Multiple sequence alignment - TraesCS5A01G448800

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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 TraesCS5A01G448800 chr5A 100.000 1610 0 0 937 2546 631259894 631258285 0.000000e+00 2974
1 TraesCS5A01G448800 chr5A 100.000 692 0 0 1 692 631260830 631260139 0.000000e+00 1279
2 TraesCS5A01G448800 chr5B 92.074 593 17 9 1 568 626193938 626193351 0.000000e+00 808
3 TraesCS5A01G448800 chr5B 88.439 692 43 16 1427 2099 631365416 631364743 0.000000e+00 800
4 TraesCS5A01G448800 chr5B 76.044 1532 281 62 1058 2542 626084848 626083356 0.000000e+00 717
5 TraesCS5A01G448800 chr5B 93.926 461 27 1 944 1404 631365865 631365406 0.000000e+00 695
6 TraesCS5A01G448800 chr5B 82.962 763 121 7 949 1706 626193186 626192428 0.000000e+00 680
7 TraesCS5A01G448800 chr5B 82.674 733 59 25 5 691 631366581 631365871 2.820000e-164 588
8 TraesCS5A01G448800 chr5B 83.333 222 30 5 454 675 626140810 626140596 5.560000e-47 198
9 TraesCS5A01G448800 chr5B 84.080 201 16 6 153 351 626140993 626140807 2.010000e-41 180
10 TraesCS5A01G448800 chr5B 80.153 262 27 16 94 351 626107390 626107150 3.370000e-39 172
11 TraesCS5A01G448800 chr5B 80.078 256 27 14 99 351 626085341 626085107 4.360000e-38 169
12 TraesCS5A01G448800 chr5B 92.793 111 8 0 579 689 626193308 626193198 7.290000e-36 161
13 TraesCS5A01G448800 chr5B 78.906 256 30 15 99 351 631379089 631378855 4.390000e-33 152
14 TraesCS5A01G448800 chr5B 78.516 256 31 13 99 351 631354617 631354383 2.040000e-31 147
15 TraesCS5A01G448800 chr5D 91.327 588 27 7 1 568 502546049 502545466 0.000000e+00 782
16 TraesCS5A01G448800 chr5D 81.378 827 128 20 1020 1822 502545272 502544448 0.000000e+00 651
17 TraesCS5A01G448800 chr5D 80.859 256 25 12 99 351 502537510 502537276 2.010000e-41 180
18 TraesCS5A01G448800 chr5D 91.667 120 10 0 570 689 502545432 502545313 1.570000e-37 167
19 TraesCS5A01G448800 chr5D 82.090 201 20 7 153 351 502365250 502365064 9.430000e-35 158


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 TraesCS5A01G448800 chr5A 631258285 631260830 2545 True 2126.500000 2974 100.000000 1 2546 2 chr5A.!!$R1 2545
1 TraesCS5A01G448800 chr5B 631364743 631366581 1838 True 694.333333 800 88.346333 5 2099 3 chr5B.!!$R7 2094
2 TraesCS5A01G448800 chr5B 626192428 626193938 1510 True 549.666667 808 89.276333 1 1706 3 chr5B.!!$R6 1705
3 TraesCS5A01G448800 chr5B 626083356 626085341 1985 True 443.000000 717 78.061000 99 2542 2 chr5B.!!$R4 2443
4 TraesCS5A01G448800 chr5D 502544448 502546049 1601 True 533.333333 782 88.124000 1 1822 3 chr5D.!!$R3 1821

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
33 34 0.184211 CGGGGTTAATAAGGGGGTGG 59.816 60.000 0.0 0.0 0.0 4.61 F
286 339 1.270252 TGCGAGACTGAAACTGATGCA 60.270 47.619 0.0 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1001 1137 0.319555 CCGAAACTCTTCCAGCGACA 60.320 55.0 0.0 0.0 0.0 4.35 R
