Multiple sequence alignment - TraesCS4A01G147400

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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 TraesCS4A01G147400 chr4A 100.000 2453 0 0 1 2453 263898375 263895923 0.000000e+00 4530.0
1 TraesCS4A01G147400 chr4A 87.862 898 88 8 553 1447 391151119 391151998 0.000000e+00 1035.0
2 TraesCS4A01G147400 chr4A 92.520 615 42 3 3 614 54347517 54348130 0.000000e+00 878.0
3 TraesCS4A01G147400 chr4A 92.988 599 36 6 3 601 54310310 54310902 0.000000e+00 869.0
4 TraesCS4A01G147400 chr4A 88.055 586 61 9 1873 2453 172284875 172284294 0.000000e+00 686.0
5 TraesCS4A01G147400 chr4A 79.795 782 104 36 1680 2446 331715413 331714671 1.010000e-143 520.0
6 TraesCS4A01G147400 chr4A 79.257 781 111 33 1680 2446 331723498 331722755 4.710000e-137 497.0
7 TraesCS4A01G147400 chr4A 78.927 783 110 42 1684 2447 294283454 294284200 4.740000e-132 481.0
8 TraesCS4A01G147400 chr4A 80.130 463 65 24 1692 2143 437054344 437054790 1.090000e-83 320.0
9 TraesCS4A01G147400 chr4A 72.331 665 109 56 3 649 275114233 275114840 3.290000e-29 139.0
10 TraesCS4A01G147400 chr4A 87.324 71 9 0 1543 1613 296703024 296702954 5.620000e-12 82.4
11 TraesCS4A01G147400 chr4A 97.143 35 1 0 989 1023 263345838 263345804 2.630000e-05 60.2
12 TraesCS4A01G147400 chr3A 91.730 1185 81 12 522 1695 422737591 422738769 0.000000e+00 1629.0
13 TraesCS4A01G147400 chr3A 89.295 1149 77 14 553 1695 288745712 288746820 0.000000e+00 1399.0
14 TraesCS4A01G147400 chr3A 87.076 472 52 5 1283 1747 400954697 400955166 2.160000e-145 525.0
15 TraesCS4A01G147400 chr3A 90.496 242 19 4 740 979 298396066 298395827 1.420000e-82 316.0
16 TraesCS4A01G147400 chr3A 88.506 261 24 2 1440 1695 166611336 166611595 6.590000e-81 311.0
17 TraesCS4A01G147400 chr3A 85.350 314 29 6 1440 1747 166619265 166619567 2.370000e-80 309.0
18 TraesCS4A01G147400 chr3A 88.115 244 24 5 740 981 298371037 298370797 3.990000e-73 285.0
19 TraesCS4A01G147400 chr3A 83.128 243 17 12 740 981 298403757 298403538 1.490000e-47 200.0
20 TraesCS4A01G147400 chr3A 91.935 62 3 2 1018 1077 299497727 299497666 4.350000e-13 86.1
21 TraesCS4A01G147400 chr3A 88.710 62 5 1 1018 1077 466571712 466571651 9.410000e-10 75.0
22 TraesCS4A01G147400 chr3A 95.122 41 2 0 699 739 331333231 331333191 5.660000e-07 65.8
23 TraesCS4A01G147400 chr5A 88.590 780 76 9 1684 2453 240755480 240754704 0.000000e+00 935.0
24 TraesCS4A01G147400 chr5A 87.949 780 80 10 1684 2453 240694197 240693422 0.000000e+00 907.0
