Multiple sequence alignment - TraesCS3D01G347200

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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 TraesCS3D01G347200 chr3D 100.000 4059 0 0 1 4059 458886954 458882896 0.000000e+00 7496.0
1 TraesCS3D01G347200 chr3D 81.437 2505 327 69 1045 3496 549061928 549059509 0.000000e+00 1923.0
2 TraesCS3D01G347200 chr3D 80.115 2268 307 61 1280 3497 549109532 549107359 0.000000e+00 1557.0
3 TraesCS3D01G347200 chr3D 79.588 1891 273 59 1002 2839 548694334 548696164 0.000000e+00 1249.0
4 TraesCS3D01G347200 chr3D 82.574 1360 198 23 996 2338 549349813 549348476 0.000000e+00 1162.0
5 TraesCS3D01G347200 chr3D 93.785 708 42 2 1 706 429087128 429086421 0.000000e+00 1062.0
6 TraesCS3D01G347200 chr3D 81.873 1164 160 33 986 2123 549468029 549466891 0.000000e+00 933.0
7 TraesCS3D01G347200 chr3D 80.030 1342 182 44 995 2278 548725546 548726859 0.000000e+00 915.0
8 TraesCS3D01G347200 chr3D 81.207 1176 169 29 1042 2183 549074044 549072887 0.000000e+00 900.0
9 TraesCS3D01G347200 chr3D 80.236 1103 135 42 2173 3232 549052533 549051471 0.000000e+00 752.0
10 TraesCS3D01G347200 chr3D 80.728 742 94 29 975 1679 549056896 549056167 2.150000e-147 532.0
11 TraesCS3D01G347200 chr3D 79.656 698 92 27 2816 3496 548727328 548727992 1.330000e-124 457.0
12 TraesCS3D01G347200 chr3D 96.759 216 7 0 760 975 569104996 569105211 1.070000e-95 361.0
13 TraesCS3D01G347200 chr3D 83.333 186 14 12 3621 3799 549065823 549065648 5.430000e-34 156.0
14 TraesCS3D01G347200 chr3D 93.684 95 6 0 3496 3590 369404927 369404833 4.230000e-30 143.0
15 TraesCS3D01G347200 chr3D 88.776 98 7 3 3497 3594 184587425 184587518 2.560000e-22 117.0
16 TraesCS3D01G347200 chr3D 87.500 80 8 1 3979 4058 549463011 549462934 1.550000e-14 91.6
17 TraesCS3D01G347200 chr3B 94.456 2940 121 22 1154 4059 605912628 605909697 0.000000e+00 4488.0
18 TraesCS3D01G347200 chr3B 79.008 2420 351 86 1000 3339 727740594 727742936 0.000000e+00 1509.0
19 TraesCS3D01G347200 chr3B 79.173 2007 290 62 1283 3257 728617857 728615947 0.000000e+00 1273.0
20 TraesCS3D01G347200 chr3B 80.151 1456 205 41 1049 2468 728754009 728752602 0.000000e+00 1011.0
21 TraesCS3D01G347200 chr3B 78.553 1175 139 58 2341 3474 728502854 728501752 0.000000e+00 669.0
22 TraesCS3D01G347200 chr3B 81.452 744 117 8 1378 2112 727794138 727794869 1.260000e-164 590.0
23 TraesCS3D01G347200 chr3B 82.095 525 71 17 2889 3404 728888772 728888262 1.040000e-115 427.0
24 TraesCS3D01G347200 chr3B 87.398 246 26 5 3253 3497 728615868 728615627 1.110000e-70 278.0
25 TraesCS3D01G347200 chr3B 82.069 290 44 5 2341 2626 728584572 728584287 1.460000e-59 241.0
26 TraesCS3D01G347200 chr3B 79.624 319 35 18 3201 3497 769431191 769431501 6.880000e-48 202.0
27 TraesCS3D01G347200 chr3B 87.179 156 11 4 1214 1360 727792808 727792963 6.980000e-38 169.0
28 TraesCS3D01G347200 chr3B 76.389 360 57 18 3621 3964 728583342 728582995 6.980000e-38 169.0
29 TraesCS3D01G347200 chr3B 91.089 101 5 3 3494 3594 263260938 263261034 2.550000e-27 134.0
30 TraesCS3D01G347200 chr3B 86.250 80 9 1 3979 4058 728888231 728888154 7.230000e-13 86.1
31 TraesCS3D01G347200 chr3A 95.827 1989 75 4 976 2959 601133994 601132009 0.000000e+00 3206.0
32 TraesCS3D01G347200 chr3A 81.301 2551 334 67 1003 3496 686539264 686536800 0.000000e+00 1936.0
33 TraesCS3D01G347200 chr3A 96.179 1073 33 4 2955 4020 601131968 601130897 0.000000e+00 1748.0
34 TraesCS3D01G347200 chr3A 81.083 1718 247 45 1002 2679 686183074 686184753 0.000000e+00 1301.0
35 TraesCS3D01G347200 chr3A 81.577 1319 197 32 986 2280 686749870 686748574 0.000000e+00 1048.0
36 TraesCS3D01G347200 chr3A 77.814 1866 282 69 1061 2852 686617383 686615576 0.000000e+00 1031.0
37 TraesCS3D01G347200 chr3A 79.835 1334 194 39 995 2275 686189708 686191019 0.000000e+00 904.0
38 TraesCS3D01G347200 chr3A 85.473 888 104 10 2622 3497 686583634 686582760 0.000000e+00 902.0
39 TraesCS3D01G347200 chr3A 85.549 865 93 16 2649 3490 686708925 686708070 0.000000e+00 876.0
40 TraesCS3D01G347200 chr3A 88.472 720 79 4 9 724 693247190 693247909 0.000000e+00 867.0
41 TraesCS3D01G347200 chr3A 80.249 1124 158 41 975 2053 686535376 686534272 0.000000e+00 787.0
42 TraesCS3D01G347200 chr3A 83.491 848 107 23 1808 2644 686549832 686549007 0.000000e+00 760.0
43 TraesCS3D01G347200 chr3A 81.852 810 100 25 975 1756 686551652 686550862 4.420000e-179 638.0
44 TraesCS3D01G347200 chr3A 81.427 813 103 33 2722 3497 686548981 686548180 4.460000e-174 621.0
45 TraesCS3D01G347200 chr3A 78.099 968 121 41 2174 3098 686533975 686533056 2.780000e-146 529.0
46 TraesCS3D01G347200 chr3A 81.696 519 72 13 2342 2847 686748480 686747972 1.050000e-110 411.0
47 TraesCS3D01G347200 chr3A 97.685 216 5 0 760 975 20040432 20040217 4.950000e-99 372.0
48 TraesCS3D01G347200 chr3A 95.789 95 4 0 3496 3590 490614485 490614391 1.950000e-33 154.0
49 TraesCS3D01G347200 chr3A 90.244 82 5 2 3506 3584 635387586 635387505 2.000000e-18 104.0
50 TraesCS3D01G347200 chr3A 84.615 91 14 0 3503 3593 490614398 490614488 1.550000e-14 91.6
51 TraesCS3D01G347200 chr3A 86.250 80 9 1 3979 4058 686747356 686747279 7.230000e-13 86.1
52 TraesCS3D01G347200 chr7B 82.083 1306 185 27 1004 2275 543186975 543188265 0.000000e+00 1070.0
53 TraesCS3D01G347200 chr7B 91.159 690 56 4 42 726 648727949 648728638 0.000000e+00 931.0
54 TraesCS3D01G347200 chr7B 79.495 317 35 20 3203 3497 615100964 615100656 8.900000e-47 198.0