2236 2405 0.037160 GGCGGTAGAGGAAACCCAAA 59.963 55.0 0.0 0.0 33.1 3.28 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
33 34 0.184211 CGGGGTTAATAAGGGGGTGG 59.816 60.000 0.00 0.00 0.00 4.61
284 337 1.392853 GCTGCGAGACTGAAACTGATG 59.607 52.381 0.00 0.00 0.00 3.07
285 338 1.392853 CTGCGAGACTGAAACTGATGC 59.607 52.381 0.00 0.00 0.00 3.91
286 339 1.270252 TGCGAGACTGAAACTGATGCA 60.270 47.619 0.00 0.00 0.00 3.96
332 390 3.723348 GGGTTGTGCTCGTTCCGC 61.723 66.667 0.00 0.00 0.00 5.54
465 526 3.560068 ACACGACTGTCAATTCTGGTTTC 59.440 43.478 8.73 0.00 0.00 2.78
527 588 5.393866 TGGCCCCTAATAAATGATTTCTCC 58.606 41.667 0.00 0.00 0.00 3.71
574 668 3.958822 ATCAACGGCGTCGGTCGAC 62.959 63.158 15.17 7.13 46.20 4.20
589 683 2.434185 GACCGCGCACCAATCTCA 60.434 61.111 8.75 0.00 0.00 3.27
954 1048 4.733725 CCCCCTCCCCCGTCTCAA 62.734 72.222 0.00 0.00 0.00 3.02
1016 1152 3.425578 CGATGTCGCTGGAAGAGTT 57.574 52.632 0.00 0.00 34.36 3.01
1018 1154 1.656095 CGATGTCGCTGGAAGAGTTTC 59.344 52.381 0.00 0.00 34.36 2.78
1236 1372 4.920340 CAGATTCGGATCAAGGATAAGTCG 59.080 45.833 6.44 0.00 34.60 4.18
1264 1400 3.529533 GAGATCATCTATTGGGCGATGG 58.470 50.000 0.00 0.00 38.02 3.51
1272 1408 2.914734 ATTGGGCGATGGAGGAGGGA 62.915 60.000 0.00 0.00 0.00 4.20
1277 1413 1.420138 GGCGATGGAGGAGGGAAAATA 59.580 52.381 0.00 0.00 0.00 1.40
1279 1418 2.104963 GCGATGGAGGAGGGAAAATACT 59.895 50.000 0.00 0.00 0.00 2.12
1315 1454 3.047877 GGTGGAAACGTGAGCCGG 61.048 66.667 0.00 0.00 42.24 6.13
1337 1479 5.757850 GATGATTGGTTTCCATCCTACAC 57.242 43.478 0.00 0.00 31.53 2.90
1340 1482 2.489938 TGGTTTCCATCCTACACAGC 57.510 50.000 0.00 0.00 0.00 4.40
1354 1496 2.144952 ACAGCCAGTGATGGTGTGA 58.855 52.632 3.79 0.00 30.24 3.58
1374 1516 1.221840 GGTGGTGATCATGACGGCT 59.778 57.895 0.00 0.00 0.00 5.52
1565 1707 2.202946 GTCTTCCCGGCTAGCAGC 60.203 66.667 18.24 0.00 41.46 5.25
1611 1753 1.758514 TCTGGCGATGAGGACTCCC 60.759 63.158 0.00 0.00 0.00 4.30
1656 1800 8.099537 TCTTTTCAGTAAGATTGCTGATCTCTT 58.900 33.333 13.10 0.00 46.65 2.85
1719 1882 6.100279 AGGATTGTAGCTAGGATGTGATTTGA 59.900 38.462 0.00 0.00 0.00 2.69
1720 1883 6.203723 GGATTGTAGCTAGGATGTGATTTGAC 59.796 42.308 0.00 0.00 0.00 3.18
1795 1959 9.407380 TGTTGATTTGGATTATAGTATTGCTGT 57.593 29.630 0.00 0.00 0.00 4.40
1835 1999 5.036117 TGGCTCTTTCTAAAGTTGACACT 57.964 39.130 2.58 0.00 37.31 3.55
1840 2008 7.012044 GGCTCTTTCTAAAGTTGACACTTAACA 59.988 37.037 2.58 0.00 42.89 2.41
1957 2125 2.093869 CCTGCCAATTGGACAAAGGATG 60.094 50.000 29.02 11.46 37.39 3.51
1969 2137 5.299949 GGACAAAGGATGTGCTTCATTTTT 58.700 37.500 0.00 0.00 46.03 1.94
1984 2152 7.105588 GCTTCATTTTTGGGTGGATTTCTTAT 58.894 34.615 0.00 0.00 0.00 1.73
2055 2223 0.983467 AATTTCATGGGTTGGGGCAC 59.017 50.000 0.00 0.00 0.00 5.01
2101 2270 3.914645 TGGGCAGTTGGGCTAGAA 58.085 55.556 0.00 0.00 42.84 2.10
