Multiple sequence alignment - TraesCS1B01G166200

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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 TraesCS1B01G166200 chr1B 100.000 2993 0 0 1 2993 289693185 289696177 0.000000e+00 5528.0
1 TraesCS1B01G166200 chr3B 93.728 1435 76 6 247 1674 775659331 775657904 0.000000e+00 2139.0
2 TraesCS1B01G166200 chr3B 92.157 612 36 3 1642 2250 60387593 60388195 0.000000e+00 854.0
3 TraesCS1B01G166200 chr3B 93.127 582 27 5 1718 2296 775657913 775657342 0.000000e+00 841.0
4 TraesCS1B01G166200 chr3B 89.764 508 24 14 2488 2993 775656770 775656289 2.530000e-175 625.0
5 TraesCS1B01G166200 chr3B 89.516 248 12 8 6 247 775659609 775659370 4.850000e-78 302.0
6 TraesCS1B01G166200 chr2D 93.327 1034 64 4 247 1278 29096269 29095239 0.000000e+00 1522.0
7 TraesCS1B01G166200 chr2D 92.402 816 54 5 1352 2164 519247 520057 0.000000e+00 1157.0
8 TraesCS1B01G166200 chr2D 93.038 632 39 5 1622 2250 29095243 29094614 0.000000e+00 918.0
9 TraesCS1B01G166200 chr4D 92.947 1035 68 5 247 1278 85851713 85850681 0.000000e+00 1502.0
10 TraesCS1B01G166200 chr4D 93.382 136 9 0 112 247 85851885 85851750 5.060000e-48 202.0
11 TraesCS1B01G166200 chr4D 81.818 209 28 6 2289 2492 20280267 20280064 1.850000e-37 167.0
12 TraesCS1B01G166200 chr4D 82.400 125 22 0 2369 2493 502732494 502732618 3.150000e-20 110.0
13 TraesCS1B01G166200 chr2B 92.761 1036 67 7 247 1278 134342413 134343444 0.000000e+00 1491.0
14 TraesCS1B01G166200 chr2B 91.216 444 35 3 2552 2993 100090950 100090509 4.270000e-168 601.0
15 TraesCS1B01G166200 chr7D 92.643 1033 71 5 247 1278 530740776 530739748 0.000000e+00 1482.0
16 TraesCS1B01G166200 chr7D 91.876 1034 78 6 247 1278 340173797 340174826 0.000000e+00 1439.0
17 TraesCS1B01G166200 chr7D 89.723 253 16 6 1 244 340173506 340173757 6.230000e-82 315.0
18 TraesCS1B01G166200 chr7D 89.062 256 18 6 1 247 530741067 530740813 2.900000e-80 309.0
19 TraesCS1B01G166200 chr6D 92.263 1034 74 6 247 1278 450189173 450188144 0.000000e+00 1461.0
20 TraesCS1B01G166200 chr6D 87.578 966 74 27 1351 2290 13477610 13478555 0.000000e+00 1077.0
21 TraesCS1B01G166200 chr6D 89.062 256 18 7 1 247 450189464 450189210 2.900000e-80 309.0
22 TraesCS1B01G166200 chr6D 80.519 231 33 9 2271 2493 82549965 82549739 1.850000e-37 167.0
23 TraesCS1B01G166200 chr5D 92.263 1034 74 6 247 1278 127939837 127938808 0.000000e+00 1461.0
24 TraesCS1B01G166200 chr5D 87.578 966 76 25 1351 2290 14031170 14032117 0.000000e+00 1079.0
25 TraesCS1B01G166200 chr5D 93.443 671 38 3 1623 2290 510553992 510554659 0.000000e+00 990.0
26 TraesCS1B01G166200 chr5D 92.814 668 42 3 1626 2290 445024663 445023999 0.000000e+00 963.0