55 TraesCS3D01G347200 chr7B 81.522 184 18 12 3621 3799 650204117 650203945 1.970000e-28 137.0
56 TraesCS3D01G347200 chr7B 95.082 61 3 0 3532 3592 591873493 591873553 3.340000e-16 97.1
57 TraesCS3D01G347200 chr2D 92.995 728 49 2 1 726 287695402 287696129 0.000000e+00 1061.0
58 TraesCS3D01G347200 chr6B 92.022 727 53 2 1 726 463563846 463563124 0.000000e+00 1016.0
59 TraesCS3D01G347200 chr6B 89.306 720 74 3 9 726 77718388 77717670 0.000000e+00 900.0
60 TraesCS3D01G347200 chr6B 81.522 184 18 12 3621 3799 696866924 696866752 1.970000e-28 137.0
61 TraesCS3D01G347200 chr6A 91.690 722 57 2 6 726 509579234 509578515 0.000000e+00 998.0
62 TraesCS3D01G347200 chr6A 81.283 187 19 12 3618 3799 471745675 471745850 1.970000e-28 137.0
63 TraesCS3D01G347200 chr5A 90.659 728 63 4 1 726 136642758 136643482 0.000000e+00 963.0
64 TraesCS3D01G347200 chr5A 89.167 720 76 2 9 726 690342138 690341419 0.000000e+00 896.0
65 TraesCS3D01G347200 chr1A 98.148 216 4 0 760 975 540115629 540115414 1.060000e-100 377.0
66 TraesCS3D01G347200 chr1A 96.759 216 7 0 760 975 466370948 466370733 1.070000e-95 361.0
67 TraesCS3D01G347200 chr5D 97.222 216 6 0 760 975 529820433 529820218 2.310000e-97 366.0
68 TraesCS3D01G347200 chr7D 95.370 216 9 1 760 975 32610159 32609945 3.880000e-90 342.0
69 TraesCS3D01G347200 chr2B 93.427 213 14 0 763 975 69056470 69056258 2.350000e-82 316.0
70 TraesCS3D01G347200 chr7A 92.593 216 16 0 760 975 584385442 584385657 1.100000e-80 311.0
71 TraesCS3D01G347200 chr4B 92.488 213 16 0 763 975 315056154 315055942 5.100000e-79 305.0
72 TraesCS3D01G347200 chrUn 81.522 184 18 12 3621 3799 361109898 361109726 1.970000e-28 137.0
73 TraesCS3D01G347200 chr5B 81.421 183 20 11 3621 3799 332838771 332838599 1.970000e-28 137.0


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 TraesCS3D01G347200 chr3D 458882896 458886954 4058 True 7496.000000 7496 100.000000 1 4059 1 chr3D.!!$R3 4058
1 TraesCS3D01G347200 chr3D 549107359 549109532 2173 True 1557.000000 1557 80.115000 1280 3497 1 chr3D.!!$R5 2217
2 TraesCS3D01G347200 chr3D 548694334 548696164 1830 False 1249.000000 1249 79.588000 1002 2839 1 chr3D.!!$F2 1837
3 TraesCS3D01G347200 chr3D 549348476 549349813 1337 True 1162.000000 1162 82.574000 996 2338 1 chr3D.!!$R6 1342
4 TraesCS3D01G347200 chr3D 429086421 429087128 707 True 1062.000000 1062 93.785000 1 706 1 chr3D.!!$R2 705
5 TraesCS3D01G347200 chr3D 549072887 549074044 1157 True 900.000000 900 81.207000 1042 2183 1 chr3D.!!$R4 1141
6 TraesCS3D01G347200 chr3D 549051471 549065823 14352 True 840.750000 1923 81.433500 975 3799 4 chr3D.!!$R7 2824
7 TraesCS3D01G347200 chr3D 548725546 548727992 2446 False 686.000000 915 79.843000 995 3496 2 chr3D.!!$F4 2501
8 TraesCS3D01G347200 chr3D 549462934 549468029 5095 True 512.300000 933 84.686500 986 4058 2 chr3D.!!$R8 3072
9 TraesCS3D01G347200 chr3B 605909697 605912628 2931 True 4488.000000 4488 94.456000 1154 4059 1 chr3B.!!$R1 2905
10 TraesCS3D01G347200 chr3B 727740594 727742936 2342 False 1509.000000 1509 79.008000 1000 3339 1 chr3B.!!$F2 2339
11 TraesCS3D01G347200 chr3B 728752602 728754009 1407 True 1011.000000 1011 80.151000 1049 2468 1 chr3B.!!$R3 1419
12 TraesCS3D01G347200 chr3B 728615627 728617857 2230 True 775.500000 1273 83.285500 1283 3497 2 chr3B.!!$R5 2214
13 TraesCS3D01G347200 chr3B 728501752 728502854 1102 True 669.000000 669 78.553000 2341 3474 1 chr3B.!!$R2 1133
14 TraesCS3D01G347200 chr3B 727792808 727794869 2061 False 379.500000 590 84.315500 1214 2112 2 chr3B.!!$F4 898
15 TraesCS3D01G347200 chr3B 728888154 728888772 618 True 256.550000 427 84.172500 2889 4058 2 chr3B.!!$R6 1169
16 TraesCS3D01G347200 chr3B 728582995 728584572 1577 True 205.000000 241 79.229000 2341 3964 2 chr3B.!!$R4 1623
17 TraesCS3D01G347200 chr3A 601130897 601133994 3097 True 2477.000000 3206 96.003000 976 4020 2 chr3A.!!$R7 3044
18 TraesCS3D01G347200 chr3A 686183074 686184753 1679 False 1301.000000 1301 81.083000 1002 2679 1 chr3A.!!$F2 1677
19 TraesCS3D01G347200 chr3A 686533056 686539264 6208 True 1084.000000 1936 79.883000 975 3496 3 chr3A.!!$R8 2521
20 TraesCS3D01G347200 chr3A 686615576 686617383 1807 True 1031.000000 1031 77.814000 1061 2852 1 chr3A.!!$R5 1791
21 TraesCS3D01G347200 chr3A 686189708 686191019 1311 False 904.000000 904 79.835000 995 2275 1 chr3A.!!$F3 1280
22 TraesCS3D01G347200 chr3A 686582760 686583634 874 True 902.000000 902 85.473000 2622 3497 1 chr3A.!!$R4 875
23 TraesCS3D01G347200 chr3A 686708070 686708925 855 True 876.000000 876 85.549000 2649 3490 1 chr3A.!!$R6 841
24 TraesCS3D01G347200 chr3A 693247190 693247909 719 False 867.000000 867 88.472000 9 724 1 chr3A.!!$F4 715
25 TraesCS3D01G347200 chr3A 686548180 686551652 3472 True 673.000000 760 82.256667 975 3497 3 chr3A.!!$R9 2522
26 TraesCS3D01G347200 chr3A 686747279 686749870 2591 True 515.033333 1048 83.174333 986 4058 3 chr3A.!!$R10 3072
27 TraesCS3D01G347200 chr7B 543186975 543188265 1290 False 1070.000000 1070 82.083000 1004 2275 1 chr7B.!!$F1 1271
28 TraesCS3D01G347200 chr7B 648727949 648728638 689 False 931.000000 931 91.159000 42 726 1 chr7B.!!$F3 684
29 TraesCS3D01G347200 chr2D 287695402 287696129 727 False 1061.000000 1061 92.995000 1 726 1 chr2D.!!$F1 725
30 TraesCS3D01G347200 chr6B 463563124 463563846 722 True 1016.000000 1016 92.022000 1 726 1 chr6B.!!$R2 725
31 TraesCS3D01G347200 chr6B 77717670 77718388 718 True 900.000000 900 89.306000 9 726 1 chr6B.!!$R1 717
