Multiple sequence alignment - TraesCS1A01G417900

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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 TraesCS1A01G417900 chr1A 100.000 4598 0 0 1 4598 575589443 575594040 0.000000e+00 8492.0
1 TraesCS1A01G417900 chr1B 90.211 1849 131 24 906 2717 667487721 667489556 0.000000e+00 2366.0
2 TraesCS1A01G417900 chr1B 94.750 800 36 3 2876 3671 667489555 667490352 0.000000e+00 1240.0
3 TraesCS1A01G417900 chr1B 88.937 687 48 11 928 1614 667471840 667472498 0.000000e+00 822.0
4 TraesCS1A01G417900 chr1B 90.441 544 46 2 998 1541 667444504 667445041 0.000000e+00 712.0
5 TraesCS1A01G417900 chr1B 86.590 261 20 12 493 748 570290414 570290664 1.630000e-69 274.0
6 TraesCS1A01G417900 chr1B 91.613 155 13 0 337 491 570290083 570290237 1.000000e-51 215.0
7 TraesCS1A01G417900 chr1B 92.908 141 10 0 752 892 667471256 667471396 6.030000e-49 206.0
8 TraesCS1A01G417900 chr1B 84.733 131 6 2 35 165 570280516 570280632 8.080000e-23 119.0
9 TraesCS1A01G417900 chr1D 93.127 1586 64 22 908 2478 479224031 479225586 0.000000e+00 2283.0
10 TraesCS1A01G417900 chr1D 92.432 925 60 7 3675 4598 479226600 479227515 0.000000e+00 1312.0
11 TraesCS1A01G417900 chr1D 95.522 804 30 3 2876 3674 479225753 479226555 0.000000e+00 1280.0
12 TraesCS1A01G417900 chr1D 92.529 174 13 0 2712 2885 127925497 127925324 2.750000e-62 250.0
13 TraesCS1A01G417900 chr1D 90.000 180 11 3 2538 2717 479225582 479225754 4.630000e-55 226.0
14 TraesCS1A01G417900 chr3A 94.377 409 18 2 344 748 700205557 700205964 1.400000e-174 623.0
15 TraesCS1A01G417900 chr3A 96.429 196 6 1 30 225 700205111 700205305 5.740000e-84 322.0
16 TraesCS1A01G417900 chr7A 85.338 266 31 5 486 748 79161941 79162201 7.580000e-68 268.0
17 TraesCS1A01G417900 chr7A 93.023 172 12 0 2714 2885 203515052 203515223 7.640000e-63 252.0
18 TraesCS1A01G417900 chr7A 92.529 174 11 2 2709 2881 246344377 246344205 9.880000e-62 248.0
19 TraesCS1A01G417900 chr7A 81.169 308 37 14 17 309 79160559 79160860 1.290000e-55 228.0
20 TraesCS1A01G417900 chr7A 88.333 120 14 0 17 136 110351504 110351623 1.330000e-30 145.0
21 TraesCS1A01G417900 chr7A 88.889 117 9 4 17 133 12807220 12807108 1.720000e-29 141.0
22 TraesCS1A01G417900 chr7A 94.203 69 4 0 423 491 79160980 79161048 6.290000e-19 106.0
23 TraesCS1A01G417900 chr3D 94.706 170 8 1 2712 2881 238999411 238999579 3.530000e-66 263.0
24 TraesCS1A01G417900 chr3D 89.474 171 5 9 11 169 84511791 84511960 2.170000e-48 204.0
25 TraesCS1A01G417900 chr5D 84.375 288 22 16 30 302 543864906 543865185 1.270000e-65 261.0
26 TraesCS1A01G417900 chr5D 93.182 176 9 2 2714 2887 431780590 431780416 5.900000e-64 255.0
27 TraesCS1A01G417900 chr5D 92.000 175 10 3 321 491 543873116 543873290 4.600000e-60 243.0
28 TraesCS1A01G417900 chr5D 94.643 56 3 0 813 868 92171296 92171241 2.280000e-13 87.9
29 TraesCS1A01G417900 chr7B 82.838 303 37 10 23 312 20429923 20429623 1.640000e-64 257.0
30 TraesCS1A01G417900 chr7B 88.889 162 18 0 330 491 20429548 20429387 2.810000e-47 200.0
31 TraesCS1A01G417900 chr2D 94.578 166 9 0 2716 2881 445733832 445733667 1.640000e-64 257.0
32 TraesCS1A01G417900 chr2D 93.976 166 9 1 2709 2874 71262032 71262196 2.750000e-62 250.0
33 TraesCS1A01G417900 chr2D 85.106 188 13 6 4159 4332 132065764 132065950 1.310000e-40 178.0
34 TraesCS1A01G417900 chr2D 77.612 201 34 7 3950 4150 132065218 132065407 1.350000e-20 111.0
35 TraesCS1A01G417900 chr7D 94.012 167 7 2 2710 2874 235502400 235502565 2.750000e-62 250.0
36 TraesCS1A01G417900 chr7D 87.826 115 9 4 17 130 81644382 81644492 3.730000e-26 130.0
37 TraesCS1A01G417900 chr6A 93.939 165 10 0 2716 2880 73573911 73573747 2.750000e-62 250.0
38 TraesCS1A01G417900 chr6A 86.466 133 16 2 18 148 223344129 223344261 1.330000e-30 145.0
39 TraesCS1A01G417900 chr6A 93.478 46 3 0 753 798 521870975 521871020 8.250000e-08 69.4
40 TraesCS1A01G417900 chrUn 82.186 247 38 2 506 746 184665498 184665252 1.680000e-49 207.0
41 TraesCS1A01G417900 chr4B 89.677 155 15 1 337 491 5888665 5888512 3.630000e-46 196.0
42 TraesCS1A01G417900 chr2A 84.043 188 15 6 4159 4332 138916543 138916729 2.850000e-37 167.0
43 TraesCS1A01G417900 chr2A 85.714 126 12 4 4359 4480 138916812 138916935 1.340000e-25 128.0
44 TraesCS1A01G417900 chr2B 82.979 188 17 7 4159 4332 186286678 186286492 6.160000e-34 156.0
45 TraesCS1A01G417900 chr2B 84.921 126 13 4 4359 4480 186286409 186286286 6.250000e-24 122.0
46 TraesCS1A01G417900 chr5A 89.189 74 8 0 795 868 85856096 85856023 4.900000e-15 93.5
47 TraesCS1A01G417900 chr5B 92.857 56 4 0 813 868 97513881 97513826 1.060000e-11 82.4


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 TraesCS1A01G417900 chr1A 575589443 575594040 4597 False 8492.000000 8492 100.000000 1 4598 1 chr1A.!!$F1 4597
1 TraesCS1A01G417900 chr1B 667487721 667490352 2631 False 1803.000000 2366 92.480500 906 3671 2 chr1B.!!$F5 2765
2 TraesCS1A01G417900 chr1B 667444504 667445041 537 False 712.000000 712 90.441000 998 1541 1 chr1B.!!$F2 543
3 TraesCS1A01G417900 chr1B 667471256 667472498 1242 False 514.000000 822 90.922500 752 1614 2 chr1B.!!$F4 862
4 TraesCS1A01G417900 chr1B 570290083 570290664 581 False 244.500000 274 89.101500 337 748 2 chr1B.!!$F3 411
5 TraesCS1A01G417900 chr1D 479224031 479227515 3484 False 1275.250000 2283 92.770250 908 4598 4 chr1D.!!$F1 3690
6 TraesCS1A01G417900 chr3A 700205111 700205964 853 False 472.500000 623 95.403000 30 748 2 chr3A.!!$F1 718