25 TraesCS4A01G147400 chr5A 89.951 617 53 7 3 614 192874269 192873657 0.000000e+00 787.0
26 TraesCS4A01G147400 chr5A 86.325 234 16 9 531 762 219797037 219796818 8.770000e-60 241.0
27 TraesCS4A01G147400 chr5A 85.398 226 30 3 1310 1533 539846028 539846252 5.280000e-57 231.0
28 TraesCS4A01G147400 chr6A 93.729 606 30 6 3 601 510658476 510659080 0.000000e+00 902.0
29 TraesCS4A01G147400 chr6A 93.500 600 36 3 3 601 510666465 510667062 0.000000e+00 889.0
30 TraesCS4A01G147400 chr6A 92.154 599 33 10 3 591 539365267 539364673 0.000000e+00 833.0
31 TraesCS4A01G147400 chr6A 91.986 574 43 3 875 1448 546379945 546379375 0.000000e+00 802.0
32 TraesCS4A01G147400 chr6A 87.445 677 72 11 1774 2446 52110241 52109574 0.000000e+00 767.0
33 TraesCS4A01G147400 chr6A 86.336 666 79 9 1784 2446 52074460 52073804 0.000000e+00 715.0
34 TraesCS4A01G147400 chr6A 80.789 760 85 44 4 752 279088287 279088996 2.780000e-149 538.0
35 TraesCS4A01G147400 chr6A 80.395 760 97 43 2 748 279080445 279081165 4.640000e-147 531.0
36 TraesCS4A01G147400 chr6A 87.072 263 28 2 1438 1695 369600789 369601050 2.390000e-75 292.0
37 TraesCS4A01G147400 chr6A 86.692 263 28 3 1438 1695 369593076 369593336 3.990000e-73 285.0
38 TraesCS4A01G147400 chr6A 87.379 206 22 4 1203 1406 590256879 590257082 1.470000e-57 233.0
39 TraesCS4A01G147400 chr1A 91.364 660 43 13 3 655 503124930 503125582 0.000000e+00 891.0
40 TraesCS4A01G147400 chr1A 93.814 582 31 4 3 582 503088655 503089233 0.000000e+00 870.0
41 TraesCS4A01G147400 chr1A 84.810 632 78 15 1827 2453 401844736 401844118 9.640000e-174 619.0
42 TraesCS4A01G147400 chr1A 86.192 239 28 5 1310 1545 55425177 55425413 1.130000e-63 254.0
43 TraesCS4A01G147400 chr1A 86.667 225 28 2 1310 1533 55433713 55433936 5.240000e-62 248.0
44 TraesCS4A01G147400 chr1A 87.805 205 21 4 1203 1405 208466050 208466252 1.130000e-58 237.0
45 TraesCS4A01G147400 chr1A 97.917 48 1 0 1132 1179 323266910 323266863 1.560000e-12 84.2
46 TraesCS4A01G147400 chr1A 100.000 44 0 0 1136 1179 400241972 400242015 5.620000e-12 82.4
47 TraesCS4A01G147400 chr1A 95.556 45 2 0 1086 1130 339542348 339542304 3.380000e-09 73.1
48 TraesCS4A01G147400 chr2A 91.864 590 43 4 3 588 470287808 470287220 0.000000e+00 819.0
49 TraesCS4A01G147400 chr2A 88.333 600 60 10 1859 2453 417049532 417048938 0.000000e+00 712.0
50 TraesCS4A01G147400 chr2A 87.805 205 21 4 1203 1405 177358136 177358338 1.130000e-58 237.0
