Multiple sequence alignment - TraesCS2D01G554200

Loading Multiple Alignment...

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 TraesCS2D01G554200 chr2D 100.000 1854 0 0 522 2375 628593691 628591838 0.000000e+00 3424.0
1 TraesCS2D01G554200 chr2D 89.816 1738 116 31 527 2218 628251844 628253566 0.000000e+00 2172.0
2 TraesCS2D01G554200 chr2D 86.851 1696 191 21 522 2197 628587551 628585868 0.000000e+00 1868.0
3 TraesCS2D01G554200 chr2D 81.886 1739 238 40 525 2231 628264615 628266308 0.000000e+00 1395.0
4 TraesCS2D01G554200 chr2D 83.972 1148 144 26 524 1652 628258675 628259801 0.000000e+00 1064.0
5 TraesCS2D01G554200 chr2D 81.382 1085 170 21 526 1589 628663565 628664638 0.000000e+00 856.0
6 TraesCS2D01G554200 chr2D 84.891 781 86 18 1467 2231 628995460 628994696 0.000000e+00 760.0
7 TraesCS2D01G554200 chr2D 82.874 689 90 9 525 1200 628581428 628580755 5.650000e-166 593.0
8 TraesCS2D01G554200 chr2D 78.759 951 147 25 529 1440 627980653 627979719 9.460000e-164 586.0
9 TraesCS2D01G554200 chr2D 93.846 195 10 2 2003 2197 628260015 628260207 2.310000e-75 292.0
10 TraesCS2D01G554200 chr2D 96.703 91 3 0 1755 1845 628259805 628259895 4.090000e-33 152.0
11 TraesCS2D01G554200 chr2D 100.000 44 0 0 1 44 628587670 628587627 5.440000e-12 82.4
12 TraesCS2D01G554200 chr2D 100.000 44 0 0 1 44 628594212 628594169 5.440000e-12 82.4
13 TraesCS2D01G554200 chr2D 97.727 44 1 0 1 44 628258566 628258609 2.530000e-10 76.8
14 TraesCS2D01G554200 chr2B 90.471 1742 121 21 526 2231 771281604 771283336 0.000000e+00 2255.0
15 TraesCS2D01G554200 chr2B 83.492 733 102 8 523 1242 771380504 771381230 0.000000e+00 665.0
16 TraesCS2D01G554200 chr2B 77.752 872 153 18 594 1440 771048516 771047661 4.560000e-137 497.0
17 TraesCS2D01G554200 chr5D 89.027 1768 122 30 526 2231 15570275 15568518 0.000000e+00 2124.0
18 TraesCS2D01G554200 chr5D 94.483 145 7 1 2231 2375 508112125 508111982 3.070000e-54 222.0
19 TraesCS2D01G554200 chr5D 94.444 144 7 1 2232 2375 119768803 119768945 1.110000e-53 220.0
20 TraesCS2D01G554200 chr5D 95.455 44 2 0 1 44 15570389 15570346 1.180000e-08 71.3
21 TraesCS2D01G554200 chr2A 86.600 1403 137 19 525 1900 758575721 758577099 0.000000e+00 1502.0
22 TraesCS2D01G554200 chr2A 95.551 899 35 3 526 1420 758563416 758564313 0.000000e+00 1434.0
23 TraesCS2D01G554200 chr2A 81.410 1759 243 42 525 2231 758583613 758585339 0.000000e+00 1360.0
24 TraesCS2D01G554200 chr2A 88.321 822 74 11 1423 2231 758564437 758565249 0.000000e+00 966.0