7 TraesCS1A01G417900 chr7A 79160559 79162201 1642 False 200.666667 268 86.903333 17 748 3 chr7A.!!$F3 731
8 TraesCS1A01G417900 chr7B 20429387 20429923 536 True 228.500000 257 85.863500 23 491 2 chr7B.!!$R1 468

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
736 1805 0.039618 GGGGCTTGTTCCAATCCTGA 59.960 55.0 0.0 0.0 0.0 3.86 F
1544 3058 0.100682 GGCATTGTGAGCAGCAGATG 59.899 55.0 0.0 0.0 0.0 2.90 F
2179 3738 0.179004 TGTTGGAAGCAATGGTCGGT 60.179 50.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 3735 0.867746 CATCCCGTGCATCATAACCG 59.132 55.0 0.00 0.0 0.00 4.44 R
3118 4678 0.036022 GGGACAGCTTGAACTCAGCT 59.964 55.0 0.00 0.0 39.79 4.24 R
4125 5734 0.524862 CTGCCAGCAGCTTAAACCAG 59.475 55.0 6.72 0.0 44.23 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
252 272 0.602905 CGCTGAAAACTTCCCTCCGT 60.603 55.000 0.00 0.00 0.00 4.69
256 276 0.399075 GAAAACTTCCCTCCGTCCCA 59.601 55.000 0.00 0.00 0.00 4.37
284 304 3.541713 GCGGTCCTAGCCTCCCAG 61.542 72.222 0.00 0.00 0.00 4.45
290 310 2.446802 CTAGCCTCCCAGGTCCCC 60.447 72.222 0.00 0.00 37.80 4.81
291 311 4.103928 TAGCCTCCCAGGTCCCCC 62.104 72.222 0.00 0.00 37.80 5.40
328 405 4.200283 CGCTCACCGGCTCTCCTC 62.200 72.222 0.00 0.00 0.00 3.71
534 1598 1.812571 AGCAAGCCGTTGATTTGGTAG 59.187 47.619 0.00 0.00 35.46 3.18
649 1713 2.629137 TGCAATTGAGCCACATTTGAGT 59.371 40.909 10.34 0.00 40.26 3.41
698 1762 9.543018 CTTGATGAACGTTAAGTTTTTATCTCC 57.457 33.333 0.00 0.00 44.35 3.71
736 1805 0.039618 GGGGCTTGTTCCAATCCTGA 59.960 55.000 0.00 0.00 0.00 3.86
748 1817 0.911769 AATCCTGAATCCGCCACTGA 59.088 50.000 0.00 0.00 0.00 3.41
749 1818 1.135094 ATCCTGAATCCGCCACTGAT 58.865 50.000 0.00 0.00 0.00 2.90
750 1819 0.911769 TCCTGAATCCGCCACTGATT 59.088 50.000 0.00 0.00 35.21 2.57
761 1830 2.669924 CGCCACTGATTATCATCATCCG 59.330 50.000 0.00 0.00 38.81 4.18
775 1844 2.016318 TCATCCGCATGATCAACAACC 58.984 47.619 0.00 0.00 33.80 3.77
776 1845 1.744522 CATCCGCATGATCAACAACCA 59.255 47.619 0.00 0.00 30.57 3.67
792 1861 4.993905 ACAACCAAACTTTTCTTCTTCGG 58.006 39.130 0.00 0.00 0.00 4.30
809 1878 3.724508 TCGGAGCATCAAGAGAGATTC 57.275 47.619 0.00 0.00 36.25 2.52
817 1886 3.961480 TCAAGAGAGATTCGCTTCCAA 57.039 42.857 0.00 0.00 34.27 3.53
848 1917 0.865111 CAACACATCTTCCGCGTTGA 59.135 50.000 4.92 0.00 39.39 3.18
856 1925 6.260050 ACACATCTTCCGCGTTGATATAATTT 59.740 34.615 4.92 0.00 0.00 1.82
897 2385 1.019805 GCGTTGTAGCAACTCCTCCC 61.020 60.000 9.82 0.00 37.05 4.30
910 2398 1.740025 CTCCTCCCGCTGTTTGATTTC 59.260 52.381 0.00 0.00 0.00 2.17
946 2434 6.414732 AGAGGTTCGAATACCATTTGATTGA 58.585 36.000 8.93 0.00 40.82 2.57
959 2447 5.752955 CCATTTGATTGAAAAGTCAACGGTT 59.247 36.000 0.00 0.00 46.40 4.44
960 2448 6.920758 CCATTTGATTGAAAAGTCAACGGTTA 59.079 34.615 0.00 0.00 46.40 2.85
971 2459 4.091549 AGTCAACGGTTATAGTCTTCCCA 58.908 43.478 0.00 0.00 0.00 4.37
986 2476 1.813753 CCCACATCGCCACCTTACG 60.814 63.158 0.00 0.00 0.00 3.18
1544 3058 0.100682 GGCATTGTGAGCAGCAGATG 59.899 55.000 0.00 0.00 0.00 2.90
1671 3186 4.206375 TGAATCAATCCATTGTGCCGTAT 58.794 39.130 0.00 0.00 38.84 3.06
1910 3442 5.175673 GGTAAAACTGAAGCTGACAAAATGC 59.824 40.000 0.00 0.00 0.00 3.56
1919 3451 7.829725 TGAAGCTGACAAAATGCTTACATTAT 58.170 30.769 0.00 0.00 45.90 1.28
1920 3452 8.955388 TGAAGCTGACAAAATGCTTACATTATA 58.045 29.630 0.00 0.00 45.90 0.98
1922 3454 8.511604 AGCTGACAAAATGCTTACATTATACT 57.488 30.769 0.00 0.00 45.90 2.12
1923 3455 8.616076 AGCTGACAAAATGCTTACATTATACTC 58.384 33.333 0.00 0.00 45.90 2.59
1963 3505 5.352569 GGTGTGATTTTACTGTCTGGATCAG 59.647 44.000 0.00 0.00 38.68 2.90
1971 3513 2.303890 ACTGTCTGGATCAGCATCACAA 59.696 45.455 0.00 0.00 36.50 3.33
1995 3537 8.875803 CAATGTGCATTGCTTAACTGAATTTAT 58.124 29.630 10.49 0.00 41.27 1.40
2064 3608 9.102757 CAGTTAGATTAGATAGTTGCAATGTGT 57.897 33.333 0.59 0.00 0.00 3.72
2067 3611 6.573434 AGATTAGATAGTTGCAATGTGTCGA 58.427 36.000 0.59 0.00 0.00 4.20
2083 3642 2.422127 TGTCGAGTTATCTGATGACGCA 59.578 45.455 14.61 7.31 0.00 5.24
2085 3644 2.033424 TCGAGTTATCTGATGACGCAGG 59.967 50.000 14.61 2.22 36.55 4.85
2091 3650 5.812642 AGTTATCTGATGACGCAGGTTTTAG 59.187 40.000 6.88 0.00 36.55 1.85
2176 3735 2.297033 ACATGTGTTGGAAGCAATGGTC 59.703 45.455 0.00 0.00 0.00 4.02
2179 3738 0.179004 TGTTGGAAGCAATGGTCGGT 60.179 50.000 0.00 0.00 0.00 4.69
2186 3745 3.003689 GGAAGCAATGGTCGGTTATGATG 59.996 47.826 0.00 0.00 0.00 3.07
2218 3777 2.409055 GGCAACTCGCATGGCATCA 61.409 57.895 0.00 0.00 45.17 3.07
2265 3824 5.508567 TGGGCAATTCTTGAACATAGATGA 58.491 37.500 0.00 0.00 0.00 2.92
2353 3912 2.447047 AGAAAAGGTGTTCAGGGACCAT 59.553 45.455 0.00 0.00 34.36 3.55
2356 3915 2.586648 AGGTGTTCAGGGACCATTTC 57.413 50.000 0.00 0.00 34.36 2.17
2357 3916 1.165270 GGTGTTCAGGGACCATTTCG 58.835 55.000 0.00 0.00 31.97 3.46
2372 3931 4.051922 CCATTTCGACACTATGAGGTAGC 58.948 47.826 0.00 0.00 33.47 3.58
2400 3959 6.883217 AGCACTCTTCTTGTTTGATGACATAT 59.117 34.615 0.00 0.00 0.00 1.78
2437 3996 6.198029 CGATATCGATCATTTAGATGGTGCTC 59.802 42.308 20.50 0.00 43.02 4.26
2452 4011 3.055094 TGGTGCTCCTCTTTAAGATGGAC 60.055 47.826 6.34 7.21 34.23 4.02
2462 4021 2.857592 TAAGATGGACCGACGCTTAC 57.142 50.000 0.00 0.00 0.00 2.34
2506 4065 2.499289 TGGTGCACCAGAATGTTGTTTT 59.501 40.909 34.74 0.00 42.01 2.43
2511 4070 3.068024 GCACCAGAATGTTGTTTTGGAGA 59.932 43.478 4.58 0.00 33.19 3.71
