Multiple sequence alignment - TraesCS5D01G285500

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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 TraesCS5D01G285500 chr5D 100.000 2270 0 0 1 2270 386059102 386056833 0.000000e+00 4193.0
1 TraesCS5D01G285500 chr5D 91.792 597 33 4 727 1313 386046351 386045761 0.000000e+00 817.0
2 TraesCS5D01G285500 chr5D 93.258 534 31 4 1 529 460681952 460681419 0.000000e+00 782.0
3 TraesCS5D01G285500 chr5D 92.081 543 33 7 786 1321 386067601 386067062 0.000000e+00 756.0
4 TraesCS5D01G285500 chr5D 82.777 929 69 36 1370 2270 386067049 386066184 0.000000e+00 745.0
5 TraesCS5D01G285500 chr5D 90.485 536 36 6 786 1318 386036064 386035541 0.000000e+00 693.0
6 TraesCS5D01G285500 chr5D 89.339 469 27 13 873 1318 385978682 385978214 3.270000e-158 568.0
7 TraesCS5D01G285500 chr5D 92.248 387 26 4 1 383 449339271 449339657 1.530000e-151 545.0
8 TraesCS5D01G285500 chr5D 83.439 471 52 14 1810 2270 385978128 385977674 4.510000e-112 414.0
9 TraesCS5D01G285500 chr5D 88.742 302 28 3 1974 2270 386035243 386034943 4.610000e-97 364.0
10 TraesCS5D01G285500 chr5D 93.548 217 11 3 376 592 449340164 449340377 1.010000e-83 320.0
11 TraesCS5D01G285500 chr5D 96.403 139 5 0 593 731 23761465 23761603 1.750000e-56 230.0
12 TraesCS5D01G285500 chr5A 86.645 1505 99 33 786 2270 487985127 487983705 0.000000e+00 1572.0
13 TraesCS5D01G285500 chr5A 99.831 592 1 0 1 592 491700669 491700078 0.000000e+00 1088.0
14 TraesCS5D01G285500 chr5A 83.121 942 65 31 1370 2270 488008540 488007652 0.000000e+00 773.0
15 TraesCS5D01G285500 chr5A 89.081 577 36 11 750 1318 488009111 488008554 0.000000e+00 691.0
16 TraesCS5D01G285500 chr5A 85.693 678 53 29 786 1434 487918875 487918213 0.000000e+00 675.0
17 TraesCS5D01G285500 chr5A 87.768 466 43 8 866 1318 487925070 487924606 1.190000e-147 532.0
18 TraesCS5D01G285500 chr5A 84.899 543 55 17 1748 2270 487940265 487939730 7.180000e-145 523.0
19 TraesCS5D01G285500 chr5A 79.559 499 60 18 1810 2270 487947564 487947070 3.640000e-83 318.0
20 TraesCS5D01G285500 chr5A 100.000 28 0 0 1558 1585 487940327 487940300 4.000000e-03 52.8
21 TraesCS5D01G285500 chr2A 98.328 598 8 2 1 597 232429879 232430475 0.000000e+00 1048.0
22 TraesCS5D01G285500 chr2A 81.569 510 58 18 108 592 35962140 35962638 2.730000e-104 388.0
23 TraesCS5D01G285500 chr3B 98.170 601 8 3 1 600 475275196 475275794 0.000000e+00 1046.0
24 TraesCS5D01G285500 chr7B 98.314 593 9 1 1 592 679528040 679528632 0.000000e+00 1038.0
