Multiple sequence alignment - TraesCS3A01G275500

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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 TraesCS3A01G275500 chr3A 100.000 7041 0 0 1 7041 505215117 505222157 0.000000e+00 13003.0
1 TraesCS3A01G275500 chr3D 95.687 4243 130 19 818 5034 381984859 381989074 0.000000e+00 6772.0
2 TraesCS3A01G275500 chr3D 94.597 1092 36 10 5034 6108 381989155 381990240 0.000000e+00 1668.0
3 TraesCS3A01G275500 chr3D 90.887 812 71 3 1 809 413999134 413999945 0.000000e+00 1086.0
4 TraesCS3A01G275500 chr3D 95.153 392 17 2 6652 7041 381990799 381991190 1.000000e-172 617.0
5 TraesCS3A01G275500 chr3D 83.183 666 77 19 1002 1645 43583499 43582847 1.700000e-160 577.0
6 TraesCS3A01G275500 chr3D 89.362 47 4 1 5733 5778 555318733 555318779 2.740000e-04 58.4
7 TraesCS3A01G275500 chr3D 78.495 93 13 3 5744 5830 611778249 611778340 4.000000e-03 54.7
8 TraesCS3A01G275500 chr3B 94.032 3787 144 28 818 4570 497704344 497708082 0.000000e+00 5666.0
9 TraesCS3A01G275500 chr3B 94.582 1772 73 11 4599 6349 497708072 497709841 0.000000e+00 2719.0
10 TraesCS3A01G275500 chr3B 88.393 560 33 12 6507 7041 497710043 497710595 0.000000e+00 645.0
11 TraesCS3A01G275500 chr2D 91.383 824 65 4 1 818 570989365 570988542 0.000000e+00 1123.0
12 TraesCS3A01G275500 chr2D 90.887 823 70 4 1 818 57098870 57099692 0.000000e+00 1099.0
13 TraesCS3A01G275500 chr2D 90.541 814 74 3 8 818 80260325 80261138 0.000000e+00 1074.0
14 TraesCS3A01G275500 chr2D 79.208 101 18 3 5733 5831 71262860 71262959 4.560000e-07 67.6
15 TraesCS3A01G275500 chr1D 91.245 811 68 3 2 809 73733228 73732418 0.000000e+00 1101.0
16 TraesCS3A01G275500 chr1D 95.238 42 2 0 5789 5830 389427455 389427496 4.560000e-07 67.6
17 TraesCS3A01G275500 chr1D 93.023 43 3 0 5787 5829 204855515 204855557 5.900000e-06 63.9
18 TraesCS3A01G275500 chr1D 93.023 43 3 0 5787 5829 311345374 311345332 5.900000e-06 63.9
19 TraesCS3A01G275500 chr1D 94.872 39 2 0 5791 5829 37884685 37884647 2.120000e-05 62.1
20 TraesCS3A01G275500 chr1D 77.885 104 20 3 5733 5834 66630361 66630259 2.120000e-05 62.1
21 TraesCS3A01G275500 chr1D 79.167 96 8 2 5734 5829 313214481 313214564 1.000000e-03 56.5
22 TraesCS3A01G275500 chr2A 90.633 822 74 3 1 819 748702858 748703679 0.000000e+00 1088.0
23 TraesCS3A01G275500 chr2A 90.587 818 74 3 3 817 740407161 740407978 0.000000e+00 1081.0
24 TraesCS3A01G275500 chr2A 82.474 97 17 0 5734 5830 464060076 464059980 1.260000e-12 86.1
25 TraesCS3A01G275500 chr2B 90.652 813 71 5 1 809 32140276 32139465 0.000000e+00 1075.0
26 TraesCS3A01G275500 chr2B 84.735 321 49 0 3226 3546 45720395 45720075 8.810000e-84 322.0
27 TraesCS3A01G275500 chr5A 90.073 826 75 7 1 820 35025615 35024791 0.000000e+00 1064.0
28 TraesCS3A01G275500 chr1A 83.058 667 83 17 996 1645 504398613 504399266 4.740000e-161 579.0
29 TraesCS3A01G275500 chr1A 86.817 311 41 0 3231 3541 428984812 428984502 1.450000e-91 348.0
30 TraesCS3A01G275500 chr1A 85.199 277 28 8 1002 1276 525143701 525143436 9.000000e-69 272.0
31 TraesCS3A01G275500 chr4A 83.056 661 82 17 1002 1645 312732760 312732113 2.200000e-159 573.0
32 TraesCS3A01G275500 chr7A 83.002 653 81 17 1002 1637 655418094 655417455 1.330000e-156 564.0
33 TraesCS3A01G275500 chr7A 88.545 323 34 3 3226 3546 209131827 209131506 8.560000e-104 388.0
34 TraesCS3A01G275500 chr7A 88.542 96 11 0 5734 5829 250681282 250681377 4.460000e-22 117.0
35 TraesCS3A01G275500 chr7A 83.505 97 11 2 5734 5829 52966868 52966776 1.260000e-12 86.1
36 TraesCS3A01G275500 chr5B 82.132 666 86 20 1002 1648 275020877 275020226 2.230000e-149 540.0
37 TraesCS3A01G275500 chr5B 94.231 52 2 1 5787 5838 530615177 530615227 2.110000e-10 78.7
38 TraesCS3A01G275500 chr5B 97.059 34 0 1 5747 5779 404146434 404146401 1.000000e-03 56.5
39 TraesCS3A01G275500 chr6B 90.062 322 31 1 3224 3544 348089578 348089899 3.930000e-112 416.0
40 TraesCS3A01G275500 chr6B 89.377 273 28 1 3227 3499 126633812 126633541 6.760000e-90 342.0
41 TraesCS3A01G275500 chrUn 87.117 326 39 3 3224 3548 337678286 337677963 4.010000e-97 366.0
42 TraesCS3A01G275500 chrUn 86.810 326 40 3 3224 3548 384396593 384396270 1.870000e-95 361.0
43 TraesCS3A01G275500 chrUn 84.615 78 12 0 5755 5832 11035694 11035771 2.110000e-10 78.7
44 TraesCS3A01G275500 chrUn 77.228 101 16 6 5734 5830 96242079 96242176 1.300000e-02 52.8
45 TraesCS3A01G275500 chrUn 100.000 28 0 0 5803 5830 292906396 292906423 1.300000e-02 52.8
46 TraesCS3A01G275500 chr6D 87.117 326 39 3 3224 3548 467145971 467145648 4.010000e-97 366.0
47 TraesCS3A01G275500 chr6D 86.458 96 10 1 5734 5829 96747801 96747893 1.250000e-17 102.0
48 TraesCS3A01G275500 chr6D 83.505 97 15 1 5734 5829 327364355 327364451 9.730000e-14 89.8
49 TraesCS3A01G275500 chr6D 100.000 30 0 0 5731 5760 427000396 427000425 1.000000e-03 56.5
