Multiple sequence alignment - TraesCS5B01G530400

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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 TraesCS5B01G530400 chr5B 100.000 2357 0 0 1 2357 689102846 689100490 0.000000e+00 4353
1 TraesCS5B01G530400 chr5B 86.667 405 44 8 1 399 688993335 688992935 7.730000e-120 440
2 TraesCS5B01G530400 chr5B 86.173 405 46 8 1 399 689080789 689080389 1.670000e-116 429
3 TraesCS5B01G530400 chr5B 81.585 429 50 15 1951 2355 688992733 688992310 6.280000e-86 327
4 TraesCS5B01G530400 chr5B 81.585 429 50 15 1951 2355 689080187 689079764 6.280000e-86 327
5 TraesCS5B01G530400 chr5B 89.831 118 8 3 2135 2251 688985825 688985711 5.250000e-32 148
6 TraesCS5B01G530400 chr5B 89.831 118 8 3 2135 2251 689075656 689075542 5.250000e-32 148
7 TraesCS5B01G530400 chr7B 93.919 1332 64 5 638 1955 720163391 720162063 0.000000e+00 1995
8 TraesCS5B01G530400 chr2D 93.468 1332 72 3 639 1956 73126873 73125543 0.000000e+00 1964
9 TraesCS5B01G530400 chr2D 93.299 1179 60 7 794 1956 36804621 36803446 0.000000e+00 1722
10 TraesCS5B01G530400 chr1D 93.473 1333 70 5 639 1956 60171817 60170487 0.000000e+00 1964
11 TraesCS5B01G530400 chr1D 93.363 1326 68 5 640 1951 205134697 205133378 0.000000e+00 1943
12 TraesCS5B01G530400 chr1D 92.804 1334 77 6 639 1956 247505759 247504429 0.000000e+00 1914
13 TraesCS5B01G530400 chr1D 92.221 1337 80 8 640 1956 451393398 451392066 0.000000e+00 1871
14 TraesCS5B01G530400 chr5D 93.163 1331 75 4 640 1956 275171748 275170420 0.000000e+00 1940
15 TraesCS5B01G530400 chr5D 89.147 387 33 6 1 379 545941530 545941145 7.620000e-130 473
16 TraesCS5B01G530400 chr5D 82.464 211 13 6 1978 2178 545938026 545937830 1.870000e-36 163
17 TraesCS5B01G530400 chr5D 92.771 83 2 3 2168 2249 545937801 545937722 1.480000e-22 117
18 TraesCS5B01G530400 chr5D 89.744 78 6 2 2280 2356 545937720 545937644 5.360000e-17 99
19 TraesCS5B01G530400 chr3D 93.163 1331 76 9 640 1956 584701392 584700063 0.000000e+00 1940
20 TraesCS5B01G530400 chr4A 93.018 1332 74 7 636 1951 703773727 703772399 0.000000e+00 1927
21 TraesCS5B01G530400 chr4A 81.385 650 98 15 1 638 623388257 623388895 2.090000e-140 508
22 TraesCS5B01G530400 chr4A 82.710 428 44 10 1951 2355 623388882 623389302 1.040000e-93 353
23 TraesCS5B01G530400 chr7D 92.922 1328 77 11 640 1953 497560907 497562231 0.000000e+00 1916
24 TraesCS5B01G530400 chr3B 92.777 1329 79 5 639 1953 661520508 661521833 0.000000e+00 1906
25 TraesCS5B01G530400 chr1B 90.587 1328 108 5 641 1953 368916267 368914942 0.000000e+00 1744
26 TraesCS5B01G530400 chr1B 92.806 987 50 10 640 1606 14562395 14561410 0.000000e+00 1410