27 TraesCS1B01G166200 chr5D 93.354 632 37 5 1622 2250 431988305 431988934 0.000000e+00 929.0
28 TraesCS1B01G166200 chr5D 93.153 628 40 2 1626 2250 27284603 27285230 0.000000e+00 918.0
29 TraesCS1B01G166200 chr5D 94.872 273 13 1 2552 2823 445019392 445019120 2.760000e-115 425.0
30 TraesCS1B01G166200 chr5D 89.453 256 17 6 1 247 127940128 127939874 6.230000e-82 315.0
31 TraesCS1B01G166200 chr5D 95.322 171 7 1 2824 2993 510559771 510559941 1.370000e-68 270.0
32 TraesCS1B01G166200 chr5D 83.256 215 24 9 2286 2493 40693289 40693498 1.420000e-43 187.0
33 TraesCS1B01G166200 chr5D 81.579 190 28 4 2287 2473 544164887 544165072 1.860000e-32 150.0
34 TraesCS1B01G166200 chr1D 91.683 1034 80 6 247 1278 415596725 415597754 0.000000e+00 1428.0
35 TraesCS1B01G166200 chr1D 87.474 966 77 25 1351 2290 62895539 62896486 0.000000e+00 1074.0
36 TraesCS1B01G166200 chr1D 89.723 253 16 6 1 244 415596434 415596685 6.230000e-82 315.0
37 TraesCS1B01G166200 chr1D 80.000 215 30 9 2287 2493 140109654 140109445 2.400000e-31 147.0
38 TraesCS1B01G166200 chr6A 90.942 817 55 8 1351 2164 540806146 540805346 0.000000e+00 1081.0
39 TraesCS1B01G166200 chr6A 94.118 136 8 0 112 247 163167283 163167148 1.090000e-49 207.0
40 TraesCS1B01G166200 chr5A 87.957 930 76 17 1351 2262 689190269 689189358 0.000000e+00 1064.0
41 TraesCS1B01G166200 chr5A 90.453 817 59 8 1351 2164 707256031 707256831 0.000000e+00 1059.0
42 TraesCS1B01G166200 chr5A 91.801 683 53 2 1485 2164 3944198 3943516 0.000000e+00 948.0
43 TraesCS1B01G166200 chr5A 91.826 367 26 3 2552 2916 470943475 470943839 2.660000e-140 508.0
44 TraesCS1B01G166200 chr7B 93.082 636 36 4 1622 2250 228802843 228803477 0.000000e+00 924.0
45 TraesCS1B01G166200 chr7B 92.760 442 30 2 2554 2993 593328243 593327802 3.250000e-179 638.0
46 TraesCS1B01G166200 chr7B 88.672 256 19 7 1 247 593350385 593350131 1.350000e-78 303.0
47 TraesCS1B01G166200 chr7A 93.038 632 38 5 1622 2250 658272944 658273572 0.000000e+00 918.0
48 TraesCS1B01G166200 chr7A 92.809 445 29 3 2552 2993 617600200 617600644 2.520000e-180 641.0
49 TraesCS1B01G166200 chr7A 92.135 445 32 3 2552 2993 41463098 41462654 2.530000e-175 625.0
50 TraesCS1B01G166200 chr2A 92.584 445 30 3 2552 2993 756526167 756526611 1.170000e-178 636.0
51 TraesCS1B01G166200 chr3A 91.008 367 29 3 2552 2916 662571785 662571421 2.680000e-135 492.0
52 TraesCS1B01G166200 chr4A 82.278 158 22 4 2321 2473 591686786 591686630 6.730000e-27 132.0
53 TraesCS1B01G166200 chr4A 80.814 172 24 5 2289 2455 541883732 541883565 3.130000e-25 126.0
54 TraesCS1B01G166200 chr4A 97.500 40 0 1 2287 2325 5352238 5352277 1.930000e-07 67.6