25 TraesCS5D01G285500 chr7B 94.074 135 8 0 593 727 392859776 392859910 2.960000e-49 206.0
26 TraesCS5D01G285500 chr7D 93.792 596 32 5 1 592 105263705 105264299 0.000000e+00 891.0
27 TraesCS5D01G285500 chr7D 93.525 139 8 1 590 727 610206038 610206176 2.960000e-49 206.0
28 TraesCS5D01G285500 chr5B 83.671 937 64 34 1370 2270 463944752 463943869 0.000000e+00 800.0
29 TraesCS5D01G285500 chr5B 92.551 537 33 5 786 1318 463945299 463944766 0.000000e+00 763.0
30 TraesCS5D01G285500 chr5B 90.543 571 40 3 727 1289 463937991 463937427 0.000000e+00 743.0
31 TraesCS5D01G285500 chr5B 87.981 624 40 20 1 592 654933703 654933083 0.000000e+00 704.0
32 TraesCS5D01G285500 chr5B 89.552 469 34 6 873 1336 463912520 463912062 4.200000e-162 580.0
33 TraesCS5D01G285500 chr5B 86.245 458 52 8 1821 2270 463918240 463917786 9.430000e-134 486.0
34 TraesCS5D01G285500 chr5B 88.630 387 37 5 1869 2250 463937376 463936992 4.420000e-127 464.0
35 TraesCS5D01G285500 chr5B 83.710 442 47 12 1810 2241 463911921 463911495 5.880000e-106 394.0
36 TraesCS5D01G285500 chr4A 91.092 595 40 8 1 592 500913423 500912839 0.000000e+00 793.0
37 TraesCS5D01G285500 chr1D 89.577 355 33 4 1 351 335038835 335039189 4.450000e-122 448.0
38 TraesCS5D01G285500 chr1D 95.556 135 6 0 593 727 415456116 415455982 1.370000e-52 217.0
39 TraesCS5D01G285500 chr3A 77.314 767 94 37 859 1598 452981244 452980531 1.650000e-101 379.0
40 TraesCS5D01G285500 chr3D 97.778 135 3 0 593 727 568189136 568189002 1.360000e-57 233.0
41 TraesCS5D01G285500 chr3D 97.037 135 4 0 593 727 552419046 552419180 6.310000e-56 228.0
42 TraesCS5D01G285500 chr3D 96.324 136 5 0 596 731 384643385 384643250 8.160000e-55 224.0
43 TraesCS5D01G285500 chr2D 96.296 135 5 0 593 727 320484078 320484212 2.930000e-54 222.0
44 TraesCS5D01G285500 chr2D 96.296 135 5 0 593 727 451929966 451930100 2.930000e-54 222.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G285500 chr5D 386056833 386059102 2269 True 4193.0 4193 100.0000 1 2270 1 chr5D.!!$R2 2269
1 TraesCS5D01G285500 chr5D 386045761 386046351 590 True 817.0 817 91.7920 727 1313 1 chr5D.!!$R1 586
2 TraesCS5D01G285500 chr5D 460681419 460681952 533 True 782.0 782 93.2580 1 529 1 chr5D.!!$R3 528
3 TraesCS5D01G285500 chr5D 386066184 386067601 1417 True 750.5 756 87.4290 786 2270 2 chr5D.!!$R6 1484
4 TraesCS5D01G285500 chr5D 386034943 386036064 1121 True 528.5 693 89.6135 786 2270 2 chr5D.!!$R5 1484
5 TraesCS5D01G285500 chr5D 385977674 385978682 1008 True 491.0 568 86.3890 873 2270 2 chr5D.!!$R4 1397
