Multiple sequence alignment - TraesCS7D01G457600

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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 TraesCS7D01G457600 chr7D 100.000 2366 0 0 1 2366 575822192 575819827 0.000000e+00 4370.0
1 TraesCS7D01G457600 chr7D 100.000 1716 0 0 2622 4337 575819571 575817856 0.000000e+00 3169.0
2 TraesCS7D01G457600 chr7D 84.518 394 30 26 557 931 575744098 575743717 1.150000e-95 361.0
3 TraesCS7D01G457600 chr7D 83.014 365 31 16 997 1361 575774610 575774277 7.050000e-78 302.0
4 TraesCS7D01G457600 chr7D 78.826 477 66 23 676 1143 575692549 575692099 5.490000e-74 289.0
5 TraesCS7D01G457600 chr7D 78.729 362 73 4 3027 3386 575772741 575772382 5.610000e-59 239.0
6 TraesCS7D01G457600 chr7D 80.519 308 34 16 389 675 575708857 575708555 3.400000e-51 213.0
7 TraesCS7D01G457600 chr7D 86.310 168 16 6 1650 1814 575773816 575773653 4.460000e-40 176.0
8 TraesCS7D01G457600 chr7D 93.137 102 7 0 1734 1835 575691549 575691448 2.700000e-32 150.0
9 TraesCS7D01G457600 chr7D 92.537 67 5 0 2103 2169 575742246 575742180 3.570000e-16 97.1
10 TraesCS7D01G457600 chr7D 91.045 67 6 0 2103 2169 575691170 575691104 1.660000e-14 91.6
11 TraesCS7D01G457600 chr7A 90.100 1202 75 23 1 1180 666591524 666590345 0.000000e+00 1520.0
12 TraesCS7D01G457600 chr7A 90.729 960 61 3 2648 3607 666588995 666588064 0.000000e+00 1254.0
13 TraesCS7D01G457600 chr7A 89.306 720 47 10 3645 4336 666587743 666587026 0.000000e+00 876.0
14 TraesCS7D01G457600 chr7A 92.844 559 27 7 1645 2201 666589959 666589412 0.000000e+00 798.0
15 TraesCS7D01G457600 chr7A 86.589 343 28 14 557 891 666507541 666507209 3.190000e-96 363.0
16 TraesCS7D01G457600 chr7A 79.778 361 71 2 3027 3386 666565899 666565540 1.200000e-65 261.0
17 TraesCS7D01G457600 chr7A 80.381 367 47 23 792 1148 666213647 666213296 5.570000e-64 255.0
18 TraesCS7D01G457600 chr7A 93.793 145 8 1 996 1140 666568703 666568560 2.630000e-52 217.0
19 TraesCS7D01G457600 chr7A 78.736 348 35 22 568 897 666569158 666568832 3.420000e-46 196.0
20 TraesCS7D01G457600 chr7A 88.485 165 12 4 399 558 666507728 666507566 4.430000e-45 193.0
21 TraesCS7D01G457600 chr7A 95.726 117 4 1 2251 2366 666589407 666589291 2.060000e-43 187.0
22 TraesCS7D01G457600 chr7A 86.127 173 16 3 1648 1814 666567000 666566830 3.450000e-41 180.0
23 TraesCS7D01G457600 chr7A 95.098 102 5 0 1734 1835 666212655 666212554 1.250000e-35 161.0
24 TraesCS7D01G457600 chr7A 83.051 177 18 4 1235 1411 666568506 666568342 2.700000e-32 150.0
25 TraesCS7D01G457600 chr7A 79.641 167 26 4 395 558 666574607 666574446 3.540000e-21 113.0
26 TraesCS7D01G457600 chr7A 92.537 67 5 0 2103 2169 666505939 666505873 3.570000e-16 97.1
27 TraesCS7D01G457600 chr7A 91.045 67 6 0 2103 2169 666212282 666212216 1.660000e-14 91.6
28 TraesCS7D01G457600 chr7A 88.158 76 5 3 295 368 666574673 666574600 2.150000e-13 87.9
29 TraesCS7D01G457600 chr7A 95.556 45 0 1 298 340 666227210 666227166 2.160000e-08 71.3
30 TraesCS7D01G457600 chr7B 91.450 924 71 5 2674 3592 637949738 637948818 0.000000e+00 1262.0
31 TraesCS7D01G457600 chr7B 88.414 725 42 21 1645 2366 637950497 637949812 0.000000e+00 835.0
32 TraesCS7D01G457600 chr7B 95.165 455 15 5 295 748 637960643 637960195 0.000000e+00 712.0
33 TraesCS7D01G457600 chr7B 85.597 486 51 10 3645 4112 637948294 637947810 3.900000e-135 492.0
34 TraesCS7D01G457600 chr7B 82.423 421 52 19 996 1411 637916321 637915918 8.930000e-92 348.0
35 TraesCS7D01G457600 chr7B 91.736 242 19 1 4096 4336 637947780 637947539 6.950000e-88 335.0
36 TraesCS7D01G457600 chr7B 90.157 254 13 6 927 1180 637951145 637950904 1.950000e-83 320.0
37 TraesCS7D01G457600 chr7B 84.337 332 20 15 573 903 637880025 637879725 3.280000e-76 296.0
38 TraesCS7D01G457600 chr7B 81.319 364 59 9 3027 3386 637914455 637914097 1.970000e-73 287.0
39 TraesCS7D01G457600 chr7B 77.871 479 59 31 676 1145 637823957 637823517 2.000000e-63 254.0
40 TraesCS7D01G457600 chr7B 83.039 283 31 12 402 673 637880594 637880318 1.560000e-59 241.0
41 TraesCS7D01G457600 chr7B 80.333 300 35 15 389 671 637824296 637824004 5.690000e-49 206.0
42 TraesCS7D01G457600 chr7B 81.784 269 28 8 298 558 637893373 637893118 5.690000e-49 206.0
43 TraesCS7D01G457600 chr7B 81.784 269 28 8 298 558 637917139 637916884 5.690000e-49 206.0
44 TraesCS7D01G457600 chr7B 88.235 170 14 5 1648 1814 637915548 637915382 9.510000e-47 198.0
45 TraesCS7D01G457600 chr7B 90.714 140 6 3 108 240 637960779 637960640 3.450000e-41 180.0
46 TraesCS7D01G457600 chr7B 75.988 329 63 8 3068 3386 637822044 637821722 5.810000e-34 156.0
47 TraesCS7D01G457600 chr7B 74.249 466 72 33 1734 2169 637822855 637822408 7.510000e-33 152.0