51 TraesCS4A01G147400 chr2A 87.805 205 21 4 1203 1405 177370691 177370893 1.130000e-58 237.0
52 TraesCS4A01G147400 chr2A 91.083 157 14 0 1684 1840 698948892 698949048 1.910000e-51 213.0
53 TraesCS4A01G147400 chr2A 97.917 48 1 0 1132 1179 247122631 247122678 1.560000e-12 84.2
54 TraesCS4A01G147400 chr2A 100.000 45 0 0 1135 1179 384097533 384097489 1.560000e-12 84.2
55 TraesCS4A01G147400 chr7A 88.350 618 55 14 875 1490 332757818 332758420 0.000000e+00 726.0
56 TraesCS4A01G147400 chr7A 86.842 608 65 15 1849 2450 332635852 332635254 0.000000e+00 665.0
57 TraesCS4A01G147400 chr7A 89.493 276 22 3 1425 1695 549655260 549655533 2.340000e-90 342.0
58 TraesCS4A01G147400 chr7A 91.358 243 19 2 740 981 152816128 152815887 5.060000e-87 331.0
59 TraesCS4A01G147400 chr7A 90.947 243 19 3 740 981 152823728 152823488 8.460000e-85 324.0
60 TraesCS4A01G147400 chr7A 95.122 41 2 0 699 739 600538793 600538753 5.660000e-07 65.8
61 TraesCS4A01G147400 chr2B 82.188 640 96 15 1823 2453 362769979 362769349 3.590000e-148 534.0
62 TraesCS4A01G147400 chr2B 81.902 652 100 15 1811 2453 362778136 362777494 3.590000e-148 534.0
63 TraesCS4A01G147400 chr7B 81.790 648 92 23 1811 2450 103385187 103385816 1.010000e-143 520.0
64 TraesCS4A01G147400 chr6B 80.721 638 91 30 1823 2443 699249184 699249806 3.690000e-128 468.0
65 TraesCS4A01G147400 chr6B 80.438 639 92 30 1823 2443 699257083 699257706 7.990000e-125 457.0


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 TraesCS4A01G147400 chr4A 263895923 263898375 2452 True 4530 4530 100.000 1 2453 1 chr4A.!!$R3 2452
1 TraesCS4A01G147400 chr4A 391151119 391151998 879 False 1035 1035 87.862 553 1447 1 chr4A.!!$F5 894
2 TraesCS4A01G147400 chr4A 54347517 54348130 613 False 878 878 92.520 3 614 1 chr4A.!!$F2 611
3 TraesCS4A01G147400 chr4A 54310310 54310902 592 False 869 869 92.988 3 601 1 chr4A.!!$F1 598
4 TraesCS4A01G147400 chr4A 172284294 172284875 581 True 686 686 88.055 1873 2453 1 chr4A.!!$R1 580
5 TraesCS4A01G147400 chr4A 331714671 331715413 742 True 520 520 79.795 1680 2446 1 chr4A.!!$R5 766
6 TraesCS4A01G147400 chr4A 331722755 331723498 743 True 497 497 79.257 1680 2446 1 chr4A.!!$R6 766
7 TraesCS4A01G147400 chr4A 294283454 294284200 746 False 481 481 78.927 1684 2447 1 chr4A.!!$F4 763
8 TraesCS4A01G147400 chr3A 422737591 422738769 1178 False 1629 1629 91.730 522 1695 1 chr3A.!!$F5 1173
9 TraesCS4A01G147400 chr3A 288745712 288746820 1108 False 1399 1399 89.295 553 1695 1 chr3A.!!$F3 1142
