Multiple sequence alignment - TraesCS2A01G459300

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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 TraesCS2A01G459300 chr2A 100.000 3020 0 0 1 3020 706490379 706487360 0.000000e+00 5578
1 TraesCS2A01G459300 chr2A 82.333 1466 162 49 725 2152 706530805 706529399 0.000000e+00 1182
2 TraesCS2A01G459300 chr2A 80.302 995 129 37 1048 2021 706510969 706510021 0.000000e+00 689
3 TraesCS2A01G459300 chr2A 80.438 593 49 29 64 630 706511840 706511289 1.020000e-104 390
4 TraesCS2A01G459300 chr2A 93.117 247 14 1 665 911 706511289 706511046 2.860000e-95 359
5 TraesCS2A01G459300 chr2A 94.118 170 7 1 2253 2419 756213688 756213857 3.860000e-64 255
6 TraesCS2A01G459300 chr2A 92.179 179 10 3 2253 2427 38649783 38649961 1.800000e-62 250
7 TraesCS2A01G459300 chr2D 92.081 2134 114 33 109 2209 566263758 566261647 0.000000e+00 2953
8 TraesCS2A01G459300 chr2D 82.890 1391 146 45 795 2152 566656870 566655539 0.000000e+00 1166
9 TraesCS2A01G459300 chr2D 90.338 621 30 14 2420 3020 566261558 566260948 0.000000e+00 787
10 TraesCS2A01G459300 chr2D 86.239 545 62 11 1536 2079 566302380 566301848 2.020000e-161 579
11 TraesCS2A01G459300 chr2D 88.596 456 29 9 564 1010 566303373 566302932 1.590000e-147 532
12 TraesCS2A01G459300 chr2D 84.016 488 52 20 1 479 566303937 566303467 2.140000e-121 446
13 TraesCS2A01G459300 chr2D 82.263 327 41 12 1046 1368 566302935 566302622 1.780000e-67 267
14 TraesCS2A01G459300 chr2D 90.179 112 9 2 63 174 566303762 566303653 8.730000e-31 145
15 TraesCS2A01G459300 chr2D 92.857 84 4 1 499 580 566303475 566303392 1.470000e-23 121
16 TraesCS2A01G459300 chr2B 89.947 2258 135 35 1 2231 679032307 679030115 0.000000e+00 2828
17 TraesCS2A01G459300 chr2B 81.503 1011 126 29 1045 2034 679071596 679070626 0.000000e+00 774
18 TraesCS2A01G459300 chr2B 83.628 849 103 24 1298 2127 679696789 679697620 0.000000e+00 765
19 TraesCS2A01G459300 chr2B 88.215 594 60 8 1534 2127 679743830 679744413 0.000000e+00 701
20 TraesCS2A01G459300 chr2B 87.500 456 33 10 564 1010 679072032 679071592 3.470000e-139 505
21 TraesCS2A01G459300 chr2B 87.731 432 32 13 793 1212 679729837 679730259 4.530000e-133 484
22 TraesCS2A01G459300 chr2B 87.298 433 32 15 793 1212 679696308 679696730 9.800000e-130 473
23 TraesCS2A01G459300 chr2B 87.708 301 24 8 283 580 679072341 679072051 3.730000e-89 339
24 TraesCS2A01G459300 chr2B 89.600 250 14 5 2429 2667 679030061 679029813 1.050000e-79 307
25 TraesCS2A01G459300 chr2B 83.224 304 24 12 2697 2987 679029827 679029538 1.390000e-63 254
26 TraesCS2A01G459300 chr7A 94.643 168 8 1 2253 2419 701621128 701621295 2.990000e-65 259
27 TraesCS2A01G459300 chr7A 94.611 167 5 2 2253 2415 690534318 690534484 3.860000e-64 255
28 TraesCS2A01G459300 chr7A 92.655 177 11 2 2253 2428 572183341 572183166 1.390000e-63 254