25 TraesCS2D01G554200 chr2A 81.066 1088 173 20 526 1589 758693400 758692322 0.000000e+00 837.0
26 TraesCS2D01G554200 chr2A 78.682 971 144 30 532 1461 758516869 758515921 2.630000e-164 588.0
27 TraesCS2D01G554200 chr2A 79.806 515 79 11 526 1020 758596877 758597386 3.760000e-93 351.0
28 TraesCS2D01G554200 chr2A 91.329 173 11 4 1899 2070 758577142 758577311 1.420000e-57 233.0
29 TraesCS2D01G554200 chr4D 95.172 145 6 1 2232 2375 122200049 122199905 6.600000e-56 228.0
30 TraesCS2D01G554200 chr4A 95.139 144 6 1 2232 2375 448515060 448515202 2.380000e-55 226.0
31 TraesCS2D01G554200 chr7A 94.483 145 7 1 2231 2375 469986369 469986512 3.070000e-54 222.0
32 TraesCS2D01G554200 chr7D 94.444 144 7 1 2231 2374 409459118 409459260 1.110000e-53 220.0
33 TraesCS2D01G554200 chr7B 93.056 144 7 2 2232 2375 423768601 423768741 8.600000e-50 207.0
34 TraesCS2D01G554200 chr3A 91.447 152 9 4 2228 2375 601159910 601160061 3.090000e-49 206.0
35 TraesCS2D01G554200 chr3D 91.447 152 6 7 2228 2375 459069746 459069894 4.000000e-48 202.0


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 TraesCS2D01G554200 chr2D 628591838 628594212 2374 True 1753.20 3424 100.0000 1 2375 2 chr2D.!!$R5 2374
1 TraesCS2D01G554200 chr2D 628251844 628253566 1722 False 2172.00 2172 89.8160 527 2218 1 chr2D.!!$F1 1691
2 TraesCS2D01G554200 chr2D 628264615 628266308 1693 False 1395.00 1395 81.8860 525 2231 1 chr2D.!!$F2 1706
3 TraesCS2D01G554200 chr2D 628585868 628587670 1802 True 975.20 1868 93.4255 1 2197 2 chr2D.!!$R4 2196
4 TraesCS2D01G554200 chr2D 628663565 628664638 1073 False 856.00 856 81.3820 526 1589 1 chr2D.!!$F3 1063
5 TraesCS2D01G554200 chr2D 628994696 628995460 764 True 760.00 760 84.8910 1467 2231 1 chr2D.!!$R3 764
6 TraesCS2D01G554200 chr2D 628580755 628581428 673 True 593.00 593 82.8740 525 1200 1 chr2D.!!$R2 675
7 TraesCS2D01G554200 chr2D 627979719 627980653 934 True 586.00 586 78.7590 529 1440 1 chr2D.!!$R1 911
8 TraesCS2D01G554200 chr2D 628258566 628260207 1641 False 396.20 1064 93.0620 1 2197 4 chr2D.!!$F4 2196
9 TraesCS2D01G554200 chr2B 771281604 771283336 1732 False 2255.00 2255 90.4710 526 2231 1 chr2B.!!$F1 1705
10 TraesCS2D01G554200 chr2B 771380504 771381230 726 False 665.00 665 83.4920 523 1242 1 chr2B.!!$F2 719
11 TraesCS2D01G554200 chr2B 771047661 771048516 855 True 497.00 497 77.7520 594 1440 1 chr2B.!!$R1 846
12 TraesCS2D01G554200 chr5D 15568518 15570389 1871 True 1097.65 2124 92.2410 1 2231 2 chr5D.!!$R2 2230