27 TraesCS5B01G530400 chr3A 92.430 1004 54 6 640 1623 727256294 727257295 0.000000e+00 1413
28 TraesCS5B01G530400 chr4B 93.557 776 36 2 641 1402 417552462 417551687 0.000000e+00 1144
29 TraesCS5B01G530400 chr6D 92.962 682 34 2 638 1306 89225599 89226279 0.000000e+00 981
30 TraesCS5B01G530400 chrUn 86.667 405 44 8 1 399 293181415 293181015 7.730000e-120 440
31 TraesCS5B01G530400 chrUn 86.667 405 44 8 1 399 293186832 293186432 7.730000e-120 440
32 TraesCS5B01G530400 chrUn 81.585 429 50 15 1951 2355 293180813 293180390 6.280000e-86 327
33 TraesCS5B01G530400 chrUn 81.585 429 50 15 1951 2355 293186230 293185807 6.280000e-86 327


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 TraesCS5B01G530400 chr5B 689100490 689102846 2356 True 4353.0 4353 100.0000 1 2357 1 chr5B.!!$R3 2356
1 TraesCS5B01G530400 chr5B 688992310 688993335 1025 True 383.5 440 84.1260 1 2355 2 chr5B.!!$R4 2354
2 TraesCS5B01G530400 chr5B 689079764 689080789 1025 True 378.0 429 83.8790 1 2355 2 chr5B.!!$R5 2354
3 TraesCS5B01G530400 chr7B 720162063 720163391 1328 True 1995.0 1995 93.9190 638 1955 1 chr7B.!!$R1 1317
4 TraesCS5B01G530400 chr2D 73125543 73126873 1330 True 1964.0 1964 93.4680 639 1956 1 chr2D.!!$R2 1317
5 TraesCS5B01G530400 chr2D 36803446 36804621 1175 True 1722.0 1722 93.2990 794 1956 1 chr2D.!!$R1 1162
6 TraesCS5B01G530400 chr1D 60170487 60171817 1330 True 1964.0 1964 93.4730 639 1956 1 chr1D.!!$R1 1317
7 TraesCS5B01G530400 chr1D 205133378 205134697 1319 True 1943.0 1943 93.3630 640 1951 1 chr1D.!!$R2 1311
8 TraesCS5B01G530400 chr1D 247504429 247505759 1330 True 1914.0 1914 92.8040 639 1956 1 chr1D.!!$R3 1317
9 TraesCS5B01G530400 chr1D 451392066 451393398 1332 True 1871.0 1871 92.2210 640 1956 1 chr1D.!!$R4 1316
10 TraesCS5B01G530400 chr5D 275170420 275171748 1328 True 1940.0 1940 93.1630 640 1956 1 chr5D.!!$R1 1316
11 TraesCS5B01G530400 chr5D 545937644 545941530 3886 True 213.0 473 88.5315 1 2356 4 chr5D.!!$R2 2355
12 TraesCS5B01G530400 chr3D 584700063 584701392 1329 True 1940.0 1940 93.1630 640 1956 1 chr3D.!!$R1 1316
13 TraesCS5B01G530400 chr4A 703772399 703773727 1328 True 1927.0 1927 93.0180 636 1951 1 chr4A.!!$R1 1315
14 TraesCS5B01G530400 chr4A 623388257 623389302 1045 False 430.5 508 82.0475 1 2355 2 chr4A.!!$F1 2354
15 TraesCS5B01G530400 chr7D 497560907 497562231 1324 False 1916.0 1916 92.9220 640 1953 1 chr7D.!!$F1 1313
16 TraesCS5B01G530400 chr3B 661520508 661521833 1325 False 1906.0 1906 92.7770 639 1953 1 chr3B.!!$F1 1314
17 TraesCS5B01G530400 chr1B 368914942 368916267 1325 True 1744.0 1744 90.5870 641 1953 1 chr1B.!!$R2 1312
18 TraesCS5B01G530400 chr1B 14561410 14562395 985 True 1410.0 1410 92.8060 640 1606 1 chr1B.!!$R1 966