2111 2280 5.464168 CAGTTGGGCTAGAAGTTTTTGATG 58.536 41.667 0.00 0.00 0.00 3.07
2112 2281 5.010012 CAGTTGGGCTAGAAGTTTTTGATGT 59.990 40.000 0.00 0.00 0.00 3.06
2115 2284 5.876357 TGGGCTAGAAGTTTTTGATGTAGT 58.124 37.500 0.00 0.00 0.00 2.73
2119 2288 6.037281 GGCTAGAAGTTTTTGATGTAGTAGGC 59.963 42.308 0.00 0.00 0.00 3.93
2121 2290 6.128138 AGAAGTTTTTGATGTAGTAGGCCT 57.872 37.500 11.78 11.78 0.00 5.19
2125 2294 4.417426 TTTTGATGTAGTAGGCCTAGGC 57.583 45.455 26.55 26.55 41.06 3.93
2138 2307 0.838122 CCTAGGCTGGTGGGATAGGG 60.838 65.000 0.00 0.00 31.24 3.53
2141 2310 0.028642 AGGCTGGTGGGATAGGGAAT 60.029 55.000 0.00 0.00 0.00 3.01
2145 2314 2.126882 CTGGTGGGATAGGGAATCACA 58.873 52.381 0.00 0.00 46.07 3.58
2151 2320 2.373502 GGGATAGGGAATCACAGAAGGG 59.626 54.545 0.00 0.00 37.98 3.95
2152 2321 2.224646 GGATAGGGAATCACAGAAGGGC 60.225 54.545 0.00 0.00 36.20 5.19
2156 2325 2.852449 AGGGAATCACAGAAGGGCAATA 59.148 45.455 0.00 0.00 0.00 1.90
2157 2326 2.952310 GGGAATCACAGAAGGGCAATAC 59.048 50.000 0.00 0.00 0.00 1.89
2159 2328 1.668419 ATCACAGAAGGGCAATACGC 58.332 50.000 0.00 0.00 41.28 4.42
2170 2339 0.804989 GCAATACGCCTTCTGTTGCT 59.195 50.000 0.00 0.00 41.30 3.91
2173 2342 3.236816 CAATACGCCTTCTGTTGCTTTG 58.763 45.455 0.00 0.00 0.00 2.77
2174 2343 0.591170 TACGCCTTCTGTTGCTTTGC 59.409 50.000 0.00 0.00 0.00 3.68
2176 2345 1.654220 GCCTTCTGTTGCTTTGCGA 59.346 52.632 0.00 0.00 0.00 5.10
2178 2347 1.973138 CCTTCTGTTGCTTTGCGATG 58.027 50.000 0.00 0.00 0.00 3.84
2196 2365 3.065371 CGATGTTTAGATGCTTTGGTCCC 59.935 47.826 0.00 0.00 0.00 4.46
2197 2366 3.806949 TGTTTAGATGCTTTGGTCCCT 57.193 42.857 0.00 0.00 0.00 4.20
2198 2367 4.112634 TGTTTAGATGCTTTGGTCCCTT 57.887 40.909 0.00 0.00 0.00 3.95
2201 2370 1.075601 AGATGCTTTGGTCCCTTCCA 58.924 50.000 0.00 0.00 35.49 3.53
2202 2371 1.428912 AGATGCTTTGGTCCCTTCCAA 59.571 47.619 0.00 0.00 44.48 3.53
2219 2388 1.631405 CAAAGGCAGATTTGGTGGGA 58.369 50.000 0.00 0.00 36.68 4.37
2220 2389 2.181975 CAAAGGCAGATTTGGTGGGAT 58.818 47.619 0.00 0.00 36.68 3.85
2221 2390 3.364549 CAAAGGCAGATTTGGTGGGATA 58.635 45.455 0.00 0.00 36.68 2.59
2222 2391 3.962718 CAAAGGCAGATTTGGTGGGATAT 59.037 43.478 0.00 0.00 36.68 1.63
2223 2392 3.234234 AGGCAGATTTGGTGGGATATG 57.766 47.619 0.00 0.00 0.00 1.78
2225 2394 3.152341 GGCAGATTTGGTGGGATATGAG 58.848 50.000 0.00 0.00 0.00 2.90
2226 2395 2.555757 GCAGATTTGGTGGGATATGAGC 59.444 50.000 0.00 0.00 0.00 4.26
2227 2396 2.810274 CAGATTTGGTGGGATATGAGCG 59.190 50.000 0.00 0.00 0.00 5.03
2228 2397 2.705658 AGATTTGGTGGGATATGAGCGA 59.294 45.455 0.00 0.00 0.00 4.93
2229 2398 2.325583 TTTGGTGGGATATGAGCGAC 57.674 50.000 0.00 0.00 0.00 5.19
2230 2399 1.199615 TTGGTGGGATATGAGCGACA 58.800 50.000 0.00 0.00 0.00 4.35
2232 2401 1.040646 GGTGGGATATGAGCGACAGA 58.959 55.000 0.00 0.00 0.00 3.41
2233 2402 1.269831 GGTGGGATATGAGCGACAGAC 60.270 57.143 0.00 0.00 0.00 3.51
