Multiple sequence alignment - TraesCS1A01G408800

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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 TraesCS1A01G408800 chr1A 100.000 4017 0 0 1 4017 570445380 570449396 0.000000e+00 7419.0
1 TraesCS1A01G408800 chr1A 94.215 605 33 2 1486 2089 496325383 496325986 0.000000e+00 922.0
2 TraesCS1A01G408800 chr1A 81.673 251 19 9 459 704 570423805 570424033 2.470000e-42 183.0
3 TraesCS1A01G408800 chr1D 93.228 1521 55 12 2 1486 474920731 474922239 0.000000e+00 2194.0
4 TraesCS1A01G408800 chr1D 92.294 545 24 9 3480 4017 474924182 474924715 0.000000e+00 758.0
5 TraesCS1A01G408800 chr1D 94.572 479 26 0 2595 3073 474922751 474923229 0.000000e+00 741.0
6 TraesCS1A01G408800 chr1D 88.161 473 28 11 2091 2561 474922233 474922679 4.570000e-149 538.0
7 TraesCS1A01G408800 chr1D 87.654 81 3 7 3092 3167 474923219 474923297 1.990000e-13 87.9
8 TraesCS1A01G408800 chr2B 99.171 603 5 0 1487 2089 76907753 76907151 0.000000e+00 1086.0
9 TraesCS1A01G408800 chr2B 95.861 604 23 2 1486 2089 377780646 377781247 0.000000e+00 976.0
10 TraesCS1A01G408800 chr2A 97.529 607 14 1 1483 2089 202889399 202888794 0.000000e+00 1037.0
11 TraesCS1A01G408800 chr2A 95.387 607 28 0 1483 2089 62363643 62364249 0.000000e+00 966.0
12 TraesCS1A01G408800 chr2A 94.926 611 23 2 1487 2089 763918837 763918227 0.000000e+00 950.0
13 TraesCS1A01G408800 chr7A 97.181 603 17 0 1486 2088 191825612 191826214 0.000000e+00 1020.0
14 TraesCS1A01G408800 chr7A 81.250 224 35 5 3326 3547 532468167 532468385 1.480000e-39 174.0
15 TraesCS1A01G408800 chr6A 95.364 604 27 1 1486 2089 586300042 586300644 0.000000e+00 959.0
16 TraesCS1A01G408800 chr7B 95.199 604 29 0 1487 2090 646607775 646607172 0.000000e+00 955.0
17 TraesCS1A01G408800 chr7B 85.665 579 34 15 172 714 609229467 609230032 7.540000e-157 564.0
18 TraesCS1A01G408800 chr7B 81.776 214 36 2 3326 3538 135771267 135771478 4.130000e-40 176.0
19 TraesCS1A01G408800 chr1B 92.896 549 24 9 3474 4017 660107510 660108048 0.000000e+00 784.0
20 TraesCS1A01G408800 chr1B 93.103 522 35 1 965 1486 660105445 660105965 0.000000e+00 763.0
21 TraesCS1A01G408800 chr1B 89.775 577 32 17 2595 3167 660106429 660106982 0.000000e+00 713.0
22 TraesCS1A01G408800 chr1B 87.539 634 29 18 31 638 660104767 660105376 0.000000e+00 688.0
23 TraesCS1A01G408800 chr1B 94.697 264 13 1 2265 2527 660106071 660106334 3.740000e-110 409.0
24 TraesCS1A01G408800 chr1B 84.921 252 26 7 3207 3446 660107268 660107519 1.120000e-60 244.0
25 TraesCS1A01G408800 chr1B 95.506 89 4 0 2090 2178 660105958 660106046 4.180000e-30 143.0
26 TraesCS1A01G408800 chr1B 97.674 43 1 0 3166 3208 660107132 660107174 1.550000e-09 75.0
27 TraesCS1A01G408800 chr3A 93.969 514 28 3 469 982 464022424 464022934 0.000000e+00 774.0
28 TraesCS1A01G408800 chr3A 86.158 354 23 7 129 482 463999442 463999769 3.820000e-95 359.0
29 TraesCS1A01G408800 chr6B 80.907 419 33 19 270 643 397897018 397896602 1.830000e-73 287.0