32 TraesCS3D01G347200 chr6A 509578515 509579234 719 True 998.000000 998 91.690000 6 726 1 chr6A.!!$R1 720
33 TraesCS3D01G347200 chr5A 136642758 136643482 724 False 963.000000 963 90.659000 1 726 1 chr5A.!!$F1 725
34 TraesCS3D01G347200 chr5A 690341419 690342138 719 True 896.000000 896 89.167000 9 726 1 chr5A.!!$R1 717

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
828 835 0.114168 TCCCACCAATCAAACAGGGG 59.886 55.0 0.00 0.0 36.92 4.79 F
832 839 0.188342 ACCAATCAAACAGGGGCAGT 59.812 50.0 0.00 0.0 0.00 4.40 F
1871 6976 0.179073 TTATGGAAGAGAGCGCCTGC 60.179 55.0 2.29 0.0 43.24 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 6970 0.169672 CAAACCATCAGAAGCAGGCG 59.830 55.000 0.0 0.0 0.00 5.52 R
2431 10306 2.237143 ACTAGCTAATCACAGCAAGGCA 59.763 45.455 0.0 0.0 44.35 4.75 R
3831 12506 1.597663 GCAAGTATCGTCGGGGAAATG 59.402 52.381 0.0 0.0 0.00 2.32 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
48 49 2.026915 AAACCGCGTGTCGAAATTTC 57.973 45.000 4.92 8.20 41.67 2.17
169 170 5.793817 TCAATGTGTGTGCAACTAGACTAT 58.206 37.500 0.00 0.00 38.04 2.12
326 331 7.706607 TCAATATGTGTGCAACTAGACTACATC 59.293 37.037 0.00 0.00 38.04 3.06
362 367 7.121759 ACCGAGTATATGTGTGTGTAACTAGTT 59.878 37.037 13.68 13.68 38.04 2.24
381 386 8.494016 ACTAGTTCTGCCAACTAAATATCAAC 57.506 34.615 6.77 0.00 32.89 3.18
567 572 6.481954 AGTACTAAAGTTGCACAATACAGC 57.518 37.500 0.00 0.00 0.00 4.40
650 657 4.843728 TGCGGGATCTAGTTTCAAAGATT 58.156 39.130 0.00 0.00 32.60 2.40
653 660 6.882140 TGCGGGATCTAGTTTCAAAGATTTTA 59.118 34.615 0.00 0.00 32.60 1.52
734 741 9.962759 GATATGACTTTTTAAAATCACGTACGT 57.037 29.630 16.72 16.72 0.00 3.57
738 745 8.268052 TGACTTTTTAAAATCACGTACGTACTG 58.732 33.333 22.34 18.25 0.00 2.74
739 746 7.566709 ACTTTTTAAAATCACGTACGTACTGG 58.433 34.615 22.34 14.34 0.00 4.00
740 747 6.464895 TTTTAAAATCACGTACGTACTGGG 57.535 37.500 22.34 16.74 0.00 4.45
741 748 3.940209 AAAATCACGTACGTACTGGGA 57.060 42.857 22.34 20.88 0.00 4.37
742 749 4.460948 AAAATCACGTACGTACTGGGAT 57.539 40.909 22.34 21.98 0.00 3.85
743 750 3.705043 AATCACGTACGTACTGGGATC 57.295 47.619 24.96 2.29 0.00 3.36
744 751 2.408271 TCACGTACGTACTGGGATCT 57.592 50.000 22.34 0.00 0.00 2.75
745 752 3.541996 TCACGTACGTACTGGGATCTA 57.458 47.619 22.34 0.40 0.00 1.98
746 753 3.461061 TCACGTACGTACTGGGATCTAG 58.539 50.000 22.34 4.04 0.00 2.43
748 755 3.624861 CACGTACGTACTGGGATCTAGTT 59.375 47.826 22.34 0.00 0.00 2.24
749 756 4.095483 CACGTACGTACTGGGATCTAGTTT 59.905 45.833 22.34 0.00 0.00 2.66
750 757 4.333926 ACGTACGTACTGGGATCTAGTTTC 59.666 45.833 21.41 0.00 0.00 2.78
751 758 4.333649 CGTACGTACTGGGATCTAGTTTCA 59.666 45.833 22.55 0.00 0.00 2.69
752 759 5.163723 CGTACGTACTGGGATCTAGTTTCAA 60.164 44.000 22.55 0.00 0.00 2.69
753 760 5.733620 ACGTACTGGGATCTAGTTTCAAA 57.266 39.130 8.16 0.00 0.00 2.69
754 761 5.721232 ACGTACTGGGATCTAGTTTCAAAG 58.279 41.667 8.16 0.00 0.00 2.77
755 762 5.479375 ACGTACTGGGATCTAGTTTCAAAGA 59.521 40.000 8.16 0.00 0.00 2.52
756 763 6.154706 ACGTACTGGGATCTAGTTTCAAAGAT 59.845 38.462 8.16 0.00 35.15 2.40
757 764 7.341256 ACGTACTGGGATCTAGTTTCAAAGATA 59.659 37.037 8.16 0.00 32.60 1.98
758 765 8.361139 CGTACTGGGATCTAGTTTCAAAGATAT 58.639 37.037 8.16 0.00 32.60 1.63
759 766 9.482627 GTACTGGGATCTAGTTTCAAAGATATG 57.517 37.037 8.16 0.00 32.60 1.78
760 767 8.324191 ACTGGGATCTAGTTTCAAAGATATGA 57.676 34.615 0.00 0.00 32.60 2.15
761 768 8.207545 ACTGGGATCTAGTTTCAAAGATATGAC 58.792 37.037 0.00 0.00 32.60 3.06
762 769 7.509546 TGGGATCTAGTTTCAAAGATATGACC 58.490 38.462 0.00 0.00 32.60 4.02
764 771 8.214364 GGGATCTAGTTTCAAAGATATGACCTT 58.786 37.037 0.00 0.00 32.60 3.50
767 774 8.792830 TCTAGTTTCAAAGATATGACCTTTGG 57.207 34.615 13.51 0.00 46.25 3.28
768 775 8.383175 TCTAGTTTCAAAGATATGACCTTTGGT 58.617 33.333 13.51 0.00 46.25 3.67
770 777 8.934023 AGTTTCAAAGATATGACCTTTGGTTA 57.066 30.769 13.51 0.00 46.25 2.85
771 778 9.014297 AGTTTCAAAGATATGACCTTTGGTTAG 57.986 33.333 13.51 0.00 46.25 2.34
772 779 7.391148 TTCAAAGATATGACCTTTGGTTAGC 57.609 36.000 13.51 0.00 46.25 3.09
773 780 6.721318 TCAAAGATATGACCTTTGGTTAGCT 58.279 36.000 13.51 0.00 46.25 3.32
774 781 6.599244 TCAAAGATATGACCTTTGGTTAGCTG 59.401 38.462 13.51 0.00 46.25 4.24
775 782 5.957771 AGATATGACCTTTGGTTAGCTGA 57.042 39.130 0.00 0.00 35.25 4.26
777 784 5.426833 AGATATGACCTTTGGTTAGCTGAGT 59.573 40.000 0.00 0.00 35.25 3.41
778 785 6.611642 AGATATGACCTTTGGTTAGCTGAGTA 59.388 38.462 0.00 0.00 35.25 2.59
781 788 2.631545 ACCTTTGGTTAGCTGAGTACGT 59.368 45.455 0.00 0.00 27.29 3.57
782 789 3.828451 ACCTTTGGTTAGCTGAGTACGTA 59.172 43.478 0.00 0.00 27.29 3.57
783 790 4.171754 CCTTTGGTTAGCTGAGTACGTAC 58.828 47.826 18.10 18.10 0.00 3.67
784 791 3.476295 TTGGTTAGCTGAGTACGTACG 57.524 47.619 19.49 15.01 0.00 3.67
785 792 2.426522 TGGTTAGCTGAGTACGTACGT 58.573 47.619 25.98 25.98 0.00 3.57
786 793 2.160219 TGGTTAGCTGAGTACGTACGTG 59.840 50.000 30.25 14.38 0.00 4.49
787 794 2.416547 GGTTAGCTGAGTACGTACGTGA 59.583 50.000 30.25 11.87 0.00 4.35
789 796 1.085091 AGCTGAGTACGTACGTGAGG 58.915 55.000 30.25 15.68 0.00 3.86
790 797 1.081892 GCTGAGTACGTACGTGAGGA 58.918 55.000 30.25 7.93 0.00 3.71
791 798 1.466167 GCTGAGTACGTACGTGAGGAA 59.534 52.381 30.25 7.51 0.00 3.36
792 799 2.475852 GCTGAGTACGTACGTGAGGAAG 60.476 54.545 30.25 19.89 0.00 3.46
793 800 2.079158 TGAGTACGTACGTGAGGAAGG 58.921 52.381 30.25 0.00 0.00 3.46
794 801 0.807496 AGTACGTACGTGAGGAAGGC 59.193 55.000 30.25 9.84 0.00 4.35
795 802 0.523072 GTACGTACGTGAGGAAGGCA 59.477 55.000 30.25 4.26 0.00 4.75