2234 2403 1.409064 GTGGGATATGAGCGACAGACA 59.591 52.381 0.00 0.00 0.00 3.41
2236 2405 1.683917 GGGATATGAGCGACAGACAGT 59.316 52.381 0.00 0.00 0.00 3.55
2238 2407 3.430929 GGGATATGAGCGACAGACAGTTT 60.431 47.826 0.00 0.00 0.00 2.66
2239 2408 3.553511 GGATATGAGCGACAGACAGTTTG 59.446 47.826 0.00 0.00 0.00 2.93
2242 2411 0.249911 GAGCGACAGACAGTTTGGGT 60.250 55.000 0.00 0.00 0.00 4.51
2245 2414 1.002792 GCGACAGACAGTTTGGGTTTC 60.003 52.381 0.00 0.00 0.00 2.78
2246 2415 1.602377 CGACAGACAGTTTGGGTTTCC 59.398 52.381 0.00 0.00 0.00 3.13
2247 2416 2.745152 CGACAGACAGTTTGGGTTTCCT 60.745 50.000 0.00 0.00 0.00 3.36
2248 2417 2.879026 GACAGACAGTTTGGGTTTCCTC 59.121 50.000 0.00 0.00 0.00 3.71
2250 2419 3.714798 ACAGACAGTTTGGGTTTCCTCTA 59.285 43.478 0.00 0.00 0.00 2.43
2251 2420 4.065789 CAGACAGTTTGGGTTTCCTCTAC 58.934 47.826 0.00 0.00 0.00 2.59
2253 2422 2.224450 ACAGTTTGGGTTTCCTCTACCG 60.224 50.000 0.00 0.00 36.49 4.02
2254 2423 1.162698 GTTTGGGTTTCCTCTACCGC 58.837 55.000 0.00 0.00 36.49 5.68
2255 2424 0.037160 TTTGGGTTTCCTCTACCGCC 59.963 55.000 0.00 0.00 36.49 6.13
2273 2449 1.352083 CCACCTGGTGAGGAAGAAGA 58.648 55.000 27.94 0.00 42.93 2.87
2277 2453 4.026744 CACCTGGTGAGGAAGAAGAGATA 58.973 47.826 22.33 0.00 42.93 1.98
2279 2455 4.264623 ACCTGGTGAGGAAGAAGAGATAGT 60.265 45.833 0.00 0.00 42.93 2.12
2281 2457 5.395103 CCTGGTGAGGAAGAAGAGATAGTTG 60.395 48.000 0.00 0.00 42.93 3.16
2283 2459 4.712337 GGTGAGGAAGAAGAGATAGTTGGA 59.288 45.833 0.00 0.00 0.00 3.53
2284 2460 5.365314 GGTGAGGAAGAAGAGATAGTTGGAT 59.635 44.000 0.00 0.00 0.00 3.41
2288 2464 8.061920 TGAGGAAGAAGAGATAGTTGGATCTTA 58.938 37.037 0.00 0.00 36.27 2.10
2289 2465 9.088987 GAGGAAGAAGAGATAGTTGGATCTTAT 57.911 37.037 0.00 0.00 36.27 1.73
2290 2466 8.869109 AGGAAGAAGAGATAGTTGGATCTTATG 58.131 37.037 0.00 0.00 36.27 1.90
2297 2473 3.652057 AGTTGGATCTTATGGTGGTGG 57.348 47.619 0.00 0.00 0.00 4.61
2300 2476 3.129262 TGGATCTTATGGTGGTGGAGA 57.871 47.619 0.00 0.00 0.00 3.71
2301 2477 3.668821 TGGATCTTATGGTGGTGGAGAT 58.331 45.455 0.00 0.00 0.00 2.75
2303 2479 3.244700 GGATCTTATGGTGGTGGAGATGG 60.245 52.174 0.00 0.00 0.00 3.51
2304 2480 3.129262 TCTTATGGTGGTGGAGATGGA 57.871 47.619 0.00 0.00 0.00 3.41
2305 2481 2.771943 TCTTATGGTGGTGGAGATGGAC 59.228 50.000 0.00 0.00 0.00 4.02
2307 2483 0.620556 ATGGTGGTGGAGATGGACAC 59.379 55.000 0.00 0.00 36.89 3.67
2313 2489 1.471119 GTGGAGATGGACACCGTAGA 58.529 55.000 0.00 0.00 31.87 2.59
2318 2494 3.322254 GGAGATGGACACCGTAGATTCAT 59.678 47.826 0.00 0.00 0.00 2.57
2321 2498 4.590647 AGATGGACACCGTAGATTCATCAT 59.409 41.667 0.00 0.00 33.92 2.45
2324 2501 4.893524 TGGACACCGTAGATTCATCATAGT 59.106 41.667 0.00 0.00 0.00 2.12
2328 2505 4.280929 CACCGTAGATTCATCATAGTGGGA 59.719 45.833 0.00 0.00 0.00 4.37
2331 2508 5.011125 CCGTAGATTCATCATAGTGGGAAGT 59.989 44.000 0.00 0.00 0.00 3.01
2337 2514 9.927081 AGATTCATCATAGTGGGAAGTTTTAAT 57.073 29.630 0.00 0.00 0.00 1.40