55 TraesCS1B01G166200 chrUn 85.833 120 13 3 2357 2473 53431133 53431015 1.130000e-24 124.0
56 TraesCS1B01G166200 chr6B 78.404 213 30 8 2268 2474 296458545 296458747 1.130000e-24 124.0
57 TraesCS1B01G166200 chr5B 81.944 72 8 5 2287 2356 358276003 358275935 4.170000e-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 TraesCS1B01G166200 chr1B 289693185 289696177 2992 False 5528.00 5528 100.00000 1 2993 1 chr1B.!!$F1 2992
1 TraesCS1B01G166200 chr3B 775656289 775659609 3320 True 976.75 2139 91.53375 6 2993 4 chr3B.!!$R1 2987
2 TraesCS1B01G166200 chr3B 60387593 60388195 602 False 854.00 854 92.15700 1642 2250 1 chr3B.!!$F1 608
3 TraesCS1B01G166200 chr2D 29094614 29096269 1655 True 1220.00 1522 93.18250 247 2250 2 chr2D.!!$R1 2003
4 TraesCS1B01G166200 chr2D 519247 520057 810 False 1157.00 1157 92.40200 1352 2164 1 chr2D.!!$F1 812
5 TraesCS1B01G166200 chr4D 85850681 85851885 1204 True 852.00 1502 93.16450 112 1278 2 chr4D.!!$R2 1166
6 TraesCS1B01G166200 chr2B 134342413 134343444 1031 False 1491.00 1491 92.76100 247 1278 1 chr2B.!!$F1 1031
7 TraesCS1B01G166200 chr7D 530739748 530741067 1319 True 895.50 1482 90.85250 1 1278 2 chr7D.!!$R1 1277
8 TraesCS1B01G166200 chr7D 340173506 340174826 1320 False 877.00 1439 90.79950 1 1278 2 chr7D.!!$F1 1277
9 TraesCS1B01G166200 chr6D 13477610 13478555 945 False 1077.00 1077 87.57800 1351 2290 1 chr6D.!!$F1 939
10 TraesCS1B01G166200 chr6D 450188144 450189464 1320 True 885.00 1461 90.66250 1 1278 2 chr6D.!!$R2 1277
11 TraesCS1B01G166200 chr5D 14031170 14032117 947 False 1079.00 1079 87.57800 1351 2290 1 chr5D.!!$F1 939
12 TraesCS1B01G166200 chr5D 510553992 510554659 667 False 990.00 990 93.44300 1623 2290 1 chr5D.!!$F5 667
13 TraesCS1B01G166200 chr5D 445023999 445024663 664 True 963.00 963 92.81400 1626 2290 1 chr5D.!!$R2 664
14 TraesCS1B01G166200 chr5D 431988305 431988934 629 False 929.00 929 93.35400 1622 2250 1 chr5D.!!$F4 628
15 TraesCS1B01G166200 chr5D 27284603 27285230 627 False 918.00 918 93.15300 1626 2250 1 chr5D.!!$F2 624
16 TraesCS1B01G166200 chr5D 127938808 127940128 1320 True 888.00 1461 90.85800 1 1278 2 chr5D.!!$R3 1277
17 TraesCS1B01G166200 chr1D 62895539 62896486 947 False 1074.00 1074 87.47400 1351 2290 1 chr1D.!!$F1 939
18 TraesCS1B01G166200 chr1D 415596434 415597754 1320 False 871.50 1428 90.70300 1 1278 2 chr1D.!!$F2 1277
19 TraesCS1B01G166200 chr6A 540805346 540806146 800 True 1081.00 1081 90.94200 1351 2164 1 chr6A.!!$R2 813
20 TraesCS1B01G166200 chr5A 689189358 689190269 911 True 1064.00 1064 87.95700 1351 2262 1 chr5A.!!$R2 911