796 803 1.133790 GTACGTACGTGAGGAAGGCAT 59.866 52.381 30.25 1.29 0.00 4.40
797 804 0.606604 ACGTACGTGAGGAAGGCATT 59.393 50.000 22.14 0.00 0.00 3.56
798 805 1.278238 CGTACGTGAGGAAGGCATTC 58.722 55.000 7.22 1.60 34.46 2.67
799 806 1.135083 CGTACGTGAGGAAGGCATTCT 60.135 52.381 11.37 0.00 35.63 2.40
801 808 0.250513 ACGTGAGGAAGGCATTCTCC 59.749 55.000 11.37 3.90 35.63 3.71
802 809 0.539051 CGTGAGGAAGGCATTCTCCT 59.461 55.000 11.37 0.37 38.31 3.69
803 810 1.741732 CGTGAGGAAGGCATTCTCCTG 60.742 57.143 11.37 0.00 36.38 3.86
812 819 1.902938 GCATTCTCCTGCCTAATCCC 58.097 55.000 0.00 0.00 36.10 3.85
815 822 1.213296 TTCTCCTGCCTAATCCCACC 58.787 55.000 0.00 0.00 0.00 4.61
818 825 1.496429 CTCCTGCCTAATCCCACCAAT 59.504 52.381 0.00 0.00 0.00 3.16
819 826 1.494721 TCCTGCCTAATCCCACCAATC 59.505 52.381 0.00 0.00 0.00 2.67
822 829 3.364549 CTGCCTAATCCCACCAATCAAA 58.635 45.455 0.00 0.00 0.00 2.69
823 830 3.096092 TGCCTAATCCCACCAATCAAAC 58.904 45.455 0.00 0.00 0.00 2.93
824 831 3.096092 GCCTAATCCCACCAATCAAACA 58.904 45.455 0.00 0.00 0.00 2.83
825 832 3.131046 GCCTAATCCCACCAATCAAACAG 59.869 47.826 0.00 0.00 0.00 3.16
826 833 3.701040 CCTAATCCCACCAATCAAACAGG 59.299 47.826 0.00 0.00 0.00 4.00
828 835 0.114168 TCCCACCAATCAAACAGGGG 59.886 55.000 0.00 0.00 36.92 4.79
829 836 1.543944 CCCACCAATCAAACAGGGGC 61.544 60.000 0.00 0.00 32.59 5.80
830 837 0.831288 CCACCAATCAAACAGGGGCA 60.831 55.000 0.00 0.00 0.00 5.36
831 838 0.604578 CACCAATCAAACAGGGGCAG 59.395 55.000 0.00 0.00 0.00 4.85
832 839 0.188342 ACCAATCAAACAGGGGCAGT 59.812 50.000 0.00 0.00 0.00 4.40
833 840 1.341080 CCAATCAAACAGGGGCAGTT 58.659 50.000 0.00 0.00 0.00 3.16
834 841 2.158385 ACCAATCAAACAGGGGCAGTTA 60.158 45.455 0.00 0.00 0.00 2.24
836 843 3.306019 CCAATCAAACAGGGGCAGTTAAC 60.306 47.826 0.00 0.00 0.00 2.01
837 844 3.525800 ATCAAACAGGGGCAGTTAACT 57.474 42.857 1.12 1.12 0.00 2.24
838 845 2.858745 TCAAACAGGGGCAGTTAACTC 58.141 47.619 4.77 0.93 0.00 3.01
839 846 1.886542 CAAACAGGGGCAGTTAACTCC 59.113 52.381 4.77 10.00 0.00 3.85
840 847 0.404426 AACAGGGGCAGTTAACTCCC 59.596 55.000 24.24 24.24 39.67 4.30
842 849 0.253327 CAGGGGCAGTTAACTCCCTC 59.747 60.000 25.30 18.28 46.12 4.30
844 851 0.992695 GGGGCAGTTAACTCCCTCTT 59.007 55.000 27.89 0.40 39.95 2.85
845 852 2.193993 GGGGCAGTTAACTCCCTCTTA 58.806 52.381 27.89 0.00 39.95 2.10
847 854 3.009805 GGGGCAGTTAACTCCCTCTTAAA 59.990 47.826 27.89 0.00 39.95 1.52
848 855 4.507869 GGGGCAGTTAACTCCCTCTTAAAA 60.508 45.833 27.89 0.00 39.95 1.52
851 858 5.357314 GGCAGTTAACTCCCTCTTAAAATCC 59.643 44.000 8.45 0.00 0.00 3.01
852 859 5.357314 GCAGTTAACTCCCTCTTAAAATCCC 59.643 44.000 4.77 0.00 0.00 3.85
853 860 6.481643 CAGTTAACTCCCTCTTAAAATCCCA 58.518 40.000 4.77 0.00 0.00 4.37
854 861 6.374613 CAGTTAACTCCCTCTTAAAATCCCAC 59.625 42.308 4.77 0.00 0.00 4.61
855 862 6.274908 AGTTAACTCCCTCTTAAAATCCCACT 59.725 38.462 1.12 0.00 0.00 4.00
856 863 5.600669 AACTCCCTCTTAAAATCCCACTT 57.399 39.130 0.00 0.00 0.00 3.16
857 864 5.180810 ACTCCCTCTTAAAATCCCACTTC 57.819 43.478 0.00 0.00 0.00 3.01
858 865 4.852697 ACTCCCTCTTAAAATCCCACTTCT 59.147 41.667 0.00 0.00 0.00 2.85
859 866 6.030082 ACTCCCTCTTAAAATCCCACTTCTA 58.970 40.000 0.00 0.00 0.00 2.10
860 867 6.504279 ACTCCCTCTTAAAATCCCACTTCTAA 59.496 38.462 0.00 0.00 0.00 2.10
862 869 7.939781 TCCCTCTTAAAATCCCACTTCTAATT 58.060 34.615 0.00 0.00 0.00 1.40
864 871 7.416777 CCCTCTTAAAATCCCACTTCTAATTGC 60.417 40.741 0.00 0.00 0.00 3.56
865 872 7.404671 TCTTAAAATCCCACTTCTAATTGCC 57.595 36.000 0.00 0.00 0.00 4.52
866 873 7.182060 TCTTAAAATCCCACTTCTAATTGCCT 58.818 34.615 0.00 0.00 0.00 4.75
867 874 7.673926 TCTTAAAATCCCACTTCTAATTGCCTT 59.326 33.333 0.00 0.00 0.00 4.35
868 875 5.921962 AAATCCCACTTCTAATTGCCTTC 57.078 39.130 0.00 0.00 0.00 3.46
869 876 4.591321 ATCCCACTTCTAATTGCCTTCA 57.409 40.909 0.00 0.00 0.00 3.02
870 877 3.686016 TCCCACTTCTAATTGCCTTCAC 58.314 45.455 0.00 0.00 0.00 3.18
871 878 3.073798 TCCCACTTCTAATTGCCTTCACA 59.926 43.478 0.00 0.00 0.00 3.58
872 879 4.019174 CCCACTTCTAATTGCCTTCACAT 58.981 43.478 0.00 0.00 0.00 3.21
873 880 4.142315 CCCACTTCTAATTGCCTTCACATG 60.142 45.833 0.00 0.00 0.00 3.21
874 881 4.418392 CACTTCTAATTGCCTTCACATGC 58.582 43.478 0.00 0.00 0.00 4.06
875 882 4.157289 CACTTCTAATTGCCTTCACATGCT 59.843 41.667 0.00 0.00 0.00 3.79
877 884 5.945784 ACTTCTAATTGCCTTCACATGCTAA 59.054 36.000 0.00 0.00 0.00 3.09
878 885 6.434028 ACTTCTAATTGCCTTCACATGCTAAA 59.566 34.615 0.00 0.00 0.00 1.85
879 886 6.194796 TCTAATTGCCTTCACATGCTAAAC 57.805 37.500 0.00 0.00 0.00 2.01
880 887 4.870123 AATTGCCTTCACATGCTAAACA 57.130 36.364 0.00 0.00 0.00 2.83
881 888 3.921119 TTGCCTTCACATGCTAAACAG 57.079 42.857 0.00 0.00 0.00 3.16
882 889 3.138884 TGCCTTCACATGCTAAACAGA 57.861 42.857 0.00 0.00 0.00 3.41
883 890 3.076621 TGCCTTCACATGCTAAACAGAG 58.923 45.455 0.00 0.00 0.00 3.35
884 891 2.421424 GCCTTCACATGCTAAACAGAGG 59.579 50.000 0.00 0.00 0.00 3.69
886 893 4.326826 CCTTCACATGCTAAACAGAGGAA 58.673 43.478 0.00 0.00 0.00 3.36
887 894 4.946157 CCTTCACATGCTAAACAGAGGAAT 59.054 41.667 0.00 0.00 0.00 3.01
888 895 5.163683 CCTTCACATGCTAAACAGAGGAATG 60.164 44.000 0.00 0.00 0.00 2.67
890 897 3.379372 CACATGCTAAACAGAGGAATGGG 59.621 47.826 0.00 0.00 0.00 4.00
891 898 3.266772 ACATGCTAAACAGAGGAATGGGA 59.733 43.478 0.00 0.00 0.00 4.37
892 899 3.350219 TGCTAAACAGAGGAATGGGAC 57.650 47.619 0.00 0.00 0.00 4.46
893 900 2.912956 TGCTAAACAGAGGAATGGGACT 59.087 45.455 0.00 0.00 0.00 3.85