29 TraesCS2A01G459300 chr7A 91.713 181 9 5 2253 2427 642935947 642935767 2.330000e-61 246
30 TraesCS2A01G459300 chr5A 93.182 176 7 3 2253 2423 473306099 473305924 1.390000e-63 254
31 TraesCS2A01G459300 chr5A 91.620 179 11 2 2256 2430 244431702 244431524 8.360000e-61 244
32 TraesCS2A01G459300 chr3A 91.257 183 10 6 2253 2430 517285425 517285244 8.360000e-61 244


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 TraesCS2A01G459300 chr2A 706487360 706490379 3019 True 5578.000000 5578 100.000000 1 3020 1 chr2A.!!$R1 3019
1 TraesCS2A01G459300 chr2A 706529399 706530805 1406 True 1182.000000 1182 82.333000 725 2152 1 chr2A.!!$R2 1427
2 TraesCS2A01G459300 chr2A 706510021 706511840 1819 True 479.333333 689 84.619000 64 2021 3 chr2A.!!$R3 1957
3 TraesCS2A01G459300 chr2D 566260948 566263758 2810 True 1870.000000 2953 91.209500 109 3020 2 chr2D.!!$R2 2911
4 TraesCS2A01G459300 chr2D 566655539 566656870 1331 True 1166.000000 1166 82.890000 795 2152 1 chr2D.!!$R1 1357
5 TraesCS2A01G459300 chr2D 566301848 566303937 2089 True 348.333333 579 87.358333 1 2079 6 chr2D.!!$R3 2078
6 TraesCS2A01G459300 chr2B 679029538 679032307 2769 True 1129.666667 2828 87.590333 1 2987 3 chr2B.!!$R1 2986
7 TraesCS2A01G459300 chr2B 679743830 679744413 583 False 701.000000 701 88.215000 1534 2127 1 chr2B.!!$F2 593
8 TraesCS2A01G459300 chr2B 679696308 679697620 1312 False 619.000000 765 85.463000 793 2127 2 chr2B.!!$F3 1334
9 TraesCS2A01G459300 chr2B 679070626 679072341 1715 True 539.333333 774 85.570333 283 2034 3 chr2B.!!$R2 1751

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
606 669 0.610232 CAGCCCAAGGGTTCTTCCAG 60.61 60.0 7.05 0.0 38.11 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2426 2736 1.001597 AGCGACGACTCGAGAAAAAGT 60.002 47.619 21.68 10.76 43.06 2.66 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
52 53 5.287035 CGTGGCTCTCATTTTTCTTAAATGC 59.713 40.000 5.57 0.00 37.50 3.56
58 59 6.611381 TCTCATTTTTCTTAAATGCCGACTG 58.389 36.000 5.57 0.00 37.50 3.51
73 74 1.667177 CGACTGCGGGATGCTAGTATG 60.667 57.143 0.00 0.00 46.63 2.39
85 86 1.742411 GCTAGTATGCCCGAGTTTGCA 60.742 52.381 0.00 0.00 42.52 4.08
103 105 3.982475 TGCATTTTATTTTGCACCACGA 58.018 36.364 0.00 0.00 43.54 4.35
201 205 4.379918 GCAGTATCCTCAACTTTGCCTTTC 60.380 45.833 0.00 0.00 0.00 2.62
212 217 2.600470 TTGCCTTTCTTTTGCACCAG 57.400 45.000 0.00 0.00 34.16 4.00
213 218 1.484038 TGCCTTTCTTTTGCACCAGT 58.516 45.000 0.00 0.00 0.00 4.00
214 219 2.660572 TGCCTTTCTTTTGCACCAGTA 58.339 42.857 0.00 0.00 0.00 2.74
216 221 3.640967 TGCCTTTCTTTTGCACCAGTAAT 59.359 39.130 0.00 0.00 0.00 1.89
217 222 4.830046 TGCCTTTCTTTTGCACCAGTAATA 59.170 37.500 0.00 0.00 0.00 0.98
219 224 6.661377 TGCCTTTCTTTTGCACCAGTAATATA 59.339 34.615 0.00 0.00 0.00 0.86