19 TraesCS5B01G530400 chr3A 727256294 727257295 1001 False 1413.0 1413 92.4300 640 1623 1 chr3A.!!$F1 983
20 TraesCS5B01G530400 chr4B 417551687 417552462 775 True 1144.0 1144 93.5570 641 1402 1 chr4B.!!$R1 761
21 TraesCS5B01G530400 chr6D 89225599 89226279 680 False 981.0 981 92.9620 638 1306 1 chr6D.!!$F1 668
22 TraesCS5B01G530400 chrUn 293180390 293181415 1025 True 383.5 440 84.1260 1 2355 2 chrUn.!!$R1 2354
23 TraesCS5B01G530400 chrUn 293185807 293186832 1025 True 383.5 440 84.1260 1 2355 2 chrUn.!!$R2 2354

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
401 416 0.027194 CCTGCAAGCATCAATCGACG 59.973 55.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 4497 0.459489 TGGTTTGCACTCAACCAAGC 59.541 50.0 17.24 3.42 33.54 4.01 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
27 29 6.172630 ACAAAAAGACAAGAAAAGCCAACAT 58.827 32.000 0.00 0.00 0.00 2.71
89 91 4.546570 GACACCAACAAGAAACCTATTGC 58.453 43.478 0.00 0.00 0.00 3.56
182 189 4.461781 TCCTCCTAGTGGAAAGAGTTTACG 59.538 45.833 0.00 0.00 42.66 3.18
184 191 3.830755 TCCTAGTGGAAAGAGTTTACGCT 59.169 43.478 3.32 3.32 45.76 5.07
190 200 5.709164 AGTGGAAAGAGTTTACGCTAGTAGA 59.291 40.000 0.00 0.00 42.32 2.59
191 201 6.028987 GTGGAAAGAGTTTACGCTAGTAGAG 58.971 44.000 0.00 0.00 33.87 2.43
202 212 4.465886 ACGCTAGTAGAGGAGACATTCAT 58.534 43.478 0.00 0.00 0.00 2.57
208 218 5.999044 AGTAGAGGAGACATTCATGCAAAT 58.001 37.500 0.00 0.00 0.00 2.32
247 259 5.763088 AGTGCTAGCAAAGTTTAGAAAAGC 58.237 37.500 21.29 1.17 0.00 3.51
258 270 0.328258 TAGAAAAGCTGGGCCTCACC 59.672 55.000 4.53 0.00 37.93 4.02
306 320 3.842732 GTGTAGGCACAATGTTTACCC 57.157 47.619 0.00 0.00 44.64 3.69
311 325 4.762289 AGGCACAATGTTTACCCAAAAA 57.238 36.364 0.00 0.00 0.00 1.94
325 340 3.244735 ACCCAAAAATGTTGGTATTGCCC 60.245 43.478 0.95 0.00 37.88 5.36
351 366 4.817318 TTTTGGCCTCAATTAACATCCC 57.183 40.909 3.32 0.00 32.28 3.85
354 369 2.174639 TGGCCTCAATTAACATCCCGAT 59.825 45.455 3.32 0.00 0.00 4.18
393 408 3.019564 AGGTAAACATCCTGCAAGCATC 58.980 45.455 0.00 0.00 33.62 3.91
395 410 3.193267 GGTAAACATCCTGCAAGCATCAA 59.807 43.478 0.00 0.00 0.00 2.57
401 416 0.027194 CCTGCAAGCATCAATCGACG 59.973 55.000 0.00 0.00 0.00 5.12
402 417 0.723414 CTGCAAGCATCAATCGACGT 59.277 50.000 0.00 0.00 0.00 4.34
403 418 0.443478 TGCAAGCATCAATCGACGTG 59.557 50.000 0.00 0.00 0.00 4.49
409 424 1.059692 GCATCAATCGACGTGTCTGTG 59.940 52.381 0.00 0.00 0.00 3.66
412 427 1.335496 TCAATCGACGTGTCTGTGTGA 59.665 47.619 0.00 0.00 0.00 3.58
415 430 0.663269 TCGACGTGTCTGTGTGATGC 60.663 55.000 0.00 0.00 0.00 3.91
420 435 1.217001 GTGTCTGTGTGATGCGACAA 58.783 50.000 0.00 0.00 38.04 3.18