50 TraesCS3A01G275500 chr6D 100.000 28 0 0 5803 5830 91706508 91706535 1.300000e-02 52.8
51 TraesCS3A01G275500 chr4D 86.000 100 12 1 5733 5830 358476837 358476936 9.660000e-19 106.0
52 TraesCS3A01G275500 chr4D 82.292 96 7 1 5734 5829 450203706 450203791 2.720000e-09 75.0
53 TraesCS3A01G275500 chr4D 80.208 96 9 1 5734 5829 12440296 12440211 5.900000e-06 63.9
54 TraesCS3A01G275500 chr7B 84.158 101 12 4 5733 5831 680523325 680523227 2.090000e-15 95.3
55 TraesCS3A01G275500 chr5D 80.769 104 16 1 5727 5830 441127345 441127444 2.110000e-10 78.7
56 TraesCS3A01G275500 chr5D 93.750 48 3 0 5787 5834 436580050 436580097 9.800000e-09 73.1
57 TraesCS3A01G275500 chr5D 95.455 44 2 0 5786 5829 543822564 543822607 3.520000e-08 71.3
58 TraesCS3A01G275500 chr5D 97.143 35 1 0 5745 5779 540260140 540260106 7.630000e-05 60.2
59 TraesCS3A01G275500 chr5D 100.000 28 0 0 5733 5760 230411976 230412003 1.300000e-02 52.8
60 TraesCS3A01G275500 chr4B 78.788 99 18 2 5733 5829 551263519 551263616 5.900000e-06 63.9
61 TraesCS3A01G275500 chr4B 96.875 32 0 1 5730 5760 461364357 461364388 1.300000e-02 52.8


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 TraesCS3A01G275500 chr3A 505215117 505222157 7040 False 13003 13003 100.000000 1 7041 1 chr3A.!!$F1 7040
1 TraesCS3A01G275500 chr3D 381984859 381991190 6331 False 3019 6772 95.145667 818 7041 3 chr3D.!!$F4 6223
2 TraesCS3A01G275500 chr3D 413999134 413999945 811 False 1086 1086 90.887000 1 809 1 chr3D.!!$F1 808
3 TraesCS3A01G275500 chr3D 43582847 43583499 652 True 577 577 83.183000 1002 1645 1 chr3D.!!$R1 643
4 TraesCS3A01G275500 chr3B 497704344 497710595 6251 False 3010 5666 92.335667 818 7041 3 chr3B.!!$F1 6223
5 TraesCS3A01G275500 chr2D 570988542 570989365 823 True 1123 1123 91.383000 1 818 1 chr2D.!!$R1 817
6 TraesCS3A01G275500 chr2D 57098870 57099692 822 False 1099 1099 90.887000 1 818 1 chr2D.!!$F1 817
7 TraesCS3A01G275500 chr2D 80260325 80261138 813 False 1074 1074 90.541000 8 818 1 chr2D.!!$F3 810
8 TraesCS3A01G275500 chr1D 73732418 73733228 810 True 1101 1101 91.245000 2 809 1 chr1D.!!$R3 807
9 TraesCS3A01G275500 chr2A 748702858 748703679 821 False 1088 1088 90.633000 1 819 1 chr2A.!!$F2 818
10 TraesCS3A01G275500 chr2A 740407161 740407978 817 False 1081 1081 90.587000 3 817 1 chr2A.!!$F1 814
11 TraesCS3A01G275500 chr2B 32139465 32140276 811 True 1075 1075 90.652000 1 809 1 chr2B.!!$R1 808
12 TraesCS3A01G275500 chr5A 35024791 35025615 824 True 1064 1064 90.073000 1 820 1 chr5A.!!$R1 819
13 TraesCS3A01G275500 chr1A 504398613 504399266 653 False 579 579 83.058000 996 1645 1 chr1A.!!$F1 649
14 TraesCS3A01G275500 chr4A 312732113 312732760 647 True 573 573 83.056000 1002 1645 1 chr4A.!!$R1 643
15 TraesCS3A01G275500 chr7A 655417455 655418094 639 True 564 564 83.002000 1002 1637 1 chr7A.!!$R3 635
16 TraesCS3A01G275500 chr5B 275020226 275020877 651 True 540 540 82.132000 1002 1648 1 chr5B.!!$R1 646

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
130 131 0.824109 ACGATGGTGACGATGTCCAT 59.176 50.000 0.0 0.0 43.54 3.41 F
1193 1206 0.986019 TTACCATCCCACGCCCATCT 60.986 55.000 0.0 0.0 0.00 2.90 F
1477 1510 1.130749 CTGACGGTAGGAAGACTGACG 59.869 57.143 0.0 0.0 36.25 4.35 F
3004 3045 0.475632 TGGTCCCCTGTCACCTGATT 60.476 55.000 0.0 0.0 33.36 2.57 F
3751 3792 0.601046 GCGATTGGATGATGGCTCGA 60.601 55.000 0.0 0.0 0.00 4.04 F
4333 4383 3.195182 CAGTGAGAGAGAAAGATGCTGGA 59.805 47.826 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1316 1347 0.464036 TCGAAACCTATGAGCGCCAT 59.536 50.0 2.29 10.32 39.25 4.40 R
2100 2138 1.429463 GTAAACTGAGGAGTGCACCG 58.571 55.0 14.63 0.00 30.61 4.94 R
3413 3454 0.598065 GAAGAACCAATGCCAAGCGT 59.402 50.0 0.00 0.00 0.00 5.07 R
3918 3968 0.679002 CTCACCCCATGGCTGTCAAG 60.679 60.0 6.09 2.13 33.59 3.02 R
4951 5003 1.041437 AGGACCGGAGCAGCTAATAC 58.959 55.0 9.46 0.00 0.00 1.89 R
6120 6347 0.032130 GAGGATAATCGCGCTGACCA 59.968 55.0 5.56 0.00 0.00 4.02 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
130 131 0.824109 ACGATGGTGACGATGTCCAT 59.176 50.000 0.00 0.00 43.54 3.41
186 187 1.871418 TCAAGGCCACTCTCTGCTAT 58.129 50.000 5.01 0.00 0.00 2.97
230 231 1.144057 GATCGGATGACGGTGGCTT 59.856 57.895 0.00 0.00 44.45 4.35
265 267 2.361189 CCTTGGGGGCGTCATTTTT 58.639 52.632 0.00 0.00 0.00 1.94
299 301 2.600439 TCGAGGGACTAGAGGACGA 58.400 57.895 0.00 0.00 41.55 4.20
325 327 1.675641 GGTGGAGCGGTGCTTCATT 60.676 57.895 7.84 0.00 46.58 2.57
335 337 3.365868 GCGGTGCTTCATTTTACACATCA 60.366 43.478 0.00 0.00 34.69 3.07
461 463 2.274760 GCAGAGAGGCCTGGCAAT 59.725 61.111 22.05 8.33 34.82 3.56
476 479 1.880027 GGCAATGTCGGTCTTCAGTTT 59.120 47.619 0.00 0.00 0.00 2.66
484 487 1.532868 CGGTCTTCAGTTTTGCTCTGG 59.467 52.381 0.00 0.00 34.15 3.86
495 498 3.866582 GCTCTGGGGATGGACCGG 61.867 72.222 0.00 0.00 40.11 5.28
505 509 1.073783 ATGGACCGGGGGATGATGA 60.074 57.895 6.32 0.00 0.00 2.92