21 TraesCS1B01G166200 chr5A 707256031 707256831 800 False 1059.00 1059 90.45300 1351 2164 1 chr5A.!!$F2 813
22 TraesCS1B01G166200 chr5A 3943516 3944198 682 True 948.00 948 91.80100 1485 2164 1 chr5A.!!$R1 679
23 TraesCS1B01G166200 chr7B 228802843 228803477 634 False 924.00 924 93.08200 1622 2250 1 chr7B.!!$F1 628
24 TraesCS1B01G166200 chr7A 658272944 658273572 628 False 918.00 918 93.03800 1622 2250 1 chr7A.!!$F2 628

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
943 997 2.515398 CTGGTGGCAAGGTGGTCA 59.485 61.111 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 2188 0.950836 AATGCACTTGTAGCAACGCA 59.049 45.0 0.0 0.0 46.27 5.24 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
119 126 8.537016 CCATAATTTGCCATCTTGGATTGATAT 58.463 33.333 0.00 0.00 40.96 1.63
128 135 7.828223 GCCATCTTGGATTGATATAAGACAGAT 59.172 37.037 0.00 0.00 40.96 2.90
150 157 8.472413 CAGATGGACCAAAATCATCTACAATTT 58.528 33.333 0.00 0.00 43.81 1.82
210 220 6.434652 TGGTTTAGGAAAGTGACAGTTTTCAA 59.565 34.615 15.10 6.00 35.51 2.69
256 305 5.648178 ACATACAACACATGTAGGACGTA 57.352 39.130 0.00 0.00 46.63 3.57
258 307 5.184479 ACATACAACACATGTAGGACGTAGT 59.816 40.000 0.00 0.00 46.63 2.73
316 365 4.142381 CCATGGCTGCTTCCTAAAACTTAC 60.142 45.833 0.00 0.00 0.00 2.34
344 393 2.642139 AGCAGATGTTTCAATTGCCG 57.358 45.000 0.00 0.00 35.44 5.69
351 400 5.865552 CAGATGTTTCAATTGCCGAAAGATT 59.134 36.000 0.00 0.00 36.72 2.40
370 419 5.072741 AGATTGTTGTTGTTCTGCCACTAT 58.927 37.500 0.00 0.00 0.00 2.12
515 566 8.093307 TGTGCATTTAAAATGCCAGAGAAAATA 58.907 29.630 2.05 0.00 43.94 1.40
570 621 8.482943 GCTAAGGTGTTCCCCATTTATAATTTT 58.517 33.333 0.00 0.00 0.00 1.82
669 720 8.563732 TGATCTGTCAGTATCTTTCTAATCTCG 58.436 37.037 0.00 0.00 0.00 4.04
739 791 6.716628 CACCCACAAGTAATATATTCTGCCAT 59.283 38.462 0.00 0.00 0.00 4.40
792 844 9.770097 CTAGTAATCATCATTGTGTAGAATGGT 57.230 33.333 2.45 0.00 34.58 3.55
866 919 8.907222 TGCACAGATGAGCAATTATTATCTTA 57.093 30.769 2.31 0.00 38.62 2.10
943 997 2.515398 CTGGTGGCAAGGTGGTCA 59.485 61.111 0.00 0.00 0.00 4.02
983 1037 2.553028 GGGCTGTCAAGAACTCCAATGA 60.553 50.000 0.00 0.00 0.00 2.57
1000 1054 4.641541 CCAATGACATTGACATAGCCAAGA 59.358 41.667 26.36 0.00 42.83 3.02
1027 1081 5.954639 GAAGCACTCGGCAGAGAACTTCA 62.955 52.174 29.23 0.00 46.53 3.02
1089 1144 1.739562 GCTGCTCACGGAAGAGTGG 60.740 63.158 0.00 0.04 42.10 4.00
1180 1235 7.675195 AGCTCACTTCATCCTATCTTCTATCAT 59.325 37.037 0.00 0.00 0.00 2.45
1227 1282 6.949352 AAGTATCCTCATGGCTGTTATTTG 57.051 37.500 0.00 0.00 0.00 2.32
1234 1289 6.945435 TCCTCATGGCTGTTATTTGTTTTCTA 59.055 34.615 0.00 0.00 0.00 2.10
1279 1334 2.063266 TGAAGTCCGTTCGATTTTCGG 58.937 47.619 10.94 10.94 44.76 4.30