422 437 1.217001 GTCTGTGTGATGCGACAACA 58.783 50.000 0.00 0.00 0.00 3.33
423 438 1.800586 GTCTGTGTGATGCGACAACAT 59.199 47.619 0.00 0.00 0.00 2.71
424 439 1.799994 TCTGTGTGATGCGACAACATG 59.200 47.619 0.00 0.00 0.00 3.21
425 440 1.532437 CTGTGTGATGCGACAACATGT 59.468 47.619 0.00 0.00 0.00 3.21
427 442 1.264020 GTGTGATGCGACAACATGTGT 59.736 47.619 0.00 0.00 45.74 3.72
430 445 0.518636 GATGCGACAACATGTGTGCT 59.481 50.000 0.00 0.00 41.96 4.40
432 447 0.029167 TGCGACAACATGTGTGCTTG 59.971 50.000 0.00 0.00 41.96 4.01
437 452 3.236816 GACAACATGTGTGCTTGCATAC 58.763 45.455 14.14 14.14 41.96 2.39
441 456 0.448990 ATGTGTGCTTGCATACGCTG 59.551 50.000 15.55 0.00 39.64 5.18
450 465 2.961721 CATACGCTGCGCCACGAT 60.962 61.111 23.51 3.63 0.00 3.73
456 471 3.260483 CTGCGCCACGATCAGCTC 61.260 66.667 4.18 0.00 0.00 4.09
469 484 3.068732 CGATCAGCTCCACCTTCTCATAA 59.931 47.826 0.00 0.00 0.00 1.90
470 485 4.630111 GATCAGCTCCACCTTCTCATAAG 58.370 47.826 0.00 0.00 0.00 1.73
497 512 0.171007 GAACATCACAATGTGGCCCG 59.829 55.000 13.95 2.48 45.48 6.13
500 515 0.602562 CATCACAATGTGGCCCGTTT 59.397 50.000 13.95 0.00 33.87 3.60
501 516 1.000731 CATCACAATGTGGCCCGTTTT 59.999 47.619 13.95 0.00 33.87 2.43
504 519 1.045911 ACAATGTGGCCCGTTTTGGT 61.046 50.000 0.00 0.00 35.15 3.67
507 522 0.757188 ATGTGGCCCGTTTTGGTTCA 60.757 50.000 0.00 0.00 35.15 3.18
512 527 1.275010 GGCCCGTTTTGGTTCAATCAT 59.725 47.619 0.00 0.00 35.15 2.45
523 544 3.133464 CAATCATGCACCCGCCGT 61.133 61.111 0.00 0.00 37.32 5.68
537 558 2.322081 GCCGTTCCGCTTGCTAACA 61.322 57.895 7.91 0.00 0.00 2.41
541 562 0.179163 GTTCCGCTTGCTAACATGCC 60.179 55.000 0.00 0.00 42.45 4.40
542 563 0.322456 TTCCGCTTGCTAACATGCCT 60.322 50.000 0.00 0.00 42.45 4.75
543 564 0.744414 TCCGCTTGCTAACATGCCTC 60.744 55.000 0.00 0.00 42.45 4.70
544 565 1.718757 CCGCTTGCTAACATGCCTCC 61.719 60.000 0.00 0.00 42.45 4.30
545 566 1.723870 GCTTGCTAACATGCCTCCG 59.276 57.895 0.00 0.00 40.22 4.63
546 567 0.744414 GCTTGCTAACATGCCTCCGA 60.744 55.000 0.00 0.00 40.22 4.55
547 568 1.959042 CTTGCTAACATGCCTCCGAT 58.041 50.000 0.00 0.00 0.00 4.18
548 569 1.600957 CTTGCTAACATGCCTCCGATG 59.399 52.381 0.00 0.00 0.00 3.84
557 578 4.161295 CCTCCGATGGCGCTGGAA 62.161 66.667 7.64 0.00 35.83 3.53
558 579 2.892425 CTCCGATGGCGCTGGAAC 60.892 66.667 7.64 0.00 35.83 3.62
577 941 0.249615 CGCCTCCATGATGATGTCGT 60.250 55.000 0.00 0.00 0.00 4.34
579 943 1.869767 GCCTCCATGATGATGTCGTTC 59.130 52.381 0.00 0.00 0.00 3.95
580 944 2.130395 CCTCCATGATGATGTCGTTCG 58.870 52.381 0.00 0.00 0.00 3.95
581 945 2.130395 CTCCATGATGATGTCGTTCGG 58.870 52.381 0.00 0.00 0.00 4.30
583 947 1.473257 CCATGATGATGTCGTTCGGGT 60.473 52.381 0.00 0.00 0.00 5.28