633 638 1.674359 TTGGTGCGATGTCTGTTTGT 58.326 45.000 0.00 0.00 0.00 2.83
636 641 2.546368 TGGTGCGATGTCTGTTTGTTAC 59.454 45.455 0.00 0.00 0.00 2.50
676 681 4.383552 GCACACCTTCATCAAGAGGATAGT 60.384 45.833 0.00 0.00 33.95 2.12
793 798 1.552337 GTTGAGATGCAGAGGTCAGGA 59.448 52.381 0.00 0.00 0.00 3.86
862 867 7.197703 ACTTGTTTTGTGAAAAGTATAACCGG 58.802 34.615 0.00 0.00 0.00 5.28
872 878 2.395619 AGTATAACCGGGAAGGGTCTG 58.604 52.381 6.32 0.00 46.96 3.51
1095 1107 4.176851 GTCGACGACTCCGGCTCC 62.177 72.222 20.52 0.00 42.92 4.70
1193 1206 0.986019 TTACCATCCCACGCCCATCT 60.986 55.000 0.00 0.00 0.00 2.90
1196 1209 1.227764 CATCCCACGCCCATCTCTG 60.228 63.158 0.00 0.00 0.00 3.35
1290 1321 6.792326 TCGAGCTCGAAATTGATAGTAGAAA 58.208 36.000 35.16 7.24 46.30 2.52
1294 1325 6.256757 AGCTCGAAATTGATAGTAGAAACTGC 59.743 38.462 0.00 0.00 36.36 4.40
1316 1347 1.813859 CGAGATGGTCGGTAGGCAA 59.186 57.895 0.00 0.00 45.58 4.52
1343 1374 2.797156 CTCATAGGTTTCGATTGCTCCG 59.203 50.000 0.00 0.00 0.00 4.63
1383 1414 4.668151 TTGGCACCCAAAACTCGT 57.332 50.000 0.00 0.00 40.92 4.18
1390 1421 3.561503 GCACCCAAAACTCGTAACATTC 58.438 45.455 0.00 0.00 0.00 2.67
1392 1423 4.783242 CACCCAAAACTCGTAACATTCTG 58.217 43.478 0.00 0.00 0.00 3.02
1477 1510 1.130749 CTGACGGTAGGAAGACTGACG 59.869 57.143 0.00 0.00 36.25 4.35
1525 1561 1.133253 CACACTTGCAGCGATTCCG 59.867 57.895 0.00 0.00 39.16 4.30
1526 1562 1.301716 ACACTTGCAGCGATTCCGT 60.302 52.632 0.00 0.00 38.24 4.69
1621 1658 1.988293 TGATTTTGCTTGTTCCGGGA 58.012 45.000 0.00 0.00 0.00 5.14
1706 1743 2.019984 GGCCATCTCACTGAAATCACC 58.980 52.381 0.00 0.00 0.00 4.02
1745 1782 4.806247 CGATGAATTGACCTGTCCTAGAAC 59.194 45.833 0.00 0.00 0.00 3.01
1868 1906 8.902806 GTTCCATTGATGTTTATGAGGACATTA 58.097 33.333 0.00 0.00 36.67 1.90
2100 2138 3.518590 CAGATTTGCTTTCTTGGATGGC 58.481 45.455 0.00 0.00 0.00 4.40
2107 2145 1.523154 TTTCTTGGATGGCGGTGCAC 61.523 55.000 8.80 8.80 0.00 4.57
2603 2644 4.672801 GCAGCTGTTGACAAGGCTATTAAC 60.673 45.833 16.64 0.00 33.43 2.01
2671 2712 5.142061 TGTTCTTCTGCCGTGTCTTATTA 57.858 39.130 0.00 0.00 0.00 0.98
2673 2714 6.869695 TGTTCTTCTGCCGTGTCTTATTATA 58.130 36.000 0.00 0.00 0.00 0.98
2762 2803 2.415090 GCTATTGCTTCAGTTGGCACAG 60.415 50.000 0.00 0.00 38.23 3.66
2800 2841 5.565637 GCTTCTTTTTCCACAGATCCTTTCC 60.566 44.000 0.00 0.00 0.00 3.13
2992 3033 3.428664 TGGATGCCCATGGTCCCC 61.429 66.667 15.48 9.42 37.58 4.81
2998 3039 2.677228 CCCATGGTCCCCTGTCAC 59.323 66.667 11.73 0.00 0.00 3.67
3004 3045 0.475632 TGGTCCCCTGTCACCTGATT 60.476 55.000 0.00 0.00 33.36 2.57
3091 3132 3.009723 AGTGCACATGGTATACACTTGC 58.990 45.455 21.04 7.93 38.38 4.01
3326 3367 3.447229 AGGTGCTTAGTTTGTTGTTGCTT 59.553 39.130 0.00 0.00 0.00 3.91
3411 3452 6.491745 TCATTTAAGTGTTTTGCATAGGTCCA 59.508 34.615 0.00 0.00 0.00 4.02
3413 3454 3.222173 AGTGTTTTGCATAGGTCCACA 57.778 42.857 0.00 0.00 0.00 4.17
3563 3604 6.194463 CCTTAATGTGAATGCGTGTTCTATG 58.806 40.000 4.10 0.00 0.00 2.23
3564 3605 6.183360 CCTTAATGTGAATGCGTGTTCTATGT 60.183 38.462 4.10 0.00 0.00 2.29
3751 3792 0.601046 GCGATTGGATGATGGCTCGA 60.601 55.000 0.00 0.00 0.00 4.04
3851 3892 4.072131 GACATTTAGTTGAGAACCCTGCA 58.928 43.478 0.00 0.00 0.00 4.41
3960 4010 7.832685 TGAGATCCAAATCATTGAAGAAGACAT 59.167 33.333 0.00 0.00 38.94 3.06
3976 4026 3.600388 AGACATGCCTTTAAGAACTCCG 58.400 45.455 0.00 0.00 0.00 4.63
4110 4160 6.997239 TCTTGATTTGGATTCTCTGTCATG 57.003 37.500 0.00 0.00 0.00 3.07
4333 4383 3.195182 CAGTGAGAGAGAAAGATGCTGGA 59.805 47.826 0.00 0.00 0.00 3.86
4422 4472 8.373048 TGGGTTTACAATATGTACGATTCATC 57.627 34.615 0.00 0.00 31.69 2.92
4495 4545 3.412386 GTCATGTAGCAAACCTTGTCCT 58.588 45.455 0.00 0.00 0.00 3.85
4757 4809 4.401519 AGGAATTGCTTGACATTGATGGAG 59.598 41.667 0.00 0.00 0.00 3.86
4875 4927 7.653767 ACTGTTATTTAACTGAAGTTCCTCG 57.346 36.000 12.52 0.00 39.31 4.63
4922 4974 4.598036 ACCTGATGTCCCAATCTTCATT 57.402 40.909 0.00 0.00 0.00 2.57
4951 5003 6.477688 TCAGTTCTGTTTACGTGGTTTCTTAG 59.522 38.462 0.00 0.00 0.00 2.18
5162 5296 6.743575 AGATAAAACGAGCTGCAGTTTAAT 57.256 33.333 20.67 12.27 39.36 1.40
5185 5319 1.416030 GTTCTGCATGTTTTGGGGGTT 59.584 47.619 0.00 0.00 0.00 4.11
5186 5320 1.337118 TCTGCATGTTTTGGGGGTTC 58.663 50.000 0.00 0.00 0.00 3.62
5681 5827 3.325135 CCTACCCCTCTAACATGTCATCC 59.675 52.174 0.00 0.00 0.00 3.51
5713 5859 6.321181 AGTTTCATAGCTTGAACTGGAAAACA 59.679 34.615 9.83 0.00 43.99 2.83
5741 5892 4.430441 ACCTCTGTGAATTCTACTCCCTT 58.570 43.478 7.05 0.00 0.00 3.95
5841 5992 5.038033 CGGAGAGAGTACTTCTGTAATTGC 58.962 45.833 10.94 0.00 35.87 3.56
5853 6006 6.765989 ACTTCTGTAATTGCACACTCTTTGTA 59.234 34.615 0.00 0.00 35.67 2.41
5865 6018 1.798813 CTCTTTGTAACGCTGACACCC 59.201 52.381 0.00 0.00 0.00 4.61
6063 6216 1.069090 GTGGTCGTGGTTCTCAGCA 59.931 57.895 0.00 0.00 0.00 4.41