895 902 4.534500 TGCTAAACAGAGGAATGGGACTTA 59.466 41.667 0.00 0.00 0.00 2.24
897 904 4.993705 AAACAGAGGAATGGGACTTACA 57.006 40.909 0.00 0.00 0.00 2.41
899 906 5.520748 AACAGAGGAATGGGACTTACAAT 57.479 39.130 0.00 0.00 0.00 2.71
900 907 5.104259 ACAGAGGAATGGGACTTACAATC 57.896 43.478 0.00 0.00 0.00 2.67
901 908 4.536090 ACAGAGGAATGGGACTTACAATCA 59.464 41.667 0.00 0.00 0.00 2.57
904 911 6.604795 CAGAGGAATGGGACTTACAATCAATT 59.395 38.462 0.00 0.00 0.00 2.32
906 913 7.340487 AGAGGAATGGGACTTACAATCAATTTC 59.660 37.037 0.00 0.00 0.00 2.17
907 914 6.381133 AGGAATGGGACTTACAATCAATTTCC 59.619 38.462 0.00 0.00 0.00 3.13
908 915 6.406961 GGAATGGGACTTACAATCAATTTCCC 60.407 42.308 0.00 0.00 35.56 3.97
909 916 5.004361 TGGGACTTACAATCAATTTCCCA 57.996 39.130 4.90 4.90 41.99 4.37
911 918 5.421693 TGGGACTTACAATCAATTTCCCATG 59.578 40.000 4.90 0.00 39.67 3.66
912 919 5.422012 GGGACTTACAATCAATTTCCCATGT 59.578 40.000 0.00 0.00 35.13 3.21
913 920 6.405842 GGGACTTACAATCAATTTCCCATGTC 60.406 42.308 0.00 0.00 35.13 3.06
914 921 6.378280 GGACTTACAATCAATTTCCCATGTCT 59.622 38.462 0.00 0.00 0.00 3.41
915 922 7.556275 GGACTTACAATCAATTTCCCATGTCTA 59.444 37.037 0.00 0.00 0.00 2.59
916 923 8.877864 ACTTACAATCAATTTCCCATGTCTAA 57.122 30.769 0.00 0.00 0.00 2.10
917 924 9.479549 ACTTACAATCAATTTCCCATGTCTAAT 57.520 29.630 0.00 0.00 0.00 1.73
918 925 9.956720 CTTACAATCAATTTCCCATGTCTAATC 57.043 33.333 0.00 0.00 0.00 1.75
919 926 7.352079 ACAATCAATTTCCCATGTCTAATCC 57.648 36.000 0.00 0.00 0.00 3.01
920 927 6.324770 ACAATCAATTTCCCATGTCTAATCCC 59.675 38.462 0.00 0.00 0.00 3.85
921 928 5.732331 TCAATTTCCCATGTCTAATCCCT 57.268 39.130 0.00 0.00 0.00 4.20
922 929 6.091076 TCAATTTCCCATGTCTAATCCCTT 57.909 37.500 0.00 0.00 0.00 3.95
923 930 5.893255 TCAATTTCCCATGTCTAATCCCTTG 59.107 40.000 0.00 0.00 0.00 3.61
924 931 3.951563 TTCCCATGTCTAATCCCTTGG 57.048 47.619 0.00 0.00 0.00 3.61
926 933 1.215173 CCCATGTCTAATCCCTTGGCA 59.785 52.381 0.00 0.00 0.00 4.92
927 934 2.358090 CCCATGTCTAATCCCTTGGCAA 60.358 50.000 0.00 0.00 0.00 4.52
928 935 3.364549 CCATGTCTAATCCCTTGGCAAA 58.635 45.455 0.00 0.00 0.00 3.68
929 936 3.131046 CCATGTCTAATCCCTTGGCAAAC 59.869 47.826 0.00 0.00 0.00 2.93
931 938 3.686016 TGTCTAATCCCTTGGCAAACTC 58.314 45.455 0.00 0.00 0.00 3.01
932 939 3.017442 GTCTAATCCCTTGGCAAACTCC 58.983 50.000 0.00 0.00 0.00 3.85
933 940 2.025321 TCTAATCCCTTGGCAAACTCCC 60.025 50.000 0.00 0.00 0.00 4.30
934 941 0.486879 AATCCCTTGGCAAACTCCCA 59.513 50.000 0.00 0.00 0.00 4.37
938 945 1.467920 CCTTGGCAAACTCCCATCTC 58.532 55.000 0.00 0.00 31.26 2.75
939 946 1.005215 CCTTGGCAAACTCCCATCTCT 59.995 52.381 0.00 0.00 31.26 3.10
940 947 2.239654 CCTTGGCAAACTCCCATCTCTA 59.760 50.000 0.00 0.00 31.26 2.43
942 949 4.335416 CTTGGCAAACTCCCATCTCTAAA 58.665 43.478 0.00 0.00 31.26 1.85
945 952 3.942115 GGCAAACTCCCATCTCTAAACTC 59.058 47.826 0.00 0.00 0.00 3.01
946 953 3.942115 GCAAACTCCCATCTCTAAACTCC 59.058 47.826 0.00 0.00 0.00 3.85
947 954 4.518249 CAAACTCCCATCTCTAAACTCCC 58.482 47.826 0.00 0.00 0.00 4.30
948 955 3.491766 ACTCCCATCTCTAAACTCCCA 57.508 47.619 0.00 0.00 0.00 4.37
950 957 4.375313 ACTCCCATCTCTAAACTCCCATT 58.625 43.478 0.00 0.00 0.00 3.16
951 958 4.410555 ACTCCCATCTCTAAACTCCCATTC 59.589 45.833 0.00 0.00 0.00 2.67
952 959 3.716872 TCCCATCTCTAAACTCCCATTCC 59.283 47.826 0.00 0.00 0.00 3.01
954 961 3.718956 CCATCTCTAAACTCCCATTCCCT 59.281 47.826 0.00 0.00 0.00 4.20
955 962 4.202409 CCATCTCTAAACTCCCATTCCCTC 60.202 50.000 0.00 0.00 0.00 4.30
956 963 4.354208 TCTCTAAACTCCCATTCCCTCT 57.646 45.455 0.00 0.00 0.00 3.69
957 964 4.290942 TCTCTAAACTCCCATTCCCTCTC 58.709 47.826 0.00 0.00 0.00 3.20
958 965 3.385115 TCTAAACTCCCATTCCCTCTCC 58.615 50.000 0.00 0.00 0.00 3.71
959 966 1.299939 AAACTCCCATTCCCTCTCCC 58.700 55.000 0.00 0.00 0.00 4.30
960 967 0.423544 AACTCCCATTCCCTCTCCCT 59.576 55.000 0.00 0.00 0.00 4.20
961 968 0.327000 ACTCCCATTCCCTCTCCCTG 60.327 60.000 0.00 0.00 0.00 4.45
962 969 0.327000 CTCCCATTCCCTCTCCCTGT 60.327 60.000 0.00 0.00 0.00 4.00
965 972 2.021042 TCCCATTCCCTCTCCCTGTTAT 60.021 50.000 0.00 0.00 0.00 1.89
966 973 2.785857 CCCATTCCCTCTCCCTGTTATT 59.214 50.000 0.00 0.00 0.00 1.40
967 974 3.980698 CCCATTCCCTCTCCCTGTTATTA 59.019 47.826 0.00 0.00 0.00 0.98
968 975 4.202472 CCCATTCCCTCTCCCTGTTATTAC 60.202 50.000 0.00 0.00 0.00 1.89
970 977 5.844516 CCATTCCCTCTCCCTGTTATTACTA 59.155 44.000 0.00 0.00 0.00 1.82
971 978 6.329197 CCATTCCCTCTCCCTGTTATTACTAA 59.671 42.308 0.00 0.00 0.00 2.24
972 979 7.147373 CCATTCCCTCTCCCTGTTATTACTAAA 60.147 40.741 0.00 0.00 0.00 1.85
973 980 6.803366 TCCCTCTCCCTGTTATTACTAAAC 57.197 41.667 0.00 0.00 0.00 2.01
1822 6927 3.365265 GTGGTGGGCTTGGCTTCG 61.365 66.667 0.00 0.00 0.00 3.79
1871 6976 0.179073 TTATGGAAGAGAGCGCCTGC 60.179 55.000 2.29 0.00 43.24 4.85
2124 7238 1.599542 GCAGGTAATAGCAAGCCTTCG 59.400 52.381 0.00 0.00 0.00 3.79
2191 10007 2.949714 AGTTGCTCAAACGAATGTCG 57.050 45.000 0.00 0.00 46.93 4.35
2431 10306 8.567948 CAATAGTTATTTGTCACTTGTGGAAGT 58.432 33.333 0.64 0.00 43.63 3.01
2532 10410 9.039870 CAGTTTTTGGTTTTGCATGTCTTAATA 57.960 29.630 0.00 0.00 0.00 0.98
2548 10426 1.136828 AATATGCCCCGCTTGGTCTA 58.863 50.000 0.00 0.00 0.00 2.59
2583 10461 9.231297 TCAAGTTTACCAAAGATGATTTCTAGG 57.769 33.333 0.00 0.00 36.38 3.02
2719 10699 5.423704 TGAGACCCAAACAACCGAATATA 57.576 39.130 0.00 0.00 0.00 0.86
2894 10926 4.636249 AGCTCAGTGTTACTTTTCTCAGG 58.364 43.478 0.00 0.00 0.00 3.86
