Multiple sequence alignment - TraesCS3B01G369000

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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 TraesCS3B01G369000 chr3B 100.000 3585 0 0 1 3585 581129177 581125593 0.000000e+00 6621
1 TraesCS3B01G369000 chr3B 86.433 914 96 12 1690 2594 581267395 581266501 0.000000e+00 976
2 TraesCS3B01G369000 chr3B 84.809 836 89 20 1572 2392 581091723 581090911 0.000000e+00 806
3 TraesCS3B01G369000 chr3B 80.834 1007 119 41 1424 2408 710388546 710389500 0.000000e+00 723
4 TraesCS3B01G369000 chr3B 80.428 935 95 36 1474 2392 581134449 581133587 1.820000e-177 632
5 TraesCS3B01G369000 chr3B 90.610 213 20 0 1 213 581096254 581096042 2.110000e-72 283
6 TraesCS3B01G369000 chr3B 82.102 352 44 12 973 1307 581135007 581134658 2.110000e-72 283
7 TraesCS3B01G369000 chr3B 88.816 152 17 0 7 158 581088195 581088044 1.700000e-43 187
8 TraesCS3B01G369000 chr3B 90.678 118 10 1 1310 1426 29612679 29612562 4.790000e-34 156
9 TraesCS3B01G369000 chr3B 89.431 123 9 4 2477 2598 581133523 581133404 6.200000e-33 152
10 TraesCS3B01G369000 chr3B 85.417 144 17 4 2453 2594 581090875 581090734 2.880000e-31 147
11 TraesCS3B01G369000 chr3B 86.957 92 6 4 238 325 581096040 581095951 8.190000e-17 99
12 TraesCS3B01G369000 chr2B 96.025 956 35 1 2633 3585 632904199 632903244 0.000000e+00 1552
13 TraesCS3B01G369000 chr7A 94.322 951 54 0 2635 3585 229213 230163 0.000000e+00 1458
14 TraesCS3B01G369000 chr7A 93.382 952 60 2 2633 3584 546583651 546584599 0.000000e+00 1406
15 TraesCS3B01G369000 chr4A 93.927 955 58 0 2631 3585 617496132 617497086 0.000000e+00 1443
16 TraesCS3B01G369000 chr4A 88.029 969 114 2 2619 3585 100613985 100614953 0.000000e+00 1146
17 TraesCS3B01G369000 chr3D 94.067 927 47 6 388 1310 443439352 443438430 0.000000e+00 1400
18 TraesCS3B01G369000 chr3D 91.213 717 34 15 1423 2131 443438427 443437732 0.000000e+00 948
19 TraesCS3B01G369000 chr3D 82.503 983 111 33 1427 2392 443421281 443420343 0.000000e+00 806
20 TraesCS3B01G369000 chr3D 95.269 465 15 2 2130 2594 443437701 443437244 0.000000e+00 730
21 TraesCS3B01G369000 chr3D 78.677 1149 128 54 1474 2598 443430739 443429684 0.000000e+00 656
22 TraesCS3B01G369000 chr3D 81.775 845 88 39 1572 2392 443319399 443318597 0.000000e+00 647
23 TraesCS3B01G369000 chr3D 92.105 380 24 3 1 377 443440009 443439633 6.820000e-147 531
24 TraesCS3B01G369000 chr3D 88.743 382 35 4 1 377 443426408 443426030 9.070000e-126 460
25 TraesCS3B01G369000 chr3D 82.769 325 29 15 990 1307 443319787 443319483 7.630000e-67 265
26 TraesCS3B01G369000 chr3D 81.739 345 34 9 973 1307 443431272 443430947 9.870000e-66 261
27 TraesCS3B01G369000 chr3D 91.005 189 17 0 1 189 443379929 443379741 4.590000e-64 255
28 TraesCS3B01G369000 chr3D 81.197 351 32 15 974 1306 443443783 443443449 5.940000e-63 252
29 TraesCS3B01G369000 chr3D 88.482 191 21 1 7 196 443435365 443435175 2.780000e-56 230
30 TraesCS3B01G369000 chr3D 82.721 272 31 7 441 707 443372655 443372395 1.000000e-55 228
31 TraesCS3B01G369000 chr3D 82.721 272 26 12 628 878 443424648 443424377 4.660000e-54 222
32 TraesCS3B01G369000 chr3D 88.462 182 13 7 796 974 443366740 443366564 2.800000e-51 213
33 TraesCS3B01G369000 chr3D 86.598 194 20 3 184 377 443373573 443373386 3.630000e-50 209
34 TraesCS3B01G369000 chr3D 88.722 133 12 3 1184 1314 443421417 443421286 3.700000e-35 159
35 TraesCS3B01G369000 chr3D 91.304 115 9 1 2480 2594 443442488 443442375 4.790000e-34 156
36 TraesCS3B01G369000 chr3D 87.903 124 14 1 1184 1306 443364122 443363999 1.040000e-30 145
37 TraesCS3B01G369000 chr3D 84.722 144 18 4 2453 2594 443420307 443420166 1.340000e-29 141
38 TraesCS3B01G369000 chr2A 93.719 812 42 3 2774 3585 40072667 40071865 0.000000e+00 1208
39 TraesCS3B01G369000 chr2A 95.282 657 31 0 2929 3585 627925731 627925075 0.000000e+00 1042
40 TraesCS3B01G369000 chr2A 91.304 115 10 0 1319 1433 510433588 510433474 1.330000e-34 158
41 TraesCS3B01G369000 chr3A 83.368 956 153 5 2633 3584 691445001 691444048 0.000000e+00 880
42 TraesCS3B01G369000 chr3A 81.560 987 94 36 1423 2392 584377864 584376949 0.000000e+00 734
43 TraesCS3B01G369000 chr3A 83.310 701 83 21 1445 2139 584356080 584355408 1.830000e-172 616
44 TraesCS3B01G369000 chr3A 89.583 480 47 3 388 866 584447727 584447250 1.100000e-169 606
45 TraesCS3B01G369000 chr3A 89.130 460 29 7 2142 2594 584446772 584446327 1.450000e-153 553
46 TraesCS3B01G369000 chr3A 89.474 380 31 5 1 377 584448486 584448113 4.190000e-129 472