30 TraesCS1A01G408800 chr5A 81.250 112 21 0 730 841 538322870 538322981 1.540000e-14 91.6
31 TraesCS1A01G408800 chr3B 100.000 30 0 0 686 715 89816392 89816421 5.610000e-04 56.5


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 TraesCS1A01G408800 chr1A 570445380 570449396 4016 False 7419.000 7419 100.000000 1 4017 1 chr1A.!!$F3 4016
1 TraesCS1A01G408800 chr1A 496325383 496325986 603 False 922.000 922 94.215000 1486 2089 1 chr1A.!!$F1 603
2 TraesCS1A01G408800 chr1D 474920731 474924715 3984 False 863.780 2194 91.181800 2 4017 5 chr1D.!!$F1 4015
3 TraesCS1A01G408800 chr2B 76907151 76907753 602 True 1086.000 1086 99.171000 1487 2089 1 chr2B.!!$R1 602
4 TraesCS1A01G408800 chr2B 377780646 377781247 601 False 976.000 976 95.861000 1486 2089 1 chr2B.!!$F1 603
5 TraesCS1A01G408800 chr2A 202888794 202889399 605 True 1037.000 1037 97.529000 1483 2089 1 chr2A.!!$R1 606
6 TraesCS1A01G408800 chr2A 62363643 62364249 606 False 966.000 966 95.387000 1483 2089 1 chr2A.!!$F1 606
7 TraesCS1A01G408800 chr2A 763918227 763918837 610 True 950.000 950 94.926000 1487 2089 1 chr2A.!!$R2 602
8 TraesCS1A01G408800 chr7A 191825612 191826214 602 False 1020.000 1020 97.181000 1486 2088 1 chr7A.!!$F1 602
9 TraesCS1A01G408800 chr6A 586300042 586300644 602 False 959.000 959 95.364000 1486 2089 1 chr6A.!!$F1 603
10 TraesCS1A01G408800 chr7B 646607172 646607775 603 True 955.000 955 95.199000 1487 2090 1 chr7B.!!$R1 603
11 TraesCS1A01G408800 chr7B 609229467 609230032 565 False 564.000 564 85.665000 172 714 1 chr7B.!!$F2 542
12 TraesCS1A01G408800 chr1B 660104767 660108048 3281 False 477.375 784 92.013875 31 4017 8 chr1B.!!$F1 3986
13 TraesCS1A01G408800 chr3A 464022424 464022934 510 False 774.000 774 93.969000 469 982 1 chr3A.!!$F2 513

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
574 630 0.895530 TTTGGTAGAGCAGTCCCTCG 59.104 55.0 0.00 0.0 36.95 4.63 F
1481 1540 0.179103 ATGATCATCGCACTCACGCA 60.179 50.0 1.18 0.0 0.00 5.24 F
2534 2604 0.178932 TGCTCAGGGTACACACCTCT 60.179 55.0 0.00 0.0 45.04 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 2329 0.250338 ACTTCAGCTCCAAACGGTCC 60.250 55.000 0.0 0.0 0.0 4.46 R
2575 2645 0.250858 CCAGGGTGTGATGTGAGCAA 60.251 55.000 0.0 0.0 0.0 3.91 R
3893 4705 1.001633 GAGACGGTAAGCTTTCACCCA 59.998 52.381 3.2 0.0 0.0 4.51 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
21 22 3.770666 CGACATTGACCGAGTATGAGTT 58.229 45.455 0.00 0.00 0.00 3.01
25 26 2.941453 TGACCGAGTATGAGTTGAGC 57.059 50.000 0.00 0.00 0.00 4.26
32 33 4.101942 CGAGTATGAGTTGAGCTCTTGTC 58.898 47.826 16.19 8.87 44.41 3.18
150 156 3.044059 GCATCGACCAACTGCAGCC 62.044 63.158 15.27 0.00 35.96 4.85
210 222 2.037527 GGAGTCCTCCGTCCCTGT 59.962 66.667 0.41 0.00 40.36 4.00
283 296 1.065636 GTTGGTTAGTAGGGGAGTGGC 60.066 57.143 0.00 0.00 0.00 5.01
430 443 2.738695 GACGCTGCTTGCTGCTCTC 61.739 63.158 19.16 11.31 43.37 3.20
431 444 2.434534 CGCTGCTTGCTGCTCTCT 60.435 61.111 19.16 0.00 43.37 3.10
444 457 2.166050 CTGCTCTCTGCTCTGCTTCTTA 59.834 50.000 0.00 0.00 43.37 2.10