6104 6331 3.707102 AGCTGACCCAGTAACCTATCTTC 59.293 47.826 0.00 0.00 33.43 2.87
6105 6332 3.491104 GCTGACCCAGTAACCTATCTTCG 60.491 52.174 0.00 0.00 33.43 3.79
6106 6333 2.429610 TGACCCAGTAACCTATCTTCGC 59.570 50.000 0.00 0.00 0.00 4.70
6107 6334 1.761198 ACCCAGTAACCTATCTTCGCC 59.239 52.381 0.00 0.00 0.00 5.54
6108 6335 1.070289 CCCAGTAACCTATCTTCGCCC 59.930 57.143 0.00 0.00 0.00 6.13
6109 6336 1.269621 CCAGTAACCTATCTTCGCCCG 60.270 57.143 0.00 0.00 0.00 6.13
6110 6337 1.407979 CAGTAACCTATCTTCGCCCGT 59.592 52.381 0.00 0.00 0.00 5.28
6111 6338 1.407979 AGTAACCTATCTTCGCCCGTG 59.592 52.381 0.00 0.00 0.00 4.94
6112 6339 1.135721 GTAACCTATCTTCGCCCGTGT 59.864 52.381 0.00 0.00 0.00 4.49
6113 6340 1.477553 AACCTATCTTCGCCCGTGTA 58.522 50.000 0.00 0.00 0.00 2.90
6114 6341 1.477553 ACCTATCTTCGCCCGTGTAA 58.522 50.000 0.00 0.00 0.00 2.41
6115 6342 1.407979 ACCTATCTTCGCCCGTGTAAG 59.592 52.381 0.00 0.00 0.00 2.34
6116 6343 1.269621 CCTATCTTCGCCCGTGTAAGG 60.270 57.143 0.00 0.00 0.00 2.69
6123 6350 4.011517 CCCGTGTAAGGCCGTGGT 62.012 66.667 0.00 0.00 0.00 4.16
6124 6351 2.433664 CCGTGTAAGGCCGTGGTC 60.434 66.667 0.00 0.00 0.00 4.02
6125 6352 2.340809 CGTGTAAGGCCGTGGTCA 59.659 61.111 0.00 0.00 0.00 4.02
6126 6353 1.736645 CGTGTAAGGCCGTGGTCAG 60.737 63.158 0.00 0.00 0.00 3.51
6127 6354 2.033194 GTGTAAGGCCGTGGTCAGC 61.033 63.158 0.00 0.00 0.00 4.26
6128 6355 2.813908 GTAAGGCCGTGGTCAGCG 60.814 66.667 0.00 0.00 0.00 5.18
6129 6356 4.752879 TAAGGCCGTGGTCAGCGC 62.753 66.667 0.00 0.00 0.00 5.92
6134 6361 2.202690 CCGTGGTCAGCGCGATTA 60.203 61.111 12.10 0.00 0.00 1.75
6135 6362 1.591594 CCGTGGTCAGCGCGATTAT 60.592 57.895 12.10 0.00 0.00 1.28
6136 6363 1.548973 CCGTGGTCAGCGCGATTATC 61.549 60.000 12.10 0.00 0.00 1.75
6137 6364 1.548973 CGTGGTCAGCGCGATTATCC 61.549 60.000 12.10 6.26 0.00 2.59
6138 6365 0.249489 GTGGTCAGCGCGATTATCCT 60.249 55.000 12.10 0.00 0.00 3.24
6139 6366 0.032130 TGGTCAGCGCGATTATCCTC 59.968 55.000 12.10 0.00 0.00 3.71
6140 6367 0.032130 GGTCAGCGCGATTATCCTCA 59.968 55.000 12.10 0.00 0.00 3.86
6141 6368 1.337260 GGTCAGCGCGATTATCCTCAT 60.337 52.381 12.10 0.00 0.00 2.90
6142 6369 2.094700 GGTCAGCGCGATTATCCTCATA 60.095 50.000 12.10 0.00 0.00 2.15
6143 6370 3.429547 GGTCAGCGCGATTATCCTCATAT 60.430 47.826 12.10 0.00 0.00 1.78
6144 6371 4.177026 GTCAGCGCGATTATCCTCATATT 58.823 43.478 12.10 0.00 0.00 1.28
6145 6372 4.627467 GTCAGCGCGATTATCCTCATATTT 59.373 41.667 12.10 0.00 0.00 1.40
6146 6373 4.864806 TCAGCGCGATTATCCTCATATTTC 59.135 41.667 12.10 0.00 0.00 2.17
6147 6374 4.627035 CAGCGCGATTATCCTCATATTTCA 59.373 41.667 12.10 0.00 0.00 2.69
6148 6375 4.867047 AGCGCGATTATCCTCATATTTCAG 59.133 41.667 12.10 0.00 0.00 3.02
6149 6376 4.493220 GCGCGATTATCCTCATATTTCAGC 60.493 45.833 12.10 0.00 0.00 4.26
6150 6377 4.627035 CGCGATTATCCTCATATTTCAGCA 59.373 41.667 0.00 0.00 0.00 4.41
6151 6378 5.220359 CGCGATTATCCTCATATTTCAGCAG 60.220 44.000 0.00 0.00 0.00 4.24
6152 6379 5.871524 GCGATTATCCTCATATTTCAGCAGA 59.128 40.000 0.00 0.00 0.00 4.26
6153 6380 6.183360 GCGATTATCCTCATATTTCAGCAGAC 60.183 42.308 0.00 0.00 0.00 3.51
6154 6381 6.312426 CGATTATCCTCATATTTCAGCAGACC 59.688 42.308 0.00 0.00 0.00 3.85
6155 6382 3.845781 TCCTCATATTTCAGCAGACCC 57.154 47.619 0.00 0.00 0.00 4.46
6156 6383 3.114606 TCCTCATATTTCAGCAGACCCA 58.885 45.455 0.00 0.00 0.00 4.51
6157 6384 3.135348 TCCTCATATTTCAGCAGACCCAG 59.865 47.826 0.00 0.00 0.00 4.45
6158 6385 3.118112 CCTCATATTTCAGCAGACCCAGT 60.118 47.826 0.00 0.00 0.00 4.00
6159 6386 4.101585 CCTCATATTTCAGCAGACCCAGTA 59.898 45.833 0.00 0.00 0.00 2.74
6160 6387 5.396772 CCTCATATTTCAGCAGACCCAGTAA 60.397 44.000 0.00 0.00 0.00 2.24
6161 6388 5.428253 TCATATTTCAGCAGACCCAGTAAC 58.572 41.667 0.00 0.00 0.00 2.50
6162 6389 2.561478 TTTCAGCAGACCCAGTAACC 57.439 50.000 0.00 0.00 0.00 2.85
6163 6390 1.729586 TTCAGCAGACCCAGTAACCT 58.270 50.000 0.00 0.00 0.00 3.50
6164 6391 2.615986 TCAGCAGACCCAGTAACCTA 57.384 50.000 0.00 0.00 0.00 3.08
6165 6392 3.116096 TCAGCAGACCCAGTAACCTAT 57.884 47.619 0.00 0.00 0.00 2.57
6166 6393 3.031736 TCAGCAGACCCAGTAACCTATC 58.968 50.000 0.00 0.00 0.00 2.08
6167 6394 3.034635 CAGCAGACCCAGTAACCTATCT 58.965 50.000 0.00 0.00 0.00 1.98
6168 6395 3.452627 CAGCAGACCCAGTAACCTATCTT 59.547 47.826 0.00 0.00 0.00 2.40
6177 6404 2.699321 AGTAACCTATCTTCGCCTTCCC 59.301 50.000 0.00 0.00 0.00 3.97
6178 6405 0.464452 AACCTATCTTCGCCTTCCCG 59.536 55.000 0.00 0.00 0.00 5.14
6197 6424 1.661509 GAACTGCGCAACAAAGGGC 60.662 57.895 13.05 0.00 46.45 5.19
6217 6444 2.431782 GCCCCTTGTGCAATATCAATGT 59.568 45.455 0.00 0.00 0.00 2.71
6257 6486 0.611618 TGGATGTGGCCTGCGATTTT 60.612 50.000 3.32 0.00 0.00 1.82
6269 6584 4.333926 GCCTGCGATTTTGTCTAGAATTCT 59.666 41.667 13.56 13.56 0.00 2.40
6270 6585 5.163713 GCCTGCGATTTTGTCTAGAATTCTT 60.164 40.000 14.36 0.00 0.00 2.52