47 TraesCS3B01G369000 chr3A 84.419 353 32 9 973 1307 584475702 584475355 3.450000e-85 326
48 TraesCS3B01G369000 chr3A 84.384 333 34 11 976 1307 584373186 584372871 9.670000e-81 311
49 TraesCS3B01G369000 chr3A 83.095 349 27 12 973 1310 584378189 584377862 4.530000e-74 289
50 TraesCS3B01G369000 chr3A 88.742 151 17 0 7 157 584352877 584352727 6.110000e-43 185
51 TraesCS3B01G369000 chr3A 94.393 107 6 0 1319 1425 658713161 658713055 7.960000e-37 165
52 TraesCS3B01G369000 chr3A 91.304 115 10 0 1319 1433 547933304 547933418 1.330000e-34 158
53 TraesCS3B01G369000 chr3A 89.431 123 9 4 2477 2598 584376885 584376766 6.200000e-33 152
54 TraesCS3B01G369000 chr3A 98.413 63 1 0 909 971 584447256 584447194 1.050000e-20 111
55 TraesCS3B01G369000 chr6D 82.540 945 158 6 2645 3584 33434414 33433472 0.000000e+00 824
56 TraesCS3B01G369000 chr6D 92.857 112 8 0 1316 1427 467047472 467047361 2.860000e-36 163
57 TraesCS3B01G369000 chr7B 82.169 959 160 9 2633 3584 537141360 537142314 0.000000e+00 813
58 TraesCS3B01G369000 chr2D 82.227 934 157 8 2647 3574 31788032 31787102 0.000000e+00 797
59 TraesCS3B01G369000 chr5B 83.667 300 33 10 1014 1307 577366473 577366184 5.900000e-68 268
60 TraesCS3B01G369000 chr5B 86.550 171 23 0 7 177 577353121 577352951 4.730000e-44 189
61 TraesCS3B01G369000 chr6B 92.982 114 8 0 1318 1431 693130572 693130459 2.210000e-37 167
62 TraesCS3B01G369000 chr1A 93.519 108 7 0 1319 1426 186750278 186750385 1.030000e-35 161
63 TraesCS3B01G369000 chr1A 93.519 108 7 0 1319 1426 556786873 556786980 1.030000e-35 161
64 TraesCS3B01G369000 chr1A 92.105 114 8 1 1315 1428 22631682 22631570 3.700000e-35 159
65 TraesCS3B01G369000 chr5D 84.722 144 16 6 2453 2594 469728961 469728822 4.830000e-29 139


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 TraesCS3B01G369000 chr3B 581125593 581129177 3584 True 6621.000000 6621 100.000000 1 3585 1 chr3B.!!$R2 3584
1 TraesCS3B01G369000 chr3B 581266501 581267395 894 True 976.000000 976 86.433000 1690 2594 1 chr3B.!!$R3 904
2 TraesCS3B01G369000 chr3B 710388546 710389500 954 False 723.000000 723 80.834000 1424 2408 1 chr3B.!!$F1 984
3 TraesCS3B01G369000 chr3B 581088044 581091723 3679 True 380.000000 806 86.347333 7 2594 3 chr3B.!!$R4 2587
4 TraesCS3B01G369000 chr3B 581133404 581135007 1603 True 355.666667 632 83.987000 973 2598 3 chr3B.!!$R6 1625
5 TraesCS3B01G369000 chr2B 632903244 632904199 955 True 1552.000000 1552 96.025000 2633 3585 1 chr2B.!!$R1 952
6 TraesCS3B01G369000 chr7A 229213 230163 950 False 1458.000000 1458 94.322000 2635 3585 1 chr7A.!!$F1 950
7 TraesCS3B01G369000 chr7A 546583651 546584599 948 False 1406.000000 1406 93.382000 2633 3584 1 chr7A.!!$F2 951
8 TraesCS3B01G369000 chr4A 617496132 617497086 954 False 1443.000000 1443 93.927000 2631 3585 1 chr4A.!!$F2 954
9 TraesCS3B01G369000 chr4A 100613985 100614953 968 False 1146.000000 1146 88.029000 2619 3585 1 chr4A.!!$F1 966
10 TraesCS3B01G369000 chr3D 443420166 443443783 23617 True 496.571429 1400 87.247429 1 2598 14 chr3D.!!$R5 2597
11 TraesCS3B01G369000 chr3D 443318597 443319787 1190 True 456.000000 647 82.272000 990 2392 2 chr3D.!!$R2 1402
12 TraesCS3B01G369000 chr3D 443372395 443373573 1178 True 218.500000 228 84.659500 184 707 2 chr3D.!!$R4 523
13 TraesCS3B01G369000 chr2A 40071865 40072667 802 True 1208.000000 1208 93.719000 2774 3585 1 chr2A.!!$R1 811
14 TraesCS3B01G369000 chr2A 627925075 627925731 656 True 1042.000000 1042 95.282000 2929 3585 1 chr2A.!!$R3 656
15 TraesCS3B01G369000 chr3A 691444048 691445001 953 True 880.000000 880 83.368000 2633 3584 1 chr3A.!!$R3 951
16 TraesCS3B01G369000 chr3A 584446327 584448486 2159 True 435.500000 606 91.650000 1 2594 4 chr3A.!!$R6 2593
17 TraesCS3B01G369000 chr3A 584352727 584356080 3353 True 400.500000 616 86.026000 7 2139 2 chr3A.!!$R4 2132
18 TraesCS3B01G369000 chr3A 584372871 584378189 5318 True 371.500000 734 84.617500 973 2598 4 chr3A.!!$R5 1625
19 TraesCS3B01G369000 chr6D 33433472 33434414 942 True 824.000000 824 82.540000 2645 3584 1 chr6D.!!$R1 939
20 TraesCS3B01G369000 chr7B 537141360 537142314 954 False 813.000000 813 82.169000 2633 3584 1 chr7B.!!$F1 951
21 TraesCS3B01G369000 chr2D 31787102 31788032 930 True 797.000000 797 82.227000 2647 3574 1 chr2D.!!$R1 927

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
583 1260 0.033228 GATGCTCACGATCCCTCCTG 59.967 60.0 0.00 0.00 0.0 3.86 F
1189 1878 0.034337 GTGTTTAGCTCACCGGGTGA 59.966 55.0 27.17 27.17 40.5 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 2103 0.032813 TCCCTCCGTCCCGAATTACT 60.033 55.0 0.00 0.0 0.0 2.24 R