1337 1392 6.817641 CCCTCATTGCAATTTGTATTTTGCTA 59.182 34.615 9.83 2.23 46.50 3.49
1481 1542 3.731216 CGTAGTATGTATCAGCAGTGCAC 59.269 47.826 19.20 9.40 0.00 4.57
1482 1543 3.893326 AGTATGTATCAGCAGTGCACA 57.107 42.857 21.04 13.17 0.00 4.57
1556 1617 0.246635 GAAGTTGCCAGCCGAGTCTA 59.753 55.000 0.00 0.00 0.00 2.59
1565 1626 2.288825 CCAGCCGAGTCTAACACTTTGA 60.289 50.000 0.00 0.00 34.41 2.69
1585 1646 9.252962 ACTTTGATTTGTTAAGAAAATCTGCAG 57.747 29.630 7.63 7.63 42.17 4.41
1774 1839 5.063186 GCATTTGTTGACACATTTCACACAA 59.937 36.000 0.00 0.00 31.06 3.33
1854 1929 2.195741 CGATCCTACCGGACATCCTA 57.804 55.000 9.46 0.00 43.51 2.94
1866 1941 0.617820 ACATCCTAGCCAACTCCGGT 60.618 55.000 0.00 0.00 0.00 5.28
1899 1974 0.320421 GCTACTTCGAGTGGGTGCAA 60.320 55.000 0.00 0.00 0.00 4.08
1923 1998 0.552367 TCCAGGGGTTCATGTGGGAT 60.552 55.000 0.00 0.00 0.00 3.85
1978 2053 4.263905 ACATGACCCACACCTCAAACATAT 60.264 41.667 0.00 0.00 0.00 1.78
2107 2188 0.609662 ATTTCTTGCCCGCTTTGCAT 59.390 45.000 0.00 0.00 38.76 3.96
2214 2309 3.674753 GCATGCACAACCTATTTTGTCAC 59.325 43.478 14.21 0.00 37.62 3.67
2245 2340 7.510549 AGTTTAGCATCTGTTTGTACATTGT 57.489 32.000 0.00 0.00 32.86 2.71
2250 2345 6.384224 AGCATCTGTTTGTACATTGTTGATG 58.616 36.000 15.68 15.68 41.71 3.07
2306 2409 2.894387 GAGCATCTCCAGCCGTGC 60.894 66.667 0.00 0.00 37.84 5.34
2307 2410 4.479993 AGCATCTCCAGCCGTGCC 62.480 66.667 0.00 0.00 38.31 5.01
2309 2412 4.864334 CATCTCCAGCCGTGCCCC 62.864 72.222 0.00 0.00 0.00 5.80
2427 2786 3.781307 CCGGCGATCCCAGGACAA 61.781 66.667 9.30 0.00 31.45 3.18
2428 2787 2.267642 CGGCGATCCCAGGACAAA 59.732 61.111 0.00 0.00 0.00 2.83
2429 2788 2.106683 CGGCGATCCCAGGACAAAC 61.107 63.158 0.00 0.00 0.00 2.93
2430 2789 1.749258 GGCGATCCCAGGACAAACC 60.749 63.158 0.00 0.00 39.35 3.27
2431 2790 1.749258 GCGATCCCAGGACAAACCC 60.749 63.158 0.00 0.00 40.05 4.11
2432 2791 1.682849 CGATCCCAGGACAAACCCA 59.317 57.895 0.00 0.00 40.05 4.51
2433 2792 0.392998 CGATCCCAGGACAAACCCAG 60.393 60.000 0.00 0.00 40.05 4.45
2434 2793 0.698818 GATCCCAGGACAAACCCAGT 59.301 55.000 0.00 0.00 40.05 4.00
2435 2794 0.405585 ATCCCAGGACAAACCCAGTG 59.594 55.000 0.00 0.00 40.05 3.66
2436 2795 1.903404 CCCAGGACAAACCCAGTGC 60.903 63.158 0.00 0.00 40.05 4.40
2437 2796 1.152777 CCAGGACAAACCCAGTGCA 60.153 57.895 0.00 0.00 40.05 4.57
2438 2797 1.455383 CCAGGACAAACCCAGTGCAC 61.455 60.000 9.40 9.40 40.05 4.57
2439 2798 0.466189 CAGGACAAACCCAGTGCACT 60.466 55.000 15.25 15.25 40.05 4.40
2440 2799 0.466189 AGGACAAACCCAGTGCACTG 60.466 55.000 35.15 35.15 43.40 3.66
2473 2832 1.212195 GGCTCCGGTAGAAGGGAAAAT 59.788 52.381 0.00 0.00 0.00 1.82