10 TraesCS4A01G147400 chr5A 240754704 240755480 776 True 935 935 88.590 1684 2453 1 chr5A.!!$R4 769
11 TraesCS4A01G147400 chr5A 240693422 240694197 775 True 907 907 87.949 1684 2453 1 chr5A.!!$R3 769
12 TraesCS4A01G147400 chr5A 192873657 192874269 612 True 787 787 89.951 3 614 1 chr5A.!!$R1 611
13 TraesCS4A01G147400 chr6A 510658476 510659080 604 False 902 902 93.729 3 601 1 chr6A.!!$F5 598
14 TraesCS4A01G147400 chr6A 510666465 510667062 597 False 889 889 93.500 3 601 1 chr6A.!!$F6 598
15 TraesCS4A01G147400 chr6A 539364673 539365267 594 True 833 833 92.154 3 591 1 chr6A.!!$R3 588
16 TraesCS4A01G147400 chr6A 546379375 546379945 570 True 802 802 91.986 875 1448 1 chr6A.!!$R4 573
17 TraesCS4A01G147400 chr6A 52109574 52110241 667 True 767 767 87.445 1774 2446 1 chr6A.!!$R2 672
18 TraesCS4A01G147400 chr6A 52073804 52074460 656 True 715 715 86.336 1784 2446 1 chr6A.!!$R1 662
19 TraesCS4A01G147400 chr6A 279088287 279088996 709 False 538 538 80.789 4 752 1 chr6A.!!$F2 748
20 TraesCS4A01G147400 chr6A 279080445 279081165 720 False 531 531 80.395 2 748 1 chr6A.!!$F1 746
21 TraesCS4A01G147400 chr1A 503124930 503125582 652 False 891 891 91.364 3 655 1 chr1A.!!$F6 652
22 TraesCS4A01G147400 chr1A 503088655 503089233 578 False 870 870 93.814 3 582 1 chr1A.!!$F5 579
23 TraesCS4A01G147400 chr1A 401844118 401844736 618 True 619 619 84.810 1827 2453 1 chr1A.!!$R3 626
24 TraesCS4A01G147400 chr2A 470287220 470287808 588 True 819 819 91.864 3 588 1 chr2A.!!$R3 585
25 TraesCS4A01G147400 chr2A 417048938 417049532 594 True 712 712 88.333 1859 2453 1 chr2A.!!$R2 594
26 TraesCS4A01G147400 chr7A 332757818 332758420 602 False 726 726 88.350 875 1490 1 chr7A.!!$F1 615
27 TraesCS4A01G147400 chr7A 332635254 332635852 598 True 665 665 86.842 1849 2450 1 chr7A.!!$R3 601
28 TraesCS4A01G147400 chr2B 362769349 362769979 630 True 534 534 82.188 1823 2453 1 chr2B.!!$R1 630
29 TraesCS4A01G147400 chr2B 362777494 362778136 642 True 534 534 81.902 1811 2453 1 chr2B.!!$R2 642
30 TraesCS4A01G147400 chr7B 103385187 103385816 629 False 520 520 81.790 1811 2450 1 chr7B.!!$F1 639
31 TraesCS4A01G147400 chr6B 699249184 699249806 622 False 468 468 80.721 1823 2443 1 chr6B.!!$F1 620
32 TraesCS4A01G147400 chr6B 699257083 699257706 623 False 457 457 80.438 1823 2443 1 chr6B.!!$F2 620

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
333 334 0.798776 CAGCGGATTTTTGCGAGTCT 59.201 50.0 0.0 0.0 35.87 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 1711 0.037326 TCGACGGTAGTGGTACTCGT 60.037 55.0 0.0 0.0 38.18 4.18 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