2612 8685 0.387202 CCGAGTCGCTCATTCCTGAT 59.613 55.0 7.12 0.0 0.0 2.90 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
44 45 1.750399 TACCAGTCGAGGTACGGGC 60.750 63.158 0.00 0.00 43.08 6.13
68 69 2.372690 CGGGTCGACTTTGCTGACG 61.373 63.158 16.46 4.13 33.45 4.35
74 75 1.347817 CGACTTTGCTGACGAGAGGC 61.348 60.000 0.00 0.00 42.12 4.70
97 98 2.279120 CGGCAAGCTAGGCTCTCG 60.279 66.667 9.82 2.43 38.25 4.04
114 115 4.874977 GGCTCGCTGGTACTCCGC 62.875 72.222 0.00 0.00 36.30 5.54
130 131 1.576421 CGCCTTCCTCAAGCACAAC 59.424 57.895 0.00 0.00 0.00 3.32
135 136 1.532868 CTTCCTCAAGCACAACGGAAG 59.467 52.381 0.00 0.00 43.14 3.46
136 137 0.884704 TCCTCAAGCACAACGGAAGC 60.885 55.000 0.00 0.00 0.00 3.86
181 182 1.376037 GAACCAGGCCCTGAACTCG 60.376 63.158 13.74 0.00 32.44 4.18
203 204 1.609501 TCCTGACTCCCAACTCCGG 60.610 63.158 0.00 0.00 0.00 5.14
246 247 1.006825 CACGCGTGAGGTTTCGATCA 61.007 55.000 34.93 0.00 0.00 2.92
247 248 0.732880 ACGCGTGAGGTTTCGATCAG 60.733 55.000 12.93 0.00 0.00 2.90
318 322 8.092687 TCCTGTGACCACTATTTTCTTAAGTAC 58.907 37.037 1.63 0.00 0.00 2.73
371 375 6.456584 GCATGATATGGCTATGAGAAATGTCG 60.457 42.308 0.00 0.00 0.00 4.35
377 381 4.398988 TGGCTATGAGAAATGTCGCATTTT 59.601 37.500 7.48 8.49 40.97 1.82
378 382 5.105797 TGGCTATGAGAAATGTCGCATTTTT 60.106 36.000 7.48 11.67 40.97 1.94
404 1034 2.158813 TCCTGTCGCCTTTGTTTTCTCT 60.159 45.455 0.00 0.00 0.00 3.10
414 1044 1.214367 TGTTTTCTCTTCCGCACGAC 58.786 50.000 0.00 0.00 0.00 4.34
415 1045 0.161024 GTTTTCTCTTCCGCACGACG 59.839 55.000 0.00 0.00 43.15 5.12
439 1116 3.541632 AGTGTTTCTTTCTTGGCTCGAA 58.458 40.909 0.00 0.00 0.00 3.71
491 1168 2.357517 CGGGGCCACTATCGATGC 60.358 66.667 8.54 2.12 0.00 3.91
515 1192 5.353111 TGTTCGTCTGTCACTGATTGTTTA 58.647 37.500 0.00 0.00 0.00 2.01
517 1194 4.939271 TCGTCTGTCACTGATTGTTTACA 58.061 39.130 0.00 0.00 0.00 2.41
519 1196 4.084537 CGTCTGTCACTGATTGTTTACACC 60.085 45.833 0.00 0.00 0.00 4.16
527 1204 4.215399 ACTGATTGTTTACACCATTCCGTG 59.785 41.667 0.00 0.00 39.75 4.94
549 1226 3.756963 GGGAACACATTTAACCTGGAGAC 59.243 47.826 0.00 0.00 0.00 3.36
573 1250 1.642215 GCAGATGCTGATGCTCACG 59.358 57.895 0.00 0.00 39.38 4.35
583 1260 0.033228 GATGCTCACGATCCCTCCTG 59.967 60.000 0.00 0.00 0.00 3.86
584 1261 2.037620 ATGCTCACGATCCCTCCTGC 62.038 60.000 0.00 0.00 0.00 4.85
695 1376 8.253113 TCTTTTTCTTTCTTAATGGGATGATGC 58.747 33.333 0.00 0.00 0.00 3.91
717 1399 1.128692 GCTGTCTGTGGCGTATTTGAC 59.871 52.381 0.00 0.00 0.00 3.18
737 1419 1.135024 CCAAATTGGTGATTGGGCTCG 60.135 52.381 3.34 0.00 41.93 5.03
740 1422 0.680921 ATTGGTGATTGGGCTCGTGG 60.681 55.000 0.00 0.00 0.00 4.94
777 1459 2.554032 GTTGAACACATCCACCTCAAGG 59.446 50.000 0.00 0.00 42.17 3.61
785 1467 1.455822 TCCACCTCAAGGGGACAAAT 58.544 50.000 0.00 0.00 42.67 2.32
804 1486 9.139174 GGACAAATAAATGTACCATGAAAACAG 57.861 33.333 0.00 0.00 32.57 3.16
810 1492 4.015872 TGTACCATGAAAACAGAGACCC 57.984 45.455 0.00 0.00 0.00 4.46
840 1522 5.738619 ATTTATTGGAAAAGGAAAGGCGT 57.261 34.783 0.00 0.00 0.00 5.68
859 1541 4.414852 GCGTGTGCATTCAGATAAAATGT 58.585 39.130 0.00 0.00 42.15 2.71
860 1542 4.858692 GCGTGTGCATTCAGATAAAATGTT 59.141 37.500 0.00 0.00 42.15 2.71
861 1543 5.345741 GCGTGTGCATTCAGATAAAATGTTT 59.654 36.000 0.00 0.00 42.15 2.83
862 1544 6.452872 GCGTGTGCATTCAGATAAAATGTTTC 60.453 38.462 0.00 0.00 42.15 2.78
863 1545 6.033831 CGTGTGCATTCAGATAAAATGTTTCC 59.966 38.462 0.00 0.00 36.65 3.13
864 1546 6.867816 GTGTGCATTCAGATAAAATGTTTCCA 59.132 34.615 0.00 0.00 36.65 3.53
865 1547 7.546667 GTGTGCATTCAGATAAAATGTTTCCAT 59.453 33.333 0.00 0.00 36.65 3.41
866 1548 7.760794 TGTGCATTCAGATAAAATGTTTCCATC 59.239 33.333 0.00 0.00 36.65 3.51
867 1549 6.974048 TGCATTCAGATAAAATGTTTCCATCG 59.026 34.615 0.00 0.00 36.65 3.84
868 1550 7.148103 TGCATTCAGATAAAATGTTTCCATCGA 60.148 33.333 0.00 0.00 36.65 3.59
869 1551 7.701924 GCATTCAGATAAAATGTTTCCATCGAA 59.298 33.333 0.00 0.00 36.65 3.71
870 1552 9.229784 CATTCAGATAAAATGTTTCCATCGAAG 57.770 33.333 0.00 0.00 31.00 3.79
871 1553 7.921786 TCAGATAAAATGTTTCCATCGAAGT 57.078 32.000 0.00 0.00 0.00 3.01
872 1554 7.751732 TCAGATAAAATGTTTCCATCGAAGTG 58.248 34.615 0.00 0.00 0.00 3.16
873 1555 7.390440 TCAGATAAAATGTTTCCATCGAAGTGT 59.610 33.333 0.00 0.00 0.00 3.55
874 1556 7.482743 CAGATAAAATGTTTCCATCGAAGTGTG 59.517 37.037 0.00 0.00 0.00 3.82
875 1557 3.559238 AATGTTTCCATCGAAGTGTGC 57.441 42.857 0.00 0.00 0.00 4.57
876 1558 1.960417 TGTTTCCATCGAAGTGTGCA 58.040 45.000 0.00 0.00 0.00 4.57