521 568 7.028962 TGCAATCTGTACTGAAATTATTGTGC 58.971 34.615 6.54 7.13 0.00 4.57
574 630 0.895530 TTTGGTAGAGCAGTCCCTCG 59.104 55.000 0.00 0.00 36.95 4.63
588 644 2.231478 GTCCCTCGAGTGATTTGACAGA 59.769 50.000 12.31 0.00 0.00 3.41
810 868 2.499289 CAGTTCAGGGTCAGCTGTCTAT 59.501 50.000 14.67 0.00 0.00 1.98
821 879 6.206243 GGGTCAGCTGTCTATAACGTCTTATA 59.794 42.308 14.67 0.00 0.00 0.98
856 914 7.510407 GGAGGGAGTAGTAAATAATTTCTGCT 58.490 38.462 0.00 0.00 0.00 4.24
896 954 6.514947 TCAAAAGTGCAGAACAAAGCATAAT 58.485 32.000 0.00 0.00 43.44 1.28
963 1021 7.039293 TGCAAGTTCCTTCTATTGTAGTACTCA 60.039 37.037 0.00 0.00 0.00 3.41
964 1022 7.982354 GCAAGTTCCTTCTATTGTAGTACTCAT 59.018 37.037 0.00 0.00 0.00 2.90
1042 1100 4.633565 GTCCATCAGAGAAAAGGTAAGCAG 59.366 45.833 0.00 0.00 0.00 4.24
1126 1184 8.360390 TGATTAGTTGCACTCTCATCGTTATAT 58.640 33.333 0.00 0.00 0.00 0.86
1248 1306 2.683933 GGGACGAGAAGAGGGGCA 60.684 66.667 0.00 0.00 0.00 5.36
1289 1347 2.201771 GAGGAGGGGCTACCGGAT 59.798 66.667 9.46 0.00 46.96 4.18
1293 1351 1.760875 GAGGGGCTACCGGATGTCA 60.761 63.158 9.46 0.00 46.96 3.58
1294 1352 1.074471 AGGGGCTACCGGATGTCAT 60.074 57.895 9.46 0.00 46.96 3.06
1305 1363 3.273434 CCGGATGTCATGTTTCATCAGT 58.727 45.455 20.36 0.00 41.26 3.41
1348 1406 2.178890 CCGCTCATCTGGCTGCTTC 61.179 63.158 0.00 0.00 0.00 3.86
1380 1438 2.991250 AGTTCGGCAAGCTTGACATAT 58.009 42.857 31.00 11.51 35.35 1.78
1389 1447 4.396166 GCAAGCTTGACATATTGGTACAGT 59.604 41.667 30.39 0.00 42.39 3.55
1425 1483 9.903682 TTTCAAATGAAGTTTTCAATTTGCAAA 57.096 22.222 15.44 15.44 43.95 3.68
1481 1540 0.179103 ATGATCATCGCACTCACGCA 60.179 50.000 1.18 0.00 0.00 5.24
1910 1970 2.224784 GCACCCGTAAAGATTCACGTTT 59.775 45.455 0.00 0.00 36.44 3.60
2193 2262 9.017509 AGACGGTAAATTTGTCTCCGATATATA 57.982 33.333 22.56 0.00 43.22 0.86
2219 2288 6.156519 GTCGCATTCCCTTAAAATTCACTTT 58.843 36.000 0.00 0.00 0.00 2.66
2255 2324 8.429493 TGAGATCACATTTAGATACTGCTTTG 57.571 34.615 0.00 0.00 0.00 2.77
2256 2325 7.011763 TGAGATCACATTTAGATACTGCTTTGC 59.988 37.037 0.00 0.00 0.00 3.68
2260 2329 7.307694 TCACATTTAGATACTGCTTTGCTTTG 58.692 34.615 0.00 0.00 0.00 2.77
2261 2330 6.529125 CACATTTAGATACTGCTTTGCTTTGG 59.471 38.462 0.00 0.00 0.00 3.28
2263 2332 5.880054 TTAGATACTGCTTTGCTTTGGAC 57.120 39.130 0.00 0.00 0.00 4.02
2275 2344 0.593128 CTTTGGACCGTTTGGAGCTG 59.407 55.000 0.00 0.00 39.21 4.24
2278 2347 0.250295 TGGACCGTTTGGAGCTGAAG 60.250 55.000 0.00 0.00 39.21 3.02
2322 2392 3.947196 TGCATCCATGTCCATCACTTAAC 59.053 43.478 0.00 0.00 0.00 2.01
2338 2408 1.619654 TAACAACAGCTTGCAGGCAT 58.380 45.000 23.85 7.73 34.17 4.40
2360 2430 0.831288 ATGGGATGGAGAGAGCCGAG 60.831 60.000 0.00 0.00 0.00 4.63
2504 2574 3.834610 CAGAATCGTCAACGTAACCTCT 58.165 45.455 2.09 0.00 40.80 3.69
2527 2597 2.602676 GGGGCTTGCTCAGGGTACA 61.603 63.158 0.00 0.00 0.00 2.90
2528 2598 1.377333 GGGCTTGCTCAGGGTACAC 60.377 63.158 0.00 0.00 0.00 2.90
2529 2599 1.374947 GGCTTGCTCAGGGTACACA 59.625 57.895 0.00 0.00 0.00 3.72