2371 2548 8.934023 ATACAAGGGAAGATTTAACAACAGAA 57.066 30.769 0.00 0.00 0.00 3.02
2376 2553 5.321927 GGAAGATTTAACAACAGAAGGGGA 58.678 41.667 0.00 0.00 0.00 4.81
2390 2567 7.510675 ACAGAAGGGGAAGATTCAACTTATA 57.489 36.000 0.00 0.00 0.00 0.98
2415 2592 2.500392 TGTTTTTCTACCCCATCCCG 57.500 50.000 0.00 0.00 0.00 5.14
2417 2594 0.033894 TTTTTCTACCCCATCCCGGC 60.034 55.000 0.00 0.00 0.00 6.13
2420 2597 3.560251 CTACCCCATCCCGGCTGG 61.560 72.222 3.88 3.88 0.00 4.85
2436 2613 2.225467 GCTGGTGTGAAGAAAAGAGCT 58.775 47.619 0.00 0.00 0.00 4.09
2463 2640 4.724399 TCTTCATGGCTAGGTTTGTTTGA 58.276 39.130 0.00 0.00 0.00 2.69
2473 2651 4.437682 AGGTTTGTTTGACAGGAGATGA 57.562 40.909 0.00 0.00 0.00 2.92
2477 2655 5.273944 GTTTGTTTGACAGGAGATGACAAC 58.726 41.667 0.00 0.00 42.06 3.32
2525 2703 6.869206 TGGAACACTAGCTTTAGACCTAAT 57.131 37.500 0.00 0.00 0.00 1.73
2528 2706 6.981559 GGAACACTAGCTTTAGACCTAATGAG 59.018 42.308 0.00 0.00 0.00 2.90
2530 2708 4.979197 CACTAGCTTTAGACCTAATGAGCG 59.021 45.833 0.00 0.00 35.29 5.03
2531 2709 4.645588 ACTAGCTTTAGACCTAATGAGCGT 59.354 41.667 0.00 0.09 35.29 5.07
2537 2715 2.203209 CCTAATGAGCGTGGGGGC 60.203 66.667 0.00 0.00 0.00 5.80
2542 2720 1.271840 AATGAGCGTGGGGGCTTAGA 61.272 55.000 0.00 0.00 44.93 2.10
2543 2721 1.271840 ATGAGCGTGGGGGCTTAGAA 61.272 55.000 0.00 0.00 44.93 2.10
2544 2722 1.271840 TGAGCGTGGGGGCTTAGAAT 61.272 55.000 0.00 0.00 44.93 2.40
2545 2723 0.107165 GAGCGTGGGGGCTTAGAATT 60.107 55.000 0.00 0.00 44.93 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.008933 ACTCGCAGCCTCACCCAC 62.009 66.667 0.00 0.00 0.00 4.61
205 248 0.794473 GTTGTAAAACGAGGCGAGGG 59.206 55.000 0.00 0.00 0.00 4.30
262 305 0.941463 CAGTTTCAGTCTCGCAGCGT 60.941 55.000 15.93 0.00 0.00 5.07
284 337 2.425773 CAAACGTGACGCTGCTGC 60.426 61.111 4.25 5.34 0.00 5.25
285 338 2.249309 CCAAACGTGACGCTGCTG 59.751 61.111 4.25 0.00 0.00 4.41
286 339 2.203015 ACCAAACGTGACGCTGCT 60.203 55.556 4.25 0.00 0.00 4.24
332 390 0.034756 TATTGGCATCCGTCCATCCG 59.965 55.000 0.00 0.00 32.92 4.18
366 425 6.770785 ACTTAAACACCAAGCAACTCATAGAA 59.229 34.615 0.00 0.00 0.00 2.10
370 429 7.883311 ACTATACTTAAACACCAAGCAACTCAT 59.117 33.333 0.00 0.00 0.00 2.90
465 526 0.458669 GCCCAGATTGCATTCCACTG 59.541 55.000 5.00 2.79 0.00 3.66
574 668 3.197790 CCTGAGATTGGTGCGCGG 61.198 66.667 8.83 0.00 0.00 6.46
608 702 4.697828 TGCAAAAGTCGCAGGTATTCATTA 59.302 37.500 0.00 0.00 33.55 1.90
620 714 2.346099 TTAATGCCTGCAAAAGTCGC 57.654 45.000 0.00 0.00 0.00 5.19
938 1032 1.984288 GATTTGAGACGGGGGAGGGG 61.984 65.000 0.00 0.00 0.00 4.79
941 1035 0.103208 CGAGATTTGAGACGGGGGAG 59.897 60.000 0.00 0.00 0.00 4.30
942 1036 1.327690 CCGAGATTTGAGACGGGGGA 61.328 60.000 0.00 0.00 41.41 4.81
954 1048 1.305930 GCCCTTTCGTTGCCGAGATT 61.306 55.000 0.00 0.00 45.24 2.40
1001 1137 0.319555 CCGAAACTCTTCCAGCGACA 60.320 55.000 0.00 0.00 0.00 4.35