48 TraesCS7D01G457600 chr7B 87.097 124 7 6 1 116 637960927 637960805 9.790000e-27 132.0
49 TraesCS7D01G457600 chr7B 87.209 86 5 5 676 758 637880216 637880134 4.620000e-15 93.5
50 TraesCS7D01G457600 chr7B 91.803 61 5 0 237 297 361210789 361210729 7.730000e-13 86.1
51 TraesCS7D01G457600 chr7B 91.667 48 4 0 250 297 352419485 352419438 2.800000e-07 67.6
52 TraesCS7D01G457600 chr2B 81.319 364 59 9 3024 3383 296288497 296288855 1.970000e-73 287.0
53 TraesCS7D01G457600 chr2B 88.235 170 14 5 1648 1814 296287407 296287573 9.510000e-47 198.0
54 TraesCS7D01G457600 chrUn 91.045 67 6 0 2103 2169 86902820 86902886 1.660000e-14 91.6
55 TraesCS7D01G457600 chr6B 91.803 61 5 0 237 297 88375040 88374980 7.730000e-13 86.1
56 TraesCS7D01G457600 chr6B 92.727 55 2 2 247 300 475814342 475814289 1.290000e-10 78.7
57 TraesCS7D01G457600 chr2A 92.727 55 4 0 247 301 535215627 535215681 3.600000e-11 80.5
58 TraesCS7D01G457600 chr6D 95.745 47 2 0 252 298 319701424 319701470 4.650000e-10 76.8
59 TraesCS7D01G457600 chr6D 100.000 32 0 0 763 794 28268466 28268435 4.680000e-05 60.2
60 TraesCS7D01G457600 chr6D 97.143 35 1 0 760 794 449179551 449179585 4.680000e-05 60.2
61 TraesCS7D01G457600 chr6D 100.000 32 0 0 763 794 455577210 455577241 4.680000e-05 60.2
62 TraesCS7D01G457600 chr5B 91.667 48 4 0 250 297 579596247 579596200 2.800000e-07 67.6
63 TraesCS7D01G457600 chr4B 88.889 54 5 1 247 299 409939617 409939564 1.010000e-06 65.8
64 TraesCS7D01G457600 chr2D 100.000 33 0 0 762 794 220709582 220709614 1.300000e-05 62.1
65 TraesCS7D01G457600 chr1D 90.000 50 2 3 745 794 6259389 6259343 1.300000e-05 62.1
66 TraesCS7D01G457600 chr5D 100.000 32 0 0 763 794 170107387 170107418 4.680000e-05 60.2
67 TraesCS7D01G457600 chr4D 100.000 32 0 0 763 794 220323912 220323943 4.680000e-05 60.2
68 TraesCS7D01G457600 chr4D 92.308 39 2 1 756 794 507723344 507723381 2.000000e-03 54.7
69 TraesCS7D01G457600 chr3D 100.000 32 0 0 763 794 604231977 604232008 4.680000e-05 60.2


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 TraesCS7D01G457600 chr7D 575817856 575822192 4336 True 3769.500000 4370 100.000000 1 4337 2 chr7D.!!$R5 4336
1 TraesCS7D01G457600 chr7D 575772382 575774610 2228 True 239.000000 302 82.684333 997 3386 3 chr7D.!!$R4 2389
2 TraesCS7D01G457600 chr7D 575742180 575744098 1918 True 229.050000 361 88.527500 557 2169 2 chr7D.!!$R3 1612
3 TraesCS7D01G457600 chr7A 666587026 666591524 4498 True 927.000000 1520 91.741000 1 4336 5 chr7A.!!$R6 4335
4 TraesCS7D01G457600 chr7A 666505873 666507728 1855 True 217.700000 363 89.203667 399 2169 3 chr7A.!!$R3 1770
5 TraesCS7D01G457600 chr7A 666565540 666569158 3618 True 200.800000 261 84.297000 568 3386 5 chr7A.!!$R4 2818
6 TraesCS7D01G457600 chr7B 637947539 637951145 3606 True 648.800000 1262 89.470800 927 4336 5 chr7B.!!$R7 3409
7 TraesCS7D01G457600 chr7B 637960195 637960927 732 True 341.333333 712 90.992000 1 748 3 chr7B.!!$R8 747
8 TraesCS7D01G457600 chr7B 637914097 637917139 3042 True 259.750000 348 83.440250 298 3386 4 chr7B.!!$R6 3088
9 TraesCS7D01G457600 chr7B 637879725 637880594 869 True 210.166667 296 84.861667 402 903 3 chr7B.!!$R5 501
10 TraesCS7D01G457600 chr2B 296287407 296288855 1448 False 242.500000 287 84.777000 1648 3383 2 chr2B.!!$F1 1735

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
788 1348 0.034186 TTGGCAATGGCTCCTAGGTG 60.034 55.0 9.08 7.68 40.87 4.00 F
965 1617 0.537188 GAGGATCGAGTTGAAGGCCA 59.463 55.0 5.01 0.00 0.00 5.36 F
1702 4034 0.249120 CGGTCCATGAACTGGTGCTA 59.751 55.0 0.00 0.00 46.08 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 3769 0.035152 AGAGCACCGATGAATGGCAA 60.035 50.0 0.0 0.0 0.00 4.52 R
2695 5287 1.083806 TCTCCGCATCAACATGACGC 61.084 55.0 0.0 0.0 31.42 5.19 R
3627 6274 0.036765 TAACCGCCAAGTAGCACCTG 60.037 55.0 0.0 0.0 0.00 4.00 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
37 38 7.654568 CCAGCAATGGCCATATATACATATTG 58.345 38.462 21.15 11.34 42.56 1.90
180 228 2.594654 GTCTATCGAACGCAGTCAACTG 59.405 50.000 5.77 5.77 45.00 3.16
208 259 5.494632 ACGTATGTATCGACATCTCAACA 57.505 39.130 0.00 0.00 43.01 3.33
221 276 0.729116 CTCAACAAGCGTAGGCCATG 59.271 55.000 5.01 6.53 41.24 3.66
281 336 5.432885 ACAAAGTCGGGTCACTTATTTTG 57.567 39.130 0.00 0.00 35.45 2.44
461 520 1.677052 TGGTTAGTTTGTCAAACGGGC 59.323 47.619 20.04 14.03 45.88 6.13
527 594 7.918076 AGACCCAGACAAATCAATTAAGTCTA 58.082 34.615 9.21 0.00 35.13 2.59
627 1116 4.505313 ACTTTTTCTCGAATTTGGGCTC 57.495 40.909 0.00 0.00 0.00 4.70
628 1117 3.058224 ACTTTTTCTCGAATTTGGGCTCG 60.058 43.478 0.00 0.00 36.39 5.03
668 1157 2.588620 CGGCCTCTGTTCTCTAGGTAT 58.411 52.381 0.00 0.00 32.67 2.73
763 1323 2.287188 CCTTGCACATTCCATACATCGC 60.287 50.000 0.00 0.00 0.00 4.58