877 1559 1.872952 TGTTTCCATCGAAGTGTGCAG 59.127 47.619 0.00 0.00 0.00 4.41
878 1560 1.873591 GTTTCCATCGAAGTGTGCAGT 59.126 47.619 0.00 0.00 0.00 4.40
879 1561 1.511850 TTCCATCGAAGTGTGCAGTG 58.488 50.000 0.00 0.00 0.00 3.66
880 1562 0.950555 TCCATCGAAGTGTGCAGTGC 60.951 55.000 8.58 8.58 0.00 4.40
881 1563 1.229975 CCATCGAAGTGTGCAGTGCA 61.230 55.000 15.37 15.37 35.60 4.57
882 1564 0.165295 CATCGAAGTGTGCAGTGCAG 59.835 55.000 20.42 5.67 40.08 4.41
883 1565 0.952497 ATCGAAGTGTGCAGTGCAGG 60.952 55.000 20.42 4.04 40.08 4.85
884 1566 2.641559 GAAGTGTGCAGTGCAGGC 59.358 61.111 20.42 14.24 40.08 4.85
885 1567 2.124193 AAGTGTGCAGTGCAGGCA 60.124 55.556 20.42 11.52 40.08 4.75
896 1578 1.378382 TGCAGGCACACACAGTGTT 60.378 52.632 2.45 0.00 45.08 3.32
897 1579 0.964860 TGCAGGCACACACAGTGTTT 60.965 50.000 2.45 0.00 45.08 2.83
898 1580 1.021202 GCAGGCACACACAGTGTTTA 58.979 50.000 2.45 0.00 45.08 2.01
899 1581 1.403679 GCAGGCACACACAGTGTTTAA 59.596 47.619 2.45 0.00 45.08 1.52
900 1582 2.541588 GCAGGCACACACAGTGTTTAAG 60.542 50.000 2.45 0.00 45.08 1.85
901 1583 1.676006 AGGCACACACAGTGTTTAAGC 59.324 47.619 2.45 5.71 45.08 3.09
902 1584 1.676006 GGCACACACAGTGTTTAAGCT 59.324 47.619 2.45 0.00 45.08 3.74
903 1585 2.541588 GGCACACACAGTGTTTAAGCTG 60.542 50.000 2.45 0.00 45.08 4.24
904 1586 2.541588 GCACACACAGTGTTTAAGCTGG 60.542 50.000 2.45 0.00 45.08 4.85
905 1587 2.682856 CACACACAGTGTTTAAGCTGGT 59.317 45.455 2.45 0.00 45.08 4.00
906 1588 2.682856 ACACACAGTGTTTAAGCTGGTG 59.317 45.455 2.45 0.00 45.08 4.17
907 1589 1.676006 ACACAGTGTTTAAGCTGGTGC 59.324 47.619 0.00 0.00 37.07 5.01
945 1627 1.334869 GTGGTTGAGGTTGCTGTTGAG 59.665 52.381 0.00 0.00 0.00 3.02
971 1653 9.995003 GATCAACAACTCTGATATAAATCTCCT 57.005 33.333 0.00 0.00 33.63 3.69
1018 1703 0.464554 GATGGGTGCTACTGCCTTCC 60.465 60.000 0.00 0.00 38.71 3.46
1050 1738 0.836400 TGTCCCTCTGGGTTCAGGAC 60.836 60.000 2.25 0.00 44.74 3.85
1133 1821 1.230324 GGAACCTCCGCATATCAAGC 58.770 55.000 0.00 0.00 0.00 4.01
1137 1825 1.233019 CCTCCGCATATCAAGCAAGG 58.767 55.000 0.00 0.00 0.00 3.61
1148 1837 6.368516 GCATATCAAGCAAGGAGTCTTATCTC 59.631 42.308 0.00 0.00 0.00 2.75
1166 1855 3.131396 TCTCGTTTGAGCTGAAAGTTCC 58.869 45.455 0.00 0.00 44.35 3.62
1169 1858 1.947456 GTTTGAGCTGAAAGTTCCGGT 59.053 47.619 0.00 0.00 44.35 5.28
1178 1867 2.614983 TGAAAGTTCCGGTGTGTTTAGC 59.385 45.455 0.00 0.00 0.00 3.09
1182 1871 1.529865 GTTCCGGTGTGTTTAGCTCAC 59.470 52.381 0.00 0.00 39.95 3.51
1189 1878 0.034337 GTGTTTAGCTCACCGGGTGA 59.966 55.000 27.17 27.17 40.50 4.02
1191 1880 1.012486 GTTTAGCTCACCGGGTGACG 61.012 60.000 25.53 20.56 37.67 4.35
1192 1881 2.775032 TTTAGCTCACCGGGTGACGC 62.775 60.000 28.82 28.82 37.67 5.19
1194 1883 4.760047 GCTCACCGGGTGACGCAT 62.760 66.667 29.99 0.00 37.67 4.73
1196 1885 4.429212 TCACCGGGTGACGCATCG 62.429 66.667 25.53 0.00 37.67 3.84
1263 1964 1.203441 TTGCTGAGGATGGCAGGAGT 61.203 55.000 0.00 0.00 39.68 3.85
1266 1967 2.025767 CTGAGGATGGCAGGAGTCCG 62.026 65.000 2.76 0.00 37.12 4.79
1270 1971 3.781770 GATGGCAGGAGTCCGAGCG 62.782 68.421 19.22 5.33 31.95 5.03
1307 2008 1.959226 ACGCAGGTTGGTTGCTACG 60.959 57.895 0.00 0.00 39.38 3.51
1308 2009 1.959226 CGCAGGTTGGTTGCTACGT 60.959 57.895 0.00 0.00 39.38 3.57
1309 2010 0.668096 CGCAGGTTGGTTGCTACGTA 60.668 55.000 0.00 0.00 39.38 3.57
1310 2011 1.076332 GCAGGTTGGTTGCTACGTAG 58.924 55.000 18.47 18.47 38.51 3.51
1312 2013 2.353011 GCAGGTTGGTTGCTACGTAGTA 60.353 50.000 22.98 16.78 45.11 1.82
1313 2014 3.248266 CAGGTTGGTTGCTACGTAGTAC 58.752 50.000 22.98 19.41 45.11 2.73
1330 2031 3.471680 AGTACGTATTACTCCCTCCGTC 58.528 50.000 0.00 0.00 36.09 4.79
1332 2033 0.957362 CGTATTACTCCCTCCGTCCC 59.043 60.000 0.00 0.00 0.00 4.46
1333 2034 1.751733 CGTATTACTCCCTCCGTCCCA 60.752 57.143 0.00 0.00 0.00 4.37
1340 2041 1.838077 CTCCCTCCGTCCCAAATTACT 59.162 52.381 0.00 0.00 0.00 2.24
1341 2042 1.835531 TCCCTCCGTCCCAAATTACTC 59.164 52.381 0.00 0.00 0.00 2.59
1343 2044 1.206371 CCTCCGTCCCAAATTACTCGT 59.794 52.381 0.00 0.00 0.00 4.18
1344 2045 2.537401 CTCCGTCCCAAATTACTCGTC 58.463 52.381 0.00 0.00 0.00 4.20
1346 2047 0.643820 CGTCCCAAATTACTCGTCGC 59.356 55.000 0.00 0.00 0.00 5.19
1347 2048 1.717194 GTCCCAAATTACTCGTCGCA 58.283 50.000 0.00 0.00 0.00 5.10
1348 2049 1.659098 GTCCCAAATTACTCGTCGCAG 59.341 52.381 0.00 0.00 0.00 5.18
1349 2050 1.546923 TCCCAAATTACTCGTCGCAGA 59.453 47.619 0.00 0.00 0.00 4.26
1352 2053 3.374058 CCCAAATTACTCGTCGCAGAAAT 59.626 43.478 0.00 0.00 39.69 2.17