26 27 6.127535 CGAGGGAACTTACATGGTAGTTTCTA 60.128 42.308 15.87 0.00 44.43 2.10
46 47 5.932455 TCTATTTAAAACATACCCTCCCGG 58.068 41.667 0.00 0.00 37.81 5.73
133 134 2.999185 ATCCCTTGGCCTTTTCTTCA 57.001 45.000 3.32 0.00 0.00 3.02
175 176 5.721480 AGCCTTGCCAATAATTCTTTTACCT 59.279 36.000 0.00 0.00 0.00 3.08
319 320 3.343617 TCTATTTTCTTGGAACCAGCGG 58.656 45.455 0.00 0.00 0.00 5.52
333 334 0.798776 CAGCGGATTTTTGCGAGTCT 59.201 50.000 0.00 0.00 35.87 3.24
450 467 0.980423 GAGAGAAGGAGCCCAACAGT 59.020 55.000 0.00 0.00 0.00 3.55
451 468 1.349357 GAGAGAAGGAGCCCAACAGTT 59.651 52.381 0.00 0.00 0.00 3.16
494 512 1.230212 CTCCCCACCTAATTGGCCC 59.770 63.158 0.00 0.00 40.22 5.80
674 710 3.881019 TTGTCCTCCTCCCGAGCGT 62.881 63.158 0.00 0.00 37.27 5.07
706 742 2.440247 CGTGCCCAATTCCCCTCC 60.440 66.667 0.00 0.00 0.00 4.30
825 861 3.170362 CCCCACTGCTCCTTTCCA 58.830 61.111 0.00 0.00 0.00 3.53
855 891 0.979665 CTCTTCCTCAACAGCCAGGA 59.020 55.000 0.00 0.00 37.00 3.86
891 927 2.819595 CACCGCGCCATGCTACTT 60.820 61.111 0.00 0.00 43.27 2.24
1081 1117 3.452786 CTCCTGCGAGCTCCCGAA 61.453 66.667 8.47 0.00 0.00 4.30
1107 1143 1.905843 CCTCCCATCCGCGAGATCT 60.906 63.158 8.23 0.00 30.59 2.75
1134 1170 3.009115 GGCCACCAGGACCTGCTA 61.009 66.667 16.72 0.00 36.69 3.49
1205 1241 4.482684 TCCTCGCGCTGCTTCTCG 62.483 66.667 5.56 0.00 0.00 4.04
1218 1254 0.679505 CTTCTCGTTGGAGTCACCCA 59.320 55.000 0.00 0.00 41.26 4.51
1344 1381 3.501062 TGTGTTGTTTTGTGTTGGACGTA 59.499 39.130 0.00 0.00 0.00 3.57
1350 1387 4.454847 TGTTTTGTGTTGGACGTAAAGACA 59.545 37.500 8.77 8.77 0.00 3.41
1431 1468 0.898789 ACCAGTACTCGGTGACCCTG 60.899 60.000 14.00 0.00 34.69 4.45
1448 1487 4.966787 GGGGTGCGCCAAGTTCCA 62.967 66.667 19.98 0.00 36.17 3.53
1570 1609 2.774687 GGCAAGTACCTCTCCGAAAAA 58.225 47.619 0.00 0.00 0.00 1.94
1571 1610 3.344515 GGCAAGTACCTCTCCGAAAAAT 58.655 45.455 0.00 0.00 0.00 1.82
1581 1620 6.001460 ACCTCTCCGAAAAATGAACATGTAA 58.999 36.000 0.00 0.00 0.00 2.41
1623 1662 0.903454 TCCCTCAAGTCCGAAGACCC 60.903 60.000 0.00 0.00 44.72 4.46
1627 1666 2.565834 CCTCAAGTCCGAAGACCCTTAA 59.434 50.000 0.00 0.00 44.72 1.85
1637 1676 3.119388 CGAAGACCCTTAATACCACGACA 60.119 47.826 0.00 0.00 0.00 4.35
1638 1677 4.618927 CGAAGACCCTTAATACCACGACAA 60.619 45.833 0.00 0.00 0.00 3.18
1639 1678 4.895668 AGACCCTTAATACCACGACAAA 57.104 40.909 0.00 0.00 0.00 2.83