2504 3009 3.073274 CCACTACTGGGCTAGCTTTTT 57.927 47.619 15.72 0.00 33.23 1.94
2547 3052 1.300481 GGGATACAGGCGAGCTTTTC 58.700 55.000 0.00 0.00 39.74 2.29
2550 3055 0.249398 ATACAGGCGAGCTTTTCCGT 59.751 50.000 0.00 0.00 0.00 4.69
2588 3093 9.836076 GTCCCAAGTAGTGTTTACATTATTTTC 57.164 33.333 0.00 0.00 0.00 2.29
2593 3098 9.801714 AAGTAGTGTTTACATTATTTTCGAACG 57.198 29.630 0.00 0.00 0.00 3.95
2605 3110 9.409949 CATTATTTTCGAACGAATAGTCACTTC 57.590 33.333 10.33 0.00 33.79 3.01
2700 3205 2.247358 GAAAGGTTCCTTTGATGCCCA 58.753 47.619 19.73 0.00 36.53 5.36
2712 3217 4.782019 TTGATGCCCACACACTAAATTC 57.218 40.909 0.00 0.00 0.00 2.17
2714 3219 5.172687 TGATGCCCACACACTAAATTCTA 57.827 39.130 0.00 0.00 0.00 2.10
2775 3281 6.773200 TCCAAACCAGTGTTATGTTCATAACA 59.227 34.615 25.06 25.06 42.68 2.41
2790 3296 8.100508 TGTTCATAACATCAATTAAACGACCA 57.899 30.769 0.00 0.00 36.25 4.02
2791 3297 8.233868 TGTTCATAACATCAATTAAACGACCAG 58.766 33.333 0.00 0.00 36.25 4.00
2792 3298 7.915293 TCATAACATCAATTAAACGACCAGT 57.085 32.000 0.00 0.00 0.00 4.00
2793 3299 8.330466 TCATAACATCAATTAAACGACCAGTT 57.670 30.769 0.00 0.00 46.76 3.16
2806 3312 6.790285 AACGACCAGTTTTAATACGAATGT 57.210 33.333 0.00 0.00 40.88 2.71
2807 3313 6.399204 ACGACCAGTTTTAATACGAATGTC 57.601 37.500 0.00 0.00 0.00 3.06
2808 3314 5.927689 ACGACCAGTTTTAATACGAATGTCA 59.072 36.000 0.00 0.00 0.00 3.58
2809 3315 6.128742 ACGACCAGTTTTAATACGAATGTCAC 60.129 38.462 0.00 0.00 0.00 3.67
2810 3316 6.090358 CGACCAGTTTTAATACGAATGTCACT 59.910 38.462 0.00 0.00 0.00 3.41
2834 3340 8.723311 ACTACATTTTGGATTGATGCAAATTTG 58.277 29.630 14.03 14.03 45.33 2.32
2855 3361 3.176708 GCACATGCACATTTCATGAGAC 58.823 45.455 9.61 0.00 42.84 3.36
2908 3415 9.499479 TGGTACAATTTGTCAAATGCATATTTT 57.501 25.926 11.54 0.00 31.80 1.82
2961 3468 7.661437 GGTATAACCAATCAGATAGCACATTGA 59.339 37.037 4.04 0.00 38.42 2.57
2974 3481 8.746530 AGATAGCACATTGATTGAATCAGTTTT 58.253 29.630 8.01 0.00 40.94 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.547894 GTGACGAACAATATCACTGCAAATATA 58.452 33.333 0.00 0.00 39.72 0.86
33 34 5.276207 CGCTTTGTATCGTGACGAACAATAT 60.276 40.000 24.64 8.62 39.99 1.28
119 126 6.962182 AGATGATTTTGGTCCATCTGTCTTA 58.038 36.000 0.00 0.00 43.62 2.10
128 135 7.669304 TGAGAAATTGTAGATGATTTTGGTCCA 59.331 33.333 0.00 0.00 0.00 4.02
169 179 4.640771 AAACCAGAAGGATTGCAGTAGA 57.359 40.909 0.00 0.00 38.69 2.59
179 189 4.410883 TGTCACTTTCCTAAACCAGAAGGA 59.589 41.667 0.00 0.00 40.18 3.36
210 220 5.627135 TCTTCCCTCCGTCTAAACAATTTT 58.373 37.500 0.00 0.00 0.00 1.82
265 314 6.414732 TCACCTGGAAAATAACATCGAAGAT 58.585 36.000 0.00 0.00 45.12 2.40
