Multiple sequence alignment - TraesCS5D01G064100

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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 TraesCS5D01G064100 chr5D 100.000 4796 0 0 1 4796 59243240 59248035 0.000000e+00 8857.0
1 TraesCS5D01G064100 chr5D 83.620 873 109 12 2986 3824 59223754 59222882 0.000000e+00 789.0
2 TraesCS5D01G064100 chr5D 89.960 498 33 9 1044 1531 59363565 59363075 1.130000e-175 627.0
3 TraesCS5D01G064100 chr5D 82.438 763 89 24 3350 4071 59295741 59294983 4.080000e-175 625.0
4 TraesCS5D01G064100 chr5D 83.540 565 62 11 1044 1578 59358775 59358212 2.580000e-137 499.0
5 TraesCS5D01G064100 chr5D 85.523 373 46 6 1206 1574 59225555 59225187 2.710000e-102 383.0
6 TraesCS5D01G064100 chr5D 94.030 201 12 0 2594 2794 59224029 59223829 6.030000e-79 305.0
7 TraesCS5D01G064100 chr5D 76.051 547 91 26 1914 2430 59224627 59224091 1.030000e-61 248.0
8 TraesCS5D01G064100 chr5D 85.780 218 19 8 991 1206 59225813 59225606 2.250000e-53 220.0
9 TraesCS5D01G064100 chr5B 95.130 2382 83 7 2429 4796 72008853 72006491 0.000000e+00 3725.0
10 TraesCS5D01G064100 chr5B 82.257 1967 251 62 2161 4071 71675136 71673212 0.000000e+00 1609.0
11 TraesCS5D01G064100 chr5B 93.162 702 33 5 1754 2445 72009575 72008879 0.000000e+00 1016.0
12 TraesCS5D01G064100 chr5B 91.610 441 23 6 781 1208 72010482 72010043 8.880000e-167 597.0
13 TraesCS5D01G064100 chr5B 94.652 374 19 1 1206 1578 72009999 72009626 3.220000e-161 579.0
14 TraesCS5D01G064100 chr5B 85.481 551 78 2 2986 3535 72018281 72018830 1.500000e-159 573.0
15 TraesCS5D01G064100 chr5B 84.375 384 51 7 1208 1588 72016290 72016667 7.580000e-98 368.0
16 TraesCS5D01G064100 chr5B 92.537 201 15 0 2594 2794 72018009 72018209 6.070000e-74 289.0
17 TraesCS5D01G064100 chr5B 88.793 232 23 2 1358 1589 71683765 71683537 1.020000e-71 281.0
18 TraesCS5D01G064100 chr5B 88.745 231 21 4 3587 3812 72018915 72019145 1.310000e-70 278.0
19 TraesCS5D01G064100 chr5B 88.393 224 24 1 3592 3813 71672383 71672160 7.910000e-68 268.0
20 TraesCS5D01G064100 chr5B 82.707 266 35 8 1914 2171 72017197 72017459 4.830000e-55 226.0
21 TraesCS5D01G064100 chr5B 85.279 197 18 5 991 1183 72016039 72016228 4.900000e-45 193.0
22 TraesCS5D01G064100 chr5B 87.050 139 14 1 1964 2098 71675287 71675149 2.310000e-33 154.0
23 TraesCS5D01G064100 chr5A 94.216 2386 86 9 2429 4796 47651537 47653888 0.000000e+00 3594.0
24 TraesCS5D01G064100 chr5A 87.750 849 52 26 781 1578 47649984 47650831 0.000000e+00 944.0
25 TraesCS5D01G064100 chr5A 84.507 852 96 14 2986 3802 47645487 47644637 0.000000e+00 809.0
26 TraesCS5D01G064100 chr5A 94.277 332 18 1 2115 2445 47651192 47651523 1.540000e-139 507.0
27 TraesCS5D01G064100 chr5A 86.595 373 42 6 1206 1574 47647078 47646710 5.780000e-109 405.0
28 TraesCS5D01G064100 chr5A 91.781 292 17 1 1754 2038 47650887 47651178 2.690000e-107 399.0
29 TraesCS5D01G064100 chr5A 87.075 294 35 3 4039 4330 592689220 592689512 3.580000e-86 329.0
30 TraesCS5D01G064100 chr5A 93.069 202 14 0 2593 2794 47645766 47645565 3.630000e-76 296.0
31 TraesCS5D01G064100 chr5A 76.697 545 87 30 1914 2429 47646547 47646014 2.850000e-67 267.0
32 TraesCS5D01G064100 chr5A 84.932 219 22 6 991 1206 47647346 47647136 1.350000e-50 211.0
33 TraesCS5D01G064100 chr5A 97.143 35 1 0 1726 1760 47650833 47650867 5.180000e-05 60.2
34 TraesCS5D01G064100 chr2D 87.002 2185 183 40 1758 3883 41479581 41477439 0.000000e+00 2368.0
35 TraesCS5D01G064100 chr2D 89.518 477 47 2 3887 4360 41468773 41468297 6.870000e-168 601.0
36 TraesCS5D01G064100 chr2D 91.885 382 28 1 1208 1589 41781289 41780911 9.140000e-147 531.0
37 TraesCS5D01G064100 chr2D 88.346 266 20 4 950 1208 41781592 41781331 4.660000e-80 309.0
38 TraesCS5D01G064100 chr2D 82.653 98 7 3 795 892 41798546 41798459 1.430000e-10 78.7
39 TraesCS5D01G064100 chr2D 89.474 57 3 2 690 745 647524749 647524695 8.610000e-08 69.4
40 TraesCS5D01G064100 chr3D 95.612 752 20 7 1 740 481927602 481928352 0.000000e+00 1194.0
41 TraesCS5D01G064100 chr3D 95.553 742 25 3 4 742 126943106 126942370 0.000000e+00 1181.0
42 TraesCS5D01G064100 chr7D 96.783 373 10 1 4 374 63920857 63920485 5.270000e-174 621.0