220 225 7.148086 TGCCTTTCTTTTGCACCAGTAATATAG 60.148 37.037 0.00 0.00 0.00 1.31
230 235 6.429078 TGCACCAGTAATATAGTAGTACTCCG 59.571 42.308 5.96 0.00 37.46 4.63
251 257 4.265556 CCGGAATCGATTAGACATTATCGC 59.734 45.833 11.38 0.00 42.42 4.58
310 320 5.578776 TGCATCGCATAATATAGTACTCCG 58.421 41.667 0.00 0.00 31.71 4.63
531 550 8.293867 TGTTTTCTAGATGAACAATAAAACGGG 58.706 33.333 15.82 0.00 37.88 5.28
606 669 0.610232 CAGCCCAAGGGTTCTTCCAG 60.610 60.000 7.05 0.00 38.11 3.86
641 704 2.813754 CCCATTCATGTACTTATGCGGG 59.186 50.000 0.00 0.00 0.00 6.13
643 706 1.961793 TTCATGTACTTATGCGGGGC 58.038 50.000 0.00 0.00 0.00 5.80
783 856 2.696759 CCATTTCCCAACGACGGCC 61.697 63.158 0.00 0.00 0.00 6.13
791 864 1.600485 CCCAACGACGGCCATTAATAC 59.400 52.381 2.24 0.00 0.00 1.89
906 994 3.663176 CCACCACGCACTGCCAAG 61.663 66.667 0.00 0.00 0.00 3.61
948 1060 2.125912 CCCTCGGCAGAACGACAG 60.126 66.667 0.00 0.00 38.06 3.51
1214 1342 1.943116 CTGCTGGTGAGTCCTCCTCG 61.943 65.000 3.67 0.00 43.64 4.63
1221 1352 0.959553 TGAGTCCTCCTCGTGTTGTC 59.040 55.000 0.00 0.00 43.64 3.18
1296 1427 9.297586 GTTCGTCTATGTATGAACAAGATTGTA 57.702 33.333 0.00 0.00 42.46 2.41
1368 1516 3.165058 TCCTGTCCGAGATGAAATTCG 57.835 47.619 0.00 0.00 36.62 3.34
1369 1517 2.758423 TCCTGTCCGAGATGAAATTCGA 59.242 45.455 0.00 0.00 39.06 3.71
1375 1549 3.557185 TCCGAGATGAAATTCGATTGCTG 59.443 43.478 0.00 0.00 39.06 4.41
1382 1556 3.694072 TGAAATTCGATTGCTGGGTTAGG 59.306 43.478 0.00 0.00 0.00 2.69
1385 1559 2.871096 TCGATTGCTGGGTTAGGTTT 57.129 45.000 0.00 0.00 0.00 3.27
1432 1606 5.294306 TCTTTGATCGGTTTATGAGCATGAC 59.706 40.000 0.00 0.00 30.98 3.06
1437 1611 2.153817 CGGTTTATGAGCATGACGATCG 59.846 50.000 14.88 14.88 30.45 3.69
1444 1618 4.520743 TGAGCATGACGATCGAATTTTC 57.479 40.909 24.34 9.02 30.45 2.29
1463 1710 5.772825 TTTCTGGTTCTGTTGGATTGAAG 57.227 39.130 0.00 0.00 0.00 3.02
1464 1711 3.149196 TCTGGTTCTGTTGGATTGAAGC 58.851 45.455 0.00 0.00 38.30 3.86
1475 1722 4.836125 TGGATTGAAGCACAGAGTTTTC 57.164 40.909 0.00 0.00 0.00 2.29
1998 2259 1.672881 CCGAAGATTGACCTGAATGCC 59.327 52.381 0.00 0.00 0.00 4.40
2052 2313 9.739276 AAAGATGATACAGTAGACAATTGGAAA 57.261 29.630 10.83 0.00 0.00 3.13
2105 2372 6.350445 CCAGCCATTAGTTTGTTGCTTCTTAT 60.350 38.462 0.00 0.00 0.00 1.73
2219 2518 7.366513 AGTCTTTTTCTTCAATTCTTAGCTGC 58.633 34.615 0.00 0.00 0.00 5.25
2238 2548 3.414269 TGCTCTGTTCATTCAGCAATGA 58.586 40.909 0.00 0.00 45.63 2.57
2250 2560 8.975410 TCATTCAGCAATGAAAATAGTCTTTG 57.025 30.769 0.00 0.00 44.56 2.77
2251 2561 8.795513 TCATTCAGCAATGAAAATAGTCTTTGA 58.204 29.630 0.00 0.00 44.56 2.69
2252 2562 8.857216 CATTCAGCAATGAAAATAGTCTTTGAC 58.143 33.333 5.33 0.00 41.97 3.18
2253 2563 7.509141 TCAGCAATGAAAATAGTCTTTGACA 57.491 32.000 5.33 0.00 35.65 3.58