13 TraesCS2D01G554200 chr2A 758583613 758585339 1726 False 1360.00 1360 81.4100 525 2231 1 chr2A.!!$F1 1706
14 TraesCS2D01G554200 chr2A 758563416 758565249 1833 False 1200.00 1434 91.9360 526 2231 2 chr2A.!!$F3 1705
15 TraesCS2D01G554200 chr2A 758575721 758577311 1590 False 867.50 1502 88.9645 525 2070 2 chr2A.!!$F4 1545
16 TraesCS2D01G554200 chr2A 758692322 758693400 1078 True 837.00 837 81.0660 526 1589 1 chr2A.!!$R2 1063
17 TraesCS2D01G554200 chr2A 758515921 758516869 948 True 588.00 588 78.6820 532 1461 1 chr2A.!!$R1 929
18 TraesCS2D01G554200 chr2A 758596877 758597386 509 False 351.00 351 79.8060 526 1020 1 chr2A.!!$F2 494

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
962 1013 3.369892 GGCTGCTTCTACTGGATTTCAGA 60.37 47.826 0.0 0.0 46.18 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 2649 0.384309 TCGACACTGAAGTTGCGACT 59.616 50.0 0.0 0.0 37.87 4.18 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
923 974 3.445805 ACATGGAAGTTTTGGTTCGTGTT 59.554 39.130 0.00 0.00 0.00 3.32
962 1013 3.369892 GGCTGCTTCTACTGGATTTCAGA 60.370 47.826 0.00 0.00 46.18 3.27
1249 1330 3.578716 GAGGCACCTGCTCCTGTATTATA 59.421 47.826 0.00 0.00 41.70 0.98
1266 1347 0.311165 ATATTGGAGTCTCGTCGGCG 59.689 55.000 1.15 1.15 39.92 6.46
1320 1401 2.331132 GCAGCTTGAGAGGGTGTGC 61.331 63.158 0.00 0.00 35.03 4.57
1353 1440 7.040755 TGTCCAAAACAGTCACAAGTATATTGG 60.041 37.037 0.00 0.00 35.94 3.16
1373 1460 2.943033 GGAACTTCCCACCATCGTTATG 59.057 50.000 0.00 0.00 0.00 1.90
1402 1489 3.199677 CCGACAGTGTCAAGTGGTAAAA 58.800 45.455 22.66 0.00 32.09 1.52
1416 1505 4.649218 AGTGGTAAAACCTTCTGTTGCATT 59.351 37.500 0.00 0.00 39.58 3.56
1487 1699 6.648310 TCTGATACTTGCTAGCTCATTAATGC 59.352 38.462 17.23 0.00 0.00 3.56
1576 1803 7.277539 TGGTCAAGCTAATTTGTTTGTCTTTTG 59.722 33.333 14.06 0.00 31.55 2.44
1597 1830 6.909550 TTGTGTGCCATCTTAAGGTAATTT 57.090 33.333 1.85 0.00 0.00 1.82
1603 1836 7.615365 TGTGCCATCTTAAGGTAATTTGAGAAT 59.385 33.333 1.85 0.00 0.00 2.40
1656 1889 4.109766 GCATTTTAGGGGTATTGCGAAAC 58.890 43.478 0.00 0.00 0.00 2.78
1660 1893 0.675522 AGGGGTATTGCGAAACCGTG 60.676 55.000 0.00 0.00 36.57 4.94
1708 1951 9.612066 ACAACAATTGATTCAGTTTTTATGGTT 57.388 25.926 13.59 0.00 0.00 3.67
1808 2068 5.183713 CACATTTATTCCAGTCAAGCAGGAA 59.816 40.000 0.00 0.00 45.05 3.36
1855 2119 5.695816 GTGGTCACCGTTACAGTTGTAAATA 59.304 40.000 6.31 0.00 41.58 1.40
1926 2238 8.860088 AGTGGCAAAAATGACTTTTTAGTATCT 58.140 29.630 0.00 0.00 41.49 1.98