584 948 1.594397 CATGATGATGTCGTTCGGGTG 59.406 52.381 0.00 0.00 0.00 4.61
586 950 1.429148 GATGATGTCGTTCGGGTGGC 61.429 60.000 0.00 0.00 0.00 5.01
612 976 4.660938 GGGCTTCCCGGCAACACT 62.661 66.667 0.00 0.00 40.61 3.55
613 977 2.349755 GGCTTCCCGGCAACACTA 59.650 61.111 0.00 0.00 38.25 2.74
614 978 1.302993 GGCTTCCCGGCAACACTAA 60.303 57.895 0.00 0.00 38.25 2.24
615 979 1.583495 GGCTTCCCGGCAACACTAAC 61.583 60.000 0.00 0.00 38.25 2.34
616 980 1.908066 GCTTCCCGGCAACACTAACG 61.908 60.000 0.00 0.00 0.00 3.18
617 981 1.908066 CTTCCCGGCAACACTAACGC 61.908 60.000 0.00 0.00 0.00 4.84
618 982 3.428282 CCCGGCAACACTAACGCC 61.428 66.667 0.00 0.00 42.64 5.68
621 985 2.858158 GGCAACACTAACGCCGAC 59.142 61.111 0.00 0.00 35.79 4.79
623 987 2.017783 GCAACACTAACGCCGACGA 61.018 57.895 0.00 0.00 43.93 4.20
624 988 1.941476 GCAACACTAACGCCGACGAG 61.941 60.000 0.00 0.00 43.93 4.18
625 989 1.080974 AACACTAACGCCGACGAGG 60.081 57.895 0.00 0.00 43.93 4.63
634 998 3.111939 CCGACGAGGCTACTGAGG 58.888 66.667 0.00 0.00 0.00 3.86
707 1071 6.878317 ACGATGCATACAGCCACTATATTAT 58.122 36.000 0.00 0.00 44.83 1.28
740 1104 9.297037 AGCACAAAAATCCTTACAAAGTAGTAT 57.703 29.630 0.00 0.00 0.00 2.12
823 1261 1.209127 GGTGCCGAATGTCCAAACG 59.791 57.895 0.00 0.00 0.00 3.60
936 1387 4.735132 TGTCGCCGCCTTCTTCCG 62.735 66.667 0.00 0.00 0.00 4.30
1028 1479 4.007644 CAGCTCGACCACCCTGCA 62.008 66.667 0.00 0.00 0.00 4.41
1192 1899 0.178876 TCCACAACATCTCTCCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
1559 2848 0.179121 CCGAATCCAACGATCCGACA 60.179 55.000 0.00 0.00 0.00 4.35
1567 2856 1.899437 AACGATCCGACATGGCCAGT 61.899 55.000 13.05 9.77 37.80 4.00
1587 2935 1.956629 GACGATCATCACCACCCCGT 61.957 60.000 0.00 0.00 0.00 5.28
1697 3491 1.275291 CCACCTCACGACACATAGGTT 59.725 52.381 0.00 0.00 40.39 3.50
1876 3740 3.896133 GACGGCGCTATGGACGGA 61.896 66.667 6.90 0.00 0.00 4.69
1914 3780 1.456705 GGATGAGACTCGAGGGGCT 60.457 63.158 18.41 10.83 0.00 5.19
1983 4108 1.378531 GTGTTGAACCACTGTCAGCA 58.621 50.000 0.00 0.00 32.50 4.41
1997 4127 1.542915 GTCAGCAGTTTGGTGCATGAT 59.457 47.619 0.00 0.00 46.60 2.45
2025 4155 8.645110 AGAATCTTGGTGTTCTTCATGAAAATT 58.355 29.630 9.88 0.00 36.30 1.82
2031 4161 6.258287 TGGTGTTCTTCATGAAAATTTGCAAG 59.742 34.615 9.88 0.00 36.30 4.01
2032 4162 6.258507 GGTGTTCTTCATGAAAATTTGCAAGT 59.741 34.615 9.88 0.00 36.30 3.16
2076 4217 2.666272 TTCCATACACAGCCAAACCA 57.334 45.000 0.00 0.00 0.00 3.67
2088 4229 3.005684 CAGCCAAACCATAAGCTCAACAA 59.994 43.478 0.00 0.00 31.93 2.83
2233 4413 9.435688 AAGCGTACAAGATATATATGCAAATCA 57.564 29.630 0.00 0.00 34.00 2.57
2260 4453 1.068741 CTATTCTCGGTAGCCACACCC 59.931 57.143 0.00 0.00 34.90 4.61