6 TraesCS5D01G285500 chr5D 449339271 449340377 1106 False 432.5 545 92.8980 1 592 2 chr5D.!!$F2 591
7 TraesCS5D01G285500 chr5A 487983705 487985127 1422 True 1572.0 1572 86.6450 786 2270 1 chr5A.!!$R4 1484
8 TraesCS5D01G285500 chr5A 491700078 491700669 591 True 1088.0 1088 99.8310 1 592 1 chr5A.!!$R5 591
9 TraesCS5D01G285500 chr5A 488007652 488009111 1459 True 732.0 773 86.1010 750 2270 2 chr5A.!!$R7 1520
10 TraesCS5D01G285500 chr5A 487918213 487918875 662 True 675.0 675 85.6930 786 1434 1 chr5A.!!$R1 648
11 TraesCS5D01G285500 chr5A 487939730 487940327 597 True 287.9 523 92.4495 1558 2270 2 chr5A.!!$R6 712
12 TraesCS5D01G285500 chr2A 232429879 232430475 596 False 1048.0 1048 98.3280 1 597 1 chr2A.!!$F2 596
13 TraesCS5D01G285500 chr3B 475275196 475275794 598 False 1046.0 1046 98.1700 1 600 1 chr3B.!!$F1 599
14 TraesCS5D01G285500 chr7B 679528040 679528632 592 False 1038.0 1038 98.3140 1 592 1 chr7B.!!$F2 591
15 TraesCS5D01G285500 chr7D 105263705 105264299 594 False 891.0 891 93.7920 1 592 1 chr7D.!!$F1 591
16 TraesCS5D01G285500 chr5B 463943869 463945299 1430 True 781.5 800 88.1110 786 2270 2 chr5B.!!$R5 1484
17 TraesCS5D01G285500 chr5B 654933083 654933703 620 True 704.0 704 87.9810 1 592 1 chr5B.!!$R2 591
18 TraesCS5D01G285500 chr5B 463936992 463937991 999 True 603.5 743 89.5865 727 2250 2 chr5B.!!$R4 1523
19 TraesCS5D01G285500 chr5B 463911495 463912520 1025 True 487.0 580 86.6310 873 2241 2 chr5B.!!$R3 1368
20 TraesCS5D01G285500 chr4A 500912839 500913423 584 True 793.0 793 91.0920 1 592 1 chr4A.!!$R1 591
21 TraesCS5D01G285500 chr3A 452980531 452981244 713 True 379.0 379 77.3140 859 1598 1 chr3A.!!$R1 739

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
939 1472 0.810031 CCATAACCACCGGAGCTTCG 60.81 60.0 9.46 7.67 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 2418 1.49049 AGACTTGGCAAAGAGTGTGGA 59.51 47.619 8.15 0.0 36.84 4.02 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
498 1021 2.048601 TCCAGGTCCAAAAGTTACCGA 58.951 47.619 0.00 0.00 38.37 4.69
611 1135 4.110493 GCCGGACGAGGAAGATTG 57.890 61.111 5.05 0.00 0.00 2.67
612 1136 2.174319 GCCGGACGAGGAAGATTGC 61.174 63.158 5.05 0.00 0.00 3.56
613 1137 1.521681 CCGGACGAGGAAGATTGCC 60.522 63.158 0.00 0.00 0.00 4.52
614 1138 1.878522 CGGACGAGGAAGATTGCCG 60.879 63.158 0.00 0.00 0.00 5.69
615 1139 2.174319 GGACGAGGAAGATTGCCGC 61.174 63.158 0.00 0.00 0.00 6.53
616 1140 2.125106 ACGAGGAAGATTGCCGCC 60.125 61.111 0.00 0.00 0.00 6.13
617 1141 3.264897 CGAGGAAGATTGCCGCCG 61.265 66.667 0.00 0.00 0.00 6.46