2051 2373 4.345271 TTGCATTTGTCTGATCACGATG 57.655 40.909 0.00 0.00 0.00 3.84
2073 2395 3.500448 TCCTTGTTGCACCTCACAATA 57.500 42.857 2.31 0.00 0.00 1.90
2078 2400 3.749226 TGTTGCACCTCACAATACATCA 58.251 40.909 0.00 0.00 0.00 3.07
2156 2483 6.097839 GGATGCTAATGATGGGCATATTGATT 59.902 38.462 5.58 0.00 45.14 2.57
2186 2513 1.069227 GTTTGTGTCGTGGCTGGAATC 60.069 52.381 0.00 0.00 0.00 2.52
2236 2565 1.702182 TTTTTGCACTGAGCCATGGA 58.298 45.000 18.40 0.00 44.83 3.41
2237 2566 1.927487 TTTTGCACTGAGCCATGGAT 58.073 45.000 18.40 10.08 44.83 3.41
2238 2567 1.927487 TTTGCACTGAGCCATGGATT 58.073 45.000 18.40 1.53 44.83 3.01
2239 2568 2.804986 TTGCACTGAGCCATGGATTA 57.195 45.000 18.40 4.71 44.83 1.75
2240 2569 3.301794 TTGCACTGAGCCATGGATTAT 57.698 42.857 18.40 0.00 44.83 1.28
2241 2570 2.578786 TGCACTGAGCCATGGATTATG 58.421 47.619 18.40 10.29 44.83 1.90
2242 2571 2.173143 TGCACTGAGCCATGGATTATGA 59.827 45.455 18.40 0.00 44.83 2.15
2243 2572 2.812591 GCACTGAGCCATGGATTATGAG 59.187 50.000 18.40 6.82 39.21 2.90
2244 2573 3.746751 GCACTGAGCCATGGATTATGAGT 60.747 47.826 18.40 7.50 39.21 3.41
2245 2574 4.063689 CACTGAGCCATGGATTATGAGTC 58.936 47.826 18.40 0.00 39.21 3.36
2246 2575 3.072184 ACTGAGCCATGGATTATGAGTCC 59.928 47.826 18.40 0.00 39.21 3.85
2247 2576 2.373169 TGAGCCATGGATTATGAGTCCC 59.627 50.000 18.40 0.00 39.21 4.46
2248 2577 2.373169 GAGCCATGGATTATGAGTCCCA 59.627 50.000 18.40 0.00 39.21 4.37
2249 2578 2.785269 AGCCATGGATTATGAGTCCCAA 59.215 45.455 18.40 0.00 39.21 4.12
2250 2579 3.152341 GCCATGGATTATGAGTCCCAAG 58.848 50.000 18.40 0.00 39.21 3.61
2251 2580 3.759581 CCATGGATTATGAGTCCCAAGG 58.240 50.000 5.56 0.00 39.21 3.61
2252 2581 3.395607 CCATGGATTATGAGTCCCAAGGA 59.604 47.826 5.56 0.00 39.25 3.36
2253 2582 4.747931 CCATGGATTATGAGTCCCAAGGAC 60.748 50.000 5.56 5.60 41.28 3.85
2264 2593 3.544698 TCCCAAGGACTAGTCAAGACT 57.455 47.619 23.91 9.21 45.02 3.24
2265 2594 4.669866 TCCCAAGGACTAGTCAAGACTA 57.330 45.455 23.91 9.40 42.54 2.59
2290 2619 1.599576 GAGTCTCAACTCCAGGGCC 59.400 63.158 0.00 0.00 45.26 5.80
2291 2620 2.232298 GAGTCTCAACTCCAGGGCCG 62.232 65.000 0.00 0.00 45.26 6.13
2292 2621 2.119611 TCTCAACTCCAGGGCCGA 59.880 61.111 0.00 0.00 0.00 5.54
2293 2622 2.266055 CTCAACTCCAGGGCCGAC 59.734 66.667 0.00 0.00 0.00 4.79
2294 2623 2.203788 TCAACTCCAGGGCCGACT 60.204 61.111 0.00 0.00 0.00 4.18
2295 2624 0.970937 CTCAACTCCAGGGCCGACTA 60.971 60.000 0.00 0.00 0.00 2.59
2296 2625 1.218316 CAACTCCAGGGCCGACTAC 59.782 63.158 0.00 0.00 0.00 2.73