2515 4074 4.022849 CCAGAATGTTGTTTTGGAGACTCC 60.023 45.833 15.13 15.13 36.96 3.85
2537 4096 8.228206 ACTCCATACACTCTGAATCCTATTCTA 58.772 37.037 1.70 0.00 0.00 2.10
2539 4098 7.175119 TCCATACACTCTGAATCCTATTCTACG 59.825 40.741 1.70 0.00 0.00 3.51
2546 4105 4.800023 TGAATCCTATTCTACGTCAGGGA 58.200 43.478 0.00 0.00 0.00 4.20
2550 4109 4.346730 TCCTATTCTACGTCAGGGAAACA 58.653 43.478 0.00 0.00 0.00 2.83
2551 4110 4.960469 TCCTATTCTACGTCAGGGAAACAT 59.040 41.667 0.00 0.00 0.00 2.71
2678 4237 2.039084 GTGAGAAAGACATGTGGGTCCT 59.961 50.000 1.15 0.00 38.59 3.85
2721 4280 8.825667 TTTCAAAATTGCAAAATAGTACTCCC 57.174 30.769 1.71 0.00 0.00 4.30
2722 4281 7.775053 TCAAAATTGCAAAATAGTACTCCCT 57.225 32.000 1.71 0.00 0.00 4.20
2723 4282 7.826690 TCAAAATTGCAAAATAGTACTCCCTC 58.173 34.615 1.71 0.00 0.00 4.30
2724 4283 6.775594 AAATTGCAAAATAGTACTCCCTCC 57.224 37.500 1.71 0.00 0.00 4.30
2725 4284 3.536956 TGCAAAATAGTACTCCCTCCG 57.463 47.619 0.00 0.00 0.00 4.63
2726 4285 2.835764 TGCAAAATAGTACTCCCTCCGT 59.164 45.455 0.00 0.00 0.00 4.69
2727 4286 3.262405 TGCAAAATAGTACTCCCTCCGTT 59.738 43.478 0.00 0.00 0.00 4.44
2728 4287 3.869832 GCAAAATAGTACTCCCTCCGTTC 59.130 47.826 0.00 0.00 0.00 3.95
2729 4288 4.439968 CAAAATAGTACTCCCTCCGTTCC 58.560 47.826 0.00 0.00 0.00 3.62
2730 4289 3.684408 AATAGTACTCCCTCCGTTCCT 57.316 47.619 0.00 0.00 0.00 3.36
2731 4290 4.803329 AATAGTACTCCCTCCGTTCCTA 57.197 45.455 0.00 0.00 0.00 2.94
2732 4291 4.803329 ATAGTACTCCCTCCGTTCCTAA 57.197 45.455 0.00 0.00 0.00 2.69
2733 4292 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2734 4293 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2735 4294 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2736 4295 4.892345 AGTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
2737 4296 3.716431 ACTCCCTCCGTTCCTAAATACA 58.284 45.455 0.00 0.00 0.00 2.29
2738 4297 4.098894 ACTCCCTCCGTTCCTAAATACAA 58.901 43.478 0.00 0.00 0.00 2.41
2739 4298 4.161754 ACTCCCTCCGTTCCTAAATACAAG 59.838 45.833 0.00 0.00 0.00 3.16
2740 4299 4.098894 TCCCTCCGTTCCTAAATACAAGT 58.901 43.478 0.00 0.00 0.00 3.16
2741 4300 4.161001 TCCCTCCGTTCCTAAATACAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
2742 4301 4.161754 CCCTCCGTTCCTAAATACAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
2743 4302 5.338137 CCCTCCGTTCCTAAATACAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2744 4303 6.171213 CCTCCGTTCCTAAATACAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2745 4304 6.092259 CCTCCGTTCCTAAATACAAGTCTTTG 59.908 42.308 0.00 0.00 40.24 2.77
2761 4320 9.429359 ACAAGTCTTTGTAGAGATTTCACTATG 57.571 33.333 0.00 0.00 45.45 2.23
2762 4321 9.645059 CAAGTCTTTGTAGAGATTTCACTATGA 57.355 33.333 0.00 0.00 0.00 2.15
2764 4323 9.646427 AGTCTTTGTAGAGATTTCACTATGAAC 57.354 33.333 0.00 0.00 35.89 3.18
2765 4324 8.874816 GTCTTTGTAGAGATTTCACTATGAACC 58.125 37.037 0.00 0.00 35.89 3.62
2766 4325 8.593679 TCTTTGTAGAGATTTCACTATGAACCA 58.406 33.333 0.00 0.00 35.89 3.67
2767 4326 8.547967 TTTGTAGAGATTTCACTATGAACCAC 57.452 34.615 0.00 0.00 35.89 4.16
2768 4327 7.239763 TGTAGAGATTTCACTATGAACCACA 57.760 36.000 0.00 0.00 35.89 4.17
2769 4328 7.851228 TGTAGAGATTTCACTATGAACCACAT 58.149 34.615 0.00 0.00 35.89 3.21
2770 4329 8.977412 TGTAGAGATTTCACTATGAACCACATA 58.023 33.333 0.00 0.00 35.89 2.29
2771 4330 9.988815 GTAGAGATTTCACTATGAACCACATAT 57.011 33.333 0.00 0.00 40.18 1.78
2772 4331 8.899427 AGAGATTTCACTATGAACCACATATG 57.101 34.615 0.00 0.00 40.18 1.78
2809 4368 9.495754 GATGCATTTTAAAGTGTAGATTCACTC 57.504 33.333 11.77 0.00 46.25 3.51
2810 4369 8.389779 TGCATTTTAAAGTGTAGATTCACTCA 57.610 30.769 11.77 0.00 46.25 3.41
2811 4370 9.013229 TGCATTTTAAAGTGTAGATTCACTCAT 57.987 29.630 11.77 0.00 46.25 2.90
2812 4371 9.846248 GCATTTTAAAGTGTAGATTCACTCATT 57.154 29.630 11.77 0.00 46.25 2.57
2816 4375 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
2817 4376 7.516198 AAAGTGTAGATTCACTCATTTTGCT 57.484 32.000 0.00 0.00 46.25 3.91
2818 4377 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2819 4378 6.471146 AGTGTAGATTCACTCATTTTGCTCT 58.529 36.000 0.00 0.00 44.07 4.09
2820 4379 6.370994 AGTGTAGATTCACTCATTTTGCTCTG 59.629 38.462 0.00 0.00 44.07 3.35
2821 4380 6.148480 GTGTAGATTCACTCATTTTGCTCTGT 59.852 38.462 0.00 0.00 35.68 3.41
2822 4381 7.331934 GTGTAGATTCACTCATTTTGCTCTGTA 59.668 37.037 0.00 0.00 35.68 2.74
2823 4382 8.043113 TGTAGATTCACTCATTTTGCTCTGTAT 58.957 33.333 0.00 0.00 0.00 2.29
2824 4383 7.317842 AGATTCACTCATTTTGCTCTGTATG 57.682 36.000 0.00 0.00 0.00 2.39
2825 4384 6.883217 AGATTCACTCATTTTGCTCTGTATGT 59.117 34.615 0.00 0.00 0.00 2.29
2826 4385 8.043113 AGATTCACTCATTTTGCTCTGTATGTA 58.957 33.333 0.00 0.00 0.00 2.29
2827 4386 7.601073 TTCACTCATTTTGCTCTGTATGTAG 57.399 36.000 0.00 0.00 0.00 2.74
2828 4387 6.701340 TCACTCATTTTGCTCTGTATGTAGT 58.299 36.000 0.00 0.00 0.00 2.73
2829 4388 6.813649 TCACTCATTTTGCTCTGTATGTAGTC 59.186 38.462 0.00 0.00 0.00 2.59
2830 4389 6.036517 CACTCATTTTGCTCTGTATGTAGTCC 59.963 42.308 0.00 0.00 0.00 3.85
2831 4390 6.048732 TCATTTTGCTCTGTATGTAGTCCA 57.951 37.500 0.00 0.00 0.00 4.02
2832 4391 6.653020 TCATTTTGCTCTGTATGTAGTCCAT 58.347 36.000 0.00 0.00 37.58 3.41
2833 4392 7.791029 TCATTTTGCTCTGTATGTAGTCCATA 58.209 34.615 0.00 0.00 34.86 2.74
2834 4393 7.928167 TCATTTTGCTCTGTATGTAGTCCATAG 59.072 37.037 0.00 0.00 36.71 2.23
2835 4394 6.791867 TTTGCTCTGTATGTAGTCCATAGT 57.208 37.500 0.00 0.00 36.71 2.12