1003 1139 1.292223 CCCGAAACTCTTCCAGCGA 59.708 57.895 0.00 0.00 0.00 4.93
1006 1142 1.004918 ACGCCCGAAACTCTTCCAG 60.005 57.895 0.00 0.00 0.00 3.86
1011 1147 4.016706 CCCCACGCCCGAAACTCT 62.017 66.667 0.00 0.00 0.00 3.24
1236 1372 2.257894 CAATAGATGATCTCGAGCGGC 58.742 52.381 7.81 0.00 0.00 6.53
1264 1400 6.758886 CGCATATCATAGTATTTTCCCTCCTC 59.241 42.308 0.00 0.00 0.00 3.71
1272 1408 3.062099 CGCGCCGCATATCATAGTATTTT 59.938 43.478 10.75 0.00 0.00 1.82
1277 1413 4.169102 CGCGCCGCATATCATAGT 57.831 55.556 10.75 0.00 0.00 2.12
1315 1454 5.192927 TGTGTAGGATGGAAACCAATCATC 58.807 41.667 0.00 0.00 36.95 2.92
1354 1496 1.907739 CCGTCATGATCACCACCCT 59.092 57.895 0.00 0.00 0.00 4.34
1536 1678 1.112113 GGGAAGACGCCTACTCATCA 58.888 55.000 0.00 0.00 0.00 3.07
1565 1707 1.817099 GACCAGCAGCCAGAATCGG 60.817 63.158 0.00 0.00 0.00 4.18
1611 1753 2.053627 GAAAGCAGCAAAATGGTCGTG 58.946 47.619 0.00 0.00 0.00 4.35
1719 1882 4.917906 AAGAGGAACTATTTGGAGCAGT 57.082 40.909 0.00 0.00 35.85 4.40
1769 1933 9.407380 ACAGCAATACTATAATCCAAATCAACA 57.593 29.630 0.00 0.00 0.00 3.33
1778 1942 8.097038 TCATCCTCAACAGCAATACTATAATCC 58.903 37.037 0.00 0.00 0.00 3.01
1795 1959 3.091545 GCCAAGGACAAATCATCCTCAA 58.908 45.455 0.00 0.00 46.36 3.02
1911 2079 8.138074 GGGATAGCTGAAAAATTACCAATTCTC 58.862 37.037 0.00 0.00 0.00 2.87
1957 2125 3.683365 ATCCACCCAAAAATGAAGCAC 57.317 42.857 0.00 0.00 0.00 4.40
1984 2152 9.108284 CATCACCATCACAACATTAGTGTAATA 57.892 33.333 0.00 0.00 37.67 0.98
2030 2198 4.810376 GCCCCAACCCATGAAATTCATTTT 60.810 41.667 5.63 0.00 34.28 1.82
2055 2223 3.858247 CCAAGAAGGTTCTACGGGTAAG 58.142 50.000 0.00 0.00 36.28 2.34
2101 2270 5.629366 GCCTAGGCCTACTACATCAAAAACT 60.629 44.000 24.19 0.00 34.56 2.66
2111 2280 1.041437 CACCAGCCTAGGCCTACTAC 58.959 60.000 30.42 0.59 43.17 2.73
2112 2281 0.105658 CCACCAGCCTAGGCCTACTA 60.106 60.000 30.42 0.00 43.17 1.82
2115 2284 1.973346 ATCCCACCAGCCTAGGCCTA 61.973 60.000 30.42 13.09 43.17 3.93
2119 2288 0.838122 CCCTATCCCACCAGCCTAGG 60.838 65.000 3.67 3.67 0.00 3.02
2121 2290 0.645496 TTCCCTATCCCACCAGCCTA 59.355 55.000 0.00 0.00 0.00 3.93
2125 2294 2.105477 CTGTGATTCCCTATCCCACCAG 59.895 54.545 0.00 0.00 31.87 4.00
2138 2307 2.032178 GCGTATTGCCCTTCTGTGATTC 59.968 50.000 0.00 0.00 37.76 2.52
2141 2310 3.153024 GCGTATTGCCCTTCTGTGA 57.847 52.632 0.00 0.00 37.76 3.58
2151 2320 0.804989 AGCAACAGAAGGCGTATTGC 59.195 50.000 7.97 7.97 44.74 3.56
2152 2321 3.236816 CAAAGCAACAGAAGGCGTATTG 58.763 45.455 0.00 0.00 34.54 1.90
2156 2325 1.360192 GCAAAGCAACAGAAGGCGT 59.640 52.632 0.00 0.00 34.54 5.68
2157 2326 1.727022 CGCAAAGCAACAGAAGGCG 60.727 57.895 0.00 0.00 36.93 5.52
2159 2328 1.267806 ACATCGCAAAGCAACAGAAGG 59.732 47.619 0.00 0.00 0.00 3.46
2166 2335 3.191162 AGCATCTAAACATCGCAAAGCAA 59.809 39.130 0.00 0.00 0.00 3.91
2170 2339 4.022416 ACCAAAGCATCTAAACATCGCAAA 60.022 37.500 0.00 0.00 0.00 3.68