2297 2626 1.229082 AACTCCAGGGCCGACTACA 60.229 57.895 0.00 0.00 0.00 2.74
2298 2627 1.542187 AACTCCAGGGCCGACTACAC 61.542 60.000 0.00 0.00 0.00 2.90
2299 2628 1.682684 CTCCAGGGCCGACTACACT 60.683 63.158 0.00 0.00 0.00 3.55
2300 2629 1.229082 TCCAGGGCCGACTACACTT 60.229 57.895 0.00 0.00 0.00 3.16
2301 2630 0.834687 TCCAGGGCCGACTACACTTT 60.835 55.000 0.00 0.00 0.00 2.66
2302 2631 0.899720 CCAGGGCCGACTACACTTTA 59.100 55.000 0.00 0.00 0.00 1.85
2303 2632 1.134788 CCAGGGCCGACTACACTTTAG 60.135 57.143 0.00 0.00 0.00 1.85
2304 2633 1.549170 CAGGGCCGACTACACTTTAGT 59.451 52.381 0.00 0.00 0.00 2.24
2320 2649 7.304919 CACTTTAGTGTCGACTAGTCTATGA 57.695 40.000 20.34 7.99 40.96 2.15
2321 2650 7.403421 CACTTTAGTGTCGACTAGTCTATGAG 58.597 42.308 20.34 14.54 40.96 2.90
2322 2651 7.064847 CACTTTAGTGTCGACTAGTCTATGAGT 59.935 40.741 20.34 15.02 40.96 3.41
2323 2652 7.278424 ACTTTAGTGTCGACTAGTCTATGAGTC 59.722 40.741 20.34 3.58 36.03 3.36
2329 2658 4.886247 GACTAGTCTATGAGTCGCAACT 57.114 45.455 15.91 0.00 38.88 3.16
2330 2659 5.238006 GACTAGTCTATGAGTCGCAACTT 57.762 43.478 15.91 0.00 35.28 2.66
2331 2660 5.238006 ACTAGTCTATGAGTCGCAACTTC 57.762 43.478 0.00 0.00 35.28 3.01
2332 2661 4.700692 ACTAGTCTATGAGTCGCAACTTCA 59.299 41.667 0.00 0.00 35.28 3.02
2333 2662 4.103365 AGTCTATGAGTCGCAACTTCAG 57.897 45.455 0.00 0.00 35.28 3.02
2334 2663 3.508012 AGTCTATGAGTCGCAACTTCAGT 59.492 43.478 0.00 0.00 35.28 3.41
2335 2664 3.610242 GTCTATGAGTCGCAACTTCAGTG 59.390 47.826 0.00 0.00 35.28 3.66
2336 2665 2.533266 ATGAGTCGCAACTTCAGTGT 57.467 45.000 0.00 0.00 35.28 3.55
2337 2666 1.852942 TGAGTCGCAACTTCAGTGTC 58.147 50.000 0.00 0.00 35.28 3.67
2338 2667 0.778815 GAGTCGCAACTTCAGTGTCG 59.221 55.000 0.00 0.00 35.28 4.35
2339 2668 0.384309 AGTCGCAACTTCAGTGTCGA 59.616 50.000 0.00 1.12 28.74 4.20
2340 2669 0.503117 GTCGCAACTTCAGTGTCGAC 59.497 55.000 9.11 9.11 42.04 4.20
2341 2670 0.384309 TCGCAACTTCAGTGTCGACT 59.616 50.000 17.92 0.00 31.20 4.18
2342 2671 1.605232 TCGCAACTTCAGTGTCGACTA 59.395 47.619 17.92 0.00 31.20 2.59
2343 2672 1.979469 CGCAACTTCAGTGTCGACTAG 59.021 52.381 17.92 6.62 0.00 2.57
2344 2673 2.604855 CGCAACTTCAGTGTCGACTAGT 60.605 50.000 17.92 9.17 0.00 2.57
2345 2674 2.726760 GCAACTTCAGTGTCGACTAGTG 59.273 50.000 17.92 15.18 0.00 2.74
2346 2675 3.795826 GCAACTTCAGTGTCGACTAGTGT 60.796 47.826 17.92 5.50 0.00 3.55
2347 2676 3.900388 ACTTCAGTGTCGACTAGTGTC 57.100 47.619 17.92 0.78 39.70 3.67