316 365 7.742963 GCAATTGAAACATCTGCTTACAAATTG 59.257 33.333 10.34 0.00 0.00 2.32
344 393 4.504097 GTGGCAGAACAACAACAATCTTTC 59.496 41.667 0.00 0.00 0.00 2.62
351 400 4.754618 CAGTATAGTGGCAGAACAACAACA 59.245 41.667 0.00 0.00 0.00 3.33
370 419 7.775053 AAAATTTAAAGCTGGATGGTCAGTA 57.225 32.000 0.00 0.00 37.12 2.74
478 528 6.917217 TTTTAAATGCACAAAGACCAAAGG 57.083 33.333 0.00 0.00 0.00 3.11
570 621 3.750130 GCTTTGAGAAGATGCTTGTCTCA 59.250 43.478 7.96 7.96 44.60 3.27
624 675 6.994496 CAGATCAGGCATAGAACTTTGGAATA 59.006 38.462 0.00 0.00 0.00 1.75
739 791 9.382275 CATTGTGTAGGCATGCTTGTATATATA 57.618 33.333 18.92 0.00 0.00 0.86
792 844 2.093890 CTTGCTCCACAATGTATGGCA 58.906 47.619 0.00 0.00 37.72 4.92
943 997 1.836166 CCCTGTGACATCTCTGATGGT 59.164 52.381 11.55 0.00 0.00 3.55
983 1037 5.687780 TCATCATCTTGGCTATGTCAATGT 58.312 37.500 0.00 0.00 0.00 2.71
1000 1054 0.538584 TCTGCCGAGTGCTTCATCAT 59.461 50.000 0.00 0.00 42.00 2.45
1024 1078 2.795329 GTCAAAGCCCTTGATCCTGAA 58.205 47.619 2.43 0.00 45.74 3.02
1025 1079 1.339055 CGTCAAAGCCCTTGATCCTGA 60.339 52.381 2.43 0.00 45.74 3.86
1027 1081 0.035056 CCGTCAAAGCCCTTGATCCT 60.035 55.000 2.43 0.00 45.74 3.24
1089 1144 4.736896 GTCGGGGTGAGCACGTCC 62.737 72.222 6.08 0.00 0.00 4.79
1105 1160 0.042431 ATGACTCCTCCCAGAGCTGT 59.958 55.000 0.00 0.00 37.39 4.40
1252 1307 7.787935 CGAAAATCGAACGGACTTCATATTAAG 59.212 37.037 0.00 0.00 43.74 1.85
1300 1355 2.372264 CAATGAGGGTTGCTATGCTGT 58.628 47.619 0.00 0.00 0.00 4.40
1337 1392 7.333528 TCAGCAGAGTTGTGAGTTAAAATTT 57.666 32.000 0.00 0.00 0.00 1.82
1348 1403 1.869767 GTCAGGTTCAGCAGAGTTGTG 59.130 52.381 0.00 0.00 0.00 3.33
1481 1542 6.254157 GCTTTCCATGCTAATTAATGTGTGTG 59.746 38.462 0.00 0.00 0.00 3.82
1482 1543 6.153340 AGCTTTCCATGCTAATTAATGTGTGT 59.847 34.615 0.00 0.00 39.21 3.72
1496 1557 4.421948 CATTCTGAGAAAGCTTTCCATGC 58.578 43.478 30.83 19.60 37.92 4.06
1565 1626 8.409358 AGGTACTGCAGATTTTCTTAACAAAT 57.591 30.769 23.35 0.00 37.18 2.32
1585 1646 5.924825 CGGTACAATTAGAATAGGCAGGTAC 59.075 44.000 0.00 0.00 0.00 3.34
1624 1685 4.102367 GCATTGTCCCTAGGAGAAGAAGAT 59.898 45.833 11.48 0.00 38.36 2.40
1774 1839 6.004574 TGTACACTTCTCTACTGTCAGTCAT 58.995 40.000 9.26 0.00 0.00 3.06
1866 1941 2.238084 AGTAGCTCACCATCACTCCA 57.762 50.000 0.00 0.00 0.00 3.86
1899 1974 2.528564 CACATGAACCCCTGGATGTTT 58.471 47.619 0.00 0.00 0.00 2.83
1923 1998 1.195115 CCCGATTCACCTTCTCCTCA 58.805 55.000 0.00 0.00 0.00 3.86
1978 2053 9.461312 AACATACACTGCCTAAATAATCAGAAA 57.539 29.630 0.00 0.00 0.00 2.52
2035 2110 7.504403 TGAGCCAATTCTGGTTTTCAAAATAA 58.496 30.769 0.00 0.00 45.53 1.40