2836 4395 5.774498 TGCTCTGTATGTAGTCCATAGTG 57.226 43.478 0.00 0.00 36.71 2.74
2837 4396 4.038042 TGCTCTGTATGTAGTCCATAGTGC 59.962 45.833 0.00 0.00 36.71 4.40
2838 4397 4.038042 GCTCTGTATGTAGTCCATAGTGCA 59.962 45.833 0.00 0.00 36.71 4.57
2839 4398 5.451937 GCTCTGTATGTAGTCCATAGTGCAA 60.452 44.000 0.00 0.00 36.71 4.08
2840 4399 6.731292 TCTGTATGTAGTCCATAGTGCAAT 57.269 37.500 0.00 0.00 36.71 3.56
2841 4400 6.749139 TCTGTATGTAGTCCATAGTGCAATC 58.251 40.000 0.00 0.00 36.71 2.67
2842 4401 6.551227 TCTGTATGTAGTCCATAGTGCAATCT 59.449 38.462 0.00 0.00 36.71 2.40
2843 4402 6.749139 TGTATGTAGTCCATAGTGCAATCTC 58.251 40.000 0.00 0.00 36.71 2.75
2844 4403 6.551227 TGTATGTAGTCCATAGTGCAATCTCT 59.449 38.462 0.00 0.00 36.71 3.10
2845 4404 7.724061 TGTATGTAGTCCATAGTGCAATCTCTA 59.276 37.037 0.00 0.00 36.71 2.43
2846 4405 6.392625 TGTAGTCCATAGTGCAATCTCTAC 57.607 41.667 0.00 0.00 0.00 2.59
2847 4406 5.891551 TGTAGTCCATAGTGCAATCTCTACA 59.108 40.000 0.00 1.66 34.82 2.74
2848 4407 5.939764 AGTCCATAGTGCAATCTCTACAA 57.060 39.130 0.00 0.00 0.00 2.41
2849 4408 6.299805 AGTCCATAGTGCAATCTCTACAAA 57.700 37.500 0.00 0.00 0.00 2.83
2850 4409 6.344500 AGTCCATAGTGCAATCTCTACAAAG 58.656 40.000 0.00 0.00 0.00 2.77
2851 4410 6.155221 AGTCCATAGTGCAATCTCTACAAAGA 59.845 38.462 0.00 0.00 0.00 2.52
2852 4411 6.256757 GTCCATAGTGCAATCTCTACAAAGAC 59.743 42.308 0.00 0.00 0.00 3.01
2853 4412 6.155221 TCCATAGTGCAATCTCTACAAAGACT 59.845 38.462 0.00 0.00 0.00 3.24
2854 4413 6.820656 CCATAGTGCAATCTCTACAAAGACTT 59.179 38.462 0.00 0.00 0.00 3.01
2855 4414 7.981789 CCATAGTGCAATCTCTACAAAGACTTA 59.018 37.037 0.00 0.00 0.00 2.24
2856 4415 9.539825 CATAGTGCAATCTCTACAAAGACTTAT 57.460 33.333 0.00 0.00 0.00 1.73
2871 4430 9.379791 ACAAAGACTTATATTTAGAAACGGAGG 57.620 33.333 0.00 0.00 0.00 4.30
2872 4431 8.827677 CAAAGACTTATATTTAGAAACGGAGGG 58.172 37.037 0.00 0.00 0.00 4.30
2873 4432 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
2874 4433 8.493787 AGACTTATATTTAGAAACGGAGGGAT 57.506 34.615 0.00 0.00 0.00 3.85
2875 4434 8.935741 AGACTTATATTTAGAAACGGAGGGATT 58.064 33.333 0.00 0.00 0.00 3.01
2940 4500 8.787852 GGAAGGGATGAATTATGACTTGTTATC 58.212 37.037 0.00 0.00 0.00 1.75
3073 4633 6.318144 ACAATCTTGAGATACCAAGCATGAAG 59.682 38.462 0.00 0.00 42.34 3.02
3074 4634 5.682234 TCTTGAGATACCAAGCATGAAGA 57.318 39.130 0.00 0.00 42.34 2.87
3118 4678 1.556564 GCGAACGTGCTCTTATGCTA 58.443 50.000 0.00 0.00 0.00 3.49
3121 4681 2.796383 CGAACGTGCTCTTATGCTAGCT 60.796 50.000 17.23 4.07 39.53 3.32
3139 4699 1.805869 CTGAGTTCAAGCTGTCCCTG 58.194 55.000 0.00 0.00 0.00 4.45
3211 4771 8.681806 TCAGACATAATTGACTTCAACAACAAA 58.318 29.630 0.00 0.00 38.86 2.83
3261 4821 7.235079 TGTTCACCTCATTTCCAGGTTTATTA 58.765 34.615 0.00 0.00 41.95 0.98
3263 4823 7.880160 TCACCTCATTTCCAGGTTTATTATG 57.120 36.000 0.00 0.00 41.95 1.90
3287 4851 8.315391 TGAACTTTGAATATGACACTCTTGAG 57.685 34.615 0.00 0.00 0.00 3.02
3339 4903 1.271379 GGCCAGAGTTACCTTCTGCAA 60.271 52.381 0.00 0.00 40.54 4.08
3347 4911 5.247110 AGAGTTACCTTCTGCAATCTGAAGA 59.753 40.000 13.45 0.00 45.53 2.87
3351 4915 3.499918 ACCTTCTGCAATCTGAAGAAACG 59.500 43.478 13.45 1.77 41.27 3.60
3405 4969 1.926510 GCCAAACTGAACAAACTGTGC 59.073 47.619 0.00 0.00 0.00 4.57
3449 5013 0.670546 CGAGCCAATCAACTGGACGT 60.671 55.000 0.00 0.00 38.96 4.34
3465 5029 2.261671 GTGATCGTCGCACCTGGT 59.738 61.111 0.00 0.00 0.00 4.00
3562 5126 3.361917 CGTTCCTTTTGCGATTTGCTTTG 60.362 43.478 0.00 0.00 46.63 2.77
3588 5152 2.003301 GTTGAAAGGATCAGAGCCGAC 58.997 52.381 0.00 0.00 39.77 4.79
3625 5189 0.036732 ATTCCTTCGAGCAGGCAACA 59.963 50.000 0.00 0.00 41.41 3.33
3634 5198 2.548057 CGAGCAGGCAACAAAAGTTAGA 59.452 45.455 0.00 0.00 41.41 2.10
3677 5285 9.399797 AGCATTCTGTCATTTGATTGTAGAATA 57.600 29.630 0.00 0.00 33.79 1.75
3703 5311 7.609146 ACATCTGCTTCTTTGTATCTGAAATGA 59.391 33.333 0.00 0.00 0.00 2.57
3757 5365 3.106827 TGCAGATCCTGAACACCAGATA 58.893 45.455 0.00 0.00 45.78 1.98
3789 5397 8.116136 GCTTTGTTACCTTTTTCTGTTTGATTG 58.884 33.333 0.00 0.00 0.00 2.67
3894 5503 6.349611 GCTATTTCATCAAGCAAAGGAACTCA 60.350 38.462 0.00 0.00 34.85 3.41
3895 5504 6.600882 ATTTCATCAAGCAAAGGAACTCAT 57.399 33.333 0.00 0.00 38.49 2.90
3898 5507 6.409524 TCATCAAGCAAAGGAACTCATTTT 57.590 33.333 0.00 0.00 38.49 1.82
3919 5528 2.798976 TTTGGCAAGCATGTGAAGAC 57.201 45.000 0.00 0.00 0.00 3.01
3921 5530 0.953727 TGGCAAGCATGTGAAGACAC 59.046 50.000 0.00 0.00 46.09 3.67
3922 5531 0.242017 GGCAAGCATGTGAAGACACC 59.758 55.000 0.00 0.00 45.40 4.16
3923 5532 1.242076 GCAAGCATGTGAAGACACCT 58.758 50.000 0.00 0.00 45.40 4.00
3926 5535 3.635331 CAAGCATGTGAAGACACCTTTG 58.365 45.455 0.00 0.00 45.40 2.77
3927 5536 3.213206 AGCATGTGAAGACACCTTTGA 57.787 42.857 0.00 0.00 45.40 2.69
3929 5538 2.618241 GCATGTGAAGACACCTTTGACA 59.382 45.455 0.00 0.00 45.40 3.58
3930 5539 3.548818 GCATGTGAAGACACCTTTGACAC 60.549 47.826 0.00 0.00 45.40 3.67
3931 5540 2.276201 TGTGAAGACACCTTTGACACG 58.724 47.619 0.00 0.00 45.40 4.49
3932 5541 2.277084 GTGAAGACACCTTTGACACGT 58.723 47.619 0.00 0.00 40.74 4.49
3933 5542 2.676342 GTGAAGACACCTTTGACACGTT 59.324 45.455 0.00 0.00 40.74 3.99
3945 5554 6.480651 ACCTTTGACACGTTGTTTTTCTTTTT 59.519 30.769 0.00 0.00 0.00 1.94
3946 5555 7.652507 ACCTTTGACACGTTGTTTTTCTTTTTA 59.347 29.630 0.00 0.00 0.00 1.52
3947 5556 7.947830 CCTTTGACACGTTGTTTTTCTTTTTAC 59.052 33.333 0.00 0.00 0.00 2.01
3948 5557 6.599637 TGACACGTTGTTTTTCTTTTTACG 57.400 33.333 0.00 0.00 0.00 3.18