6271 6586 6.253746 CCTGCGATTTTGTCTAGAATTCTTG 58.746 40.000 14.36 12.08 0.00 3.02
6295 6610 5.928839 GCTCAAGATCAGACTTTGTTCAGTA 59.071 40.000 0.00 0.00 0.00 2.74
6297 6612 6.816136 TCAAGATCAGACTTTGTTCAGTACA 58.184 36.000 0.00 0.00 34.12 2.90
6335 6660 9.177608 TGGTTCGATTTCATCTAGAATTCAAAT 57.822 29.630 8.44 3.69 36.75 2.32
6350 6675 4.829064 TTCAAATTCCAGGTCGACTTTG 57.171 40.909 16.46 15.99 35.08 2.77
6356 6681 2.036387 TCCAGGTCGACTTTGTTCAGA 58.964 47.619 16.46 4.69 0.00 3.27
6357 6682 2.135933 CCAGGTCGACTTTGTTCAGAC 58.864 52.381 16.46 0.00 0.00 3.51
6377 6715 2.262211 CGGGTACGTGGCTTACTTTAC 58.738 52.381 0.00 0.00 34.81 2.01
6395 6733 5.521372 ACTTTACGTTGGTGTAGTTGTCTTC 59.479 40.000 0.00 0.00 0.00 2.87
6397 6735 2.140717 CGTTGGTGTAGTTGTCTTCCC 58.859 52.381 0.00 0.00 0.00 3.97
6398 6736 2.501261 GTTGGTGTAGTTGTCTTCCCC 58.499 52.381 0.00 0.00 0.00 4.81
6399 6737 1.061546 TGGTGTAGTTGTCTTCCCCC 58.938 55.000 0.00 0.00 0.00 5.40
6405 6743 3.460340 TGTAGTTGTCTTCCCCCTTTTGA 59.540 43.478 0.00 0.00 0.00 2.69
6421 6759 2.785713 TTGAGCCCAACGTAAAAAGC 57.214 45.000 0.00 0.00 0.00 3.51
6437 6775 1.767759 AAGCTTGCACAAGACACCTT 58.232 45.000 14.44 5.09 40.79 3.50
6438 6776 1.767759 AGCTTGCACAAGACACCTTT 58.232 45.000 14.44 0.00 40.79 3.11
6446 6784 5.069318 TGCACAAGACACCTTTATGATCAA 58.931 37.500 0.00 0.00 0.00 2.57
6451 6789 7.120285 CACAAGACACCTTTATGATCAACAGAT 59.880 37.037 0.00 0.00 0.00 2.90
6460 6798 6.823286 TTATGATCAACAGATAGTTCCCCA 57.177 37.500 0.00 0.00 38.74 4.96
6469 6807 6.607198 CAACAGATAGTTCCCCATAAAATGGT 59.393 38.462 5.27 0.00 43.21 3.55
6484 6822 9.483916 CCATAAAATGGTACTGTATTCGTCATA 57.516 33.333 0.00 0.00 45.54 2.15
6508 6846 7.076842 ACGATCACATCAAAAGTAAAGGATG 57.923 36.000 0.00 0.00 42.12 3.51
6532 6875 5.528690 GCCACTATGATCATACACAACATGT 59.471 40.000 11.49 3.06 46.06 3.21
6533 6876 6.293081 GCCACTATGATCATACACAACATGTC 60.293 42.308 11.49 0.00 42.09 3.06
6557 6900 6.535865 TCCGCAACTTTATTACACGATTACAT 59.464 34.615 0.00 0.00 0.00 2.29
6577 6922 0.765510 AGACCTGAAACCTGGGTGTC 59.234 55.000 3.11 3.11 33.01 3.67
6580 6925 1.966451 CTGAAACCTGGGTGTCGGC 60.966 63.158 5.90 0.00 35.20 5.54
6590 6935 1.152963 GGTGTCGGCCTGCCATTAT 60.153 57.895 9.17 0.00 35.37 1.28
6593 6938 2.294074 GTGTCGGCCTGCCATTATAAA 58.706 47.619 9.17 0.00 35.37 1.40
6594 6939 2.290641 GTGTCGGCCTGCCATTATAAAG 59.709 50.000 9.17 0.00 35.37 1.85
6595 6940 2.092646 TGTCGGCCTGCCATTATAAAGT 60.093 45.455 9.17 0.00 35.37 2.66
6596 6941 2.949644 GTCGGCCTGCCATTATAAAGTT 59.050 45.455 9.17 0.00 35.37 2.66
6597 6942 3.003378 GTCGGCCTGCCATTATAAAGTTC 59.997 47.826 9.17 0.00 35.37 3.01
6598 6943 2.948979 CGGCCTGCCATTATAAAGTTCA 59.051 45.455 9.17 0.00 35.37 3.18
6600 6945 4.037923 CGGCCTGCCATTATAAAGTTCATT 59.962 41.667 9.17 0.00 35.37 2.57
6603 6948 7.496747 GGCCTGCCATTATAAAGTTCATTTAA 58.503 34.615 2.58 0.00 35.10 1.52
6604 6949 7.653311 GGCCTGCCATTATAAAGTTCATTTAAG 59.347 37.037 2.58 0.00 35.10 1.85
6605 6950 8.413229 GCCTGCCATTATAAAGTTCATTTAAGA 58.587 33.333 0.00 0.00 36.94 2.10
6609 6954 9.237846 GCCATTATAAAGTTCATTTAAGAGTGC 57.762 33.333 0.00 0.00 36.94 4.40
6650 7031 7.101054 AGGAAATACGACTAAACAAGCATACA 58.899 34.615 0.00 0.00 0.00 2.29
6657 7056 8.090250 ACGACTAAACAAGCATACATACAAAA 57.910 30.769 0.00 0.00 0.00 2.44
6673 7072 8.475331 ACATACAAAATTACAGTCTAGGTTCG 57.525 34.615 0.00 0.00 0.00 3.95
6676 7075 5.632347 ACAAAATTACAGTCTAGGTTCGACG 59.368 40.000 0.00 0.00 36.53 5.12
6692 7091 4.131649 TCGACGGAACATTATTCATGGT 57.868 40.909 0.00 0.00 37.17 3.55
6875 7276 8.194769 AGTGCTATTAAAGAGAAAGAGAGCTAC 58.805 37.037 0.00 0.00 0.00 3.58
6915 7316 1.549203 TACCGAGGTCGTAGGCTTTT 58.451 50.000 0.00 0.00 37.74 2.27
6941 7342 3.193757 TCGAGCCGCGATGTTAGT 58.806 55.556 8.23 0.00 45.59 2.24
6981 7382 2.903135 GGAGAAGGGTGGATAGATCAGG 59.097 54.545 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 4.356436 TGATTGAAGACCTCCATCTCTCA 58.644 43.478 0.00 0.00 29.37 3.27
155 156 0.608640 GGCCTTGAACTTCTCCTCGA 59.391 55.000 0.00 0.00 0.00 4.04
203 204 3.193691 ACCGTCATCCGATCTATTGATCC 59.806 47.826 10.93 0.00 44.61 3.36
230 231 1.057851 AGGGGGAAACGACACCAGAA 61.058 55.000 0.00 0.00 34.56 3.02
265 267 4.314440 GAGCCCGTGTGCACCTCA 62.314 66.667 15.69 0.00 0.00 3.86
299 301 2.030562 CCGCTCCACCAAAGACGT 59.969 61.111 0.00 0.00 0.00 4.34
325 327 1.815613 CCGCCACCATTGATGTGTAAA 59.184 47.619 0.00 0.00 0.00 2.01
335 337 2.505982 CCGAGATCCGCCACCATT 59.494 61.111 0.00 0.00 36.84 3.16
368 370 1.550065 CGCATCAGACGTCGAATCTT 58.450 50.000 10.46 0.00 0.00 2.40
461 463 2.158957 AGAGCAAAACTGAAGACCGACA 60.159 45.455 0.00 0.00 0.00 4.35
476 479 2.669133 CGGTCCATCCCCAGAGCAA 61.669 63.158 0.00 0.00 0.00 3.91
484 487 3.570212 CATCCCCCGGTCCATCCC 61.570 72.222 0.00 0.00 0.00 3.85
495 498 2.548920 GGTCGTCATCTTCATCATCCCC 60.549 54.545 0.00 0.00 0.00 4.81
505 509 0.674895 GCTGCAAGGGTCGTCATCTT 60.675 55.000 0.00 0.00 0.00 2.40