618 1142 3.577313 GAGGAAGATTGCCGCCGC 61.577 66.667 0.00 0.00 0.00 6.53
653 1177 3.282920 GGCTTAGCCTGCGATGCC 61.283 66.667 17.16 12.09 46.69 4.40
654 1178 3.282920 GCTTAGCCTGCGATGCCC 61.283 66.667 0.00 0.00 0.00 5.36
655 1179 2.507944 CTTAGCCTGCGATGCCCT 59.492 61.111 0.00 0.00 0.00 5.19
656 1180 1.596477 CTTAGCCTGCGATGCCCTC 60.596 63.158 0.00 0.00 0.00 4.30
686 1210 4.890306 GGGAGGAGAGGGAGGCCC 62.890 77.778 0.00 0.00 45.90 5.80
745 1269 2.479730 GGGAGAGTGTGCATACGTAGTG 60.480 54.545 8.03 1.23 45.73 2.74
805 1329 7.715265 ATGTAATTAATTAGCCTCACTGACG 57.285 36.000 8.18 0.00 0.00 4.35
810 1334 2.450609 TTAGCCTCACTGACGTTTCC 57.549 50.000 0.00 0.00 0.00 3.13
819 1343 1.144093 ACTGACGTTTCCATCCCCAAA 59.856 47.619 0.00 0.00 0.00 3.28
852 1378 1.335964 CCGATACCATTCGAGCGACAT 60.336 52.381 0.00 0.00 41.62 3.06
939 1472 0.810031 CCATAACCACCGGAGCTTCG 60.810 60.000 9.46 7.67 0.00 3.79
1179 1751 4.530857 GAGGTGCGCCGCCACTAT 62.531 66.667 18.38 0.00 40.50 2.12
1222 1794 3.781770 CTGATCGACTCCGGCAGGC 62.782 68.421 0.00 0.00 36.06 4.85
1308 1884 3.578282 ACCAAAACCCAACCTGATCATTC 59.422 43.478 0.00 0.00 0.00 2.67
1312 1888 4.664688 AACCCAACCTGATCATTCTCTT 57.335 40.909 0.00 0.00 0.00 2.85
1317 1893 6.012508 ACCCAACCTGATCATTCTCTTTTCTA 60.013 38.462 0.00 0.00 0.00 2.10
1320 1896 9.050601 CCAACCTGATCATTCTCTTTTCTATAC 57.949 37.037 0.00 0.00 0.00 1.47
1322 1898 9.829507 AACCTGATCATTCTCTTTTCTATACTG 57.170 33.333 0.00 0.00 0.00 2.74
1323 1899 8.986991 ACCTGATCATTCTCTTTTCTATACTGT 58.013 33.333 0.00 0.00 0.00 3.55
1343 1926 7.228314 ACTGTACTATATGTGTGTCAACTGT 57.772 36.000 0.00 0.00 0.00 3.55
1344 1927 7.313646 ACTGTACTATATGTGTGTCAACTGTC 58.686 38.462 0.00 0.00 0.00 3.51
1364 1952 0.972883 AAGTGTCAGCAGGAGTCCTC 59.027 55.000 9.36 4.58 0.00 3.71
1388 1976 8.166422 TCGCTCAAAGATATATAGTGTTCTCA 57.834 34.615 0.00 0.00 0.00 3.27
1531 2144 2.230508 CTCCAGATGCACTGCAAACATT 59.769 45.455 8.03 0.00 43.62 2.71
1535 2148 4.163552 CAGATGCACTGCAAACATTAGTG 58.836 43.478 8.03 0.00 43.62 2.74
1536 2149 3.822735 AGATGCACTGCAAACATTAGTGT 59.177 39.130 8.03 0.00 43.62 3.55
1537 2150 3.352554 TGCACTGCAAACATTAGTGTG 57.647 42.857 0.00 0.00 42.79 3.82
1538 2151 2.948315 TGCACTGCAAACATTAGTGTGA 59.052 40.909 0.00 0.00 42.79 3.58
1539 2152 3.243035 TGCACTGCAAACATTAGTGTGAC 60.243 43.478 0.00 0.00 42.79 3.67
1540 2153 3.243035 GCACTGCAAACATTAGTGTGACA 60.243 43.478 0.00 0.00 42.79 3.58
1585 2198 2.746277 AAAGCGGATCCGGCACAC 60.746 61.111 33.98 17.69 40.19 3.82
1600 2213 2.094545 GGCACACAATTTAAGCCTGGAG 60.095 50.000 0.00 0.00 42.01 3.86