1640 1679 5.231702 AGACCCTTAATACCACGACAAAA 57.768 39.130 0.00 0.00 0.00 2.44
1641 1680 5.243207 AGACCCTTAATACCACGACAAAAG 58.757 41.667 0.00 0.00 0.00 2.27
1642 1681 4.329392 ACCCTTAATACCACGACAAAAGG 58.671 43.478 0.00 0.00 33.37 3.11
1643 1682 3.692593 CCCTTAATACCACGACAAAAGGG 59.307 47.826 3.02 3.02 44.11 3.95
1644 1683 4.581868 CCTTAATACCACGACAAAAGGGA 58.418 43.478 0.00 0.00 0.00 4.20
1645 1684 5.190677 CCTTAATACCACGACAAAAGGGAT 58.809 41.667 0.00 0.00 0.00 3.85
1646 1685 5.650703 CCTTAATACCACGACAAAAGGGATT 59.349 40.000 0.00 0.00 0.00 3.01
1647 1686 6.152154 CCTTAATACCACGACAAAAGGGATTT 59.848 38.462 0.00 0.00 0.00 2.17
1662 1701 9.196552 CAAAAGGGATTTGTATTCTTCAAGTTC 57.803 33.333 0.00 0.00 42.84 3.01
1663 1702 8.477419 AAAGGGATTTGTATTCTTCAAGTTCA 57.523 30.769 0.00 0.00 0.00 3.18
1664 1703 7.454260 AGGGATTTGTATTCTTCAAGTTCAC 57.546 36.000 0.00 0.00 0.00 3.18
1665 1704 6.434340 AGGGATTTGTATTCTTCAAGTTCACC 59.566 38.462 0.00 0.00 0.00 4.02
1666 1705 6.434340 GGGATTTGTATTCTTCAAGTTCACCT 59.566 38.462 0.00 0.00 0.00 4.00
1667 1706 7.039714 GGGATTTGTATTCTTCAAGTTCACCTT 60.040 37.037 0.00 0.00 0.00 3.50
1723 1762 0.249741 CCGTGGACGTCAAGTTCCTT 60.250 55.000 18.91 0.00 37.74 3.36
1779 1818 3.890756 TCTAAGAACGTGAACCACTACCA 59.109 43.478 0.00 0.00 31.34 3.25
1895 1937 2.036862 GCTTCGAAGGTATAACCCCGAT 59.963 50.000 25.77 0.00 41.26 4.18
1978 2050 2.612212 GTTGTTCTTTGCGAGTTCCTCA 59.388 45.455 0.00 0.00 0.00 3.86
1994 2069 5.421056 AGTTCCTCATTGCATTGTCATTGAT 59.579 36.000 8.36 0.00 0.00 2.57
2047 2126 3.946606 TCATCTTGCATGACACACTCAT 58.053 40.909 4.14 0.00 40.59 2.90
2051 2131 3.007831 TCTTGCATGACACACTCATACCA 59.992 43.478 0.00 0.00 37.53 3.25
2095 2178 0.952280 GTGAGCTACCGGATCATCGA 59.048 55.000 9.46 0.00 42.56 3.59
2344 2462 4.508492 GGTTTTACCGGAATTGTTGTTTGG 59.492 41.667 9.46 0.00 0.00 3.28
2345 2463 3.372660 TTACCGGAATTGTTGTTTGGC 57.627 42.857 9.46 0.00 0.00 4.52
2347 2465 1.281566 CCGGAATTGTTGTTTGGCGC 61.282 55.000 0.00 0.00 0.00 6.53
2450 2575 5.180868 TGTTGAGTACCTAAACGAGAGAGAC 59.819 44.000 0.00 0.00 27.69 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.555195 CGGGAGGGTATGTTTTAAATAGAAACT 59.445 37.037 0.00 0.00 37.75 2.66
133 134 5.753721 AGGCTAGAGAGTCAAAACTTGAT 57.246 39.130 0.00 0.00 42.47 2.57
175 176 3.495434 TTTGGTAGAGCTCCGGAAAAA 57.505 42.857 10.93 2.69 0.00 1.94
319 320 3.915437 TTTCCCAGACTCGCAAAAATC 57.085 42.857 0.00 0.00 0.00 2.17
638 674 0.030092 AAGGGGAATCGAGGGGATCA 60.030 55.000 0.00 0.00 33.02 2.92