2173 2342 3.487544 GGACCAAAGCATCTAAACATCGC 60.488 47.826 0.00 0.00 0.00 4.58
2174 2343 3.065371 GGGACCAAAGCATCTAAACATCG 59.935 47.826 0.00 0.00 0.00 3.84
2176 2345 4.322057 AGGGACCAAAGCATCTAAACAT 57.678 40.909 0.00 0.00 0.00 2.71
2178 2347 3.444034 GGAAGGGACCAAAGCATCTAAAC 59.556 47.826 0.00 0.00 0.00 2.01
2201 2370 2.629017 ATCCCACCAAATCTGCCTTT 57.371 45.000 0.00 0.00 0.00 3.11
2202 2371 3.205056 TCATATCCCACCAAATCTGCCTT 59.795 43.478 0.00 0.00 0.00 4.35
2204 2373 3.152341 CTCATATCCCACCAAATCTGCC 58.848 50.000 0.00 0.00 0.00 4.85
2206 2375 2.810274 CGCTCATATCCCACCAAATCTG 59.190 50.000 0.00 0.00 0.00 2.90
2207 2376 2.705658 TCGCTCATATCCCACCAAATCT 59.294 45.455 0.00 0.00 0.00 2.40
2208 2377 2.808543 GTCGCTCATATCCCACCAAATC 59.191 50.000 0.00 0.00 0.00 2.17
2219 2388 3.525537 CCAAACTGTCTGTCGCTCATAT 58.474 45.455 0.00 0.00 0.00 1.78
2220 2389 2.353704 CCCAAACTGTCTGTCGCTCATA 60.354 50.000 0.00 0.00 0.00 2.15
2221 2390 1.609061 CCCAAACTGTCTGTCGCTCAT 60.609 52.381 0.00 0.00 0.00 2.90
2222 2391 0.249868 CCCAAACTGTCTGTCGCTCA 60.250 55.000 0.00 0.00 0.00 4.26
2223 2392 0.249911 ACCCAAACTGTCTGTCGCTC 60.250 55.000 0.00 0.00 0.00 5.03
2225 2394 1.002792 GAAACCCAAACTGTCTGTCGC 60.003 52.381 0.00 0.00 0.00 5.19
2226 2395 1.602377 GGAAACCCAAACTGTCTGTCG 59.398 52.381 0.00 0.00 0.00 4.35
2227 2396 2.879026 GAGGAAACCCAAACTGTCTGTC 59.121 50.000 0.00 0.00 0.00 3.51
2228 2397 2.509964 AGAGGAAACCCAAACTGTCTGT 59.490 45.455 0.00 0.00 0.00 3.41
2229 2398 3.214696 AGAGGAAACCCAAACTGTCTG 57.785 47.619 0.00 0.00 0.00 3.51
2230 2399 3.072622 GGTAGAGGAAACCCAAACTGTCT 59.927 47.826 0.00 0.00 0.00 3.41
2232 2401 2.224450 CGGTAGAGGAAACCCAAACTGT 60.224 50.000 0.00 0.00 33.10 3.55
2233 2402 2.423577 CGGTAGAGGAAACCCAAACTG 58.576 52.381 0.00 0.00 33.10 3.16
2234 2403 1.271217 GCGGTAGAGGAAACCCAAACT 60.271 52.381 0.00 0.00 33.10 2.66
2236 2405 0.037160 GGCGGTAGAGGAAACCCAAA 59.963 55.000 0.00 0.00 33.10 3.28
2238 2407 1.536907 TGGCGGTAGAGGAAACCCA 60.537 57.895 0.00 0.00 33.10 4.51
2239 2408 1.078637 GTGGCGGTAGAGGAAACCC 60.079 63.158 0.00 0.00 33.10 4.11
2242 2411 1.550130 CCAGGTGGCGGTAGAGGAAA 61.550 60.000 0.00 0.00 0.00 3.13
2245 2414 2.683933 ACCAGGTGGCGGTAGAGG 60.684 66.667 0.00 0.00 39.32 3.69
2246 2415 1.949847 CTCACCAGGTGGCGGTAGAG 61.950 65.000 20.14 3.76 39.32 2.43
2247 2416 1.982395 CTCACCAGGTGGCGGTAGA 60.982 63.158 20.14 0.00 39.32 2.59
2248 2417 2.579201 CTCACCAGGTGGCGGTAG 59.421 66.667 20.14 5.28 39.32 3.18
2250 2419 4.954118 TCCTCACCAGGTGGCGGT 62.954 66.667 20.14 0.00 41.28 5.68
2251 2420 3.612247 CTTCCTCACCAGGTGGCGG 62.612 68.421 20.14 18.98 41.28 6.13
2253 2422 0.322008 CTTCTTCCTCACCAGGTGGC 60.322 60.000 20.14 0.00 41.28 5.01
2254 2423 1.277557 CTCTTCTTCCTCACCAGGTGG 59.722 57.143 20.14 10.16 41.28 4.61
2255 2424 2.251818 TCTCTTCTTCCTCACCAGGTG 58.748 52.381 14.19 14.19 41.28 4.00