2255 2565 7.013178 TCAGCAATGAAAATAGTCTTTGACACA 59.987 33.333 5.33 0.00 35.65 3.72
2258 2568 8.025445 GCAATGAAAATAGTCTTTGACACATCT 58.975 33.333 5.33 0.00 35.65 2.90
2287 2597 9.973450 ATGTGCTCTAGTTATTACACATCTAAG 57.027 33.333 0.00 0.00 43.27 2.18
2288 2598 8.967918 TGTGCTCTAGTTATTACACATCTAAGT 58.032 33.333 0.00 0.00 33.41 2.24
2289 2599 9.239002 GTGCTCTAGTTATTACACATCTAAGTG 57.761 37.037 0.00 0.00 44.93 3.16
2290 2600 9.185680 TGCTCTAGTTATTACACATCTAAGTGA 57.814 33.333 0.57 0.00 42.05 3.41
2291 2601 9.672086 GCTCTAGTTATTACACATCTAAGTGAG 57.328 37.037 0.57 0.00 42.05 3.51
2292 2602 9.672086 CTCTAGTTATTACACATCTAAGTGAGC 57.328 37.037 0.57 0.00 42.05 4.26
2293 2603 8.343366 TCTAGTTATTACACATCTAAGTGAGCG 58.657 37.037 0.57 0.00 42.05 5.03
2294 2604 7.096884 AGTTATTACACATCTAAGTGAGCGA 57.903 36.000 0.57 0.00 42.05 4.93
2295 2605 7.544622 AGTTATTACACATCTAAGTGAGCGAA 58.455 34.615 0.57 0.00 42.05 4.70
2296 2606 8.198109 AGTTATTACACATCTAAGTGAGCGAAT 58.802 33.333 0.57 0.00 42.05 3.34
2297 2607 8.480853 GTTATTACACATCTAAGTGAGCGAATC 58.519 37.037 0.57 0.00 42.05 2.52
2298 2608 4.456280 ACACATCTAAGTGAGCGAATCA 57.544 40.909 0.57 0.00 42.05 2.57
2299 2609 4.820897 ACACATCTAAGTGAGCGAATCAA 58.179 39.130 0.57 0.00 42.05 2.57
2300 2610 4.867047 ACACATCTAAGTGAGCGAATCAAG 59.133 41.667 0.57 0.00 42.05 3.02
2301 2611 4.867047 CACATCTAAGTGAGCGAATCAAGT 59.133 41.667 0.00 0.00 42.05 3.16
2302 2612 6.036470 CACATCTAAGTGAGCGAATCAAGTA 58.964 40.000 0.00 0.00 42.05 2.24
2303 2613 6.699204 CACATCTAAGTGAGCGAATCAAGTAT 59.301 38.462 0.00 0.00 42.05 2.12
2304 2614 7.862873 CACATCTAAGTGAGCGAATCAAGTATA 59.137 37.037 0.00 0.00 42.05 1.47
2305 2615 8.414003 ACATCTAAGTGAGCGAATCAAGTATAA 58.586 33.333 0.00 0.00 40.43 0.98
2306 2616 9.249457 CATCTAAGTGAGCGAATCAAGTATAAA 57.751 33.333 0.00 0.00 40.43 1.40
2307 2617 8.858003 TCTAAGTGAGCGAATCAAGTATAAAG 57.142 34.615 0.00 0.00 40.43 1.85
2308 2618 8.683615 TCTAAGTGAGCGAATCAAGTATAAAGA 58.316 33.333 0.00 0.00 40.43 2.52
2309 2619 7.763172 AAGTGAGCGAATCAAGTATAAAGAG 57.237 36.000 0.00 0.00 40.43 2.85
2310 2620 7.101652 AGTGAGCGAATCAAGTATAAAGAGA 57.898 36.000 0.00 0.00 40.43 3.10
2311 2621 7.548097 AGTGAGCGAATCAAGTATAAAGAGAA 58.452 34.615 0.00 0.00 40.43 2.87
2312 2622 8.035394 AGTGAGCGAATCAAGTATAAAGAGAAA 58.965 33.333 0.00 0.00 40.43 2.52
2313 2623 8.656849 GTGAGCGAATCAAGTATAAAGAGAAAA 58.343 33.333 0.00 0.00 40.43 2.29
2314 2624 9.214957 TGAGCGAATCAAGTATAAAGAGAAAAA 57.785 29.630 0.00 0.00 34.02 1.94
2353 2663 9.599866 AATATTCACACGAATCTCAATGTAAGA 57.400 29.630 0.00 0.00 41.09 2.10
2354 2664 9.770097 ATATTCACACGAATCTCAATGTAAGAT 57.230 29.630 0.00 0.00 41.09 2.40
2355 2665 7.525688 TTCACACGAATCTCAATGTAAGATC 57.474 36.000 0.00 0.00 32.29 2.75
2356 2666 6.630071 TCACACGAATCTCAATGTAAGATCA 58.370 36.000 0.00 0.00 32.29 2.92