764 1324 0.936600 TGCACATTCCATACATCGCG 59.063 50.000 0.00 0.00 0.00 5.87
765 1325 0.235665 GCACATTCCATACATCGCGG 59.764 55.000 6.13 0.00 0.00 6.46
766 1326 1.864565 CACATTCCATACATCGCGGA 58.135 50.000 6.13 0.00 0.00 5.54
767 1327 2.209273 CACATTCCATACATCGCGGAA 58.791 47.619 6.13 0.00 42.77 4.30
768 1328 2.611751 CACATTCCATACATCGCGGAAA 59.388 45.455 6.13 0.00 41.93 3.13
769 1329 3.250762 CACATTCCATACATCGCGGAAAT 59.749 43.478 6.13 0.00 41.93 2.17
770 1330 3.882888 ACATTCCATACATCGCGGAAATT 59.117 39.130 6.13 0.00 41.93 1.82
771 1331 3.961477 TTCCATACATCGCGGAAATTG 57.039 42.857 6.13 0.00 35.89 2.32
772 1332 2.217750 TCCATACATCGCGGAAATTGG 58.782 47.619 6.13 9.09 0.00 3.16
773 1333 1.334960 CCATACATCGCGGAAATTGGC 60.335 52.381 6.13 0.00 0.00 4.52
774 1334 1.333308 CATACATCGCGGAAATTGGCA 59.667 47.619 6.13 0.00 0.00 4.92
775 1335 1.454201 TACATCGCGGAAATTGGCAA 58.546 45.000 6.13 0.68 0.00 4.52
776 1336 0.817013 ACATCGCGGAAATTGGCAAT 59.183 45.000 6.96 6.96 0.00 3.56
777 1337 1.202203 CATCGCGGAAATTGGCAATG 58.798 50.000 14.47 2.00 0.00 2.82
778 1338 0.102844 ATCGCGGAAATTGGCAATGG 59.897 50.000 14.47 5.09 0.00 3.16
779 1339 2.166579 CGCGGAAATTGGCAATGGC 61.167 57.895 14.47 13.45 40.13 4.40
780 1340 1.218854 GCGGAAATTGGCAATGGCT 59.781 52.632 14.47 1.24 40.87 4.75
781 1341 0.807275 GCGGAAATTGGCAATGGCTC 60.807 55.000 14.47 10.59 40.87 4.70
782 1342 0.179103 CGGAAATTGGCAATGGCTCC 60.179 55.000 14.47 17.49 40.87 4.70
783 1343 1.197812 GGAAATTGGCAATGGCTCCT 58.802 50.000 14.47 0.00 40.87 3.69
784 1344 2.387757 GGAAATTGGCAATGGCTCCTA 58.612 47.619 14.47 0.00 40.87 2.94
785 1345 2.363359 GGAAATTGGCAATGGCTCCTAG 59.637 50.000 14.47 0.00 40.87 3.02
786 1346 2.077687 AATTGGCAATGGCTCCTAGG 57.922 50.000 14.47 0.82 40.87 3.02
787 1347 0.929244 ATTGGCAATGGCTCCTAGGT 59.071 50.000 12.82 0.00 40.87 3.08
788 1348 0.034186 TTGGCAATGGCTCCTAGGTG 60.034 55.000 9.08 7.68 40.87 4.00
789 1349 1.825622 GGCAATGGCTCCTAGGTGC 60.826 63.158 24.68 24.68 40.87 5.01
790 1350 1.077501 GCAATGGCTCCTAGGTGCA 60.078 57.895 31.19 19.96 36.47 4.57
823 1392 9.958285 GTACGCTTGTACTTTTAAAATAGTACC 57.042 33.333 20.10 9.60 43.80 3.34
904 1473 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
905 1474 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
906 1475 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
907 1476 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
908 1477 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
909 1478 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
944 1596 4.258543 GGAACTTGGGTTTGTGATCGATA 58.741 43.478 0.00 0.00 35.58 2.92
945 1597 4.332819 GGAACTTGGGTTTGTGATCGATAG 59.667 45.833 0.00 0.00 35.58 2.08
946 1598 3.873910 ACTTGGGTTTGTGATCGATAGG 58.126 45.455 0.00 0.00 0.00 2.57
947 1599 3.517901 ACTTGGGTTTGTGATCGATAGGA 59.482 43.478 0.00 0.00 0.00 2.94
965 1617 0.537188 GAGGATCGAGTTGAAGGCCA 59.463 55.000 5.01 0.00 0.00 5.36
984 1638 1.055040 AGATAGCTTAGCTGCAGGGG 58.945 55.000 17.97 0.00 40.10 4.79
998 1653 1.143073 GCAGGGGGAGGACGATAAAAT 59.857 52.381 0.00 0.00 0.00 1.82
999 1654 2.810767 GCAGGGGGAGGACGATAAAATC 60.811 54.545 0.00 0.00 0.00 2.17
1011 1669 8.195165 AGGACGATAAAATCATGAGAGGATTA 57.805 34.615 0.09 0.00 34.02 1.75
1020 1678 4.996793 TCATGAGAGGATTAGAGAGGAGG 58.003 47.826 0.00 0.00 0.00 4.30
1047 1705 1.217244 GCAGTACAACCGGTCGGAT 59.783 57.895 16.90 0.61 38.96 4.18
1145 1803 3.549625 GGTCAGTTCTTGCTTCTTGCTTG 60.550 47.826 0.00 0.00 43.37 4.01
1148 1806 2.692041 AGTTCTTGCTTCTTGCTTGCTT 59.308 40.909 0.00 0.00 43.37 3.91
1149 1807 3.048501 GTTCTTGCTTCTTGCTTGCTTC 58.951 45.455 0.00 0.00 43.37 3.86
1150 1808 2.579873 TCTTGCTTCTTGCTTGCTTCT 58.420 42.857 0.00 0.00 43.37 2.85
1151 1809 2.551459 TCTTGCTTCTTGCTTGCTTCTC 59.449 45.455 0.00 0.00 43.37 2.87
1152 1810 1.971481 TGCTTCTTGCTTGCTTCTCA 58.029 45.000 0.00 0.00 43.37 3.27
1153 1811 1.605710 TGCTTCTTGCTTGCTTCTCAC 59.394 47.619 0.00 0.00 43.37 3.51
1154 1812 1.605710 GCTTCTTGCTTGCTTCTCACA 59.394 47.619 0.00 0.00 38.95 3.58
1155 1813 2.604132 GCTTCTTGCTTGCTTCTCACAC 60.604 50.000 0.00 0.00 38.95 3.82
1156 1814 1.220529 TCTTGCTTGCTTCTCACACG 58.779 50.000 0.00 0.00 0.00 4.49
1158 1816 1.331756 CTTGCTTGCTTCTCACACGTT 59.668 47.619 0.00 0.00 0.00 3.99
1160 1818 1.742831 TGCTTGCTTCTCACACGTTTT 59.257 42.857 0.00 0.00 0.00 2.43
1162 1820 3.375610 TGCTTGCTTCTCACACGTTTTTA 59.624 39.130 0.00 0.00 0.00 1.52
1206 1887 1.921243 CACAGTTGCATGCATGGATG 58.079 50.000 27.34 21.79 0.00 3.51
1207 1888 1.474879 CACAGTTGCATGCATGGATGA 59.525 47.619 29.10 12.45 0.00 2.92
1228 2107 6.812879 TGATATGCATGAACCTTGATGATC 57.187 37.500 10.16 0.00 0.00 2.92
1253 2132 2.240612 GATTTGCACTGCCGGACGAC 62.241 60.000 5.05 0.00 0.00 4.34