2262 4455 1.255667 TTCTCGGTAGCCACACCCTC 61.256 60.000 0.00 0.00 34.90 4.30
2281 4474 1.810151 TCGCTCAACATTTAACCCTGC 59.190 47.619 0.00 0.00 0.00 4.85
2282 4475 1.465689 CGCTCAACATTTAACCCTGCG 60.466 52.381 0.00 0.00 35.22 5.18
2292 4485 5.010213 ACATTTAACCCTGCGTGTACAAAAT 59.990 36.000 0.00 0.00 0.00 1.82
2297 4490 1.468520 CCTGCGTGTACAAAATGGGAG 59.531 52.381 0.00 0.00 0.00 4.30
2300 4493 1.467342 GCGTGTACAAAATGGGAGGTC 59.533 52.381 0.00 0.00 0.00 3.85
2304 4497 3.058501 GTGTACAAAATGGGAGGTCAACG 60.059 47.826 0.00 0.00 0.00 4.10
2335 4528 3.380320 AGTGCAAACCAACAAGTTAGGTC 59.620 43.478 0.00 0.00 33.74 3.85
2346 4539 5.195848 ACAAGTTAGGTCCTCTAGCTAGT 57.804 43.478 20.10 2.65 38.35 2.57
2349 4542 4.784177 AGTTAGGTCCTCTAGCTAGTGTC 58.216 47.826 20.10 12.20 39.29 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 29 7.658179 TTTTGTTAACATGCTTTTGTTGTGA 57.342 28.000 9.56 0.00 40.00 3.58
139 146 9.981460 AGGAGGATAATTTGTTGATAAGTTCTT 57.019 29.630 0.00 0.00 0.00 2.52
152 159 7.569240 ACTCTTTCCACTAGGAGGATAATTTG 58.431 38.462 6.98 0.71 46.74 2.32
182 189 4.038522 TGCATGAATGTCTCCTCTACTAGC 59.961 45.833 0.00 0.00 0.00 3.42
184 191 6.544928 TTTGCATGAATGTCTCCTCTACTA 57.455 37.500 0.00 0.00 0.00 1.82
190 200 5.503927 ACACTATTTGCATGAATGTCTCCT 58.496 37.500 0.00 0.00 0.00 3.69
191 201 5.355071 TGACACTATTTGCATGAATGTCTCC 59.645 40.000 15.38 0.00 0.00 3.71
202 212 5.163703 ACTCGTTTTTGTGACACTATTTGCA 60.164 36.000 7.20 0.00 0.00 4.08
208 218 3.527533 AGCACTCGTTTTTGTGACACTA 58.472 40.909 7.20 0.00 36.38 2.74
247 259 2.140405 CCTAGATGGTGAGGCCCAG 58.860 63.158 0.00 0.00 38.07 4.45
274 286 0.748005 GCCTACACATGCCGGTCAAT 60.748 55.000 1.90 0.00 0.00 2.57
306 320 4.013267 TGGGGCAATACCAACATTTTTG 57.987 40.909 0.00 0.00 42.05 2.44
311 325 4.925390 AAATTTGGGGCAATACCAACAT 57.075 36.364 0.00 0.00 46.94 2.71
354 369 3.162666 ACCTTTGTGTAGATCCGAGACA 58.837 45.455 0.00 0.00 0.00 3.41
393 408 1.766069 TCACACAGACACGTCGATTG 58.234 50.000 0.00 0.00 34.09 2.67
395 410 1.982612 CATCACACAGACACGTCGAT 58.017 50.000 0.00 0.00 34.09 3.59
401 416 1.070577 GTTGTCGCATCACACAGACAC 60.071 52.381 0.00 0.00 42.44 3.67
402 417 1.217001 GTTGTCGCATCACACAGACA 58.783 50.000 0.00 0.00 41.24 3.41
403 418 1.217001 TGTTGTCGCATCACACAGAC 58.783 50.000 0.00 0.00 0.00 3.51
409 424 1.954437 CACACATGTTGTCGCATCAC 58.046 50.000 0.00 0.00 35.67 3.06
412 427 0.953727 AAGCACACATGTTGTCGCAT 59.046 45.000 0.00 0.00 35.67 4.73
415 430 0.029167 TGCAAGCACACATGTTGTCG 59.971 50.000 0.00 0.00 35.67 4.35
420 435 0.168788 GCGTATGCAAGCACACATGT 59.831 50.000 4.23 0.00 42.15 3.21
422 437 0.448990 CAGCGTATGCAAGCACACAT 59.551 50.000 10.11 0.00 46.23 3.21