2360 2689 5.154215 GACTAGTGTCGATTAGTTACGCT 57.846 43.478 0.00 0.00 37.67 5.07
2361 2690 5.557891 ACTAGTGTCGATTAGTTACGCTT 57.442 39.130 0.00 0.00 35.67 4.68
2362 2691 6.668541 ACTAGTGTCGATTAGTTACGCTTA 57.331 37.500 0.00 0.00 35.67 3.09
2363 2692 6.713520 ACTAGTGTCGATTAGTTACGCTTAG 58.286 40.000 0.00 0.00 35.67 2.18
2364 2693 5.557891 AGTGTCGATTAGTTACGCTTAGT 57.442 39.130 0.00 0.00 30.02 2.24
2365 2694 5.567552 AGTGTCGATTAGTTACGCTTAGTC 58.432 41.667 0.00 0.00 30.02 2.59
2366 2695 5.353678 AGTGTCGATTAGTTACGCTTAGTCT 59.646 40.000 0.00 0.00 30.02 3.24
2367 2696 6.536582 AGTGTCGATTAGTTACGCTTAGTCTA 59.463 38.462 0.00 0.00 30.02 2.59
2368 2697 7.226325 AGTGTCGATTAGTTACGCTTAGTCTAT 59.774 37.037 0.00 0.00 30.02 1.98
2369 2698 7.320797 GTGTCGATTAGTTACGCTTAGTCTATG 59.679 40.741 0.00 0.00 0.00 2.23
2370 2699 7.225341 TGTCGATTAGTTACGCTTAGTCTATGA 59.775 37.037 0.00 0.00 0.00 2.15
2371 2700 7.741216 GTCGATTAGTTACGCTTAGTCTATGAG 59.259 40.741 0.00 0.00 0.00 2.90
2372 2701 7.440556 TCGATTAGTTACGCTTAGTCTATGAGT 59.559 37.037 7.21 7.21 0.00 3.41
2373 2702 7.741216 CGATTAGTTACGCTTAGTCTATGAGTC 59.259 40.741 5.58 0.00 0.00 3.36
2374 2703 8.680039 ATTAGTTACGCTTAGTCTATGAGTCT 57.320 34.615 5.58 2.19 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
962 1013 4.324402 GCACGAGCAATTTTTCAATCGAAT 59.676 37.500 0.00 0.00 41.58 3.34
1249 1330 2.044555 TCGCCGACGAGACTCCAAT 61.045 57.895 0.00 0.00 45.12 3.16
1266 1347 1.332375 TGCGTGTAACAACCTTGCTTC 59.668 47.619 0.00 0.00 35.74 3.86
1320 1401 6.558771 TGTGACTGTTTTGGACATGAATAG 57.441 37.500 0.00 0.00 37.69 1.73
1353 1440 3.869065 TCATAACGATGGTGGGAAGTTC 58.131 45.455 0.00 0.00 33.49 3.01
1402 1489 5.246307 GGTAACTAGAATGCAACAGAAGGT 58.754 41.667 0.00 0.00 0.00 3.50
1540 1762 1.969862 GCTTGACCAGCTTTGCCAT 59.030 52.632 0.00 0.00 46.27 4.40
1597 1830 6.215431 TGTTAGATCCTCCCTTTCAATTCTCA 59.785 38.462 0.00 0.00 0.00 3.27
1603 1836 4.263331 GGTGTGTTAGATCCTCCCTTTCAA 60.263 45.833 0.00 0.00 0.00 2.69
1660 1893 5.163663 TGTGACTTGTGATCCAGTGTTTTTC 60.164 40.000 0.00 0.00 0.00 2.29
1708 1951 9.753674 AACTTGTATCCAATCTCCATTTTCTTA 57.246 29.630 0.00 0.00 0.00 2.10
1749 1992 6.102897 ACACTACAAAGATGAACTGCTAGT 57.897 37.500 0.00 0.00 0.00 2.57
1808 2068 8.099537 CCACATAAGACTTCCAGATAGCATAAT 58.900 37.037 0.00 0.00 0.00 1.28
1902 2213 8.855110 TCAGATACTAAAAAGTCATTTTTGCCA 58.145 29.630 8.55 0.00 45.80 4.92
2051 2373 1.896220 TGTGAGGTGCAACAAGGATC 58.104 50.000 3.64 0.00 39.98 3.36
2126 2452 2.453521 CCCATCATTAGCATCCCATGG 58.546 52.381 4.14 4.14 0.00 3.66