1298 2177 7.762615 GGATATTTCACGGTATGGATCGATTTA 59.237 37.037 0.00 0.00 0.00 1.40
1307 2209 5.642491 GGTATGGATCGATTTAAAGGGTAGC 59.358 44.000 0.00 0.00 0.00 3.58
1389 2342 3.976015 AGGAAACAAAGAAAGTCCCACA 58.024 40.909 0.00 0.00 0.00 4.17
1418 2371 7.652300 ATGCATGCATGATGAAAAATGATAC 57.348 32.000 31.74 7.50 35.03 2.24
1421 2374 6.365247 GCATGCATGATGAAAAATGATACTCC 59.635 38.462 30.64 1.71 33.31 3.85
1495 2652 8.723365 TCTGTCTCTCTCTAATCTCTCCTTTAT 58.277 37.037 0.00 0.00 0.00 1.40
1527 3633 3.925453 TGGCAATAAGTGACAGCGA 57.075 47.368 0.00 0.00 41.83 4.93
1548 3656 1.939255 ACCTGCCGTTTTGCAAAAATG 59.061 42.857 25.40 19.55 41.51 2.32
1559 3667 6.183360 CGTTTTGCAAAAATGAAACACCACTA 60.183 34.615 25.40 0.00 32.91 2.74
1639 3810 0.601057 TTCATCGGTGCTCTCGTCAA 59.399 50.000 0.00 0.00 0.00 3.18
1688 4014 1.376812 ATTTCTTCACGGCCGGTCC 60.377 57.895 31.76 2.02 0.00 4.46
1702 4034 0.249120 CGGTCCATGAACTGGTGCTA 59.751 55.000 0.00 0.00 46.08 3.49
1865 4394 4.982701 GCAGCAGCAACCCACCCT 62.983 66.667 0.00 0.00 41.58 4.34
1934 4487 1.664965 GCAACGTCGGCTTCAGACT 60.665 57.895 5.03 0.00 36.53 3.24
1964 4523 2.163818 TCCCTCTTACGCTGTGTTTG 57.836 50.000 0.00 0.00 0.00 2.93
2016 4575 4.154195 GTGCCAAATGTGAGTACTACCAAG 59.846 45.833 0.00 0.00 0.00 3.61
2055 4624 9.961266 AATTCCGCTTTTAATTAATTTTTACGC 57.039 25.926 5.91 3.12 0.00 4.42
2100 4674 6.981762 ACATGCTAGCTATTATCTCATTGC 57.018 37.500 17.23 0.00 0.00 3.56
2201 4775 5.453480 GCTAAATACACCAGAGAAGGTAGGG 60.453 48.000 0.00 0.00 40.77 3.53
2203 4777 0.252742 ACACCAGAGAAGGTAGGGGG 60.253 60.000 0.00 0.00 40.77 5.40
2209 4783 3.301274 CAGAGAAGGTAGGGGGAACTAG 58.699 54.545 0.00 0.00 0.00 2.57
2214 4788 5.049294 AGAAGGTAGGGGGAACTAGTAGTA 58.951 45.833 2.50 0.00 0.00 1.82
2215 4789 5.134169 AGAAGGTAGGGGGAACTAGTAGTAG 59.866 48.000 2.50 2.87 0.00 2.57
2216 4790 4.388156 AGGTAGGGGGAACTAGTAGTAGT 58.612 47.826 2.50 4.29 41.61 2.73
2231 4805 9.837525 ACTAGTAGTAGTTATCAAGTGTTTTCG 57.162 33.333 0.00 0.00 35.88 3.46
2232 4806 9.837525 CTAGTAGTAGTTATCAAGTGTTTTCGT 57.162 33.333 0.00 0.00 0.00 3.85
2237 4811 9.538508 AGTAGTTATCAAGTGTTTTCGTTAGTT 57.461 29.630 0.00 0.00 0.00 2.24
2311 4889 1.338973 TGTACTCACACGGACTGGTTC 59.661 52.381 0.00 0.00 0.00 3.62
2695 5287 4.431809 CTGATGTCTTGACTAGCTCTTGG 58.568 47.826 0.00 0.00 0.00 3.61
2957 5599 5.195001 GCTTCTAGCTAGAATGTGCTACT 57.805 43.478 31.24 0.00 41.12 2.57
2958 5600 6.320494 GCTTCTAGCTAGAATGTGCTACTA 57.680 41.667 31.24 9.95 41.12 1.82
2959 5601 6.378582 GCTTCTAGCTAGAATGTGCTACTAG 58.621 44.000 31.24 18.66 41.12 2.57
2960 5602 6.569610 GCTTCTAGCTAGAATGTGCTACTAGG 60.570 46.154 31.24 18.02 41.12 3.02
2961 5603 6.189036 TCTAGCTAGAATGTGCTACTAGGA 57.811 41.667 21.26 0.00 40.35 2.94
2962 5604 6.602278 TCTAGCTAGAATGTGCTACTAGGAA 58.398 40.000 21.26 0.00 40.35 3.36
2964 5606 6.095432 AGCTAGAATGTGCTACTAGGAATG 57.905 41.667 0.00 0.00 37.81 2.67
2965 5607 5.600484 AGCTAGAATGTGCTACTAGGAATGT 59.400 40.000 0.00 0.00 37.81 2.71
2966 5608 5.923684 GCTAGAATGTGCTACTAGGAATGTC 59.076 44.000 0.00 0.00 35.54 3.06
2967 5609 5.939764 AGAATGTGCTACTAGGAATGTCA 57.060 39.130 0.00 0.00 0.00 3.58
2968 5610 6.299805 AGAATGTGCTACTAGGAATGTCAA 57.700 37.500 0.00 0.00 0.00 3.18
2969 5611 6.344500 AGAATGTGCTACTAGGAATGTCAAG 58.656 40.000 0.00 0.00 0.00 3.02
2970 5612 5.939764 ATGTGCTACTAGGAATGTCAAGA 57.060 39.130 0.00 0.00 0.00 3.02
2971 5613 5.330455 TGTGCTACTAGGAATGTCAAGAG 57.670 43.478 0.00 0.00 0.00 2.85
2972 5614 4.116238 GTGCTACTAGGAATGTCAAGAGC 58.884 47.826 0.00 0.00 0.00 4.09
2973 5615 3.133003 TGCTACTAGGAATGTCAAGAGCC 59.867 47.826 0.00 0.00 0.00 4.70
2974 5616 3.133003 GCTACTAGGAATGTCAAGAGCCA 59.867 47.826 0.00 0.00 0.00 4.75
2975 5617 3.902881 ACTAGGAATGTCAAGAGCCAG 57.097 47.619 0.00 0.00 0.00 4.85
2976 5618 3.177228 ACTAGGAATGTCAAGAGCCAGT 58.823 45.455 0.00 0.00 0.00 4.00
2977 5619 2.777832 AGGAATGTCAAGAGCCAGTC 57.222 50.000 0.00 0.00 0.00 3.51
2978 5620 1.980765 AGGAATGTCAAGAGCCAGTCA 59.019 47.619 0.00 0.00 0.00 3.41
2979 5621 2.373169 AGGAATGTCAAGAGCCAGTCAA 59.627 45.455 0.00 0.00 0.00 3.18
2980 5622 2.746362 GGAATGTCAAGAGCCAGTCAAG 59.254 50.000 0.00 0.00 0.00 3.02
2981 5623 3.557898 GGAATGTCAAGAGCCAGTCAAGA 60.558 47.826 0.00 0.00 0.00 3.02
2982 5624 2.533266 TGTCAAGAGCCAGTCAAGAC 57.467 50.000 0.00 0.00 33.85 3.01
3089 5731 4.314440 GGCGACTGGCTGGTCACA 62.314 66.667 10.61 0.00 42.94 3.58
3118 5760 1.527034 TGGCAAGATGTGTCAGAAGC 58.473 50.000 0.00 0.00 36.75 3.86
3148 5790 4.329545 CGGTGGGGTGTGACCTGG 62.330 72.222 0.00 0.00 38.64 4.45
3157 5799 2.279517 GTGACCTGGCGCTATCGG 60.280 66.667 7.64 1.60 35.95 4.18
3159 5801 2.355986 TGACCTGGCGCTATCGGTT 61.356 57.895 7.64 0.00 35.95 4.44