43 TraesCS5D01G064100 chr7D 93.824 340 11 1 407 736 63920496 63920157 1.990000e-138 503.0
44 TraesCS5D01G064100 chr2A 91.281 367 30 2 384 749 22188602 22188237 2.580000e-137 499.0
45 TraesCS5D01G064100 chr2A 90.736 367 32 2 10 374 22188935 22188569 5.580000e-134 488.0
46 TraesCS5D01G064100 chr2A 90.741 54 2 2 690 742 772955889 772955940 8.610000e-08 69.4
47 TraesCS5D01G064100 chr6A 83.461 393 56 7 7 395 62605679 62606066 1.640000e-94 357.0
48 TraesCS5D01G064100 chr6A 82.653 392 60 7 7 395 62638037 62638423 1.650000e-89 340.0
49 TraesCS5D01G064100 chr4B 88.530 279 28 4 4040 4317 374729995 374729720 7.690000e-88 335.0
50 TraesCS5D01G064100 chr6B 88.364 275 31 1 4042 4315 465696550 465696276 3.580000e-86 329.0
51 TraesCS5D01G064100 chr4A 86.379 301 37 4 4032 4329 117703103 117703402 4.630000e-85 326.0
52 TraesCS5D01G064100 chr4A 82.192 73 9 3 669 740 37772861 37772930 5.180000e-05 60.2
53 TraesCS5D01G064100 chr4D 87.814 279 31 3 4040 4317 301022202 301021926 1.660000e-84 324.0
54 TraesCS5D01G064100 chr6D 86.577 298 31 8 4038 4328 472683988 472683693 2.150000e-83 320.0
55 TraesCS5D01G064100 chr1D 84.091 176 26 2 1255 1429 4823669 4823843 8.250000e-38 169.0
56 TraesCS5D01G064100 chr1D 75.138 362 65 22 1072 1419 90148702 90149052 3.870000e-31 147.0
57 TraesCS5D01G064100 chr2B 88.235 68 2 5 679 744 796840896 796840833 5.150000e-10 76.8
58 TraesCS5D01G064100 chr7B 87.500 64 5 2 679 742 648042016 648042076 2.390000e-08 71.3


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 TraesCS5D01G064100 chr5D 59243240 59248035 4795 False 8857.000000 8857 100.000000 1 4796 1 chr5D.!!$F1 4795
1 TraesCS5D01G064100 chr5D 59294983 59295741 758 True 625.000000 625 82.438000 3350 4071 1 chr5D.!!$R1 721
2 TraesCS5D01G064100 chr5D 59358212 59358775 563 True 499.000000 499 83.540000 1044 1578 1 chr5D.!!$R2 534
3 TraesCS5D01G064100 chr5D 59222882 59225813 2931 True 389.000000 789 85.000800 991 3824 5 chr5D.!!$R4 2833
4 TraesCS5D01G064100 chr5B 72006491 72010482 3991 True 1479.250000 3725 93.638500 781 4796 4 chr5B.!!$R3 4015
5 TraesCS5D01G064100 chr5B 71672160 71675287 3127 True 677.000000 1609 85.900000 1964 4071 3 chr5B.!!$R2 2107
6 TraesCS5D01G064100 chr5B 72016039 72019145 3106 False 321.166667 573 86.520667 991 3812 6 chr5B.!!$F1 2821
7 TraesCS5D01G064100 chr5A 47649984 47653888 3904 False 1100.840000 3594 93.033400 781 4796 5 chr5A.!!$F2 4015
8 TraesCS5D01G064100 chr5A 47644637 47647346 2709 True 397.600000 809 85.160000 991 3802 5 chr5A.!!$R1 2811
9 TraesCS5D01G064100 chr2D 41477439 41479581 2142 True 2368.000000 2368 87.002000 1758 3883 1 chr2D.!!$R2 2125
10 TraesCS5D01G064100 chr2D 41780911 41781592 681 True 420.000000 531 90.115500 950 1589 2 chr2D.!!$R5 639
11 TraesCS5D01G064100 chr3D 481927602 481928352 750 False 1194.000000 1194 95.612000 1 740 1 chr3D.!!$F1 739
12 TraesCS5D01G064100 chr3D 126942370 126943106 736 True 1181.000000 1181 95.553000 4 742 1 chr3D.!!$R1 738
13 TraesCS5D01G064100 chr7D 63920157 63920857 700 True 562.000000 621 95.303500 4 736 2 chr7D.!!$R1 732
14 TraesCS5D01G064100 chr2A 22188237 22188935 698 True 493.500000 499 91.008500 10 749 2 chr2A.!!$R1 739

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
458 467 1.202533 CGTGGAGCCGGTGAGAAATAT 60.203 52.381 1.90 0.0 0.00 1.28 F
1024 1081 0.249657 GAGCCGCCTCTTCCACTATG 60.250 60.000 0.00 0.0 35.16 2.23 F
2208 3109 0.037232 GTCCTCAGTGGTTTCCCTCG 60.037 60.000 0.00 0.0 37.07 4.63 F
3385 4569 1.489230 GGGTTACCCGGATCTGTCATT 59.511 52.381 3.99 0.0 32.13 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2655 0.611062 CCCCGTCACTCTAGTCACCA 60.611 60.0 0.0 0.0 0.0 4.17 R
2267 3185 0.727398 GCACAAAGATCGGCACTACC 59.273 55.0 0.0 0.0 0.0 3.18 R
3618 4849 1.888436 TAGGCACCTTCCACTCAGCG 61.888 60.0 0.0 0.0 0.0 5.18 R
4751 5987 0.883833 GACTTGTACGAACCCGAGGA 59.116 55.0 0.0 0.0 39.5 3.71 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
88 89 3.999001 CCATACGCAGATGTGATTAGCAT 59.001 43.478 0.00 0.00 0.00 3.79
458 467 1.202533 CGTGGAGCCGGTGAGAAATAT 60.203 52.381 1.90 0.00 0.00 1.28
472 481 4.818005 TGAGAAATATAGTAGACGACGGCA 59.182 41.667 2.19 0.00 0.00 5.69