2357 2667 7.096551 TCACACGAATCTCAATGTAAGATCAA 58.903 34.615 0.00 0.00 32.29 2.57
2358 2668 7.765819 TCACACGAATCTCAATGTAAGATCAAT 59.234 33.333 0.00 0.00 32.29 2.57
2359 2669 7.849515 CACACGAATCTCAATGTAAGATCAATG 59.150 37.037 0.00 0.00 32.29 2.82
2360 2670 7.765819 ACACGAATCTCAATGTAAGATCAATGA 59.234 33.333 0.00 0.00 32.29 2.57
2361 2671 8.060679 CACGAATCTCAATGTAAGATCAATGAC 58.939 37.037 0.00 0.00 32.29 3.06
2362 2672 7.765819 ACGAATCTCAATGTAAGATCAATGACA 59.234 33.333 0.00 0.00 32.29 3.58
2363 2673 8.771766 CGAATCTCAATGTAAGATCAATGACAT 58.228 33.333 0.00 0.00 32.29 3.06
2446 2756 1.001597 ACTTTTTCTCGAGTCGTCGCT 60.002 47.619 13.13 0.00 46.39 4.93
2468 2778 8.083462 TCGCTATTAATAACACGATTGGTATGA 58.917 33.333 9.58 0.00 35.66 2.15
2476 2793 3.133691 CACGATTGGTATGACCTGGATG 58.866 50.000 0.00 0.00 39.58 3.51
2483 2800 4.843728 TGGTATGACCTGGATGTTCTTTC 58.156 43.478 0.00 0.00 39.58 2.62
2502 2819 9.691362 GTTCTTTCCAAAATTAATGCAGTTCTA 57.309 29.630 0.00 0.00 0.00 2.10
2527 2844 8.696043 AGGTACACCACGTATATAAATAGTGA 57.304 34.615 0.38 0.00 38.89 3.41
2592 2920 5.898972 ACGAGTACCCTGGTATTTTATACCA 59.101 40.000 15.67 15.67 44.62 3.25
2627 2956 4.255833 AGTGTGGTACCATGCAAAAATG 57.744 40.909 19.72 0.00 0.00 2.32
2646 2975 8.987729 CAAAAATGAAATAAAATACGCATGTGC 58.012 29.630 6.08 0.00 37.78 4.57
2672 3001 4.223659 ACAAAACCACGATACAAAATCGC 58.776 39.130 7.27 0.00 44.60 4.58
2686 3015 4.202010 ACAAAATCGCAAGTGTAGTTTGCT 60.202 37.500 8.15 0.00 46.62 3.91
2689 3018 1.136690 CGCAAGTGTAGTTTGCTCGA 58.863 50.000 8.15 0.00 46.62 4.04
2708 3037 7.909267 TGCTCGATGTAGAAAAATCACAATAG 58.091 34.615 0.00 0.00 0.00 1.73
2758 3087 5.167121 CCTTATCAAGTGGAGAGCGATATG 58.833 45.833 0.00 0.00 0.00 1.78
2782 3111 2.092323 GGTGCCCTATTGGACAAGAAC 58.908 52.381 0.00 0.00 35.39 3.01
2793 3122 3.427573 TGGACAAGAACCGATAGACTGA 58.572 45.455 0.00 0.00 39.76 3.41
2860 3199 7.064728 GTGATTAGTCTTTTCTGTGGATGGTAC 59.935 40.741 0.00 0.00 0.00 3.34
2885 3224 9.762933 ACAAATTTACTCTACCGTGTAAAACTA 57.237 29.630 0.00 0.00 40.42 2.24
2890 3229 3.564511 TCTACCGTGTAAAACTACGCAC 58.435 45.455 0.00 0.00 38.87 5.34
2923 3262 6.682113 GCAGATTGCATTCAGGAATATGTTGT 60.682 38.462 10.98 0.00 45.53 3.32
2961 3300 4.982295 GTGCCACTTGTAAAATTCCTTCAC 59.018 41.667 0.00 0.00 0.00 3.18
2971 3310 5.343307 AAAATTCCTTCACACACTTTGCT 57.657 34.783 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.376037 GGGCATACTAGCATCCCGC 60.376 63.158 0.00 0.00 42.91 6.13
73 74 4.668941 GCAAAATAAAATGCAAACTCGGGC 60.669 41.667 0.00 0.00 42.12 6.13
85 86 8.682710 ACTATATGTCGTGGTGCAAAATAAAAT 58.317 29.630 0.00 0.00 0.00 1.82
86 87 8.046294 ACTATATGTCGTGGTGCAAAATAAAA 57.954 30.769 0.00 0.00 0.00 1.52
189 193 3.270027 GGTGCAAAAGAAAGGCAAAGTT 58.730 40.909 0.00 0.00 39.57 2.66
212 217 8.709386 TCGATTCCGGAGTACTACTATATTAC 57.291 38.462 3.34 0.00 36.24 1.89