3179 5821 4.400251 CCGGTGGGAGGAGGAGGT 62.400 72.222 0.00 0.00 34.06 3.85
3246 5889 2.044352 GTGCCGGCAAGGGGTTAT 60.044 61.111 34.66 0.00 41.48 1.89
3249 5892 2.123897 CCGGCAAGGGGTTATGGG 60.124 66.667 0.00 0.00 35.97 4.00
3252 5895 2.689813 GCAAGGGGTTATGGGGCT 59.310 61.111 0.00 0.00 0.00 5.19
3294 5937 1.933247 CTTCCGCTGATCTGAACCTC 58.067 55.000 3.42 0.00 0.00 3.85
3346 5989 5.188555 TCTTCTTGGCTCTGATGTGTTATCT 59.811 40.000 0.00 0.00 0.00 1.98
3354 5997 6.870965 GGCTCTGATGTGTTATCTATAACCTG 59.129 42.308 9.72 0.92 41.41 4.00
3357 6000 8.706322 TCTGATGTGTTATCTATAACCTGCTA 57.294 34.615 9.72 0.00 41.41 3.49
3482 6129 6.698380 TGACTAATCCTTTGGTCTAGTTGAC 58.302 40.000 0.00 0.00 42.20 3.18
3523 6170 3.138798 GCCACCCTGCTGAGCATG 61.139 66.667 7.94 4.90 38.13 4.06
3548 6195 7.041780 TGCCAGAATCGCTAATCTTCTTAATTC 60.042 37.037 0.00 0.00 0.00 2.17
3603 6250 5.692814 TGAGCTTGAAGTTGAATTTCATCG 58.307 37.500 3.94 0.92 34.76 3.84
3607 6254 7.820648 AGCTTGAAGTTGAATTTCATCGTATT 58.179 30.769 3.94 0.00 34.76 1.89
3609 6256 7.750458 GCTTGAAGTTGAATTTCATCGTATTGA 59.250 33.333 3.94 0.00 34.76 2.57
3610 6257 9.270576 CTTGAAGTTGAATTTCATCGTATTGAG 57.729 33.333 3.94 0.00 34.76 3.02
3611 6258 7.243487 TGAAGTTGAATTTCATCGTATTGAGC 58.757 34.615 0.00 0.00 30.03 4.26
3612 6259 6.741992 AGTTGAATTTCATCGTATTGAGCA 57.258 33.333 0.00 0.00 0.00 4.26
3613 6260 7.325660 AGTTGAATTTCATCGTATTGAGCAT 57.674 32.000 0.00 0.00 0.00 3.79
3614 6261 8.437360 AGTTGAATTTCATCGTATTGAGCATA 57.563 30.769 0.00 0.00 0.00 3.14
3615 6262 8.892723 AGTTGAATTTCATCGTATTGAGCATAA 58.107 29.630 0.00 0.00 0.00 1.90
3616 6263 9.502145 GTTGAATTTCATCGTATTGAGCATAAA 57.498 29.630 0.00 0.00 0.00 1.40
3617 6264 9.720667 TTGAATTTCATCGTATTGAGCATAAAG 57.279 29.630 0.00 0.00 0.00 1.85
3618 6265 8.892723 TGAATTTCATCGTATTGAGCATAAAGT 58.107 29.630 0.00 0.00 0.00 2.66
3619 6266 9.722056 GAATTTCATCGTATTGAGCATAAAGTT 57.278 29.630 0.00 0.00 0.00 2.66
3620 6267 9.507280 AATTTCATCGTATTGAGCATAAAGTTG 57.493 29.630 0.00 0.00 0.00 3.16
3621 6268 6.603237 TCATCGTATTGAGCATAAAGTTGG 57.397 37.500 0.00 0.00 0.00 3.77
3622 6269 6.345298 TCATCGTATTGAGCATAAAGTTGGA 58.655 36.000 0.00 0.00 0.00 3.53
3623 6270 6.992123 TCATCGTATTGAGCATAAAGTTGGAT 59.008 34.615 0.00 0.00 0.00 3.41
3624 6271 6.844696 TCGTATTGAGCATAAAGTTGGATC 57.155 37.500 0.00 0.00 0.00 3.36
3625 6272 6.582636 TCGTATTGAGCATAAAGTTGGATCT 58.417 36.000 0.00 0.00 0.00 2.75
3626 6273 7.722363 TCGTATTGAGCATAAAGTTGGATCTA 58.278 34.615 0.00 0.00 0.00 1.98
3627 6274 7.652105 TCGTATTGAGCATAAAGTTGGATCTAC 59.348 37.037 0.00 0.00 0.00 2.59
3628 6275 7.438160 CGTATTGAGCATAAAGTTGGATCTACA 59.562 37.037 0.00 0.00 0.00 2.74
3629 6276 7.798596 ATTGAGCATAAAGTTGGATCTACAG 57.201 36.000 0.00 0.00 0.00 2.74
3630 6277 5.674525 TGAGCATAAAGTTGGATCTACAGG 58.325 41.667 0.00 0.00 0.00 4.00
3631 6278 5.189736 TGAGCATAAAGTTGGATCTACAGGT 59.810 40.000 0.00 0.00 0.00 4.00
3632 6279 5.431765 AGCATAAAGTTGGATCTACAGGTG 58.568 41.667 0.00 0.00 0.00 4.00
3633 6280 4.035675 GCATAAAGTTGGATCTACAGGTGC 59.964 45.833 0.00 0.00 0.00 5.01
3634 6281 5.431765 CATAAAGTTGGATCTACAGGTGCT 58.568 41.667 0.00 0.00 0.00 4.40
3635 6282 6.582636 CATAAAGTTGGATCTACAGGTGCTA 58.417 40.000 0.00 0.00 0.00 3.49
3636 6283 4.473477 AAGTTGGATCTACAGGTGCTAC 57.527 45.455 0.00 0.00 0.00 3.58
3637 6284 3.714144 AGTTGGATCTACAGGTGCTACT 58.286 45.455 0.00 0.00 0.00 2.57
3638 6285 4.097418 AGTTGGATCTACAGGTGCTACTT 58.903 43.478 0.00 0.00 0.00 2.24
3639 6286 4.081420 AGTTGGATCTACAGGTGCTACTTG 60.081 45.833 0.00 0.00 0.00 3.16
3640 6287 2.766263 TGGATCTACAGGTGCTACTTGG 59.234 50.000 0.00 0.00 28.38 3.61
3641 6288 2.483889 GGATCTACAGGTGCTACTTGGC 60.484 54.545 0.00 0.00 28.38 4.52
3642 6289 0.530744 TCTACAGGTGCTACTTGGCG 59.469 55.000 0.00 0.00 34.52 5.69
3643 6290 0.460284 CTACAGGTGCTACTTGGCGG 60.460 60.000 0.00 0.00 34.52 6.13
3664 6782 7.107542 GGCGGTTATACTATGGGATTTTATCA 58.892 38.462 0.00 0.00 0.00 2.15
3699 6817 7.010183 CGACTAATCATGGTAGTTTCGACAAAT 59.990 37.037 10.25 0.00 31.88 2.32
3747 6867 8.598041 ACAGGATAGACAACAAGAAGAAATACT 58.402 33.333 0.00 0.00 0.00 2.12
3799 6920 1.077993 CAAAACCTATGGGGGTTGGGA 59.922 52.381 0.00 0.00 45.78 4.37
3847 6968 8.579850 ACAAATGTATAATCATGAAGTGGTGT 57.420 30.769 0.00 0.00 0.00 4.16
3870 6991 0.659427 CGCATTCACCATGATTCGCT 59.341 50.000 0.00 0.00 34.31 4.93
3899 7036 6.493458 AGTGTTATGGCTTAAACTCCAAATGT 59.507 34.615 0.00 0.00 35.75 2.71
3903 7040 3.826157 TGGCTTAAACTCCAAATGTCCAG 59.174 43.478 0.00 0.00 0.00 3.86
3911 7048 6.994421 AACTCCAAATGTCCAGGTATTTTT 57.006 33.333 2.77 0.00 0.00 1.94
3928 7074 4.627284 TTTTTCTGACGTGGATCCCTTA 57.373 40.909 9.90 0.00 0.00 2.69
3937 7083 2.099098 CGTGGATCCCTTAAATGCCAAC 59.901 50.000 9.90 0.00 0.00 3.77