559 588 1.684386 CGCAGGAGAGGAGGAAGCAT 61.684 60.000 0.00 0.00 0.00 3.79
603 632 4.002506 ATCCATGGCGGCGCGATA 62.003 61.111 28.26 15.19 33.14 2.92
670 699 4.100981 GCGGCTGCAAACAAACAA 57.899 50.000 14.08 0.00 42.15 2.83
743 772 3.369756 CGCAGAGTACTCGCCAAAAATAA 59.630 43.478 24.20 0.00 34.09 1.40
745 774 5.615984 CGCAGAGTACTCGCCAAAAATAAAA 60.616 40.000 24.20 0.00 34.09 1.52
746 775 5.795441 GCAGAGTACTCGCCAAAAATAAAAG 59.205 40.000 21.53 2.19 34.09 2.27
747 776 6.567891 GCAGAGTACTCGCCAAAAATAAAAGT 60.568 38.462 21.53 0.00 34.09 2.66
748 777 6.797033 CAGAGTACTCGCCAAAAATAAAAGTG 59.203 38.462 17.07 0.63 34.09 3.16
750 779 5.766174 AGTACTCGCCAAAAATAAAAGTGGA 59.234 36.000 0.00 0.00 32.54 4.02
751 780 5.523438 ACTCGCCAAAAATAAAAGTGGAA 57.477 34.783 0.00 0.00 32.54 3.53
752 781 5.286438 ACTCGCCAAAAATAAAAGTGGAAC 58.714 37.500 0.00 0.00 32.54 3.62
753 782 5.163499 ACTCGCCAAAAATAAAAGTGGAACA 60.163 36.000 0.00 0.00 41.43 3.18
754 783 5.848406 TCGCCAAAAATAAAAGTGGAACAT 58.152 33.333 0.00 0.00 44.52 2.71
755 784 5.694006 TCGCCAAAAATAAAAGTGGAACATG 59.306 36.000 0.00 0.00 44.52 3.21
756 785 5.465056 CGCCAAAAATAAAAGTGGAACATGT 59.535 36.000 0.00 0.00 44.52 3.21
757 786 6.018343 CGCCAAAAATAAAAGTGGAACATGTT 60.018 34.615 11.78 11.78 44.52 2.71
758 787 7.466590 CGCCAAAAATAAAAGTGGAACATGTTT 60.467 33.333 13.36 0.00 44.52 2.83
759 788 8.187480 GCCAAAAATAAAAGTGGAACATGTTTT 58.813 29.630 13.36 4.38 44.52 2.43
760 789 9.715123 CCAAAAATAAAAGTGGAACATGTTTTC 57.285 29.630 13.36 9.03 44.52 2.29
763 792 9.665719 AAAATAAAAGTGGAACATGTTTTCACT 57.334 25.926 27.95 27.95 44.52 3.41
764 793 9.665719 AAATAAAAGTGGAACATGTTTTCACTT 57.334 25.926 32.51 32.51 44.52 3.16
768 797 8.702163 AAAGTGGAACATGTTTTCACTTAAAG 57.298 30.769 35.02 0.00 44.52 1.85
769 798 7.404671 AGTGGAACATGTTTTCACTTAAAGT 57.595 32.000 27.95 14.89 44.52 2.66
770 799 8.514330 AGTGGAACATGTTTTCACTTAAAGTA 57.486 30.769 27.95 2.82 44.52 2.24
771 800 8.962679 AGTGGAACATGTTTTCACTTAAAGTAA 58.037 29.630 27.95 2.29 44.52 2.24
772 801 9.575783 GTGGAACATGTTTTCACTTAAAGTAAA 57.424 29.630 25.60 0.55 44.52 2.01
773 802 9.575783 TGGAACATGTTTTCACTTAAAGTAAAC 57.424 29.630 13.36 0.00 30.96 2.01
774 803 9.027129 GGAACATGTTTTCACTTAAAGTAAACC 57.973 33.333 13.36 0.00 29.82 3.27
775 804 9.797556 GAACATGTTTTCACTTAAAGTAAACCT 57.202 29.630 13.36 0.00 29.82 3.50
874 904 3.243839 GGTGTTCATGCATCCAACAAGTT 60.244 43.478 18.24 0.00 31.95 2.66
932 962 3.443925 CGAGCAGAGGACGGCAGA 61.444 66.667 0.00 0.00 39.53 4.26
974 1017 1.244019 GCAAGCAACCGATCCCAGTT 61.244 55.000 0.00 0.00 0.00 3.16
979 1022 1.882352 GCAACCGATCCCAGTTGTTCT 60.882 52.381 15.44 0.00 44.17 3.01
1024 1081 0.249657 GAGCCGCCTCTTCCACTATG 60.250 60.000 0.00 0.00 35.16 2.23
1030 1087 1.115467 CCTCTTCCACTATGCCTCGT 58.885 55.000 0.00 0.00 0.00 4.18
1032 1089 2.693591 CCTCTTCCACTATGCCTCGTTA 59.306 50.000 0.00 0.00 0.00 3.18
1184 1256 3.558321 CCCAACAACGATCTCCTGGTAAA 60.558 47.826 0.00 0.00 0.00 2.01
1186 1258 4.332819 CCAACAACGATCTCCTGGTAAATC 59.667 45.833 0.00 0.00 0.00 2.17
1190 1262 3.782046 ACGATCTCCTGGTAAATCAACG 58.218 45.455 0.00 0.00 0.00 4.10
1191 1263 3.194968 ACGATCTCCTGGTAAATCAACGT 59.805 43.478 0.00 0.00 0.00 3.99
1221 1377 4.177165 TGCATATGGCTCTGTGTTTTTG 57.823 40.909 4.56 0.00 45.15 2.44
1243 1400 2.434185 TTGACCGATCAGCACGCC 60.434 61.111 0.00 0.00 35.83 5.68
1392 1554 1.675641 AAGCTGTGGCGGATCAACC 60.676 57.895 0.00 0.00 44.37 3.77
1505 1667 0.452987 CCGAGACGTTCCGATTGGTA 59.547 55.000 11.30 0.00 36.30 3.25
1570 1732 1.454201 GGGCTCTTCTTGCAGGTAAC 58.546 55.000 0.00 0.00 0.00 2.50
1578 1740 6.144724 GCTCTTCTTGCAGGTAACGATAATAG 59.855 42.308 0.00 0.00 46.39 1.73
1579 1741 7.108841 TCTTCTTGCAGGTAACGATAATAGT 57.891 36.000 0.00 0.00 46.39 2.12
1581 1743 8.133627 TCTTCTTGCAGGTAACGATAATAGTAC 58.866 37.037 0.00 0.00 46.39 2.73
1582 1744 6.432936 TCTTGCAGGTAACGATAATAGTACG 58.567 40.000 0.00 0.00 46.39 3.67
1583 1745 6.260714 TCTTGCAGGTAACGATAATAGTACGA 59.739 38.462 0.00 0.00 46.39 3.43
1585 1747 6.794374 TGCAGGTAACGATAATAGTACGAAA 58.206 36.000 0.00 0.00 46.39 3.46
1586 1748 7.428020 TGCAGGTAACGATAATAGTACGAAAT 58.572 34.615 0.00 0.00 46.39 2.17