423 438 1.868306 CAGCGTATGCAAGCACACA 59.132 52.632 10.11 0.00 46.23 3.72
424 439 4.751539 CAGCGTATGCAAGCACAC 57.248 55.556 10.11 0.00 46.23 3.82
441 456 4.819761 TGGAGCTGATCGTGGCGC 62.820 66.667 0.00 0.00 0.00 6.53
449 464 4.036518 ACTTATGAGAAGGTGGAGCTGAT 58.963 43.478 0.00 0.00 0.00 2.90
450 465 3.196469 CACTTATGAGAAGGTGGAGCTGA 59.804 47.826 0.00 0.00 0.00 4.26
469 484 3.181440 ACATTGTGATGTTCCAGTCCACT 60.181 43.478 0.00 0.00 43.92 4.00
470 485 3.058016 CACATTGTGATGTTCCAGTCCAC 60.058 47.826 11.45 0.00 43.92 4.02
504 519 2.405805 CGGCGGGTGCATGATTGAA 61.406 57.895 0.00 0.00 45.35 2.69
507 522 2.361104 AACGGCGGGTGCATGATT 60.361 55.556 13.24 0.00 45.35 2.57
523 544 0.322456 AGGCATGTTAGCAAGCGGAA 60.322 50.000 0.64 0.00 39.93 4.30
541 562 2.892425 GTTCCAGCGCCATCGGAG 60.892 66.667 2.29 0.00 35.95 4.63
542 563 4.812476 CGTTCCAGCGCCATCGGA 62.812 66.667 2.29 1.90 35.95 4.55
554 575 1.233019 CATCATCATGGAGGCGTTCC 58.767 55.000 0.00 1.61 46.98 3.62
556 577 1.807755 CGACATCATCATGGAGGCGTT 60.808 52.381 0.00 0.00 33.82 4.84
557 578 0.249615 CGACATCATCATGGAGGCGT 60.250 55.000 0.00 0.00 33.82 5.68
558 579 0.249615 ACGACATCATCATGGAGGCG 60.250 55.000 4.22 4.22 33.82 5.52
563 927 1.220529 CCCGAACGACATCATCATGG 58.779 55.000 0.00 0.00 33.82 3.66
564 928 1.594397 CACCCGAACGACATCATCATG 59.406 52.381 0.00 0.00 35.92 3.07
565 929 1.473257 CCACCCGAACGACATCATCAT 60.473 52.381 0.00 0.00 0.00 2.45
568 932 1.449601 GCCACCCGAACGACATCAT 60.450 57.895 0.00 0.00 0.00 2.45
569 933 2.047655 GCCACCCGAACGACATCA 60.048 61.111 0.00 0.00 0.00 3.07
597 961 1.873863 GTTAGTGTTGCCGGGAAGC 59.126 57.895 9.39 5.26 0.00 3.86
598 962 1.908066 GCGTTAGTGTTGCCGGGAAG 61.908 60.000 9.39 0.00 0.00 3.46
599 963 1.962306 GCGTTAGTGTTGCCGGGAA 60.962 57.895 3.37 3.37 0.00 3.97
600 964 2.357760 GCGTTAGTGTTGCCGGGA 60.358 61.111 2.18 0.00 0.00 5.14
601 965 3.428282 GGCGTTAGTGTTGCCGGG 61.428 66.667 2.18 0.00 39.30 5.73
604 968 2.858158 GTCGGCGTTAGTGTTGCC 59.142 61.111 6.85 0.00 45.39 4.52
605 969 1.941476 CTCGTCGGCGTTAGTGTTGC 61.941 60.000 10.18 0.00 39.49 4.17
606 970 1.342082 CCTCGTCGGCGTTAGTGTTG 61.342 60.000 10.18 0.00 39.49 3.33
607 971 1.080974 CCTCGTCGGCGTTAGTGTT 60.081 57.895 10.18 0.00 39.49 3.32
608 972 2.564975 CCTCGTCGGCGTTAGTGT 59.435 61.111 10.18 0.00 39.49 3.55
617 981 0.463295 TACCTCAGTAGCCTCGTCGG 60.463 60.000 0.00 0.00 0.00 4.79
618 982 0.938713 CTACCTCAGTAGCCTCGTCG 59.061 60.000 0.00 0.00 39.66 5.12
740 1104 3.201930 TGGTGGCTTCAGGCTTATTGATA 59.798 43.478 1.64 0.00 41.69 2.15
745 1109 1.849039 AGATGGTGGCTTCAGGCTTAT 59.151 47.619 1.64 0.00 41.69 1.73
823 1261 5.048364 TGGTGCAATGTCTGTTTGGTATTAC 60.048 40.000 0.00 0.00 0.00 1.89