213 218 9.896645 AATCGATTCCGGAGTACTACTATATTA 57.103 33.333 3.34 0.00 36.24 0.98
214 219 8.804912 AATCGATTCCGGAGTACTACTATATT 57.195 34.615 3.34 0.00 36.24 1.28
216 221 8.753133 TCTAATCGATTCCGGAGTACTACTATA 58.247 37.037 15.25 0.00 36.24 1.31
217 222 7.548780 GTCTAATCGATTCCGGAGTACTACTAT 59.451 40.741 15.25 0.00 36.24 2.12
219 224 5.700373 GTCTAATCGATTCCGGAGTACTACT 59.300 44.000 15.25 0.00 36.24 2.57
220 225 5.468072 TGTCTAATCGATTCCGGAGTACTAC 59.532 44.000 15.25 0.00 36.24 2.73
230 235 6.194876 CGTAGCGATAATGTCTAATCGATTCC 59.805 42.308 15.25 4.74 46.08 3.01
284 291 7.062956 CGGAGTACTATATTATGCGATGCAAAA 59.937 37.037 0.00 0.00 43.62 2.44
291 301 6.238293 CGATTCCGGAGTACTATATTATGCGA 60.238 42.308 3.34 0.00 0.00 5.10
401 416 4.337763 CCGCGTCGTATAATACATACTCC 58.662 47.826 4.92 0.00 0.00 3.85
402 417 3.782893 GCCGCGTCGTATAATACATACTC 59.217 47.826 4.92 0.00 0.00 2.59
403 418 3.189080 TGCCGCGTCGTATAATACATACT 59.811 43.478 4.92 0.00 0.00 2.12
404 419 3.491356 TGCCGCGTCGTATAATACATAC 58.509 45.455 4.92 0.00 0.00 2.39
405 420 3.828060 TGCCGCGTCGTATAATACATA 57.172 42.857 4.92 0.00 0.00 2.29
406 421 2.710220 TGCCGCGTCGTATAATACAT 57.290 45.000 4.92 0.00 0.00 2.29
407 422 2.488639 TTGCCGCGTCGTATAATACA 57.511 45.000 4.92 0.00 0.00 2.29
531 550 8.971321 CATTGATCCATTCCATTTAATCGTTTC 58.029 33.333 0.00 0.00 0.00 2.78
538 557 6.541934 TGTGCATTGATCCATTCCATTTAA 57.458 33.333 0.00 0.00 0.00 1.52
641 704 6.369615 TCCGTTTAAAGTAGTCATTTACTGCC 59.630 38.462 0.00 0.00 41.41 4.85
643 706 9.590088 GTTTCCGTTTAAAGTAGTCATTTACTG 57.410 33.333 0.00 0.00 39.39 2.74
906 994 3.083997 AGAGATCGGTGGGGGTGC 61.084 66.667 0.00 0.00 0.00 5.01
948 1060 4.096382 TGCTTCCTCTTTTCTGTGTTTGTC 59.904 41.667 0.00 0.00 0.00 3.18
1214 1342 0.949105 ACGAATGGGCGAGACAACAC 60.949 55.000 0.00 0.00 34.83 3.32
1221 1352 0.108138 AGGAGAAACGAATGGGCGAG 60.108 55.000 0.00 0.00 34.83 5.03
1316 1464 2.845967 CGCGAATTGATTAAGCACCAAC 59.154 45.455 0.00 0.00 0.00 3.77
1368 1516 3.365969 CGACAAAACCTAACCCAGCAATC 60.366 47.826 0.00 0.00 0.00 2.67
1369 1517 2.556622 CGACAAAACCTAACCCAGCAAT 59.443 45.455 0.00 0.00 0.00 3.56
1375 1549 0.879090 CTGCCGACAAAACCTAACCC 59.121 55.000 0.00 0.00 0.00 4.11
1382 1556 3.057596 TGGATTTGATCTGCCGACAAAAC 60.058 43.478 8.88 7.14 37.14 2.43
1385 1559 2.488204 TGGATTTGATCTGCCGACAA 57.512 45.000 0.00 0.00 0.00 3.18
1432 1606 4.928661 ACAGAACCAGAAAATTCGATCG 57.071 40.909 9.36 9.36 0.00 3.69
1437 1611 6.748132 TCAATCCAACAGAACCAGAAAATTC 58.252 36.000 0.00 0.00 0.00 2.17
1444 1618 2.886523 TGCTTCAATCCAACAGAACCAG 59.113 45.455 0.00 0.00 0.00 4.00
1599 1854 4.021925 AGGTTGAGGTCCGGCTGC 62.022 66.667 0.00 0.00 0.00 5.25
1604 1859 2.266055 GAGGCAGGTTGAGGTCCG 59.734 66.667 0.00 0.00 0.00 4.79
2010 2271 3.502123 TCTTTTCCCATTCACTCGGTT 57.498 42.857 0.00 0.00 0.00 4.44