538 542 1.610673 ACCGATCTGGCACACTCCT 60.611 57.895 3.85 0.00 43.94 3.69
633 638 2.173519 CCGAATATCCGGGCCTAGTAA 58.826 52.381 0.84 0.00 45.43 2.24
657 662 6.492087 GCTACTACTATCCTCTTGATGAAGGT 59.508 42.308 0.00 0.00 34.76 3.50
676 681 3.068448 TCTTGACAACACCGTTGCTACTA 59.932 43.478 6.77 0.00 0.00 1.82
757 762 7.247929 CATCTCAACTATGCATATAGCCATG 57.752 40.000 6.92 2.64 44.83 3.66
772 777 1.554160 CCTGACCTCTGCATCTCAACT 59.446 52.381 0.00 0.00 0.00 3.16
776 781 1.484038 ACTCCTGACCTCTGCATCTC 58.516 55.000 0.00 0.00 0.00 2.75
821 826 7.332678 ACAAAACAAGTACAGTACTCTCGTTTT 59.667 33.333 25.41 25.41 41.27 2.43
825 830 5.975344 TCACAAAACAAGTACAGTACTCTCG 59.025 40.000 13.86 8.19 38.26 4.04
826 831 7.766219 TTCACAAAACAAGTACAGTACTCTC 57.234 36.000 13.86 0.00 38.26 3.20
846 851 3.943381 CCCTTCCCGGTTATACTTTTCAC 59.057 47.826 0.00 0.00 0.00 3.18
859 864 0.912486 AGATTTCAGACCCTTCCCGG 59.088 55.000 0.00 0.00 0.00 5.73
862 867 4.262617 GTTGGTAGATTTCAGACCCTTCC 58.737 47.826 0.00 0.00 31.80 3.46
872 878 4.156739 CCTTCAGGCTTGTTGGTAGATTTC 59.843 45.833 0.00 0.00 0.00 2.17
927 933 1.599576 GCACTCCCCACTTCTCCTC 59.400 63.158 0.00 0.00 0.00 3.71
928 934 1.920835 GGCACTCCCCACTTCTCCT 60.921 63.158 0.00 0.00 0.00 3.69
929 935 2.671682 GGCACTCCCCACTTCTCC 59.328 66.667 0.00 0.00 0.00 3.71
1044 1056 1.440893 CTCCTCCATGTCCAGCTCG 59.559 63.158 0.00 0.00 0.00 5.03
1095 1107 1.820481 GACGTCGGAGGAGGAGGAG 60.820 68.421 0.00 0.00 0.00 3.69
1193 1206 3.160585 CAGAAGGCACACCCCAGA 58.839 61.111 0.00 0.00 36.11 3.86
1280 1294 3.066900 TCTCGGCAGCAGTTTCTACTATC 59.933 47.826 0.00 0.00 31.96 2.08
1290 1321 2.581354 GACCATCTCGGCAGCAGT 59.419 61.111 0.00 0.00 39.03 4.40
1316 1347 0.464036 TCGAAACCTATGAGCGCCAT 59.536 50.000 2.29 10.32 39.25 4.40
1343 1374 9.586435 CCAAATCACCTTAAACCAAATAGATTC 57.414 33.333 0.00 0.00 0.00 2.52
1390 1421 7.303182 TGACTCCTAATTGATGTATACCCAG 57.697 40.000 0.00 0.00 0.00 4.45
1392 1423 7.162082 CCTTGACTCCTAATTGATGTATACCC 58.838 42.308 0.00 0.00 0.00 3.69
1495 1528 4.734402 GCTGCAAGTGTGAGAAATTGTGAA 60.734 41.667 0.00 0.00 35.30 3.18
1525 1561 3.037431 AGGCGCATCTAATCATCAGAC 57.963 47.619 10.83 0.00 0.00 3.51
1526 1562 3.323115 AGAAGGCGCATCTAATCATCAGA 59.677 43.478 10.83 0.00 0.00 3.27
1621 1658 3.181458 GCTGATGCCCAATTCAATCCATT 60.181 43.478 0.00 0.00 0.00 3.16
1767 1804 3.133183 TGGACTAATAGCGCATGGTGTAA 59.867 43.478 11.47 0.00 0.00 2.41
1868 1906 6.215227 AGAAGAATGAGGAAAAGGATCAGAGT 59.785 38.462 0.00 0.00 0.00 3.24
2100 2138 1.429463 GTAAACTGAGGAGTGCACCG 58.571 55.000 14.63 0.00 30.61 4.94
2107 2145 5.983540 AGAAAGCATAGGTAAACTGAGGAG 58.016 41.667 0.00 0.00 0.00 3.69
2603 2644 5.715434 TCATGCATGGATTATCAACATGG 57.285 39.130 25.97 0.00 41.62 3.66
2671 2712 9.793259 TGGAGAACTGTCAGAAAATAAAACTAT 57.207 29.630 6.91 0.00 0.00 2.12
2673 2714 8.406297 GTTGGAGAACTGTCAGAAAATAAAACT 58.594 33.333 6.91 0.00 0.00 2.66
2762 2803 2.970974 GAAGCAACACCTCCGCTGC 61.971 63.158 0.00 0.00 35.79 5.25
2826 2867 8.865090 ACAAATAACAGATGAATTACCAAACCA 58.135 29.630 0.00 0.00 0.00 3.67
3004 3045 9.457436 CATCATCATTTCCCTTGATGTATATCA 57.543 33.333 12.03 0.00 46.78 2.15
3055 3096 7.015584 ACCATGTGCACTATCTAGTAATGATGA 59.984 37.037 19.41 0.00 34.13 2.92
3056 3097 7.157347 ACCATGTGCACTATCTAGTAATGATG 58.843 38.462 19.41 8.08 34.13 3.07
3057 3098 7.308450 ACCATGTGCACTATCTAGTAATGAT 57.692 36.000 19.41 0.00 34.13 2.45
3091 3132 2.642139 ATTTGCAAGCATCAACTCGG 57.358 45.000 0.00 0.00 0.00 4.63
3156 3197 6.489127 TCTGTTGATTAACATACAAACCCG 57.511 37.500 3.22 0.00 45.16 5.28
3326 3367 7.504238 TGTTGAACAATTAAAGGAAGGAAGCTA 59.496 33.333 0.00 0.00 0.00 3.32
3411 3452 0.823356 AGAACCAATGCCAAGCGTGT 60.823 50.000 0.00 0.00 0.00 4.49
3413 3454 0.598065 GAAGAACCAATGCCAAGCGT 59.402 50.000 0.00 0.00 0.00 5.07
3563 3604 8.244113 CCTTGAAAGTTTGGGATAATACAAGAC 58.756 37.037 0.00 0.00 34.81 3.01
3564 3605 8.167392 TCCTTGAAAGTTTGGGATAATACAAGA 58.833 33.333 0.00 0.00 34.81 3.02
3751 3792 5.147330 TGACCTCGAGTGATAACATTTGT 57.853 39.130 12.31 0.00 0.00 2.83
3851 3892 4.898265 TCTGGCTCATAGCATTAGAGAACT 59.102 41.667 0.78 0.00 44.75 3.01
3918 3968 0.679002 CTCACCCCATGGCTGTCAAG 60.679 60.000 6.09 2.13 33.59 3.02
3960 4010 1.278127 CCCTCGGAGTTCTTAAAGGCA 59.722 52.381 4.02 0.00 0.00 4.75
3976 4026 2.134789 ACTGTCCAAATGCATCCCTC 57.865 50.000 0.00 0.00 0.00 4.30
4110 4160 4.252971 TGGTCACTTGAAGTACTAGTGC 57.747 45.455 16.34 3.75 46.36 4.40
4178 4228 4.383444 CCAAGACAGTTCAGGCATGAGATA 60.383 45.833 0.00 0.00 36.61 1.98
4333 4383 2.037251 AGCACGGTATTGTCTCTGTTGT 59.963 45.455 0.00 0.00 0.00 3.32
4523 4573 9.784531 GACAGAAATGGAAGGAATATTATCTGA 57.215 33.333 0.00 0.00 35.67 3.27
4757 4809 2.663602 CTCGCTGCAACCGATATGATAC 59.336 50.000 9.24 0.00 33.83 2.24
4875 4927 6.490381 AGAAGTGGGAAAAGAACCTGAAATAC 59.510 38.462 0.00 0.00 0.00 1.89