1353 2054 4.569162 CCCAAATTACTCGTCGCAGAAATA 59.431 41.667 0.00 0.00 39.69 1.40
1354 2055 5.276868 CCCAAATTACTCGTCGCAGAAATAG 60.277 44.000 0.00 0.00 39.69 1.73
1355 2056 5.518847 CCAAATTACTCGTCGCAGAAATAGA 59.481 40.000 0.00 0.00 39.69 1.98
1357 2058 6.755461 AATTACTCGTCGCAGAAATAGATG 57.245 37.500 0.00 0.00 39.69 2.90
1359 2060 4.895224 ACTCGTCGCAGAAATAGATGTA 57.105 40.909 0.00 0.00 39.69 2.29
1361 2062 5.453648 ACTCGTCGCAGAAATAGATGTATC 58.546 41.667 0.00 0.00 39.69 2.24
1362 2063 5.239744 ACTCGTCGCAGAAATAGATGTATCT 59.760 40.000 0.00 0.00 39.69 1.98
1364 2065 7.041303 ACTCGTCGCAGAAATAGATGTATCTAA 60.041 37.037 5.75 0.00 39.88 2.10
1365 2066 7.645402 TCGTCGCAGAAATAGATGTATCTAAA 58.355 34.615 5.75 0.00 39.88 1.85
1366 2067 8.132995 TCGTCGCAGAAATAGATGTATCTAAAA 58.867 33.333 5.75 0.00 39.88 1.52
1367 2068 8.916654 CGTCGCAGAAATAGATGTATCTAAAAT 58.083 33.333 5.75 0.00 39.88 1.82
1398 2099 6.971602 ACATCTAGATATATTCATACCCGCG 58.028 40.000 4.54 0.00 0.00 6.46
1399 2100 6.771267 ACATCTAGATATATTCATACCCGCGA 59.229 38.462 8.23 0.00 0.00 5.87
1400 2101 6.615264 TCTAGATATATTCATACCCGCGAC 57.385 41.667 8.23 0.00 0.00 5.19
1401 2102 6.117488 TCTAGATATATTCATACCCGCGACA 58.883 40.000 8.23 0.00 0.00 4.35
1402 2103 5.654603 AGATATATTCATACCCGCGACAA 57.345 39.130 8.23 0.00 0.00 3.18
1403 2104 5.651530 AGATATATTCATACCCGCGACAAG 58.348 41.667 8.23 0.00 0.00 3.16
1409 2156 3.450578 TCATACCCGCGACAAGTAATTC 58.549 45.455 8.23 0.00 0.00 2.17
1412 2159 2.003672 CCGCGACAAGTAATTCGGG 58.996 57.895 8.23 1.47 45.06 5.14
1435 2182 2.711542 GGAGGGAGTACATGTTTGTGG 58.288 52.381 2.30 0.00 36.53 4.17
1462 2209 5.645056 TGTATCTGGCTTTCCCATATGAA 57.355 39.130 3.65 0.00 44.33 2.57
1532 2335 3.437049 GCAACTTGTGATCAGGTTACCTC 59.563 47.826 0.00 0.00 40.91 3.85
1533 2336 4.804261 GCAACTTGTGATCAGGTTACCTCT 60.804 45.833 0.00 0.00 40.91 3.69
1645 2457 6.014327 AGAGTAATTGAACATGGCAAATTGGT 60.014 34.615 7.25 0.00 0.00 3.67
1646 2458 5.933463 AGTAATTGAACATGGCAAATTGGTG 59.067 36.000 7.25 0.00 0.00 4.17
1649 2461 4.148128 TGAACATGGCAAATTGGTGTTT 57.852 36.364 3.67 0.00 33.55 2.83
1680 2497 2.664851 CCAGAACTTGACGCGGCA 60.665 61.111 12.71 12.71 0.00 5.69
1682 2499 2.357517 AGAACTTGACGCGGCAGG 60.358 61.111 24.00 24.00 0.00 4.85
1711 2529 4.207165 AGTGTTTGTTGCAGTTAGGTCAT 58.793 39.130 0.00 0.00 0.00 3.06
2025 7891 9.341899 CCGGTTTTGTTTTCTAATTTATCTCAG 57.658 33.333 0.00 0.00 0.00 3.35
2431 8503 0.240945 AACAACTACATTGCAGCGGC 59.759 50.000 0.31 0.31 42.62 6.53
2595 8668 4.463891 AGTTTGGAAATAGGGTTGCATCAG 59.536 41.667 0.00 0.00 0.00 2.90
2597 8670 2.580322 TGGAAATAGGGTTGCATCAGGA 59.420 45.455 0.00 0.00 0.00 3.86
2598 8671 3.205056 TGGAAATAGGGTTGCATCAGGAT 59.795 43.478 0.00 0.00 0.00 3.24
2599 8672 4.218312 GGAAATAGGGTTGCATCAGGATT 58.782 43.478 0.00 0.00 0.00 3.01
2602 8675 2.431954 AGGGTTGCATCAGGATTGAG 57.568 50.000 0.00 0.00 36.61 3.02
2604 8677 2.019984 GGGTTGCATCAGGATTGAGTC 58.980 52.381 0.00 0.00 36.61 3.36
2605 8678 1.667724 GGTTGCATCAGGATTGAGTCG 59.332 52.381 0.00 0.00 36.61 4.18
2606 8679 2.621338 GTTGCATCAGGATTGAGTCGA 58.379 47.619 0.00 0.00 36.61 4.20
2607 8680 3.002791 GTTGCATCAGGATTGAGTCGAA 58.997 45.455 0.00 0.00 36.61 3.71
2609 8682 3.673902 TGCATCAGGATTGAGTCGAAAA 58.326 40.909 0.00 0.00 36.61 2.29
2611 8684 3.064545 GCATCAGGATTGAGTCGAAAAGG 59.935 47.826 0.00 0.00 36.61 3.11
2612 8685 4.507710 CATCAGGATTGAGTCGAAAAGGA 58.492 43.478 0.00 0.00 36.61 3.36
2613 8686 4.826274 TCAGGATTGAGTCGAAAAGGAT 57.174 40.909 0.00 0.00 0.00 3.24
2614 8687 4.759782 TCAGGATTGAGTCGAAAAGGATC 58.240 43.478 0.00 0.00 0.00 3.36
2616 8689 4.569966 CAGGATTGAGTCGAAAAGGATCAG 59.430 45.833 0.00 0.00 0.00 2.90
2617 8690 3.873952 GGATTGAGTCGAAAAGGATCAGG 59.126 47.826 0.00 0.00 0.00 3.86
2622 8695 4.222810 TGAGTCGAAAAGGATCAGGAATGA 59.777 41.667 0.00 0.00 0.00 2.57
2624 8697 3.311048 GTCGAAAAGGATCAGGAATGAGC 59.689 47.826 0.00 0.00 0.00 4.26
2629 8702 1.686052 AGGATCAGGAATGAGCGACTC 59.314 52.381 0.00 0.00 0.00 3.36
2842 18539 4.918201 GGATCCGCCGCTTCCTGG 62.918 72.222 0.00 0.00 0.00 4.45
2852 18549 1.364626 CGCTTCCTGGTGATCTGCAC 61.365 60.000 0.00 0.00 46.98 4.57
2914 18612 3.335729 TTCCCCGCTTTCCCCTCC 61.336 66.667 0.00 0.00 0.00 4.30
3003 18738 2.521224 ATAGGGAGACGGGGCGAC 60.521 66.667 0.00 0.00 0.00 5.19
3108 19198 4.380531 TCTCAACGTTGATGAAGAGCTTT 58.619 39.130 29.79 0.00 36.46 3.51
3545 27017 6.101296 GGAGAAAGAAGAAAGGGGGTCATATA 59.899 42.308 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.012486 GCAAAGTCGACCCGGTACAG 61.012 60.000 13.01 0.00 0.00 2.74