2197 2495 7.537991 CAGAGCAGCTAAGAATTGAAGAAAAAG 59.462 37.037 0.00 0.00 0.00 2.27
2262 2572 8.967918 ACTTAGATGTGTAATAACTAGAGCACA 58.032 33.333 0.00 0.00 40.42 4.57
2263 2573 9.239002 CACTTAGATGTGTAATAACTAGAGCAC 57.761 37.037 0.00 0.00 33.61 4.40
2264 2574 9.185680 TCACTTAGATGTGTAATAACTAGAGCA 57.814 33.333 0.00 0.00 38.90 4.26
2265 2575 9.672086 CTCACTTAGATGTGTAATAACTAGAGC 57.328 37.037 0.00 0.00 38.90 4.09
2266 2576 9.672086 GCTCACTTAGATGTGTAATAACTAGAG 57.328 37.037 0.00 0.00 38.90 2.43
2269 2579 8.217131 TCGCTCACTTAGATGTGTAATAACTA 57.783 34.615 0.00 0.00 38.90 2.24
2271 2581 7.751047 TTCGCTCACTTAGATGTGTAATAAC 57.249 36.000 0.00 0.00 38.90 1.89
2273 2583 7.712797 TGATTCGCTCACTTAGATGTGTAATA 58.287 34.615 0.00 0.00 38.90 0.98
2274 2584 6.573434 TGATTCGCTCACTTAGATGTGTAAT 58.427 36.000 0.00 0.00 38.90 1.89
2275 2585 5.961272 TGATTCGCTCACTTAGATGTGTAA 58.039 37.500 0.00 0.00 38.90 2.41
2276 2586 5.576447 TGATTCGCTCACTTAGATGTGTA 57.424 39.130 0.00 0.00 38.90 2.90
2277 2587 4.456280 TGATTCGCTCACTTAGATGTGT 57.544 40.909 0.00 0.00 38.90 3.72
2278 2588 4.867047 ACTTGATTCGCTCACTTAGATGTG 59.133 41.667 0.00 0.00 39.15 3.21
2279 2589 5.078411 ACTTGATTCGCTCACTTAGATGT 57.922 39.130 0.00 0.00 32.17 3.06
2280 2590 8.803201 TTATACTTGATTCGCTCACTTAGATG 57.197 34.615 0.00 0.00 32.17 2.90
2281 2591 9.469807 CTTTATACTTGATTCGCTCACTTAGAT 57.530 33.333 0.00 0.00 32.17 1.98
2282 2592 8.683615 TCTTTATACTTGATTCGCTCACTTAGA 58.316 33.333 0.00 0.00 32.17 2.10
2283 2593 8.858003 TCTTTATACTTGATTCGCTCACTTAG 57.142 34.615 0.00 0.00 32.17 2.18
2284 2594 8.683615 TCTCTTTATACTTGATTCGCTCACTTA 58.316 33.333 0.00 0.00 32.17 2.24
2285 2595 7.548097 TCTCTTTATACTTGATTCGCTCACTT 58.452 34.615 0.00 0.00 32.17 3.16
2286 2596 7.101652 TCTCTTTATACTTGATTCGCTCACT 57.898 36.000 0.00 0.00 32.17 3.41
2287 2597 7.757097 TTCTCTTTATACTTGATTCGCTCAC 57.243 36.000 0.00 0.00 32.17 3.51
2288 2598 8.771920 TTTTCTCTTTATACTTGATTCGCTCA 57.228 30.769 0.00 0.00 0.00 4.26
2327 2637 9.599866 TCTTACATTGAGATTCGTGTGAATATT 57.400 29.630 0.00 0.00 44.79 1.28
2328 2638 9.770097 ATCTTACATTGAGATTCGTGTGAATAT 57.230 29.630 0.00 0.00 44.79 1.28
2329 2639 9.249457 GATCTTACATTGAGATTCGTGTGAATA 57.751 33.333 0.00 0.00 44.79 1.75
2331 2641 7.096551 TGATCTTACATTGAGATTCGTGTGAA 58.903 34.615 0.00 0.00 38.76 3.18
2332 2642 6.630071 TGATCTTACATTGAGATTCGTGTGA 58.370 36.000 0.00 0.00 34.13 3.58
2333 2643 6.892310 TGATCTTACATTGAGATTCGTGTG 57.108 37.500 0.00 0.00 34.13 3.82
2334 2644 7.765819 TCATTGATCTTACATTGAGATTCGTGT 59.234 33.333 0.00 0.00 34.13 4.49
2335 2645 8.060679 GTCATTGATCTTACATTGAGATTCGTG 58.939 37.037 0.00 0.00 34.13 4.35
2336 2646 7.765819 TGTCATTGATCTTACATTGAGATTCGT 59.234 33.333 0.00 0.00 34.13 3.85
2337 2647 8.134905 TGTCATTGATCTTACATTGAGATTCG 57.865 34.615 0.00 0.00 34.13 3.34