2156 2483 3.125487 CCACGACACAAACTACAACACAA 59.875 43.478 0.00 0.00 0.00 3.33
2231 2560 4.712051 TCCTTGGGACTCATAATCCATG 57.288 45.455 0.00 0.00 38.06 3.66
2244 2573 3.544698 AGTCTTGACTAGTCCTTGGGA 57.455 47.619 20.11 8.06 0.00 4.37
2245 2574 3.131400 GCTAGTCTTGACTAGTCCTTGGG 59.869 52.174 28.01 10.65 41.20 4.12
2246 2575 3.131400 GGCTAGTCTTGACTAGTCCTTGG 59.869 52.174 28.01 11.20 41.20 3.61
2247 2576 4.020543 AGGCTAGTCTTGACTAGTCCTTG 58.979 47.826 28.29 11.23 43.81 3.61
2248 2577 4.325084 AGGCTAGTCTTGACTAGTCCTT 57.675 45.455 28.29 15.18 43.81 3.36
2249 2578 5.132985 TCATAGGCTAGTCTTGACTAGTCCT 59.867 44.000 31.50 31.50 43.81 3.85
2250 2579 5.378332 TCATAGGCTAGTCTTGACTAGTCC 58.622 45.833 28.29 26.95 43.81 3.85
2251 2580 6.059484 ACTCATAGGCTAGTCTTGACTAGTC 58.941 44.000 26.09 26.09 43.27 2.59
2252 2581 6.008696 ACTCATAGGCTAGTCTTGACTAGT 57.991 41.667 28.01 17.49 41.20 2.57
2253 2582 6.554334 GACTCATAGGCTAGTCTTGACTAG 57.446 45.833 25.33 25.33 41.84 2.57
2273 2602 2.286523 CGGCCCTGGAGTTGAGACT 61.287 63.158 0.00 0.00 39.32 3.24
2274 2603 2.266055 CGGCCCTGGAGTTGAGAC 59.734 66.667 0.00 0.00 0.00 3.36
2275 2604 2.119611 TCGGCCCTGGAGTTGAGA 59.880 61.111 0.00 0.00 0.00 3.27
2276 2605 0.970937 TAGTCGGCCCTGGAGTTGAG 60.971 60.000 0.00 0.00 0.00 3.02
2277 2606 1.077805 TAGTCGGCCCTGGAGTTGA 59.922 57.895 0.00 0.00 0.00 3.18
2278 2607 1.218316 GTAGTCGGCCCTGGAGTTG 59.782 63.158 0.00 0.00 0.00 3.16
2279 2608 1.229082 TGTAGTCGGCCCTGGAGTT 60.229 57.895 0.00 0.00 0.00 3.01
2280 2609 1.982938 GTGTAGTCGGCCCTGGAGT 60.983 63.158 0.00 0.00 0.00 3.85
2281 2610 1.258445 AAGTGTAGTCGGCCCTGGAG 61.258 60.000 0.00 0.00 0.00 3.86
2282 2611 0.834687 AAAGTGTAGTCGGCCCTGGA 60.835 55.000 0.00 0.00 0.00 3.86
2283 2612 0.899720 TAAAGTGTAGTCGGCCCTGG 59.100 55.000 0.00 0.00 0.00 4.45
2284 2613 1.549170 ACTAAAGTGTAGTCGGCCCTG 59.451 52.381 0.00 0.00 0.00 4.45
2285 2614 1.549170 CACTAAAGTGTAGTCGGCCCT 59.451 52.381 0.00 0.00 40.96 5.19
2286 2615 2.005971 CACTAAAGTGTAGTCGGCCC 57.994 55.000 0.00 0.00 40.96 5.80
2296 2625 7.064847 ACTCATAGACTAGTCGACACTAAAGTG 59.935 40.741 19.50 8.56 42.19 3.16
2297 2626 7.104939 ACTCATAGACTAGTCGACACTAAAGT 58.895 38.462 19.50 16.77 34.53 2.66
2298 2627 7.542534 ACTCATAGACTAGTCGACACTAAAG 57.457 40.000 19.50 16.28 34.53 1.85
2299 2628 7.536895 GACTCATAGACTAGTCGACACTAAA 57.463 40.000 19.50 7.54 34.53 1.85
2308 2637 4.886247 AGTTGCGACTCATAGACTAGTC 57.114 45.455 15.41 15.41 39.00 2.59