4922 4974 5.266733 ACCACGTAAACAGAACTGAAGTA 57.733 39.130 8.87 0.00 0.00 2.24
4951 5003 1.041437 AGGACCGGAGCAGCTAATAC 58.959 55.000 9.46 0.00 0.00 1.89
5022 5074 7.715249 CAGCATACCAAATACTAGTATTGTGGT 59.285 37.037 34.52 34.52 42.49 4.16
5162 5296 2.896685 CCCCCAAAACATGCAGAACTTA 59.103 45.455 0.00 0.00 0.00 2.24
5174 5308 2.547855 GCACTGAATGAACCCCCAAAAC 60.548 50.000 0.00 0.00 0.00 2.43
5185 5319 1.800586 GCGAACTGAAGCACTGAATGA 59.199 47.619 0.00 0.00 0.00 2.57
5186 5320 1.135859 GGCGAACTGAAGCACTGAATG 60.136 52.381 0.00 0.00 34.54 2.67
5538 5684 1.135603 CAACAACGGCATGACATGAGG 60.136 52.381 19.76 11.50 0.00 3.86
5713 5859 2.175202 AGAATTCACAGAGGTCGCTCT 58.825 47.619 8.44 0.00 0.00 4.09
5741 5892 6.045072 ACTATGACACTTATTTTGGGACGA 57.955 37.500 0.00 0.00 0.00 4.20
5841 5992 2.863740 TGTCAGCGTTACAAAGAGTGTG 59.136 45.455 0.00 0.00 41.89 3.82
5853 6006 1.407656 TTCCTCTGGGTGTCAGCGTT 61.408 55.000 0.00 0.00 43.06 4.84
5865 6018 4.219507 ACGTATATCTGCAGGATTCCTCTG 59.780 45.833 15.13 2.96 35.98 3.35
6063 6216 6.991531 GTCAGCTGAAAGATAAGGAGAATCAT 59.008 38.462 20.19 0.00 32.23 2.45
6074 6301 4.081087 GGTTACTGGGTCAGCTGAAAGATA 60.081 45.833 20.19 4.96 34.37 1.98
6106 6333 3.945304 GACCACGGCCTTACACGGG 62.945 68.421 0.00 0.00 0.00 5.28
6107 6334 2.433664 GACCACGGCCTTACACGG 60.434 66.667 0.00 0.00 0.00 4.94
6108 6335 1.736645 CTGACCACGGCCTTACACG 60.737 63.158 0.00 0.00 0.00 4.49
6109 6336 2.033194 GCTGACCACGGCCTTACAC 61.033 63.158 0.00 0.00 42.05 2.90
6110 6337 2.345991 GCTGACCACGGCCTTACA 59.654 61.111 0.00 0.00 42.05 2.41
6111 6338 2.813908 CGCTGACCACGGCCTTAC 60.814 66.667 0.00 0.00 44.72 2.34
6112 6339 4.752879 GCGCTGACCACGGCCTTA 62.753 66.667 0.00 0.00 44.72 2.69
6117 6344 1.548973 GATAATCGCGCTGACCACGG 61.549 60.000 5.56 0.00 0.00 4.94
6118 6345 1.548973 GGATAATCGCGCTGACCACG 61.549 60.000 5.56 0.00 0.00 4.94
6119 6346 0.249489 AGGATAATCGCGCTGACCAC 60.249 55.000 5.56 0.00 0.00 4.16
6120 6347 0.032130 GAGGATAATCGCGCTGACCA 59.968 55.000 5.56 0.00 0.00 4.02
6121 6348 0.032130 TGAGGATAATCGCGCTGACC 59.968 55.000 5.56 0.76 0.00 4.02
6122 6349 2.071688 ATGAGGATAATCGCGCTGAC 57.928 50.000 5.56 0.00 0.00 3.51
6123 6350 4.456280 AATATGAGGATAATCGCGCTGA 57.544 40.909 5.56 4.94 0.00 4.26
6124 6351 4.627035 TGAAATATGAGGATAATCGCGCTG 59.373 41.667 5.56 0.00 0.00 5.18
6125 6352 4.820897 TGAAATATGAGGATAATCGCGCT 58.179 39.130 5.56 0.00 0.00 5.92
6126 6353 4.493220 GCTGAAATATGAGGATAATCGCGC 60.493 45.833 0.00 0.00 0.00 6.86
6127 6354 4.627035 TGCTGAAATATGAGGATAATCGCG 59.373 41.667 0.00 0.00 0.00 5.87
6128 6355 5.871524 TCTGCTGAAATATGAGGATAATCGC 59.128 40.000 0.00 0.00 0.00 4.58
6129 6356 6.312426 GGTCTGCTGAAATATGAGGATAATCG 59.688 42.308 0.00 0.00 0.00 3.34
6130 6357 6.597280 GGGTCTGCTGAAATATGAGGATAATC 59.403 42.308 0.00 0.00 0.00 1.75
6131 6358 6.044754 TGGGTCTGCTGAAATATGAGGATAAT 59.955 38.462 0.00 0.00 0.00 1.28
6132 6359 5.369404 TGGGTCTGCTGAAATATGAGGATAA 59.631 40.000 0.00 0.00 0.00 1.75
6133 6360 4.907269 TGGGTCTGCTGAAATATGAGGATA 59.093 41.667 0.00 0.00 0.00 2.59
6134 6361 3.718434 TGGGTCTGCTGAAATATGAGGAT 59.282 43.478 0.00 0.00 0.00 3.24
6135 6362 3.114606 TGGGTCTGCTGAAATATGAGGA 58.885 45.455 0.00 0.00 0.00 3.71
6136 6363 3.118112 ACTGGGTCTGCTGAAATATGAGG 60.118 47.826 0.00 0.00 0.00 3.86
6137 6364 4.148128 ACTGGGTCTGCTGAAATATGAG 57.852 45.455 0.00 0.00 0.00 2.90
6138 6365 5.428253 GTTACTGGGTCTGCTGAAATATGA 58.572 41.667 0.00 0.00 0.00 2.15
6139 6366 4.576463 GGTTACTGGGTCTGCTGAAATATG 59.424 45.833 0.00 0.00 0.00 1.78
6140 6367 4.475016 AGGTTACTGGGTCTGCTGAAATAT 59.525 41.667 0.00 0.00 0.00 1.28
6141 6368 3.844211 AGGTTACTGGGTCTGCTGAAATA 59.156 43.478 0.00 0.00 0.00 1.40
6142 6369 2.644798 AGGTTACTGGGTCTGCTGAAAT 59.355 45.455 0.00 0.00 0.00 2.17
6143 6370 2.054799 AGGTTACTGGGTCTGCTGAAA 58.945 47.619 0.00 0.00 0.00 2.69
6144 6371 1.729586 AGGTTACTGGGTCTGCTGAA 58.270 50.000 0.00 0.00 0.00 3.02
6145 6372 2.615986 TAGGTTACTGGGTCTGCTGA 57.384 50.000 0.00 0.00 0.00 4.26
6146 6373 3.034635 AGATAGGTTACTGGGTCTGCTG 58.965 50.000 0.00 0.00 0.00 4.41
6147 6374 3.406512 AGATAGGTTACTGGGTCTGCT 57.593 47.619 0.00 0.00 0.00 4.24
6148 6375 3.491104 CGAAGATAGGTTACTGGGTCTGC 60.491 52.174 0.00 0.00 0.00 4.26
6149 6376 3.491104 GCGAAGATAGGTTACTGGGTCTG 60.491 52.174 0.00 0.00 0.00 3.51
6150 6377 2.694109 GCGAAGATAGGTTACTGGGTCT 59.306 50.000 0.00 0.00 0.00 3.85
6151 6378 2.223994 GGCGAAGATAGGTTACTGGGTC 60.224 54.545 0.00 0.00 0.00 4.46
6152 6379 1.761198 GGCGAAGATAGGTTACTGGGT 59.239 52.381 0.00 0.00 0.00 4.51
6153 6380 2.040178 AGGCGAAGATAGGTTACTGGG 58.960 52.381 0.00 0.00 0.00 4.45
6154 6381 3.492829 GGAAGGCGAAGATAGGTTACTGG 60.493 52.174 0.00 0.00 0.00 4.00
6155 6382 3.492829 GGGAAGGCGAAGATAGGTTACTG 60.493 52.174 0.00 0.00 0.00 2.74
6156 6383 2.699321 GGGAAGGCGAAGATAGGTTACT 59.301 50.000 0.00 0.00 0.00 2.24