936 1387 1.005156 GCTCTGGAGATGGATCGGC 60.005 63.158 1.35 0.00 0.00 5.54
1028 1479 4.148825 GCGGCTGGATGGACGAGT 62.149 66.667 0.00 0.00 40.66 4.18
1103 1562 1.739929 TGGTGCGGCGTTGTATCTG 60.740 57.895 9.37 0.00 0.00 2.90
1292 2570 1.384082 CTATCCACCCCCGAACCCT 60.384 63.158 0.00 0.00 0.00 4.34
1559 2848 0.832626 TGATGATCGTCACTGGCCAT 59.167 50.000 13.75 0.00 0.00 4.40
1567 2856 1.904771 GGGGTGGTGATGATCGTCA 59.095 57.895 13.75 13.75 0.00 4.35
1587 2935 3.052082 GGACTCCGTCGACCGTCA 61.052 66.667 21.37 1.24 32.65 4.35
1769 3594 2.722201 GCGGGATCCAGAGGAACGT 61.722 63.158 16.86 0.00 34.34 3.99
1857 3721 4.246206 CGTCCATAGCGCCGTCGA 62.246 66.667 2.29 0.00 38.10 4.20
1876 3740 4.150454 CTCTCCCCCTCCTCGCCT 62.150 72.222 0.00 0.00 0.00 5.52
1895 3761 2.503382 GCCCCTCGAGTCTCATCCC 61.503 68.421 12.31 0.00 0.00 3.85
1914 3780 1.298667 GGAGAAAACCCTAGCCGCA 59.701 57.895 0.00 0.00 0.00 5.69
1977 4102 0.953727 TCATGCACCAAACTGCTGAC 59.046 50.000 0.00 0.00 38.07 3.51
1978 4103 1.542472 CATCATGCACCAAACTGCTGA 59.458 47.619 0.00 0.00 38.07 4.26
1979 4104 1.542472 TCATCATGCACCAAACTGCTG 59.458 47.619 0.00 0.00 38.07 4.41
1980 4105 1.816835 CTCATCATGCACCAAACTGCT 59.183 47.619 0.00 0.00 38.07 4.24
1981 4106 1.814394 TCTCATCATGCACCAAACTGC 59.186 47.619 0.00 0.00 37.70 4.40
1982 4107 4.398358 AGATTCTCATCATGCACCAAACTG 59.602 41.667 0.00 0.00 0.00 3.16
1983 4108 4.597004 AGATTCTCATCATGCACCAAACT 58.403 39.130 0.00 0.00 0.00 2.66
1997 4127 5.868454 TCATGAAGAACACCAAGATTCTCA 58.132 37.500 0.00 0.00 34.01 3.27
2068 4200 3.658757 TTGTTGAGCTTATGGTTTGGC 57.341 42.857 0.00 0.00 0.00 4.52
2088 4229 7.456725 AGTTAATTCCTGCATACATAGCTCAT 58.543 34.615 0.00 0.00 0.00 2.90
2142 4283 8.736244 TGAATGGAATACTAAAGTTAAAGGCAC 58.264 33.333 0.00 0.00 0.00 5.01
2150 4291 7.611467 TGCTGACATGAATGGAATACTAAAGTT 59.389 33.333 0.00 0.00 0.00 2.66
2239 4419 1.538419 GGTGTGGCTACCGAGAATAGC 60.538 57.143 0.00 0.00 43.66 2.97
2240 4420 1.068741 GGGTGTGGCTACCGAGAATAG 59.931 57.143 0.00 0.00 41.79 1.73
2260 4453 2.159517 GCAGGGTTAAATGTTGAGCGAG 60.160 50.000 0.00 0.00 0.00 5.03
2262 4455 1.465689 CGCAGGGTTAAATGTTGAGCG 60.466 52.381 0.00 0.00 36.62 5.03
2281 4474 2.773487 TGACCTCCCATTTTGTACACG 58.227 47.619 0.00 0.00 0.00 4.49
2282 4475 3.058501 CGTTGACCTCCCATTTTGTACAC 60.059 47.826 0.00 0.00 0.00 2.90
2292 4485 1.990160 AACCAAGCGTTGACCTCCCA 61.990 55.000 0.15 0.00 31.79 4.37
2304 4497 0.459489 TGGTTTGCACTCAACCAAGC 59.541 50.000 17.24 3.42 33.54 4.01
2335 4528 4.062677 AGTCTACGACACTAGCTAGAGG 57.937 50.000 27.45 19.34 34.60 3.69


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

AutoCloner maintained by Alex Coulton.