3987 7133 5.725362 TCTGGAAATTTTTGGTGAACGTTT 58.275 33.333 0.46 0.00 0.00 3.60
3999 7145 5.655488 TGGTGAACGTTTGTGATGAATTTT 58.345 33.333 0.46 0.00 0.00 1.82
4004 7150 7.009174 GTGAACGTTTGTGATGAATTTTGTTCT 59.991 33.333 0.46 0.00 34.61 3.01
4005 7151 7.543868 TGAACGTTTGTGATGAATTTTGTTCTT 59.456 29.630 0.46 0.00 34.61 2.52
4013 7159 7.492020 TGTGATGAATTTTGTTCTTTGGTCAAG 59.508 33.333 0.00 0.00 0.00 3.02
4113 7307 5.683681 TCCCCGGTTATGTTTTCCTATTAC 58.316 41.667 0.00 0.00 0.00 1.89
4118 7312 8.373220 CCCGGTTATGTTTTCCTATTACTCTAT 58.627 37.037 0.00 0.00 0.00 1.98
4171 7366 6.071051 GCTAATAACTGGGATTTTGGTTTCCA 60.071 38.462 0.00 0.00 33.43 3.53
4237 7432 0.178961 GCCCTGTTCCCAAACCTCTT 60.179 55.000 0.00 0.00 34.28 2.85
4312 7507 5.484715 TGTTAAGTCCCTTTACTCCAATCG 58.515 41.667 0.00 0.00 0.00 3.34
4320 7515 3.306166 CCTTTACTCCAATCGTTGCGTAG 59.694 47.826 0.00 0.00 0.00 3.51
4328 7523 4.728102 CGTTGCGTAGGGGCGACA 62.728 66.667 0.00 0.00 45.70 4.35
4336 7531 0.252197 GTAGGGGCGACACTCCAATT 59.748 55.000 0.00 0.00 45.07 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.316308 GGCAATGGGATGTAGTGAATGTC 59.684 47.826 0.00 0.00 0.00 3.06
180 228 6.129088 TGAGATGTCGATACATACGTACGTAC 60.129 42.308 28.99 17.12 46.49 3.67
208 259 1.153168 ATTCGCATGGCCTACGCTT 60.153 52.632 3.32 0.00 34.44 4.68
221 276 4.822026 AGGGAGTATATAGCAACATTCGC 58.178 43.478 0.00 0.00 0.00 4.70
257 312 6.368213 CAAAATAAGTGACCCGACTTTGTAC 58.632 40.000 0.00 0.00 37.38 2.90
281 336 4.031636 ACTATAGTACTCCATCCGTCCC 57.968 50.000 2.75 0.00 0.00 4.46
461 520 4.811024 ACAGGCATATATGTGAACAGTTCG 59.189 41.667 14.14 0.00 0.00 3.95
527 594 0.537143 TGCGTCAACCCATCAAGCTT 60.537 50.000 0.00 0.00 0.00 3.74
627 1116 1.661112 GGAAGAATCAAGAGGAACGCG 59.339 52.381 3.53 3.53 0.00 6.01
628 1117 2.010497 GGGAAGAATCAAGAGGAACGC 58.990 52.381 0.00 0.00 0.00 4.84
668 1157 5.955959 TCCATGCTCACTTAACTTAGGTAGA 59.044 40.000 0.00 0.00 0.00 2.59
763 1323 0.179103 GGAGCCATTGCCAATTTCCG 60.179 55.000 0.00 0.00 38.69 4.30
764 1324 1.197812 AGGAGCCATTGCCAATTTCC 58.802 50.000 4.85 4.85 38.69 3.13
765 1325 2.363359 CCTAGGAGCCATTGCCAATTTC 59.637 50.000 1.05 0.00 38.69 2.17
766 1326 2.292455 ACCTAGGAGCCATTGCCAATTT 60.292 45.455 17.98 0.00 38.69 1.82
767 1327 1.288932 ACCTAGGAGCCATTGCCAATT 59.711 47.619 17.98 0.00 38.69 2.32
768 1328 0.929244 ACCTAGGAGCCATTGCCAAT 59.071 50.000 17.98 0.00 38.69 3.16
769 1329 0.034186 CACCTAGGAGCCATTGCCAA 60.034 55.000 17.98 0.00 38.69 4.52
770 1330 1.609239 CACCTAGGAGCCATTGCCA 59.391 57.895 17.98 0.00 38.69 4.92
771 1331 1.825622 GCACCTAGGAGCCATTGCC 60.826 63.158 19.57 0.00 38.69 4.52
772 1332 0.466922 ATGCACCTAGGAGCCATTGC 60.467 55.000 25.94 18.71 37.95 3.56
773 1333 2.936919 TATGCACCTAGGAGCCATTG 57.063 50.000 25.94 9.40 0.00 2.82
774 1334 5.966935 ACTATATATGCACCTAGGAGCCATT 59.033 40.000 25.94 14.38 0.00 3.16
775 1335 5.533112 ACTATATATGCACCTAGGAGCCAT 58.467 41.667 25.94 20.41 0.00 4.40
776 1336 4.947883 ACTATATATGCACCTAGGAGCCA 58.052 43.478 25.94 15.42 0.00 4.75
777 1337 5.008811 CGTACTATATATGCACCTAGGAGCC 59.991 48.000 25.94 10.55 0.00 4.70
778 1338 5.505985 GCGTACTATATATGCACCTAGGAGC 60.506 48.000 22.91 22.91 0.00 4.70
779 1339 5.823570 AGCGTACTATATATGCACCTAGGAG 59.176 44.000 17.98 9.24 32.18 3.69
780 1340 5.752650 AGCGTACTATATATGCACCTAGGA 58.247 41.667 17.98 0.00 32.18 2.94
781 1341 6.127703 ACAAGCGTACTATATATGCACCTAGG 60.128 42.308 7.41 7.41 32.18 3.02
782 1342 6.853720 ACAAGCGTACTATATATGCACCTAG 58.146 40.000 0.00 0.00 32.18 3.02
783 1343 6.829229 ACAAGCGTACTATATATGCACCTA 57.171 37.500 0.00 0.00 32.18 3.08
784 1344 5.723672 ACAAGCGTACTATATATGCACCT 57.276 39.130 0.00 0.00 32.18 4.00
785 1345 6.866179 GTACAAGCGTACTATATATGCACC 57.134 41.667 0.00 0.00 43.97 5.01
812 1381 6.770746 ACTCGAAGCTCAGGTACTATTTTA 57.229 37.500 0.00 0.00 36.02 1.52
823 1392 3.931468 ACAATGATGAACTCGAAGCTCAG 59.069 43.478 0.00 0.00 0.00 3.35
906 1475 9.615660 ACCCAAGTTCCAATATATATGTAGAGA 57.384 33.333 0.00 0.00 0.00 3.10
944 1596 0.827368 GCCTTCAACTCGATCCTCCT 59.173 55.000 0.00 0.00 0.00 3.69
945 1597 0.179070 GGCCTTCAACTCGATCCTCC 60.179 60.000 0.00 0.00 0.00 4.30
946 1598 0.537188 TGGCCTTCAACTCGATCCTC 59.463 55.000 3.32 0.00 0.00 3.71
947 1599 0.539051 CTGGCCTTCAACTCGATCCT 59.461 55.000 3.32 0.00 0.00 3.24
965 1617 1.055040 CCCCTGCAGCTAAGCTATCT 58.945 55.000 8.66 0.00 36.40 1.98
984 1638 5.011125 TCCTCTCATGATTTTATCGTCCTCC 59.989 44.000 0.00 0.00 0.00 4.30
998 1653 4.202663 CCCTCCTCTCTAATCCTCTCATGA 60.203 50.000 0.00 0.00 0.00 3.07
999 1654 4.088634 CCCTCCTCTCTAATCCTCTCATG 58.911 52.174 0.00 0.00 0.00 3.07
1011 1669 4.824515 CGGACGCCCCTCCTCTCT 62.825 72.222 0.00 0.00 0.00 3.10