2532 2602 0.687354 CTTGCTCAGGGTACACACCT 59.313 55.000 0.00 0.00 45.04 4.00
2534 2604 0.178932 TGCTCAGGGTACACACCTCT 60.179 55.000 0.00 0.00 45.04 3.69
2535 2605 0.533032 GCTCAGGGTACACACCTCTC 59.467 60.000 0.00 0.00 45.04 3.20
2536 2606 1.924731 CTCAGGGTACACACCTCTCA 58.075 55.000 0.00 0.00 45.04 3.27
2537 2607 2.461695 CTCAGGGTACACACCTCTCAT 58.538 52.381 0.00 0.00 45.04 2.90
2538 2608 2.428890 CTCAGGGTACACACCTCTCATC 59.571 54.545 0.00 0.00 45.04 2.92
2540 2610 2.428890 CAGGGTACACACCTCTCATCTC 59.571 54.545 0.00 0.00 45.04 2.75
2541 2611 1.757699 GGGTACACACCTCTCATCTCC 59.242 57.143 0.00 0.00 45.04 3.71
2543 2613 3.034635 GGTACACACCTCTCATCTCCAT 58.965 50.000 0.00 0.00 42.11 3.41
2544 2614 3.181471 GGTACACACCTCTCATCTCCATG 60.181 52.174 0.00 0.00 42.11 3.66
2545 2615 2.544721 ACACACCTCTCATCTCCATGT 58.455 47.619 0.00 0.00 0.00 3.21
2546 2616 3.713003 ACACACCTCTCATCTCCATGTA 58.287 45.455 0.00 0.00 0.00 2.29
2547 2617 3.703556 ACACACCTCTCATCTCCATGTAG 59.296 47.826 0.00 0.00 0.00 2.74
2548 2618 3.956848 CACACCTCTCATCTCCATGTAGA 59.043 47.826 0.00 0.00 0.00 2.59
2549 2619 4.037803 CACACCTCTCATCTCCATGTAGAG 59.962 50.000 0.00 0.00 35.81 2.43
2561 2631 7.239763 TCTCCATGTAGAGTATTTCACAACA 57.760 36.000 0.00 0.00 35.28 3.33
2563 2633 8.154203 TCTCCATGTAGAGTATTTCACAACAAA 58.846 33.333 0.00 0.00 35.28 2.83
2566 2636 9.345517 CCATGTAGAGTATTTCACAACAAATTG 57.654 33.333 0.00 0.00 41.98 2.32
2572 2642 9.868277 AGAGTATTTCACAACAAATTGAAACAA 57.132 25.926 0.00 0.00 42.87 2.83
2588 2658 5.658468 TGAAACAAATTTGCTCACATCACA 58.342 33.333 18.12 3.61 0.00 3.58
2589 2659 5.519566 TGAAACAAATTTGCTCACATCACAC 59.480 36.000 18.12 0.00 0.00 3.82
2590 2660 3.981211 ACAAATTTGCTCACATCACACC 58.019 40.909 18.12 0.00 0.00 4.16
2592 2662 2.592102 ATTTGCTCACATCACACCCT 57.408 45.000 0.00 0.00 0.00 4.34
2602 2710 0.250901 ATCACACCCTGGCTGTTCAC 60.251 55.000 0.00 0.00 0.00 3.18
2603 2711 1.898574 CACACCCTGGCTGTTCACC 60.899 63.158 0.00 0.00 0.00 4.02
2721 2829 3.775654 CCTCGAGGACCTGGGCAC 61.776 72.222 28.21 0.00 37.39 5.01
2903 3011 0.108992 GATGAACGACTACACCGGCA 60.109 55.000 0.00 0.00 0.00 5.69
2911 3019 1.144057 CTACACCGGCATCCTCACC 59.856 63.158 0.00 0.00 0.00 4.02
2950 3058 2.474712 GCGGTTGTAGTTGCGCTC 59.525 61.111 9.73 1.40 0.00 5.03
2986 3094 3.145551 ACCGGCGCCTACTTCGAT 61.146 61.111 26.68 0.00 0.00 3.59
3160 3268 8.879342 TGTTTTGTTCACTTCTTTTTCTTTCA 57.121 26.923 0.00 0.00 0.00 2.69
3161 3269 8.977505 TGTTTTGTTCACTTCTTTTTCTTTCAG 58.022 29.630 0.00 0.00 0.00 3.02
3162 3270 9.191995 GTTTTGTTCACTTCTTTTTCTTTCAGA 57.808 29.630 0.00 0.00 0.00 3.27
3163 3271 9.757227 TTTTGTTCACTTCTTTTTCTTTCAGAA 57.243 25.926 0.00 0.00 31.28 3.02
3164 3272 8.742554 TTGTTCACTTCTTTTTCTTTCAGAAC 57.257 30.769 0.00 0.00 33.26 3.01
3253 3780 3.864789 ACAAATATACAGCAGGGGGAG 57.135 47.619 0.00 0.00 0.00 4.30
3281 3808 6.412072 GCATTCTCGACATTTTATTTCCTTCG 59.588 38.462 0.00 0.00 0.00 3.79
3289 3816 6.795399 ACATTTTATTTCCTTCGATGCGAAT 58.205 32.000 2.53 0.00 44.85 3.34