1614 2227 1.818642 CTGGAGCAGGAACCTTGAAG 58.181 55.000 0.00 0.00 0.00 3.02
1615 2228 0.401738 TGGAGCAGGAACCTTGAAGG 59.598 55.000 10.24 10.24 42.49 3.46
1616 2229 0.962855 GGAGCAGGAACCTTGAAGGC 60.963 60.000 11.96 0.00 39.63 4.35
1617 2230 0.037447 GAGCAGGAACCTTGAAGGCT 59.963 55.000 11.96 0.00 39.63 4.58
1671 2299 4.814147 CATGGATGCGCTAATCTTAGAGA 58.186 43.478 9.73 0.00 33.12 3.10
1678 2306 3.305676 GCGCTAATCTTAGAGATCCTGCA 60.306 47.826 0.00 0.00 32.89 4.41
1683 2311 2.614259 TCTTAGAGATCCTGCATCCCC 58.386 52.381 0.00 0.00 30.71 4.81
1695 2323 1.149174 CATCCCCGCATAAGGCTGT 59.851 57.895 0.00 0.00 41.67 4.40
1719 2347 4.989279 ATTGAAGTCTGTTTTGCACACT 57.011 36.364 0.00 0.00 0.00 3.55
1734 2362 2.288213 GCACACTCTTTAGGGCCAAAAC 60.288 50.000 6.18 0.00 0.00 2.43
1736 2364 2.091555 ACACTCTTTAGGGCCAAAACCA 60.092 45.455 6.18 0.00 0.00 3.67
1737 2365 3.165071 CACTCTTTAGGGCCAAAACCAT 58.835 45.455 6.18 0.00 0.00 3.55
1739 2367 2.497273 CTCTTTAGGGCCAAAACCATGG 59.503 50.000 11.19 11.19 43.70 3.66
1741 2369 3.076182 TCTTTAGGGCCAAAACCATGGTA 59.924 43.478 20.12 0.00 42.75 3.25
1742 2370 2.517998 TAGGGCCAAAACCATGGTAC 57.482 50.000 20.12 5.54 42.75 3.34
1743 2371 0.252057 AGGGCCAAAACCATGGTACC 60.252 55.000 20.12 14.27 42.75 3.34
1744 2372 1.261938 GGGCCAAAACCATGGTACCC 61.262 60.000 20.12 19.17 42.75 3.69
1745 2373 1.261938 GGCCAAAACCATGGTACCCC 61.262 60.000 20.12 10.74 42.75 4.95
1746 2374 0.252057 GCCAAAACCATGGTACCCCT 60.252 55.000 20.12 0.00 42.75 4.79
1747 2375 1.829666 GCCAAAACCATGGTACCCCTT 60.830 52.381 20.12 5.22 42.75 3.95
1748 2376 1.899142 CCAAAACCATGGTACCCCTTG 59.101 52.381 20.12 15.41 35.65 3.61
1749 2377 2.491825 CCAAAACCATGGTACCCCTTGA 60.492 50.000 20.12 0.00 37.97 3.02
1750 2378 2.825532 CAAAACCATGGTACCCCTTGAG 59.174 50.000 20.12 1.39 37.97 3.02
1751 2379 2.053747 AACCATGGTACCCCTTGAGA 57.946 50.000 20.12 0.00 37.97 3.27
1752 2380 1.584724 ACCATGGTACCCCTTGAGAG 58.415 55.000 18.10 0.00 37.97 3.20
1771 2399 4.146058 CAGCGCTGCATATCCCAA 57.854 55.556 26.68 0.00 0.00 4.12
1774 2402 1.068748 CAGCGCTGCATATCCCAAATC 60.069 52.381 26.68 0.00 0.00 2.17
1775 2403 0.953727 GCGCTGCATATCCCAAATCA 59.046 50.000 0.00 0.00 0.00 2.57
1784 2412 5.300034 TGCATATCCCAAATCACAGAACATC 59.700 40.000 0.00 0.00 0.00 3.06
1785 2413 5.300034 GCATATCCCAAATCACAGAACATCA 59.700 40.000 0.00 0.00 0.00 3.07
1787 2415 7.631161 GCATATCCCAAATCACAGAACATCAAA 60.631 37.037 0.00 0.00 0.00 2.69
1789 2417 6.669125 TCCCAAATCACAGAACATCAAAAT 57.331 33.333 0.00 0.00 0.00 1.82