3012 11098 5.770417 ACTTATTATGCTCGTAGGTACTGC 58.230 41.667 0.00 0.00 41.52 4.40
3189 11303 2.792947 GCATGGGCTTGGCTGATGG 61.793 63.158 0.00 0.00 36.96 3.51
3399 11638 7.118971 AGTCAATTTCTCAACTTGATCACTAGC 59.881 37.037 0.00 0.00 32.05 3.42
3510 11752 6.259608 CGATATTATATACTCCTTCCGTCCGT 59.740 42.308 0.00 0.00 0.00 4.69
3526 11768 2.601763 GTCCGTAATTAACTGTCGCTGG 59.398 50.000 0.00 0.00 0.00 4.85
3580 11835 0.643820 GCGACAGTTAATTCCGGACG 59.356 55.000 1.83 1.53 0.00 4.79
3652 11907 4.272991 GGCATAAAGCTCTGATCTGACTTG 59.727 45.833 13.85 7.51 44.79 3.16
3893 12573 6.415280 CGTGATATTCTAGACAGTTGCAGTAC 59.585 42.308 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 170 2.046796 TCAGTTGGCGCGGCAATA 60.047 55.556 43.73 30.63 0.00 1.90
338 343 8.396390 AGAACTAGTTACACACACATATACTCG 58.604 37.037 8.42 0.00 0.00 4.18
362 367 5.121611 CACACGTTGATATTTAGTTGGCAGA 59.878 40.000 0.00 0.00 0.00 4.26
381 386 3.007979 TGTAGTCTAGTTGCACACACG 57.992 47.619 0.00 0.00 0.00 4.49
567 572 6.260714 TGGTGCTATATGATGCAACTTTAGTG 59.739 38.462 13.60 0.00 46.08 2.74
650 657 3.002791 CTGCTGGAACTCTTGCGATAAA 58.997 45.455 0.00 0.00 0.00 1.40
653 660 0.322975 ACTGCTGGAACTCTTGCGAT 59.677 50.000 0.00 0.00 0.00 4.58
695 702 2.936498 AGTCATATCTTTCAAACCGCGG 59.064 45.455 26.86 26.86 0.00 6.46
726 733 3.201290 ACTAGATCCCAGTACGTACGTG 58.799 50.000 30.25 13.99 0.00 4.49
727 734 3.550437 ACTAGATCCCAGTACGTACGT 57.450 47.619 25.98 25.98 0.00 3.57
728 735 4.333649 TGAAACTAGATCCCAGTACGTACG 59.666 45.833 19.49 15.01 0.00 3.67
729 736 5.824904 TGAAACTAGATCCCAGTACGTAC 57.175 43.478 18.10 18.10 0.00 3.67
730 737 6.660521 TCTTTGAAACTAGATCCCAGTACGTA 59.339 38.462 0.00 0.00 0.00 3.57
732 739 5.962433 TCTTTGAAACTAGATCCCAGTACG 58.038 41.667 0.00 0.00 0.00 3.67
733 740 9.482627 CATATCTTTGAAACTAGATCCCAGTAC 57.517 37.037 0.00 0.00 33.38 2.73
734 741 9.434275 TCATATCTTTGAAACTAGATCCCAGTA 57.566 33.333 0.00 0.00 33.38 2.74
735 742 8.207545 GTCATATCTTTGAAACTAGATCCCAGT 58.792 37.037 0.00 0.00 33.38 4.00
736 743 7.659390 GGTCATATCTTTGAAACTAGATCCCAG 59.341 40.741 0.00 0.00 33.38 4.45
738 745 7.740805 AGGTCATATCTTTGAAACTAGATCCC 58.259 38.462 0.00 0.00 33.38 3.85
739 746 9.620259 AAAGGTCATATCTTTGAAACTAGATCC 57.380 33.333 0.00 0.00 33.68 3.36
750 757 6.599244 TCAGCTAACCAAAGGTCATATCTTTG 59.401 38.462 5.80 5.80 46.22 2.77
751 758 6.721318 TCAGCTAACCAAAGGTCATATCTTT 58.279 36.000 0.00 0.00 33.12 2.52
752 759 6.069963 ACTCAGCTAACCAAAGGTCATATCTT 60.070 38.462 0.00 0.00 33.12 2.40
753 760 5.426833 ACTCAGCTAACCAAAGGTCATATCT 59.573 40.000 0.00 0.00 33.12 1.98
754 761 5.675538 ACTCAGCTAACCAAAGGTCATATC 58.324 41.667 0.00 0.00 33.12 1.63
755 762 5.700402 ACTCAGCTAACCAAAGGTCATAT 57.300 39.130 0.00 0.00 33.12 1.78
756 763 5.393787 CGTACTCAGCTAACCAAAGGTCATA 60.394 44.000 0.00 0.00 33.12 2.15
757 764 4.620803 CGTACTCAGCTAACCAAAGGTCAT 60.621 45.833 0.00 0.00 33.12 3.06
758 765 3.305813 CGTACTCAGCTAACCAAAGGTCA 60.306 47.826 0.00 0.00 33.12 4.02
759 766 3.251571 CGTACTCAGCTAACCAAAGGTC 58.748 50.000 0.00 0.00 33.12 3.85
760 767 2.631545 ACGTACTCAGCTAACCAAAGGT 59.368 45.455 0.00 0.00 37.65 3.50
761 768 3.314541 ACGTACTCAGCTAACCAAAGG 57.685 47.619 0.00 0.00 0.00 3.11
762 769 3.850273 CGTACGTACTCAGCTAACCAAAG 59.150 47.826 22.55 0.00 0.00 2.77
764 771 2.813754 ACGTACGTACTCAGCTAACCAA 59.186 45.455 21.41 0.00 0.00 3.67
766 773 2.416547 TCACGTACGTACTCAGCTAACC 59.583 50.000 22.34 0.00 0.00 2.85
767 774 3.484886 CCTCACGTACGTACTCAGCTAAC 60.485 52.174 22.34 0.00 0.00 2.34
768 775 2.674852 CCTCACGTACGTACTCAGCTAA 59.325 50.000 22.34 1.73 0.00 3.09
770 777 1.085091 CCTCACGTACGTACTCAGCT 58.915 55.000 22.34 0.00 0.00 4.24
771 778 1.081892 TCCTCACGTACGTACTCAGC 58.918 55.000 22.34 0.00 0.00 4.26
772 779 2.095532 CCTTCCTCACGTACGTACTCAG 59.904 54.545 22.34 13.74 0.00 3.35
773 780 2.079158 CCTTCCTCACGTACGTACTCA 58.921 52.381 22.34 2.75 0.00 3.41
774 781 1.202121 GCCTTCCTCACGTACGTACTC 60.202 57.143 22.34 0.00 0.00 2.59
775 782 0.807496 GCCTTCCTCACGTACGTACT 59.193 55.000 22.34 7.87 0.00 2.73
777 784 1.466856 ATGCCTTCCTCACGTACGTA 58.533 50.000 22.34 1.84 0.00 3.57
778 785 0.606604 AATGCCTTCCTCACGTACGT 59.393 50.000 16.72 16.72 0.00 3.57
781 788 1.480954 GGAGAATGCCTTCCTCACGTA 59.519 52.381 0.00 0.00 31.27 3.57
782 789 0.250513 GGAGAATGCCTTCCTCACGT 59.749 55.000 0.00 0.00 31.27 4.49
783 790 0.539051 AGGAGAATGCCTTCCTCACG 59.461 55.000 0.00 0.00 33.46 4.35
784 791 2.016096 GCAGGAGAATGCCTTCCTCAC 61.016 57.143 0.00 0.00 40.43 3.51
785 792 0.254178 GCAGGAGAATGCCTTCCTCA 59.746 55.000 0.00 0.00 40.43 3.86
786 793 3.092851 GCAGGAGAATGCCTTCCTC 57.907 57.895 0.00 0.00 40.43 3.71
793 800 1.143684 TGGGATTAGGCAGGAGAATGC 59.856 52.381 0.00 0.00 45.74 3.56
794 801 2.487986 GGTGGGATTAGGCAGGAGAATG 60.488 54.545 0.00 0.00 0.00 2.67
795 802 1.777272 GGTGGGATTAGGCAGGAGAAT 59.223 52.381 0.00 0.00 0.00 2.40
796 803 1.213296 GGTGGGATTAGGCAGGAGAA 58.787 55.000 0.00 0.00 0.00 2.87
797 804 0.044092 TGGTGGGATTAGGCAGGAGA 59.956 55.000 0.00 0.00 0.00 3.71
798 805 0.918983 TTGGTGGGATTAGGCAGGAG 59.081 55.000 0.00 0.00 0.00 3.69
799 806 1.494721 GATTGGTGGGATTAGGCAGGA 59.505 52.381 0.00 0.00 0.00 3.86
801 808 2.734755 TGATTGGTGGGATTAGGCAG 57.265 50.000 0.00 0.00 0.00 4.85
802 809 3.096092 GTTTGATTGGTGGGATTAGGCA 58.904 45.455 0.00 0.00 0.00 4.75
803 810 3.096092 TGTTTGATTGGTGGGATTAGGC 58.904 45.455 0.00 0.00 0.00 3.93
806 813 3.565449 CCCCTGTTTGATTGGTGGGATTA 60.565 47.826 0.00 0.00 36.90 1.75