3291 3818 8.567948 ACATTTTATTTCCTTCGATGCGAATAT 58.432 29.630 2.53 0.00 44.85 1.28
3294 3821 7.827819 TTATTTCCTTCGATGCGAATATAGG 57.172 36.000 2.53 1.22 44.85 2.57
3296 3823 5.462530 TTCCTTCGATGCGAATATAGGAA 57.537 39.130 13.63 13.63 44.85 3.36
3297 3824 5.462530 TCCTTCGATGCGAATATAGGAAA 57.537 39.130 2.53 0.00 44.85 3.13
3303 3838 7.392494 TCGATGCGAATATAGGAAACTCTAT 57.608 36.000 0.00 0.00 35.63 1.98
3406 3941 5.471797 TGCAGGTTCAATTAAAAGATCACGA 59.528 36.000 0.00 0.00 0.00 4.35
3444 3980 8.827832 TGAGATGAAAACTTTATCCAATGGAT 57.172 30.769 19.73 19.73 45.40 3.41
3454 3990 9.566432 AACTTTATCCAATGGATGATACTCTTC 57.434 33.333 24.13 0.00 43.06 2.87
3455 3991 8.717717 ACTTTATCCAATGGATGATACTCTTCA 58.282 33.333 24.13 0.00 43.06 3.02
3466 4002 7.093156 TGGATGATACTCTTCAGACTTGTCAAT 60.093 37.037 3.49 0.00 0.00 2.57
3483 4019 5.323581 TGTCAATTCTCAACCATTGGATGA 58.676 37.500 14.25 14.25 33.54 2.92
3495 4289 7.946219 TCAACCATTGGATGAAGCATATCTAAT 59.054 33.333 12.81 0.00 36.54 1.73
3525 4319 9.283768 TGACATTTGAAGTTATTGTCACACTAT 57.716 29.630 0.24 0.00 41.11 2.12
3604 4412 2.362736 ACAGTGCACATAAGGCATGAG 58.637 47.619 21.04 0.00 44.11 2.90
3609 4417 2.739292 GCACATAAGGCATGAGCAATG 58.261 47.619 0.00 0.00 46.81 2.82
3610 4418 2.359848 GCACATAAGGCATGAGCAATGA 59.640 45.455 0.00 0.00 46.81 2.57
3746 4554 1.246056 TACACCCGAGAAGGACACCG 61.246 60.000 0.00 0.00 45.00 4.94
3852 4660 6.935208 ACCTTTAAAAGAACAGAAGCGAGTAT 59.065 34.615 0.00 0.00 0.00 2.12
3871 4679 1.583556 TCTTAGCAGCCATCAAGGGA 58.416 50.000 0.00 0.00 38.09 4.20
4009 4821 2.471815 ATGTCCCCGAGGATAAGTCA 57.528 50.000 0.00 0.00 46.41 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.422417 ACTCATACTCGGTCAATGTCG 57.578 47.619 0.00 0.00 0.00 4.35
21 22 1.066358 CCATGCTGAGACAAGAGCTCA 60.066 52.381 17.77 0.00 39.90 4.26
25 26 0.747283 GGGCCATGCTGAGACAAGAG 60.747 60.000 4.39 0.00 0.00 2.85
32 33 0.471191 TATCACTGGGCCATGCTGAG 59.529 55.000 6.72 0.00 0.00 3.35
192 204 2.760385 CAGGGACGGAGGACTCCC 60.760 72.222 12.54 0.00 46.96 4.30
193 205 2.037527 ACAGGGACGGAGGACTCC 59.962 66.667 8.33 8.33 46.18 3.85
194 206 1.304217 TGACAGGGACGGAGGACTC 60.304 63.158 0.00 0.00 0.00 3.36
207 219 3.604582 GAAGAAGGGATCAACCTGACAG 58.395 50.000 0.00 0.00 40.87 3.51
210 222 2.840651 GAGGAAGAAGGGATCAACCTGA 59.159 50.000 0.00 0.00 40.87 3.86
283 296 2.650116 CCTCACCGACCACCTCCTG 61.650 68.421 0.00 0.00 0.00 3.86
395 408 3.898509 CCCAGCTCTCTCGCTCGG 61.899 72.222 0.00 0.00 38.41 4.63
430 443 3.871485 ACCAGAATAAGAAGCAGAGCAG 58.129 45.455 0.00 0.00 0.00 4.24
431 444 3.988976 ACCAGAATAAGAAGCAGAGCA 57.011 42.857 0.00 0.00 0.00 4.26
603 661 8.937884 CCATGATCTTCACAATTTTGCATTTTA 58.062 29.630 0.00 0.00 0.00 1.52
610 668 6.916440 TCAGTCCATGATCTTCACAATTTTG 58.084 36.000 0.00 0.00 31.12 2.44
754 812 9.046296 ACTGTCTGAACTGTATAAAACTTCTTG 57.954 33.333 0.00 0.00 35.98 3.02
881 939 8.725148 AGACTTTCAGTATTATGCTTTGTTCTG 58.275 33.333 0.00 0.00 0.00 3.02
906 964 6.957635 GCTTTTGAGCTGTTTGAAAGAAAAAG 59.042 34.615 0.00 5.73 35.96 2.27