1587 1749 8.567104 TGCAGGTAACGATAATAGTACGAAATA 58.433 33.333 0.00 0.00 46.39 1.40
1588 1750 8.844690 GCAGGTAACGATAATAGTACGAAATAC 58.155 37.037 0.00 0.00 46.39 1.89
1589 1751 9.334693 CAGGTAACGATAATAGTACGAAATACC 57.665 37.037 0.00 0.00 46.39 2.73
1590 1752 8.230486 AGGTAACGATAATAGTACGAAATACCG 58.770 37.037 0.00 0.00 46.39 4.02
1592 1754 6.000891 ACGATAATAGTACGAAATACCGCA 57.999 37.500 0.00 0.00 33.85 5.69
1593 1755 6.615088 ACGATAATAGTACGAAATACCGCAT 58.385 36.000 0.00 0.00 33.85 4.73
1594 1756 7.751732 ACGATAATAGTACGAAATACCGCATA 58.248 34.615 0.00 0.00 33.85 3.14
1595 1757 8.400947 ACGATAATAGTACGAAATACCGCATAT 58.599 33.333 0.00 0.00 33.85 1.78
1596 1758 9.868389 CGATAATAGTACGAAATACCGCATATA 57.132 33.333 0.00 0.00 33.85 0.86
1600 1762 8.867112 ATAGTACGAAATACCGCATATATTGG 57.133 34.615 0.00 0.11 33.85 3.16
1601 1763 6.694447 AGTACGAAATACCGCATATATTGGT 58.306 36.000 10.48 10.48 39.80 3.67
1602 1764 6.810182 AGTACGAAATACCGCATATATTGGTC 59.190 38.462 9.22 0.00 37.20 4.02
1603 1765 5.543714 ACGAAATACCGCATATATTGGTCA 58.456 37.500 9.22 0.00 37.20 4.02
1604 1766 5.637810 ACGAAATACCGCATATATTGGTCAG 59.362 40.000 9.22 2.71 37.20 3.51
1605 1767 5.445939 CGAAATACCGCATATATTGGTCAGC 60.446 44.000 9.22 0.00 37.20 4.26
1606 1768 2.928801 ACCGCATATATTGGTCAGCA 57.071 45.000 1.28 0.00 0.00 4.41
1607 1769 2.494059 ACCGCATATATTGGTCAGCAC 58.506 47.619 1.28 0.00 0.00 4.40
1608 1770 2.104792 ACCGCATATATTGGTCAGCACT 59.895 45.455 1.28 0.00 0.00 4.40
1618 1780 1.269723 TGGTCAGCACTTCACTACTCG 59.730 52.381 0.00 0.00 0.00 4.18
1619 1781 1.269998 GGTCAGCACTTCACTACTCGT 59.730 52.381 0.00 0.00 0.00 4.18
1620 1782 2.486982 GGTCAGCACTTCACTACTCGTA 59.513 50.000 0.00 0.00 0.00 3.43
1621 1783 3.490399 GTCAGCACTTCACTACTCGTAC 58.510 50.000 0.00 0.00 0.00 3.67
1622 1784 3.188873 GTCAGCACTTCACTACTCGTACT 59.811 47.826 0.00 0.00 0.00 2.73
1623 1785 4.391216 GTCAGCACTTCACTACTCGTACTA 59.609 45.833 0.00 0.00 0.00 1.82
1624 1786 4.391216 TCAGCACTTCACTACTCGTACTAC 59.609 45.833 0.00 0.00 0.00 2.73
1625 1787 3.370366 AGCACTTCACTACTCGTACTACG 59.630 47.826 1.93 1.93 44.19 3.51
1626 1788 3.484886 GCACTTCACTACTCGTACTACGG 60.485 52.174 8.71 2.71 42.81 4.02
1627 1789 3.928992 CACTTCACTACTCGTACTACGGA 59.071 47.826 8.71 0.00 42.81 4.69
1628 1790 4.389992 CACTTCACTACTCGTACTACGGAA 59.610 45.833 8.71 2.89 42.81 4.30
1629 1791 4.997395 ACTTCACTACTCGTACTACGGAAA 59.003 41.667 8.71 0.00 42.81 3.13
1630 1792 5.470098 ACTTCACTACTCGTACTACGGAAAA 59.530 40.000 8.71 0.00 42.81 2.29
1631 1793 6.150140 ACTTCACTACTCGTACTACGGAAAAT 59.850 38.462 8.71 0.00 42.81 1.82
1632 1794 7.334421 ACTTCACTACTCGTACTACGGAAAATA 59.666 37.037 8.71 0.00 42.81 1.40
1633 1795 7.792374 TCACTACTCGTACTACGGAAAATAT 57.208 36.000 8.71 0.00 42.81 1.28
1634 1796 8.887036 TCACTACTCGTACTACGGAAAATATA 57.113 34.615 8.71 0.00 42.81 0.86
1635 1797 8.982685 TCACTACTCGTACTACGGAAAATATAG 58.017 37.037 8.71 0.00 42.81 1.31
1636 1798 8.768955 CACTACTCGTACTACGGAAAATATAGT 58.231 37.037 8.71 4.98 42.81 2.12
1637 1799 9.982651 ACTACTCGTACTACGGAAAATATAGTA 57.017 33.333 8.71 5.78 42.81 1.82
1640 1802 8.286097 ACTCGTACTACGGAAAATATAGTAAGC 58.714 37.037 8.71 0.00 42.81 3.09
1641 1803 8.383318 TCGTACTACGGAAAATATAGTAAGCT 57.617 34.615 8.71 0.00 42.81 3.74
1642 1804 9.489084 TCGTACTACGGAAAATATAGTAAGCTA 57.511 33.333 8.71 0.00 42.81 3.32
1643 1805 9.752274 CGTACTACGGAAAATATAGTAAGCTAG 57.248 37.037 0.26 0.00 38.08 3.42
1646 1808 9.962783 ACTACGGAAAATATAGTAAGCTAGTTG 57.037 33.333 0.00 0.00 0.00 3.16
1647 1809 9.962783 CTACGGAAAATATAGTAAGCTAGTTGT 57.037 33.333 0.00 0.00 0.00 3.32
1649 1811 9.662947 ACGGAAAATATAGTAAGCTAGTTGTTT 57.337 29.630 0.00 0.00 0.00 2.83
1659 1821 8.535690 AGTAAGCTAGTTGTTTAACACAGATC 57.464 34.615 0.00 0.00 39.30 2.75
1660 1822 8.368668 AGTAAGCTAGTTGTTTAACACAGATCT 58.631 33.333 0.00 0.00 39.30 2.75
1661 1823 7.659652 AAGCTAGTTGTTTAACACAGATCTC 57.340 36.000 0.00 0.00 39.30 2.75
1662 1824 6.759272 AGCTAGTTGTTTAACACAGATCTCA 58.241 36.000 0.00 0.00 39.30 3.27
1663 1825 7.217200 AGCTAGTTGTTTAACACAGATCTCAA 58.783 34.615 0.00 0.00 39.30 3.02
1664 1826 7.715249 AGCTAGTTGTTTAACACAGATCTCAAA 59.285 33.333 0.00 0.00 39.30 2.69