2107 2188 0.950836 AATGCACTTGTAGCAACGCA 59.049 45.000 0.00 0.00 46.27 5.24
2167 2248 6.049955 TCTTCTGTTCCATACTAAAGGTGG 57.950 41.667 0.00 0.00 0.00 4.61
2214 2309 5.152097 CAAACAGATGCTAAACTTGCTCAG 58.848 41.667 0.00 0.00 0.00 3.35
2245 2340 7.701539 ACAATAAGAACCAGCATAACATCAA 57.298 32.000 0.00 0.00 0.00 2.57
2250 2345 6.151144 AGGACAACAATAAGAACCAGCATAAC 59.849 38.462 0.00 0.00 0.00 1.89
2410 2769 3.323758 TTTGTCCTGGGATCGCCGG 62.324 63.158 13.28 13.28 33.83 6.13
2412 2771 1.749258 GGTTTGTCCTGGGATCGCC 60.749 63.158 7.38 0.12 0.00 5.54
2417 2776 1.843421 CACTGGGTTTGTCCTGGGA 59.157 57.895 0.00 0.00 36.25 4.37
2461 2820 2.426738 CAATGCGCCATTTTCCCTTCTA 59.573 45.455 4.18 0.00 31.05 2.10
2462 2821 1.205417 CAATGCGCCATTTTCCCTTCT 59.795 47.619 4.18 0.00 31.05 2.85
2490 2995 1.657751 GCCCGAAAAAGCTAGCCCAG 61.658 60.000 12.13 0.00 0.00 4.45
2496 3001 1.019278 CAGAGCGCCCGAAAAAGCTA 61.019 55.000 2.29 0.00 40.39 3.32
2535 3040 3.050275 GCACGGAAAAGCTCGCCT 61.050 61.111 0.00 0.00 0.00 5.52
2547 3052 2.364632 TGGGACAATAATTCAGCACGG 58.635 47.619 0.00 0.00 31.92 4.94
2588 3093 6.389622 TTCAATGAAGTGACTATTCGTTCG 57.610 37.500 0.00 0.00 34.46 3.95
2605 3110 6.309712 AGTCTCACAATTGTCACTTCAATG 57.690 37.500 8.48 0.00 37.96 2.82
2676 3181 3.766051 GGCATCAAAGGAACCTTTCATCT 59.234 43.478 14.89 0.00 43.56 2.90
2775 3281 9.763465 CGTATTAAAACTGGTCGTTTAATTGAT 57.237 29.630 6.68 0.00 44.77 2.57
2785 3291 6.090358 AGTGACATTCGTATTAAAACTGGTCG 59.910 38.462 0.00 0.00 0.00 4.79
2786 3292 7.360575 AGTGACATTCGTATTAAAACTGGTC 57.639 36.000 0.00 0.00 0.00 4.02
2787 3293 7.874016 TGTAGTGACATTCGTATTAAAACTGGT 59.126 33.333 0.00 0.00 0.00 4.00
2788 3294 8.246908 TGTAGTGACATTCGTATTAAAACTGG 57.753 34.615 0.00 0.00 0.00 4.00
2804 3310 5.476254 TGCATCAATCCAAAATGTAGTGACA 59.524 36.000 0.00 0.00 40.72 3.58
2805 3311 5.953183 TGCATCAATCCAAAATGTAGTGAC 58.047 37.500 0.00 0.00 0.00 3.67
2806 3312 6.587206 TTGCATCAATCCAAAATGTAGTGA 57.413 33.333 0.00 0.00 0.00 3.41
2807 3313 7.837202 ATTTGCATCAATCCAAAATGTAGTG 57.163 32.000 0.00 0.00 34.93 2.74
2808 3314 8.723311 CAAATTTGCATCAATCCAAAATGTAGT 58.277 29.630 5.01 0.00 34.93 2.73
2834 3340 3.176708 GTCTCATGAAATGTGCATGTGC 58.823 45.455 0.00 0.00 46.80 4.57
2839 3345 2.885894 TGCTTGTCTCATGAAATGTGCA 59.114 40.909 0.00 2.65 46.80 4.57
2879 3385 7.798596 ATGCATTTGACAAATTGTACCAAAA 57.201 28.000 10.77 7.36 31.07 2.44
2908 3415 8.585018 CAGGTACATGTACAACTATATGATGGA 58.415 37.037 31.52 0.00 37.78 3.41
2930 3437 5.013183 GCTATCTGATTGGTTATACCCAGGT 59.987 44.000 0.00 0.00 37.50 4.00
2961 3468 7.234355 ACCCTGAACTCTAAAACTGATTCAAT 58.766 34.615 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.