1020 1678 4.382320 TTGTACTGCCGGACGCCC 62.382 66.667 5.05 0.00 36.24 6.13
1199 1880 5.475564 TCAAGGTTCATGCATATCATCCATG 59.524 40.000 0.00 2.09 38.10 3.66
1200 1881 5.637127 TCAAGGTTCATGCATATCATCCAT 58.363 37.500 0.00 0.00 31.79 3.41
1201 1882 5.051409 TCAAGGTTCATGCATATCATCCA 57.949 39.130 0.00 0.00 31.79 3.41
1202 1883 5.708697 TCATCAAGGTTCATGCATATCATCC 59.291 40.000 0.00 0.00 31.79 3.51
1204 1885 7.175797 AGATCATCAAGGTTCATGCATATCAT 58.824 34.615 0.00 0.00 35.31 2.45
1205 1886 6.540083 AGATCATCAAGGTTCATGCATATCA 58.460 36.000 0.00 0.00 0.00 2.15
1206 1887 6.653740 TGAGATCATCAAGGTTCATGCATATC 59.346 38.462 0.00 0.00 34.02 1.63
1207 1888 6.540083 TGAGATCATCAAGGTTCATGCATAT 58.460 36.000 0.00 0.00 34.02 1.78
1228 2107 0.027194 CGGCAGTGCAAATCGATGAG 59.973 55.000 18.61 0.00 0.00 2.90
1253 2132 2.621055 TCCACAATTTTTGACAGGTCGG 59.379 45.455 0.00 0.00 0.00 4.79
1307 2209 2.268298 ACCGCACGACTAAAGCAATAG 58.732 47.619 0.00 0.00 0.00 1.73
1389 2342 8.093927 TCATTTTTCATCATGCATGCATATCAT 58.906 29.630 31.73 20.26 34.91 2.45
1418 2371 1.094785 AATTTGATGGAACGGCGGAG 58.905 50.000 13.24 0.00 0.00 4.63
1421 2374 2.849880 ATCAATTTGATGGAACGGCG 57.150 45.000 11.06 4.80 35.43 6.46
1495 2652 5.480073 ACTTATTGCCAAAGTCAGCCAATAA 59.520 36.000 0.00 0.00 31.56 1.40
1527 3633 2.100605 TTTTTGCAAAACGGCAGGTT 57.899 40.000 23.79 0.00 45.88 3.50
1548 3656 9.294030 GATCAAAATCATGATTAGTGGTGTTTC 57.706 33.333 21.00 11.25 40.08 2.78
1596 3745 4.400884 TGGCAAATAAAGGATGTACGCAAT 59.599 37.500 0.00 0.00 0.00 3.56
1614 3769 0.035152 AGAGCACCGATGAATGGCAA 60.035 50.000 0.00 0.00 0.00 4.52
1688 4014 5.571784 ATTGATGTTAGCACCAGTTCATG 57.428 39.130 0.00 0.00 0.00 3.07
1702 4034 8.579006 ACAAGATGTGTGAACATAATTGATGTT 58.421 29.630 16.85 0.00 46.26 2.71
1851 4362 2.418083 GCATAGGGTGGGTTGCTGC 61.418 63.158 0.00 0.00 32.41 5.25
1865 4394 3.181491 TGACGACGATTCACTGATGCATA 60.181 43.478 0.00 0.00 0.00 3.14
1934 4487 2.361119 CGTAAGAGGGAATGTCGATCCA 59.639 50.000 5.92 0.00 38.06 3.41
2090 4664 2.159099 GGACGGTCTGTGCAATGAGATA 60.159 50.000 8.23 0.00 39.04 1.98
2100 4674 1.139734 CCTCGATGGACGGTCTGTG 59.860 63.158 8.23 0.00 42.82 3.66
2201 4775 8.291191 ACACTTGATAACTACTACTAGTTCCC 57.709 38.462 0.00 0.00 41.51 3.97
2311 4889 8.774586 CCTAATTACAATCCTTGAATCCGTAAG 58.225 37.037 0.00 0.00 0.00 2.34
2636 5221 9.838339 CAACAATAATCCTAGAAGAATACAGGT 57.162 33.333 0.00 0.00 0.00 4.00
2695 5287 1.083806 TCTCCGCATCAACATGACGC 61.084 55.000 0.00 0.00 31.42 5.19
2700 5292 1.487976 ACCTGATCTCCGCATCAACAT 59.512 47.619 0.00 0.00 32.24 2.71
2710 5302 9.566432 AAAAGATATCAATTACACCTGATCTCC 57.434 33.333 5.32 0.00 34.21 3.71
2805 5397 7.541122 TGTTAACTTTTAATGGTTGGTTTGC 57.459 32.000 7.22 0.00 0.00 3.68
2957 5599 3.173151 TGACTGGCTCTTGACATTCCTA 58.827 45.455 0.00 0.00 30.70 2.94
2958 5600 1.980765 TGACTGGCTCTTGACATTCCT 59.019 47.619 0.00 0.00 30.70 3.36
2959 5601 2.479566 TGACTGGCTCTTGACATTCC 57.520 50.000 0.00 0.00 30.70 3.01
2960 5602 3.434984 GTCTTGACTGGCTCTTGACATTC 59.565 47.826 0.00 0.00 32.21 2.67
2961 5603 3.181451 TGTCTTGACTGGCTCTTGACATT 60.181 43.478 2.35 0.00 31.48 2.71
2962 5604 2.369860 TGTCTTGACTGGCTCTTGACAT 59.630 45.455 2.35 0.00 31.48 3.06
2964 5606 2.533266 TGTCTTGACTGGCTCTTGAC 57.467 50.000 2.35 0.00 0.00 3.18
2965 5607 2.634453 TGATGTCTTGACTGGCTCTTGA 59.366 45.455 2.35 0.00 0.00 3.02
2966 5608 3.049708 TGATGTCTTGACTGGCTCTTG 57.950 47.619 2.35 0.00 0.00 3.02
2967 5609 3.777106 TTGATGTCTTGACTGGCTCTT 57.223 42.857 2.35 0.00 0.00 2.85
2968 5610 3.777106 TTTGATGTCTTGACTGGCTCT 57.223 42.857 2.35 0.00 0.00 4.09
2969 5611 6.073331 GCTATATTTGATGTCTTGACTGGCTC 60.073 42.308 2.35 0.00 0.00 4.70
2970 5612 5.762218 GCTATATTTGATGTCTTGACTGGCT 59.238 40.000 2.35 0.00 0.00 4.75
2971 5613 5.528690 TGCTATATTTGATGTCTTGACTGGC 59.471 40.000 2.35 0.00 0.00 4.85
2972 5614 7.558161 TTGCTATATTTGATGTCTTGACTGG 57.442 36.000 2.35 0.00 0.00 4.00
2973 5615 8.833493 TCATTGCTATATTTGATGTCTTGACTG 58.167 33.333 2.35 0.00 0.00 3.51
2974 5616 8.969260 TCATTGCTATATTTGATGTCTTGACT 57.031 30.769 2.35 0.00 0.00 3.41
2975 5617 9.661187 CTTCATTGCTATATTTGATGTCTTGAC 57.339 33.333 0.00 0.00 0.00 3.18
2976 5618 9.617523 TCTTCATTGCTATATTTGATGTCTTGA 57.382 29.630 0.00 0.00 0.00 3.02
3157 5799 4.410400 CTCCTCCCACCGGCCAAC 62.410 72.222 0.00 0.00 0.00 3.77
3179 5821 0.516001 GTCAGTGTCACTACTCGCGA 59.484 55.000 9.26 9.26 0.00 5.87
3294 5937 1.914634 CAAGATCGAGGTTCAGGTCG 58.085 55.000 0.00 0.00 37.54 4.79
3449 6092 5.192927 CCAAAGGATTAGTCAACTGCCATA 58.807 41.667 0.00 0.00 0.00 2.74
3482 6129 2.252260 CAAAGGTGCGGCAGTTCG 59.748 61.111 1.18 0.00 0.00 3.95
3523 6170 6.793492 ATTAAGAAGATTAGCGATTCTGGC 57.207 37.500 0.00 0.00 33.67 4.85