1665 1827 8.012241 GCTAGTTGTTTAACACAGATCTCAAAG 58.988 37.037 0.00 0.00 39.30 2.77
1666 1828 6.729187 AGTTGTTTAACACAGATCTCAAAGC 58.271 36.000 0.00 0.00 39.30 3.51
1667 1829 6.543831 AGTTGTTTAACACAGATCTCAAAGCT 59.456 34.615 0.00 0.00 39.30 3.74
1668 1830 7.715249 AGTTGTTTAACACAGATCTCAAAGCTA 59.285 33.333 0.00 0.00 39.30 3.32
1669 1831 8.507249 GTTGTTTAACACAGATCTCAAAGCTAT 58.493 33.333 0.00 0.00 36.48 2.97
1670 1832 9.719355 TTGTTTAACACAGATCTCAAAGCTATA 57.281 29.630 0.00 0.00 36.48 1.31
1671 1833 9.890629 TGTTTAACACAGATCTCAAAGCTATAT 57.109 29.630 0.00 0.00 0.00 0.86
1699 1861 9.958180 TGAGGATAAAGATAAAAGTGTTCATGA 57.042 29.630 0.00 0.00 0.00 3.07
1706 1868 7.138692 AGATAAAAGTGTTCATGAGACAAGC 57.861 36.000 10.87 2.90 0.00 4.01
1707 1869 6.939163 AGATAAAAGTGTTCATGAGACAAGCT 59.061 34.615 10.87 4.64 0.00 3.74
1708 1870 5.429957 AAAAGTGTTCATGAGACAAGCTC 57.570 39.130 10.87 0.00 44.21 4.09
1709 1871 4.348863 AAGTGTTCATGAGACAAGCTCT 57.651 40.909 10.87 3.85 44.27 4.09
1710 1872 5.474578 AAGTGTTCATGAGACAAGCTCTA 57.525 39.130 10.87 0.00 44.27 2.43
1711 1873 5.474578 AGTGTTCATGAGACAAGCTCTAA 57.525 39.130 10.87 0.00 44.27 2.10
1712 1874 5.858381 AGTGTTCATGAGACAAGCTCTAAA 58.142 37.500 10.87 0.00 44.27 1.85
1713 1875 6.291377 AGTGTTCATGAGACAAGCTCTAAAA 58.709 36.000 10.87 0.00 44.27 1.52
1714 1876 6.767902 AGTGTTCATGAGACAAGCTCTAAAAA 59.232 34.615 10.87 0.00 44.27 1.94
1715 1877 7.446625 AGTGTTCATGAGACAAGCTCTAAAAAT 59.553 33.333 10.87 0.00 44.27 1.82
1716 1878 7.748241 GTGTTCATGAGACAAGCTCTAAAAATC 59.252 37.037 10.87 0.00 44.27 2.17
1717 1879 6.992063 TCATGAGACAAGCTCTAAAAATCC 57.008 37.500 0.00 0.00 44.27 3.01
1718 1880 6.475504 TCATGAGACAAGCTCTAAAAATCCA 58.524 36.000 0.00 0.00 44.27 3.41
1719 1881 6.372659 TCATGAGACAAGCTCTAAAAATCCAC 59.627 38.462 0.00 0.00 44.27 4.02
1720 1882 4.690748 TGAGACAAGCTCTAAAAATCCACG 59.309 41.667 0.00 0.00 44.27 4.94
1721 1883 4.642429 AGACAAGCTCTAAAAATCCACGT 58.358 39.130 0.00 0.00 0.00 4.49
1722 1884 4.691216 AGACAAGCTCTAAAAATCCACGTC 59.309 41.667 0.00 0.00 0.00 4.34
1723 1885 3.751698 ACAAGCTCTAAAAATCCACGTCC 59.248 43.478 0.00 0.00 0.00 4.79
1724 1886 3.983044 AGCTCTAAAAATCCACGTCCT 57.017 42.857 0.00 0.00 0.00 3.85
1727 1889 4.000988 GCTCTAAAAATCCACGTCCTTCA 58.999 43.478 0.00 0.00 0.00 3.02
1814 2476 3.084786 GCCTCCAATGTTGACTAGCTTT 58.915 45.455 0.00 0.00 0.00 3.51
2000 2662 1.066918 GTCGGTGTTCGTGGTGACT 59.933 57.895 0.00 0.00 40.32 3.41
2108 2787 1.792301 CATCACTGCTCCACTTGCG 59.208 57.895 0.00 0.00 0.00 4.85
2176 3072 7.809665 TGTACATTATGCTTATCATGCATCAC 58.190 34.615 0.00 0.00 46.80 3.06
2208 3109 0.037232 GTCCTCAGTGGTTTCCCTCG 60.037 60.000 0.00 0.00 37.07 4.63
2217 3118 2.228103 GTGGTTTCCCTCGTCATTTTCC 59.772 50.000 0.00 0.00 0.00 3.13
2267 3185 1.946768 TGCACAAGGAAACGAGAAAGG 59.053 47.619 0.00 0.00 0.00 3.11
2280 3201 1.757699 GAGAAAGGGTAGTGCCGATCT 59.242 52.381 0.00 0.00 38.44 2.75
2299 3220 5.220397 CGATCTTTGTGCAGCGAATAACTTA 60.220 40.000 0.00 0.00 0.00 2.24
2305 3226 2.869801 TGCAGCGAATAACTTAATCGGG 59.130 45.455 8.08 0.00 37.08 5.14
2310 3235 5.521010 CAGCGAATAACTTAATCGGGTACAA 59.479 40.000 8.08 0.00 37.08 2.41
2313 3238 6.036408 GCGAATAACTTAATCGGGTACAACTT 59.964 38.462 8.08 0.00 37.08 2.66
2510 3484 8.834004 TGACAAGGTAGATACTTATAGTTGGT 57.166 34.615 0.00 0.00 0.00 3.67
2856 4023 5.487433 TGAAATCAAAGATCGGCTCAACTA 58.513 37.500 0.00 0.00 0.00 2.24
2939 4113 8.340443 CCGTTATCTAATTAACTTTTGGCCTAC 58.660 37.037 3.32 0.00 31.28 3.18
3347 4531 2.765705 ATCCCCGGACCCAACAGAGT 62.766 60.000 0.73 0.00 0.00 3.24
3385 4569 1.489230 GGGTTACCCGGATCTGTCATT 59.511 52.381 3.99 0.00 32.13 2.57
4003 5237 3.806949 AGGCTTGGGTGAACTATTTGA 57.193 42.857 0.00 0.00 0.00 2.69
4059 5294 0.103208 CTAGGTGATTTCTCCGCGCT 59.897 55.000 5.56 0.00 34.85 5.92
4085 5320 4.741676 GCTGCGGGATTTCAAAGATTAATG 59.258 41.667 0.00 0.00 0.00 1.90
4358 5593 7.278868 GCATTATGCTTAACAGTCTCTAGTTGT 59.721 37.037 10.27 0.00 40.96 3.32
4420 5655 8.892723 TCAGAATGGAAATCAATACACACATAC 58.107 33.333 0.00 0.00 36.16 2.39
4439 5674 1.684734 GCACGAACTAGGGGAGGGA 60.685 63.158 0.00 0.00 0.00 4.20
4465 5701 5.377478 AGGTCTTTGAGTAACCTCCAAAAG 58.623 41.667 0.00 0.00 39.17 2.27