809 816 0.114168 CCCCTGTTTGATTGGTGGGA 59.886 55.000 0.00 0.00 36.90 4.37
811 818 0.831288 TGCCCCTGTTTGATTGGTGG 60.831 55.000 0.00 0.00 0.00 4.61
812 819 0.604578 CTGCCCCTGTTTGATTGGTG 59.395 55.000 0.00 0.00 0.00 4.17
815 822 3.573967 AGTTAACTGCCCCTGTTTGATTG 59.426 43.478 7.48 0.00 0.00 2.67
818 825 2.488347 GGAGTTAACTGCCCCTGTTTGA 60.488 50.000 14.14 0.00 0.00 2.69
819 826 1.886542 GGAGTTAACTGCCCCTGTTTG 59.113 52.381 14.14 0.00 0.00 2.93
828 835 5.357314 GGGATTTTAAGAGGGAGTTAACTGC 59.643 44.000 18.07 18.07 0.00 4.40
829 836 6.374613 GTGGGATTTTAAGAGGGAGTTAACTG 59.625 42.308 14.14 0.00 0.00 3.16
830 837 6.274908 AGTGGGATTTTAAGAGGGAGTTAACT 59.725 38.462 8.13 8.13 0.00 2.24
831 838 6.482524 AGTGGGATTTTAAGAGGGAGTTAAC 58.517 40.000 0.00 0.00 0.00 2.01
832 839 6.713731 AGTGGGATTTTAAGAGGGAGTTAA 57.286 37.500 0.00 0.00 0.00 2.01
833 840 6.504279 AGAAGTGGGATTTTAAGAGGGAGTTA 59.496 38.462 0.00 0.00 0.00 2.24
834 841 5.313506 AGAAGTGGGATTTTAAGAGGGAGTT 59.686 40.000 0.00 0.00 0.00 3.01
836 843 5.443230 AGAAGTGGGATTTTAAGAGGGAG 57.557 43.478 0.00 0.00 0.00 4.30
837 844 6.963117 TTAGAAGTGGGATTTTAAGAGGGA 57.037 37.500 0.00 0.00 0.00 4.20
838 845 7.416777 GCAATTAGAAGTGGGATTTTAAGAGGG 60.417 40.741 0.00 0.00 0.00 4.30
839 846 7.416777 GGCAATTAGAAGTGGGATTTTAAGAGG 60.417 40.741 0.00 0.00 0.00 3.69
840 847 7.340487 AGGCAATTAGAAGTGGGATTTTAAGAG 59.660 37.037 0.00 0.00 0.00 2.85
841 848 7.182060 AGGCAATTAGAAGTGGGATTTTAAGA 58.818 34.615 0.00 0.00 0.00 2.10
842 849 7.410120 AGGCAATTAGAAGTGGGATTTTAAG 57.590 36.000 0.00 0.00 0.00 1.85
844 851 6.951198 TGAAGGCAATTAGAAGTGGGATTTTA 59.049 34.615 0.00 0.00 0.00 1.52
845 852 5.779771 TGAAGGCAATTAGAAGTGGGATTTT 59.220 36.000 0.00 0.00 0.00 1.82
847 854 4.706962 GTGAAGGCAATTAGAAGTGGGATT 59.293 41.667 0.00 0.00 0.00 3.01
848 855 4.263905 TGTGAAGGCAATTAGAAGTGGGAT 60.264 41.667 0.00 0.00 0.00 3.85
851 858 4.676196 GCATGTGAAGGCAATTAGAAGTGG 60.676 45.833 0.00 0.00 0.00 4.00
852 859 4.157289 AGCATGTGAAGGCAATTAGAAGTG 59.843 41.667 0.00 0.00 0.00 3.16
853 860 4.338879 AGCATGTGAAGGCAATTAGAAGT 58.661 39.130 0.00 0.00 0.00 3.01
854 861 4.978083 AGCATGTGAAGGCAATTAGAAG 57.022 40.909 0.00 0.00 0.00 2.85
855 862 6.208402 TGTTTAGCATGTGAAGGCAATTAGAA 59.792 34.615 0.00 0.00 0.00 2.10
856 863 5.709631 TGTTTAGCATGTGAAGGCAATTAGA 59.290 36.000 0.00 0.00 0.00 2.10
857 864 5.953183 TGTTTAGCATGTGAAGGCAATTAG 58.047 37.500 0.00 0.00 0.00 1.73
858 865 5.709631 TCTGTTTAGCATGTGAAGGCAATTA 59.290 36.000 0.00 0.00 0.00 1.40
859 866 4.523943 TCTGTTTAGCATGTGAAGGCAATT 59.476 37.500 0.00 0.00 0.00 2.32
860 867 4.081406 TCTGTTTAGCATGTGAAGGCAAT 58.919 39.130 0.00 0.00 0.00 3.56
862 869 3.076621 CTCTGTTTAGCATGTGAAGGCA 58.923 45.455 0.00 0.00 0.00 4.75
864 871 3.942829 TCCTCTGTTTAGCATGTGAAGG 58.057 45.455 0.00 0.00 0.00 3.46
865 872 5.163683 CCATTCCTCTGTTTAGCATGTGAAG 60.164 44.000 0.00 0.00 0.00 3.02
866 873 4.701651 CCATTCCTCTGTTTAGCATGTGAA 59.298 41.667 0.00 0.00 0.00 3.18
867 874 4.264253 CCATTCCTCTGTTTAGCATGTGA 58.736 43.478 0.00 0.00 0.00 3.58
868 875 3.379372 CCCATTCCTCTGTTTAGCATGTG 59.621 47.826 0.00 0.00 0.00 3.21
869 876 3.266772 TCCCATTCCTCTGTTTAGCATGT 59.733 43.478 0.00 0.00 0.00 3.21
870 877 3.629398 GTCCCATTCCTCTGTTTAGCATG 59.371 47.826 0.00 0.00 0.00 4.06
871 878 3.525199 AGTCCCATTCCTCTGTTTAGCAT 59.475 43.478 0.00 0.00 0.00 3.79
872 879 2.912956 AGTCCCATTCCTCTGTTTAGCA 59.087 45.455 0.00 0.00 0.00 3.49
873 880 3.636153 AGTCCCATTCCTCTGTTTAGC 57.364 47.619 0.00 0.00 0.00 3.09
874 881 6.049955 TGTAAGTCCCATTCCTCTGTTTAG 57.950 41.667 0.00 0.00 0.00 1.85
875 882 6.442541 TTGTAAGTCCCATTCCTCTGTTTA 57.557 37.500 0.00 0.00 0.00 2.01
877 884 4.993705 TTGTAAGTCCCATTCCTCTGTT 57.006 40.909 0.00 0.00 0.00 3.16
878 885 4.536090 TGATTGTAAGTCCCATTCCTCTGT 59.464 41.667 0.00 0.00 0.00 3.41
879 886 5.102953 TGATTGTAAGTCCCATTCCTCTG 57.897 43.478 0.00 0.00 0.00 3.35
880 887 5.779241 TTGATTGTAAGTCCCATTCCTCT 57.221 39.130 0.00 0.00 0.00 3.69
881 888 7.410120 AAATTGATTGTAAGTCCCATTCCTC 57.590 36.000 0.00 0.00 0.00 3.71
882 889 6.381133 GGAAATTGATTGTAAGTCCCATTCCT 59.619 38.462 0.00 0.00 0.00 3.36
883 890 6.406961 GGGAAATTGATTGTAAGTCCCATTCC 60.407 42.308 0.00 0.00 35.13 3.01
884 891 6.154363 TGGGAAATTGATTGTAAGTCCCATTC 59.846 38.462 4.40 0.00 39.67 2.67
886 893 5.588845 TGGGAAATTGATTGTAAGTCCCAT 58.411 37.500 4.40 0.00 39.67 4.00
887 894 5.004361 TGGGAAATTGATTGTAAGTCCCA 57.996 39.130 4.40 4.40 41.99 4.37
888 895 5.422012 ACATGGGAAATTGATTGTAAGTCCC 59.578 40.000 0.00 0.00 35.56 4.46
890 897 7.396540 AGACATGGGAAATTGATTGTAAGTC 57.603 36.000 0.00 0.00 0.00 3.01
891 898 8.877864 TTAGACATGGGAAATTGATTGTAAGT 57.122 30.769 0.00 0.00 0.00 2.24
892 899 9.956720 GATTAGACATGGGAAATTGATTGTAAG 57.043 33.333 0.00 0.00 0.00 2.34
893 900 8.912988 GGATTAGACATGGGAAATTGATTGTAA 58.087 33.333 0.00 0.00 0.00 2.41
895 902 6.324770 GGGATTAGACATGGGAAATTGATTGT 59.675 38.462 0.00 0.00 0.00 2.71
897 904 6.686544 AGGGATTAGACATGGGAAATTGATT 58.313 36.000 0.00 0.00 0.00 2.57
899 906 5.732331 AGGGATTAGACATGGGAAATTGA 57.268 39.130 0.00 0.00 0.00 2.57
900 907 5.069516 CCAAGGGATTAGACATGGGAAATTG 59.930 44.000 0.00 0.00 0.00 2.32
901 908 5.211201 CCAAGGGATTAGACATGGGAAATT 58.789 41.667 0.00 0.00 0.00 1.82
904 911 2.091885 GCCAAGGGATTAGACATGGGAA 60.092 50.000 0.00 0.00 0.00 3.97
906 913 1.215173 TGCCAAGGGATTAGACATGGG 59.785 52.381 0.00 0.00 0.00 4.00
907 914 2.734755 TGCCAAGGGATTAGACATGG 57.265 50.000 0.00 0.00 0.00 3.66