97 98 4.874977 GCGGAGTACCAGCGAGCC 62.875 72.222 0.00 0.00 35.59 4.70
114 115 0.250295 TCCGTTGTGCTTGAGGAAGG 60.250 55.000 0.00 0.00 0.00 3.46
130 131 3.710722 ACCAGGGCAGAGCTTCCG 61.711 66.667 0.00 0.00 0.00 4.30
135 136 3.655810 CTCGACACCAGGGCAGAGC 62.656 68.421 0.00 0.00 0.00 4.09
136 137 1.536073 TTCTCGACACCAGGGCAGAG 61.536 60.000 0.00 0.00 0.00 3.35
172 173 1.609501 TCAGGACCCCGAGTTCAGG 60.610 63.158 0.00 0.00 0.00 3.86
181 182 1.539124 AGTTGGGAGTCAGGACCCC 60.539 63.158 15.18 15.18 45.01 4.95
196 197 1.407656 TTGCACTGGACTCCGGAGTT 61.408 55.000 36.55 19.46 42.66 3.01
197 198 1.837051 TTGCACTGGACTCCGGAGT 60.837 57.895 36.89 36.89 45.84 3.85
203 204 3.414700 CGCGGTTGCACTGGACTC 61.415 66.667 0.00 0.00 42.97 3.36
227 228 1.006825 TGATCGAAACCTCACGCGTG 61.007 55.000 32.76 32.76 0.00 5.34
228 229 0.732880 CTGATCGAAACCTCACGCGT 60.733 55.000 5.58 5.58 0.00 6.01
230 231 1.135373 TCTCTGATCGAAACCTCACGC 60.135 52.381 0.00 0.00 0.00 5.34
233 234 3.589988 GCTTTCTCTGATCGAAACCTCA 58.410 45.455 0.00 0.00 0.00 3.86
236 237 2.092838 CACGCTTTCTCTGATCGAAACC 59.907 50.000 0.00 0.00 0.00 3.27
246 247 1.819288 TCCGAGAATCACGCTTTCTCT 59.181 47.619 16.05 0.00 44.46 3.10
247 248 2.279582 TCCGAGAATCACGCTTTCTC 57.720 50.000 10.84 10.84 43.63 2.87
318 322 7.331026 TCATATCACTGGTGTCCTAAAGAAAG 58.669 38.462 0.53 0.00 0.00 2.62
377 381 2.650322 ACAAAGGCGACAGGAAGAAAA 58.350 42.857 0.00 0.00 0.00 2.29
378 382 2.341846 ACAAAGGCGACAGGAAGAAA 57.658 45.000 0.00 0.00 0.00 2.52
380 384 2.341846 AAACAAAGGCGACAGGAAGA 57.658 45.000 0.00 0.00 0.00 2.87
381 385 2.618709 AGAAAACAAAGGCGACAGGAAG 59.381 45.455 0.00 0.00 0.00 3.46
382 386 2.616842 GAGAAAACAAAGGCGACAGGAA 59.383 45.455 0.00 0.00 0.00 3.36
384 388 2.222027 AGAGAAAACAAAGGCGACAGG 58.778 47.619 0.00 0.00 0.00 4.00
404 1034 0.248990 AACACTTACGTCGTGCGGAA 60.249 50.000 8.47 3.85 46.52 4.30
414 1044 4.608445 CGAGCCAAGAAAGAAACACTTACG 60.608 45.833 0.00 0.00 37.93 3.18
415 1045 4.510340 TCGAGCCAAGAAAGAAACACTTAC 59.490 41.667 0.00 0.00 37.93 2.34
420 1050 2.878406 CCTTCGAGCCAAGAAAGAAACA 59.122 45.455 0.00 0.00 0.00 2.83
477 1154 1.221414 GAACAGCATCGATAGTGGCC 58.779 55.000 0.00 0.00 37.02 5.36
491 1168 3.384668 ACAATCAGTGACAGACGAACAG 58.615 45.455 0.00 0.00 0.00 3.16
519 1196 4.481463 GTTAAATGTGTTCCCACGGAATG 58.519 43.478 0.00 0.00 44.04 2.67
527 1204 3.756963 GTCTCCAGGTTAAATGTGTTCCC 59.243 47.826 0.00 0.00 0.00 3.97
533 1210 2.236395 CCCTCGTCTCCAGGTTAAATGT 59.764 50.000 0.00 0.00 0.00 2.71
549 1226 1.597302 CATCAGCATCTGCCCCTCG 60.597 63.158 0.00 0.00 43.38 4.63
573 1250 0.250513 AACAACGAGCAGGAGGGATC 59.749 55.000 0.00 0.00 0.00 3.36
717 1399 1.135024 CGAGCCCAATCACCAATTTGG 60.135 52.381 14.02 14.02 45.02 3.28
730 1412 4.100084 CAGCATCCCACGAGCCCA 62.100 66.667 0.00 0.00 0.00 5.36
737 1419 2.440980 GCCCCTTCAGCATCCCAC 60.441 66.667 0.00 0.00 0.00 4.61
740 1422 1.000396 AACTGCCCCTTCAGCATCC 60.000 57.895 0.00 0.00 40.04 3.51
794 1476 1.453155 CCGGGGTCTCTGTTTTCATG 58.547 55.000 0.00 0.00 0.00 3.07
804 1486 4.533311 TCCAATAAATATACCCGGGGTCTC 59.467 45.833 27.92 0.00 37.09 3.36
810 1492 7.826918 TTCCTTTTCCAATAAATATACCCGG 57.173 36.000 0.00 0.00 0.00 5.73
840 1522 6.990798 TGGAAACATTTTATCTGAATGCACA 58.009 32.000 0.00 0.00 37.89 4.57
859 1541 1.872952 CACTGCACACTTCGATGGAAA 59.127 47.619 3.12 0.00 0.00 3.13
860 1542 1.511850 CACTGCACACTTCGATGGAA 58.488 50.000 3.12 0.00 0.00 3.53
861 1543 0.950555 GCACTGCACACTTCGATGGA 60.951 55.000 3.12 0.00 0.00 3.41
862 1544 1.229975 TGCACTGCACACTTCGATGG 61.230 55.000 0.00 0.00 31.71 3.51
863 1545 0.165295 CTGCACTGCACACTTCGATG 59.835 55.000 0.00 0.00 33.79 3.84
864 1546 0.952497 CCTGCACTGCACACTTCGAT 60.952 55.000 0.00 0.00 33.79 3.59
865 1547 1.595109 CCTGCACTGCACACTTCGA 60.595 57.895 0.00 0.00 33.79 3.71
866 1548 2.941333 CCTGCACTGCACACTTCG 59.059 61.111 0.00 0.00 33.79 3.79
867 1549 2.188829 TGCCTGCACTGCACACTTC 61.189 57.895 0.00 0.00 33.79 3.01
868 1550 2.124193 TGCCTGCACTGCACACTT 60.124 55.556 0.00 0.00 33.79 3.16
873 1555 3.211245 GTGTGTGCCTGCACTGCA 61.211 61.111 21.62 16.96 46.30 4.41
874 1556 3.190323 CTGTGTGTGCCTGCACTGC 62.190 63.158 21.62 14.88 46.30 4.40
875 1557 1.820906 ACTGTGTGTGCCTGCACTG 60.821 57.895 21.62 9.96 46.30 3.66
876 1558 1.820906 CACTGTGTGTGCCTGCACT 60.821 57.895 21.62 0.00 46.30 4.40
877 1559 1.656818 AACACTGTGTGTGCCTGCAC 61.657 55.000 15.11 15.15 46.79 4.57
878 1560 0.964860 AAACACTGTGTGTGCCTGCA 60.965 50.000 15.11 0.00 46.79 4.41
879 1561 1.021202 TAAACACTGTGTGTGCCTGC 58.979 50.000 15.11 0.00 46.79 4.85