696 732 0.029577 GAGGGAGGAGGAGGGGAATT 60.030 60.000 0.00 0.00 0.00 2.17
825 861 1.006631 AGGAAGAGGGGGATGGCAT 59.993 57.895 0.00 0.00 0.00 4.40
891 927 2.896854 GCGGCGAATGGATGCAGA 60.897 61.111 12.98 0.00 0.00 4.26
1012 1048 2.530151 AGTCCTGGCCTGGCAGAA 60.530 61.111 23.46 3.59 0.00 3.02
1058 1094 2.999648 AGCTCGCAGGAGAAGGCA 61.000 61.111 0.00 0.00 43.27 4.75
1081 1117 3.415087 GGATGGGAGGCTGGTGCT 61.415 66.667 0.00 0.00 39.59 4.40
1130 1166 4.457496 GCGGCCAGAGCAGTAGCA 62.457 66.667 2.24 0.00 45.49 3.49
1201 1237 0.608130 CATGGGTGACTCCAACGAGA 59.392 55.000 0.00 0.00 40.62 4.04
1205 1241 1.813513 CTGACATGGGTGACTCCAAC 58.186 55.000 0.00 0.00 40.62 3.77
1218 1254 1.071299 TCGTGCTGGTTGCTGACAT 59.929 52.632 0.00 0.00 43.37 3.06
1249 1285 0.768221 TGTGCAGGGGAAAGGAGAGT 60.768 55.000 0.00 0.00 0.00 3.24
1344 1381 0.759346 AGTCGACCTTGCCTGTCTTT 59.241 50.000 13.01 0.00 0.00 2.52
1350 1387 1.258445 CCCTGTAGTCGACCTTGCCT 61.258 60.000 13.01 0.00 0.00 4.75
1431 1468 4.966787 TGGAACTTGGCGCACCCC 62.967 66.667 10.83 1.38 33.59 4.95
1435 1472 1.000385 CTTTCAATGGAACTTGGCGCA 60.000 47.619 10.83 0.00 31.35 6.09
1524 1563 1.197036 TCGTCTCGCAGTGTAGTCAAG 59.803 52.381 0.00 0.00 0.00 3.02
1551 1590 4.000988 TCATTTTTCGGAGAGGTACTTGC 58.999 43.478 0.00 0.00 41.55 4.01
1570 1609 3.267483 GGGCGTAGTGTTACATGTTCAT 58.733 45.455 2.30 0.00 0.00 2.57
1571 1610 2.690786 GGGCGTAGTGTTACATGTTCA 58.309 47.619 2.30 1.04 0.00 3.18
1607 1646 3.955650 TTAAGGGTCTTCGGACTTGAG 57.044 47.619 0.00 0.00 43.94 3.02
1623 1662 6.753107 AATCCCTTTTGTCGTGGTATTAAG 57.247 37.500 0.00 0.00 0.00 1.85
1637 1676 8.923270 TGAACTTGAAGAATACAAATCCCTTTT 58.077 29.630 0.00 0.00 0.00 2.27
1638 1677 8.360390 GTGAACTTGAAGAATACAAATCCCTTT 58.640 33.333 0.00 0.00 0.00 3.11
1639 1678 7.039714 GGTGAACTTGAAGAATACAAATCCCTT 60.040 37.037 0.00 0.00 0.00 3.95
1640 1679 6.434340 GGTGAACTTGAAGAATACAAATCCCT 59.566 38.462 0.00 0.00 0.00 4.20
1641 1680 6.434340 AGGTGAACTTGAAGAATACAAATCCC 59.566 38.462 0.00 0.00 0.00 3.85
1642 1681 7.454260 AGGTGAACTTGAAGAATACAAATCC 57.546 36.000 0.00 0.00 0.00 3.01
1657 1696 4.573607 GGTACTCGTTTTCAAGGTGAACTT 59.426 41.667 0.00 0.00 35.89 2.66
1658 1697 4.124970 GGTACTCGTTTTCAAGGTGAACT 58.875 43.478 0.00 0.00 35.89 3.01
1659 1698 3.872771 TGGTACTCGTTTTCAAGGTGAAC 59.127 43.478 0.00 0.00 35.89 3.18
1660 1699 3.872771 GTGGTACTCGTTTTCAAGGTGAA 59.127 43.478 0.00 0.00 34.03 3.18
1661 1700 3.133362 AGTGGTACTCGTTTTCAAGGTGA 59.867 43.478 0.00 0.00 0.00 4.02