1790 2418 7.065120 TCCCAAATCACAGAACATCAAAATT 57.935 32.000 0.00 0.00 0.00 1.82
1791 2419 7.153985 TCCCAAATCACAGAACATCAAAATTC 58.846 34.615 0.00 0.00 0.00 2.17
1792 2420 6.369615 CCCAAATCACAGAACATCAAAATTCC 59.630 38.462 0.00 0.00 0.00 3.01
1794 2422 7.095523 CCAAATCACAGAACATCAAAATTCCAC 60.096 37.037 0.00 0.00 0.00 4.02
1795 2423 6.653526 ATCACAGAACATCAAAATTCCACA 57.346 33.333 0.00 0.00 0.00 4.17
1796 2424 5.830912 TCACAGAACATCAAAATTCCACAC 58.169 37.500 0.00 0.00 0.00 3.82
1808 3177 2.435372 TTCCACACTCTTTGCCAAGT 57.565 45.000 0.00 0.00 0.00 3.16
1816 3185 4.020218 ACACTCTTTGCCAAGTCTAGCATA 60.020 41.667 0.00 0.00 39.11 3.14
1817 3186 5.121811 CACTCTTTGCCAAGTCTAGCATAT 58.878 41.667 0.00 0.00 39.11 1.78
1836 3205 6.317140 AGCATATTCACACAACACTATCCAAG 59.683 38.462 0.00 0.00 0.00 3.61
1865 3242 3.495806 GGGGCATGATTCTCCTACTGAAG 60.496 52.174 0.00 0.00 0.00 3.02
1907 3288 6.043243 TCCCAGTTCTAGATTTGAGAAGTTGT 59.957 38.462 0.00 0.00 34.94 3.32
2001 3448 4.391830 TCCTGCAAACACGATAATCTGTTC 59.608 41.667 0.00 0.00 30.11 3.18
2172 3634 1.539827 GGTTTTGCAGACGGTAGCATT 59.460 47.619 8.32 0.00 40.94 3.56
2251 3735 5.129485 CAGTGATGTAAATCCCCAGTACTCT 59.871 44.000 0.00 0.00 0.00 3.24
2252 3736 5.364157 AGTGATGTAAATCCCCAGTACTCTC 59.636 44.000 0.00 0.00 0.00 3.20
2255 3739 4.684724 TGTAAATCCCCAGTACTCTCTGT 58.315 43.478 0.00 0.00 34.02 3.41
2256 3740 5.834460 TGTAAATCCCCAGTACTCTCTGTA 58.166 41.667 0.00 0.00 34.02 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
593 1117 1.878522 CAATCTTCCTCGTCCGGCG 60.879 63.158 11.37 11.37 43.01 6.46
594 1118 2.174319 GCAATCTTCCTCGTCCGGC 61.174 63.158 0.00 0.00 0.00 6.13
596 1120 1.878522 CGGCAATCTTCCTCGTCCG 60.879 63.158 0.00 0.00 0.00 4.79
597 1121 2.174319 GCGGCAATCTTCCTCGTCC 61.174 63.158 0.00 0.00 0.00 4.79
598 1122 2.174319 GGCGGCAATCTTCCTCGTC 61.174 63.158 3.07 0.00 0.00 4.20
599 1123 2.125106 GGCGGCAATCTTCCTCGT 60.125 61.111 3.07 0.00 0.00 4.18
600 1124 3.264897 CGGCGGCAATCTTCCTCG 61.265 66.667 10.53 0.00 0.00 4.63
601 1125 3.577313 GCGGCGGCAATCTTCCTC 61.577 66.667 9.78 0.00 39.62 3.71
637 1161 3.282920 GGGCATCGCAGGCTAAGC 61.283 66.667 0.00 0.00 0.00 3.09
638 1162 1.596477 GAGGGCATCGCAGGCTAAG 60.596 63.158 0.00 0.00 0.00 2.18
639 1163 2.505982 GAGGGCATCGCAGGCTAA 59.494 61.111 0.00 0.00 0.00 3.09
640 1164 3.916544 CGAGGGCATCGCAGGCTA 61.917 66.667 9.16 0.00 45.98 3.93
669 1193 4.890306 GGGCCTCCCTCTCCTCCC 62.890 77.778 0.84 0.00 41.34 4.30
721 1245 0.802222 CGTATGCACACTCTCCCGTG 60.802 60.000 0.00 0.00 40.67 4.94