3951 5560 7.377928 TGACACGTTGTTTTTCTTTTTACGAAA 59.622 29.630 0.00 0.00 0.00 3.46
3953 5562 8.367396 ACACGTTGTTTTTCTTTTTACGAAATC 58.633 29.630 0.00 0.00 31.17 2.17
3967 5576 6.903883 TTACGAAATCCTTCTCAGTTATGC 57.096 37.500 0.00 0.00 0.00 3.14
3969 5578 3.302740 CGAAATCCTTCTCAGTTATGCGC 60.303 47.826 0.00 0.00 0.00 6.09
3979 5588 4.697828 TCTCAGTTATGCGCAACCAAAATA 59.302 37.500 17.11 0.00 0.00 1.40
3992 5601 5.294060 GCAACCAAAATATAAGCCACCATTG 59.706 40.000 0.00 0.00 0.00 2.82
3993 5602 6.638610 CAACCAAAATATAAGCCACCATTGA 58.361 36.000 0.00 0.00 0.00 2.57
3997 5606 7.102346 CCAAAATATAAGCCACCATTGAACAA 58.898 34.615 0.00 0.00 0.00 2.83
3998 5607 7.769970 CCAAAATATAAGCCACCATTGAACAAT 59.230 33.333 0.00 0.00 0.00 2.71
4003 5612 4.046286 AGCCACCATTGAACAATAAGGA 57.954 40.909 9.75 0.00 0.00 3.36
4004 5613 4.415596 AGCCACCATTGAACAATAAGGAA 58.584 39.130 9.75 0.00 0.00 3.36
4032 5641 4.602340 TTTCTGAGTGAGGTAAGGTCAC 57.398 45.455 0.00 0.00 44.02 3.67
4057 5666 8.630037 ACTACACCTTTATTTTTATATGCCTGC 58.370 33.333 0.00 0.00 0.00 4.85
4215 5824 0.107214 TTCTCCGGTGGGAATCATGC 60.107 55.000 0.00 0.00 43.27 4.06
4216 5825 0.982852 TCTCCGGTGGGAATCATGCT 60.983 55.000 0.00 0.00 43.27 3.79
4232 5841 1.571955 TGCTCTCATTGGCTGGAGTA 58.428 50.000 0.00 0.00 32.93 2.59
4264 5873 0.036732 CAGACCCAAGGTGCTGCTAA 59.963 55.000 0.00 0.00 35.25 3.09
4273 5882 0.598065 GGTGCTGCTAAAGTTGTGGG 59.402 55.000 0.00 0.00 0.00 4.61
4319 5928 0.543277 TGCCAAGCTGATAGGAGTGG 59.457 55.000 0.00 0.00 0.00 4.00
4349 5958 1.873591 CTGTCACACTGCCAGGTTAAC 59.126 52.381 0.00 0.00 0.00 2.01
4437 6046 7.039993 ACAAAGATGTTGGTAACCATTACCTTC 60.040 37.037 16.64 10.81 43.88 3.46
4456 6065 0.649475 CTTCGCCATCTTTGCTCTCG 59.351 55.000 0.00 0.00 0.00 4.04
4490 6099 5.407502 TGATTGATAGGTATGTAATCGCCG 58.592 41.667 0.00 0.00 32.01 6.46
4493 6102 3.192001 TGATAGGTATGTAATCGCCGTCC 59.808 47.826 0.00 0.00 0.00 4.79
4497 6106 2.482490 GGTATGTAATCGCCGTCCTGTT 60.482 50.000 0.00 0.00 0.00 3.16
4503 6112 2.467566 ATCGCCGTCCTGTTAAAACT 57.532 45.000 0.00 0.00 0.00 2.66
4523 6132 4.901868 ACTCTTTAATCACCCGCAGTTTA 58.098 39.130 0.00 0.00 0.00 2.01
4530 6139 1.944024 TCACCCGCAGTTTACACTTTG 59.056 47.619 0.00 0.00 0.00 2.77
4539 6148 4.037690 CAGTTTACACTTTGCAGTTCAGC 58.962 43.478 0.00 0.00 0.00 4.26
4573 6182 2.823196 TGTTTTGCAGTCAAGTCACG 57.177 45.000 0.00 0.00 33.12 4.35
4579 6188 1.286501 GCAGTCAAGTCACGTCAACA 58.713 50.000 0.00 0.00 0.00 3.33
4580 6189 1.004927 GCAGTCAAGTCACGTCAACAC 60.005 52.381 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.087031 GCCCCTGATGATAATGATGGTG 58.913 50.000 0.00 0.00 0.00 4.17
5 6 2.269023 TCCGCCCCTGATGATAATGAT 58.731 47.619 0.00 0.00 0.00 2.45
6 7 1.728323 TCCGCCCCTGATGATAATGA 58.272 50.000 0.00 0.00 0.00 2.57
7 8 2.238144 AGATCCGCCCCTGATGATAATG 59.762 50.000 0.00 0.00 0.00 1.90
8 9 2.238144 CAGATCCGCCCCTGATGATAAT 59.762 50.000 0.00 0.00 32.37 1.28
9 10 1.625315 CAGATCCGCCCCTGATGATAA 59.375 52.381 0.00 0.00 32.37 1.75
10 11 1.269958 CAGATCCGCCCCTGATGATA 58.730 55.000 0.00 0.00 32.37 2.15
11 12 1.486997 CCAGATCCGCCCCTGATGAT 61.487 60.000 0.00 0.00 32.37 2.45
12 13 2.142761 CCAGATCCGCCCCTGATGA 61.143 63.158 0.00 0.00 32.37 2.92
13 14 2.429058 CCAGATCCGCCCCTGATG 59.571 66.667 0.00 0.00 32.37 3.07
14 15 2.851102 CCCAGATCCGCCCCTGAT 60.851 66.667 0.00 0.00 32.37 2.90
105 106 2.203337 GCCCTGGCTGTGTGTTGA 60.203 61.111 0.00 0.00 38.26 3.18
232 252 1.298859 CGGAGGGAAGTTTTCAGCGG 61.299 60.000 0.00 0.00 0.00 5.52
233 253 0.602905 ACGGAGGGAAGTTTTCAGCG 60.603 55.000 0.00 0.00 0.00 5.18
235 255 1.610886 GGGACGGAGGGAAGTTTTCAG 60.611 57.143 0.00 0.00 0.00 3.02
236 256 0.399075 GGGACGGAGGGAAGTTTTCA 59.601 55.000 0.00 0.00 0.00 2.69
237 257 0.399075 TGGGACGGAGGGAAGTTTTC 59.601 55.000 0.00 0.00 0.00 2.29
269 289 1.762858 GACCTGGGAGGCTAGGACC 60.763 68.421 8.80 0.00 39.63 4.46
312 332 4.200283 CGAGGAGAGCCGGTGAGC 62.200 72.222 1.90 0.00 39.96 4.26
313 333 4.200283 GCGAGGAGAGCCGGTGAG 62.200 72.222 1.90 0.00 39.96 3.51
314 334 3.339738 TAGCGAGGAGAGCCGGTGA 62.340 63.158 1.90 0.00 39.96 4.02
315 335 2.829003 TAGCGAGGAGAGCCGGTG 60.829 66.667 1.90 0.00 39.96 4.94
316 336 2.517402 CTAGCGAGGAGAGCCGGT 60.517 66.667 1.90 0.00 39.96 5.28
319 339 1.528309 AGAGCTAGCGAGGAGAGCC 60.528 63.158 9.55 0.00 36.87 4.70
325 402 2.727544 GGAGCAGAGCTAGCGAGG 59.272 66.667 9.55 3.58 39.88 4.63
327 404 3.212682 CCGGAGCAGAGCTAGCGA 61.213 66.667 9.55 0.00 39.88 4.93
328 405 4.940593 GCCGGAGCAGAGCTAGCG 62.941 72.222 5.05 0.00 39.88 4.26
491 1555 7.877612 TGCTTCATCAGTGTCTTTGATAACTTA 59.122 33.333 0.00 0.00 33.67 2.24
673 1737 8.508875 GGGAGATAAAAACTTAACGTTCATCAA 58.491 33.333 2.82 0.00 33.90 2.57
736 1805 4.356405 TGATGATAATCAGTGGCGGATT 57.644 40.909 0.00 4.63 38.46 3.01
761 1830 5.754890 AGAAAAGTTTGGTTGTTGATCATGC 59.245 36.000 0.00 0.00 0.00 4.06
775 1844 4.552166 TGCTCCGAAGAAGAAAAGTTTG 57.448 40.909 0.00 0.00 0.00 2.93
776 1845 4.821805 TGATGCTCCGAAGAAGAAAAGTTT 59.178 37.500 0.00 0.00 0.00 2.66
792 1861 3.096489 AGCGAATCTCTCTTGATGCTC 57.904 47.619 0.00 0.00 0.00 4.26
817 1886 2.751259 AGATGTGTTGATTTGCATCGCT 59.249 40.909 0.00 0.00 41.64 4.93
820 1889 4.100529 CGGAAGATGTGTTGATTTGCATC 58.899 43.478 0.00 0.00 38.30 3.91
821 1890 3.674138 GCGGAAGATGTGTTGATTTGCAT 60.674 43.478 0.00 0.00 0.00 3.96
897 2385 3.012518 AGATCCCAGAAATCAAACAGCG 58.987 45.455 0.00 0.00 0.00 5.18