2376 2686 6.173427 TCTAGATGTGCCATAAGTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
2377 2687 7.069852 CATCTAGATGTGCCATAAGTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
2415 2725 9.640974 CGACTCGAGAAAAAGTTTTATTTACAA 57.359 29.630 21.68 0.00 0.00 2.41
2416 2726 8.819974 ACGACTCGAGAAAAAGTTTTATTTACA 58.180 29.630 21.68 0.00 0.00 2.41
2417 2727 9.299276 GACGACTCGAGAAAAAGTTTTATTTAC 57.701 33.333 21.68 0.00 0.00 2.01
2418 2728 8.209869 CGACGACTCGAGAAAAAGTTTTATTTA 58.790 33.333 21.68 0.00 43.06 1.40
2419 2729 7.061634 CGACGACTCGAGAAAAAGTTTTATTT 58.938 34.615 21.68 0.00 43.06 1.40
2420 2730 6.578691 CGACGACTCGAGAAAAAGTTTTATT 58.421 36.000 21.68 0.00 43.06 1.40
2421 2731 5.388164 GCGACGACTCGAGAAAAAGTTTTAT 60.388 40.000 21.68 0.00 43.06 1.40
2422 2732 4.085415 GCGACGACTCGAGAAAAAGTTTTA 60.085 41.667 21.68 0.00 43.06 1.52
2423 2733 3.302286 GCGACGACTCGAGAAAAAGTTTT 60.302 43.478 21.68 0.00 43.06 2.43
2424 2734 2.218075 GCGACGACTCGAGAAAAAGTTT 59.782 45.455 21.68 0.00 43.06 2.66
2425 2735 1.785430 GCGACGACTCGAGAAAAAGTT 59.215 47.619 21.68 0.00 43.06 2.66
2426 2736 1.001597 AGCGACGACTCGAGAAAAAGT 60.002 47.619 21.68 10.76 43.06 2.66
2427 2737 1.687628 AGCGACGACTCGAGAAAAAG 58.312 50.000 21.68 8.43 43.06 2.27
2437 2747 5.160699 TCGTGTTATTAATAGCGACGACT 57.839 39.130 21.18 0.00 29.82 4.18
2446 2756 9.483916 CAGGTCATACCAATCGTGTTATTAATA 57.516 33.333 0.00 0.00 41.95 0.98
2476 2793 8.593492 AGAACTGCATTAATTTTGGAAAGAAC 57.407 30.769 0.00 0.00 0.00 3.01
2483 2800 7.968405 GTGTACCTAGAACTGCATTAATTTTGG 59.032 37.037 0.00 0.00 0.00 3.28
2502 2819 8.696043 TCACTATTTATATACGTGGTGTACCT 57.304 34.615 0.00 0.00 35.44 3.08
2527 2844 6.744112 TGAGAAAATACAAAAGCAACGGATT 58.256 32.000 0.00 0.00 0.00 3.01
2530 2847 5.746245 TGTTGAGAAAATACAAAAGCAACGG 59.254 36.000 0.00 0.00 37.71 4.44
2592 2920 1.202114 CCACACTTGCGTATTTGCCAT 59.798 47.619 0.00 0.00 0.00 4.40
2614 2942 8.174422 GCGTATTTTATTTCATTTTTGCATGGT 58.826 29.630 0.00 0.00 0.00 3.55
2646 2975 7.364441 CGATTTTGTATCGTGGTTTTGTACCG 61.364 42.308 0.00 0.00 40.04 4.02
2672 3001 5.161358 TCTACATCGAGCAAACTACACTTG 58.839 41.667 0.00 0.00 0.00 3.16
2708 3037 0.801067 GATGAGACCACGTACGCACC 60.801 60.000 16.72 2.20 0.00 5.01
2711 3040 0.029035 ATCGATGAGACCACGTACGC 59.971 55.000 16.72 0.00 0.00 4.42
2782 3111 0.311165 ATTCGGCGTCAGTCTATCGG 59.689 55.000 6.85 0.00 0.00 4.18
2793 3122 1.024271 CATGGATTTGGATTCGGCGT 58.976 50.000 6.85 0.00 0.00 5.68
2885 3224 0.750850 AATCTGCCTATACGGTGCGT 59.249 50.000 0.00 0.00 44.35 5.24
2886 3225 1.139989 CAATCTGCCTATACGGTGCG 58.860 55.000 0.00 0.00 34.25 5.34
2890 3229 3.402110 TGAATGCAATCTGCCTATACGG 58.598 45.455 2.94 0.00 44.23 4.02
2961 3300 5.200368 AGTATTTTGGGAAGCAAAGTGTG 57.800 39.130 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.