722 1246 1.248785 ACGTATGCACACTCTCCCGT 61.249 55.000 0.00 0.00 0.00 5.28
723 1247 0.736636 TACGTATGCACACTCTCCCG 59.263 55.000 0.00 0.00 0.00 5.14
724 1248 1.749634 ACTACGTATGCACACTCTCCC 59.250 52.381 0.00 0.00 0.00 4.30
725 1249 2.422479 TCACTACGTATGCACACTCTCC 59.578 50.000 0.00 0.00 0.00 3.71
737 1261 2.089980 GAAGGAGCTGGTCACTACGTA 58.910 52.381 9.30 0.00 0.00 3.57
745 1269 2.496899 TTTGGATGAAGGAGCTGGTC 57.503 50.000 0.00 0.00 0.00 4.02
805 1329 1.476488 CATCGGTTTGGGGATGGAAAC 59.524 52.381 0.00 0.00 37.09 2.78
810 1334 0.969917 TTGCCATCGGTTTGGGGATG 60.970 55.000 2.82 0.00 39.74 3.51
819 1343 0.034896 GTATCGGGATTGCCATCGGT 59.965 55.000 0.00 0.00 35.15 4.69
939 1472 4.320608 TTCTGATGGTTTTTGCACTTCC 57.679 40.909 0.00 0.00 0.00 3.46
1179 1751 3.891366 TGATGTCGCTATCAAGGATCTCA 59.109 43.478 0.00 0.00 34.32 3.27
1222 1794 2.107552 TGTTGTACTTGGGGAAAGGGAG 59.892 50.000 0.00 0.00 40.51 4.30
1317 1893 8.967918 ACAGTTGACACACATATAGTACAGTAT 58.032 33.333 0.00 0.00 0.00 2.12
1320 1896 7.312899 TGACAGTTGACACACATATAGTACAG 58.687 38.462 0.00 0.00 0.00 2.74
1322 1898 7.813148 ACTTGACAGTTGACACACATATAGTAC 59.187 37.037 0.00 0.00 0.00 2.73
1323 1899 7.812669 CACTTGACAGTTGACACACATATAGTA 59.187 37.037 0.00 0.00 0.00 1.82
1325 1906 6.646653 ACACTTGACAGTTGACACACATATAG 59.353 38.462 0.00 0.00 0.00 1.31
1337 1920 1.600957 CCTGCTGACACTTGACAGTTG 59.399 52.381 9.84 4.19 39.42 3.16
1339 1922 1.069823 CTCCTGCTGACACTTGACAGT 59.930 52.381 9.84 0.00 39.42 3.55
1340 1923 1.069823 ACTCCTGCTGACACTTGACAG 59.930 52.381 4.57 4.57 40.02 3.51
1341 1924 1.069204 GACTCCTGCTGACACTTGACA 59.931 52.381 0.00 0.00 0.00 3.58
1343 1926 0.681733 GGACTCCTGCTGACACTTGA 59.318 55.000 0.00 0.00 0.00 3.02
1344 1927 0.683973 AGGACTCCTGCTGACACTTG 59.316 55.000 0.00 0.00 29.57 3.16
1364 1952 8.803201 TTGAGAACACTATATATCTTTGAGCG 57.197 34.615 0.00 0.00 0.00 5.03
1388 1976 9.976511 CCATTATTATGACAAGAGCAATTGATT 57.023 29.630 10.34 0.00 33.37 2.57
1392 1980 9.851686 TCTACCATTATTATGACAAGAGCAATT 57.148 29.630 0.00 0.00 33.37 2.32
1394 1982 7.715249 GGTCTACCATTATTATGACAAGAGCAA 59.285 37.037 11.67 0.00 35.07 3.91
1396 1984 7.217200 TGGTCTACCATTATTATGACAAGAGC 58.783 38.462 0.00 10.50 42.01 4.09
1450 2060 6.400940 CGGCATTCCATTGTTGTTTATTTGTC 60.401 38.462 0.00 0.00 0.00 3.18
1456 2066 2.560542 AGCGGCATTCCATTGTTGTTTA 59.439 40.909 1.45 0.00 0.00 2.01
1462 2072 0.527565 GACAAGCGGCATTCCATTGT 59.472 50.000 1.45 2.44 41.76 2.71
1600 2213 0.600057 CAAGCCTTCAAGGTTCCTGC 59.400 55.000 5.03 0.00 37.80 4.85