910 2398 0.103937 GAACCTCTCGCAGATCCCAG 59.896 60.000 0.00 0.00 33.89 4.45
946 2434 5.936372 GGGAAGACTATAACCGTTGACTTTT 59.064 40.000 0.00 0.00 0.00 2.27
959 2447 2.364324 GTGGCGATGTGGGAAGACTATA 59.636 50.000 0.00 0.00 0.00 1.31
960 2448 1.139058 GTGGCGATGTGGGAAGACTAT 59.861 52.381 0.00 0.00 0.00 2.12
971 2459 1.740296 GTGCGTAAGGTGGCGATGT 60.740 57.895 0.00 0.00 38.28 3.06
986 2476 2.048877 GCATTGCCAGTGGTGTGC 60.049 61.111 11.74 14.46 0.00 4.57
1064 2560 4.069232 CCTCCAGCACGAAGGCGA 62.069 66.667 0.00 0.00 41.64 5.54
1068 2564 2.125350 GCCTCCTCCAGCACGAAG 60.125 66.667 0.00 0.00 0.00 3.79
1544 3058 3.002371 CAAGAGGGGAAGGGGAGC 58.998 66.667 0.00 0.00 0.00 4.70
1629 3144 4.425772 TCAGAGTCAGAATTCACCCCTTA 58.574 43.478 8.44 0.00 0.00 2.69
1671 3186 1.537348 GCTGACGGCACATACGGATTA 60.537 52.381 0.00 0.00 41.35 1.75
1845 3377 2.005451 GATATGATGATCACGCCAGCC 58.995 52.381 0.00 0.00 0.00 4.85
1848 3380 2.899256 TGGAGATATGATGATCACGCCA 59.101 45.455 0.00 0.00 0.00 5.69
1923 3455 4.087182 TCACACCACTCTCCTTAACTAGG 58.913 47.826 0.00 0.00 46.27 3.02
1933 3465 5.406780 CAGACAGTAAAATCACACCACTCTC 59.593 44.000 0.00 0.00 0.00 3.20
1971 3513 9.439500 AAATAAATTCAGTTAAGCAATGCACAT 57.561 25.926 8.35 0.00 0.00 3.21
1995 3537 5.526846 GTGGATGCCATGTTTTTGAAAGAAA 59.473 36.000 0.00 0.00 35.28 2.52
2004 3548 4.142403 CGACATAAGTGGATGCCATGTTTT 60.142 41.667 0.00 0.00 35.28 2.43
2064 3608 2.033424 CCTGCGTCATCAGATAACTCGA 59.967 50.000 0.00 0.00 36.19 4.04
2067 3611 3.895232 AACCTGCGTCATCAGATAACT 57.105 42.857 0.00 0.00 36.19 2.24
2176 3735 0.867746 CATCCCGTGCATCATAACCG 59.132 55.000 0.00 0.00 0.00 4.44
2265 3824 1.566231 CAACCCTCTTGCCCCTTAGAT 59.434 52.381 0.00 0.00 0.00 1.98
2353 3912 4.014406 TGAGCTACCTCATAGTGTCGAAA 58.986 43.478 0.00 0.00 42.98 3.46
2356 3915 2.287308 GCTGAGCTACCTCATAGTGTCG 60.287 54.545 0.00 0.00 46.44 4.35
2357 3916 2.690497 TGCTGAGCTACCTCATAGTGTC 59.310 50.000 5.83 0.00 46.44 3.67
2372 3931 4.753610 TCATCAAACAAGAAGAGTGCTGAG 59.246 41.667 0.00 0.00 0.00 3.35
2437 3996 2.810650 CGTCGGTCCATCTTAAAGAGG 58.189 52.381 0.00 0.00 0.00 3.69
2452 4011 2.031314 TCTGACTTATCGTAAGCGTCGG 59.969 50.000 0.00 0.00 39.49 4.79
2462 4021 6.860539 CCACTCATTAGATGTCTGACTTATCG 59.139 42.308 9.51 0.00 0.00 2.92
2511 4070 7.072562 AGAATAGGATTCAGAGTGTATGGAGT 58.927 38.462 2.27 0.00 0.00 3.85
2515 4074 7.877003 ACGTAGAATAGGATTCAGAGTGTATG 58.123 38.462 2.27 0.00 0.00 2.39
2520 4079 5.533154 CCTGACGTAGAATAGGATTCAGAGT 59.467 44.000 0.00 0.00 33.82 3.24
2537 4096 7.521748 CGAGAGTATAATATGTTTCCCTGACGT 60.522 40.741 0.00 0.00 0.00 4.34
2539 4098 7.883217 TCGAGAGTATAATATGTTTCCCTGAC 58.117 38.462 0.00 0.00 0.00 3.51
2678 4237 5.238624 TGAAAAATGGCATTTTGGGATGA 57.761 34.783 32.24 13.25 41.30 2.92
2717 4276 4.161754 ACTTGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2718 4277 4.098894 ACTTGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2719 4278 4.161754 AGACTTGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2720 4279 5.340439 AGACTTGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2721 4280 6.649557 ACAAAGACTTGTATTTAGGAACGGAG 59.350 38.462 0.00 0.00 44.14 4.63
2722 4281 6.527423 ACAAAGACTTGTATTTAGGAACGGA 58.473 36.000 0.00 0.00 44.14 4.69
2723 4282 6.796705 ACAAAGACTTGTATTTAGGAACGG 57.203 37.500 0.00 0.00 44.14 4.44
2724 4283 8.752766 TCTACAAAGACTTGTATTTAGGAACG 57.247 34.615 0.00 0.00 44.95 3.95
2725 4284 9.924650 TCTCTACAAAGACTTGTATTTAGGAAC 57.075 33.333 0.00 0.00 44.95 3.62
2736 4295 9.645059 TCATAGTGAAATCTCTACAAAGACTTG 57.355 33.333 0.00 0.00 38.61 3.16
2738 4297 9.646427 GTTCATAGTGAAATCTCTACAAAGACT 57.354 33.333 0.00 0.00 38.22 3.24
2739 4298 8.874816 GGTTCATAGTGAAATCTCTACAAAGAC 58.125 37.037 0.00 0.00 38.22 3.01
2740 4299 8.593679 TGGTTCATAGTGAAATCTCTACAAAGA 58.406 33.333 0.00 0.00 38.22 2.52
2741 4300 8.660373 GTGGTTCATAGTGAAATCTCTACAAAG 58.340 37.037 0.00 0.00 38.22 2.77
2742 4301 8.154203 TGTGGTTCATAGTGAAATCTCTACAAA 58.846 33.333 0.00 0.00 38.22 2.83
2743 4302 7.676004 TGTGGTTCATAGTGAAATCTCTACAA 58.324 34.615 0.00 0.00 38.22 2.41
2744 4303 7.239763 TGTGGTTCATAGTGAAATCTCTACA 57.760 36.000 0.00 0.00 38.22 2.74
2745 4304 9.988815 ATATGTGGTTCATAGTGAAATCTCTAC 57.011 33.333 0.00 0.00 41.55 2.59
2746 4305 9.987272 CATATGTGGTTCATAGTGAAATCTCTA 57.013 33.333 0.00 0.00 41.55 2.43
2747 4306 7.935755 CCATATGTGGTTCATAGTGAAATCTCT 59.064 37.037 0.00 0.00 41.55 3.10
2748 4307 7.933577 TCCATATGTGGTTCATAGTGAAATCTC 59.066 37.037 8.51 0.00 46.16 2.75
2749 4308 7.805163 TCCATATGTGGTTCATAGTGAAATCT 58.195 34.615 8.51 0.00 46.16 2.40
2750 4309 8.509690 CATCCATATGTGGTTCATAGTGAAATC 58.490 37.037 8.51 0.00 46.16 2.17
2751 4310 8.000709 ACATCCATATGTGGTTCATAGTGAAAT 58.999 33.333 8.51 0.00 44.79 2.17
2752 4311 7.345691 ACATCCATATGTGGTTCATAGTGAAA 58.654 34.615 8.51 0.00 44.79 2.69
2753 4312 6.899089 ACATCCATATGTGGTTCATAGTGAA 58.101 36.000 8.51 0.00 44.79 3.18
2754 4313 6.499106 ACATCCATATGTGGTTCATAGTGA 57.501 37.500 8.51 0.00 44.79 3.41
2761 4320 9.265901 GCATCTATATACATCCATATGTGGTTC 57.734 37.037 8.51 0.00 45.99 3.62
2762 4321 8.771286 TGCATCTATATACATCCATATGTGGTT 58.229 33.333 8.51 0.00 45.99 3.67
2763 4322 8.322905 TGCATCTATATACATCCATATGTGGT 57.677 34.615 8.51 0.00 45.99 4.16
2764 4323 9.788889 AATGCATCTATATACATCCATATGTGG 57.211 33.333 0.00 1.19 45.99 4.17
2796 4355 6.148480 ACAGAGCAAAATGAGTGAATCTACAC 59.852 38.462 0.00 0.00 40.60 2.90
2797 4356 6.233434 ACAGAGCAAAATGAGTGAATCTACA 58.767 36.000 0.00 0.00 0.00 2.74