922 980 3.853475 ACTTGCATAATGGCTTTTGAGC 58.147 40.909 0.00 0.00 34.04 4.26
963 1021 8.989131 TCTAGTCCTGTAGGTTTTGCTTATTAT 58.011 33.333 0.00 0.00 36.34 1.28
964 1022 8.370266 TCTAGTCCTGTAGGTTTTGCTTATTA 57.630 34.615 0.00 0.00 36.34 0.98
965 1023 7.253905 TCTAGTCCTGTAGGTTTTGCTTATT 57.746 36.000 0.00 0.00 36.34 1.40
1042 1100 5.655488 TCTGCTATTACTCAGACAGAAAGC 58.345 41.667 0.00 0.00 34.69 3.51
1248 1306 1.968540 GCTTTTCGGCTGCCTCAGT 60.969 57.895 17.92 0.00 33.43 3.41
1284 1342 3.273434 ACTGATGAAACATGACATCCGG 58.727 45.455 20.14 0.00 41.21 5.14
1289 1347 4.971939 TCTCCAACTGATGAAACATGACA 58.028 39.130 0.00 0.00 0.00 3.58
1293 1351 4.639310 GCTGATCTCCAACTGATGAAACAT 59.361 41.667 0.00 0.00 0.00 2.71
1294 1352 4.005650 GCTGATCTCCAACTGATGAAACA 58.994 43.478 0.00 0.00 0.00 2.83
1305 1363 2.903357 GGGCTCGCTGATCTCCAA 59.097 61.111 0.00 0.00 0.00 3.53
1348 1406 2.432444 TGCCGAACTTGTCCTTTATGG 58.568 47.619 0.00 0.00 37.10 2.74
1380 1438 9.606631 ATTTGAAAATTTAAGCAACTGTACCAA 57.393 25.926 0.00 0.00 0.00 3.67
1415 1473 7.599621 TCTGTATCACAAATCCTTTGCAAATTG 59.400 33.333 13.23 15.88 44.39 2.32
1425 1483 4.574674 TGCCTTCTGTATCACAAATCCT 57.425 40.909 0.00 0.00 0.00 3.24
1481 1540 1.208776 GTTTCCGGCTACTATGGGTGT 59.791 52.381 0.00 0.00 0.00 4.16
1528 1587 1.070134 GATTCCGGGTCGATGAATCCA 59.930 52.381 0.00 0.00 38.82 3.41
1910 1970 1.745087 GTACGGTACCATGGAACGAGA 59.255 52.381 21.47 10.10 0.00 4.04
1941 2001 3.074412 GCGATCCAATCAATTCCGGTAT 58.926 45.455 0.00 0.00 0.00 2.73
2096 2164 2.616330 ATTGTTGACCTGCGGTGCG 61.616 57.895 4.94 0.00 35.25 5.34
2193 2262 5.418840 AGTGAATTTTAAGGGAATGCGACAT 59.581 36.000 0.00 0.00 0.00 3.06
2219 2288 8.539544 TCTAAATGTGATCTCAATGTACTCCAA 58.460 33.333 0.90 0.00 0.00 3.53
2231 2300 7.226325 AGCAAAGCAGTATCTAAATGTGATCTC 59.774 37.037 0.00 0.00 0.00 2.75
2255 2324 1.172812 AGCTCCAAACGGTCCAAAGC 61.173 55.000 0.00 0.00 0.00 3.51
2256 2325 0.593128 CAGCTCCAAACGGTCCAAAG 59.407 55.000 0.00 0.00 0.00 2.77
2260 2329 0.250338 ACTTCAGCTCCAAACGGTCC 60.250 55.000 0.00 0.00 0.00 4.46
2261 2330 2.067013 GTACTTCAGCTCCAAACGGTC 58.933 52.381 0.00 0.00 0.00 4.79
2263 2332 2.457366 AGTACTTCAGCTCCAAACGG 57.543 50.000 0.00 0.00 0.00 4.44
2275 2344 6.053650 ACCAAACAACCTCAGTAAGTACTTC 58.946 40.000 12.39 4.24 33.46 3.01
2278 2347 5.505159 GCAACCAAACAACCTCAGTAAGTAC 60.505 44.000 0.00 0.00 0.00 2.73
2322 2392 1.080093 CCATGCCTGCAAGCTGTTG 60.080 57.895 9.08 3.93 36.67 3.33
2338 2408 0.765903 GGCTCTCTCCATCCCATCCA 60.766 60.000 0.00 0.00 0.00 3.41
2388 2458 2.191641 GTCCTCTGCATCCTGGGC 59.808 66.667 0.00 0.00 0.00 5.36
2513 2583 3.233355 GGTGTGTACCCTGAGCAAG 57.767 57.895 0.00 0.00 41.36 4.01
2527 2597 4.214310 CTCTACATGGAGATGAGAGGTGT 58.786 47.826 8.45 0.00 34.02 4.16
2528 2598 4.214310 ACTCTACATGGAGATGAGAGGTG 58.786 47.826 8.45 0.00 37.74 4.00
2529 2599 4.534647 ACTCTACATGGAGATGAGAGGT 57.465 45.455 8.45 0.00 37.74 3.85
2532 2602 7.561356 TGTGAAATACTCTACATGGAGATGAGA 59.439 37.037 8.45 0.00 37.13 3.27