908 915 4.019174 AGTTTGCCAAGGGATTAGACATG 58.981 43.478 0.00 0.00 0.00 3.21
909 916 4.273318 GAGTTTGCCAAGGGATTAGACAT 58.727 43.478 0.00 0.00 0.00 3.06
911 918 3.017442 GGAGTTTGCCAAGGGATTAGAC 58.983 50.000 0.00 0.00 0.00 2.59
912 919 2.025321 GGGAGTTTGCCAAGGGATTAGA 60.025 50.000 0.00 0.00 0.00 2.10
913 920 2.291540 TGGGAGTTTGCCAAGGGATTAG 60.292 50.000 0.00 0.00 33.84 1.73
914 921 1.713647 TGGGAGTTTGCCAAGGGATTA 59.286 47.619 0.00 0.00 33.84 1.75
915 922 0.486879 TGGGAGTTTGCCAAGGGATT 59.513 50.000 0.00 0.00 33.84 3.01
916 923 0.712380 ATGGGAGTTTGCCAAGGGAT 59.288 50.000 0.00 0.00 42.59 3.85
917 924 0.039618 GATGGGAGTTTGCCAAGGGA 59.960 55.000 0.00 0.00 42.59 4.20
918 925 0.040204 AGATGGGAGTTTGCCAAGGG 59.960 55.000 0.00 0.00 42.59 3.95
919 926 1.005215 AGAGATGGGAGTTTGCCAAGG 59.995 52.381 0.00 0.00 42.59 3.61
920 927 2.503895 AGAGATGGGAGTTTGCCAAG 57.496 50.000 0.00 0.00 42.59 3.61
921 928 4.079253 GTTTAGAGATGGGAGTTTGCCAA 58.921 43.478 0.00 0.00 42.59 4.52
922 929 3.330701 AGTTTAGAGATGGGAGTTTGCCA 59.669 43.478 0.00 0.00 43.78 4.92
923 930 3.942115 GAGTTTAGAGATGGGAGTTTGCC 59.058 47.826 0.00 0.00 0.00 4.52
924 931 3.942115 GGAGTTTAGAGATGGGAGTTTGC 59.058 47.826 0.00 0.00 0.00 3.68
926 933 4.175962 TGGGAGTTTAGAGATGGGAGTTT 58.824 43.478 0.00 0.00 0.00 2.66
927 934 3.803340 TGGGAGTTTAGAGATGGGAGTT 58.197 45.455 0.00 0.00 0.00 3.01
928 935 3.491766 TGGGAGTTTAGAGATGGGAGT 57.508 47.619 0.00 0.00 0.00 3.85
929 936 4.202409 GGAATGGGAGTTTAGAGATGGGAG 60.202 50.000 0.00 0.00 0.00 4.30
931 938 3.181439 GGGAATGGGAGTTTAGAGATGGG 60.181 52.174 0.00 0.00 0.00 4.00
932 939 3.718956 AGGGAATGGGAGTTTAGAGATGG 59.281 47.826 0.00 0.00 0.00 3.51
933 940 4.657969 AGAGGGAATGGGAGTTTAGAGATG 59.342 45.833 0.00 0.00 0.00 2.90
934 941 4.901927 AGAGGGAATGGGAGTTTAGAGAT 58.098 43.478 0.00 0.00 0.00 2.75
938 945 2.439880 GGGAGAGGGAATGGGAGTTTAG 59.560 54.545 0.00 0.00 0.00 1.85
939 946 2.047296 AGGGAGAGGGAATGGGAGTTTA 59.953 50.000 0.00 0.00 0.00 2.01
940 947 1.203622 AGGGAGAGGGAATGGGAGTTT 60.204 52.381 0.00 0.00 0.00 2.66
942 949 0.327000 CAGGGAGAGGGAATGGGAGT 60.327 60.000 0.00 0.00 0.00 3.85
945 952 1.893315 TAACAGGGAGAGGGAATGGG 58.107 55.000 0.00 0.00 0.00 4.00
946 953 4.660771 AGTAATAACAGGGAGAGGGAATGG 59.339 45.833 0.00 0.00 0.00 3.16
947 954 5.896073 AGTAATAACAGGGAGAGGGAATG 57.104 43.478 0.00 0.00 0.00 2.67
948 955 7.404980 TGTTTAGTAATAACAGGGAGAGGGAAT 59.595 37.037 0.00 0.00 32.15 3.01
950 957 6.266080 TGTTTAGTAATAACAGGGAGAGGGA 58.734 40.000 0.00 0.00 32.15 4.20
951 958 6.555463 TGTTTAGTAATAACAGGGAGAGGG 57.445 41.667 0.00 0.00 32.15 4.30
960 967 6.588756 CGCAACTCCTCTGTTTAGTAATAACA 59.411 38.462 0.00 0.00 34.55 2.41
961 968 6.455246 GCGCAACTCCTCTGTTTAGTAATAAC 60.455 42.308 0.30 0.00 0.00 1.89
962 969 5.579511 GCGCAACTCCTCTGTTTAGTAATAA 59.420 40.000 0.30 0.00 0.00 1.40
965 972 3.006537 AGCGCAACTCCTCTGTTTAGTAA 59.993 43.478 11.47 0.00 0.00 2.24
966 973 2.561419 AGCGCAACTCCTCTGTTTAGTA 59.439 45.455 11.47 0.00 0.00 1.82
967 974 1.344763 AGCGCAACTCCTCTGTTTAGT 59.655 47.619 11.47 0.00 0.00 2.24
968 975 1.728971 CAGCGCAACTCCTCTGTTTAG 59.271 52.381 11.47 0.00 0.00 1.85
970 977 1.510480 GCAGCGCAACTCCTCTGTTT 61.510 55.000 11.47 0.00 0.00 2.83
971 978 1.963338 GCAGCGCAACTCCTCTGTT 60.963 57.895 11.47 0.00 0.00 3.16
972 979 1.536073 TAGCAGCGCAACTCCTCTGT 61.536 55.000 11.47 0.00 0.00 3.41
973 980 0.390340 TTAGCAGCGCAACTCCTCTG 60.390 55.000 11.47 0.00 0.00 3.35
1173 4059 0.756815 GGCACTGGAATTGGGGATCC 60.757 60.000 1.92 1.92 36.21 3.36
1375 5432 0.996727 CACAAAACTAAGCGGCGCAC 60.997 55.000 35.02 5.34 0.00 5.34
1822 6927 3.244215 TGGAAGTGTTGTGAGAGATGGAC 60.244 47.826 0.00 0.00 0.00 4.02
1865 6970 0.169672 CAAACCATCAGAAGCAGGCG 59.830 55.000 0.00 0.00 0.00 5.52
1871 6976 3.379372 CCATACAGCCAAACCATCAGAAG 59.621 47.826 0.00 0.00 0.00 2.85
2183 9999 5.763444 AACACTCAAAGATACGACATTCG 57.237 39.130 0.00 0.00 46.93 3.34
2191 10007 7.776933 TCATCAGCATAACACTCAAAGATAC 57.223 36.000 0.00 0.00 0.00 2.24
2196 10022 7.175467 ACTTCAATCATCAGCATAACACTCAAA 59.825 33.333 0.00 0.00 0.00 2.69
2248 10075 7.807977 TCTTTTAAAGAACTCATCAAGCAGT 57.192 32.000 4.77 0.00 33.83 4.40
2431 10306 2.237143 ACTAGCTAATCACAGCAAGGCA 59.763 45.455 0.00 0.00 44.35 4.75
2548 10426 6.059484 TCTTTGGTAAACTTGATTCCTCGTT 58.941 36.000 0.00 0.00 0.00 3.85
2583 10461 4.504858 TCCCGCAAGAGAAAAGATACTTC 58.495 43.478 0.00 0.00 43.02 3.01
2644 10616 5.239306 ACTGTTATGTGTCACATTGTCAAGG 59.761 40.000 23.05 11.22 39.88 3.61
2719 10699 3.315191 CCGAAAAGTGTCAATGGAGTTGT 59.685 43.478 0.00 0.00 38.95 3.32
2814 10802 6.232581 ACTCCTCACTTCAGGAAGATATTG 57.767 41.667 15.51 3.90 42.35 1.90
2894 10926 6.574350 ACTGAGAGGTGCATAGTTATGTAAC 58.426 40.000 0.00 0.00 36.42 2.50
3501 11743 3.500982 CGACAGTTAATTACGGACGGAA 58.499 45.455 0.00 0.00 36.75 4.30
3510 11752 5.580691 CACTCATTCCAGCGACAGTTAATTA 59.419 40.000 0.00 0.00 0.00 1.40
3526 11768 3.499048 TCTAGACGCGTTTCACTCATTC 58.501 45.455 15.53 0.00 0.00 2.67
3580 11835 5.589050 AGAAAGTTCACAAACTACAACCTCC 59.411 40.000 0.00 0.00 45.07 4.30
3652 11907 8.532977 ACATTTTAACCTTTGCATGACATTAC 57.467 30.769 0.00 0.00 0.00 1.89
3688 11944 7.709149 AAAATAGTAGCATTCTTTCAGCCTT 57.291 32.000 0.00 0.00 0.00 4.35
3831 12506 1.597663 GCAAGTATCGTCGGGGAAATG 59.402 52.381 0.00 0.00 0.00 2.32
3893 12573 0.519519 TTTTATGCACGACGGGCAAG 59.480 50.000 30.72 0.00 45.60 4.01
3943 12628 1.148157 CCGCGACTTAGCCACATCTG 61.148 60.000 8.23 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.