880 1562 2.541588 GCTTAAACACTGTGTGTGCCTG 60.542 50.000 15.11 4.64 46.79 4.85
881 1563 1.676006 GCTTAAACACTGTGTGTGCCT 59.324 47.619 15.11 0.00 46.79 4.75
882 1564 1.676006 AGCTTAAACACTGTGTGTGCC 59.324 47.619 15.11 2.12 46.79 5.01
883 1565 2.541588 CCAGCTTAAACACTGTGTGTGC 60.542 50.000 15.11 15.09 46.79 4.57
884 1566 2.682856 ACCAGCTTAAACACTGTGTGTG 59.317 45.455 15.11 6.32 46.79 3.82
885 1567 5.034365 GCACCAGCTTAAACACTGTGTGT 62.034 47.826 15.11 11.87 42.66 3.72
886 1568 2.541588 GCACCAGCTTAAACACTGTGTG 60.542 50.000 15.11 2.82 37.75 3.82
887 1569 1.676006 GCACCAGCTTAAACACTGTGT 59.324 47.619 7.80 7.80 37.91 3.72
888 1570 2.405892 GCACCAGCTTAAACACTGTG 57.594 50.000 6.19 6.19 37.91 3.66
900 1582 0.895100 TGGTCATGGAAAGCACCAGC 60.895 55.000 0.00 0.00 43.49 4.85
901 1583 1.475280 CATGGTCATGGAAAGCACCAG 59.525 52.381 7.64 0.00 42.22 4.00
902 1584 1.075212 TCATGGTCATGGAAAGCACCA 59.925 47.619 10.61 4.34 43.10 4.17
903 1585 1.838112 TCATGGTCATGGAAAGCACC 58.162 50.000 10.61 0.00 39.24 5.01
904 1586 2.165030 CCTTCATGGTCATGGAAAGCAC 59.835 50.000 10.61 0.00 39.24 4.40
905 1587 2.449464 CCTTCATGGTCATGGAAAGCA 58.551 47.619 10.61 0.00 39.24 3.91
945 1627 9.995003 AGGAGATTTATATCAGAGTTGTTGATC 57.005 33.333 0.00 0.00 36.68 2.92
991 1673 4.444306 GGCAGTAGCACCCATCTATGTTTA 60.444 45.833 0.00 0.00 44.61 2.01
1018 1703 0.032615 AGGGACAGCAGGAGGTAGAG 60.033 60.000 0.00 0.00 0.00 2.43
1050 1738 2.393768 AAGATCAGCGGCAGTTGCG 61.394 57.895 1.45 0.00 43.26 4.85
1122 1810 2.831333 AGACTCCTTGCTTGATATGCG 58.169 47.619 0.00 0.00 0.00 4.73
1133 1821 4.564769 GCTCAAACGAGATAAGACTCCTTG 59.435 45.833 0.00 0.00 33.83 3.61
1137 1825 4.987832 TCAGCTCAAACGAGATAAGACTC 58.012 43.478 0.00 0.00 31.68 3.36
1148 1837 1.069906 CCGGAACTTTCAGCTCAAACG 60.070 52.381 0.00 0.00 0.00 3.60
1169 1858 0.250124 CACCCGGTGAGCTAAACACA 60.250 55.000 12.68 0.00 39.65 3.72
1178 1867 2.509336 GATGCGTCACCCGGTGAG 60.509 66.667 21.05 15.00 43.57 3.51
1182 1871 0.528901 TAAATCGATGCGTCACCCGG 60.529 55.000 6.75 0.00 36.94 5.73
1184 1873 2.869801 TCATTAAATCGATGCGTCACCC 59.130 45.455 6.75 0.00 0.00 4.61
1189 1878 8.633075 AATCAAAATTCATTAAATCGATGCGT 57.367 26.923 0.00 0.00 0.00 5.24
1217 1915 3.770933 ACCCTCATACTGCATGCAAAATT 59.229 39.130 22.88 8.80 34.35 1.82
1218 1916 3.131577 CACCCTCATACTGCATGCAAAAT 59.868 43.478 22.88 14.73 34.35 1.82
1263 1964 3.998672 GTGTCCCAACCGCTCGGA 61.999 66.667 15.95 0.00 38.96 4.55
1266 1967 0.534203 TGAAAGTGTCCCAACCGCTC 60.534 55.000 0.00 0.00 0.00 5.03
1270 1971 1.947456 GTGAGTGAAAGTGTCCCAACC 59.053 52.381 0.00 0.00 0.00 3.77
1307 2008 4.381411 ACGGAGGGAGTAATACGTACTAC 58.619 47.826 6.08 6.08 43.45 2.73
1308 2009 4.503296 GGACGGAGGGAGTAATACGTACTA 60.503 50.000 0.00 0.00 43.45 1.82
1309 2010 3.471680 GACGGAGGGAGTAATACGTACT 58.528 50.000 0.00 0.00 46.23 2.73
1310 2011 2.550180 GGACGGAGGGAGTAATACGTAC 59.450 54.545 0.00 0.00 34.43 3.67
1311 2012 2.487265 GGGACGGAGGGAGTAATACGTA 60.487 54.545 0.00 0.00 34.43 3.57
1312 2013 1.685148 GGACGGAGGGAGTAATACGT 58.315 55.000 0.00 0.00 37.26 3.57
1313 2014 0.957362 GGGACGGAGGGAGTAATACG 59.043 60.000 0.00 0.00 0.00 3.06
1314 2015 2.077687 TGGGACGGAGGGAGTAATAC 57.922 55.000 0.00 0.00 0.00 1.89
1315 2016 2.852714 TTGGGACGGAGGGAGTAATA 57.147 50.000 0.00 0.00 0.00 0.98
1316 2017 1.961133 TTTGGGACGGAGGGAGTAAT 58.039 50.000 0.00 0.00 0.00 1.89
1317 2018 1.961133 ATTTGGGACGGAGGGAGTAA 58.039 50.000 0.00 0.00 0.00 2.24
1318 2019 1.961133 AATTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
1319 2020 1.558294 GTAATTTGGGACGGAGGGAGT 59.442 52.381 0.00 0.00 0.00 3.85
1320 2021 1.838077 AGTAATTTGGGACGGAGGGAG 59.162 52.381 0.00 0.00 0.00 4.30
1330 2031 2.004583 TCTGCGACGAGTAATTTGGG 57.995 50.000 0.00 0.00 0.00 4.12
1332 2033 6.569228 TCTATTTCTGCGACGAGTAATTTG 57.431 37.500 0.00 0.00 0.00 2.32
1333 2034 6.757010 ACATCTATTTCTGCGACGAGTAATTT 59.243 34.615 0.00 0.00 0.00 1.82
1340 2041 5.690997 AGATACATCTATTTCTGCGACGA 57.309 39.130 0.00 0.00 34.85 4.20
1341 2042 7.853377 TTTAGATACATCTATTTCTGCGACG 57.147 36.000 0.00 0.00 39.02 5.12
1375 2076 7.078851 GTCGCGGGTATGAATATATCTAGATG 58.921 42.308 15.79 0.00 0.00 2.90
1377 2078 6.117488 TGTCGCGGGTATGAATATATCTAGA 58.883 40.000 6.13 0.00 0.00 2.43
1378 2079 6.373186 TGTCGCGGGTATGAATATATCTAG 57.627 41.667 6.13 0.00 0.00 2.43
1379 2080 6.376299 ACTTGTCGCGGGTATGAATATATCTA 59.624 38.462 6.13 0.00 0.00 1.98
1380 2081 5.185249 ACTTGTCGCGGGTATGAATATATCT 59.815 40.000 6.13 0.00 0.00 1.98