4480 5716 6.883756 ACCTCCAAAAGCAAATTTCTTGAAAA 59.116 30.769 0.00 0.00 0.00 2.29
4481 5717 7.392953 ACCTCCAAAAGCAAATTTCTTGAAAAA 59.607 29.630 0.00 0.00 0.00 1.94
4550 5786 7.410120 TCTATTAGCACTCACAATTCTCTCA 57.590 36.000 0.00 0.00 0.00 3.27
4646 5882 6.275335 CCTGAATGTTGCTTTTCTTTCTTCA 58.725 36.000 0.00 0.00 0.00 3.02
4720 5956 1.340893 TGGATCGTGCAATCCCACAAT 60.341 47.619 13.71 0.00 43.99 2.71
4751 5987 6.127140 ACAAGTCTAATAGGCCTACAAACGAT 60.127 38.462 16.61 0.00 0.00 3.73
4759 5995 0.822164 CCTACAAACGATCCTCGGGT 59.178 55.000 1.29 0.00 45.59 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.976255 GTGTCGTTTGTAGCATAAATAAACATA 57.024 29.630 0.00 0.00 32.36 2.29
161 165 2.927477 CGCCATCGTAGCAAAAACTCTA 59.073 45.455 0.00 0.00 0.00 2.43
458 467 1.020861 TTCGCTGCCGTCGTCTACTA 61.021 55.000 0.00 0.00 35.54 1.82
559 588 1.153066 TTGAAGCACTGCCCAACGA 60.153 52.632 0.00 0.00 0.00 3.85
603 632 7.505258 GTCTTCTTCTATGAGAAAATAGCCCT 58.495 38.462 0.00 0.00 35.38 5.19
665 694 1.812571 CCAGCAGCGTAGGATTTGTTT 59.187 47.619 0.00 0.00 0.00 2.83
670 699 1.450312 GCACCAGCAGCGTAGGATT 60.450 57.895 8.37 0.00 41.58 3.01
743 772 8.311109 ACTTTAAGTGAAAACATGTTCCACTTT 58.689 29.630 36.75 27.71 34.12 2.66
745 774 7.404671 ACTTTAAGTGAAAACATGTTCCACT 57.595 32.000 27.31 27.31 0.00 4.00
746 775 9.575783 TTTACTTTAAGTGAAAACATGTTCCAC 57.424 29.630 24.85 24.85 0.00 4.02
747 776 9.575783 GTTTACTTTAAGTGAAAACATGTTCCA 57.424 29.630 12.39 10.31 30.78 3.53
748 777 9.027129 GGTTTACTTTAAGTGAAAACATGTTCC 57.973 33.333 19.01 7.71 31.56 3.62
759 788 9.382275 ACGAAGTTTTAGGTTTACTTTAAGTGA 57.618 29.630 8.00 0.00 37.78 3.41
924 954 2.813042 GTGCTCTGCTCTGCCGTC 60.813 66.667 0.00 0.00 0.00 4.79
1024 1081 1.002366 CACAGCATGAGTAACGAGGC 58.998 55.000 0.00 0.00 39.69 4.70
1030 1087 2.568956 AGAGGAAGCACAGCATGAGTAA 59.431 45.455 0.00 0.00 39.69 2.24
1032 1089 0.982704 AGAGGAAGCACAGCATGAGT 59.017 50.000 0.00 0.00 39.69 3.41
1184 1256 1.790755 TGCAAAGCTACGACGTTGAT 58.209 45.000 13.63 3.74 31.65 2.57
1186 1258 3.544048 CCATATGCAAAGCTACGACGTTG 60.544 47.826 5.50 5.22 32.95 4.10
1190 1262 2.213499 AGCCATATGCAAAGCTACGAC 58.787 47.619 2.73 0.00 44.83 4.34
1191 1263 2.103094 AGAGCCATATGCAAAGCTACGA 59.897 45.455 4.43 0.00 44.83 3.43
1221 1377 1.079503 GTGCTGATCGGTCAAGAACC 58.920 55.000 0.00 0.00 45.45 3.62
1243 1400 1.717937 CCGTCCTGTAGGTACGTCG 59.282 63.158 16.16 0.00 37.17 5.12
1251 1411 2.507102 CTGCGTGCCGTCCTGTAG 60.507 66.667 0.00 0.00 0.00 2.74
1392 1554 6.275335 ACACTTTGAAATTGAATGTCACCTG 58.725 36.000 0.00 0.00 0.00 4.00
1570 1732 8.778141 ATATGCGGTATTTCGTACTATTATCG 57.222 34.615 0.00 0.00 33.64 2.92
1578 1740 6.587226 TGACCAATATATGCGGTATTTCGTAC 59.413 38.462 7.00 0.00 31.63 3.67
1579 1741 6.689554 TGACCAATATATGCGGTATTTCGTA 58.310 36.000 7.00 0.00 31.63 3.43
1581 1743 5.445939 GCTGACCAATATATGCGGTATTTCG 60.446 44.000 7.00 0.00 31.63 3.46
1582 1744 5.411361 TGCTGACCAATATATGCGGTATTTC 59.589 40.000 7.00 0.00 31.63 2.17
1583 1745 5.181245 GTGCTGACCAATATATGCGGTATTT 59.819 40.000 7.00 0.00 31.63 1.40
1585 1747 4.020218 AGTGCTGACCAATATATGCGGTAT 60.020 41.667 7.00 0.00 31.63 2.73
1586 1748 3.323691 AGTGCTGACCAATATATGCGGTA 59.676 43.478 7.00 0.00 31.63 4.02
1587 1749 2.104792 AGTGCTGACCAATATATGCGGT 59.895 45.455 6.77 6.77 35.12 5.68
1588 1750 2.771089 AGTGCTGACCAATATATGCGG 58.229 47.619 0.77 0.77 0.00 5.69
1589 1751 3.809279 TGAAGTGCTGACCAATATATGCG 59.191 43.478 0.00 0.00 0.00 4.73
1590 1752 4.818546 AGTGAAGTGCTGACCAATATATGC 59.181 41.667 0.00 0.00 0.00 3.14
1592 1754 7.366847 AGTAGTGAAGTGCTGACCAATATAT 57.633 36.000 0.00 0.00 0.00 0.86
1593 1755 6.459710 CGAGTAGTGAAGTGCTGACCAATATA 60.460 42.308 0.00 0.00 0.00 0.86
1594 1756 5.665459 GAGTAGTGAAGTGCTGACCAATAT 58.335 41.667 0.00 0.00 0.00 1.28
1595 1757 4.380550 CGAGTAGTGAAGTGCTGACCAATA 60.381 45.833 0.00 0.00 0.00 1.90
1596 1758 3.615110 CGAGTAGTGAAGTGCTGACCAAT 60.615 47.826 0.00 0.00 0.00 3.16
1597 1759 2.288213 CGAGTAGTGAAGTGCTGACCAA 60.288 50.000 0.00 0.00 0.00 3.67
1598 1760 1.269723 CGAGTAGTGAAGTGCTGACCA 59.730 52.381 0.00 0.00 0.00 4.02
1599 1761 1.269998 ACGAGTAGTGAAGTGCTGACC 59.730 52.381 0.00 0.00 0.00 4.02