2534 2604 7.660030 TGTGAAATACTCTACATGGAGATGA 57.340 36.000 8.45 0.00 37.13 2.92
2535 2605 7.765819 TGTTGTGAAATACTCTACATGGAGATG 59.234 37.037 8.45 5.51 37.13 2.90
2536 2606 7.851228 TGTTGTGAAATACTCTACATGGAGAT 58.149 34.615 8.45 1.66 37.13 2.75
2537 2607 7.239763 TGTTGTGAAATACTCTACATGGAGA 57.760 36.000 7.60 7.60 37.13 3.71
2538 2608 7.905604 TTGTTGTGAAATACTCTACATGGAG 57.094 36.000 0.00 0.00 39.09 3.86
2540 2610 9.345517 CAATTTGTTGTGAAATACTCTACATGG 57.654 33.333 0.00 0.00 30.94 3.66
2546 2616 9.868277 TTGTTTCAATTTGTTGTGAAATACTCT 57.132 25.926 2.50 0.00 43.56 3.24
2561 2631 8.124199 GTGATGTGAGCAAATTTGTTTCAATTT 58.876 29.630 21.27 13.05 0.00 1.82
2563 2633 6.762187 TGTGATGTGAGCAAATTTGTTTCAAT 59.238 30.769 21.27 17.41 0.00 2.57
2566 2636 5.050837 GGTGTGATGTGAGCAAATTTGTTTC 60.051 40.000 19.03 16.28 0.00 2.78
2569 2639 3.243839 GGGTGTGATGTGAGCAAATTTGT 60.244 43.478 19.03 6.52 0.00 2.83
2570 2640 3.006110 AGGGTGTGATGTGAGCAAATTTG 59.994 43.478 14.03 14.03 0.00 2.32
2571 2641 3.006110 CAGGGTGTGATGTGAGCAAATTT 59.994 43.478 0.00 0.00 0.00 1.82
2572 2642 2.559668 CAGGGTGTGATGTGAGCAAATT 59.440 45.455 0.00 0.00 0.00 1.82
2573 2643 2.165167 CAGGGTGTGATGTGAGCAAAT 58.835 47.619 0.00 0.00 0.00 2.32
2575 2645 0.250858 CCAGGGTGTGATGTGAGCAA 60.251 55.000 0.00 0.00 0.00 3.91
2576 2646 1.376086 CCAGGGTGTGATGTGAGCA 59.624 57.895 0.00 0.00 0.00 4.26
2577 2647 2.042831 GCCAGGGTGTGATGTGAGC 61.043 63.158 0.00 0.00 0.00 4.26
2579 2649 1.376086 CAGCCAGGGTGTGATGTGA 59.624 57.895 10.82 0.00 0.00 3.58
2580 2650 0.538057 AACAGCCAGGGTGTGATGTG 60.538 55.000 25.16 0.00 43.73 3.21
2582 2652 0.250858 TGAACAGCCAGGGTGTGATG 60.251 55.000 25.16 0.00 43.73 3.07
2588 2658 1.151450 CAAGGTGAACAGCCAGGGT 59.849 57.895 0.29 0.00 0.00 4.34
2589 2659 2.270986 GCAAGGTGAACAGCCAGGG 61.271 63.158 0.29 0.00 0.00 4.45
2590 2660 1.108727 TTGCAAGGTGAACAGCCAGG 61.109 55.000 0.00 0.00 0.00 4.45
2592 2662 1.189752 TTTTGCAAGGTGAACAGCCA 58.810 45.000 0.00 0.00 0.00 4.75
2602 2710 5.390145 GCTGAAATACTGCATTTTTGCAAGG 60.390 40.000 0.00 0.00 44.88 3.61
2603 2711 5.614760 GCTGAAATACTGCATTTTTGCAAG 58.385 37.500 0.00 0.03 44.88 4.01
2843 2951 3.276091 CACGCAGTTGACCCGCAA 61.276 61.111 0.00 0.00 41.61 4.85
2876 2984 0.813184 TAGTCGTTCATCCCGGTGAC 59.187 55.000 0.00 0.00 0.00 3.67
2940 3048 2.867333 CTTCTCCGCGAGCGCAACTA 62.867 60.000 11.47 0.00 42.06 2.24
2965 3073 2.995574 AAGTAGGCGCCGGTGACT 60.996 61.111 29.52 29.52 0.00 3.41
2986 3094 2.343758 GCTCCCAGTTCAGTGCGA 59.656 61.111 0.00 0.00 0.00 5.10
3077 3185 9.979578 TTGTGTTATTGCAAAAGATCAAGTAAT 57.020 25.926 1.71 0.00 0.00 1.89
3078 3186 9.979578 ATTGTGTTATTGCAAAAGATCAAGTAA 57.020 25.926 1.71 0.00 0.00 2.24
3079 3187 9.409312 CATTGTGTTATTGCAAAAGATCAAGTA 57.591 29.630 1.71 0.00 0.00 2.24
3080 3188 7.927629 ACATTGTGTTATTGCAAAAGATCAAGT 59.072 29.630 1.71 5.18 0.00 3.16
3081 3189 8.301730 ACATTGTGTTATTGCAAAAGATCAAG 57.698 30.769 1.71 4.65 0.00 3.02
3082 3190 7.924947 TGACATTGTGTTATTGCAAAAGATCAA 59.075 29.630 1.71 7.63 0.00 2.57