1662 1701 3.463944 AGTGGTACTCGTTTTCAAGGTG 58.536 45.455 0.00 0.00 0.00 4.00
1663 1702 3.832615 AGTGGTACTCGTTTTCAAGGT 57.167 42.857 0.00 0.00 0.00 3.50
1664 1703 3.992427 GGTAGTGGTACTCGTTTTCAAGG 59.008 47.826 0.00 0.00 0.00 3.61
1665 1704 3.671928 CGGTAGTGGTACTCGTTTTCAAG 59.328 47.826 0.00 0.00 0.00 3.02
1666 1705 3.068024 ACGGTAGTGGTACTCGTTTTCAA 59.932 43.478 0.00 0.00 34.42 2.69
1667 1706 2.622942 ACGGTAGTGGTACTCGTTTTCA 59.377 45.455 0.00 0.00 34.42 2.69
1668 1707 3.237628 GACGGTAGTGGTACTCGTTTTC 58.762 50.000 0.00 0.00 36.67 2.29
1669 1708 2.350772 CGACGGTAGTGGTACTCGTTTT 60.351 50.000 0.00 0.00 36.67 2.43
1670 1709 1.197721 CGACGGTAGTGGTACTCGTTT 59.802 52.381 0.00 0.00 36.67 3.60
1671 1710 0.798776 CGACGGTAGTGGTACTCGTT 59.201 55.000 0.00 0.00 36.67 3.85
1672 1711 0.037326 TCGACGGTAGTGGTACTCGT 60.037 55.000 0.00 0.00 38.18 4.18
1673 1712 0.371645 GTCGACGGTAGTGGTACTCG 59.628 60.000 0.00 0.00 31.36 4.18
1674 1713 0.729690 GGTCGACGGTAGTGGTACTC 59.270 60.000 9.92 0.00 0.00 2.59
1675 1714 0.678048 GGGTCGACGGTAGTGGTACT 60.678 60.000 9.92 0.00 0.00 2.73
1676 1715 0.678048 AGGGTCGACGGTAGTGGTAC 60.678 60.000 9.92 0.00 0.00 3.34
1677 1716 0.392998 GAGGGTCGACGGTAGTGGTA 60.393 60.000 9.92 0.00 0.00 3.25
1678 1717 1.676967 GAGGGTCGACGGTAGTGGT 60.677 63.158 9.92 0.00 0.00 4.16
1723 1762 1.067142 GTAGATGTTCAGGGTCACGCA 60.067 52.381 0.00 0.00 0.00 5.24
1779 1818 1.279271 CCGAGTCCTTCAGGGTTTGAT 59.721 52.381 0.00 0.00 35.27 2.57
1895 1937 4.403137 CGTTCACGGGCGGTCGTA 62.403 66.667 0.00 0.00 41.86 3.43
1978 2050 5.599242 TCCCACATATCAATGACAATGCAAT 59.401 36.000 7.17 0.00 36.54 3.56
1994 2069 1.529796 GATGCCGGGTTCCCACATA 59.470 57.895 2.18 0.00 0.00 2.29
2047 2126 2.955660 CCAGTGCAAAAGGAAGTTGGTA 59.044 45.455 0.00 0.00 0.00 3.25
2051 2131 3.826729 GGATACCAGTGCAAAAGGAAGTT 59.173 43.478 7.28 0.00 0.00 2.66
2230 2345 6.183360 CGGATGACATTTGCAAGTTTTATGTG 60.183 38.462 16.36 1.07 30.14 3.21
2231 2346 5.863397 CGGATGACATTTGCAAGTTTTATGT 59.137 36.000 12.36 12.36 32.49 2.29
2344 2462 1.373590 TTTAAATGAGGCCGGAGCGC 61.374 55.000 5.05 0.00 41.24 5.92
2345 2463 0.377203 GTTTAAATGAGGCCGGAGCG 59.623 55.000 5.05 0.00 41.24 5.03
2347 2465 2.159379 GCAAGTTTAAATGAGGCCGGAG 60.159 50.000 5.05 0.00 0.00 4.63
2380 2503 5.359292 GGCAAGAGGAGAAGCATAAAGAAAT 59.641 40.000 0.00 0.00 0.00 2.17
2395 2518 4.211125 TGTTGTTAAACATGGCAAGAGGA 58.789 39.130 0.00 0.00 41.41 3.71


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

AutoCloner maintained by Alex Coulton.