2266 2442 8.646900 ACCATAAGATCCAACTATCTCTTCTTC 58.353 37.037 0.00 0.00 35.10 2.87
2273 2449 5.072329 CCACCACCATAAGATCCAACTATCT 59.928 44.000 0.00 0.00 37.84 1.98
2277 2453 3.189606 TCCACCACCATAAGATCCAACT 58.810 45.455 0.00 0.00 0.00 3.16
2279 2455 3.459828 TCTCCACCACCATAAGATCCAA 58.540 45.455 0.00 0.00 0.00 3.53
2281 2457 3.244700 CCATCTCCACCACCATAAGATCC 60.245 52.174 0.00 0.00 0.00 3.36
2283 2459 3.392616 GTCCATCTCCACCACCATAAGAT 59.607 47.826 0.00 0.00 0.00 2.40
2284 2460 2.771943 GTCCATCTCCACCACCATAAGA 59.228 50.000 0.00 0.00 0.00 2.10
2288 2464 0.620556 GTGTCCATCTCCACCACCAT 59.379 55.000 0.00 0.00 0.00 3.55
2289 2465 2.066340 GTGTCCATCTCCACCACCA 58.934 57.895 0.00 0.00 0.00 4.17
2297 2473 4.038042 TGATGAATCTACGGTGTCCATCTC 59.962 45.833 0.00 0.00 32.53 2.75
2300 2476 4.963318 ATGATGAATCTACGGTGTCCAT 57.037 40.909 0.00 0.00 0.00 3.41
2301 2477 4.893524 ACTATGATGAATCTACGGTGTCCA 59.106 41.667 0.00 0.00 0.00 4.02
2303 2479 5.223382 CCACTATGATGAATCTACGGTGTC 58.777 45.833 0.00 0.00 0.00 3.67
2304 2480 4.039245 CCCACTATGATGAATCTACGGTGT 59.961 45.833 0.00 0.00 0.00 4.16
2305 2481 4.280929 TCCCACTATGATGAATCTACGGTG 59.719 45.833 0.00 0.00 0.00 4.94
2307 2483 5.011125 ACTTCCCACTATGATGAATCTACGG 59.989 44.000 0.00 0.00 0.00 4.02
2308 2484 6.090483 ACTTCCCACTATGATGAATCTACG 57.910 41.667 0.00 0.00 0.00 3.51
2345 2522 8.934023 TCTGTTGTTAAATCTTCCCTTGTATT 57.066 30.769 0.00 0.00 0.00 1.89
2346 2523 8.934023 TTCTGTTGTTAAATCTTCCCTTGTAT 57.066 30.769 0.00 0.00 0.00 2.29
2347 2524 7.447238 CCTTCTGTTGTTAAATCTTCCCTTGTA 59.553 37.037 0.00 0.00 0.00 2.41
2348 2525 6.265422 CCTTCTGTTGTTAAATCTTCCCTTGT 59.735 38.462 0.00 0.00 0.00 3.16
2349 2526 6.294731 CCCTTCTGTTGTTAAATCTTCCCTTG 60.295 42.308 0.00 0.00 0.00 3.61
2350 2527 5.775195 CCCTTCTGTTGTTAAATCTTCCCTT 59.225 40.000 0.00 0.00 0.00 3.95
2353 2530 5.321927 TCCCCTTCTGTTGTTAAATCTTCC 58.678 41.667 0.00 0.00 0.00 3.46
2390 2567 6.314917 GGGATGGGGTAGAAAAACATCATAT 58.685 40.000 0.00 0.00 39.63 1.78
2415 2592 1.268079 GCTCTTTTCTTCACACCAGCC 59.732 52.381 0.00 0.00 0.00 4.85
2417 2594 6.566197 AATTAGCTCTTTTCTTCACACCAG 57.434 37.500 0.00 0.00 0.00 4.00
2436 2613 7.775053 AACAAACCTAGCCATGAAGAAATTA 57.225 32.000 0.00 0.00 0.00 1.40
2489 2667 6.720288 AGCTAGTGTTCCACTTTACTAAGAGA 59.280 38.462 1.74 0.00 42.59 3.10
2491 2669 6.912951 AGCTAGTGTTCCACTTTACTAAGA 57.087 37.500 1.74 0.00 42.59 2.10
2501 2679 4.538746 AGGTCTAAAGCTAGTGTTCCAC 57.461 45.455 0.00 0.00 34.10 4.02
2503 2681 6.875076 TCATTAGGTCTAAAGCTAGTGTTCC 58.125 40.000 0.00 0.00 41.42 3.62
2511 2689 3.430929 CCACGCTCATTAGGTCTAAAGCT 60.431 47.826 10.72 0.00 37.01 3.74
2513 2691 3.458189 CCCACGCTCATTAGGTCTAAAG 58.542 50.000 0.00 0.00 0.00 1.85
2525 2703 1.271840 ATTCTAAGCCCCCACGCTCA 61.272 55.000 0.00 0.00 38.44 4.26
2528 2706 4.657952 AATTCTAAGCCCCCACGC 57.342 55.556 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.