2309 2638 4.700692 TGAAGTTGCGACTCATAGACTAGT 59.299 41.667 7.17 0.00 34.21 2.57
2310 2639 5.163703 ACTGAAGTTGCGACTCATAGACTAG 60.164 44.000 7.17 0.57 34.21 2.57
2311 2640 4.700692 ACTGAAGTTGCGACTCATAGACTA 59.299 41.667 7.17 0.00 34.21 2.59
2312 2641 3.508012 ACTGAAGTTGCGACTCATAGACT 59.492 43.478 7.17 0.00 34.21 3.24
2313 2642 3.610242 CACTGAAGTTGCGACTCATAGAC 59.390 47.826 7.17 0.00 34.21 2.59
2314 2643 3.255888 ACACTGAAGTTGCGACTCATAGA 59.744 43.478 7.17 0.00 34.21 1.98
2315 2644 3.579709 ACACTGAAGTTGCGACTCATAG 58.420 45.455 7.17 8.64 34.21 2.23
2316 2645 3.575630 GACACTGAAGTTGCGACTCATA 58.424 45.455 7.17 0.00 34.21 2.15
2317 2646 2.408050 GACACTGAAGTTGCGACTCAT 58.592 47.619 7.17 0.00 34.21 2.90
2318 2647 1.852942 GACACTGAAGTTGCGACTCA 58.147 50.000 7.17 6.57 34.21 3.41
2319 2648 0.778815 CGACACTGAAGTTGCGACTC 59.221 55.000 7.17 1.94 34.21 3.36
2320 2649 0.384309 TCGACACTGAAGTTGCGACT 59.616 50.000 0.00 0.00 37.87 4.18
2321 2650 0.503117 GTCGACACTGAAGTTGCGAC 59.497 55.000 11.55 14.99 41.41 5.19
2322 2651 0.384309 AGTCGACACTGAAGTTGCGA 59.616 50.000 19.50 1.52 0.00 5.10
2323 2652 1.979469 CTAGTCGACACTGAAGTTGCG 59.021 52.381 19.50 0.00 33.62 4.85
2324 2653 2.726760 CACTAGTCGACACTGAAGTTGC 59.273 50.000 19.50 0.00 33.62 4.17
2325 2654 3.966154 ACACTAGTCGACACTGAAGTTG 58.034 45.455 19.50 5.48 33.62 3.16
2326 2655 4.226113 GACACTAGTCGACACTGAAGTT 57.774 45.455 19.50 0.00 34.60 2.66
2327 2656 3.900388 GACACTAGTCGACACTGAAGT 57.100 47.619 19.50 9.69 34.60 3.01
2338 2667 5.154215 AGCGTAACTAATCGACACTAGTC 57.846 43.478 0.00 0.00 41.46 2.59
2339 2668 5.557891 AAGCGTAACTAATCGACACTAGT 57.442 39.130 0.00 0.00 0.00 2.57
2340 2669 6.713520 ACTAAGCGTAACTAATCGACACTAG 58.286 40.000 0.00 0.00 0.00 2.57
2341 2670 6.536582 AGACTAAGCGTAACTAATCGACACTA 59.463 38.462 0.00 0.00 0.00 2.74
2342 2671 5.353678 AGACTAAGCGTAACTAATCGACACT 59.646 40.000 0.00 0.00 0.00 3.55
2343 2672 5.567552 AGACTAAGCGTAACTAATCGACAC 58.432 41.667 0.00 0.00 0.00 3.67
2344 2673 5.808042 AGACTAAGCGTAACTAATCGACA 57.192 39.130 0.00 0.00 0.00 4.35
2345 2674 7.571026 TCATAGACTAAGCGTAACTAATCGAC 58.429 38.462 0.00 0.00 0.00 4.20
2346 2675 7.440556 ACTCATAGACTAAGCGTAACTAATCGA 59.559 37.037 0.00 0.00 0.00 3.59
2347 2676 7.574496 ACTCATAGACTAAGCGTAACTAATCG 58.426 38.462 0.00 0.00 0.00 3.34
2348 2677 8.776470 AGACTCATAGACTAAGCGTAACTAATC 58.224 37.037 0.00 0.00 0.00 1.75
2349 2678 8.680039 AGACTCATAGACTAAGCGTAACTAAT 57.320 34.615 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.