2798 4357 6.734104 ACAGAGCAAAATGAGTGAATCTAC 57.266 37.500 0.00 0.00 0.00 2.59
2799 4358 8.043113 ACATACAGAGCAAAATGAGTGAATCTA 58.957 33.333 0.00 0.00 0.00 1.98
2800 4359 6.883217 ACATACAGAGCAAAATGAGTGAATCT 59.117 34.615 0.00 0.00 0.00 2.40
2801 4360 7.081526 ACATACAGAGCAAAATGAGTGAATC 57.918 36.000 0.00 0.00 0.00 2.52
2802 4361 7.826252 ACTACATACAGAGCAAAATGAGTGAAT 59.174 33.333 0.00 0.00 0.00 2.57
2803 4362 7.161404 ACTACATACAGAGCAAAATGAGTGAA 58.839 34.615 0.00 0.00 0.00 3.18
2804 4363 6.701340 ACTACATACAGAGCAAAATGAGTGA 58.299 36.000 0.00 0.00 0.00 3.41
2805 4364 6.036517 GGACTACATACAGAGCAAAATGAGTG 59.963 42.308 0.00 0.00 0.00 3.51
2806 4365 6.109359 GGACTACATACAGAGCAAAATGAGT 58.891 40.000 0.00 0.00 0.00 3.41
2807 4366 6.108687 TGGACTACATACAGAGCAAAATGAG 58.891 40.000 0.00 0.00 0.00 2.90
2808 4367 6.048732 TGGACTACATACAGAGCAAAATGA 57.951 37.500 0.00 0.00 0.00 2.57
2809 4368 6.932356 ATGGACTACATACAGAGCAAAATG 57.068 37.500 0.00 0.00 38.26 2.32
2810 4369 7.712639 CACTATGGACTACATACAGAGCAAAAT 59.287 37.037 0.00 0.00 41.03 1.82
2811 4370 7.041721 CACTATGGACTACATACAGAGCAAAA 58.958 38.462 0.00 0.00 41.03 2.44
2812 4371 6.573434 CACTATGGACTACATACAGAGCAAA 58.427 40.000 0.00 0.00 41.03 3.68
2813 4372 5.451937 GCACTATGGACTACATACAGAGCAA 60.452 44.000 0.00 0.00 41.03 3.91
2814 4373 4.038042 GCACTATGGACTACATACAGAGCA 59.962 45.833 0.00 0.00 41.03 4.26
2815 4374 4.038042 TGCACTATGGACTACATACAGAGC 59.962 45.833 0.00 0.00 41.03 4.09
2816 4375 5.774498 TGCACTATGGACTACATACAGAG 57.226 43.478 0.00 0.00 41.03 3.35
2817 4376 6.551227 AGATTGCACTATGGACTACATACAGA 59.449 38.462 0.00 0.00 41.03 3.41
2818 4377 6.753180 AGATTGCACTATGGACTACATACAG 58.247 40.000 0.00 0.00 41.03 2.74
2819 4378 6.551227 AGAGATTGCACTATGGACTACATACA 59.449 38.462 0.00 0.00 41.03 2.29
2820 4379 6.987386 AGAGATTGCACTATGGACTACATAC 58.013 40.000 0.00 0.00 41.03 2.39
2821 4380 7.724061 TGTAGAGATTGCACTATGGACTACATA 59.276 37.037 0.00 0.00 41.03 2.29
2822 4381 6.551227 TGTAGAGATTGCACTATGGACTACAT 59.449 38.462 0.00 0.00 43.68 2.29
2823 4382 5.891551 TGTAGAGATTGCACTATGGACTACA 59.108 40.000 0.00 0.00 36.46 2.74
2824 4383 6.392625 TGTAGAGATTGCACTATGGACTAC 57.607 41.667 0.00 0.00 0.00 2.73
2825 4384 7.342026 TCTTTGTAGAGATTGCACTATGGACTA 59.658 37.037 0.00 0.00 0.00 2.59
2826 4385 5.939764 TTGTAGAGATTGCACTATGGACT 57.060 39.130 0.00 0.00 0.00 3.85
2827 4386 6.256757 GTCTTTGTAGAGATTGCACTATGGAC 59.743 42.308 0.00 0.00 0.00 4.02
2828 4387 6.155221 AGTCTTTGTAGAGATTGCACTATGGA 59.845 38.462 0.00 0.00 0.00 3.41
2829 4388 6.344500 AGTCTTTGTAGAGATTGCACTATGG 58.656 40.000 0.00 0.00 0.00 2.74
2830 4389 7.840342 AAGTCTTTGTAGAGATTGCACTATG 57.160 36.000 0.00 0.00 0.00 2.23
2845 4404 9.379791 CCTCCGTTTCTAAATATAAGTCTTTGT 57.620 33.333 0.00 0.00 0.00 2.83
2846 4405 8.827677 CCCTCCGTTTCTAAATATAAGTCTTTG 58.172 37.037 0.00 0.00 0.00 2.77
2847 4406 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
2848 4407 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
2849 4408 7.909485 TCCCTCCGTTTCTAAATATAAGTCT 57.091 36.000 0.00 0.00 0.00 3.24
2855 4414 9.101325 TCATCTAATCCCTCCGTTTCTAAATAT 57.899 33.333 0.00 0.00 0.00 1.28
2856 4415 8.365647 GTCATCTAATCCCTCCGTTTCTAAATA 58.634 37.037 0.00 0.00 0.00 1.40
2857 4416 7.147549 TGTCATCTAATCCCTCCGTTTCTAAAT 60.148 37.037 0.00 0.00 0.00 1.40
2858 4417 6.155565 TGTCATCTAATCCCTCCGTTTCTAAA 59.844 38.462 0.00 0.00 0.00 1.85
2859 4418 5.659525 TGTCATCTAATCCCTCCGTTTCTAA 59.340 40.000 0.00 0.00 0.00 2.10
2860 4419 5.205821 TGTCATCTAATCCCTCCGTTTCTA 58.794 41.667 0.00 0.00 0.00 2.10
2861 4420 4.030913 TGTCATCTAATCCCTCCGTTTCT 58.969 43.478 0.00 0.00 0.00 2.52
2862 4421 4.402056 TGTCATCTAATCCCTCCGTTTC 57.598 45.455 0.00 0.00 0.00 2.78
2863 4422 4.837093 TTGTCATCTAATCCCTCCGTTT 57.163 40.909 0.00 0.00 0.00 3.60
2864 4423 6.270000 TGATATTGTCATCTAATCCCTCCGTT 59.730 38.462 0.00 0.00 0.00 4.44
2865 4424 5.780282 TGATATTGTCATCTAATCCCTCCGT 59.220 40.000 0.00 0.00 0.00 4.69
2866 4425 6.286240 TGATATTGTCATCTAATCCCTCCG 57.714 41.667 0.00 0.00 0.00 4.63
2867 4426 7.453393 TGTTGATATTGTCATCTAATCCCTCC 58.547 38.462 0.00 0.00 36.54 4.30
2868 4427 9.160496 GATGTTGATATTGTCATCTAATCCCTC 57.840 37.037 0.00 0.00 36.54 4.30
2869 4428 7.821359 CGATGTTGATATTGTCATCTAATCCCT 59.179 37.037 0.00 0.00 36.54 4.20
2870 4429 7.065085 CCGATGTTGATATTGTCATCTAATCCC 59.935 40.741 0.00 0.00 36.54 3.85
2871 4430 7.819415 TCCGATGTTGATATTGTCATCTAATCC 59.181 37.037 0.00 0.00 36.54 3.01
2872 4431 8.763049 TCCGATGTTGATATTGTCATCTAATC 57.237 34.615 0.00 0.00 36.54 1.75
2873 4432 7.821359 CCTCCGATGTTGATATTGTCATCTAAT 59.179 37.037 0.00 0.00 36.54 1.73
2874 4433 7.015195 TCCTCCGATGTTGATATTGTCATCTAA 59.985 37.037 0.00 0.00 36.54 2.10
2875 4434 6.493458 TCCTCCGATGTTGATATTGTCATCTA 59.507 38.462 0.00 0.00 36.54 1.98
2876 4435 5.305386 TCCTCCGATGTTGATATTGTCATCT 59.695 40.000 0.00 0.00 36.54 2.90
3073 4633 5.422666 TTTGTACCGCATCATTGATGATC 57.577 39.130 26.94 11.49 45.23 2.92
3118 4678 0.036022 GGGACAGCTTGAACTCAGCT 59.964 55.000 0.00 0.00 39.79 4.24
3121 4681 1.423584 TCAGGGACAGCTTGAACTCA 58.576 50.000 0.00 0.00 0.00 3.41
3139 4699 4.449405 GCCAGTTCAGACAAGTAAGAGTTC 59.551 45.833 0.00 0.00 0.00 3.01
3211 4771 4.529377 TGAGTAATTACCTCGACAGGGTTT 59.471 41.667 12.05 0.00 45.53 3.27
3261 4821 8.853077 TCAAGAGTGTCATATTCAAAGTTCAT 57.147 30.769 0.00 0.00 0.00 2.57
