
2858 2977 7.319052 TGTCCAATAGTAAGGTCCTTGTTTA 57.681 36.000 14.84 4.45 0.00 2.01
2859 2978 6.195600 TGTCCAATAGTAAGGTCCTTGTTT 57.804 37.500 14.84 2.30 0.00 2.83
2860 2979 5.836024 TGTCCAATAGTAAGGTCCTTGTT 57.164 39.130 14.84 4.77 0.00 2.83
2861 2980 6.180472 CAATGTCCAATAGTAAGGTCCTTGT 58.820 40.000 14.84 4.05 0.00 3.16
2862 2981 5.590259 CCAATGTCCAATAGTAAGGTCCTTG 59.410 44.000 14.84 0.00 0.00 3.61
2990 3113 0.322456 GTTGCTCAGGTGGGCATACA 60.322 55.000 5.12 0.00 38.30 2.29
3156 3280 9.660544 ACTAAATTCCATCCCATATTAAGCTTT 57.339 29.630 3.20 0.00 0.00 3.51
3222 3348 1.864082 GGTTTGGGCAAATTTCACACG 59.136 47.619 0.00 0.00 32.36 4.49
3263 3424 9.653516 ATGGAAGAGAAGAAATATACTCTCTGA 57.346 33.333 1.42 0.00 38.53 3.27
3317 3478 9.311916 CACAGGTGAATAAACAAAATTTCTTCA 57.688 29.630 0.00 0.00 0.00 3.02
3340 3501 2.792500 CCTTGACACTGGCAACACA 58.208 52.632 0.00 0.00 46.17 3.72
3462 3623 3.689649 CCAGGACATTACTTTTCTTCCCG 59.310 47.826 0.00 0.00 0.00 5.14
3531 3692 5.627135 TGTTTGACCCTAAACTCCCTAAAG 58.373 41.667 0.00 0.00 40.36 1.85
3604 3765 2.544486 GCTGTTGCTTCCTCAACCAAAG 60.544 50.000 4.46 0.00 44.15 2.77
3610 3771 1.677576 CTTGTGCTGTTGCTTCCTCAA 59.322 47.619 0.00 0.00 40.48 3.02
3615 3776 2.589014 GCATACTTGTGCTGTTGCTTC 58.411 47.619 0.00 0.00 41.82 3.86
3650 3811 6.869913 CAAGCAATACAACTTGATGGAACATT 59.130 34.615 0.00 0.00 44.89 2.71
3658 3819 6.828273 TGGTATAGCAAGCAATACAACTTGAT 59.172 34.615 1.19 2.98 44.89 2.57
3660 3821 6.435430 TGGTATAGCAAGCAATACAACTTG 57.565 37.500 1.19 0.00 44.88 3.16
3711 3875 5.745227 CCTAAGCAGTATCCTCTTTTGGAA 58.255 41.667 0.00 0.00 39.85 3.53
3727 3891 3.196039 TGATTTACACTACGGCCTAAGCA 59.804 43.478 0.00 0.00 42.56 3.91


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

AutoCloner maintained by Alex Coulton.