3083 3191 7.432059 TGACATTGTGTTATTGCAAAAGATCA 58.568 30.769 1.71 0.00 0.00 2.92
3084 3192 7.872163 TGACATTGTGTTATTGCAAAAGATC 57.128 32.000 1.71 0.00 0.00 2.75
3085 3193 8.089597 TCATGACATTGTGTTATTGCAAAAGAT 58.910 29.630 1.71 0.00 0.00 2.40
3086 3194 7.432059 TCATGACATTGTGTTATTGCAAAAGA 58.568 30.769 1.71 0.00 0.00 2.52
3087 3195 7.383029 ACTCATGACATTGTGTTATTGCAAAAG 59.617 33.333 1.71 0.00 0.00 2.27
3088 3196 7.208777 ACTCATGACATTGTGTTATTGCAAAA 58.791 30.769 1.71 0.00 0.00 2.44
3102 3210 4.581309 ATCTGGACCAACTCATGACATT 57.419 40.909 0.00 0.00 0.00 2.71
3157 3265 9.958180 TGACATTGGAAATATTCTAGTTCTGAA 57.042 29.630 0.00 0.00 33.61 3.02
3160 3268 9.401058 CCTTGACATTGGAAATATTCTAGTTCT 57.599 33.333 0.00 0.00 33.61 3.01
3161 3269 9.178758 ACCTTGACATTGGAAATATTCTAGTTC 57.821 33.333 2.47 0.00 32.41 3.01
3194 3459 6.757947 ACGTACACTTTGCTAGTAGTTTCAAA 59.242 34.615 0.00 0.78 34.56 2.69
3233 3593 3.393687 TCTCCCCCTGCTGTATATTTGT 58.606 45.455 0.00 0.00 0.00 2.83
3253 3780 7.420800 AGGAAATAAAATGTCGAGAATGCATC 58.579 34.615 0.00 0.00 0.00 3.91
3292 3819 8.919145 AGAACAATCTCGATTATAGAGTTTCCT 58.081 33.333 2.49 0.00 37.07 3.36
3340 3875 6.674694 TCTAGAAGCATCTTTTTCTCATGC 57.325 37.500 0.00 0.00 42.81 4.06
3367 3902 6.233434 TGAACCTGCATTCTATCATCCATAC 58.767 40.000 1.98 0.00 0.00 2.39
3384 3919 7.095229 TGACTCGTGATCTTTTAATTGAACCTG 60.095 37.037 0.00 0.00 0.00 4.00
3385 3920 6.934645 TGACTCGTGATCTTTTAATTGAACCT 59.065 34.615 0.00 0.00 0.00 3.50
3444 3980 7.901029 AGAATTGACAAGTCTGAAGAGTATCA 58.099 34.615 16.85 0.00 33.49 2.15
3451 3987 5.528690 TGGTTGAGAATTGACAAGTCTGAAG 59.471 40.000 21.92 0.00 35.72 3.02
3454 3990 5.954296 ATGGTTGAGAATTGACAAGTCTG 57.046 39.130 21.92 0.00 35.72 3.51
3455 3991 5.242393 CCAATGGTTGAGAATTGACAAGTCT 59.758 40.000 17.51 17.51 38.75 3.24
3466 4002 3.765381 TGCTTCATCCAATGGTTGAGAA 58.235 40.909 12.27 5.91 33.64 2.87
3483 4019 6.774170 TCAAATGTCAGCCATTAGATATGCTT 59.226 34.615 0.00 0.00 43.04 3.91
3495 4289 5.534278 TGACAATAACTTCAAATGTCAGCCA 59.466 36.000 3.01 0.00 43.79 4.75
3540 4334 9.100554 CTGCTTACGTATGCTACTAGTCTATAT 57.899 37.037 27.42 0.00 0.00 0.86
3547 4341 7.598189 TCTATCTGCTTACGTATGCTACTAG 57.402 40.000 27.42 22.58 0.00 2.57
3548 4342 7.822822 TGATCTATCTGCTTACGTATGCTACTA 59.177 37.037 27.42 16.81 0.00 1.82
3558 4352 6.072452 TCCAGTACATGATCTATCTGCTTACG 60.072 42.308 0.00 0.00 0.00 3.18
3632 4440 9.959749 GTAAATTGTCTGGTGTAAAAAGAATGA 57.040 29.630 0.00 0.00 0.00 2.57
3746 4554 1.584308 GCTCGACGAAACATAGTGAGC 59.416 52.381 0.00 0.00 40.31 4.26
3852 4660 1.583556 TCCCTTGATGGCTGCTAAGA 58.416 50.000 0.00 0.00 0.00 2.10
3880 4688 3.304911 TTCACCCATGTTCAACAGGAA 57.695 42.857 3.10 0.00 30.30 3.36
3881 4689 3.221771 CTTTCACCCATGTTCAACAGGA 58.778 45.455 3.10 0.00 30.30 3.86
3882 4690 2.288395 GCTTTCACCCATGTTCAACAGG 60.288 50.000 0.00 0.00 0.00 4.00
3893 4705 1.001633 GAGACGGTAAGCTTTCACCCA 59.998 52.381 3.20 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.