3603 6250 8.662781 TGTAGATCCAACTTTATGCTCAATAC 57.337 34.615 0.00 0.00 0.00 1.89
3607 6254 5.189736 ACCTGTAGATCCAACTTTATGCTCA 59.810 40.000 0.00 0.00 0.00 4.26
3609 6256 5.431765 CACCTGTAGATCCAACTTTATGCT 58.568 41.667 0.00 0.00 0.00 3.79
3610 6257 4.035675 GCACCTGTAGATCCAACTTTATGC 59.964 45.833 0.00 0.00 0.00 3.14
3611 6258 5.431765 AGCACCTGTAGATCCAACTTTATG 58.568 41.667 0.00 0.00 0.00 1.90
3612 6259 5.700402 AGCACCTGTAGATCCAACTTTAT 57.300 39.130 0.00 0.00 0.00 1.40
3613 6260 5.720041 AGTAGCACCTGTAGATCCAACTTTA 59.280 40.000 0.00 0.00 0.00 1.85
3614 6261 4.532521 AGTAGCACCTGTAGATCCAACTTT 59.467 41.667 0.00 0.00 0.00 2.66
3615 6262 4.097418 AGTAGCACCTGTAGATCCAACTT 58.903 43.478 0.00 0.00 0.00 2.66
3616 6263 3.714144 AGTAGCACCTGTAGATCCAACT 58.286 45.455 0.00 0.00 0.00 3.16
3617 6264 4.184629 CAAGTAGCACCTGTAGATCCAAC 58.815 47.826 0.00 0.00 0.00 3.77
3618 6265 3.197766 CCAAGTAGCACCTGTAGATCCAA 59.802 47.826 0.00 0.00 0.00 3.53
3619 6266 2.766263 CCAAGTAGCACCTGTAGATCCA 59.234 50.000 0.00 0.00 0.00 3.41
3620 6267 2.483889 GCCAAGTAGCACCTGTAGATCC 60.484 54.545 0.00 0.00 0.00 3.36
3621 6268 2.799917 CGCCAAGTAGCACCTGTAGATC 60.800 54.545 0.00 0.00 0.00 2.75
3622 6269 1.137086 CGCCAAGTAGCACCTGTAGAT 59.863 52.381 0.00 0.00 0.00 1.98
3623 6270 0.530744 CGCCAAGTAGCACCTGTAGA 59.469 55.000 0.00 0.00 0.00 2.59
3624 6271 0.460284 CCGCCAAGTAGCACCTGTAG 60.460 60.000 0.00 0.00 0.00 2.74
3625 6272 1.189524 ACCGCCAAGTAGCACCTGTA 61.190 55.000 0.00 0.00 0.00 2.74
3626 6273 2.052047 AACCGCCAAGTAGCACCTGT 62.052 55.000 0.00 0.00 0.00 4.00
3627 6274 0.036765 TAACCGCCAAGTAGCACCTG 60.037 55.000 0.00 0.00 0.00 4.00
3628 6275 0.909623 ATAACCGCCAAGTAGCACCT 59.090 50.000 0.00 0.00 0.00 4.00
3629 6276 2.159000 AGTATAACCGCCAAGTAGCACC 60.159 50.000 0.00 0.00 0.00 5.01
3630 6277 3.175109 AGTATAACCGCCAAGTAGCAC 57.825 47.619 0.00 0.00 0.00 4.40
3631 6278 4.262292 CCATAGTATAACCGCCAAGTAGCA 60.262 45.833 0.00 0.00 0.00 3.49
3632 6279 4.243270 CCATAGTATAACCGCCAAGTAGC 58.757 47.826 0.00 0.00 0.00 3.58
3633 6280 4.525487 TCCCATAGTATAACCGCCAAGTAG 59.475 45.833 0.00 0.00 0.00 2.57
3634 6281 4.482030 TCCCATAGTATAACCGCCAAGTA 58.518 43.478 0.00 0.00 0.00 2.24
3635 6282 3.311091 TCCCATAGTATAACCGCCAAGT 58.689 45.455 0.00 0.00 0.00 3.16
3636 6283 4.553330 ATCCCATAGTATAACCGCCAAG 57.447 45.455 0.00 0.00 0.00 3.61
3637 6284 4.986054 AATCCCATAGTATAACCGCCAA 57.014 40.909 0.00 0.00 0.00 4.52
3638 6285 4.986054 AAATCCCATAGTATAACCGCCA 57.014 40.909 0.00 0.00 0.00 5.69
3639 6286 7.065443 GTGATAAAATCCCATAGTATAACCGCC 59.935 40.741 0.00 0.00 0.00 6.13
3640 6287 7.065443 GGTGATAAAATCCCATAGTATAACCGC 59.935 40.741 0.00 0.00 0.00 5.68
3641 6288 8.319146 AGGTGATAAAATCCCATAGTATAACCG 58.681 37.037 0.00 0.00 32.75 4.44
3664 6782 3.055094 ACCATGATTAGTCGCAGAAAGGT 60.055 43.478 0.00 0.00 39.69 3.50
3699 6817 8.511321 CCTGTTACAGTAAAAAGCATTGTGATA 58.489 33.333 11.68 0.00 0.00 2.15
3724 6844 9.606631 ATCAGTATTTCTTCTTGTTGTCTATCC 57.393 33.333 0.00 0.00 0.00 2.59
3752 6872 8.992073 GGTCTGCAAATGATTTTTCATTTAACT 58.008 29.630 12.22 0.00 45.34 2.24
3771 6891 2.214376 CCATAGGTTTTGGGTCTGCA 57.786 50.000 0.00 0.00 0.00 4.41
3794 6915 8.757877 CATTAAGGAGGTTTTAATGATTCCCAA 58.242 33.333 10.63 0.00 45.07 4.12
3870 6991 6.065374 TGGAGTTTAAGCCATAACACTTGAA 58.935 36.000 0.00 0.00 0.00 2.69
3899 7036 3.325425 TCCACGTCAGAAAAATACCTGGA 59.675 43.478 0.00 0.00 0.00 3.86
3903 7040 3.626217 GGGATCCACGTCAGAAAAATACC 59.374 47.826 15.23 0.00 0.00 2.73
3911 7048 3.681594 GCATTTAAGGGATCCACGTCAGA 60.682 47.826 15.23 0.00 0.00 3.27
3973 7119 4.703645 TCATCACAAACGTTCACCAAAA 57.296 36.364 0.00 0.00 0.00 2.44
3983 7129 7.118724 CCAAAGAACAAAATTCATCACAAACG 58.881 34.615 0.00 0.00 0.00 3.60
3987 7133 6.871844 TGACCAAAGAACAAAATTCATCACA 58.128 32.000 0.00 0.00 0.00 3.58
3999 7145 3.130340 GCCTCAAACTTGACCAAAGAACA 59.870 43.478 0.00 0.00 39.38 3.18
4004 7150 4.164843 ACTAGCCTCAAACTTGACCAAA 57.835 40.909 0.00 0.00 32.90 3.28
4005 7151 3.857157 ACTAGCCTCAAACTTGACCAA 57.143 42.857 0.00 0.00 32.90 3.67
4013 7159 2.552743 GGTCACCAAACTAGCCTCAAAC 59.447 50.000 0.00 0.00 0.00 2.93
4089 7237 4.866327 ATAGGAAAACATAACCGGGGAA 57.134 40.909 6.32 0.00 0.00 3.97
4091 7239 5.687780 AGTAATAGGAAAACATAACCGGGG 58.312 41.667 6.32 0.00 0.00 5.73
4118 7312 7.285401 GCTACCTTTGAAATGGAGATATTTGGA 59.715 37.037 0.00 0.00 30.78 3.53
4124 7319 5.104360 AGCAGCTACCTTTGAAATGGAGATA 60.104 40.000 0.00 0.00 0.00 1.98
4171 7366 0.033796 TACGGGAGACAAGGATCGGT 60.034 55.000 0.00 0.00 0.00 4.69
4237 7432 2.091389 AGGAGCTGATCAGAAGCCTCTA 60.091 50.000 27.04 0.00 41.82 2.43
4312 7507 3.116531 GTGTCGCCCCTACGCAAC 61.117 66.667 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.