1600 1762 2.708386 ACGAGTAGTGAAGTGCTGAC 57.292 50.000 0.00 0.00 0.00 3.51
1601 1763 3.409570 AGTACGAGTAGTGAAGTGCTGA 58.590 45.455 0.00 0.00 0.00 4.26
1602 1764 3.833545 AGTACGAGTAGTGAAGTGCTG 57.166 47.619 0.00 0.00 0.00 4.41
1603 1765 3.370366 CGTAGTACGAGTAGTGAAGTGCT 59.630 47.826 17.85 0.00 46.05 4.40
1604 1766 3.484886 CCGTAGTACGAGTAGTGAAGTGC 60.485 52.174 23.95 0.00 46.05 4.40
1605 1767 3.928992 TCCGTAGTACGAGTAGTGAAGTG 59.071 47.826 23.95 2.77 46.05 3.16
1606 1768 4.193826 TCCGTAGTACGAGTAGTGAAGT 57.806 45.455 23.95 0.00 46.05 3.01
1607 1769 5.536554 TTTCCGTAGTACGAGTAGTGAAG 57.463 43.478 23.95 4.00 46.05 3.02
1608 1770 5.940192 TTTTCCGTAGTACGAGTAGTGAA 57.060 39.130 23.95 13.81 46.05 3.18
1620 1782 9.962783 CAACTAGCTTACTATATTTTCCGTAGT 57.037 33.333 0.00 0.00 33.55 2.73
1621 1783 9.962783 ACAACTAGCTTACTATATTTTCCGTAG 57.037 33.333 0.00 0.00 0.00 3.51
1623 1785 9.662947 AAACAACTAGCTTACTATATTTTCCGT 57.337 29.630 0.00 0.00 0.00 4.69
1633 1795 9.635520 GATCTGTGTTAAACAACTAGCTTACTA 57.364 33.333 0.00 0.00 38.67 1.82
1634 1796 8.368668 AGATCTGTGTTAAACAACTAGCTTACT 58.631 33.333 0.00 0.00 38.67 2.24
1635 1797 8.535690 AGATCTGTGTTAAACAACTAGCTTAC 57.464 34.615 0.00 0.00 38.67 2.34
1636 1798 8.364894 TGAGATCTGTGTTAAACAACTAGCTTA 58.635 33.333 0.00 0.00 38.67 3.09
1637 1799 7.217200 TGAGATCTGTGTTAAACAACTAGCTT 58.783 34.615 0.00 0.00 38.67 3.74
1638 1800 6.759272 TGAGATCTGTGTTAAACAACTAGCT 58.241 36.000 0.00 0.00 38.67 3.32
1639 1801 7.421530 TTGAGATCTGTGTTAAACAACTAGC 57.578 36.000 0.00 0.00 38.67 3.42
1640 1802 8.012241 GCTTTGAGATCTGTGTTAAACAACTAG 58.988 37.037 0.00 0.00 38.67 2.57
1641 1803 7.715249 AGCTTTGAGATCTGTGTTAAACAACTA 59.285 33.333 0.00 0.00 38.67 2.24
1642 1804 6.543831 AGCTTTGAGATCTGTGTTAAACAACT 59.456 34.615 0.00 0.00 38.67 3.16
1643 1805 6.729187 AGCTTTGAGATCTGTGTTAAACAAC 58.271 36.000 0.00 0.00 38.67 3.32
1644 1806 6.942532 AGCTTTGAGATCTGTGTTAAACAA 57.057 33.333 0.00 0.00 38.67 2.83
1645 1807 9.890629 ATATAGCTTTGAGATCTGTGTTAAACA 57.109 29.630 0.00 0.00 37.22 2.83
1673 1835 9.958180 TCATGAACACTTTTATCTTTATCCTCA 57.042 29.630 0.00 0.00 0.00 3.86
1680 1842 8.078596 GCTTGTCTCATGAACACTTTTATCTTT 58.921 33.333 9.36 0.00 0.00 2.52
1681 1843 7.446625 AGCTTGTCTCATGAACACTTTTATCTT 59.553 33.333 9.36 0.00 0.00 2.40
1682 1844 6.939163 AGCTTGTCTCATGAACACTTTTATCT 59.061 34.615 9.36 0.00 0.00 1.98
1683 1845 7.118971 AGAGCTTGTCTCATGAACACTTTTATC 59.881 37.037 9.36 4.64 44.35 1.75
1684 1846 6.939163 AGAGCTTGTCTCATGAACACTTTTAT 59.061 34.615 9.36 0.00 44.35 1.40
1685 1847 6.291377 AGAGCTTGTCTCATGAACACTTTTA 58.709 36.000 9.36 0.00 44.35 1.52
1686 1848 5.128919 AGAGCTTGTCTCATGAACACTTTT 58.871 37.500 9.36 0.00 44.35 2.27
1687 1849 4.712476 AGAGCTTGTCTCATGAACACTTT 58.288 39.130 9.36 0.62 44.35 2.66
1688 1850 4.348863 AGAGCTTGTCTCATGAACACTT 57.651 40.909 9.36 1.25 44.35 3.16
1689 1851 5.474578 TTAGAGCTTGTCTCATGAACACT 57.525 39.130 9.36 5.85 44.35 3.55
1690 1852 6.545504 TTTTAGAGCTTGTCTCATGAACAC 57.454 37.500 9.36 4.35 44.35 3.32
1691 1853 7.094634 GGATTTTTAGAGCTTGTCTCATGAACA 60.095 37.037 0.00 1.78 44.35 3.18
1692 1854 7.094634 TGGATTTTTAGAGCTTGTCTCATGAAC 60.095 37.037 0.00 0.00 44.35 3.18
1693 1855 6.942005 TGGATTTTTAGAGCTTGTCTCATGAA 59.058 34.615 0.00 0.00 44.35 2.57
1694 1856 6.372659 GTGGATTTTTAGAGCTTGTCTCATGA 59.627 38.462 0.00 0.00 44.35 3.07
1695 1857 6.549952 GTGGATTTTTAGAGCTTGTCTCATG 58.450 40.000 0.00 0.00 44.35 3.07
1696 1858 5.352569 CGTGGATTTTTAGAGCTTGTCTCAT 59.647 40.000 0.00 0.00 44.35 2.90
1697 1859 4.690748 CGTGGATTTTTAGAGCTTGTCTCA 59.309 41.667 0.00 0.00 44.35 3.27
1698 1860 4.691216 ACGTGGATTTTTAGAGCTTGTCTC 59.309 41.667 0.00 0.00 42.21 3.36
1699 1861 4.642429 ACGTGGATTTTTAGAGCTTGTCT 58.358 39.130 0.00 0.00 39.59 3.41
1700 1862 4.142881 GGACGTGGATTTTTAGAGCTTGTC 60.143 45.833 0.00 0.00 0.00 3.18
1701 1863 3.751698 GGACGTGGATTTTTAGAGCTTGT 59.248 43.478 0.00 0.00 0.00 3.16
1702 1864 4.003648 AGGACGTGGATTTTTAGAGCTTG 58.996 43.478 0.00 0.00 0.00 4.01
1703 1865 4.287766 AGGACGTGGATTTTTAGAGCTT 57.712 40.909 0.00 0.00 0.00 3.74
1704 1866 3.983044 AGGACGTGGATTTTTAGAGCT 57.017 42.857 0.00 0.00 0.00 4.09