3263 4823 8.439286 GTCTCAAGAGTGTCATATTCAAAGTTC 58.561 37.037 0.00 0.00 0.00 3.01
3287 4851 5.622233 GCCATCCTTTCCTGTAACAAATGTC 60.622 44.000 0.00 0.00 0.00 3.06
3339 4903 2.163818 TGCCGTTCGTTTCTTCAGAT 57.836 45.000 0.00 0.00 0.00 2.90
3347 4911 0.536460 AGGACCAATGCCGTTCGTTT 60.536 50.000 0.00 0.00 0.00 3.60
3351 4915 1.675641 AGCAGGACCAATGCCGTTC 60.676 57.895 2.19 0.00 44.97 3.95
3405 4969 0.898320 TCTTCTCAAGGCCTTCCTCG 59.102 55.000 17.29 4.34 43.40 4.63
3449 5013 2.261361 CACCAGGTGCGACGATCA 59.739 61.111 6.67 0.00 0.00 2.92
3465 5029 1.142531 CAGGCTATGAGCAGACGCA 59.857 57.895 0.21 0.00 44.75 5.24
3588 5152 6.551385 AGGAATAAGCAATCTCAATAAGCG 57.449 37.500 0.00 0.00 0.00 4.68
3625 5189 8.646900 TGCAATATTGGAGGTTTTCTAACTTTT 58.353 29.630 17.02 0.00 34.59 2.27
3634 5198 5.188359 AGAATGCTGCAATATTGGAGGTTTT 59.812 36.000 30.73 13.72 45.44 2.43
3677 5285 7.609146 TCATTTCAGATACAAAGAAGCAGATGT 59.391 33.333 0.00 0.00 0.00 3.06
3691 5299 6.420903 TGCGCACTATTACTCATTTCAGATAC 59.579 38.462 5.66 0.00 0.00 2.24
3703 5311 3.056107 TCAGTCCTTTGCGCACTATTACT 60.056 43.478 11.12 7.74 0.00 2.24
3711 5319 3.122297 CAAAAATTCAGTCCTTTGCGCA 58.878 40.909 5.66 5.66 0.00 6.09
3713 5321 6.616260 GCATAACAAAAATTCAGTCCTTTGCG 60.616 38.462 0.00 0.00 33.08 4.85
3757 5365 7.555965 ACAGAAAAAGGTAACAAAGCTGAAAT 58.444 30.769 0.00 0.00 35.65 2.17
3822 5430 1.807142 TGCACAAAACAACGTGTCAGA 59.193 42.857 0.00 0.00 35.51 3.27
3827 5435 4.143242 TGTCATTTTGCACAAAACAACGTG 60.143 37.500 10.53 5.57 42.32 4.49
3898 5507 3.118847 TGTCTTCACATGCTTGCCAAAAA 60.119 39.130 0.00 0.00 0.00 1.94
3919 5528 4.481463 AGAAAAACAACGTGTCAAAGGTG 58.519 39.130 0.00 0.00 0.00 4.00
3921 5530 6.460664 AAAAGAAAAACAACGTGTCAAAGG 57.539 33.333 0.00 0.00 0.00 3.11
3922 5531 7.676826 CGTAAAAAGAAAAACAACGTGTCAAAG 59.323 33.333 0.00 0.00 0.00 2.77
3923 5532 7.377928 TCGTAAAAAGAAAAACAACGTGTCAAA 59.622 29.630 0.00 0.00 0.00 2.69
3926 5535 6.835719 TCGTAAAAAGAAAAACAACGTGTC 57.164 33.333 0.00 0.00 0.00 3.67
3927 5536 7.620397 TTTCGTAAAAAGAAAAACAACGTGT 57.380 28.000 0.00 0.00 35.00 4.49
3929 5538 7.756272 AGGATTTCGTAAAAAGAAAAACAACGT 59.244 29.630 0.00 0.00 40.44 3.99
3930 5539 8.110970 AGGATTTCGTAAAAAGAAAAACAACG 57.889 30.769 0.00 0.00 40.44 4.10
3931 5540 9.895894 GAAGGATTTCGTAAAAAGAAAAACAAC 57.104 29.630 0.00 0.00 40.44 3.32
3932 5541 9.863845 AGAAGGATTTCGTAAAAAGAAAAACAA 57.136 25.926 0.00 0.00 40.44 2.83
3933 5542 9.511144 GAGAAGGATTTCGTAAAAAGAAAAACA 57.489 29.630 0.00 0.00 40.44 2.83
3945 5554 5.041287 CGCATAACTGAGAAGGATTTCGTA 58.959 41.667 0.00 0.00 38.38 3.43
3946 5555 3.865745 CGCATAACTGAGAAGGATTTCGT 59.134 43.478 0.00 0.00 38.38 3.85
3947 5556 3.302740 GCGCATAACTGAGAAGGATTTCG 60.303 47.826 0.30 0.00 38.38 3.46
3948 5557 3.623060 TGCGCATAACTGAGAAGGATTTC 59.377 43.478 5.66 0.00 0.00 2.17
3951 5560 2.939103 GTTGCGCATAACTGAGAAGGAT 59.061 45.455 12.75 0.00 0.00 3.24
3953 5562 1.398390 GGTTGCGCATAACTGAGAAGG 59.602 52.381 12.75 0.00 0.00 3.46
3967 5576 3.119316 TGGTGGCTTATATTTTGGTTGCG 60.119 43.478 0.00 0.00 0.00 4.85
3969 5578 6.638610 TCAATGGTGGCTTATATTTTGGTTG 58.361 36.000 0.00 0.00 0.00 3.77
3979 5588 6.194235 TCCTTATTGTTCAATGGTGGCTTAT 58.806 36.000 8.11 0.00 0.00 1.73
3997 5606 9.401058 CCTCACTCAGAAAATAATGTTCCTTAT 57.599 33.333 0.00 0.00 0.00 1.73
3998 5607 8.383175 ACCTCACTCAGAAAATAATGTTCCTTA 58.617 33.333 0.00 0.00 0.00 2.69
4003 5612 8.164070 ACCTTACCTCACTCAGAAAATAATGTT 58.836 33.333 0.00 0.00 0.00 2.71
4004 5613 7.690256 ACCTTACCTCACTCAGAAAATAATGT 58.310 34.615 0.00 0.00 0.00 2.71
4032 5641 8.082242 GGCAGGCATATAAAAATAAAGGTGTAG 58.918 37.037 0.00 0.00 0.00 2.74
4057 5666 4.376340 AAAAGAAGTCAAGTTGCAGTGG 57.624 40.909 0.00 0.00 0.00 4.00
4112 5721 0.963962 AAACCAGATGGCTGCAACTG 59.036 50.000 0.50 7.41 40.91 3.16
4125 5734 0.524862 CTGCCAGCAGCTTAAACCAG 59.475 55.000 6.72 0.00 44.23 4.00
4186 5795 0.810031 CACCGGAGAACTAATGCCCG 60.810 60.000 9.46 0.00 39.85 6.13
4190 5799 3.118408 TGATTCCCACCGGAGAACTAATG 60.118 47.826 9.46 0.00 40.10 1.90
4215 5824 3.875727 CACATTACTCCAGCCAATGAGAG 59.124 47.826 7.98 0.00 34.48 3.20
4216 5825 3.264193 ACACATTACTCCAGCCAATGAGA 59.736 43.478 7.98 0.00 34.48 3.27
4232 5841 1.219213 TGGGTCTGGGGAAAACACATT 59.781 47.619 0.00 0.00 0.00 2.71
4264 5873 1.833934 CCTTGCAGGCCCACAACTT 60.834 57.895 0.00 0.00 0.00 2.66
4332 5941 1.136828 AGGTTAACCTGGCAGTGTGA 58.863 50.000 26.57 1.33 46.55 3.58
4333 5942 3.725754 AGGTTAACCTGGCAGTGTG 57.274 52.632 26.57 0.23 46.55 3.82
4349 5958 2.568623 ACTGCTTTACACCCTTCAGG 57.431 50.000 0.00 0.00 43.78 3.86
4425 6034 2.871096 TGGCGAAGAAGGTAATGGTT 57.129 45.000 0.00 0.00 0.00 3.67
4426 6035 2.505819 AGATGGCGAAGAAGGTAATGGT 59.494 45.455 0.00 0.00 0.00 3.55
4437 6046 0.649475 CGAGAGCAAAGATGGCGAAG 59.351 55.000 0.00 0.00 36.08 3.79
4438 6047 0.037326 ACGAGAGCAAAGATGGCGAA 60.037 50.000 0.00 0.00 36.08 4.70
4439 6048 0.815095 TACGAGAGCAAAGATGGCGA 59.185 50.000 0.00 0.00 36.08 5.54
4490 6099 7.572539 CGGGTGATTAAAGAGTTTTAACAGGAC 60.573 40.741 0.00 0.00 40.51 3.85
4493 6102 6.084277 GCGGGTGATTAAAGAGTTTTAACAG 58.916 40.000 0.00 0.00 40.51 3.16
4497 6106 5.310451 ACTGCGGGTGATTAAAGAGTTTTA 58.690 37.500 0.00 0.00 0.00 1.52
4503 6112 4.453136 GTGTAAACTGCGGGTGATTAAAGA 59.547 41.667 0.00 0.00 0.00 2.52
4573 6182 6.851609 TCACATTATAATTGGCTGTGTTGAC 58.148 36.000 13.25 0.00 38.61 3.18


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

AutoCloner maintained by Alex Coulton.