1381 2082 5.408356 ACTTGTCGCGGGTATGAATATATC 58.592 41.667 6.13 0.00 0.00 1.63
1382 2083 5.401531 ACTTGTCGCGGGTATGAATATAT 57.598 39.130 6.13 0.00 0.00 0.86
1384 2085 3.746045 ACTTGTCGCGGGTATGAATAT 57.254 42.857 6.13 0.00 0.00 1.28
1386 2087 3.530265 TTACTTGTCGCGGGTATGAAT 57.470 42.857 6.13 0.00 0.00 2.57
1387 2088 3.530265 ATTACTTGTCGCGGGTATGAA 57.470 42.857 6.13 0.00 0.00 2.57
1388 2089 3.450578 GAATTACTTGTCGCGGGTATGA 58.549 45.455 6.13 0.00 0.00 2.15
1389 2090 2.217847 CGAATTACTTGTCGCGGGTATG 59.782 50.000 6.13 0.00 0.00 2.39
1392 2093 0.738412 CCGAATTACTTGTCGCGGGT 60.738 55.000 6.13 3.16 35.93 5.28
1393 2094 2.003672 CCGAATTACTTGTCGCGGG 58.996 57.895 6.13 0.00 35.93 6.13
1394 2095 0.458889 TCCCGAATTACTTGTCGCGG 60.459 55.000 6.13 0.00 35.93 6.46
1395 2096 0.643820 GTCCCGAATTACTTGTCGCG 59.356 55.000 0.00 0.00 35.93 5.87
1397 2098 1.135315 TCCGTCCCGAATTACTTGTCG 60.135 52.381 0.00 0.00 37.01 4.35
1398 2099 2.537401 CTCCGTCCCGAATTACTTGTC 58.463 52.381 0.00 0.00 0.00 3.18
1399 2100 1.206371 CCTCCGTCCCGAATTACTTGT 59.794 52.381 0.00 0.00 0.00 3.16
1400 2101 1.472728 CCCTCCGTCCCGAATTACTTG 60.473 57.143 0.00 0.00 0.00 3.16
1401 2102 0.828677 CCCTCCGTCCCGAATTACTT 59.171 55.000 0.00 0.00 0.00 2.24
1402 2103 0.032813 TCCCTCCGTCCCGAATTACT 60.033 55.000 0.00 0.00 0.00 2.24
1403 2104 0.388294 CTCCCTCCGTCCCGAATTAC 59.612 60.000 0.00 0.00 0.00 1.89
1409 2156 1.455217 ATGTACTCCCTCCGTCCCG 60.455 63.158 0.00 0.00 0.00 5.14
1412 2159 2.028385 ACAAACATGTACTCCCTCCGTC 60.028 50.000 0.00 0.00 0.00 4.79
1420 2167 8.730680 AGATACAAATTCCACAAACATGTACTC 58.269 33.333 0.00 0.00 29.16 2.59
1435 2182 5.859205 ATGGGAAAGCCAGATACAAATTC 57.141 39.130 0.00 0.00 35.15 2.17
1462 2209 4.363991 GGAAATATCCAGAGTCTGCCAT 57.636 45.455 15.10 10.77 45.79 4.40
1532 2335 7.168302 GTCTTAAATATCCACTCGACACATCAG 59.832 40.741 0.00 0.00 0.00 2.90
1533 2336 6.978659 GTCTTAAATATCCACTCGACACATCA 59.021 38.462 0.00 0.00 0.00 3.07
1538 2341 5.356190 AGTCGTCTTAAATATCCACTCGACA 59.644 40.000 14.33 0.00 44.49 4.35
1645 2457 2.557924 CTGGTCTTGGCTATTGCAAACA 59.442 45.455 1.71 0.00 41.91 2.83
1646 2458 2.819608 TCTGGTCTTGGCTATTGCAAAC 59.180 45.455 1.71 0.00 41.91 2.93
1649 2461 2.040278 AGTTCTGGTCTTGGCTATTGCA 59.960 45.455 0.66 0.00 41.91 4.08
1680 2497 1.136891 GCAACAAACACTTCTTGGCCT 59.863 47.619 3.32 0.00 0.00 5.19
1682 2499 2.195922 CTGCAACAAACACTTCTTGGC 58.804 47.619 0.00 0.00 0.00 4.52
1711 2529 6.034470 GCAAGAACAAATCGAACTGTCAAAAA 59.966 34.615 3.49 0.00 0.00 1.94
2025 7891 5.578727 GCAAACCCAAAATTTTCCCAAAAAC 59.421 36.000 0.00 0.00 37.20 2.43
2031 7897 3.814625 TCTGCAAACCCAAAATTTTCCC 58.185 40.909 0.00 0.00 0.00 3.97
2034 7900 4.821260 GTCCATCTGCAAACCCAAAATTTT 59.179 37.500 0.00 0.00 0.00 1.82
2074 7941 7.181485 AGGTTGTTGTAATACTCTAGCCCTTTA 59.819 37.037 0.00 0.00 0.00 1.85
2431 8503 3.951775 TGATTCCCCCAAAAACAATCG 57.048 42.857 0.00 0.00 0.00 3.34
2595 8668 3.873952 CCTGATCCTTTTCGACTCAATCC 59.126 47.826 0.00 0.00 0.00 3.01
2597 8670 4.826274 TCCTGATCCTTTTCGACTCAAT 57.174 40.909 0.00 0.00 0.00 2.57
2598 8671 4.617253 TTCCTGATCCTTTTCGACTCAA 57.383 40.909 0.00 0.00 0.00 3.02
2599 8672 4.222810 TCATTCCTGATCCTTTTCGACTCA 59.777 41.667 0.00 0.00 0.00 3.41
2602 8675 3.311048 GCTCATTCCTGATCCTTTTCGAC 59.689 47.826 0.00 0.00 0.00 4.20
2604 8677 2.286294 CGCTCATTCCTGATCCTTTTCG 59.714 50.000 0.00 0.00 0.00 3.46
2605 8678 3.311048 GTCGCTCATTCCTGATCCTTTTC 59.689 47.826 0.00 0.00 0.00 2.29
2606 8679 3.054802 AGTCGCTCATTCCTGATCCTTTT 60.055 43.478 0.00 0.00 0.00 2.27
2607 8680 2.503356 AGTCGCTCATTCCTGATCCTTT 59.497 45.455 0.00 0.00 0.00 3.11
2609 8682 1.686052 GAGTCGCTCATTCCTGATCCT 59.314 52.381 2.53 0.00 0.00 3.24
2611 8684 1.601663 CCGAGTCGCTCATTCCTGATC 60.602 57.143 7.12 0.00 0.00 2.92
2612 8685 0.387202 CCGAGTCGCTCATTCCTGAT 59.613 55.000 7.12 0.00 0.00 2.90
2613 8686 0.965866 ACCGAGTCGCTCATTCCTGA 60.966 55.000 7.12 0.00 0.00 3.86
2614 8687 0.803768 CACCGAGTCGCTCATTCCTG 60.804 60.000 7.12 0.00 0.00 3.86
2616 8689 1.519455 CCACCGAGTCGCTCATTCC 60.519 63.158 7.12 0.00 0.00 3.01
2617 8690 1.519455 CCCACCGAGTCGCTCATTC 60.519 63.158 7.12 0.00 0.00 2.67
2914 18612 0.975135 ATCCGCTGATGAGGGATCTG 59.025 55.000 0.00 0.00 35.71 2.90
3003 18738 2.230025 AGTAGATCGAGCCATTGATCCG 59.770 50.000 0.00 0.00 44.57 4.18
3108 19198 5.340403 CGATTATTAAACGCTTACCGATCGA 59.660 40.000 18.66 0.00 41.02 3.59
3545 27017 1.358725 CCGGCGATCGTTGTGACAAT 61.359 55.000 17.81 0.00 37.11 2.71


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

AutoCloner maintained by Alex Coulton.