6157 6384 2.545322 CGGGAAGGCGAAGATAGGTTAC 60.545 54.545 0.00 0.00 0.00 2.50
6158 6385 1.684983 CGGGAAGGCGAAGATAGGTTA 59.315 52.381 0.00 0.00 0.00 2.85
6159 6386 0.464452 CGGGAAGGCGAAGATAGGTT 59.536 55.000 0.00 0.00 0.00 3.50
6160 6387 1.400530 CCGGGAAGGCGAAGATAGGT 61.401 60.000 0.00 0.00 0.00 3.08
6161 6388 1.113517 TCCGGGAAGGCGAAGATAGG 61.114 60.000 0.00 0.00 40.77 2.57
6162 6389 0.750850 TTCCGGGAAGGCGAAGATAG 59.249 55.000 5.09 0.00 40.77 2.08
6163 6390 0.462789 GTTCCGGGAAGGCGAAGATA 59.537 55.000 10.35 0.00 40.77 1.98
6164 6391 1.221021 GTTCCGGGAAGGCGAAGAT 59.779 57.895 10.35 0.00 40.77 2.40
6165 6392 1.911766 AGTTCCGGGAAGGCGAAGA 60.912 57.895 10.35 0.00 40.77 2.87
6166 6393 1.741770 CAGTTCCGGGAAGGCGAAG 60.742 63.158 10.35 0.00 40.77 3.79
6167 6394 2.345991 CAGTTCCGGGAAGGCGAA 59.654 61.111 10.35 0.00 40.77 4.70
6168 6395 4.388499 GCAGTTCCGGGAAGGCGA 62.388 66.667 10.35 0.00 40.77 5.54
6177 6404 1.370414 CCTTTGTTGCGCAGTTCCG 60.370 57.895 11.31 0.26 0.00 4.30
6178 6405 1.007387 CCCTTTGTTGCGCAGTTCC 60.007 57.895 11.31 0.43 0.00 3.62
6197 6424 3.956199 AGACATTGATATTGCACAAGGGG 59.044 43.478 4.74 0.00 33.13 4.79
6217 6444 0.318699 CGTGGTCTCAAACGAGCAGA 60.319 55.000 0.00 0.00 41.53 4.26
6269 6584 5.125356 TGAACAAAGTCTGATCTTGAGCAA 58.875 37.500 8.21 0.00 0.00 3.91
6270 6585 4.707105 TGAACAAAGTCTGATCTTGAGCA 58.293 39.130 8.21 0.00 0.00 4.26
6271 6586 4.754114 ACTGAACAAAGTCTGATCTTGAGC 59.246 41.667 8.21 0.00 0.00 4.26
6297 6612 9.690428 GATGAAATCGAACCACATTCAGCATGT 62.690 40.741 0.00 0.00 39.33 3.21
6313 6628 9.394767 TGGAATTTGAATTCTAGATGAAATCGA 57.605 29.630 14.20 0.00 45.01 3.59
6335 6660 2.432874 TCTGAACAAAGTCGACCTGGAA 59.567 45.455 13.01 0.01 0.00 3.53
6338 6663 1.787155 CGTCTGAACAAAGTCGACCTG 59.213 52.381 13.01 12.68 31.58 4.00
6350 6675 1.735559 GCCACGTACCCGTCTGAAC 60.736 63.158 0.00 0.00 46.28 3.18
6357 6682 2.262211 GTAAAGTAAGCCACGTACCCG 58.738 52.381 0.00 0.00 40.83 5.28
6364 6689 2.874086 ACACCAACGTAAAGTAAGCCAC 59.126 45.455 0.00 0.00 0.00 5.01
6366 6691 4.309933 ACTACACCAACGTAAAGTAAGCC 58.690 43.478 0.00 0.00 0.00 4.35
6374 6712 4.370917 GGAAGACAACTACACCAACGTAA 58.629 43.478 0.00 0.00 0.00 3.18
6377 6715 2.140717 GGGAAGACAACTACACCAACG 58.859 52.381 0.00 0.00 0.00 4.10
6395 6733 2.275380 CGTTGGGCTCAAAAGGGGG 61.275 63.158 0.00 0.00 34.28 5.40
6397 6735 1.611519 TTACGTTGGGCTCAAAAGGG 58.388 50.000 0.00 0.00 34.28 3.95
6398 6736 3.719173 TTTTACGTTGGGCTCAAAAGG 57.281 42.857 0.00 0.00 34.28 3.11
6399 6737 3.489416 GCTTTTTACGTTGGGCTCAAAAG 59.511 43.478 0.00 0.53 35.33 2.27
6405 6743 1.269569 GCAAGCTTTTTACGTTGGGCT 60.270 47.619 0.00 0.00 0.00 5.19
6421 6759 5.181811 TGATCATAAAGGTGTCTTGTGCAAG 59.818 40.000 5.63 5.63 39.71 4.01
6437 6775 6.823286 TGGGGAACTATCTGTTGATCATAA 57.177 37.500 0.00 0.00 39.30 1.90
6438 6776 8.504811 TTATGGGGAACTATCTGTTGATCATA 57.495 34.615 0.00 0.00 39.30 2.15
6460 6798 9.188588 CGTATGACGAATACAGTACCATTTTAT 57.811 33.333 11.63 0.00 46.05 1.40
6478 6816 5.702622 ACTTTTGATGTGATCGTATGACG 57.297 39.130 0.00 0.00 44.19 4.35
6479 6817 8.116753 CCTTTACTTTTGATGTGATCGTATGAC 58.883 37.037 0.00 0.00 0.00 3.06
6484 6822 6.403636 GCATCCTTTACTTTTGATGTGATCGT 60.404 38.462 0.00 0.00 37.51 3.73
6495 6833 7.118723 TGATCATAGTGGCATCCTTTACTTTT 58.881 34.615 0.00 0.00 0.00 2.27
6508 6846 5.528690 ACATGTTGTGTATGATCATAGTGGC 59.471 40.000 15.83 5.01 39.91 5.01
6532 6875 5.868258 TGTAATCGTGTAATAAAGTTGCGGA 59.132 36.000 0.00 0.00 0.00 5.54
6533 6876 6.097156 TGTAATCGTGTAATAAAGTTGCGG 57.903 37.500 0.00 0.00 0.00 5.69
6557 6900 1.975680 GACACCCAGGTTTCAGGTCTA 59.024 52.381 0.00 0.00 0.00 2.59
6577 6922 2.948979 TGAACTTTATAATGGCAGGCCG 59.051 45.455 5.74 0.00 39.42 6.13
6580 6925 9.956720 CTCTTAAATGAACTTTATAATGGCAGG 57.043 33.333 0.00 0.00 0.00 4.85
6603 6948 9.851686 TTCCTTTGTTATCATATTATGCACTCT 57.148 29.630 0.00 0.00 0.00 3.24
6625 7006 7.101054 TGTATGCTTGTTTAGTCGTATTTCCT 58.899 34.615 0.00 0.00 0.00 3.36
6650 7031 7.487189 CGTCGAACCTAGACTGTAATTTTGTAT 59.513 37.037 0.00 0.00 36.53 2.29
6657 7056 3.614092 TCCGTCGAACCTAGACTGTAAT 58.386 45.455 0.00 0.00 36.53 1.89
6673 7072 5.116180 TCTGACCATGAATAATGTTCCGTC 58.884 41.667 0.00 0.00 34.11 4.79
6676 7075 7.933577 TCATACTCTGACCATGAATAATGTTCC 59.066 37.037 0.00 0.00 34.11 3.62
6687 7086 1.871408 GCGCCTCATACTCTGACCATG 60.871 57.143 0.00 0.00 0.00 3.66
6688 7087 0.390860 GCGCCTCATACTCTGACCAT 59.609 55.000 0.00 0.00 0.00 3.55
6692 7091 0.390492 CATGGCGCCTCATACTCTGA 59.610 55.000 29.70 2.45 0.00 3.27
6694 7093 1.750930 CCATGGCGCCTCATACTCT 59.249 57.895 29.70 0.00 0.00 3.24
6875 7276 6.535508 CGGTAAAATCTTCTTTCCTAGACCTG 59.464 42.308 0.00 0.00 30.90 4.00
6941 7342 4.903649 TCTCCAGCATCAGGAAGATATCAA 59.096 41.667 5.32 0.00 34.43 2.57


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

AutoCloner maintained by Alex Coulton.