1705 1867 4.000988 TGAAGGACGTGGATTTTTAGAGC 58.999 43.478 0.00 0.00 0.00 4.09
1706 1868 7.042335 AGTATGAAGGACGTGGATTTTTAGAG 58.958 38.462 0.00 0.00 0.00 2.43
1707 1869 6.942976 AGTATGAAGGACGTGGATTTTTAGA 58.057 36.000 0.00 0.00 0.00 2.10
1708 1870 7.980099 AGTAGTATGAAGGACGTGGATTTTTAG 59.020 37.037 0.00 0.00 0.00 1.85
1709 1871 7.844009 AGTAGTATGAAGGACGTGGATTTTTA 58.156 34.615 0.00 0.00 0.00 1.52
1710 1872 6.708285 AGTAGTATGAAGGACGTGGATTTTT 58.292 36.000 0.00 0.00 0.00 1.94
1711 1873 6.295719 AGTAGTATGAAGGACGTGGATTTT 57.704 37.500 0.00 0.00 0.00 1.82
1712 1874 5.934402 AGTAGTATGAAGGACGTGGATTT 57.066 39.130 0.00 0.00 0.00 2.17
1713 1875 6.550108 ACATAGTAGTATGAAGGACGTGGATT 59.450 38.462 21.86 0.00 38.76 3.01
1714 1876 6.069331 ACATAGTAGTATGAAGGACGTGGAT 58.931 40.000 21.86 0.00 38.76 3.41
1715 1877 5.443283 ACATAGTAGTATGAAGGACGTGGA 58.557 41.667 21.86 0.00 38.76 4.02
1716 1878 5.769484 ACATAGTAGTATGAAGGACGTGG 57.231 43.478 21.86 0.00 38.76 4.94
1717 1879 6.019801 GCAAACATAGTAGTATGAAGGACGTG 60.020 42.308 21.86 10.34 38.76 4.49
1718 1880 6.040878 GCAAACATAGTAGTATGAAGGACGT 58.959 40.000 21.86 0.00 38.76 4.34
1719 1881 5.462398 GGCAAACATAGTAGTATGAAGGACG 59.538 44.000 21.86 7.04 38.76 4.79
1720 1882 6.346096 TGGCAAACATAGTAGTATGAAGGAC 58.654 40.000 21.86 13.09 38.76 3.85
1721 1883 6.553953 TGGCAAACATAGTAGTATGAAGGA 57.446 37.500 21.86 0.99 38.76 3.36
1722 1884 6.823689 AGTTGGCAAACATAGTAGTATGAAGG 59.176 38.462 21.86 11.85 38.76 3.46
1723 1885 7.201644 CCAGTTGGCAAACATAGTAGTATGAAG 60.202 40.741 21.86 12.41 38.76 3.02
1724 1886 6.597672 CCAGTTGGCAAACATAGTAGTATGAA 59.402 38.462 21.86 4.22 38.76 2.57
1727 1889 5.437060 CCCAGTTGGCAAACATAGTAGTAT 58.563 41.667 6.76 0.00 38.88 2.12
1814 2476 3.196901 TGCGCTAGTCAAAATCCCTAGAA 59.803 43.478 9.73 0.00 31.78 2.10
1943 2605 2.633657 GTGCGCTGGCCATAATCG 59.366 61.111 5.51 9.23 38.85 3.34
1946 2608 2.438254 CTGGTGCGCTGGCCATAA 60.438 61.111 5.51 0.00 38.85 1.90
1993 2655 0.611062 CCCCGTCACTCTAGTCACCA 60.611 60.000 0.00 0.00 0.00 4.17
2000 2662 1.471119 CTTGTAGCCCCGTCACTCTA 58.529 55.000 0.00 0.00 0.00 2.43
2108 2787 3.444034 GCTCTGAATTAAAACAGGGGTCC 59.556 47.826 12.06 0.00 35.42 4.46
2267 3185 0.727398 GCACAAAGATCGGCACTACC 59.273 55.000 0.00 0.00 0.00 3.18
2280 3201 5.320723 CGATTAAGTTATTCGCTGCACAAA 58.679 37.500 12.68 0.00 0.00 2.83
2299 3220 5.838531 TTTCAAACAAGTTGTACCCGATT 57.161 34.783 9.37 0.00 38.47 3.34
2305 3226 7.462109 TGCAATGATTTCAAACAAGTTGTAC 57.538 32.000 9.37 0.00 38.47 2.90
2856 4023 2.308866 CCCCTGGCCTAAATATTCCGAT 59.691 50.000 3.32 0.00 0.00 4.18
2939 4113 9.476202 AAAAAGAATAAAAAGGAGGATCAAACG 57.524 29.630 0.00 0.00 36.25 3.60
2978 4162 5.827568 ACAAATTGAGCATTTACAAAGCG 57.172 34.783 0.00 0.00 32.90 4.68
3149 4333 2.103263 ACCTGGATGCGAGGAAATCTAC 59.897 50.000 0.00 0.00 33.49 2.59
3385 4569 2.287393 ACGCGTAGTAATGCACATCA 57.713 45.000 11.67 0.00 37.49 3.07
3526 4711 9.292195 TCTAAAACCAAAAGGGAATAGTTACAG 57.708 33.333 0.00 0.00 41.15 2.74
3618 4849 1.888436 TAGGCACCTTCCACTCAGCG 61.888 60.000 0.00 0.00 0.00 5.18
4003 5237 6.076653 TGGACCCATATTGAATTACATGCAT 58.923 36.000 0.00 0.00 0.00 3.96
4059 5294 1.959985 TCTTTGAAATCCCGCAGCAAA 59.040 42.857 0.00 0.00 0.00 3.68
4136 5371 2.223456 TGTTCACACACAATTGCTTCCG 60.223 45.455 5.05 0.00 0.00 4.30
4210 5445 6.094719 ACAACTATTTTGTAGCACATGCATG 58.905 36.000 25.09 25.09 45.16 4.06
4271 5506 6.887013 ACTCTAATTCTCTCAACATGCATCT 58.113 36.000 0.00 0.00 0.00 2.90
4358 5593 5.680619 AGTTCACACAACTTTCATGACCTA 58.319 37.500 0.00 0.00 0.00 3.08
4420 5655 2.494918 CCTCCCCTAGTTCGTGCG 59.505 66.667 0.00 0.00 0.00 5.34
4502 5738 3.435275 TGCCTTTTGCCAACACCATATA 58.565 40.909 0.00 0.00 40.16 0.86
4550 5786 6.179040 CAAAAACAGAGAGAGGGATCAAGAT 58.821 40.000 0.00 0.00 0.00 2.40
4646 5882 8.196771 TGTTTGCTTTCTGTTGAGAAATAACAT 58.803 29.630 0.00 0.00 45.25 2.71
4720 5956 4.279145 AGGCCTATTAGACTTGTTCTCGA 58.721 43.478 1.29 0.00 35.55 4.04
4751 5987 0.883833 GACTTGTACGAACCCGAGGA 59.116 55.000 0.00 0.00 39.50 3.71
4759 5995 4.539870 CTTTAGGACGTGACTTGTACGAA 58.460 43.478 0.00 0.00 43.82 3.85


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

AutoCloner maintained by Alex Coulton.