1616 2229 1.891178 CGTGCATGATGCTGTTCAAG 58.109 50.000 19.19 0.00 45.31 3.02
1617 2230 0.109643 GCGTGCATGATGCTGTTCAA 60.110 50.000 19.19 0.00 45.31 2.69
1678 2306 1.149174 CACAGCCTTATGCGGGGAT 59.851 57.895 0.00 0.00 41.63 3.85
1695 2323 5.101628 GTGTGCAAAACAGACTTCAATTCA 58.898 37.500 0.00 0.00 40.26 2.57
1719 2347 2.158234 ACCATGGTTTTGGCCCTAAAGA 60.158 45.455 13.00 0.00 40.68 2.52
1739 2367 1.222113 GCTGCCTCTCAAGGGGTAC 59.778 63.158 0.00 0.00 43.58 3.34
1741 2369 3.710722 CGCTGCCTCTCAAGGGGT 61.711 66.667 0.00 0.00 43.58 4.95
1743 2371 4.093291 AGCGCTGCCTCTCAAGGG 62.093 66.667 10.39 0.00 43.58 3.95
1744 2372 2.818714 CAGCGCTGCCTCTCAAGG 60.819 66.667 26.68 0.00 46.44 3.61
1759 2387 4.641541 TGTTCTGTGATTTGGGATATGCAG 59.358 41.667 0.00 0.00 0.00 4.41
1771 2399 6.925165 GTGTGGAATTTTGATGTTCTGTGATT 59.075 34.615 0.00 0.00 0.00 2.57
1774 2402 5.835257 AGTGTGGAATTTTGATGTTCTGTG 58.165 37.500 0.00 0.00 0.00 3.66
1775 2403 5.829924 AGAGTGTGGAATTTTGATGTTCTGT 59.170 36.000 0.00 0.00 0.00 3.41
1784 2412 4.057406 TGGCAAAGAGTGTGGAATTTTG 57.943 40.909 0.00 0.00 33.18 2.44
1785 2413 4.162131 ACTTGGCAAAGAGTGTGGAATTTT 59.838 37.500 8.15 0.00 36.84 1.82
1787 2415 3.299503 ACTTGGCAAAGAGTGTGGAATT 58.700 40.909 8.15 0.00 36.84 2.17
1789 2417 2.092429 AGACTTGGCAAAGAGTGTGGAA 60.092 45.455 8.15 0.00 36.84 3.53
1790 2418 1.490490 AGACTTGGCAAAGAGTGTGGA 59.510 47.619 8.15 0.00 36.84 4.02
1791 2419 1.972872 AGACTTGGCAAAGAGTGTGG 58.027 50.000 8.15 0.00 36.84 4.17
1792 2420 2.481952 GCTAGACTTGGCAAAGAGTGTG 59.518 50.000 8.15 0.00 36.84 3.82
1794 2422 2.771089 TGCTAGACTTGGCAAAGAGTG 58.229 47.619 8.15 0.00 37.91 3.51
1795 2423 3.710209 ATGCTAGACTTGGCAAAGAGT 57.290 42.857 8.15 0.00 44.38 3.24
1796 2424 5.819379 TGAATATGCTAGACTTGGCAAAGAG 59.181 40.000 8.15 0.00 44.38 2.85
1808 3177 7.147742 TGGATAGTGTTGTGTGAATATGCTAGA 60.148 37.037 0.00 0.00 0.00 2.43
1816 3185 5.241403 TCCTTGGATAGTGTTGTGTGAAT 57.759 39.130 0.00 0.00 0.00 2.57
1817 3186 4.698201 TCCTTGGATAGTGTTGTGTGAA 57.302 40.909 0.00 0.00 0.00 3.18
1836 3205 1.966354 GAGAATCATGCCCCCATTTCC 59.034 52.381 0.00 0.00 33.17 3.13
1865 3242 8.034804 AGAACTGGGATAAATTAACATTTGCAC 58.965 33.333 0.00 0.00 34.29 4.57
1917 3299 2.754002 ACGAGAGAGGTACCTTGTAAGC 59.246 50.000 17.53 1.37 0.00 3.09
1956 3344 6.947158 AGGATCTTCAGAATTCAGAAGCTTTT 59.053 34.615 27.16 15.79 38.76 2.27
2001 3448 5.296151 TCCCAGCTAAGGACTTGATTATG 57.704 43.478 0.43 0.00 0.00 1.90
2070 3523 7.175104 TCTTTTATTCCTAACCAAGTGCTCAT 58.825 34.615 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.